Abstract: Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.

Abstract: Nonthermal plasma is a promising alternative for ammonia synthesis at gentle conditions. Metal meshes of Fe, Cu, Pd, Ag, and Au were employed as catalysts in radio frequency plasma for ammonia synthesis. The energy yield for all these transition metal catalysts ranged between 0.12 and 0.19 g-NH3/kWh at 300 W and, thus, needs further improvement. In addition, a semimetal, pure gallium, was used for the first time as catalyst for ammonia synthesis, with energy yield of 0.22 g-NH3/kWh and with a maximum yield of ∼10% at 150 W. The emission spectra, as well as computer simulations, revealed hydrogen recombination as a primary governing parameter, which depends on the concentration or flux of H atoms in the plasma and on the catalyst surface. The simulations helped to elucidate the underlying mechanism, implicating the dominance of surface reactions and surface adsorbed species. The rate limiting step appears to be NH2 formation on the surface of the reactor wall and on the catalyst surface, which is different from classical catalysis.

Abstract: Ammonia is a crucial nutrient used for plant growth and as a building block in pharmaceutical and chemical industry, produced via nitrogen fixation of the ubiquitous atmospheric N2. Current industrial ammonia production relies heavily on fossil resources, but a lot of work is put into developing non-fossil based pathways. Among these is the use of nonequilibrium plasma. In this work, we investigated water vapor as H source for nitrogen fixation into NH3 by non-equilibrium plasma. The highest selectivity towards NH3 was observed with low amounts of added H2O vapor, but the highest production rate was reached at high H2O vapor.

Abstract: The continuous miniaturization of nanodevices, such as transistors, solar cells, and optical fibers, requires the controlled synthesis of (ultra)thin gate oxides (<10 nm), including Si gate-oxide (SiO2) with high quality at the atomic scale. Traditional thermal growth of SiO2 on planar Si surfaces, however, does not allow one to obtain such ultrathin oxide due to either the high oxygen diffusivity at high temperature or the very low sticking ability of incident oxygen at low temperature. Two recent techniques, both operative at low (room) temperature, have been put forward to overcome these obstacles: (i) hyperthermal oxidation of planar Si surfaces and (ii) thermal or plasma-assisted oxidation of nonplanar Si surfaces, including Si nanowires (SiNWs). These nanooxidation processes are, however, often difficult to study experimentally, due to the key intermediate processes taking place on the nanosecond time scale.
In this Account, these Si nano-oxidation techniques are discussed from a computational point of view and compared to both hyperthermal and thermal oxidation experiments, as well as to well-known models of thermal oxidation, including the Deal−Grove, Cabrera−Mott, and Kao models and several alternative mechanisms. In our studies, we use reactive molecular dynamics (MD) and hybrid MD/Monte Carlo simulation techniques, applying the Reax force field. The incident energy of oxygen species is chosen in the range of 1−5 eV in hyperthermal oxidation of planar Si surfaces in order to prevent energy-induced damage. It turns out that hyperthermal growth allows for two growth modes, where the ultrathin oxide thickness depends on either (1) only the kinetic energy of the incident oxygen species at a growth temperature below Ttrans = 600 K, or (2) both the incident energy and the growth temperature at a growth temperature above Ttrans. These modes are specific to such ultrathin oxides, and are not observed in traditional thermal oxidation, nor theoretically considered by already existing models. In the case of thermal or plasma-assisted oxidation of small Si nanowires, on the other hand, the thickness of the ultrathin oxide is a function of the growth temperature and the nanowire diameter. Below Ttrans, which varies with the nanowire diameter, partially oxidized SiNW are formed, whereas complete oxidation to a SiO2 nanowire occurs only above Ttrans. In both nano-oxidation processes at lower temperature (T < Ttrans), final sandwich c-Si|SiOx|a-SiO2 structures are obtained due to a competition between overcoming the energy barrier to penetrate into Si subsurface layers and the compressive stress (∼2−3 GPa) at the Si crystal/oxide interface. The overall atomic-simulation results strongly indicate that the thickness of the intermediate SiOx (x < 2) region is very limited (∼0.5 nm) and constant irrespective of oxidation parameters. Thus, control over the ultrathin SiO2 thickness with good quality is indeed possible by accurately tuning the oxidant energy, oxidation temperature and surface curvature.
In general, we discuss and put in perspective these two oxidation mechanisms for obtaining controllable ultrathin gate-oxide films, offering a new route toward the fabrication of nanodevices via selective nano-oxidation.

Abstract: Synchrotron radiation (SR)-based X-ray methods are powerful analytical tools for several purposes. They are widely used to probe the degradation mechanisms of inorganic artists' pigments in paintings, including chrome yellows (PbCr1-xSxO4; 0 <= x <= 0.8), a class of compounds often found in Van Gogh masterpieces. However, the high intensity and brightness of SR beams raise important issues regarding the potential damage inflicted on the analyzed samples. A thorough knowledge of the SR X-ray sensitivity of each class of pigment in the painting matrix is therefore required to find analytical strategies that seek to minimize the damage for preserving the integrity of the analyzed samples and to avoid data misinterpretation. Here, we employ a combination of Cr K-edge X-ray absorption near-edge structure spectroscopy, Cr-K-beta X-ray emission spectroscopy, and X-ray diffraction to monitor and quantify the effects of SR X-rays on the stability of chrome yellows and related Cr compounds and to define mitigation strategies. We found that the SR X-ray beam exposure induces changes in the oxidation state and local coordination environment of Cr ions and leads to a loss of the compound's crystalline structure. The extent of X-ray damage depends on some intrinsic properties of the samples (chemical composition of the pigment and the presence/absence and nature of the binder). It can be minimized by optimizing the overall fluence/dose released to the samples and by working in vacuum and under cryogenic conditions.

Abstract: Detection of antigenic biomarkers present in trace amounts is of crucial importance for medical diagnosis. A parasitic disease, human toxocariasis, lacks an adequate diagnostic method despite its worldwide occurrence. The currently used serology tests may stay positive even years after a possibly unnoticed infection, whereas the direct detection of a re-infection or a still active infection remains a diagnostic challenge due to the low concentration of circulating parasitic antigens. We report a time-efficient sandwich immunosensor using small recombinant single-domain antibodies (nanobodies) derived from camelid heavy-chain antibodies specific to Toxocara canis antigens. An enhanced sensitivity to pg/mL levels is achieved by using a redox cycle consisting of a photocatalytic oxidation and electrochemical reduction steps. The photocatalytic oxidation is achieved by a photosensitizer generating singlet oxygen (1O2) that, in turn, readily reacts with p-nitrophenol enzymatically produced under alkaline conditions. The photooxidation produces benzoquinone that is electrochemically reduced to hydroquinone, generating an amperometric response. The light-driven process could be easily separated from the background, thus making amperometric detection more reliable. The proposed method for detection of the toxocariasis antigen marker shows superior performances compared to other detection schemes with the same nanobodies and outperforms by at least two orders of magnitude the assays based on regular antibodies, thus suggesting new opportunities for electrochemical immunoassays of challenging low levels of antigens.

Abstract: Formation and aggregation of metal carboxylates (metal soaps) can degrade the appearance and integrity of oil paints, challenging efforts to conserve painted works of art. Endeavors to understand the root cause of metal soap formation have been hampered by the limited spatial resolution of Fourier transform infrared microscopy (mu-FTIR). We overcome this limitation using optical photothermal infrared spectroscopy (O-PTIR) and photothermal-induced resonance (PTIR), two novel methods that provide IR spectra with approximate to 500 and approximate to 10 nm spatial resolutions, respectively. The distribution of chemical phases in thin sections from the top layer of a 19th-century painting is investigated at multiple scales (mu-FTIR approximate to 10(2) mu m(3), O-PTIR approximate to 10(-1) mu m(3), PTIR approximate to 10(-5) mu m(3)). The paint samples analyzed here are found to be mixtures of pigments (cobalt green, lead white), cured oil, and a rich array of intermixed, small (often << 0.1 mu m(3)) zinc soap domains. We identify Zn stearate and Zn oleate crystalline soaps with characteristic narrow IR peaks (approximate to 1530-1558 cm(-1)) and a heterogeneous, disordered, water-permeable, tetrahedral zinc soap phase, with a characteristic broad peak centered at approximate to 1596 cm(-1). We show that the high signal-to-noise ratio and spatial resolution afforded by O-PTIR are ideal for identifying phase-separated (or locally concentrated) species with low average concentration, while PTIR provides an unprecedented nanoscale view of distributions and associations of species in paint. This newly accessible nanocompositional information will advance our knowledge of chemical processes in oil paint and will stimulate new art conservation practices.

Abstract: This study aims at sensing in situ reactive oxygen and nitrogen species (RONS) and specifically superoxide anion (O-2(center dot-)) in aqueous buffer solutions exposed to cold atmospheric plasmas (CAPs). CAPs were generated by ionizing He gas shielded with variable N-2/O-2 mixtures. Thanks to ultramicroelectrodes protected against the high electric fields transported by the ionization waves of CAPs, the production of superoxide and several RONS was electrochemically directly detected in liquids during their plasma exposure. Complementarily, optical emissive spectroscopy (OES) was used to study the plasma phase composition and its correlation with the chemistry in the exposed liquid. The specific production of O-2(center dot-), a biologically reactive redox species, was analyzed by cyclic voltammetry (CV), in both alkaline (pH 11), where the species is fairly stable, and physiological (pH 7.4) conditions, where it is unstable. To understand its generation with respect to the plasma chemistry, we varied the shielding gas composition of CAPs to directly impact on the RONS composition at the plasma-liquid interface. We observed that the production and accumulation of RONS in liquids, including O(2)(center dot-)depends on the plasma composition, with N-2-based shieldings providing the highest superoxide concentrations (few 10s of micromolar at most) and of its derivatives (hundreds of micromolar). In situ spectroscopic and electrochemical analyses provide a high resolution kinetic and quantitative understanding of the interactions between CAPs and physiological solutions for biomedical applications.

Abstract: Mixed hemi/ad-micelle sodium dodecyl sulfate (SDS)-coated magnetic iron oxide nanoparticles (MHAMS-MIONPs) were used as an efficient adsorbent for both removal and preconcentration of two important carcinogenic xanthine dyes named rhodamine-B (RB) and rhodamine-6G (RG). To gain insight in the configuration of SDS molecules on the surface of MIONPs, zeta potential measurements were performed in different [SDS]/[MIONP] ratios. Zeta potential data indicated that mixed hemi/ad-micelle MHAM was formed in [SDS]/[MIONP] ratios over the range of 1.1 to 7.3. Parameters affecting the adsorption of dyes were optimized as removal efficiency by one variable at-a-time and response surface methodology; the obtained removal efficiencies were ∼100%. Adsorption kinetic and equilibrium studies, under the optimum condition (pH = 2; amount of MIONPs = 87.15 mg; [SDS]/[MIONP] ratio = 2.9), showed that adsorption of both dyes are based on the pseudo-second-order and the Langmuir isotherm models, respectively. The maximum adsorption capacities for RB and RG were 385 and 323 mg g1, respectively. MHAMS-MIONPs were also applied for extraction of RB and RG. Under optimum conditions (pH = 2; amount of damped MHAMS-MIONPs = 90 mg; eluent solvent volume = 2.6 mL of 3% acetic acid in acetonitrile), extraction recoveries for 0.5 mg L1 of RB and RG were 98% and 99%, with preconcentration factors of 327 and 330, respectively. Limit of detection obtained for rhodamine dyes were <0.7 ng mL1. Finally, MHAMS-MIONPs were successfully applied for both removal and trace determination of RB and RG in environmental and wastewater samples.

Abstract: We have computationally investigated the introduction of copper elemental particles in an inductively coupled plasma torch connected to a sampling cone, including for the first time the ionization of the sample. The sample is inserted as liquid particles, which are followed inside the entire torch, i.e., from the injector inlet up to the ionization and reaching the sampler. The spatial position of the ion clouds inside the torch as well as detailed information on the copper species fluxes at the position of the sampler orifice and the exhausts of the torch are provided. The effect of on- and off-axis injection is studied. We clearly show that the ion clouds of on-axis injected material are located closer to the sampler with less radial diffusion. This guarantees a higher transport efficiency through the sampler cone. Moreover, our model reveals the optimum ranges of applied power and flow rates, which ensure the proper position of ion clouds inside the torch, i.e., close enough to the sampler to increase the fraction that can enter the mass spectrometer and with minimum loss of material toward the exhausts as well as a sufficiently high plasma temperature for efficient ionization.

Abstract: Synchrotron radiation phase-contrast computed nanotomography (nano-CT) and two-and three-dimensional (2D and 3D) nanoscopic X-ray fluorescence (nano-XRF) were used to investigate the internal distribution of engineered-cobalt nanoparticles (Co NPs) in exposed individuals of the nematode Caenorhabditis elegans. Whole-nematodes and selected tissues and organs were 3D-rendered: anatomical 3D renderings with 50 nm voxel size enabled the visualization of spherical nanoparticle aggregates. with size tip to 200 nm within intact C. elegans. A 20 X 37 nm(2) high-brilliance beam was employed to obtain XRF elemental distribution maps of entire nematodes or anatomical details such as embryos, which could be compared with the CT data, These maps showed Co NPs to be predominantly present within the intestine and the epithelium, and they were not colocalized with Zn granules found in the lysosonie-containing vesicles or Fe agglomerates in the intestine. Iterated XRF scanning of a specimen at 0 degrees and 90 degrees angles suggested that NP aggregates were translocated into tissues outside of the intestinal lumen. Virtual-slicing by means of 2D XRF tomography, combined with holotomography, indicated presumable presence of individual NP aggregates inside the uterus and within embryos.

Abstract: In the past decade macroscopic X-ray fluorescence imaging (MA-XRF) has become established as a method for the noninvasive investigation of flat painted surfaces, yielding large scale elemental maps. MA-XRF is limited by a lack of specificity, only allowing for indirect pigment identification based on the simultaneous presence of chemical elements. The high specificity of X-ray powder diffraction (XRPD) mapping is already being exploited at synchrotron facilities for investigations at the (sub)microscopic scale, but the technique has not yet been employed using lab sources. In this paper we present the development of a novel MA-XRPD/XRF instrument based on a laboratory X-ray source. Several combinations of X-ray sources and area detectors are evaluated in terms of their spatial and angular resolution and their sensitivity. The highly specific imaging capability of the combined MA-XRPD/XRF instrument is demonstrated on a 15th/16th century illuminated manuscript directly revealing the distribution of a large number of inorganic pigments, including the uncommon yellow pigment massicot (o-PbO). The case study illustrates the wealth of new mapping information that can be obtained in a noninvasive manner using the laboratory MA-XRPD/XRF instrument.

Abstract: This paper presents electrochemical strategies for the fast screening of cocaine and most common cutting agents found in seized drug samples. First, a study on the performance of Scott color tests on cocaine and a wide range of cutting agents is described. The cutting agents causing false positive or false negative results when in mixture with cocaine are identified. To overcome the lack of specificity of color tests, we further propose a fast screening strategy by means of square wave voltammetry on disposable graphite screen printed electrodes, which reveals the unique fingerprint of cocaine and cutting agents. By employing a forward and backward scan and by a dual pH strategy, we enrich the electrochemical fingerprint and enable the simultaneous detection of cocaine and cutting agents. The effectiveness of the developed strategies was tested for the detection of cocaine in seized cocaine samples and compared with the color tests. Moreover, we prove the usefulness of square wave voltammetry for predicting possible interfering agents in color tests, based on the reduction peak of cobalt thiocyanate. The developed electrochemical strategies allow for a quick screening of seized cocaine samples resulting in a selective identification of drugs and cutting agents.

Abstract: This Feature addresses the analysis of the reactive species generated by nonthermal atmospheric
pressure plasmas, which are widely employed in industrial and biomedical research, as well as first
clinical applications. We summarize the progress in detection of plasma-generated short-lived
reactive oxygen and nitrogen species in aqueous solutions, discuss the potential and limitations of
various analytical methods in plasma−liquid systems, and provide an outlook on the possible future
research goals in development of short-lived reactive species analysis methods for a general
nonspecialist audience.