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1.
Radiat Prot Dosimetry ; 200(11-12): 1207-1215, 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-39016515

ABSTRACT

In the present study, we have prepared six glass samples of bismuth borate using the melt-quenching method with the composition (70-x)B2O3-10CaO-20Na2O-xBi2O3; x = 0, 3, 6, 9, 12 and 15 mol%. The density of the prepared glasses was determined using Archimedes principle. The X-ray diffraction patterns provide confirmation of the amorphous nature of the prepared samples, whereas the Fourier transform infrared measurements pointed to the existence of structural units like BO3, BO4, BiO3 and BiO6 within the glass network. An assessment of the optical absorption spectra unveiled that with the increase in the bismuth oxide content, there was a decrease observed in both the direct and indirect band gap energies. Specifically, they decreased from 3.40 to 2.79 eV and from 3.10 to 2.46 eV, respectively. The properties related to gamma ray attenuation, including the mass attenuation coefficient (µm), effective atomic number (Zeff), half-value layer (HVL) and mean free path (MFP), were examined for all the glass samples. This investigation was carried out using the Phy-X/PSD software, covering the energy range from 0.511 to 1.332 MeV. Out of all the samples, Bi-15, featuring the highest Bi2O3 content, demonstrated the highest µm, Zeff, the smallest HVL and MFP. These results suggest that the glass with 15 mol% of Bi2O3 offers the most effective gamma radiation shielding performance. Moreover, the glasses examined in this study exhibit superior radiation shielding characteristics compared with specific concrete types, namely, ordinary concrete, Hematite serpentine concrete and barite concrete, as well as commercial glasses such as RS-360 and RS-253.


Subject(s)
Bismuth , Borates , Gamma Rays , Glass , Radiation Protection , Bismuth/chemistry , Glass/chemistry , Borates/chemistry , Radiation Protection/methods , Calcium/chemistry , Sodium/chemistry , X-Ray Diffraction , Materials Testing , Spectroscopy, Fourier Transform Infrared
2.
J Mol Graph Model ; 131: 108808, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38852428

ABSTRACT

Hydrogen energy has attracted a lot of interest from researchers as a sustainable and renewable energy source, but there are some technical challenges related to its storage. Hydride materials demonstrate the ability to store hydrogen adequately and safely. In the current study, we have investigated the structural and optoelectronic properties of the XCuH3 (where X = Li, Na and K) perovskite-type hydride using LDA and GGA formalisms for hydrogen storage application. Electronic properties such as band structure, density of states reveal the metallic character of the studied XCuH3 hydrides. Various optical parameters such as the complex dielectric function, refractive index, extinction coefficient, absorption coefficient, reflectivity, optical conductivity, energy loss function, and joint density of states have been computed and compared. The gravimetric hydrogen storage capacity for LiCuH3, NaCuH3 and KCuH3 are found to be 4.11, 3.37 and 2.86 wt%, respectively. The computed values of the gravimetric ratio manifest that XCuH3 hydrides are potential candidates for hydrogen storage applications. These calculations are made for the first time for XCuH3 hydrides and will be inspirational in the future for comparison and for hydrogen storage purposes.


Subject(s)
Calcium Compounds , Hydrogen , Oxides , Titanium , Hydrogen/chemistry , Calcium Compounds/chemistry , Titanium/chemistry , Oxides/chemistry , Sodium/chemistry , Lithium/chemistry , Potassium/chemistry , Models, Molecular
3.
Environ Sci Pollut Res Int ; 31(31): 44191-44204, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38937355

ABSTRACT

Red mud is a highly alkaline solid waste discharged from the alumina industry, and its high sodium content is the key factor limiting its wide utilization. Therefore, effective control of the "frosting" phenomenon during the application of red mud has received significant attention. In this study, the changes of particle size, phase, morphology, and pore size of red mud after sodium removal with different amounts of citric acid pretreatment were investigated. The single-factor experiment shows that the Na+ leaching rate is 86.33% under a citric acid dosage of 15%, liquid-to-solid ratio of 7 mL/g, leaching temperature of 80 °C, stirring speed of 300 rpm, and leaching time of 10 min. The leachate is characterized through X-ray diffraction (XRD), scanning electron microscopy (SEM), and Brunauer-Emmett-Teller (BET) surface area analysis. The results reveal that Na+ mainly exists in a combined state in the form of cancrinite. With the increase of citric acid dosage, red mud agglomerates, calcite, and cancrinite are dissolved, and new phases such as calcium oxalate and magnesium aluminum hydroxide are formed. The specific surface area, pore volume, and pore diameter show irregular changes with the increase in the citric acid dosage. Citric acid pretreatment can effectively reduce the sodium content in red mud, the treatment cost of leaching solution is low, and the leaching residue is neutral, which is helpful to promote the practical application of red mud.


Subject(s)
Citric Acid , Sodium , Citric Acid/chemistry , Sodium/chemistry , X-Ray Diffraction , Solid Waste , Microscopy, Electron, Scanning
4.
PLoS One ; 19(6): e0304512, 2024.
Article in English | MEDLINE | ID: mdl-38829838

ABSTRACT

The Organic Cation Transporter Novel 1 (OCTN1), also known as SLC22A4, is widely expressed in various human tissues, and involved in numerous physiological and pathological processes remains. It facilitates the transport of organic cations, zwitterions, with selectivity for positively charged solutes. Ergothioneine, an antioxidant compound, and acetylcholine (Ach) are among its substrates. Given the lack of experimentally solved structures of this protein, this study aimed at generating a reliable 3D model of OCTN1 to shed light on its substrate-binding preferences and the role of sodium in substrate recognition and transport. A chimeric model was built by grafting the large extracellular loop 1 (EL1) from an AlphaFold-generated model onto a homology model. Molecular dynamics simulations revealed domain-specific mobility, with EL1 exhibiting the highest impact on overall stability. Molecular docking simulations identified cytarabine and verapamil as highest affinity ligands, consistent with their known inhibitory effects on OCTN1. Furthermore, MM/GBSA analysis allowed the categorization of substrates into weak, good, and strong binders, with molecular weight strongly correlating with binding affinity to the recognition site. Key recognition residues, including Tyr211, Glu381, and Arg469, were identified through interaction analysis. Ach demonstrated a low interaction energy, supporting the hypothesis of its one-directional transport towards to outside of the membrane. Regarding the role of sodium, our model suggested the involvement of Glu381 in sodium binding. Molecular dynamics simulations of systems at increasing levels of Na+ concentrations revealed increased sodium occupancy around Glu381, supporting experimental data associating Na+ concentration to molecule transport. In conclusion, this study provides valuable insights into the 3D structure of OCTN1, its substrate-binding preferences, and the role of sodium in the recognition. These findings contribute to the understanding of OCTN1 involvement in various physiological and pathological processes and may have implications for drug development and disease management.


Subject(s)
Molecular Docking Simulation , Molecular Dynamics Simulation , Organic Cation Transport Proteins , Humans , Organic Cation Transport Proteins/chemistry , Organic Cation Transport Proteins/metabolism , Organic Cation Transport Proteins/genetics , Symporters/chemistry , Symporters/metabolism , Binding Sites , Protein Binding , Ergothioneine/chemistry , Ergothioneine/metabolism , Sodium/metabolism , Sodium/chemistry , Computer Simulation , Acetylcholine/metabolism , Acetylcholine/chemistry , Ligands
5.
J Phys Chem B ; 128(25): 5950-5965, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38875355

ABSTRACT

The guanine-rich telomeric repeats can form G-quadruplexes (G4s) that alter the accessibility of the single-stranded telomeric overhang. In this study, we investigated the effects of Na+ and K+ on G4 folding and accessibility through cation introduction and exchange. We combined differential scanning calorimetry (DSC), circular dichroism (CD), and single molecule Förster resonance energy transfer (smFRET) to monitor the stability, conformational dynamics, and complementary strand binding accessibility of G4 formed by single-stranded telomeric DNA. Our data showed that G4 formed through heating and slow cooling in K+ solution exhibited fewer conformational dynamics than G4 formed in Na+ solution, which is consistent with the higher thermal stability of G4 in K+. Monitoring cation exchange with real time smFRET at room temperature shows that Na+ and K+ can replace each other in G4. When encountering high K+ at room or body temperature, G4 undergoes a slow conformational rearrangement process which is mostly complete by 2 h. The slow conformational rearrangement ends with a stable G4 that is unable to be unfolded by a complementary strand. This study provides new insights into the accessibility of G4 forming sequences at different time points after introduction to a high K+ environment in cells, which may affect how the nascent telomeric overhang interacts with proteins and telomerase.


Subject(s)
DNA, Single-Stranded , G-Quadruplexes , Potassium , Telomere , Potassium/chemistry , Potassium/metabolism , Telomere/chemistry , Telomere/metabolism , Humans , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/metabolism , Fluorescence Resonance Energy Transfer , Sodium/chemistry , Sodium/metabolism , Nucleic Acid Conformation , Circular Dichroism , Calorimetry, Differential Scanning
6.
Methods ; 228: 55-64, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38782295

ABSTRACT

Metal ions, including biologically prevalent sodium ions, can modulate electrostatic interactions frequently involved in the stability of condensed compartments in cells. Quantitative characterization of heterogeneous ion dynamics inside biomolecular condensates demands new experimental approaches. Here we develop a 23Na NMR relaxation-based integrative approach to probe dynamics of sodium ions inside agarose gels as a model system. We exploit the electric quadrupole moment of spin-3/2 23Na nuclei and, through combination of single-quantum and triple-quantum-filtered 23Na NMR relaxation methods, disentangle the relaxation contribution of different populations of sodium ions inside gels. Three populations of sodium ions are identified: a population with bi-exponential relaxation representing ions within the slow motion regime and two populations with mono-exponential relaxation but at different rates. Our study demonstrates the dynamical heterogeneity of sodium ions inside agarose gels and presents a new experimental approach for monitoring dynamics of sodium and other spin-3/2 ions (e.g. chloride) in condensed environments.


Subject(s)
Gels , Sepharose , Sodium , Sepharose/chemistry , Sodium/chemistry , Gels/chemistry , Magnetic Resonance Spectroscopy/methods , Ions/chemistry , Quantum Theory
7.
Anal Chem ; 96(21): 8518-8527, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38711366

ABSTRACT

Accurate structural determination of proteins is critical to understanding their biological functions and the impact of structural disruption on disease progression. Gas-phase cross-linking mass spectrometry (XL-MS) via ion/ion reactions between multiply charged protein cations and singly charged cross-linker anions has previously been developed to obtain low-resolution structural information on proteins. This method significantly shortens experimental time relative to conventional solution-phase XL-MS but has several technical limitations: (1) the singly deprotonated N-hydroxysulfosuccinimide (sulfo-NHS)-based cross-linker anions are restricted to attachment at neutral amine groups of basic amino acid residues and (2) analyzing terminal cross-linked fragment ions is insufficient to unambiguously localize sites of linker attachment. Herein, we demonstrate enhanced structural information for alcohol-denatured A-state ubiquitin obtained from an alternative gas-phase XL-MS approach. Briefly, singly sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linker anions enable covalent cross-linking at both ammonium and amine groups. Additionally, covalently modified internal fragment ions, along with terminal b-/y-type counterparts, improve the determination of linker attachment sites. Molecular dynamics simulations validate experimentally obtained gas-phase conformations of denatured ubiquitin. This method has identified four cross-linking sites across 8+ ubiquitin, including two new sites in the N-terminal region of the protein that were originally inaccessible in prior gas-phase XL approaches. The two N-terminal cross-linking sites suggest that the N-terminal half of ubiquitin is more compact in gas-phase conformations. By comparison, the two C-terminal linker sites indicate the signature transformation of this region of the protein from a native to a denatured conformation. Overall, the results suggest that the solution-phase secondary structures of the A-state ubiquitin are conserved in the gas phase. This method also provides sufficient sensitivity to differentiate between two gas-phase conformers of the same charge state with subtle structural variations.


Subject(s)
Cross-Linking Reagents , Ubiquitin , Ubiquitin/chemistry , Cross-Linking Reagents/chemistry , Sodium/chemistry , Gases/chemistry , Cations/chemistry , Succinimides/chemistry , Mass Spectrometry , Ions/chemistry
8.
Nat Commun ; 15(1): 4218, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38760331

ABSTRACT

DNAzymes - synthetic enzymes made of DNA - have long attracted attention as RNA-targeting therapeutic agents. Yet, as of now, no DNAzyme-based drug has been approved, partially due to our lacking understanding of their molecular mode of action. In this work we report the solution structure of 8-17 DNAzyme bound to a Zn2+ ion solved through NMR spectroscopy. Surprisingly, it turned out to be very similar to the previously solved Pb2+-bound form (catalytic domain RMSD = 1.28 Å), despite a long-standing literature consensus that Pb2+ recruits a different DNAzyme fold than other metal ion cofactors. Our follow-up NMR investigations in the presence of other ions - Mg2+, Na+, and Pb2+ - suggest that at DNAzyme concentrations used in NMR all these ions induce a similar tertiary fold. Based on these findings, we propose a model for 8-17 DNAzyme interactions with metal ions postulating the existence of only a single catalytically-active structure, yet populated to a different extent depending on the metal ion cofactor. Our results provide structural information on the 8-17 DNAzyme in presence of non-Pb2+ cofactors, including the biologically relevant Mg2+ ion.


Subject(s)
DNA, Catalytic , Lead , Magnesium , Zinc , DNA, Catalytic/chemistry , DNA, Catalytic/metabolism , Magnesium/metabolism , Magnesium/chemistry , Zinc/metabolism , Zinc/chemistry , Lead/chemistry , Lead/metabolism , Nucleic Acid Conformation , Catalytic Domain , Models, Molecular , Sodium/metabolism , Sodium/chemistry , Metals/metabolism , Metals/chemistry , Magnetic Resonance Spectroscopy , Ions
9.
J Biol Chem ; 300(6): 107382, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38763337

ABSTRACT

ASCT2 (alanine serine cysteine transporter 2), a member of the solute carrier 1 family, mediates Na+-dependent exchange of small neutral amino acids across cell membranes. ASCT2 was shown to be highly expressed in tumor cells, making it a promising target for anticancer therapies. In this study, we explored the binding mechanism of the high-affinity competitive inhibitor L-cis hydroxyproline biphenyl ester (Lc-BPE) with ASCT2, using electrophysiological and rapid kinetic methods. Our investigations reveal that Lc-BPE binding requires one or two Na+ ions initially bound to the apo-transporter with high affinity, with Na1 site occupancy being more critical for inhibitor binding. In contrast to the amino acid substrate bound form, the final, third Na+ ion cannot bind, due to distortion of its binding site (Na2), thus preventing the formation of a translocation-competent complex. Based on the rapid kinetic analysis, the application of Lc-BPE generated outward transient currents, indicating that despite its net neutral nature, the binding of Lc-BPE in ASCT2 is weakly electrogenic, most likely because of asymmetric charge distribution within the amino acid moiety of the inhibitor. The preincubation with Lc-BPE also led to a decrease of the turnover rate of substrate exchange and a delay in the activation of substrate-induced anion current, indicating relatively slow Lc-BPE dissociation kinetics. Overall, our results provide new insight into the mechanism of binding of a prototypical competitive inhibitor to the ASCT transporters.


Subject(s)
Amino Acid Transport System ASC , Minor Histocompatibility Antigens , Amino Acid Transport System ASC/metabolism , Amino Acid Transport System ASC/antagonists & inhibitors , Amino Acid Transport System ASC/genetics , Amino Acid Transport System ASC/chemistry , Kinetics , Minor Histocompatibility Antigens/metabolism , Minor Histocompatibility Antigens/genetics , Minor Histocompatibility Antigens/chemistry , Humans , Sodium/metabolism , Sodium/chemistry , Animals , Binding, Competitive
10.
Sensors (Basel) ; 24(9)2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38732822

ABSTRACT

Magnetic resonance (MR) with sodium (23Na) is a noninvasive tool providing quantitative biochemical information regarding physiology, cellular metabolism, and viability, with the potential to extend MR beyond anatomical proton imaging. However, when using clinical scanners, the low detectable 23Na signal and the low 23Na gyromagnetic ratio require the design of dedicated radiofrequency (RF) coils tuned to the 23Na Larmor frequency and sequences, as well as the development of dedicated phantoms for testing the image quality, and an MR scanner with multinuclear spectroscopy (MNS) capabilities. In this work, we propose a hardware and software setup for evaluating the potential of 23Na magnetic resonance imaging (MRI) with a clinical scanner. In particular, the reliability of the proposed setup and the reproducibility of the measurements were verified by multiple acquisitions from a 3T MR scanner using a homebuilt RF volume coil and a dedicated sequence for the imaging of a phantom specifically designed for evaluating the accuracy of the technique. The final goal of this study is to propose a setup for standardizing clinical and research 23Na MRI protocols.


Subject(s)
Magnetic Resonance Imaging , Phantoms, Imaging , Software , Magnetic Resonance Imaging/methods , Magnetic Resonance Imaging/instrumentation , Sodium/chemistry , Humans , Sodium Isotopes , Image Processing, Computer-Assisted/methods , Reproducibility of Results
11.
Molecules ; 29(10)2024 May 08.
Article in English | MEDLINE | ID: mdl-38792055

ABSTRACT

The present study aimed to develop low-sodium curing agents for dry-cured meat products. Four low-sodium formulations (SPMA, SPM, SP, and SM) were used for dry-curing meat. The physicochemical properties and flavor of the dry-cured meat were investigated. The presence of Mg2+ ions hindered the penetration of Na+ into the meat. The weight loss, moisture content, and pH of all low-sodium salt groups were lower than those of S. Mg2+ addition increased the water activity (Aw) of SPMA, SPM, and SM. Dry-curing meat with low-sodium salts promoted the production of volatile flavor compounds, with Mg2+ playing a more prominent role. Furthermore, low-sodium salts also promoted protein degradation and increased the content of free amino acids in dry-cured meat, especially in SM. Principal component analysis (PCA) showed that the low-sodium salts containing Mg2+ were conducive to improving the quality of dry-cured meat products. Therefore, low-sodium salts enriched with Mg2+ become a desirable low-sodium curing agent for achieving salt reduction in dry-cured meat products.


Subject(s)
Magnesium , Meat Products , Meat Products/analysis , Magnesium/analysis , Magnesium/chemistry , Animals , Sodium/analysis , Sodium/chemistry , Salts/chemistry , Taste , Flavoring Agents/analysis , Flavoring Agents/chemistry , Hydrogen-Ion Concentration , Amino Acids/analysis , Amino Acids/chemistry , Food Handling/methods
12.
Magn Reson Med ; 92(3): 900-915, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38650306

ABSTRACT

PURPOSE: Sodium triple quantum (TQ) signal has been shown to be a valuable biomarker for cell viability. Despite its clinical potential, application of Sodium TQ signal is hindered by complex pulse sequences with long scan times. This study proposes a method to approximate the TQ signal using a single excitation pulse without phase cycling. METHODS: The proposed method is based on a single excitation pulse and a comparison of the free induction decay (FID) with the integral of the FID combined with a shifting reconstruction window. The TQ signal is calculated from this FID only. As a proof of concept, the method was also combined with a multi-echo UTE imaging sequence on a 9.4 T preclinical MRI scanner for the possibility of fast TQ MRI. RESULTS: The extracted Sodium TQ signals of single-pulse and spin echo FIDs were in close agreement with theory and TQ measurement by traditional three-pulse sequence (TQ time proportional phase increment [TQTPPI)]. For 2%, 4%, and 6% agar samples, the absolute deviations of the maximum TQ signals between SE and theoretical (time proportional phase increment TQTPPI) TQ signals were less than 1.2% (2.4%), and relative deviations were less than 4.6% (6.8%). The impact of multi-compartment systems and noise on the accuracy of the TQ signal was small for simulated data. The systematic error was <3.4% for a single quantum (SQ) SNR of 5 and at maximum <2.5% for a multi-compartment system. The method also showed the potential of fast in vivo SQ and TQ imaging. CONCLUSION: Simultaneous SQ and TQ MRI using only a single-pulse sequence and SQ time efficiency has been demonstrated. This may leverage the full potential of the Sodium TQ signal in clinical applications.


Subject(s)
Algorithms , Magnetic Resonance Imaging , Phantoms, Imaging , Sodium , Magnetic Resonance Imaging/methods , Sodium/chemistry , Signal Processing, Computer-Assisted , Image Processing, Computer-Assisted/methods , Humans , Signal-To-Noise Ratio , Animals
13.
Chem Asian J ; 19(11): e202400163, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38606886

ABSTRACT

Pollution from harmful heavy metal ions such as Pb(II) and Cu(II) is causing serious environmental and health problems. In this study, Sodium and nitrogen co-doped porous carbon material (Na/NABc) was successfully prepared from seaweed, sodium hydroxide, and dicyandiamide. The experimental results showed that Na/NABc is an excellent adsorbent for the effective removal of Pb(II) and Cu(II) from water bodies. Specifically, 99.8% of Pb(II) and 64.6% Cu(II) (100 mg/L) were removed within 12 h using 10 mg Na/NABc(10%) at 25 °C. The adsorption of Pb(II) and Cu(II) in aqueous solution by Na/NABc(10%) was efficient and rapid in the first stage. The theoretical maximum removal capacities of Na/NABc for Pb(II) and Cu(II) were 959.6 and 299.1 mg/g, respectively. Pb(II) and Cu(II) ions were adsorbed quickly in the first 60 min, and the kinetics data were generally consistent with a pseudo-second-order model. Na/NABc(10%) had a large distribution coefficient for Pb(II) (8.38 L/mg) and Cu(II) (1.17 L/mg). The possible mechanisms were precipitation, Ion exchange, and surface complexation. The removal rate can reach about 70% after five cycles, and the release of sodium meets the standard. The results of this study demonstrate the potential applicability of Na/NABc(10%) for adsorption of heavy metals from aqueous solution.


Subject(s)
Charcoal , Copper , Lead , Nitrogen , Seaweed , Sodium , Water Pollutants, Chemical , Copper/chemistry , Lead/chemistry , Lead/isolation & purification , Seaweed/chemistry , Charcoal/chemistry , Water Pollutants, Chemical/isolation & purification , Water Pollutants, Chemical/chemistry , Adsorption , Sodium/chemistry , Nitrogen/chemistry , Water Purification/methods , Kinetics , Water/chemistry
14.
Biochemistry (Mosc) ; 89(Suppl 1): S262-S277, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38621755

ABSTRACT

Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.


Subject(s)
G-Quadruplexes , DNA/metabolism , Sodium/chemistry , Cations, Monovalent/chemistry , Thermodynamics
15.
Int J Biol Macromol ; 267(Pt 1): 131273, 2024 May.
Article in English | MEDLINE | ID: mdl-38569994

ABSTRACT

The nanopore-based translocation of a single-stranded RNA (ssRNA) in mixed salt solution has garnered increasing interest for its biological and technological significance. However, it is challenging to comprehensively understand the effects of the mixed ion species on the translocation dynamics due to their cooperation and competition, which can be directly reflected by the ion screening and neutralizing effects, respectively. In this study, Langevin dynamics simulation is employed to investigate the properties of ssRNA conformation and translocation in mixed Na+-Mg2+ ion environments. Simulation results reveal that the ion screening effect dominates the change in the ssRNA conformational size, the ion neutralizing effect controls the capture rate of the ssRNA by the nanopore, and both of them take charge of the different changes in translocation time of the ssRNA under various mixed ion environments. Under high Na+ ion concentration, as Mg2+ concentration increases, the ion neutralizing effect strengthens, weakening the driving force inside the nanopore, leading to longer translocation time. Conversely, at low Na+ concentration, an increase in Mg2+ concentration enhances the ion screening effect, aiding in faster translocation. Furthermore, these simulation results will be explained by quantitative analysis, advancing a deeper understanding of the complicated effects of the mixed Na+-Mg2+ ions.


Subject(s)
Magnesium , Nucleic Acid Conformation , Sodium , Sodium/chemistry , Sodium/metabolism , Magnesium/chemistry , Nanopores , Molecular Dynamics Simulation , Ions/chemistry , RNA/chemistry
16.
Bioresour Technol ; 402: 130755, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38688394

ABSTRACT

Carbothermal reduction is a promising method for the industrial preparation of nano-zero-valent iron. Preparing it also involves very high pyrolysis temperatures, which leads to a significant amount of energy consumption. The temperature required for the preparation of nano-zero-valent iron by carbothermal reduction was reduced by 200 °C by the addition of sodium salt. Carbon-loaded nano zero-valent iron (Fe0/CB-Na) was prepared by carbothermal reduction through the addition of sodium salt. The results showed that Fe0/CB-Na@700 had the same activation performance as Fe0/CB@900 and the newly prepared nano-zero-valent iron. The addition of sodium salt promoted the transfer of oxygen from the iron oxide to the carbon structure during the roasting process so that the iron oxide was reduced to as much Fe0 as possible. Thus, sodium salts were optimized for the preparation of nano-zero-valent iron by carbothermal reduction through interfacial amorphization and oxygen transfer, thus reducing the preparation cost.


Subject(s)
Anti-Bacterial Agents , Iron , Iron/chemistry , Anti-Bacterial Agents/chemistry , Sulfates/chemistry , Oxidation-Reduction , Temperature , Sodium/chemistry
17.
J Mol Graph Model ; 130: 108775, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38642499

ABSTRACT

In this paper, we have performed an all-atom molecular dynamics simulation to understand the structure and dynamics of Na+ ions in water mixed Ionic liquids (Water in Ionic liquid). Two ionic liquid (IL) systems consist of (1) 1-butyl-3-methylimidazolium [BMIM] tetrafluoroborate [BF4] and (2) 1-butyl-3-methylimidazolium [BMIM] hexafluorophosphate [PF6] were considered in this work. We understand various inter-molecular structures and dynamic and thermodynamic behaviours of Na+ ions in the water-mixed IL systems. The water (H2O) mole fractions (x) varied from 0.33 to 0.71. The neat ILs [BMIM][BF4] and [BMIM][PF6] pairwise radial distribution functions show a decrease with an increase in x. The [BMIM][PF6] exhibits a strong coordination structure with Na+ ions across the entire range of x values. The rdf between the pairs of Na+-[PF6] presents a significant interaction compared to Na+ and [BF4]. The Na + ions manifested greater coordination with H2O In H2O-[BMIM][PF6] compared to H2O-[BMIM][BF4]. The self-diffusion coefficient (D) values of Na + ions increase with the rise in x in both ILs. The D values of Na + ions are 10-fold higher in [BMIM][BF4] than [BMIM][PF6]. The ionic conductivity values are higher for [BMIM][BF4]. Overall, this paper unveils molecular-level insights for understanding the behavior of Na+ ions in the water in ionic liquid systems.


Subject(s)
Imidazoles , Ionic Liquids , Molecular Dynamics Simulation , Sodium , Water , Ionic Liquids/chemistry , Imidazoles/chemistry , Sodium/chemistry , Water/chemistry , Ions/chemistry , Thermodynamics , Electrolytes/chemistry , Molecular Structure
18.
J Recept Signal Transduct Res ; 44(1): 8-18, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38529713

ABSTRACT

PURPOSE: The G-protein coupled receptor (GPCR) family, implicated in neurological disorders and drug targets, includes the sensitive serotonin receptor subtype, 5-HT2B. The influence of sodium ions on ligand binding at the receptor's allosteric region is being increasingly studied for its impact on receptor structure. METHODS: High-throughput virtual screening of three libraries, specifically the Asinex-GPCR library, which contains 8,532 compounds and FDA-approved (2466 compounds) and investigational compounds (2731)) against the modeled receptor [4IB4-5HT2BRM] using the standard agonist/antagonist (Ergotamine/Methysergide), as previously selected from our studies based on ADMET profiling, and further on basis of binding free energy a single compound - dihydroergotamine is chosen. RESULTS: This compound displayed strong interactions with the conserved active site. Ions influence ligand binding, with stronger interactions (3-H-bonds and 1-π-bond around 3.35 Å) observed when an agonist and ions are present. Ions entry is guided by conserved motifs in helices III, IV, and VII, which regulate the receptor. Dihydroergotamine, the selected drug, showed binding variance based on ions presence/absence, affecting amino acid residues in these motifs. DCCM and PCA confirmed the stabilization of ligands, with a greater correlation (∼46.6%-PC1) observed with ions. Dihydroergotamine-modified interaction sites within the receptor necessary for activation, serving as a potential 5HT2BRM agonist. RDF analysis showed the sodium ions density around the active site during dihydroergotamine binding. CONCLUSION: Our study provides insights into sodium ion mobility's role in controlling ligand binding affinity in 5HT2BR, offering therapeutic development insights.


Subject(s)
Drug Discovery , Protein Binding , Receptor, Serotonin, 5-HT2B , Sodium , Ligands , Receptor, Serotonin, 5-HT2B/metabolism , Receptor, Serotonin, 5-HT2B/chemistry , Humans , Sodium/metabolism , Sodium/chemistry , Drug Development , Molecular Docking Simulation , Binding Sites , Allosteric Site , Receptors, G-Protein-Coupled/metabolism , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/genetics , Catalytic Domain/drug effects
19.
Environ Sci Pollut Res Int ; 31(19): 28166-28177, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38532210

ABSTRACT

Taihu Lake, the third largest freshwater lake in China, has experienced rapid salinization in the past decades; however, little is known about the impact of sodium (Na) on ion exchange in the lake environment. To explore the potential effect of increased Na on the migration of base cations (Ca and Mg) and resulting redistribution between the water and sediment, we used the adsorption-exchange experiment, MINTEQ modeling to explore the cation exchange induced by high Na input, and its impact on the redistribution of Ca and Mg in Taihu different media. The results indicated that exchanged quantity of Ca and Mg increased with time, and the exchange process reached 90% during 0-4 h and reached equilibrium after 24 h under 100 mg/L Na (the maximum Na concentration in Taihu sediment pore water). Our MINTEQ modeled result indicated that the exchanged quantity of Ca and Mg increased with the increasing Na concentration, with Ca being preferably exchanged over Mg at the same Na concentration. The MINTEQ model further predicted that, in the Taihu lake environment, the exchange adsorption would reach the equilibrium at the concentration of 6000 mg/L Na, with exchanged Ca2+ and Mg2+ accounting for 47% and 55% of the total exchangeable Ca and Mg in the sediment, respectively. Although current Na-induced exchange in the Taihu lake has been far from the equilibrium, the MINTEQ result confirmed the existence of this reaction and predicted the potential redistribution of base cations or Ca/Mg ratio in the lake sediment and water phase with further Na increase. Furthermore, our field observations not only confirmed the existence of Na-induced cation exchange in this lake environment but also were generally in agreement with our experimental and modeled results. The increased salinization-induced ion exchange would alter the re-distribution of base cations and the resulting potential ecosystem consequences should be given close attention in this large freshwater lake.


Subject(s)
Environmental Monitoring , Lakes , Models, Theoretical , China , Lakes/chemistry , Salinity , Geologic Sediments/analysis , Geologic Sediments/chemistry , Sodium/analysis , Sodium/chemistry , Ion Exchange , Calcium/analysis , Calcium/chemistry , Magnesium/analysis , Magnesium/chemistry , Cations/chemistry
20.
Environ Sci Pollut Res Int ; 31(18): 27403-27415, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38512568

ABSTRACT

The critical impact of sodium-doped molybdenum (MoNa) in shaping the MoSe2 interfacial layer, influencing the electrical properties of CIGSe/Mo heterostructures, and achieving optimal MoSe2 formation conditions, leading to improved hetero-contact quality. Notably, samples with a 600-nm-thick MoNa layer demonstrate the highest resistivity (73 µΩcm) and sheet resistance (0.45 Ω/square), highlighting the substantial impact of MoNa layer thickness on electrical conductivity. Controlled sodium diffusion through MoNa layers is essential for achieving desirable electrical characteristics, influencing Na diffusion rates, grain sizes, and overall morphology, as elucidated by EDX and FESEM analyses. Additionally, XRD results provide insights into the spontaneous peeling-off phenomenon, with the sample featuring a ~ 600-nm MoNa layer displaying the strongest diffraction peak and the largest crystal size, indicative of enhanced Mo to MoSe2 conversion facilitated by sodium presence. Raman spectra further confirm the presence of MoSe2, with its thickness correlating with MoNa layer thickness. The observed increase in resistance and decrease in conductivity with rising MoSe2 layer thickness underscore the critical importance of optimal MoSe2 formation for transitioning from Schottky to ohmic contact in CIGSe/Mo heterostructures. Ultimately, significant factors to the advancement of CIGSe thin-film solar cell production are discussed, providing nuanced insights into the interplay of MoNa and MoSe2, elucidating their collective impact on the electrical characteristics of CIGSe/Mo heterostructures.


Subject(s)
Molybdenum , Sodium , Molybdenum/chemistry , Sodium/chemistry , Electric Conductivity
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