Neutral Species Research Articles

Data processing and visualization tool for atomic and molecular data for collisional radiative models

The Monte Carlo kinetic code EIRENE (Sect. 2) is used for simulating the behavior of neutral species in the edge of tokamak plasma and coupled with fluid plasma codes for a self-consistent description to be compared with measured experimental conditions. The data and visualization toolbox HYDKIN (Sect. 3) has been developed as a pre-processing tool for validation of those atomic and molecular (A &M) data used in EIRENE simulations, such as cross sections and reaction rates for plasma-neutral and neutral-neutral collisions. The restructuring that is being performed to increase HYDKIN readability and usability is here presented (Sect. 4).Graphic

Solv: An Alternative Continuum Model Implementation Based on Fixed Atomic Charges, Scaled Particle Theory, and the Atom-Atom Potential Method.

An alternative continuum model implementation is reported. The electrostatic contribution to the solvation Gibbs free energy utilizes the noniterative conductor-like screening model of Vyboishchikov and Voityuk (DOI: 10.1002/jcc.26531) based on the fixed partial atomic charges. The nonelectrostatic solute-solvent dispersion-repulsion energy is calculated through the Caillet-Claverie atom-atom potential method employing the grid-based approach. The nonelectrostatic cavitation energy is computed within the scaled particle theory (SPT) formalism with the solute hard-sphere radius obtained via the Pierotti-Claverie (PC) scheme, from the solute molecular surface (SPT-S) or volume (SPT-V). The solvent hard-sphere radius is derived through the fitting to the experimental total solvation free energies of 2530 neutral species in 92 solvents. Application of the model to reproduce both the absolute and relative (reaction net) solvation free energies indicates that the SPT-V approach based on the CM5 charges is the best performer. The method is suggested for the solvation free energy calculation in the nonaqueous solvents.

Vaporization of Intact Neutral Biomolecules Using Laser-Based Thermal Desorption.

The production of a clean neutral molecular sample is a crucial step in many gas-phase spectroscopy and reaction dynamics experiments investigating neutral species. Unfortunately, conventional methods based on heating cannot be used with most nonvolatile biomolecules due to their thermal instability. In this paper, we demonstrate the application of laser-based thermal desorption (LBTD) to produce neutral molecular plumes of biomolecules such as dipeptides and lipids. Specifically, we report mass spectra of glycylglycine, glycyl-l-alanine, and cholesterol obtained using LBTD vaporization, followed by soft femtosecond multiphoton ionization (fs-MPI) at 400 nm. For all molecules, the signal from the intact precursor ion was observed, highlighting the softness and applicability of the LBTD and fs-MPI approach. In more detail, cholesterol underwent hardly any fragmentation. Both dipeptides fragmented significantly, although mostly through only a single channel, which we attribute to the fs-MPI process.

Ab Initio Calculations on the Ground and Excited Electronic States of Thorium-Ammonia, Thorium-Aza-Crown, and Thorium-Crown Ether Complexes.

Positively charged metal-ammonia complexes are known to host peripheral, diffuse electrons around their molecular skeleton. The resulting neutral species form materials known as expanded or liquid metals. Alkali, alkaline earth, and transition metals have been investigated previously in experimental and theoretical studies of both the gas and condensed phase. This work is the first ab initio exploration of an f-block metal-ammonia complex. The ground and excited states are calculated for Th0-3+ complexes with ammonia, crown ethers, and aza-crown ethers. For Th3+ complexes, the one valence electron Th populates the metal's 6d or 7f orbitals. For Th0-2+, the additional electrons prefer occupation of the outer s- and p-type orbitals of the complex, except Th(NH3)10, which uniquely places all four electrons in outer orbitals of the complex. Although thorium coordinates up to ten ammonia ligands, octa-coordinated complexes are more stable. Crown ether complexes have a similar electronic spectrum to ammonia complexes, but excitations of electrons in the outer orbitals of the complex are higher in energy. Aza-crown ethers disfavor the orbitals perpendicular to the crowns, attributed to the N-H bonds pointing along the plane of the crowns.

Persistence of Growth Enhancement Induced by Oxygen Plasma Irradiation Seed and Leaf

The variation of gene expression of seeds or leaves of Arabidopsis thaliana was investigated by irradiation with oxygen and air plasmas. The irradiation with oxygen plasma reported on the growth promotion and induced the consequence of gene expression in plant cells by neutral active oxygen species. The increase in leaf area ratio by oxygen plasma to seeds was due to epigenetics such as activation of DNA demethylation transcription factors and the growth enhancement effect induced by the plasma irradiation of seeds was inherited by next-generation cells through cell division even after germination. In oxygen irradiation for 10 s, expression of each de-DNA methylation-related gene increased, and DNA methylation-related genes decreased in expression. DNA acetylation that induces gene expressions was suppressed. However, irradiated for 20 s by oxygen, both demethylation suppression and promotion and methylation/acetylation suppression and promotion were obtained. On the other hand, methylation and demethylation may occur at the same time but were not significant and the acetylation was suppressed by air plasma irradiation. In both cases, active oxygen species was the key factor for the variation of gene expression.

Ambipolar Charge Transport in Organic Semiconductors: How Intramolecular Reorganization Energy Is Controlled by Diradical Character.

The charged forms of π-conjugated chromophores are relevant in the field of organic electronics as charge carriers in optoelectronic devices, but also as energy storage substrates in organic batteries. In this context, intramolecular reorganization energy plays an important role in controlling material efficiency. In this work, we investigate how the diradical character influences the reorganization energies of holes and electrons by considering a library of diradicaloid chromophores. We determine the reorganization energies with the four-point adiabatic potential method using quantum-chemical calculations at density functional theory (DFT) level. To assess the role of diradical character, we compare the results obtained, assuming both closed-shell and open-shell representations of the neutral species. The study shows how the diradical character impacts the geometrical and electronic structure of neutral species, which in turn control the magnitude of reorganization energies for both charge carriers. Based on computed geometries of neutral and charged species, we propose a simple scheme to rationalize the small, computed reorganization energies for both n-type and p-type charge transport. The study is supplemented with the calculation of intermolecular electronic couplings governing charge transport for selected diradicals, further supporting the ambipolar character of the investigated diradicals.

Investigation on the correlation of stability, reactivity, and structural properties of C/C2-doped neutral and charged Aln (n = 2–7) clusters

The equilibrium geometries, electronic structures, reactivity, and stability of C/C2-doped Aln0,± (n = 2–7) clusters were investigated computationally at B3LYP-D4/def2-TZVPP and CCSD(T)/def2-TZVPP levels of theory. The lowest energy structures of AlnC1,20,± clusters were the carbon atoms inserted inside the aluminium clusters. The stability of the neutral and charged clusters were investigated under various reaction conditions, such as dissociation of the clusters via Al0,+,C0,-,C20,--elimination and electron elimination from neutral (ionization) and anionic species (electron detachment). The dominant dissociation reaction channels are the Al-elimination from the neutral and anionic clusters, Al+-elimination from cationic clusters, rather than the C/C2-elimintion reaction. On the other hand, C-elimination are were more favorable compared to C2-elimination due to the stronger CC and Al-C bonds. In addition, binding energy, second-order difference of energy, chemical hardness, and electron affinity parameters were used to determine the stability and reactivity. The results show the singlet cluster (Al2,4,6C1,2 and Al3,5,7C0-20,±) have the greater stability than the doublet clusters (Al3,5,7C0-2 and Al2,4,6C1,20,±) and triplet clusters (Al2,4,6). It has been demonstrated that anionic clusters are more stable than the neutral species, and cationic species are less stable than that of neutral species. The current study could be useful in understanding the stability and reactivity of metal clusters after carbon doping, which is important in combustion, material science, and the astrochemical community.

Nitrogen partitioning between silicate phases and aqueous fluid depends on concentration

The distribution of nitrogen in geologic systems is modulated by its partitioning between silicate (mineral and melt) and fluid phases. Under geologically applicable oxygen fugacity, pressure, and temperatures, nitrogen can be multiply-speciated, with N2 coexisting with reduced nitride (N−3) species. Non-polar, neutral species, including N2, tend to concentrate in fluids, while charged nitride species have a greater propensity to concentrate in silicate phases. The stoichiometry of converting N2 to single N atom nitride species implies that nitrogen speciation may depend on its concentration, and this leads to the hypothesis that the partitioning of nitrogen between silicate and fluid phases also depends on concentration, potentially biasing prior experimental work in doped systems and influencing the behavior of nitrogen in geologic systems. To test this hypothesis, we have completed a series high pressure (∼1.75 GPa, 800 °C) experiments that react minerals, melts, and fluids with variable nitrogen concentrations (3.1–17.1 wt% N). Our results imply order-of-magnitude-scale increases in mineral/melt and melt/fluid partitioning as nitrogen concentrations decrease within natural ranges. For example, decreasing the N concentration from 2500 to 2 ppm increases predicted Dmelt/fluidN values by over an order of magnitude at constant PT conditions. This means that loss of nitrogen from a degassing magma or dehydrating slab is a self-limiting process that becomes increasingly inefficient as nitrogen concentration falls. Despite this, nitrogen remains highly concentrated in the atmosphere, which receives N from fluids exsolved from slabs and magmas. To maintain a nitrogen-rich atmosphere we therefore suggest that warm and oxidizing conditions have prevailed over subduction zones because warm slabs dehydrate under lower pressures where nitrogen is more easily partitioned into fluids, and oxidizing conditions also promote nitrogen partitioning into fluids. Concentration-dependent partitioning of nitrogen will also serve to moderate any initial variations of N/K in slab materials upon dehydration, and this may help to explain the relatively uniform N/K ratio of MORB mantle. We supplement our nitrogen concentration experiments with a temperature series (1.5–2 GPa, 750–950 °C). Our temperature series data reveal that at high temperature nitrogen favors melts over fluids, while temperature has no resolvable effect of biotite-fluid partitioning.

Evidence of 1000 eV positive oxygen ion flux generated in reactive HiPIMS plasma

The arrival of highly energetic (near 1000 eV) positive atomic oxygen ions at the substrate region has been detected in a unipolar reactive high-power impulse magnetron sputtering process operated with an uncooled copper target in argon–oxygen mixtures. Examination of the ion fluxes from discharge plasma was performed with a magnetic sector mass-spectrometer and an electrostatic energy analyzer. The energy of fast positive O+ ions is close to the value of eV d (e—elementary charge, V d—discharge voltage), which indicates their connection to the well-studied fraction of negative O− ions, which undergo acceleration in the cathode sheath. After switching the oxygen gas supply off, the flux of energetic O+ species decreases gradually as the poisoned target surface layers become depleted of oxygen due to sputtering in pure argon. Presumably, the observed energetic O+ ions originate as a result of low-angle scattering of fast negative O− ions from other charged or neutral species in the plasma followed by electron detachment, ionization, or charge exchange.

Solar-wind electron precipitation on weakly magnetized bodies: The planet Mercury

Rocky objects in the Solar System (such as planets, asteroids, moons, and comets) undergo a complex interaction with the flow of magnetized, supersonic plasma emitted from the Sun called solar wind. We address the interaction of such a flow with the planet Mercury, considered here as the archetype of a weakly magnetized, airless, telluric body immersed in the solar wind. Due to the lack of dense atmosphere, a considerable fraction of solar-wind particles precipitate on Mercury. The interaction processes between precipitating electrons and other nonionized parts of the system remain poorly understood. Shading light on such processes is the goal of this work. Using a 3D fully kinetic self-consistent plasma model, we show for the first time that solar-wind electron precipitation drives (i) efficient ionization of multiple neutral exosphere species and (ii) emission of X-rays from the surface of the planet. We conclude that, compared to photoionization, electron-impact ionization should not be considered a secondary process for the H, He, O, and Mn exosphere. Moreover, we provide the first, independent evidence of X-ray aurora-like emission on Mercury using a numerical approach.

Utilizing Helium Ion Chemistry to Derive Mixing Ratios of Heavier Neutral Species in Saturn's Equatorial Ionosphere

AbstractA surprisingly strong influx of organic‐rich material into Saturn's upper atmosphere from its rings was observed during the proximal obits of the Grand Finale of the Cassini mission. Measurements by the Ion and Neutral Mass Spectrometer (INMS) gave insights into the composition of the material, but it remains to be resolved what fraction of the inferred heavy volatiles should be attributed as originating from the fragmentation of dust particles in the instrument versus natural ablation of grains in the atmosphere. In the present study, we utilize measured light ion and neutral densities to further constrain the abundances of heavy volatiles in Saturn's ionosphere through a steady‐state model focusing on helium ion chemistry. We first show that the principal loss mechanism of He+ in Saturn's equatorial ionosphere is through reactions with species other than H2. Based on the assumption of photochemical equilibrium at altitudes below 2,500 km, we then proceed by estimating the mixing ratio of heavier volatiles down to the closest approaches for Cassini's proximal orbits 288 and 292. Our derived mixing ratios for the inbound part of both orbits fall below those reported from direct measurements by the INMS, with values of ∼2 × 10−4 at closest approaches and order‐of‐magnitude variations in either direction over the orbits. This aligns with previous suggestions that a large fraction of the neutrals measured by the INMS stems from the fragmentation of infalling dust particles that do not significantly ablate in the considered part of Saturn's atmosphere and are thus unavailable for reactions.

Multifluid Simulation of Solar Chromospheric Turbulence and Heating Due to Thermal Farley–Buneman Instability

Models fail to reproduce observations of the coldest parts of the Sun’s atmosphere, where interactions between multiple ionized and neutral species prevent an accurate MHD representation. This paper argues that a meter-scale electrostatic plasma instability develops in these regions and causes heating. We refer to this instability as the Thermal Farley–Buneman Instability (TFBI). Using parameters from a 2.5D radiative MHD Bifrost simulation, we show that the TFBI develops in many of the colder regions in the chromosphere. This paper also presents the first multifluid simulation of the TFBI and validates this new result by demonstrating close agreement with theory during the linear regime. The simulation eventually develops turbulence, and we characterize the resulting wave-driven heating, plasma transport, and turbulent motions. These results all contend that the effects of the TFBI contribute to the discrepancies between solar observations and radiative MHD models.

Determination of thermochemical properties of stainless steels type D-9 and T-91 using Knudsen Effusion Mass Spectrometry

High temperature vaporisation thermodynamic studies over D-9 and T-91 stainless steel samples were carried out in the temperature range 1202–1529 K and 1232–1530 K respectively, by using Knudsen Effusion Mass Spectrometry (KEMS). These studies revealed that both the alloys undergo incongruent vaporisation. Cr(g), Mn(g), Fe(g) and Ni(g) were the neutral vapour species observed over the D-9 alloy. Cr(g), Mn(g) and Fe(g) were the neutral vapour species observed over the T-91alloy. Partial pressure-Temperature relations were derived using KEMS for the first time. Apparent enthalpies of vaporisation data were deduced by second law method. Chemical activities of all the major metallic elements (Fe, Cr, Ni and Mn) in the commercial grade D-9 austenitic stainless steel were determined in the temperature range of 1202–1529 K. In case of T-91 ferritic steel, chemical activities of Fe, Cr and Mn were determined in the temperature range of 1232 -1530 K.

Experimental Determination of Air/Water Partition Coefficients for 21 Per- and Polyfluoroalkyl Substances Reveals Variable Performance of Property Prediction Models.

Per- and polyfluoroalkyl substances (PFAS) are a group of chemicals of high environmental concern. However, reliable data for the air/water partition coefficients (Kaw), which are required for fate, exposure, and risk analysis, are available for only a few PFAS. In this study, Kaw values at 25 °C were determined for 21 neutral PFAS by using the hexadecane/air/water thermodynamic cycle. Hexadecane/water partition coefficients (KHxd/w) were measured with batch partition, shared-headspace, and/or modified variable phase ratio headspace methods and were divided by hexadecane/air partition coefficients (KHxd/air) to obtain Kaw values over 7 orders of magnitude (10-4.9 to 102.3). Comparison to predicted Kaw values by four models showed that the quantum chemically based COSMOtherm model stood out for accuracy with a root-mean-squared error (RMSE) of 0.42 log units, as compared to HenryWin, OPERA, and the linear solvation energy relationship with predicted descriptors (RMSE, 1.28-2.23). The results indicate the advantage of a theoretical model over empirical models for a data-poor class like PFAS and the importance of experimentally filling data gaps in the chemical domain of environmental interest. Kaw values for 222 neutral (or neutral species of) PFAS were predicted using COSMOtherm as current best estimates for practical and regulatory use.

Anomalous salting-out, self-association and pKa effects in the practically-insoluble bromothymol blue.

The widely-used and practically insoluble diprotic acidic dye, bromothymol blue (BTB), is a neutral molecule in strongly acidic aqueous solutions. The Schill (1964) extensive solubility-pH measurement of bromothymol blue in 0.1 and 1.0 M NaCl solutions, with pH adjusted with HCl from 0.0 to 5.4, featured several unusual findings. The data suggest that the difference in solubility of the neutral-form molecule in 1M NaCl is more than 0.7 log unit lower than the solubility in pure water. This could be considered as uncharacteristically high for a salting-out effect. Also, the study reported two apparent values of pKa1, 1.48 and 1.00, in 0.1 M and 1.0 M NaCl solutions, respectively. The only other measured value found for pKa1 in the literature is -0.66 (Gupta and Cadwallader, 1968). It was reasoned that the there can be only a single pKa1 for BTB. Also, it was hypothesized that salting-out alone might not account for such a large difference in solubility observed at the two levels of salt. A generalized mass action approach incorporating activity corrections for charged species using the Stokes-Robinson hydration equation and for neutral species using the Setschenow equation, was selected to analyze the Schill solubility-pH data to seek a rationalization of these unusual results. BTB reveals complex speciation chemistry in saturated aqueous solutions which had been poorly understood for many years. The appearance of two different values of pKa1 at different levels of NaCl and the anomalously high value of the empirical salting-out constant could be rationalized to normal values by invoking the formation of a very stable neutral dimer (log K2 = 10.0 ± 0.1 M-1). A 'normal' salting-out constant, 0.25 M-1 was then derived. It was also possible to estimate the 'self-interaction' constant. The data analysis in the present study critically depended on the pKa1 = -0.66 reported by Gupta and Cadwallader. A more reasonable salting-out constant and a consistent single value for pKa1 have been determined by considering a self-interacting (aggregation) model involving an uncharged form of the molecule, which is likely a zwitterion, as suggested by literature spectrophotometric studies.

Computational DFT analysis and molecular modeling on imidazole derivatives used as corrosion inhibitors for aluminum in acidic media

The corrosion inhibiting effect of imidazole derivatives on aluminum was studied using density functional theory (DFT) calculations to assess the relationship between molecular structures and their corresponding efficiencies. The chemical reactivity of the neutral and protonated species (IM, Me-IM, IMH+ and Me-IMH+) was investigated, and the impact of methyl group substitution on the adsorption ability onto Al(111) surface was examined. Results revealed that the neutral species can be absorbed onto Al(111) surface by forming covalent bond N–Al, implying chemisorption as the mechanism of adsorption. It was also established that, the IMH+ and Me-IMH+ can be adsorbed via the Cl− anion, which was already firstly adsorbed onto the Al(111) surface. The DFT calculations align well with the experimental results, suggesting that introduction of a methyl group at the 2-position of the imidazole ring enhances the adsorption ability.

Theoretical understanding of stability of the oxygen electrode in a proton-conductor based solid oxide electrolysis cell

The oxygen electrode in a proton-conductor based solid oxide cells is often a triple-conducting material that enables the transport and exchange of electrons (e−), oxygen ions (O2−), and protons (H+), thus expanding active areas to enhance the oxygen electrode activity. In this work, a theoretical model was developed to understand stability of tri-conducting oxygen electrode by studying chemical potentials of neutral species (i.e., μO2, μH2, and μH2O) as functions of transport properties, operating parameters, and cell geometry. Our theoretical understanding shows that (1): In a conventional oxygen-ion based solid oxide cell, a high μO2 (thus high oxygen partial pressure) exists in the oxygen electrode during the electrolysis mode, which may lead to the formation of cracks at the electrode/electrolyte interface. While in a proton-conductor based solid oxide cell, the μO2 is reduced significantly, suppressing the crack formation, and resulting in improved performance stability (2). In a typical proton-conductor based solid oxide electrolyzer, the dependence of μO2 on the Faradaic efficiency is negligible. Hence, approaches to block the electronic current can improve the electrolysis efficiency while achieving stability (3). The difference of the μO2 (thus pO2) between the oxygen electrode and gas phase can be reduced by using higher ionic conducting components and improving electrode kinetics, which lead to further improvement of electrode stability.

Retrieval Survey of Metals in Six Ultrahot Jupiters: Trends in Chemistry, Rain-out, Ionization, and Atmospheric Dynamics

Ground-based high-resolution spectroscopy (HRS) has detected numerous chemical species and atmospheric dynamics in exoplanets, most notably ultrahot Jupiters (UHJs). However, quantitative estimates on abundances have been challenging but are essential for accurate comparative characterization and to determine formation scenarios. In this work, we retrieve the atmospheres of six UHJs (WASP-76 b, MASCARA-4 b, MASCARA-2 b, WASP-121 b, HAT-P-70 b, and WASP-189 b) with ESPRESSO and HARPS-N/HARPS observations, exploring trends in eleven neutral species and dynamics. While Fe abundances agree well with stellar values, Mg, Ni, Cr, Mn, and V show more variation, highlighting the difficulty in using a single species as a proxy for metallicity. We find that Ca, Na, Ti, and TiO are underabundant, potentially due to ionization and/or nightside rain-out. Our retrievals also show that relative abundances between species are more robust, consistent with previous works. We perform spatially resolved and phase-resolved retrievals for WASP-76 b and WASP-121 b given their high signal-to-noise observations, and find the chemical abundances in each of the terminator regions are broadly consistent. We additionally constrain dynamics for our sample through Doppler shifts and broadening of the planetary signals during the primary eclipse, with median blueshifts between ∼0.9 and 9.0 km s−1 due to day–night winds. Furthermore, we constrain spectroscopic masses for MASCARA-2 b and HAT-P-70 b consistent with their known upper limits, but we note that these may be biased due to degeneracies. This work highlights the importance of future HRS studies to further probe differences and trends between exoplanets.

Bisazapentalene Dication: Global Aromaticity and Open-Shell Singlet Ground State

Antiaromatic moieties fused in polycyclic π-conjugated molecules usually exhibit strong localized antiaromaticiy. Herein, we reported the synthesis and properties of a bisazapentalene dication (BAP2+) obtained from in situ two-electron oxidation of neutral species 8. Noteworthily, it possesses global aromaticity and an open-shell singlet ground state. This study underlines the importance of heteroatoms in determining the delocalization of π-electrons and the aromaticity of molecules in their oxidized states.

Beltrami fields in partially ionized magnetized dusty plasma

The relaxed state of a magnetized four-component partially ionized dusty (PID) plasma is explored. PID plasma is composed of inertial electrons, positive ions, neutrals, and static negatively charged dust particles. When the neutrals are dragged along with the ions, the steady-state solution of vortex dynamic equations for inertial electron and ion species yields a triple Beltrami relaxed state, which is a linear combination of three single force-free fields and is characterized by three self-organized structures. The impact of plasma parameters such as Beltrami parameters and neutral (degree of ionization) and dust species densities on the nature of the relaxed state is investigated. Furthermore, the role of scale separation and its implication in space plasma are also presented. The present research will aid in elucidating the role of neutral and dust species in space, astrophysical, and laboratory plasmas.