Experimental Molecular Dynamics Research Articles

Study on the Thermal Stability of Urea‐Formaldehyde Resin Microcapsules with Nanosilica Incorporation by Molecular Dynamics Simulation and Experiments

AbstractIt is an innovation to self‐heal the microdefects inside materials by doping microcapsules. Urea‐formaldehyde resin (UF) microcapsule is widely used in self‐healing materials owing to its excellent mechanical properties. However, when it is used in electrical insulation materials, the thermal stability of the microcapsules need to be enhanced owing to the relatively high internal temperature of the material under the long‐term action of electric field. In this paper, molecular dynamics simulation is used to calculate the properties related to the thermal stability of UF microcapsule with and without nanosilica incorporation. The simulation result shows that incorporating nanosilica can increase the density and glass transition temperature, decrease the fractional free volume of UF materials. The UF microcapsules with and without nanosilica incorporation are prepared experimentally, and thermogravimetric test result shows that incorporating nanosilica can enhance the thermal stability of UF microcapsule; scanning electron microscope result shows nanocomposite microcapsule has more UF debris adhered on its surface. By establishing the interface model of UF and nanosilica to explore the internal mechanism, it is found that the interface interaction between UF and nanosilica is conducive to enhancing the thermal stability of UF material.

Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments

In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.

Novel 1,3,4-oxadiazole compounds inhibit the tyrosinase and melanin level: Synthesis, in-vitro, and in-silico studies

In this research work, we have designed and synthesized some biologically useful of 1,3,4-Oxadiazoles. The structural interpretation of the synthesized compounds has been validated by using FT-IR, LC-MS, HRMS, 1H NMR and 13C NMR techniques. Moreover, the in-vitro mushroom tyrosinase inhibitory potential of the target compounds was assessed. The in-vitro study reveals that, all compounds demonstrate an excellent tyrosinase inhibitory activity. Especially, 2-(5-(2-methoxyphenyl)-1,3,4-oxadiazol-2-ylthio)-N-phenylacetamide (IC50 = 0.003 ± 0.00 µM) confirms much more significant potent inhibition activity compared with standard drug kojic acid (IC50 = 16.83 ± 1.16 µM). Subsequently, the most potent five oxadiazole compounds were screened for cytotoxicity study against B16F10 melanoma cells using an MTT assay method. The survival rate for the most potent compound was more pleasant than other compounds. Furthermore, the western blot results proved that the most potent compound considerably decreased the expression level of tyrosinase at 50 µM (P < 0.05). The molecular docking investigation exposed that the utmost potent compound displayed the significant interactions pattern within the active region of the tyrosinase enzyme and which might be responsible for the decent inhibitory activity towards the enzyme. A molecular dynamic simulation experiment was presented to recognize the residual backbone stability of protein structure.

Comprehensive evaluation of the role of phenolate based ionic liquid on extracting pyrrole from diverse sources: A combined molecular dynamics simulation study and experiment validation

Ionic liquids have acted as a hopeful solvent in separation field over the past decade due to its functional groups contributed in separation process. Thus, to test the effect of the phenolate anion on extracting typical heterocyclic N-compound, pyrrole was selected as the representative compounds due to its high content from diverse sources. In this work, the simple structure and easy prepared functional phenolate-based ionic liquid, 1-ethyl-3-methylimidazolium phenolate ([emim][Phe]), is evaluated to separate pyrrole with the polarity analysis by COSMO-SAC model. After understanding the H-bond donor or acceptor relationship of the studied regents, the interaction mechanism between the phenolate based ionic liquid extractant itself and its complex system with pyrrole are visual demonstrated by the RDF, SDF plots etc. analysis and experimental research, which can contribute to understand the H-bonds interaction, hydrogen atom connected to the heteroatoms in pyrrole and oxygen atom in phenolate anion, more indicative. Additionally, the liquid–liquid phase behavior of the methylbenzene + pyrrole + [emim][Phe] system was determined to verify the effect at the perspective of phase equilibrium, the values of D and S was calculated and a highly selectivity for pyrrole could be confirmed. This will lay a solid foundation for developing a new separation technology about the extraction of heterocyclic N-compounds such as pyrrole.

Ion effects on the extraction of cesium (I) by 1,3-Diisopropoxycalix [4] arenecrown-6(BPC6) and the highly efficient extraction under neutral conditions

ABSTRACT The effect of ion species and concentration on the extraction percent of Cs+ by 1,3-Diisopropoxycalix [4] arenecrown-6 (BPC6) in octanol/water solvent extraction system has been studied by molecular dynamics simulations and experiments. The results show that the anionic species play an important role on the enhancement of the extraction percent of Cs+. Specifically, the order in which anions promote the extraction percent is different at different total anion concentrations. At a relatively low anion concentration of 0.5 M, the extraction percent follows the sequence: ClO4 −> I−> NO3 −> Br−> Cl−> SO4 2−> F−. At a relatively high concentration of 2 M, the extraction percent of Cs+ follows the following sequence: I−> ClO4 −> Br−~ NO3 −> Cl−> SO4 2−> F−. It is indicated that the extraction percent is dominated by the anion’s interface propensity, which is the probability of anion distribution in the interface compared to the water phase. However, at low concentration of anions, strong coordination effect of NO3 − promotes the extraction effect compared to Br−. At the high anion’s concentration, the stronger salting-out capacity of Br− leads to a considerable increase of extraction percent. In addition, the cations also slightly affect the extraction percent. The extraction percent is affected by both cations’ concentration and the salt-out effect. On this basis, a neutral Cs+ extraction system has been established, and one stage extraction percent could reach 62.5%.

Enhancement of Diffusion Assisted Bonding of the Bimetal Composite of Austenitic/Ferric Steels via Intrinsic Interlayers.

We investigate the effect of the intrinsic interlayers on the diffusion assisted bonding properties of the austenitic steel (stainless steel 316L) and ferric steels (Low-carbon steel Q345R) in a hot rolling process by molecular dynamics simulations and experiment. The introduction of an intrinsic interlayer (Cr or Ni) widens the diffusion region, leading to enhancement of bonding. The thickness of the diffusion region enlarges with an increase of temperature, with an enhancement factor of 195% and 108%, for Cr and Ni interlayer, respectively, at the temperature of 1800 K. Further diffusion analysis reveals the unsymmetrical diffusion near the interface. Our experimental investigation evidenced our computation discovery.

Atomic-Resolution 1.3 Å Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE.

We report the atomic-resolution (1.3 Å) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the starting point for targeted molecular dynamics experiments revealing the conformational change from the open form to the closed form that occurs when DapE binds l,l-SDAP and cleaves the amide bond. These simulations demonstrated closure from the open to the closed conformation, the change in RMS throughout the closure, and the independence in the movement of the two DapE subunits. This conformational change occurred in two phases with the catalytic domains moving toward the dimerization domains first, followed by a rotation of catalytic domains relative to the dimerization domains. Although there were no targeting forces, the substrate moved closer to the active site and bound more tightly during the closure event.

Enhanced interfacial and mechanical properties of carbon fiber/PEEK composites by hydroxylated PEEK and carbon nanotubes

The interfacial adhesion between carbon fiber (CF) and polyetheretherketone (PEEK) is poor due to their inert nature, limiting the mechanical properties of CF/PEEK composites. This study improved the interactions between CF and PEEK by sizing hydroxylated PEEK grafted multi-walled carbon nanotubes (HPEEK-g-MWCNT) synthesized via an esterification reaction. Molecular dynamics simulations and experiments were conducted to evaluate the microstructure and characterize the mechanical properties of CF/PEEK composites. A slightly decreased crystallinity of PEEK within modified composites resulted from the reduced nucleation effect of CF and inhibited PEEK mobility by HPEEK-g-MWCNT sizing. Hydrogen bonding and mechanical interlocking enhanced interface adhesion, and covalent bonds of HPEEK-g-MWCNT increased load transfer. These factors led to the flexural strength and interlaminar shear strength of HPEEK-g-MWCNT modified composites increased by 94.2% (669.7 MPa) and 55.2% (79.1 MPa) compared with control ones. The modification method of using chemically treated and grafted polymers like HPEEK-g-MWCNT would have great potential applications in thermoplastic composites.

Effect of interlayer cations on montmorillonite swelling: Comparison between molecular dynamic simulations and experiments

The understanding of the swelling phenomenon of montmorillonite is essential to predict the physical and chemical behavior of clay-based barriers in geoenvironmental engineering. This study investigated the crystalline swelling behavior of montmorillonite with different interlayer cations including monovalent Na, K, and Cs and divalent Ca and Sr by molecular dynamics simulations and experimental measurements including X-ray diffraction and water vapor adsorption. The stepwise swelling behavior for Na- and Ca/Sr-montmorillonite demonstrated good agreement between molecular dynamics (MD) simulated and experimental results. The swelling curves of K- and Cs-montmorillonite remaining in the 1-hydrated state even at high relative humidity showed systematic discrepancies between MD simulations and experimental results. The comparative discussion between the experimental and MD derived swelling curves offer insights that may help to understand the swelling mechanism of montmorillonite and the dependence on interlayer cations. The water content in the interlayer and external surface in five homoionic montmorillonite was strongly correlated to the hydration number of each ion. On the basis of these comparisons, the hydration free energy of interlayer cations seems to contribute greatly to the total driving force for the crystalline swelling of montmorillonite. An additional key factor is the preference of an outer- or inner-sphere complex of interlayer cations and the distribution of cations in the interlayer space. This effect has a considerable impact in the case of monovalent cations and results in different swelling behavior between the outer-sphere Na and inner-sphere K and Cs ions.

Compressed cylindrical shell with a rigid core and a gap

Compressed cylindrical shells are common in our daily life, such as rolled-up sleeves and a retreated package of drinking straws. The deformations on these cylindrical shells with a rigid core are often random and unpredictable. In contrast, compressed beer can exhibit uniform arrays of diamonds, called the Yoshimura pattern. To elucidate the difference between these systems, we combine molecular dynamics simulations and experiments to study the deformation on a compressed cylindrical shell with a rigid core. By thoroughly exploring different material parameters, we are able to pin down the mode diagram.

Generation mechanism of irregular microstructures on the machined surface in single-point diamond turning

Polycrystalline copper is widely applied to the manufacture of optical components. Our previous experiments found that some irregular microstructures appeared on the machined surface; however, it had lacked sufficient studies about generation mechanism. The present research conducted a theoretical and experimental study on the generation mechanism of irregular microstructures. Firstly, the appearance and distribution of irregular microstructures on the machined surface was studied. Secondly, the effects of crystal orientations on the generation of irregular microstructures were investigated. Finally, the cutting performances were investigated by both molecular dynamics simulations and experiments. Theoretical and experimental results show that (1) material properties under different grain orientations are the major cause of the appearance of irregular microstructures; (2) with the changes of crystal orientations, the force signal, chip morphology, shear slip of material, and subsurface defect are also different; and (3) higher cutting velocities have the suppression effect on the generation of irregular microstructures. The present research provides a deep insight into the generation mechanism and suppression method of irregular microstructures in single point diamond turning polycrystalline copper.

Secondary structure dependence of amyloid-β(1-40) on simulation techniques and force field parameters.

Our recent studies revealed that none of the selected widely used force field parameters and molecular dynamics simulation techniques yield structural properties for the intrinsically disordered α-synuclein that are in agreement with various experiments via testing different force field parameters. Here, we extend our studies on the secondary structure properties of the disordered amyloid-β(1-40) peptide in aqueous solution. For these purposes, we conducted extensive replica exchange molecular dynamics simulations and obtained extensive molecular dynamics simulation trajectories from David E. Shaw group. Specifically, these molecular dynamics simulations were conducted using various force field parameters and obtained results are compared to our replica exchange molecular dynamics simulations and experiments. In this study, we calculated the secondary structure abundances and radius of gyration values for amyloid-β(1-40) that were simulated using varying force field parameter sets and different simulation techniques. In addition, the intrinsic disorder propensity, as well as sequence-based secondary structure predisposition of amyloid-β(1-40) and compared the findings with the results obtained from molecular simulations using various force field parameters and different simulation techniques. Our studies clearly show that the epitope region identification of amyloid-β(1-40) depends on the chosen simulation technique and chosen force field parameters. Based on comparison with experiments, we find that best computational results in agreement with experiments are obtained using the a99sb*-ildn, charmm36m, and a99sb-disp parameters for the amyloid-β(1-40) peptide in molecular dynamics simulations without parallel tempering or via replica exchange molecular dynamics simulations.

Research on the miscibility, mechanical properties and printability of polylactic acid/poly (ε-caprolactone) blends: insights from molecular dynamics simulation and experiments

As known, the poor toughness of Polylactic acid (PLA) limits its further application, especially as a bone implant withstanding complex loadings. Blending PLA with Poly (e-caprolactone) (PCL) under the action of compatibilizers is a proven method to improve the toughness of PLA, while the excess compatibilizers is hard to remove and easy to contaminate the matrix material. This study employed a molecular dynamics simulation combining experimental testing method to investigate the miscibility, mechanical properties and printability of PLA/PCL blends at different compositions without adding any compatibilizers, so as to obtain an ideal PLA/PCL filament for FDM printing bone scaffolds. Results of binding energy distribution and intermolecular interaction show that the miscibility of PLA and PCL is not very good, only the blend of 9PLA/1PCL is miscible. The calculated static mechanical properties and tensile testing results indicate the stiffness or hardness of blends decrease with the addition of PCL, while the toughness firstly increases and then decreases with the introduction of PCL, and the blend of 9PLA/1PCL possesses the best ductility and toughness. Moreover, the results of surface morphology confirm the miscible of 9PLA/1PCL blend and explain why the tensile properties of 9PLA/1PCL is the best, a better miscibility indicating better mechanical properties. Finally, the results of printability indicates that, due to the fluidity of PCL, the printability of blend becomes worse with the increase of PCL content, and the blend of 9PLA/1PCL possesses a relatively good printability. This work provides a practical guidance to the design of PLA/PCL blend filament for FDM printing bone scaffolds.

Doping effects of metal cation on sulfide solid electrolyte/lithium metal interface

Doping modification is usually used to improve the ionic conductivity of sulfide solid electrolytes, but its effects on the interface between the electrolyte/lithium (Li) metal seem not sufficiently studied and understood. In this work, the advantages and disadvantages of sulfide electrolyte doped with MoS 2 , ZnS, FeS 2 , SnS 2 and SiS 2 are systematically studied. The ab initio molecular dynamics (AIMD) calculations and experiments show that MoS 4 4- can preferentially replace the P 2 S 7 4- in Li 7 P 3 S 11 , thereby broadening Li + channels and creating Li vacancies to promote ion conduction. However, the doping of MoS 2 can lead to the introduction of Mo metal into the solid electrolyte/Li interface layer (SEI), resulting in the reduction of the SEI’s interface energy and migration rate of Li atoms at SEI, as well as the accumulation of electrons, thereby accelerating the thickening of the SEI and growth of Li dendrites. The doping results of different sulfides show that the critical current density is positively related to the resistivity of the doping element. The doping of non-metallic silicon will not cause a decrease in the critical current density. This work provides an important reference for the selection of solid electrolyte dopants and the construction of electrolyte/Li interface. • Metal cations doping of Li7P3S11 will replace P2S74- and increase ion conductivity. • Metallic Mo will reduce interface energy and increase Li diffusion barrier of SEI, accelerating Li dendrites growth. • Mo will turn SEI into a mixed conductor of ions and electrons, thus thickening SEI. • Critical current density is positively correlated with resistivity of the doping elements, rather than ion conductivity. • Non-metallic Si-doping will cause an increasement in electrochemical performance.

Influence of Nanoparticles on the Evaporation of a Nanodroplet from Solid Substrates: An Experimental and Molecular Dynamics Investigation

Molecular Dynamic simulations and experiments have been performed to investigate the evaporative behavior of a liquid droplet in the presence of nanoparticles on a smooth, heated flat plate. Nanofluids of different volume fractions with CuO and Al2O3 nanoparticles were prepared to obtain liquid droplets. Experiments were conducted for droplets of both nanofluids and base fluid (DI water). The results showed that in the pinned region of evaporation, droplets of nanofluids with higher volume fractions of dense nanoparticles evaporated by keeping their base pinned at the triple point contact line. It is also observed that the evaporation rate of nanofluid droplets with nanoparticles having higher density is slower and promoted a typical pattern formation. Molecular Dynamic simulations were further performed to analyse the influence of various nanoparticle-liquid interaction strengths (εnp−l) on evaporative behavior. The simulation results suggest that in the pinned evaporation stage, for higher values of εnp−l, the droplet undergoes a delay on evaporation while subjected to higher heat flux on the substrate.

Additives-directed lyotropic liquid crystals architecture: Simulations and experiments

In this study, alkanes and sucrose esters are employed to investigate the influence of additives on lyotropic liquid crystal architecture. After molecular dynamic simulations and experiment characterization, we showed how the additives control the structure of LLCs. By controlling the polarity of additives, the phase behavior of LLCs can be engineered to form the required structure. Dissipative particle dynamics (DPD) is introduced for simulating the self-assembly of phytantriol (PT), providing intuitionistic images and structure information, which shows that additives with low-polarity complicate the internal structure of liquid crystal systems. Then the ternary phase diagrams of additives, PT, and water are constructed to systematically study the effects of additives on the phase behavior of LLCs. Consistent with DPD simulation results, there is a certain regularity in the effects of additives on the structure of liquid crystals. The difference in the structure of LLCs is due to the variability in the critical packing parameter (CPP) obtained by changing the polarity of additives. Our findings demonstrate that additives polarity is a key factor in LLCs structure, and may pave a promising avenue for novel LLCs development and translation, determining the self-assembly process and the resulting phase of LLCs.

Discovery of drug-like acetylcholinesterase inhibitors by rapid virtual screening of a 6.9million compound database.

Cholinesterase inhibitors remain the mainstay of Alzheimer's disease treatment, and the search for new inhibitors with better efficacy and side effect profiles is ongoing. Virtual screening (VS) is a powerful technique for searching large compound databases for potential hits. This study used a sequential VS workflow combining ligand-based VS, molecular docking and physicochemical filtering to screen for central nervous system (CNS) drug-like acetylcholinesterase inhibitors (AChEIs) amongst the 6.9million compounds of the CoCoCo database. Eleven in silico hits were initially selected, resulting in the discovery of an AChEI with a Ki of 3.2µM. In vitro kinetics and in silico molecular dynamics experiments informed the selection of an additional seven analogues. This led to the discovery of two further AChEIs, with Ki values of 2.9µM and 0.65µM. All three compounds exhibited reversible, mixed inhibition of acetylcholinesterase. Importantly, the in silico physicochemical filter facilitated the discovery of CNS drug-like compounds, such that all three inhibitors displayed high in vitro blood-brain barrier model permeability.

Synthesis, antibacterial action, and ribosome inhibition of deoxyspectinomycins

Spectinomycin, an aminocyclitol antibiotic, is subject to inactivation by aminoglycoside modifying enzymes (AMEs) through adenylylation or phosphorylation of the 6-hydroxy group position. In this study, the effects of deoxygenation of the 2- and 6-hydroxy group positions on the spectinomycin actinamine ring are probed to evaluate their relationship to ribosomal binding and the antimicrobial activities of spectinomycin, semisynthetic aminomethyl spectinomycins (amSPCs), and spectinamides. To generate these analogs, an improved synthesis of 6-deoxyspectinomycin was developed using the Barton deoxygenation reaction. 6-Dehydrospectinamide was also synthesized from spectinamide 4 to evaluate the H-bond acceptor character on the C-6 position. All the synthesized analogs were tested for antibacterial activity against a panel of Gram (+) and Gram (−) pathogens, plus Mycobacterium tuberculosis. The molecular contribution of the 2- and 6-hydroxy group and the aryl functionalities of all analogs were examined by measuring inhibition of ribosomal translation and molecular dynamics experiments with MM/GBSA analysis. The results of this work indicate that the 6-hydroxy group, which is the primary target of AMEs, is a required motif for antimicrobial activity in current analogs. Removal of the 6-hydroxy group could be partially rescued by offsetting ribosomal binding contributions made by the aryl side chains found in the spectinamide and amSPCs. This study builds on the knowledge of the structure–activity relationships of spectinomycin analogs and is being used to aid the design of next-generation spectinomycins.

Study on preparation and properties of mineral surfactant – microbial dust suppressant

In order to solve the problem of coal dust pollution and further improve the dust suppression performance of microbial dust suppressant, a surfactant-microbial dust suppressant is prepared through the addition of surfactant to microbial dust suppressant. The optimal formula is as follows: mineralized bacteria (OD600 ≈ 1.6) cultivated for 48 h, 0.5 mol/L of cementing fluid and 0.08% cocamidopropyl betaine (CAB). Compared with microbial dust suppressant, surfactant (CAB)-microbial dust suppressant has better anti-evaporation and wind erosion resistance. Molecular dynamic simulations and contact angle experiments verified the improvement of the wettability of microbial dust suppressants by surfactants. XRD and SEM-EDS results show that calcium carbonate precipitates in coal dust treated with CAB-microbial dust suppressant, which can consolidate the coal dust particles into a whole. In summary, the addition of surfactants improves the dust suppression efficiency of microbial dust suppressants.

The effects of the van der Waals potential energy on the Young’s modulus of a polymer: comparison between molecular dynamics simulation and experiment

Molecular dynamics simulation were employed to investigate the effect of changing the potential energies describing primary and secondary bonds on the Young’s modulus of a polymer. The energies were changed by arbitrarily modifying the parameters of the potential energy model function. The parameters influence the structure of the polymer and its global energy, eventually causing changes to the Young’s modulus. The van der Waals energy describing secondary bonds gives the most significant contribution to the changes. Increasing the energy increases the density and Young’s modulus. The trends are in agreement with experimental data.