Interaction Of Ions Research Articles

Molecular Insights into the Effect of Cholesterol on the Binding of Bicarbonate Ions in Band 3 Protein.

Band 3, or anion exchanger 1 (AE1), is one of the indispensable transmembrane proteins involved in the effective respiratory process of the human body and is primarily responsible for the exchange of bicarbonate and chloride anions across the plasma membrane of erythrocyte. However, the molecular mechanism of ion transport of Band 3 is not completely understood, yet. In this work, we systematically investigate the key binding sites of bicarbonate ions in Band 3 and the impact of cholesterol (CHOL) in lipid bilayers on bicarbonate ion binding using all-atom molecular dynamics (MD) simulations. We examine the dynamics of interactions of bicarbonate ions with Band 3 in the microsecond time scale and calculate the binding free energy of the anion in Band 3. The results indicate that the residue R730 of Band 3 is the most probable binding site for bicarbonate ions. CHOL enhances the bicarbonate ion binding by influencing the conformational stability of Band 3 and compressing the volume of the Band 3 cavity. These findings provide some insights into the bicarbonate ion binding in Band 3 and are helpful for understanding the anion exchange of Band 3.

Enhanced adsorption and removal of Cd(II) from aqueous solution by amino-functionalized ZIF-8

Zeolite imidazolate framework-8 (ZIF-8), which is a special subgroup of metal–organic frameworks (MOFs), was synthesized and modified by ethylenediamine (ZIF-8-EDA) to prepare an efficient adsorbent for the high sorption of Cd2+ ions from solution. The synthesized and modified ZIF-8 (ZIF-8-EDA) were characterized by X-ray diffraction (XRD), Fourier-transform infrared (FT-IR) spectroscopy, Brunauer–Emmett–Teller (BET), field emission scanning electron microscopy (FE-SEM) with energy dispersive spectroscopy (EDS), and transmission electron microscopy (TEM) analysis. The optimum conditions for dosage of adsorbent, initial ion concentration, pH, and contact time were 0.05 g/l, 50 mg/l, 6, and 60 min, respectively, for cadmium ion sorption from aqueous solutions with a removal efficiency of 89.7% for ZIF-8 and 93.5% for ZIF-8-EDA. Adsorption kinetics and equilibrium data were analyzed using the Langmuir and Freundlich equations. The Langmuir model fitted the equilibrium data better than the Freundlich model. According to the Langmuir equation, the maximum uptake for the cadmium ions was 294.11(mg/g). The calculated thermodynamic parameters (ΔG°, ΔH°, and ΔS°) indicated that the adsorption process was feasible, spontaneous, and endothermic at 20–50 °C. Based on the results, the amino functionalized ZIF-8 had improved adsorption performance due to the replacing of the starting linker with organic ligands that had effective functional groups, leading to chemical coordination due to the interaction of metal ions with the non-bonding pair of electrons on the N atoms of the amino functional group. The selectivity toward metal ion adsorption by ZIF-8-EDA was Cd2+ > Pb2+ > Ni2+‏.

Influence of sawtooth oscillations on fast ions in a stellarator

Sawtooth oscillations in tokamaks frequently lead to the redistribution of energetic ions, mainly on passing orbits, causing their expulsion from the core. This paper discusses the first measurements of the interaction of fast ions and sawteeth in the Large Helical Device. The crashes were caused by the plasma current induced by Electron Cyclotron Current Drive and Neutral Beam Current Drive. Despite these crashes, there was no detectable redistribution effect on fast ions in either the core or at the edge of the plasma.

Use of Particle Induced X-Ray Emission (PIXE), Particle Induced Gamma–Ray Emission (PIGE), Energy Dispersive X-Ray Analysis (EDXRF) for Detecting Trace Elements in Soil Sample

This review paper provides a comprehensive overview of trace element analysis utilizing ion-atom interaction techniques, focusing on the principles, applications, and recent advancements in the field. Ion- atom interaction techniques, including Particle Induced X- Ray Emission (PIXE), Particle Induced Gamma–Ray Emission (PIGE), Energy Dispersive X-Ray Analysis (EDXRF), Rutherford backscattering spectroscopy (RBS), and ion beam analysis (IBA), offer unique capabilities for trace element analysis with high sensitivity and minimal sample preparation requirements. The paper begins by discussing the fundamental principles underlying ion-atom interaction techniques, such as the interaction of energetic ions with matter and the subsequent detection of emitted X-rays or backscattered particles. It explores the various analytical parameters that influence the sensitivity, resolution, and depth profiling capabilities of these techniques. Furthermore, the review highlights the diverse applications of ion-atom interaction techniques in fields such as environmental monitoring, forensic science, biomedical research, and materials science. It showcases how these techniques have been utilized to address specific analytical challenges, such as the detection of trace contaminants in environmental samples or the characterization of thin films and semiconductor materials.

Sulfite ion and gold (111) surface interaction mechanism

The interaction of a sulfite ion (SO32−) with the Au (111) surface has been studied using density functional theory. The results of the geometry optimization, the charge density distribution, and the density of states showed that sulfite ions exhibit a strong interaction with the Au (111) surface atoms, and they are adsorbed by forming a strong ionic bond that leads to the rearrangement of Au surface atoms. Consequently, this interaction leads to a charge transfer from the sulfite ion to Au surface atoms. The results proved a change in the geometry of the adsorbed sulfite ion, but it is not degraded on the gold surface because of the covalent bonds between sulfur and oxygen atoms.

Impact of Hydrostatic Pressure on Molecular Structure and Dynamics of the Sodium and Chloride Ions in Portlandite Nanopores.

In order to address the issues of energy depletion, more resources are being searched for in the deep sea. Therefore, research into how the deep-sea environment affects cement-based materials for underwater infrastructure is required. This paper examines the impact of ocean depth (0, 500, 1000, and 1500 m) on the ion interaction processes in concrete nanopores using molecular dynamics simulations. At the portlandite interface, the local structural and kinetic characteristics of ions and water molecules are examined. The findings show that the portlandite surface hydrophilicity is unaffected by increasing depth. The density profile and coordination number of ions alter as depth increases, and the diffusion speed noticeably decreases. The main cause of the ions' reduced diffusion velocity is expected to be the low temperature. This work offers a thorough understanding of the cement hydration products' microstructure in deep sea, which may help explain why cement-based underwater infrastructure deteriorates over time.

Exploring Bimetallic Nanoparticles in Alzheimer's Therapy: A Novel Bio-Assisted Synthesis with Multitarget Potential.

Unlocking the potential of metal nanoparticles (NPs) in biomedical applications represents a leading endeavor in contemporary research. Among these, gold NPs (AuNPs) and silver NPs (AgNPs) have shown promising strides in combatting complex neurodegenerative ailments like Alzheimer's disease. Yet, the unexplored realm of bimetallic Au/Ag-NP harbors immense potential, concealing undiscovered opportunities for enhanced therapeutic effectiveness through the synergistic interaction of metal ions. Nonetheless, the limitations of traditional synthesis methods have restricted the preparation, biocompatibility, and versatility of these NPs, prompting an urgent requirement for innovative approaches. Biobased synthetic methodologies have emerged as a noteworthy solution to address these challenges. Our study ventures into uncharted terrain, harnessing collagen-mimicking peptide nanofibers as a bioactive template for the synthesis of bimetallic NPs. These green NPs exhibit remarkable activity in inhibiting amyloid β (Aβ) protein aggregation with almost 74% inhibition, surpassing the individual impacts of Au and Ag NPs, which show inhibition percentages of 66 and 43, respectively. The bimetallic Au/Ag-NPs not only demonstrate powerful inhibition of Aβ, but they also demonstrate inhibitory activity against esterase (∼50%) and against reactive oxygen species (ROS) (∼75%), metamorphosing into multifaceted therapeutic agents for Alzheimer's disease. Au/Ag-NPs have proven highly beneficial in surpassing cellular barriers, as evidenced by studies on tissue penetration, 3D uptake, and endosomal escape, and these attributes also hold promise for the future treatment modalities. The findings indicate that the intrinsic traits of Au/Ag-NPs provide numerous mechanistic benefits, such as inhibiting Aβ and acetylcholinesterase (AChE), and reducing stress related to ROS, in addition to their advantageous internalization properties. This research represents a notable advancement in the development of multitargeted treatments for neurodegenerative disorders using bimetallic NPs, diverging from the prevalent emphasis on AuNPs in the current literature.

Controlled fabrication of upright and inverted pyramid arrays of silicon via the interaction of copper ions and oxidants in hydrofluoric acid

Recent advances in chemical etching of silicon have allowed its widespread use in the fabrication of microelectronic devices and energy converters, in which shaped silicon exhibits outstanding properties and functions. The texturing process used to fabricate light-trapping structures on silicon surfaces is an indispensable step in preparing solar cells. Here, this manuscript describes the use of a one-step wet chemical etching method with copper as a catalyst to manufacture different structures, including inverted pyramid structures and upright pyramid structures, on silicon surfaces, which can be easily controlled by varying the solution composition and etching time. Moreover, this manuscript demonstrates an exciting method for fabricating random inverted pyramid and random upright pyramid arrays of silicon. The findings provide important contributions that can help improve the fabrication methods for silicon-based solar cell devices and optimize the light trapping structure on the cell surface.

Mean force emission theory for classical bremsstrahlung in strongly coupled plasmas

This work presents mean force emission theory, which extends the classical theory of bremsstrahlung emission to strongly coupled plasmas. In the high-frequency limit, the theory reduces to solving for the electron trajectory during a binary collision, but where the electron–ion interactions occur through the potential of mean force. In the low-frequency limit, it uses an autocorrelation formalism that captures effects of multiple collisions and strongly correlated motion. The predictions are benchmarked by comparison with first-principles classical molecular dynamics simulations of a fully ionized hydrogen plasma in which all interactions are repulsive. The comparison shows good agreement up to Coulomb coupling strengths of Γ∼30. The theory improves upon traditional models by including strong coupling effects and systematically including the effect of multiple collisions. Furthermore, mean force emission theory provides evidence that the Drude correction factor commonly used in quantum calculations of optical quantities may not be adequate at strong coupling.

Ion transport mechanism and diffusion model establishment in recycled aggregate concrete subjected to magnesium, sulfate, and chloride attack

Recycled aggregate concrete (RAC), which is used in Northwest China, is inevitably subjected to various aggressive environments. However, the aggressive ions of chloride, sulfate, and magnesium and the original ions of calcium and hydroxide in RAC under the combined action of magnesium-sulfate-chloride attack and dry–wet (D&W) cycles have received little attention in previous studies. Therefore, in this study, the content of aggressive and original ions in exposed RAC was quantified, and the influence of the replacement ratio of supplementary cementitious materials (SCMs) on diffusion was investigated. Results showed that the contents of chloride, sulfate, and magnesium in exposed RAC increased with an increase in the replacement ratio of silica fume (SF) and metakaolin (MK). In contrast, the contents decreased with the increase in the replacement ratio of granulated blast furnace slag (GBFS). At the same exposure time and depth, the content of RAC with ternary cementitious materials from the highest to the lowest was in the order of cement–fly ash –SF, cement–fly ash–MK, and cement–fly ash–GBFS. Visual appearance, relative compressive strength, and the diffusion coefficient exhibited a similar change law. An exponential relationship was observed between the diffusion and time delay coefficients and the replacement ratio of SCMs, and the content of aggressive ions on the exposed surface decreased linearly with increasing exposure time. Diffusion models of aggressive ions were established to consider the multiple effects. Aggressive ion–original ion interaction influenced the mineral phases’ composition in the corrosive zone and led to a difference in the diffusion process and depth.

Effect of bonding description and strain regulation on the conductive transition of Bi semimetal

Due to the differences in the treatment methods of the electron–ion interaction and the critical strain mode of the transition from semimetals to semiconductors, the corresponding strain modulation mechanism in layered bismuth (Bi) crystals remains elusive. In this work, the effects of van der Waals (vdW) correction on the crystal structure and electrical properties of Bi in an equilibrium/strained state are comparatively studied based on the density functional theory. It is found that vdW corrections can better describe the layered crystal and bandgap structure of Bi under equilibrium/strain conditions. With the vdW modification, bismuth can be converted from a semimetal to a semiconductor within a small compression range that is experimentally available. This transition is induced by the transfer of the conduction band minimum and the valence band maximum and is related to the competition of the near-band edge energy state near the Fermi level of bismuth. The present results not only provide guidance for the accurate study of the crystal structure and electronic properties of complex model systems, such as Bi or Bi-based inherently nanostructured materials, but also reveal strain regulation mechanism of Bi and predict its potential application in the semiconductor electronic devices.

Theory of Majorana-Type Heavy Ion Double Charge Exchange Reactions by Pion–Nucleon Isotensor Interactions

The theory of heavy ion double charge exchange (DCE) reactions proceeding by effective rank-2 isotensor interactions is presented. Virtual pion–nucleon charge exchange interactions are investigated as the source for induced isotensor interactions, giving rise to the Majorana DCE (MDCE) reaction mechanism. MDCE is of a generic character, proceeding through pairs of complementary (π±,π∓) reactions in the projectile and target nucleus. The dynamics of the elementary processes is discussed, where the excitation of pion–nucleon resonances are of central importance. Investigations of initial and final state ion–ion interactions show that these effects are acting as vertex renormalizations. In closure approximation, well justified by the finite pion mass, the second-order transition matrix elements reduce to pion potentials and effective two-body isotensor DCE interactions, giving rise also to two-body correlations in either of the participating nuclei. Connections to neutrinoless Majorana double beta decay (MDBD) are elucidated at various levels of the dynamics, from the underlying fundamental electro-weak and QCD scales to the physical scales of nuclear MDBD and MDCE physics. It is pointed out that heavy ion MDCE reactions may also proceed by competing electro-weak charge exchange processes, leading to lepton MDCE by electrons, positrons, and neutrinos.

Surface Tension Estimation of Steel above Boiling Temperature

Surface tension is an important characteristic of materials. In particular at high temperatures, surface tension values are often unknown. However, for metals, these values are highly relevant in order to enable efficient industrial processing or simulation of material behavior. Plasma, electron or laser beam processes can induce such high energy inputs, which increase the metal temperatures to, and even above, boiling temperatures, e.g., during deep penetration welding or remote cutting. Unfortunately, both theoretical and experimental methods experience challenges in deriving surface tension values at high temperatures. Material models of metals have limitations in explaining complex ion interactions, and experimentally measuring temperature and surface tension at high temperatures is a challenge for methods and equipment. Therefore, surface wave analysis was conducted in this work to derive surface tension values around the boiling temperature of steel and identify trends. In addition, a simple ion interaction calculation was used to simulate the impacting parameters that define the surface tension. Since both the experimental values and simulation results indicate an increasing trend in surface tension above the boiling temperature, it is concluded that the dominating attractive forces above this temperature should increase with increasing temperature and lead to increasing surface tension forces in the surface layers of liquid metal.

The study of iron- and copper-binding proteome of Fusarium oxysporum and its effector candidates.

Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron-binding proteins (IBPs) and copper-binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high-throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron-binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate-binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen-host interactions. The insights gained from this report on the role of metal ions in plant-pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.

Probing Ion-Receptor Interactions in Halide Complexes of Octamethyl Calix[4]Pyrrole.

Ion receptors are molecular hosts that bind ionic guests, often with great selectivity. The interplay of solvation and ion binding in anion host-guest complexes in solution governs the binding efficiency and selectivity of such ion receptors. To gain molecular-level insight into the intrinsic binding properties of octamethyl calix[4]pyrrole (omC4P) host molecules with halide guest ions, we performed cryogenic ion vibrational spectroscopy (CIVS) of omC4P in complexes with fluoride, chloride, and bromide ions. We interpret the spectra using density functional theory, describing the infrared spectra of these complexes with both harmonic and anharmonic second-order vibrational perturbation theory (VPT2) calculations. The NH stretching modes of the pyrrole moieties serve as sensitive probes of the ion binding properties, as their frequencies encode the ion-receptor interactions. While scaled harmonic spectra reproduce the experimental NH stretching modes of the chloride and bromide complexes in broad strokes, the high proton affinity of fluoride introduces strong anharmonic effects. As a result, the spectrum of F-·omC4P is not even qualitatively captured by harmonic calculations, but it is recovered very well by VPT2 calculations. In addition, the VPT2 calculations recover the intricate coupling of the NH stretching modes with overtones and combination bands of CH stretching and NH bending modes and with low-frequency vibrations of the omC4P macrocycle, which are apparent for all of the halide ion complexes investigated here. A comparison of the CIVS spectra with infrared spectra of solutions of the same ion-receptor complexes in d3-acetonitrile and d6-acetone shows how ion solvation changes the ion-receptor interactions for the different halide ions.

Optical control of 4f orbital state in rare-earth metals.

A change of orbital state alters the coupling between ions and their surroundings drastically. Orbital excitations are hence key to understand and control interaction of ions. Rare-earth elements with strong magneto-crystalline anisotropy (MCA) are important ingredients for magnetic devices. Thus, control of their localized 4f magnetic moments and anisotropy is one major challenge in ultrafast spin physics. With time-resolved x-ray absorption and resonant inelastic scattering experiments, we show for Tb metal that 4f-electronic excitations out of the ground-state multiplet occur after optical pumping. These excitations are driven by inelastic 5d-4f-electron scattering, altering the 4f-orbital state and consequently the MCA with important implications for magnetization dynamics in 4f-metals and more general for the excitation of localized electronic states in correlated materials.

Investigation of cathinone analogs targeting human dopamine transporter using molecular modeling

In a step towards understanding the structure–property relationship among Synthetic Cathinones (SCs), a combined methodology based on Density Functional Theory (DFT), Administration, Distribution, Metabolism, Excretion, and Toxicity (ADMET) predictions, docking and molecular dynamics simulations have been applied to correlate physicochemical descriptors of various SCs to their biological activity. The results from DFT and molecular docking studies correlate well with each other explaining the biological activity trends of the studied SCs. Quantum mechanical descriptors viz. polarizability, electron affinity, ionization potential, chemical hardness, electronegativity, molecular electrostatic potential, and ion interaction studies unravel the distinguishingly reactive nature of Group D (pyrrolidine substituted) and Group E (methylenedioxy and pyrrolidine substituted) compounds. According to ADMET analysis, Group D and Group E molecules have a higher probability of permeating through the blood–brain barrier. Molecular docking results indicate that Phe76, Ala77, Asp79, Val152, Tyr156, Phe320, and Phe326 constitute the binding pocket residues of hDAT in which the most active ligands MDPV, MDPBP, and MDPPP are bound. Finally, to validate the derived quantum chemical descriptors and docking results, Molecular Dynamics (MD) simulations are performed with homology-modelled hDAT (human dopamine transporter). The MD simulation results revealed that the majority of SCs remain stable within the hDAT protein’s active sites via non-bonded interactions after 100 ns long simulations. The findings from DFT, ADMET analysis, molecular docking, and molecular dynamics simulation studies complement each other suggesting that pyrrolidine-substituted SCs (Group D and E), specifically, MPBP and PVN are proven potent SCs along with MDPV, validating various experimental observations. Communicated by Ramaswamy H. Sarma

Toward Modeling the Structure of Electrolytes at Charged Mineral Interfaces Using Classical Density Functional Theory.

The organization of water molecules and ions between charged mineral surfaces determines the stability of colloidal suspensions and the strength of phase-separated particulate gels. In this article, we assemble a density functional that measures the free energy due to the interaction of water molecules and ions in electric double layers. The model accounts for the finite size of the particles using fundamental measure theory, hydrogen-bonding between water molecules using Wertheim's statistical association theory, long-range dispersion interactions using Barker and Henderson's high-temperature expansion, electrostatic correlations using a functionalized mean-spherical approximation, and Coulomb forces through the Poisson equation. These contributions are shown to produce highly correlated structures, aptly rendering the layering of counterions and co-ions at highly charged surfaces and permitting the solvation of ions and surfaces to be measured by a combination of short-range associations and long-ranged attractions. The model is tested in a planar geometry near soft, charged surfaces to reproduce the structure of water near graphene and mica. For mica surfaces, explicitly representing the density of the outer oxygen layer of the exposed silica tetrahedra allows water molecules to hydrogen-bond to the solid. When electrostatic interactions are included, water molecules assume a hybrid character, being accounted for implicitly in the dielectric constant but explicitly otherwise. The disjoining pressure between approaching like-charged surfaces is calculated, demonstrating the model's ability to probe pressure oscillations that arise during the expulsion of ions and water layers from the interfacial gap and predict strong interattractive stresses that form at narrow interfacial spacing when the surface charge is overscreened. This interattractive stress arises not due to in-plane correlations under strong electrostatic coupling but due to the out-of-plane structuring of associating ions and water molecules.

Selective and Effective Sensing of Cyanide Ion with no Interference in Water by Phenothiazine-indolium Fused Optical Sensor.

The sensor with electron donor phenothiazine-2-carbaldehyde and electron acceptor indolium carboxylic acid, is developed with an intramolecular charge transfer transition between them. The synthesized molecule senses cyanide ion in water. The cyanide ion reacts with the molecule via nucleophilic addition in the indolium ring with a noticeable purple to colorless change in the solution observed. Also with the cyanide ion interaction, the sensor exhibits change in UV-visible absorption and fluorescence spectra. While the other ion does not show spectral and visual changes when interacts with the sensor molecule. Also the interference study reveals that the molecule is highly selective towards cyanide ion. Different source of water samples confirms the CN- ion sensing efficiency of the molecule. 1:1 interaction between the molecule PTI and cyanide ion is confirmed from the results of Jobs plot, 1H NMR and HRMS. Paper strips were prepared and this can act as a simple tool to sense cyanide ion in various water samples.

Toward Distinguishing between the Superchaotropic and Hydrophobic Characters of Nanometric-Sized Ions in Interaction with PEGylated Surfaces.

In this study, we explore the superchaotropic effect of various polyoxometalate or boron cluster nano-ions on hydrophilic neutral surfaces. Nano-ions, characterized by low charge densities, exhibit strong adsorption on non-ionic hydrophilic surfaces like PEGylated micelles. This adsorption phenomenon was attributed to the enthalpically favorable dehydration of nano-ions, the so-called superchaotropic effect. Here, we investigate the adsorption of three nano-ions, α-SiW12O404-, α-PW12O403-, and B12I122-, with decreasing charge density or increasing superchaotropicity (or hydrophobicity), on hydrophilic solid surfaces, PEGylated gold nanoparticles, and PEGylated gold-coated quartz crystal. Solid surfaces are devoid of hydrophobic regions, enabling the study of the subtle nuance between hydrophobic and superchaotropic effects. Unlike adsorption on PEGylated micelles, the adsorption constant decreases with a reduced charge density, aligning with the well-established principle that hydrophobic ions do not adsorb on hydrophilic surfaces. This research improves our understanding of the subtle difference between superchaotropic and hydrophobic effects in nano-ion adsorption phenomena.