Intercalation Of Small Molecules Research Articles

Intercalation of small molecules in the selective layer of polyamide nanofiltration membranes facilitates the separation of Mg2+/Li+

In addressing lithium supply shortages driven by increased energy demand, nanofiltration membrane technology is crucial for recovering lithium from salt lake brines. Overcoming the challenge of achieving high selectivity for Li+ and water permeability in polymer nanofiltration membranes, this study proposes a simple approach using Aminomalononitrile (AMN) intercalation to modify polyamide layers. Density functional theory simulations predict AMN's superior selectivity and enhanced hydrophilicity. Stable intercalation of AMN between polyethyleneimine (PEI) molecules is demonstrated, synergistically enhancing water permeability and Li+ selectivity. The resulting PEI/AMN-TMC membrane exhibits exceptional Li+ selectivity and improved water permeability (13.1 L·m−2·h−1·bar−1), 2.9 times higher than traditional PEI-TMC membranes. Stable performance for over seven days, along with anti-scaling and anti-bacterial properties, underscores its practicality. This investigation sheds light on membrane structure regulation through small-molecule intercalation, offering insights into precise adjustments for enhanced water permeability and ion selectivity.

(Invited) Probing the Single Molecular Structural and Interactional Properties

Single molecule study, where science and engineering met, applies the tools and measurement techniques of nanoscale physics and chemistry to generate remarkable new insights into how physical, chemical, and biological systems function. It permits direct observation of molecular behavior that can be obscured by ensemble averaging and enables the study of important problems ranging from the fundamental physics of electronic transport in single molecule junctions and biophysics of single molecule interactions, such as the energetics and nonequilibrium transport mechanisms in single molecule junctions and the energy landscape of biomolecular reactions, associated lifetimes, and free energy, to the study and design of single molecules as devices-molecular wires, rectifiers and transistors and high‐affinity, anti‐cancer drugs.In this talk, we present two of our recent researches using the legendary scanning probe microscope Dr. Stuart Lindsay and the Late Dr. Nongjian Tao pioneered. One studies the small molecule-DNA interactions electronically by STM-breakjunction measurements of site-specific intercalation of small molecules (coralyne) into a custom-designed 11-base-pair DNA duplex. The results show that a single molecule DNA electrical rectifier is realized and the coralyne-induced spatial asymmetry in the electron state distribution caused the observed rectification. The other study elucidated the in situ single-molecule interaction of heparan sulfate (HS) with antithrombin (AT) on the endothelial cell membrane surface under near-physiological conditions, especially the role of sulfate groups in specific binding sites of HS for AT, using AFM recognition imaging and dynamic force spectroscopy measurements.

Intercalation, decomposition, entrapment - a new route to graphene nanobubbles.

Graphene nanobubbles (GNBs) have become the subject of recent research due to their novel physical properties. However, present methods to create them involve either extreme conditions or complex sample fabrication. We present a novel approach which relies on the intercalation of small molecules (NH3), their surface-mediated decomposition and the formation of larger molecules (N2) which are then entrapped beneath the graphene in bubbles. Our hypothesised reaction mechanism requires the copper substrate, on which our graphene is grown via chemical vapour deposition (CVD), to be oxidised before the reaction can occur. This was confirmed through X-ray photoelectron spectroscopy (XPS) data of both oxidised and reduced Cu substrate samples. The GNBs have been analysed through atomic force microscopy (AFM, after NH3 treatment) and XPS, which reveals the formation of five distinct N 1s peaks, attributed to N2 entrapment, N doping species and atomic nitrogen bonded with the Cu within the substrate. This method is simple, occurs at low temperatures (520 K) and integrates very easily with conventional CVD graphene growth, so presents an opportunity to open up this field of research further.

Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint.

The restricted access of regulatory factors to their binding sites on DNA wrapped around the nucleosomes is generally interpreted in terms of molecular shielding exerted by nucleosomal structure and internucleosomal interactions. Binding of proteins to DNA often includes intercalation of hydrophobic amino acids into the DNA. To assess the role of constrained superhelicity in limiting these interactions, we studied the binding of small molecule intercalators to chromatin in close to native conditions by laser scanning cytometry. We demonstrate that the nucleosome-constrained superhelical configuration of DNA is the main barrier to intercalation. As a result, intercalating compounds are virtually excluded from the nucleosome-occupied regions of the chromatin. Binding of intercalators to extranucleosomal regions is limited to a smaller degree, in line with the existence of net supercoiling in the regions comprising linker and nucleosome free DNA. Its relaxation by inducing as few as a single nick per ~50 kb increases intercalation in the entire chromatin loop, demonstrating the possibility for long-distance effects of regulatory potential.

Performance and mechanisms of wastewater sludge conditioning with slag-based hydrotalcite-like minerals (Ca/Mg/Al-LDH)

Extracellular polymeric substances (EPS) in wastewater sludge form a network structure that is highly hydrophilic and compressible. Thus chemical conditioning is always required to improve sludge dewaterability by changing the gelatinous structure of sludge flocs. Layered double hydroxides (LDH) are generally characterized by large surface area and high anion exchange capacity, so we prepared three types of hydrotalcite-like compounds (Ca/Mg/Al-LDHs) from a typical solid waste, blast furnace slag, using NaOH precipitation (giving LDHa), a hydrothermal method (LDHb), and NaOH–Na2CO3 precipitation (LDHc). The physicochemical properties of the three LDH were comprehensively characterized, and their effectiveness as sludge conditioners was evaluated. The results showed that LDH conditioning was able to promote sludge dewaterability, and conditioning efficiency was strongly dependent on LDH structural properties. LDH neutralized the negative charges onto sludge particles and interacted with EPS to increase floc strength. LDH also formed a skeletal structure that reduced sludge compressibility. In addition, there were interactions between the LDH surfaces and the OC–OH in EPS proteins, which altered the secondary structure of protein molecules, consequently increasing sludge dewaterability. The biomolecules of low-molecular-weight fractions (such as peptides and humic acids) in soluble EPS intercalated LDH. Both the surface complexation of organic matter containing carboxyl groups and the intercalation of small molecules in soluble EPS were responsible for EPS–LDH interactions. The combination of skeleton formation, electrostatic interaction, and EPS–LDH interactions resulted in compression of gel-like structure and improved sludge dewatering performance. We finally suggested a novel sludge treatment process that increases sludge dewaterability using slag-derived Ca/Mg/Al-LDH to condition the sludge, and it could be combined with pyrolysis to prepare multi-functional materials or bio-oil.

Unraveling the Role of Lithium in Enhancing the Hydrogen Evolution Activity of MoS2: Intercalation versus Adsorption.

Molybdenum disulfide (MoS2) is a highly promising catalyst for the hydrogen evolution reaction (HER) to realize large-scale artificial photosynthesis. The metallic 1T′-MoS2 phase, which is stabilized via the adsorption or intercalation of small molecules or cations such as Li, shows exceptionally high HER activity, comparable to that of noble metals, but the effect of cation adsorption on HER performance has not yet been resolved. Here we investigate in detail the effect of Li adsorption and intercalation on the proton reduction properties of MoS2. By combining spectroscopy methods (infrared of adsorbed NO, 7Li solid-state nuclear magnetic resonance, and X-ray photoemission and absorption) with catalytic activity measurements and theoretical modeling, we infer that the enhanced HER performance of LixMoS2 is predominantly due to the catalytic promotion of edge sites by Li.

Conformation of graphene folding around single-walled carbon nanotubes

The low bending rigidity of graphene facilitates the formation of folds into the structure. This curvature change affects the reactivity and electron transport of the sheet. One novel extension of this is the intercalation of small molecules into these folds. We construct a model incorporating a single-walled carbon nanotube into a sheet of folded graphene. Variational calculus techniques are employed to determine the minimum energy structure and the resulting curves are shown to agree well with molecular dynamics study. Graphical Abstract Using calculus of variations, the elastic bending energy and van der Waals energy are minimised giving rise to Euler-Lagrange equation for which analytical solutions are derived to determine the optimal curved sturctures of graphene wrapped around carbon nanotubes . Overall agreement between the analytical solutions (with different values of bending rigidities) and results from molecular dynamics simulations (grey) is shown here for (6,6), (8,8) and (10,10) armchair nanotubes, respectively.

Molecular rectifier composed of DNA with high rectification ratio enabled by intercalation.

The predictability, diversity and programmability of DNA make it a leading candidate for the design of functional electronic devices that use single molecules, yet its electron transport properties have not been fully elucidated. This is primarily because of a poor understanding of how the structure of DNA determines its electron transport. Here, we demonstrate a DNA-based molecular rectifier constructed by site-specific intercalation of small molecules (coralyne) into a custom-designed 11-base-pair DNA duplex. Measured current-voltage curves of the DNA-coralyne molecular junction show unexpectedly large rectification with a rectification ratio of about 15 at 1.1 V, a counter-intuitive finding considering the seemingly symmetrical molecular structure of the junction. A non-equilibrium Green's function-based model-parameterized by density functional theory calculations-revealed that the coralyne-induced spatial asymmetry in the electron state distribution caused the observed rectification. This inherent asymmetry leads to changes in the coupling of the molecular HOMO-1 level to the electrodes when an external voltage is applied, resulting in an asymmetric change in transmission.

The Occurrence of Plectonemes in Supercoiled DNA Depends on DNA Sequence

The supercoiling state of chromosomal DNA needs to be precisely controlled by cells as it is important to many essential cellular processes such as DNA replication and gene expression. The extrusion of coiled loop structures termed plectonemes are one of the characteristic features of supercoiled DNA. Despite their fundamental importance, many basic properties of plectonemes are unknown mainly because of the lack of proper experimental tools to probe them. Our previous study, based on a side-pulling magnetic tweezers combined with wide-field fluorescence microscopy, revealed that DNA plectonemes are highly dynamic in nature. Here, we extend this technique to study the sequence-dependent localization of plectonemes. Moreover, we developed another single-molecule technique to probe plectonemes in DNA of which supercoiling state is carefully controlled by intercalation of small molecules. While the side-pulling magnetic tweezers technique allows precise control of force and supercoil density, this new technique provides high-throughput measurements by simultaneous visualization of many single DNA molecules in parallel. Using both techniques, we study the DNA sequence dependence of plectonemes and the influence of local structures such as bound proteins on the plectoneme formation. Analysis of the positions and sizes of the individual plectonemes reveals that plectonemes are either localized to or excluded from certain regions of DNA, depending on the nature of the sequence. Furthermore, we find that plectonemes can be pinned to local structures such as a bound protein or a local bubble formed by base pair mismatches. These first biophysics experiments on the sequence dependence on plectonemic supercoils have clear consequences for the non-homogenous distribution of supercoiling across the genome in biological cells.(∗ The first two authors contributed equally)

Exfoliated Molybdenum Disulfide for TiO2 Based Dye Sensitized Solar Cells

Photochemical properties of transition metal dichalcogenides have been studied for more than 30 years, providing promising results as photocatalysts for energy applications. Recent works on these layered materials, particularly on molybdenum disulfide (MoS2), demonstrate that structural changes provoke different electron transitions in the system. MoS2 is a nonprecious metal, relatively earth abundant, and stable, which possess three main crystalline structure types: 2H, 3R and 1T; with hexagonal, rhombohedral, and trigonal unit cells, respectively. The thermodynamically stable 2H phase can be affected by chemical reactions such as the intercalation of small molecules. A common reactive used to complete this intercalation is n-butyllithium (n-BuLi), since lithium ions strongly interact with MoS2 layers. The quantity of lithium ions inside the layers may fluctuate depending on the duration of the reaction and the concentration of n-BuLi. This interaction produce a LixMoS2 specie that can react with water to exfoliate the MoS2 layers. MoS2 chemical treatments can affect the oxidation state of MoS2 and its photoabsorption behavior, hence altering its physicochemical properties. These changes provide the opportunity to produce new materials and interfaces, improving properties such as radiation absorption and electron mobility range. These two characteristics make exfoliated MoS2 an excellent material to be tested in dye sensitized solar cells (DSC), especially for the anode of this device. Solar cells normally use expensive organometallic ruthenium based dyes, which decompose under high temperature. In contrast, exfoliated MoS2 (E-MoS2) is a stable inorganic compound, which can also absorb in the visible region where a relatively high concentration of sunlight photons are available. Two approaches are studied in this work; 1) the use of exfoliated MoS2 as enhancer for electron transfer reactions and 2) as a substitute of ruthenium based dyes. Exhaustive physicochemical characterization of the MoS2 during the intercalation and exfoliation process was accomplished using X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), X-ray Photoelectron Spectroscopy (XPS), Raman Spectroscopy and Ultraviolet and Visible Absorption (UV/Vis). The E-MoS2 was further tested in a dye sensitized solar cell. Finally, Electrochemical Impedance Spectroscopy (EIS) was done to obtain an insight of the electron process occurring in these two approaches. Previous results provide evidence of the potential use of exfoliated MoS2 in this photovoltaic devices E-MoS2 layers were produced after a lithium intercalation, exfoliation and purification synthesis, and an exhaustive physicochemical characterization was completed. The characterization demonstrated structural and chemical modifications, which affect electron transitions in the E-MoS2 product. DSCs devices were employed to test this E-MoS2 in two different setups: 1) as a layered formation with TiO2 thin film and 2) as a dye-substitute in a hybrid form with TiO2, both at the anode. In the first approach, an increase in photovoltage was detected on the DSC device during testing. Between a 10 fold increase at low wavelength (e.g. 330 nm) and two-fold at higher wavelength (e.g. 370nm). EIS results show lower resistances and higher effective lifetime. In this layered structured thin film between E-MoS2 and TiO2 a MoS2 optical-reflection effect may have caused an increases in the number of electron-hole pairs produced in the cell. Improvements in the electron transfer processes between the iodide/E-MoS2/TiO2 interphase are also a possible explanation of these results. Surprisingly, EIS shows higher resistances compared with the device having an E-MoS2-TiO2 layered structured thin film DSC. A possible explanation is a low E-MoS2 chemisorb process on TiO2, where the nanocomposite may be degraded while the photochemistry develops. We can conclude that E-MoS2 could offer an alternative material in DSC by enhancing the photochemical behavior, yet further studies are needed to attend stability concerns of the material.

Adsorption and Intercalation of Small Molecules on Kaolinite from Molecular Modelling Studies

Kaolinite is an abundant natural material with considerable industrial potential. Despite its simple composition (Al2Si2O5(OH)4 and layered structure being a phyllosilicate), it is notable that only little known about the interaction of kaolinite sheets with small organic reagents at the molecular level. These assumed to govern intercalation, delamination, and then the complete exfoliation processes. A common methodology to model the molecular structure of kaolinite is the employment of periodic boundary conditions. The application of molecular cluster models gained importance nowadays by capitalizing on the availability of wide range of theoretical tools for describing structural features and reaction mechanisms. In this study, we present our results using theoretical methodologies and modelling strategies from literature that are applied for adsorption and intercalation of urea, ethylene glycol, and potassium acetate.

1,8-Pyrenylene-Ethynylene Macrocycles

A concise, highly regioselective synthesis of 1,8-dibromo-4,5-dialkoxypyrenes has been developed and exploited in the synthesis of some 1,8-pyrenylene−ethynylene macrocycles. The 1H NMR data and NICS calculations indicate that there is little or no macrocyclic ring current. Concentration-dependent UV−visible studies indicate no aggregation at low concentration, but 8b forms dimers with voids suitable for intercalation of small molecules in the solid state.

1,8-Pyrenylene−Ethynylene Macrocycles

A concise, highly regioselective synthesis of 1,8-dibromo-4,5-dialkoxypyrenes has been developed and exploited in the synthesis of some 1,8-pyrenylene-ethynylene macrocycles. The (1)H NMR data and NICS calculations indicate that there is little or no macrocyclic ring current. Concentration-dependent UV-visible studies indicate no aggregation at low concentration, but 8b forms dimers with voids suitable for intercalation of small molecules in the solid state.

Photochemically driven intercalation of small molecules into DNA by in situ irradiation

Intercalation of small molecules into DNA is photochemically achieved by in situ irradiation of a tetraaryl-pyridinium species. Such a "DNA intercalation on demand" process could highlight an alternative pathway to anticancer basic research, based on photo-activable DNA binders.

Recent Developments in the Chemistry of Deoxyribonucleic Acid (DNA) Intercalators: Principles, Design, Synthesis, Applications and Trends

In the present overview, we describe the bases of intercalation of small molecules (cationic and polar neutral compounds) in DNA. We briefly describe the importance of DNA structure and principles of intercalation. Selected syntheses, possibilities and applications are shown to exemplify the importance, drawbacks and challenges in this pertinent, new, and exciting research area. Additionally, some clinical applications (molecular processes, cancer therapy and others) and trends are described.

Molecular simulation study of intercalation of small molecules in kaolinite

Molecular simulations are used to study the intercalation of simple fluids of different dipole moments (dimethyl sulphoxide, formamide, methanol, water) in kaolinite at two temperatures. Mechanically stable basal spacings are determined from constant chemical potential Monte Carlo simulations and the results are compared with experimental data. The structure and thermodynamics of the different kaolinite/fluid intercalates with single or double fluid layers are studied. The calculations suggest the existence of more than one stable state for most of the intercalate systems investigated.

Design of Tetrathiafulvalene-Based Phosphazenes Combining a Good Electron-Donor Capacity and Possible Inclusion Adduct Formation (Part II)

Physical properties of intercalated porous material can be modulated by intercalation of small molecules, as this was demonstrated through the iodine (I2) intercalation into tris(o-phenylenedioxy)cyclotriphosphazene (TPP) crystals. This work describes in depth theoretical considerations of TPP derivatives. The core ring [(NP)3] substitution by [(CO)3], [(CNH)3], and [(CS)3], as well as the side group modification in size and composition (containing tetrathiafulvalene-like fragments), is well described from the most important aspects as their geometry optimization, their highest occupied molecular orbital (HOMO)−lowest unoccupied molecular orbital (LUMO) consideration together with ionization potentials (IP), and their charged forms. On the basis of PBE0/6-31G(d,p) calculations, the neutral forms of the [(CO)3], [(CNH)3], and [(CS)3] containing derivatives are predicted in a distorted caplike conformation. In the first two series, planar (or nearly planar) conformations are predicted upon oxidation, while ...

Design of TTF-Based Phosphazenes Combining a Good Electron-Donor Capacity and Possible Inclusion Adduct Formation

The physical properties of porous material can be modulated by intercalation of small molecules, whose size, in the case of tris-o-phenylenedioxy)cyclotriphosphazene (TPP)-based materials, vary with the different side groups. Starting from the TPP structure, a series of new derivatives were constructed through the core ring [(NP)(3)] substitution by [(CNH)(3)], [(CO)(3)], and [(CS)(3)] or/and the side group substitution by tetrathiafulvalene and a series of related fragments including bis(ethylenedithio)tetrathiafulvalene, 2-methylene-1, 3-dithiole, and 2-methylene-5,6-dihydro[1,3]dithiolo[4,5-b][1,4]dithiine. In the side fragment, such a substitution corresponds to the replacement of a ring heteroatom, an addition of substituents, or both. With use of theoretical methodologies based on DFT-B3LYP/6-31G* and HF/6-31G*//B3LYP/6-31G* approaches, molecular geometries and electronic properties including the LUMO and HOMO energies, the HOMO-LUMO gap, as well as the ionization potential (IP) were calculated. In comparison with the commonly used organic superconductors, most of the molecules investigated were predicted to show comparable or better electron-donor strength. Interestingly, a number of cyclophosphazene [(NP)(3)]-containing compounds were predicted to show the "paddle wheel" shape responsible for inclusion adducts formation, making these compounds to be potential candidates for organic superconductors with the ease of modulating their conducting properties by intercalation of suitable acceptors.

From Self-Affine to Logarithmic: Interfacial Fluctuation of a Stearic Acid Film upon Swelling in Water

The interfacial structures of a solution-cast stearic acid film before and after immersion in water were studied by X-ray scattering combined with atomic force microscopy. It is shown that the interfaces of the as-deposited film are self-affine. After the film is immersed in water for a long time, water molecules penetrate into the hydrophilic interfaces, enlarging the distance between the adjacent bilayers. Theoretical fit indicates that the film takes on a liquid crystal character after being swollen by water. The interfaces in both cases are partially correlated and are well represented by the given correlation functions, except for a small discrepancy between the theory and the experiment on length scales shorter than 60 nm. The results help to provide a deeper insight into the interfaces of lipid multilayers during the intercalation of small molecules.

Identification of Binding Mechanisms in Single Molecule–DNA Complexes

Changes in the elastic properties of single deoxyribonucleic acid (DNA) molecules in the presence of different DNA-binding agents are identified using atomic force microscope single molecule force spectroscopy. We investigated the binding of poly(dG-dC) dsDNA with the minor groove binder distamycin A, two supposed major groove binders, an α-helical and a 310-helical peptide, the intercalants daunomycin, ethidium bromide and YO, and the bis-intercalant YOYO. Characteristic mechanical fingerprints in the overstretching behavior of the studied single DNA-ligand complexes were observed allowing the distinction between different binding modes. Docking of ligands to the minor or major groove of DNA has the effect that the intramolecular B-S transition remains visible as a distinct plateau in the force-extension trace. By contrast, intercalation of small molecules into the double helix is characterized by the vanishing of the B-S plateau. These findings lead to the conclusion that atomic force microscope force spectroscopy can be regarded as a single molecule biosensor and is a potent tool for the characterization of binding motives of small ligands to DNA.