Search Results (48)

Streptococcus pneumoniae (S. pneumoniae) Sortase A (SrtA) anchors virulence proteins to the surface of the cell wall by recognizing and cleaving the LPXTG motif. These toxins help bacteria adhere to and colonize host cells, promote biofilm formation, and trigger host inflammatory responses. Therefore, SrtA is an ideal target for the development of new preparations for S. pneumoniae. In this study, we found that phloretin (pht) and phlorizin (phz) exhibited excellent affinities for SrtA based on virtual screening experiments. We analyzed the interactive mechanism between pht, phz, and alnusone (aln, a reported S. pneumoniae SrtA inhibitor) and SrtA based on molecular dynamics simulation experiments. The results showed that these inhibitors bound to the active pocket of SrtA, and the root mean square deviation (RMSD) and distance analyses showed that these compounds and SrtA maintained stable configuration and binding during the assay. The binding free energy analysis showed that both electrostatic forces (ele), van der Waals forces (vdw), and hydrogen bonds (Hbonds) promoted the binding between pht, phz, and SrtA; however, for the binding of aln and SrtA, the vdw force was much stronger than ele, and Hbonds were not found. The binding free energy decomposition showed that HIS141, ILE143, and PHE119 contributed more energy to promote pht and SrtA binding; ARG215, ASP188, and LEU210 contributed more energy to promote phz and SrtA binding; and HIS141, ASP209, and ARG215 contributed more energy to promote aln and SrtA binding. Finally, the transpeptidase activity of SrtA decreased significantly when treated with different concentrations of pht, phz, or aln, which inhibited S. pneumoniae biofilm formation and adhesion to A549 cells without affecting normal bacterial growth. These results suggest that pht, phtz, and aln are potential materials for the development of novel inhibitors against S. pneumoniae infection. Full article

Tocols are commonly known as vitamin E, which comprise tocopherols and tocotrienols. Although vegetable oils are natural sources of tocols, deodorizer distillates (DDs) are attractive feedstock due to their potential abundance from oil refining processes and economic price. Deep eutectic solvents (DESs) are a family of neoteric solvents that show promising performance for tocols extraction. Besides their characters occupying the green chemistry concept, this review presents the current research on the potential performances of DESs in extracting tocols selectively and efficiently from DDs. The application of DESs in tocols extraction is presented considering three different ways: mono-phasic, in situ DESs formation, and bi-phasic systems. The basic principles of intermolecular interactions (H-bond, van der Walls bond, and misfit interaction) between DESs or their components with tocols are discussed to understand the mechanism by which DESs selectively extract tocols from the mixture. This is mainly observed to be a function of the intrinsic properties of DESs and/or tocols, which could be beneficial for tuning the appropriate DESs for extracting tocols selectively and effectively under mild operation conditions. This review is expected to provide insight in the potential application of DESs in the extracting of natural compounds with a phenolic structure and also briefly discusses the toxicity of DESs. Full article

To improve the poor thermal conductivity of microencapsulated phase change materials (MPCMs), a strategy was designed with effective combinations between graphene nanosheets (GNs) and shells to prepare thermally conductive MPCMs–GNs by using cellulose nanofibers (CNFs) to assist GN dispersion. The experiments and theoretical calculations both illustrated that CNFs effectively prevented GNs from aggregating due to the strong Van der Walls interactions between CNFs and GNs. The morphologies and structures of MPCMs with and without GNs were characterized by SEM, FTIR and XRD. The thermal properties of MPCMs were evaluated by DSC, TG, and a thermal conductivity test. The MPCMs with 10 wt.% GNs exhibited a melting enthalpy as high as 187.2 J/g and a thermal conductivity as high as 1.214 (W/m⋅K). The results indicate that the prepared MPCMs possessed a good thermal stability. In addition, MPCMs–GNs exhibited outstanding mechanical properties using a nano-indentation test. With an excellent melting enthalpy and thermal conductivity, the prepared MPCMs–GNs/textile showed a potential ability to be used for comfort thermal regulation. Full article

The application of nanomaterials as modifiers in the field of asphalt is increasingly widespread, and this paper aims to systematically review research on the impact of nanomaterials on asphalt viscosity. The results find that nanomaterials tend to increase asphalt’s viscosity, enhancing its resistance to high-temperature rutting and low-temperature cracking. Zero-dimension nanomaterials firmly adhere to the asphalt surface, augmenting non-bonding interactions through van der Waals forces and engaging in chemical reactions to form a spatial network structure. One-dimensional nanomaterials interact with non-polar asphalt molecules, forming bonds between tube walls, thereby enhancing adhesion, stability, and resistance to cyclic loading. Meanwhile, these bundled materials act as reinforcement to transmit stress, preventing or delaying crack propagation. Two-dimensional nanomaterials, such as graphene and graphene oxide, participate in chemical interactions, forming hydrogen bonds and aromatic deposits with asphalt molecules, affecting asphalt’s surface roughness and aggregate movement, which exhibit strong adsorption capacity and increase the viscosity of asphalt. Polymers reduce thermal movement and compact asphalt structures, absorbing light components and promoting the formation of a cross-linked network, thus enhancing high-temperature deformation resistance. However, challenges such as poor compatibility and dispersion, high production costs, and environmental and health concerns currently hinder the widespread application of nanomaterial-modified asphalt. Consequently, addressing these issues through comprehensive economic and ecological evaluations is crucial before large-scale practical implementation. Full article

Bovine serum albumin (BSA) was ³H-labeled via a tritium thermal activation method that allowed quantifying BSA adsorption on single-walled carbon nanotubes (SWCNTs) to be 740 mg/mg, which leads to the ζ-potential of the BSA–SWCNT complex changing from −10 to −16 mV. Supercomputer simulations were carried out with Gromacs and PM7 with MOPAC2016 with Berendsen, Nosè–Hoover and Parrinello–Rahman algorithms. The dominant interactions between BSA and SWCNTs are found to be hydrophobic, and hydrogen bonds are also present. The mean total energy of the Coulomb and Van der Waals interactions is −646 ± 8 kJ/mol, by gmx energy. Full article

Inhibiting MDM2-p53 interaction is considered an efficient mode of cancer treatment. In our current study, Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and binding free energy calculations were combined together to probe the binding mechanism of non-peptide inhibitors K23 and 0Y7 and peptide ones PDI6W and PDI to MDM2. The GaMD trajectory-based DL approach successfully identified significant functional domains, predominantly located at the helixes α2 and α2’, as well as the β-strands and loops between α2 and α2’. The post-processing analysis of the GaMD simulations indicated that inhibitor binding highly influences the structural flexibility and collective motions of MDM2. Calculations of molecular mechanics–generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) not only suggest that the ranking of the calculated binding free energies is in agreement with that of the experimental results, but also verify that van der Walls interactions are the primary forces responsible for inhibitor–MDM2 binding. Our findings also indicate that peptide inhibitors yield more interaction contacts with MDM2 compared to non-peptide inhibitors. Principal component analysis (PCA) and free energy landscape (FEL) analysis indicated that the piperidinone inhibitor 0Y7 shows the most pronounced impact on the free energy profiles of MDM2, with the piperidinone inhibitor demonstrating higher fluctuation amplitudes along primary eigenvectors. The hot spots of MDM2 revealed by residue-based free energy estimation provide target sites for drug design toward MDM2. This study is expected to provide useful theoretical aid for the development of selective inhibitors of MDM2 family members. Full article

Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calculations are integrated to probe the binding modes of three inhibitors (H1B, JQ1 and TVU) to BRD4 and BRD9. The MD trajectory-based DL successfully identify significant functional function domains, such as BC-loop and ZA-loop. The information from the post-processing analysis of MD simulations indicates that inhibitor binding highly influences the structural flexibility and dynamic behavior of BRD4 and BRD9. The results of the MM-GBSA calculations not only suggest that the binding ability of H1B, JQ1 and TVU to BRD9 are stronger than to BRD4, but they also verify that van der Walls interactions are the primary forces responsible for inhibitor binding. The hot spots of BRD4 and BRD9 revealed by residue-based free energy estimation provide target sites of drug design in regard to BRD4 and BRD9. This work is anticipated to provide useful theoretical aids for the development of selective inhibitors over BRD family members. Full article

The paper concerns the dynamics and stability of double-walled carbon nanotubes conveying fluid. The equations of motion adopted in the current study to describe the dynamics of such nano-pipes stem from the classical Bernoulli–Euler beam theory. Several additional terms are included in the basic equations in order to take into account the influence of the conveyed fluid, the impact of the surrounding medium and the effect of the van der Waals interaction between the inner and outer single-walled carbon nanotubes constituting a double-walled one. In the present work, the flow-induced vibrations of the considered nano-pipes are studied for different values of the length of the pipe, its inner radius, the characteristics of the ambient medium and the velocity of the fluid flow, which is assumed to be constant. The critical fluid flow velocities are obtained at which such a cantilevered double-walled carbon nanotube embedded in an elastic medium loses stability. Full article

A 3D hydrogen-bonded metal-organic framework, [Cu(apc)₂]_n (TJU-Dan-5, Hapc = 2-aminopyrimidine-5-carboxylic acid), was synthesized via a solvothermal reaction. The activated TJU-Dan-5 with permanent porosity exhibits a moderate uptake of 1.52 wt% of hydrogen gas at 77 K. The appropriate BET surface areas and decoration of the internal polar pore surfaces with groups that form extensive hydrogen bonds offer a more favorable environment for selective C₂H₆ adsorption, with a predicted selectivity for C₂H₆/CH₄ of around 101 in C₂H₆/CH₄ (5:95, v/v) mixtures at 273 K under 100 kPa. The molecular model calculation demonstrates a C–H···π interaction and a van der Waals host–guest interaction of C₂H₆ with the pore walls. This work provides a strategy for the construction of 3D hydrogen-bonded MOFs, which may have great potential in the purification of natural gas. Full article

Alzheimer’s disease (AD), the most common type of dementia in older people, causes neurological problems associated with memory and thinking. The key enzymes involved in Alzheimer’s disease pathways are acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). Because of this, there is a lot of interest in finding new AChE inhibitors. Among compounds that are not alkaloids, flavonoids have stood out as good candidates. The apple fruit, Malus domestica (Rosaceae), is second only to cranberries regarding total phenolic compound concentration. Computational tools and biological databases were used to investigate enzymes and natural compounds. Molecular docking techniques were used to analyze the interactions of natural compounds of the apple with enzymes involved in the central nervous system (CNS), acetylcholinesterase, and butyrylcholinesterase, followed by binding affinity calculations using the AutoDock tool. The molecular docking results revealed that CID: 107905 exhibited the best interactions with AChE, with a binding affinity of −12.2 kcal/mol, and CID: 163103561 showed the highest binding affinity with BuChE, i.e., −11.2 kcal/mol. Importantly, it was observed that amino acid residue Trp286 of AChE was involved in hydrogen bond formation, Van Der Walls interactions, and Pi–Sigma/Pi–Pi interactions in the studied complexes. Moreover, the results of the Molecular Dynamics Simulation (MDS) analysis indicated interaction stability. This study shows that CID: 12000657 could be used as an AChE inhibitor and CID: 135398658 as a BuChE inhibitor to treat Alzheimer’s disease and other neurological disorders. Full article

The flavin derivatives 10-methyl-isoalloxazine (MIA) and 6-fluoro-10-methyl-isoalloxazine (6F-MIA) were incorporated in two alternative metal-organic frameworks, (MOFs) MIL-53(Al) and MOF-5. We used a post-synthetic, diffusion-based incorporation into microcrystalline MIL-53 powders with one-dimensional (1D) pores and an in-situ approach during the synthesis of MOF-5 with its 3D channel network. The maximum amount of flavin dye incorporation is 3.9 wt% for MIA@MIL-53(Al) and 1.5 wt% for 6F-MIA@MIL-53(Al), 0.85 wt% for MIA@MOF-5 and 5.2 wt% for 6F-MIA@MOF-5. For the high incorporation yields the probability to have more than one dye molecule in a pore volume is significant. As compared to the flavins in solution, the fluorescence spectrum of these flavin@MOF composites is broadened at the bathocromic side especially for MIA. Time-resolved spectroscopy showed that multi-exponential fluorescence lifetimes were needed to describe the decays. The fluorescence-weighted lifetime of flavin@MOF of 4 ± 1 ns also corresponds to those in solution but is significantly prolonged compared to the solid flavin dyes with less than 1 ns, thereby confirming the concept of “solid solutions” for dye@MOF composites. The fluorescence quantum yield (Φ_F) of the flavin@MOF composites is about half of the solution but is significantly higher compared to the solid flavin dyes. Both the fluorescence lifetime and quantum yield of flavin@MOF decrease with the flavin loading in MIL-53 due to the formation of various J-aggregates. Theoretical calculations using plane-wave and QM/MM methods are in good correspondence with the experimental results and explain the electronic structures as well as the photophysical properties of crystalline MIA and the flavin@MOF composites. In the solid flavins, π-stacking interactions of the molecules lead to a charge transfer state with low oscillator strength resulting in aggregation-caused quenching (ACQ) with low lifetimes and quantum yields. In the MOF pores, single flavin molecules represent a major population and the computed MIA@MOF structures do not find π-stacking interactions with the pore walls but only weak van-der-Waals contacts which reasons the enhanced fluorescence lifetime and quantum yield of the flavins in the composites compared to their neat solid state. To analyze the orientation of flavins in MOFs, we measured fluorescence anisotropy images of single flavin@MOF-5 crystals and a static ensemble flavin@MIL53 microcrystals, respectively. Based on image information, anisotropy distributions and overall curve of the time-resolved anisotropy curves combined with theoretical calculations, we can prove that all fluorescent flavins species have a defined and rather homogeneous orientation in the MOF framework. In MIL-53, the transition dipole moments of flavins are orientated along the 1D channel axis, whereas in MOF-5 we resolved an average orientation that is tilted with respect to the cubic crystal lattice. Notably, the more hydrophobic 6F-MIA exhibits a higher degree order than MIA. The flexible MOF MIL-53(Al) was optimized essentially to the experimental large-pore form in the guest-free state with QuantumEspresso (QE) and with MIA molecules in the pores the structure contracted to close to the experimental narrow-pore form which was also confirmed by PXRD. In summary, the incorporation of flavins in MOFs yields solid-state materials with enhanced rigidity, stabilized conformation, defined orientation and reduced aggregations of the flavins, leading to increased fluorescence lifetime and quantum yield as controllable photo-luminescent and photo-physical properties. Full article

TiO₂ is one of the most investigated materials due to its abundance, lack of toxicity, high faradaic capacitance, and high chemical and physical stability; however, its potential use in energy storage devices is constrained by its high internal resistance and weak van der Waals interaction between the particles. Carbon nanotubes are especially well suited for solving these issues due to their strong mechanical strength, superior electrical conductivity, high electron mobilities, excellent chemical and thermal stability, and enormous specific nanoporous surface. The hydrothermal approach was followed by chemical vapor deposition to produce a network composite of titanium dioxide nanoribbons (TNRs) and multi-walled carbon nanotubes (MWCNTs). The nanocomposite was characterized using a variety of methods. One phase of TiO₂-B nanoribbons has porous pits on its surface, and MWCNTs are grown in these pits to produce a network-like structure in the nanocomposite. With a two-electrode supercapacitor configuration, the TNR/CNT gave a gravimetric capacitance of 33.33 F g⁻¹, which was enhanced to 68.18 F g⁻¹ in a redox-active electrolyte containing hydroquinone (HQ). Additionally, the areal capacitance per footprint was increased from 80 mF cm⁻² in H₂SO₄ to 163.63 mF cm⁻² in H₂SO₄/HQ. The TNR/CNT supercapacitor has superior cyclic stability than the previously reported TiO₂-based electrodes, with 97.5% capacitance retention after 5000 cycles. Based on these results, it looks like the TNR/CNT supercapacitor could provide portable electronic power supplies with new ways to work in the future. Full article

In traditional Chinese medicine, soft-shelled turtle protein and peptides serve as a nutraceutical for prolonging the lifespan. However, their effects on anti-aging have not been clarified scientifically in vivo. This study aimed to determine whether soft-shelled turtle peptides (STP) could promote the lifespan and healthspan in Drosophila melanogaster and the underlying molecular mechanisms. Herein, STP supplementation prolonged the mean lifespan by 20.23% and 9.04% in males and females, respectively, delaying the aging accompanied by climbing ability decline, enhanced gut barrier integrity, and improved anti-oxidation, starvation, and heat stress abilities, while it did not change the daily food intake. Mechanistically, STP enhanced autophagy and decreased oxidative stress by downregulating the target of rapamycin (TOR) signaling pathway. In addition, 95.18% of peptides from the identified sequences in STP could exert potential inhibitory effects on TOR through hydrogen bonds, van der Walls, hydrophobic interactions, and electrostatic interactions. The current study could provide a theoretical basis for the full exploitation of soft-shelled turtle aging prevention. Full article

This study was devoted to an investigation on the dynamics of double-walled carbon nanotubes (DWCNTs) under the influence of Winkler–Pasternak foundation near the primary resonance. Two Euler–Bernoulli beams embedded on nonlinear foundation, interacting through van der Waals forces, subjected to mechanical impact are considered. By means of Hamilton’s principle, Eringen’s nonlocal elastic theory, and taking into account the moving nanoparticles, the Galerkin–Bubnov method is applied and accordingly, governing partial differential equations are reduced to two differential equations with variable coefficients. The nonlinear damped and forced vibration is studied using the optimal auxiliary functions method (OAFM). An explicit and very accurate analytical solution is obtained by means of OAFM without considering simplifying hypotheses. An accurate analysis is for the first time reported considering the cumulated effects of nonlinearities simultaneously induced by the Winkler–Pasternak foundation, the curvature of beams and van der Waals force, and also the effect of discontinuities marked by the presence of the Dirac function. Finally, a stability analysis of the considered model is developed by means of the homotopy perturbation method (HPM) using the condition of existence of the two frequencies. It was shown that an increasing of some constitutive parameters substantially reduces the area of stability, all these being of much help in guiding the design of advanced nanoelectromechanical devices, in which nanotubes act as basic elements. Full article

Twisted van der Waals heterostructures were recently found to possess unique physical properties, such as superconductivity in magic angle bilayer graphene. Owing to the nonhomogeneous stacking, the energy of twisted van der Waals heterostructures are often higher than their AA or AB stacking counterpart, therefore, fabricating such structures remains a great challenge in experiments. On the other hand, one dimensional (1D) coaxial van der Waals structures has less freedom to undergo phase transition, thus offer opportunity for fabricating the 1D cousin of twisted bilayer graphene. In this work, we show by molecular dynamic simulations that graphene nanoribbons can self-assemble onto the surface of carbon nanotubes driven by van der Waals interactions. By modifying the size of the carbon nanotubes or graphene nanoribbons, the resultant configurations can be controlled. Of particular interest is the formation of twisted double walled carbon nanotubes whose chiral angle difference can be tuned, including the 1.1° magic angle. Upon the longitudinal unzipping of such structures, twisted bilayer graphene nanoribbons can be obtained. As the longitudinal unzipping of carbon nanotubes is a mature technique, we expect the strategy proposed in this study to stimulate experimental efforts and promote the fast growing research in twistronics. Full article