Search Results (315)

Under normal conditions, the novel zinc blende beryllium oxide (zb BeO) exhibits in a metastable crystalline phase, which is less stable than its wurtzite counterpart. Ultrathin zb BeO epifilms have recently gained significant interest to create a wide range of advanced high-resolution, high-frequency, flexible, transparent, nano-electronic and nanophotonic modules. BeO-based ultraviolet photodetectors and biosensors are playing important roles in providing safety and efficiency to nuclear reactors for their optimum operations. In thermal management, BeO epifilms have also been used for many high-tech devices including medical equipment. Phonon characteristics of zb BeO at ambient and high-pressure P ≠ 0 GPa are required in the development of electronics that demand enhanced heat dissipation for improving heat sink performance to lower the operating temperature. Here, we have reported methodical simulations to comprehend P-dependent structural, phonon and thermodynamical properties by using a realistic rigid-ion model (RIM). Unlike zb ZnO, the study of the Grüneisen parameter γ(T) and thermal expansion coefficient α(T) in zb BeO has revealed atypical behavior. Possible reasons for such peculiar trends are attributed to the combined effect of the short bond length and strong localization of electron charge close to the small core size Be atom in BeO. Results of RIM calculations are compared/contrasted against the limited experimental and first-principle data. Full article

The mechanism by which voltage-gated ion channels open and close has been the subject of intensive investigation for decades. For a large class of potassium channels and related sodium channels, the consensus has been that the gating current preceding the main ionic current is a large movement of positively charged segments of protein from voltage-sensing domains that are mechanically connected to the gate through linker sections of the protein, thus opening and closing the gate. We have pointed out that this mechanism is based on evidence that has alternate interpretations in which protons move. Very little literature considers the role of water and protons in gating, although water must be present, and there is evidence that protons can move in related channels. It is known that water has properties in confined spaces and at the surface of proteins different from those in bulk water. In addition, there is the possibility of quantum properties that are associated with mobile protons and the hydrogen bonds that must be present in the pore; these are likely to be of major importance in gating. In this review, we consider the evidence that indicates a central role for water and the mobility of protons, as well as alternate ways to interpret the evidence of the standard model in which a segment of protein moves. We discuss evidence that includes the importance of quantum effects and hydrogen bonding in confined spaces. K⁺ must be partially dehydrated as it passes the gate, and a possible mechanism for this is considered; added protons could prevent this mechanism from operating, thus closing the channel. The implications of certain mutations have been unclear, and we offer consistent interpretations for some that are of particular interest. Evidence for proton transport in response to voltage change includes a similarity in sequence to the H_v1 channel; this appears to be conserved in a number of K⁺ channels. We also consider evidence for a switch in -OH side chain orientation in certain key serines and threonines. Full article

The solvatochromic properties of 48 solvents of three benzo-[f]-quinolinium methylids (BfQs) were analyzed within the theories of the variational model and Abe’s model of the liquid. The electro-optical properties of BfQs in the first excited state were determined based on the charge transfer process that occurs from the ylid carbon to the nitrogen atom. The dipole moments and the polarizabilities in the first excited state were calculated according to the two models. The quantum chemical calculations helped in understanding the relationship between the molecular structure and absorption properties of the ground state. It is concluded that several key parameters modulate the strength of the charge transfer and they work in synergy, and the most important are as follows: (i) isomerism around the single polar bond, and (ii) the properties of the solvent. The link between geometrical conformation and the zwitterionic character make the studied BfQs very sensitive chromophores for sensors and optical switching devices. Full article

The dynamic phosphorylation of the human RNA Pol II CTD establishes a code applicable to all eukaryotic transcription processes. However, the ability of these specific post-translational modifications to convey molecular signals through structural changes remains unclear. We previously explained that each gene can be modeled as a combination of n circuits connected in parallel. RNA Pol II accesses these circuits and, through a series of pulses, matches the resonance frequency of the DNA qubits, enabling it to extract genetic information and quantum teleport it. Negatively charged phosphates react under RNA Pol II catalysis, which increases the electron density on the deoxyribose acceptor carbon (2’C in the DNA sugar backbone). The phosphorylation effect on the stability of a carbon radical connects tyrosine to the nitrogenous base, while the subsequent pulses link the protein to molecular water through hydrogen bonds. The selective activation of inert C(sp³)–H bonds begins by reading the quantum information stored in the nitrogenous bases. The coupling of hydrogen proton transfer with electron transfer in water generates a supercurrent, which is explained by the correlation of pairs of the same type of fermions exchanging a boson. All these changes lead to the formation of a molecular protein–DNA–water transcriptional condensate. Full article

The one-dimensional (1D) Sb(III)-based organic–inorganic hybrid perovskite (AImd)₂¹_∞[SbI₅] (AImd = 1-allylimidazolium) crystallizes in the orthorhombic, centrosymmetric space group Pnma. The structure consists of corner-sharing [SbI₆] octahedra forming 1D chains separated by allylimidazolium cations. Void analysis through Mercury CSD software confirmed a densely packed lattice with a calculated void volume of 1.1%. Integrated quantum theory of atoms in molecules (QTAIM) and non-covalent interactions index (NCI) analyses showed that C–H···I interactions between the cations and the ¹_∞[SbI₅]²⁻ network predominantly stabilize the supramolecular assembly followed by N–H···I hydrogen bonds. The calculated growth morphology (GM) model fits very well to the experimental morphology. UV–Vis diffuse reflectance spectroscopy allowed us to determine the optical band gap to 3.15 eV. Density functional theory (DFT) calculations employing the B3LYP, CAM-B3LYP, and PBE0 functionals were benchmarked against experimental data. CAM-B3LYP best reproduced Sb–I bond lengths, while PBE0 more accurately captured the HOMO–LUMO gap and the associated electronic descriptors. These results support the assignment of an inorganic-to-organic [Sb–I] → π* charge-transfer excitation, and clarify how structural dimensionality and cation identity shape the material’s optoelectronic properties. Full article

This study examines the environmental challenges posed by azo-dye pollutants and aluminum industrial waste. Aluminum oxide nanoparticles (P/Al₂O₃-NPs) were produced using a green method that utilized pharmaceutical packaging waste as an aluminum source and marine algae extract (Padina pavonica) as reducing and stabilizing agents and that was characterized by XRD, EDX, SEM, TEM, and zeta potential. Batch biosorption studies were performed to assess the effectiveness of P/Al₂O₃-NPs in removing CR dye from aqueous solutions. The results demonstrate that the particle sizes range from 58.63 to 86.70 nm and morphologies vary from spherical to elliptical. FTIR analysis revealed Al–O lattice vibrations at 988 and 570 cm⁻¹. The nanoparticles displayed a negative surface charge (−13 mV) and a pH_zpc of 4.8. Adsorption experiments optimized parameters for CR dye removal, achieving 97.81% efficiency under native pH (6.95), with a dye concentration of 30 mg/L, an adsorbent dosage of 0.1 g/L, and a contact time of 30 min. Thermodynamic studies confirmed that the process is exothermic and spontaneous. Kinetic data fit well with the pseudo-second-order model, while equilibrium data aligned with the Langmuir isotherm. The adsorption mechanism involved van der Waals forces, hydrogen bonding, and π–π interactions, as supported by the influence of pH, isotherm data, and FTIR spectra. Overall, the study demonstrates the potential of eco-friendly P/Al₂O₃-NPs to efficiently remove CR dye from aqueous solutions. Full article

This study presents the synthesis, physicochemical characterization, and biological evaluation of a novel ternary nickel(II) complex with isoleucine and 1,10-phenanthroline ligands, [Ni(Phen)(Ile)₂]∙6H₂O, designed as a potential antitumor agent. Single-crystal X-ray diffraction revealed a monoclinic structure (C2-space group) with an octahedral Ni(II) coordination involving Phen and Ile ligands. A Hirshfeld surface analysis highlighted intermolecular interactions stabilizing the crystal lattice, with hydrogen bonds (H···H and O···H/H···O) dominating (99.1% of contacts). Density functional theory (DFT) calculations, including solvation effects (in water and methanol), demonstrated strong agreement with the experimental geometric parameters and revealed higher affinity to the water solvent. The electronic properties of the complex, such as HOMO−LUMO gaps (3.20–4.26 eV) and electrophilicity (4.54–5.88 eV), indicated a charge-transfer potential suitable for biological applications through interactions with biomolecules. Raman and infrared spectroscopic studies showed vibrational modes associated with Ni–N/O bonds and ligand-specific deformations, with solvation-induced shifts observed. A study using ultraviolet–visible–near-infrared absorption spectroscopy demonstrated that the complex remains stable in solution. In vitro cytotoxicity assays against MCF-7 (breast adenocarcinoma) and HCT-116 (colorectal carcinoma) cells showed dose-dependent activity, achieving 47.6% and 65.3% viability reduction at 100 μM (48 h), respectively, with lower toxicity to non-tumor lung fibroblasts (GM07492A, 39.8%). Supporting the experimental data, we performed computational modeling to examine the pharmacokinetic profile, with particular focus on the absorption, distribution, metabolism, and excretion properties and drug-likeness potential. Full article

Recently, it has been proposed that plant melatonin receptors belong to the superfamily of G protein-coupled receptors (GPCRs). However, a detailed description of the phylogeny, protein structure, and binding properties of melatonin, which is still lacking, can help determine the signaling and function of this compound. Melatonin receptor homologs (PMTRs) were identified in 90 Viridiplantae sensu lato proteomes using profile Hidden Markov Models (HMM), which yielded 174 receptors across 87 species. Phylogenetic analysis revealed an expansion of PMTR sequences in angiosperms, which were grouped into three clades. Docking studies uncovered a conserved internal melatonin-binding site in PMTRs, which was analogous to the site in human MT1 receptors. Binding affinity simulations indicated this internal site exhibits stronger melatonin binding compared to a previously reported superficial pocket. Ligand–receptor interaction analysis and alanine scanning highlighted a major role of hydrophobic interactions, with hydrogen bonds contributing predominantly at the internal site, while non-interacting charged residues stabilize the binding pocket. Tunnel and ligand transport simulations suggested melatonin moves favorably through the internal cavity to access the binding site. Also, we presented for the first time details of these pockets in a non-model species, Capsicum chinense. Taken together, the structural analyses presented here illustrate opportunities and theoretical evidence for performing structure–function studies via mutations in specific residues within the proposed new melatonin-binding site in PMTRs, shedding light on their role in plant melatonin signaling. Full article

Black, needle-like single crystals of [Pd@Bi₁₀][AlCl₄]₄ were synthesized in a one-pot reaction between PdCl₂, Bi, and BiCl₃ at 180 °C in the Lewis acidic ionic liquid (LAIL) medium [BMIm]Cl∙4.2AlCl₄ (BMIm = 1-n-butyl-3-methylimidazolium). Single-crystal X-ray diffraction revealed that the compound crystallizes in the triclinic space group P$\overline{1}$ with the unit cell parameters a = 11.0233(5) Å, b = 26.1892(14) Å, c = 26.2687(14) Å, α = 90.842(2)°, β = 92.1940(10)°, γ = 91.164(2)°, closely matching its platinum-containing analog. The structure features pentagonal antiprismatic [Pd@Bi₁₀]⁴⁺ cluster cations charge-balanced by tetrahedral [AlCl₄]⁻ anions. Bonding and charge analysis reveal unoptimized Pd–Bi and strong Bi–Bi covalent interactions consistent with electronegativity trends and the previously reported host–guest model. Electronic structure calculations performed with the TB-LMTO-ASA program show that [Pd@Bi₁₀][AlCl₄]₄ exhibits semiconducting behavior, suggesting a bandgap opening of 0.71 eV. Full article

This study investigated strontium (Sr²⁺) adsorption by Taiwan Zhi-Shin bentonite (cation exchange capacity (CEC): 80–86 meq 100 g⁻¹) using Sr(NO₃)₂-simulated nuclear waste. Kinetic analysis revealed pseudo-second-order adsorption kinetics, achieving 95% Sr²⁺ removal within 5 min at pH 9. Isothermal studies showed a maximum capacity of 0.28 mmol g⁻¹ (56 meq 100 g⁻¹) at 15 mmol L⁻¹ Sr²⁺, accounting for 65–70% CEC and fitting the Freundlich model. Cation exchange was the dominant mechanism (84% contribution), driven by Sr²⁺ displacing interlayer Ca²⁺. Alkaline conditions (pH > 9) enhanced adsorption through improved surface charge and electrostatic attraction. Thermodynamic studies demonstrated temperature-dependent behavior: increasing temperature reduced adsorption at 0.01 mM Sr²⁺ but increased efficiency at 10 mM. Na⁺ addition suppressed adsorption, aligning with cation exchange mechanisms. Molecular dynamics simulations identified hydrated Ca²⁺-Sr²⁺ water bridges interacting with bentonite via hydrogen-bonding networks. The material exhibits rapid kinetics (5 min equilibrium), alkaline pH optimization, and resistance to ion interference, making it suitable for emergency Sr²⁺ treatment. It shows promise as a cost-effective and good performing adsorbent for radioactive waste solutions. Full article

Polymer coatings as thin films stand out as a commonly used strategy to modify biosensor surfaces for improving detection performance; however, nonspecific biomolecule interactions and the limited degree of ligand conjugation on the surface have necessitated the development of innovative methods for surface modification. To this end, methacrylated tethered telechelic polyethylene glycol (PEG-diMA) chains of three different molecular weights (2, 6, and 10 kDa) were synthesized herein and used for obtaining thiolated nanoparticles (NPs) upon adding excess amounts of a tetra-thiol crosslinker. Characterized according to their size, surface charge, morphology, and thiol amounts, these nanoparticles were immobilized on gold surfaces that mimicked gold-coated mass sensor platforms. The PEG-based nanoparticles, prepared especially by PEG6K-diMA polymers, were shown to result in the preparation of a monolayer and smooth coating of 80–120 nm thickness. Cysteine-modified NTS(8–13) peptide (RRPYIL) was conjugated to thiolated NP with reversible disulfide bonds and it was demonstrated that its cleavage with a reducing agent such as dithiothreitol (DTT) restores the NP-immobilized gold surface for at least two cycles. Together with its binding studies to NTSR2 antibodies, it was revealed that the peptide-conjugated NP-modified gold surface could be employed as a model for a reusable sensor surface for the detection of biomarkers of same or different types. Full article

Novel wide-bandgap ZnO, BeO, and ZnBeO materials have recently gained considerable interest due to their stellar optoelectronic properties. These semiconductors are being used in developing high-resolution, flexible, transparent nanoelectronics/photonics and achieving high-power radio frequency modules for sensors/biosensors, photodetectors/solar cells, and resistive random-access memory applications. Despite earlier evidence of attaining p-type wz ZnO with N doping, the problem persists in achieving reproducible p-type conductivity. This issue is linked to charging compensation by intrinsic donors and/or background impurities. In ZnO: Al (Li), the vibrational features by infrared and Raman spectroscopy have been ascribed to the presence of isolated ${\mathrm{A}\mathrm{l}}_{\mathrm{Z}\mathrm{n}}{(\mathrm{L}\mathrm{i}}_{\mathrm{Z}\mathrm{n}})$ defects, nearest-neighbor (NN) ${[\mathrm{A}\mathrm{l}}_{\mathrm{Z}\mathrm{n}}{-\mathrm{N}}_{\mathrm{O}}$] pairs, and second NN ${[\mathrm{A}\mathrm{l}}_{\mathrm{Z}\mathrm{n}}{-\mathrm{O}-\mathrm{L}\mathrm{i}}_{\mathrm{Z}\mathrm{n}};{\mathrm{V}}_{\mathrm{Z}\mathrm{n}}-\mathrm{O}{-\mathrm{L}\mathrm{i}}_{\mathrm{Z}\mathrm{n}}]$ complexes. However, no firm identification has been established. By integrating accurate perturbation models in a realistic Green’s function method, we have meticulously simulated the impurity vibrational modes of ${\mathrm{A}\mathrm{l}}_{\mathrm{Z}\mathrm{n}}$${(\mathrm{L}\mathrm{i}}_{\mathrm{Z}\mathrm{n}})$ and their bonding to form complexes with dopants as well as intrinsic defects. We strongly feel that these phonon features in doped ZnO will encourage spectroscopists to perform similar measurements to check our theoretical conjectures. Full article

The main goal of the present study was to verify in detail whether the use of a cluster model for Stone–Wales (SW) defect-containing graphene (SWG) to study the adsorption of Ln atoms yields results similar to those previously obtained by employing a periodic model. We addressed this question by analyzing the optimized geometries of SWG + Ln complexes, their formation energies, and selected electronic parameters (in particular, the frontier orbital energies and atomic charges and spins). Within the frame of density functional theory, we used the computational methodology of the PBE-D2/DNP theoretical level using ECP pseudopotentials. The most important conclusion is that the use of a cluster model gives qualitatively similar results to those of the periodic model. While the corresponding plots of the dihedral angles θ versus the Ln atoms differ considerably, the two models have many common features in the trends of the bonding strength despite the use of two very different theoretical tools, namely periodic (plane waves) versus cluster calculations (localized basis sets). In comparing the results for SW defect-free and SW defect-containing cluster models, it is evident that SW defects serve as much more preferential adsorption sites compared to the conditions in the defect-free graphene model. Full article

SARS-CoV-2 remains a severe threat to worldwide public health, particularly as the virus continues to evolve and diversify into variants of concern (VOCs). Among these VOCs, Omicron variants exhibit unique phenotypic traits, such as immune evasion, transmissibility, and severity, due to numerous spike protein mutations and the rapid subvariant evolution. These Omicron subvariants have more than 15 mutations in the receptor-binding domain (RBD), a region of the SARS-CoV-2 spike protein that is important for recognition and binding with the angiotensin-converting enzyme 2 (ACE2) human receptor. To address the impact of these high numbers of Omicron mutations on the binding process, we have developed a novel method to precisely quantify amino acid interactions via the amino acid–amino acid bond pair (AABP). We applied this concept to investigate the interface interactions of the RBD–ACE2 complex in four Omicron Variants (BA.1, BA.2, BA.5, and XBB.1.16) with its Wild Type counterpart. Based on the AABP analysis, we have identified all the sites that are affected by mutation and have provided evidence that unmutated sites are also impacted by mutation. We have calculated that the binding between RBD and ACE2 is strongest in OV BA.1, followed by OV BA.2, WT, OV BA.5, and OV XBB.1.16. We also present the partial charge values for all 311 residues across these five models. Our analysis provides a detailed understanding of changes caused by mutation in each Omicron interface complex. Full article

A novel 3-amino-5-mercapto-1,2,4-triazole functionalized graphene oxide composite (GO-ATT) was successfully prepared via a covalent coupling method, then employed for the removal of p-nitrophenol (PNP) from wastewater. The morphology as well as the composition of GO-ATT composite were investigated using Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), X-ray diffraction spectroscopy (XRD), and X-ray photoelectron spectroscopy (XPS). The surface charge of GO-ATT composite was evaluated by Zeta potential analyses. The surface area and pore size distribution of GO-ATT composite were analyzed using specific surface analyses using the Brunauer–Emmett–Teller (BET) method. Batch adsorption experiments were performed to investigate the effects of conditional factors, including contact time, solution pH, initial PNP concentration, and contact temperature, on the adsorption process. A maximum adsorption capacity of PNP by GO-ATT composite (0.287 mmol g⁻¹) could be obtained at 25 °C. Freundlich isotherm (R² > 0.92505) can better describe the adsorption behavior of PNP on GO-ATT composite. The thermodynamic functions (ΔG°, ΔH°, ΔS°) indicate that adsorption is a spontaneous, endothermic, entropy-increasing process and features physisorption. The adsorption behavior of PNP on GO-ATT composite conformed to the nonlinear pseudo-second-order kinetic model. Adsorption mechanism investigation indicated that the electrostatic, π-π stacking, and hydrogen bonding interactions were involved in the adsorption process. After 10 adsorption–desorption cycles, the adsorbent exhibited a stable and efficient removal rate (94%) for PNP. Due to its advantages of a high efficiency, excellent reusability, and high stability, the covalently coupled GO-ATT composite might be used as an effective adsorbent for the removal of phenolic contaminants from wastewater. Full article