Results Of Molecular Dynamics Simulations Research Articles

Association parameters for Cubic-Plus-Association equation of state determined by molecular dynamics and Petroleomics: Prediction of asphaltene precipitation

In this study, petroleomics characterization, molecular dynamics (MD) simulations, and a cubic-plus-association (CPA) equation of state (EoS) were conducted to understand how the structural characteristics affect the phase behavior of a fluid. To do this, the asphaltene onset pressure (AOP) was estimated by CPA EoS using association parameters determined from MD simulations. Petroleomics characterization and gas chromatography were conducted to identify appropriate representative molecular structures for describing a live crude oil. The American Petroleum Institute (API) gravity, dead and live crude oil densities, and viscosities at reservoir conditions were calculated from the MD simulation results and were found to differ from the experimental measurements by less than 5%, indicating accurate characterizations for both real dead and live crude oil. A formation damage diagnosis from a compositional perspective was conducted because oxygenated aromatic compounds, which are highly active in aggregation terms, were identified in the aromatic fraction by Fourier-transform ion cyclotron resonance mass spectrometry (FT–ICR MS). The association parameters for the self-associating organics (So: asphaltenes and oxygenated aromatics) and the cross-interaction between these Sos and the maltenes were calculated from the MD simulation results. To the best of our knowledge, this is the first time that association parameters have been obtained from an MD model and successfully implemented in a CPA EoS, allowing the prediction of AOP with an accuracy close to 1% compared to the experimentally determined value for live crude oil. This study provides a promising framework to develop an EoS for crude oils based on their molecular characteristics, reducing the need to perform parametric tuning with experimental data. In addition, this structural characterization proposed could be important to other key topics such as enhanced oil recovery (EOR) and carbon capture use and storage (CCUS), relating the structural composition to phase behavior.

Development of NaCl-MgCl2-CaCl2 Ternary Salt for High-Temperature Thermal Energy Storage Using Machine Learning.

NaCl-MgCl2-CaCl2 eutectic ternary chloride salts are potential heat transfer and storage materials for high-temperature thermal energy storage. In this study, first-principles molecular dynamics simulation results were used as a data set to develop an interatomic potential for ternary chloride salts using a neural network machine learning method. Deep potential molecular dynamics (DPMD) simulations were performed to predict the microstructure and thermophysical properties of the NaCl-MgCl2-CaCl2 ternary salt. This work reveals that DPMD simulations can accurately calculate the microstructure and thermophysical properties of ternary chloride salts. The association strength of chloride ions and cations follows the order of Mg2+ > Ca2+ > Na+, and the coordination number decreases gradually with increasing temperature, indicating a progressively looser and more disordered molten structure. Furthermore, thermophysical properties, such as density, specific heat capacity, thermal conductivity, and viscosity, are in good agreement with the experimental measurements. Machine learning molecular dynamics will provide a feasible multivariate molten salt exploration method for the design of next-generation solar power plants and thermal energy storage systems.

Constructing a screening model to obtain the functional herbs for the treatment of active ulcerative colitis based on herb-compound-target network and immuno-infiltration analysis

The therapeutic effect of most traditional Chinese medicines (TCM) on ulcerative colitis is unclear, The objective of this study was to develop a core herbal screening model aimed at facilitating the transition from active ulcerative colitis (UC) to inactive. We obtained the gene expression dataset GSE75214 for UC from the GEO database and analysed the differentially expressed genes (DEGs) between active and inactive groups. Gene modules associated with the active group were screened using WGCNA, and immune-related genes (IRGs) were obtained from the ImmPort database. The TCMSP database was utilized to acquire the herb-molecule-target network and identify the herb-related targets (HRT). We performed intersection operations on HRTs, DEGs, IRGs, and module genes to identify candidate genes and conducted enrichment analyses. Subsequently, three machine learning algorithms (SVM-REF analysis, Random Forest analysis, and LASSO regression analysis) were employed to refine the hubgene from the candidate genes. Based on the hub genes identified in this study, we conducted compound and herb matching and further screened herbs related to abdominal pain and blood in stool using the Symmap database.Besides, the stability between molecules and targets were assessed using molecular docking and molecular dynamic simulation methods. An intersection operation was performed on HRT, DEGs, IRGs, and module genes, leading to the identification of 23 candidate genes. Utilizing three algorithms (RandomForest, SVM-REF, and LASSO) for analyzing the candidate genes and identifying the intersection, we identified five core targets (CXCL2, DUOX2, LYZ, MMP9, and AGT) and 243 associated herbs. Hedysarum Multijugum Maxim. (Huangqi), Sophorae Flavescentis Radix (Kushen), Cotyledon Fimbriata Turcz. (Wasong), and Granati Pericarpium (Shiliupi) were found to be capable of relieving abdominal pain and hematochezia during active UC. Molecular docking demonstrated that the compounds of the four aforementioned herbs showed positive docking activity with their core targets. The results of molecular dynamic simulations indicated that well-docked active molecules had a more stable structure when bound to their target complexes. The study has shed light on the potential of TCMs in treating active UC from an immunomodulatory perspective, consequently, 5 core targets and 4 key herbs has been identified. These findings can provide a theoretical basis for subsequent management and treatment of active UC with TCM, as well as offer original ideas for further research and development of innovative drugs for alleviating UC.

Theoretical and experimental study of 5-ethoxymethylfurfural and ethyl levulinate production from cellulose

Theoretical simulations and experiments were taken to explore the mechanism of cellulose conversion into 5-ethoxymethylfurfural (EMF) and ethyl levulinate (EL) catalyzed by a mixed acid of Lewis acid and Brønsted acid. Up to 64.8 % total yield of EMF and EL can be obtained when the ratios of Lewis/Brønsted acid and water/ethanol (v/v) were 1:2 and 3:7 respectively. The results showed that Lewis acid and water could reduce the activation energy of EMF formation from 75.6 to 47.9 kJ mol−1, and mixed acids and water/ethanol system were beneficial to the accumulation of EMF. Moreover, the results of molecular dynamics (MD) simulation indicated that Lewis acid could promote the distribution of Bronsted acid around the β-1,4 glycosidic bond of cellobiose. The combination of DFT and frontier molecular orbital (FMO) calculation demonstrated that the breakage of the β-1,4 glycosidic bond was the main rate-limiting step of cellulose hydrolysis. Meanwhile, the mixed acid and water/ethanol system could accelerate the hydrolysis due to the reducing energy barrier and HOMO-LUMO gap. This study gave a deep insight into the mechanism of Lewis acid with Brønsted acid on cellulose conversion into EMF and EL.

The effect of pre-corrosion on corrosion inhibition performance and mechanism of quinoline quaternary ammonium salts

The influence of pre-corrosion on the corrosion inhibition performance and corrosion inhibition mechanism of quinoline quaternary ammonium salt (QQAS) on Q235 carbon steel in 1 wt% HCl solution at 60 °C were investigated by weight loss experiment, molecular dynamics simulation. The results of IR vibrational spectra and NMR hydrogen spectra indicate the successful synthesis of QQAS. The results of weight loss experiments show that the corrosion inhibition performance of the synthesized QQAS increase with the increasing of the concentration under the condition of Q235 carbon steel with and without pre-corrosion. But the pre-corrosion obviously decreases the corrosion inhibition efficiency by 17.28% when the concentration is 50 mg·L−1. Analysis of thermodynamic parameters shows that the adsorption of QQAS on the steel surface is a spontaneous and exothermic process, which conforms to the Langmuir isothermal formula and is mainly based on chemical adsorption. The results of molecular dynamics simulation indicate that pre-corrosion changes the equilibrium adsorption conformations of QQAS molecules, and decreases the adsorption energies, and decreases the density of the film for the different oxidization extent of Q235 carbon steel. As a result, the corrosion inhibition performance of QQAS is decreased by the pre-corrosion. The results are in good agreement with the results of weight loss experiments. The corrosion inhibition performance of QQAS is the best when the number of QQAS molecules is 18. The corrosion inhibition mechanism is a single molecular layer adsorption mechanism. The results of this study can provide a reference for studying the corrosion inhibition performance and corrosion inhibition mechanism of corrosion inhibitors under the action of pre-corrosion.

Heterogeneous-elasticity theory of instantaneous normal modes in liquids

Since decades, the concept of vibrational density of states in glasses has been mirrored in liquids by the instantaneous-normal-mode spectrum. In glasses instantaneous configurations are believed to be situated close to minima of the potential-energy hypersurface and all eigenvalues of the associated Hessian matrix are positive. In liquids this is no longer true, and modes corresponding to both positive and negative eigenvalues exist. The instantaneous-normal-mode spectrum has been numerically investigated in the past, and it has been demonstrated to bring important information on the liquid dynamics and transport properties. A systematic deeper theoretical understanding is now needed. Heterogeneous-elasticity theory has proven to be particularly successful in explaining many details of the low-frequency excitations in glasses, ranging from the thoroughly studied boson peak, to other anomalies related to the crossover between wave-like and random-matrix-like excitations. Here we present an extension of heterogeneous-elasticity theory to the liquid state, and show that the outcome of the theory agrees well to the results of extensive molecular-dynamics simulations of a model liquid at different temperatures. We find that the spectrum of eigenvalues ρ(λ)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\rho (\\lambda )$$\\end{document} has a sharp maximum close to (but not at) λ=0\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\lambda =0$$\\end{document}, and decreases monotonically with |λ|\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$|\\lambda |$$\\end{document} on both its stable and unstable side. We show that the spectral shape strongly depends on temperature, being symmetric at high temperatures and becoming rather asymmetric at low temperatures, close to the dynamical critical temperature. Most importantly, we demonstrate that the theory naturally reproduces a surprising phenomenon, a zero-energy spectral singularity with a cusp-like character developing in the vibrational spectra upon cooling. This feature, known from a few previous numerical studies, has been generally overlooked in the past due to a misleading representation of the data. We provide a thorough analysis of this issue, based on both very accurate predictions of our theory, and computational studies of model liquid systems with extended size.

Pulsed electric field enhances glucose glycation and emulsifying properties of bovine serum albumin: Focus on polarization and ionization effects at a high reaction temperature

Previous studies demonstrated that the non-thermal effects of pulsed electric fields can promote protein glycation below 40 °C, but it does not always enhance the emulsifying properties of proteins, such as in the bovine serum albumin/glucose model. Therefore, the aim of this study was to investigate the impact of non-thermal effects on the glucose glycation and emulsification properties of bovine serum albumin at 90 °C. The results of circular dichroism, surface hydrophobicity, and molecular dynamics simulations showed that the polarization effect increased the degree of glycation of bovine serum albumin-glucose conjugates from 12.82 % to 21.10 % by unfolding protein molecule, while the emulsifying stability index was increased from 79.17 to 100.73 compared with the control. Furthermore, the results of principal component analysis and Pearson correlation analysis indicated that the ionization effect and the free radicals generated by pulsed electric fields significantly (p < 0.05) inhibited browning and reduced free sulfhydryl content. This study demonstrated that pulsed electric fields combined with heating can prepare glycated proteins with good emulsifying properties in a short period of time and at temperatures lower than conventional heating while reducing energy consumption. This processing strategy has potential applications in improving the emulsifying performance of highly stable proteins.

Mechanistic insights into the selectivity of bicyclophosphorothionate antagonists for housefly versus rat GABA receptors.

γ-Aminobutyric acid (GABA) receptors (GABARs) are validated targets of insecticides. Bicyclophosphorothionates are a group of insecticidal compounds that act as noncompetitive antagonists of GABARs. We previously reported that the analogs exhibit various degrees of selectivity for housefly versus rat GABARs, depending on substitutions at the 3- and 4-positions. We here sought to elucidate the unsolved mechanisms of the receptor selectivity using quantitative structure-activity relationship (QSAR), molecular docking, and molecular dynamics approaches. Three-dimensional (3D)-QSAR studies using Topomer comparative molecular field analysis quantitatively demonstrated how the introduction of a small alkyl group at the 3-position of bicyclophosphorothionates contributes to the housefly versus rat GABAR selectivity. To investigate the molecular mechanisms of the selective action, bicyclophosphorothionates were docked into housefly Resistance to dieldrin (RDL) GABAR and rat α1β2γ2 GABAR homology models built using the published 3D-structures of human GABARs as templates. The results of molecular docking and molecular dynamics simulations revealed that the 2'Ala and 6'Thr residues of the RDL subunit within the channel are the key amino acids for binding to the housefly GABARs, whereas the 2'Ser residue of γ2 subunit plays a crucial role in binding to rat GABARs. We revealed the molecular mechanisms underlying the selective antagonistic action of bicyclophosphorothionates on housefly versus rat GABARs. The information presented should help design and develop novel, safe GABAR-targeting insecticides. © 2023 Society of Chemical Industry.

Force field study of catechol dimers and catechol-(H2O)n clusters

Force field parameters were developed for catechol and used to produce optimized structures of catechol dimers and catechol-(H2O)n clusters. The force field optimized structures for the catechol dimer and catechol-(H2O)n (with n = 1 and 2) clusters are benchmarked against quantum chemistry calculations at the B3LYP and w97XD levels of theory; with the quantum chemistry calculations taking into account basis set superposition error. The force field predicts, in agreement with B3LYP and w97XD reasonable structures and relative binding energies for two dimer structures and six catechol-(H2O)n clusters (with n = 1, 2). The developed forcefield parameters are then used to conduct molecular dynamics (MD) simulations for catechol-(H2O)15 cluster to highlight the effect of increased coordination number on the H-bond network around catechol with potential impact on the reactivity of catechol towards ozone in wet conditions. The result of MD simulations suggests that water molecules form a cage of H-bonds network around the hydroxyl groups of catechol, thereby blocking the active sites on catechol.

Dispersion stability and tribological behavior of nanocomposite supramolecular gel lubricants and molecular dynamic simulation

The poor dispersion stability of nanoparticles in oils limited their application. To address this problem, diverse of nanoparticles were introduced to supramolecular gels to fabricate a new lubricant (Nano-Gel). The results of molecular dynamics simulation show that gelators adsorbed onto the surface of nanoparticles at the non-covalent interaction. Besides, the intricate networks of supramolecular gels show spatial confinement to nanoparticles, which improved the dispersion stability of nanoparticles. Compared with supramolecular gels lubricant, Nano-Gel shows good anti-friction and anti-wear properties. The excellent tribological properties would be contributed to the self-repairing and tribo-film formed by nanoparticles and gelators. The Nano-Gels provide effective solution to the application of nanoparticles in lubricating oil, which have great values to prolong the life of mechanisms.

Experimental studies and molecular dynamics simulation of the compatibility between thermoplastic polyurethane elastomer (TPU) and asphalt

Compatibility between polymer and asphalt is an important issue to be considered when the polymer is added to base asphalt as a modifier. It determines the stability of the modified asphalt system. The purpose of this paper is to investigate the effect of shearing temperature and the content of thermoplastic polyurethane elastomer (TPU) on the compatibility between TPU and asphalt by means of experiments and molecular dynamics simulations. Firstly, the molecular models of base asphalt, TPU chain and TPU/asphalt blends were constructed by using Materials Studio 8.0. Based on the rational construction of the model, the effect of shearing temperature on the storage stability of TPU modified asphalt was evaluated by the calculation of solubility parameter (δ) and mean square displacement (MSD). In addition, the effect of different TPU admixtures on the compatibility of TPU with asphalt was characterized by interaction energy and radial distribution function (RDF). The results of molecular dynamics calculation were compared with the results of fluorescence microscopy test (FM) and segregation test. It showed that the minimum difference in solubility parameters between TPU and asphalt occurs when the shearing temperature was 170 °C, at which the diffusion movement of TPU in asphalt was the most active. The interaction energy between TPU and asphalt reached the peak when the content of TPU in asphalt was 17 wt%. Furthermore, the RDF results also indicated that the optimum dispersion effect of TPU in asphalt is achieved at this TPU content. The molecular dynamics simulation results are in agreement with the experimental results.

High carrier mobility ZrSSe/SnX (X=S, Se, S2, Se2) vdW heterostructures for photocatalytic overall water splitting: A first-principles study

Recently, the assembly of novel two-dimensional materials via van der Waals (vdW) interactions to form heterostructures is considered an effective strategy for producing materials with enhanced photocatalytic activities. This study systematically explored the optoelectronic and photocatalytic properties and carrier mobilities of novel ZrSSe/SnX (X = S, Se, S2, Se2) vdW heterostructures using density functional theory. The formation energies, elastic constants, phonon dispersions, and results of ab-initio molecular dynamic simulations indicate structural, mechanical, dynamic, and thermal stability. The electronic band structure and optical properties are calculated using hybrid functional HSE06 for accurate calculations. The results of calculations using the bandgap center technique based on density functional theory show that ZrSSe/SnSe, ZrSSe/SnS2, and ZrSSe/SnSe2 heterostructures possess suitable band edges for photocatalytic overall water splitting. The optical absorption spectrum covers a broad range from 104 in the visible region and increases to 105 in the UV region. Furthermore, the ZrSSe/SnX (X = S, Se, S2, Se2) heterostructures have high carrier mobilities of the order of 105. High mobilities help carriers to move quickly and reduce the recombination rate of holes and electrons. The findings indicate that ZrSSe/SnX (X = S, Se, S2, Se2) heterostructures are potentially efficient visible-light photocatalysts for overall water splitting.

The Influence Mechanism of Interfacial Characteristics between CSH and Montmorillonite on the Strength Properties of Cement-Stabilized Montmorillonite Soil.

To elucidate the impact mechanism of the interfacial characteristics of Calcium Silicate Hydrate gel (CSH)-Montmorillonite (MMT) at the nanoscale on the strength of cement-stabilized montmorillonite soil, this paper begins by examining the interfacial energy. Through Molecular Dynamics (MD) simulation methods, the energy at the MMT and CSH binding interface is quantitatively calculated, and the correlation between the interfacial energy and macroscopic strength is determined in conjunction with grey relational analysis. Finally, based on the characterization results from X-ray diffraction (XRD), the accuracy and sources of deviation in the MD simulation results are discussed. The study shows the CSH-MMT interfacial energy is composed of van der Waals forces, hydrogen bond energy, and electrostatic interactions, which are influenced by the migration of cations; there is a good consistency between the CSH-MMT interfacial energy and the unconfined compressive strength (UCS) of cement-stabilized soil (cemented soil), with the interfacial energy decreasing as the number of water molecules increases and first decreasing then increasing as the number of MMT layers grows; by adjusting the mix proportions, the magnitude of the CSH-MMT interfacial energy can be altered, thereby optimizing the strength of the cemented soil.

Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells

Activation-induced cytidine deaminase (AID) is the key mediator of antibody diversification in activated B-cells by the process of somatic hypermutation (SHM) and class switch recombination (CSR). Targeting AID to the Ig genes requires transcription (initiation and elongation), enhancers, and its interaction with numerous factors. Furthermore, the HIRA chaperon complex, a regulator of chromatin architecture, is indispensable for SHM. The HIRA chaperon complex consists of UBN1, ASF1a, HIRA, and CABIN1 that deposit H3.3 onto the DNA, the SHM hallmark. We explored whether UBN1 interacts with AID using computational and in-vitro experiments. Interestingly, our in-silico studies, such as molecular docking and molecular dynamics simulation results, predict that AID interacts with UBN1. Subsequently, co-immunoprecipitation and pull-down experiments established interactions between UBN1 and AID inside B-cells. Additionally, a double immunofluorescence assay confirmed that AID and UBN1 were co-localized in the human and chicken B-cell lines. Moreover, proximity ligation assay studies validated that AID interacts with UBN1. Ours is the first report on the interaction of genome mutator enzyme AID with UBN1. Nevertheless, the fate of interaction between UBN1 and AID is yet to be explored in the context of SHM or CSR.

Ionization‐engineered two‐dimensional confined channels in GO membranes for highly efficient OH− separation

AbstractOH− sieving membranes provide a valuable means for treating alkaline effluents but their development presents several challenges. In this study, the concept of ionization engineering is applied to two‐dimensional (2D) laminated membranes to facilitate OH− separation. This concept is demonstrated through the stacking of the self‐designed sulfonated graphene oxide (SGO) nanosheets to fabricate 2D membranes. The SGO membranes enhance synergistically the OH− dialysis coefficients and separation factors when treating simulated NaOH/Na2WO4 alkaline wastewater, compared with the performance of 2D GO membranes and commonly adopted polymeric cation exchange membranes. Furthermore, the separation factor achieved by the SGO membranes is considerably higher than that of most of the existing alkali recovery membranes. Results of molecular dynamics simulations indicate that the high efficiency of OH− separation in the 2D SGO confined channels is attributable to dehydration effects and intensified electrostatic repulsion. Overall, this research provides an alternative strategy for achieving rapid OH− sieving through the ionization of 2D confined channels.

Diffusion Behavior of Carbon and Silicon in the Process of Preparing Silicon Steel Using Solid-State Decarburization

In this study, we investigated the relationship between the decarburization effect of the solid-state decarburization method for preparing silicon steel and the atomic diffusion behavior in the matrix, focusing on 1 mm thick Fe-0.18 wt% C-Si (1.5, 3.5 wt%) alloy strips as the research object. Solid-state decarburization experiments were carried out in an Ar-H2O-H2 atmosphere, and the self-diffusion behavior of C and Si in Fe-C-Si alloy system was simulated by molecular dynamics. The results show that the molecular dynamics simulation results are consistent with the decarburization experimental results. When the temperature is lower than 800 °C, the atoms maintain a compact bcc structure, so the migration rate of carbon is low. When the temperature rises, the atoms move violently, resulting in the destruction of the crystal structure. Because the atomic arrangement tends towards a disordered structure, the migration rate of C is high and the diffusion coefficient increases. The experimental results showed that the decarburization rate was accelerated. At the same temperature, the diffusion activation energy Q = 48.7 kJ·mol−1 of carbon in an Fe-3.5 wt% Si-C alloy matrix can be calculated. The diffusion activation energy of carbon Q = 47.3 kJ·mol−1 was calculated using a molecular dynamics simulation. When the content of Si is 3.5 wt% and 1.5 wt%, the diffusion series of Si can be expressed as D3.5Si, Si = 8.54 × 10−10 exp(−33,089.7/RT) m2/s and D1.5Si, Si = 2.06 × 10−9 exp(−46,641.5/RT) m2/s, respectively. When the Si content is 3.5 wt%, the diffusion coefficient of Si is larger. After diffusion to the near surface, it combines with the remaining O to form a continuous strip of SiO2. When the Si content is 1.5 wt%, the diffusion coefficient of Si is small. The remaining O diffuses in the matrix and will oxidize when encountering Si; it cannot aggregate in a highly-dispersed distribution. The lattice transition from face centered cubic lattice austenite to body centered cubic lattice ferrite occurred in the matrix of the thin strip. The diffusion coefficient of C in ferrite is much larger than that in austenite. Therefore, the decarburization rate suddenly increases before decarburization stagnation. With the increase in Si content, the diffusion activation energy of C decreases, which promotes the decarburization effect.

Interactions studies of CYP2D6 with quercetin and hyperoside by spectral analysis and molecular dynamics simulations.

Some ingredients from herbal medicine can significantly affect the activity of CYP2D6, thus leading to serious interactions between herbs and drugs. Quercetin and hyperoside are active ingredients widely found in vegetables, fruits, and herbal medicines. Quercetin and hyperoside have many biological activities. In this work, the characteristic bindings of CYP2D6 with quercetin/hyperoside are revealed by multi-spectroscopy analysis, molecular docking, and molecular dynamics simulations. The fluorescence of CYP2D6 is statically quenched by quercetin and hyperoside. The binding constant (Ka ) values of CYP2D6-quercetin/hyperoside range from 104 L mol-1 , which indicates that these two flavonoids bind moderately to CYP2D6. Meanwhile, quercetin has a stronger quenching ability to CYP2D6 than that of hyperoside. The secondary structure of CYP2D6 is obviously changed by binding with quercetin/hyperoside. The docking results reveal that the quercetin/hyperoside enters the active site of CYP2D6 near heme and binds to CYP2D6 by hydrogen bonds and van der Waals forces. The molecular dynamics simulation results indicate that the binding of quercetin/hyperoside can stabilize the two complexes, enhance the flexibility of CYP2D6 backbone atoms, and make a more unfolded and looser structure of CYP2D6.

Drug repurposing for targeting fibronectin in treatment of endometriosis and cancers

Increased concentrations of the fibronectin glycoprotein can cause ectopic tissue growth patients with endometriosis and the formation of various cancerous tumors. Furthermore, fibronectin binding to its receptors from the EDA (Extra Domain A) region contributes to promote tumorigenesis, metastasis and vasculogenesis. Thus, the EDA region can be considered a unique target for therapeutic intervention. Therefore, the present study used computational methods to identify the best fibronectin inhibitor(s) among FDA-approved drugs. First, docking-based virtual screening was performed using PyRx 0.8. Next, FDA-approved drugs that obtained favorable results in the docking phase were selected for further studies and analysis using molecular dynamics (MD) simulation. The preliminary findings of the virtual screening showed that 17 FDA-approved drugs (from 2471) had more favorable energy with their binding energy less than −9 kcal/mol. The MD simulation results of these 17 drugs showed that Avapritinib had a lower RMSD value and higher binding energy and hydrogen bonding than the other complexes in the EDA domain. Also, analyses related to the second structure changes displayed that Avapritinib in the EDA domain led to more changes in the second structure. According to the results, the anticancer drug Avapritinib forms a more stable complex with fibronectin than other FDA-approved drugs. Furthermore, this drug leads to more changes in the second EDA structure, which may have more serious potential for inhibiting EDA fibronectin. Communicated by Ramaswamy H. Sarma

Structures and dynamics of protic [EtNH3][NO3] and aprotic [Emim][NO3] ionic liquid mixtures around the single-walled carbon nanotubes: The critical role of imidazolium-based cations

Molecular dynamics (MD) simulations and a series of ab initio calculations have been applied to systematically investigate the structural and dynamic properties for ionic liquid (IL) mixture of equimolar protic [EtNH3][NO3] and aprotic [Emim][NO3] around the single-walled carbon nanotubes (SWCNTs) of (4,4), (8,8) and (12,12). Our simulation results demonstrated that ions of IL mixtures display a well-defined shell structures at the interface irrespective of the diameters of SWCNTs. The aprotic [Emim]+ cations adsorb preferentially over protic [EtNH3]+ at the interface of SWCNTs irrespective of its diameters. Further analysis reveals that these two cations and the [NO3]– anions display ordered arrangement in the first solvation shell. Accordantly, the rotational dynamics of interfacial [Emim]+ and [EtNH3]+ cations decay much slower than those of the bulk curves, suggesting the rotational motions of these two cations at the interface of the SWCNTs are significantly restricted. Interfacial [Emim]+ cations decay much slower rotational motions as the SWCNTs diameter increases. However, for interfacial [EtNH3]+ cations, because they are far from the interface, they display similar rotations regardless of the SWCNTs diameters. More importantly, the HB lifetime of interfacial [Emim]+–[NO3]– and [EtNH3]+–[NO3]– are much longer than the corresponding bulk values due to the restrictions on the rotational motions of cations, suggesting the strength of these two HBs are enhanced at the interface. The binding energies for the above HBs were determined by the ab initio calculations, which are in accordance with the MD simulation results. Our results provide a molecular-level understanding the structural and dynamic properties of [EtNH3][NO3] and [Emim][NO3] IL mixtures around the SWCNTs, which highlighted the critical role of the imidazolium-based cations.

How polymer infiltration affects metal-organic frameworks-based facilitated hybrid membrane performances for CO2 separation

Membrane separation technology has been widely used in the separation and capture of CO2 to reduce carbon emissions. The performances of facilitated hybrid membranes (FHMs) can be improved by properly adding metal-organic framework (MOF)-based nanoparticles (NPs) and modifying polymers to the polymer matrix. Grafting and blending methods are widely used to introduce modifying polymers to improve the compatibility between NPs and the polymer matrix, and the performance of FHMs for CO2 separation. However, the separation performance of FHMs decreases significantly when the long chains of the polymer infiltrate into the pores of the MOF at the interface between the modifying polymer and MOF. To in-depth understand the nano-scale polymer-NPs interfacial interaction mechanism of the grafting and blending methods, we herein employed molecular dynamic (MD) simulation method combined with experiments to investigate the interface between NPs of Cu-MOF (Cu-BDC) and four commonly used modifying polymers (PEG, polyethylene glycol; PEI, polyethylenimine; PVA, polyvinyl alcohol; PPy, polypyrrole) with PVDF (polyvinylidene difluoride) as the polymer matrix. The results showed that the blending method for modification can effectively avoid the polymer blockage in Cu-BDC pores by using four modifying polymers, while the grafting method caused polymer infiltration for PEG and PEI. The relationship between the polymer diameter and the pore limiting diameter (PLD) of the Cu-BDC was evaluated to analyze the polymer infiltration effect. FHMs of Cu-BDC/PEG@PVDF were synthesized based on the MD simulation results, which showed excellent CO2 separation performance due to the good compatibility between the Cu-BDC and the modified matrix polymer. This work offers an insight in nano-scale into the interface design between the MOF and the polymer for FHMs separating CO2.