Effects of mussel-inspired co-deposition of 2-hydroxymethyl methacrylate and poly (2-methoxyethyl acrylate) on the hydrophilicity and binding tendency of common hemodialysis membranes: Molecular dynamics simulations and molecular docking studies

Despite advances in the field, hemoincompatibility remains a critical issue for hemodialysis (HD) as interactions between various human blood constituents and the polymeric structure of HD membranes results in complications such as activation of immune system cascades. Adding hydrophilic polymer structures to the membranes is one modification approach that can decrease the extent of protein adsorption. This study conducted molecular dynamics (MD) simulations to understand the interactions between three human serum proteins (fibrinogen [FB], human serum albumin, and transferrin) and common HD membranes in untreated and modified forms. Poly(aryl ether sulfone) (PAES) and cellulose triacetate were used as the common dialyzer polymers, and membrane modifications were performed with 2-hydroxymethyl methacrylate (HEMA) and poly (2-methoxyethyl acrylate) (PMEA), using polydopamine-assisted co-deposition. The MD simulations were used as the framework for binding energy simulations, and molecular docking simulations were also performed to conduct molecular-level investigations between the two modifying polymers (HEMA and PMEA) and FB. Each of the three proteins acted differently with the membranes due to their unique nature and surface chemistry. The simulations show PMEA binds less intensively to FB with a higher number of hydrogen bonds, which reflects PMEA's superior performance compared to HEMA. The simulations suggest PAES membranes could be used in modified forms for blood-contact applications as they reflect the lowest binding energy to blood proteins.     

A sustainable method of mitigating acid corrosion of mild steel using jackfruit pectin (JP) as green inhibitor: Theoretical and electrochemical studies

This study is attempted to develop a green corrosion inhibitor from a waste material of Jack fruit (Artocarpus heterophyllus). This method is therefore quite valuable to health, environment, and economic point of view. Pectin is isolated from the jackfruit peel waste using 0.05 ?N oxalic acid and used as an inhibitor for mild steel corrosion in acidic environment as it is highly water soluble. 250–1000 ?ppm of pectin was used in this study at a temperature range of 303–323 ?K. The protection efficiency of jack fruit pectin (JP) in 0.5 ?M HCl was evaluated by conventional weight loss and electrochemical techniques. The potentiodynamic polarization results revealed that JP could effectively reduce the corrosion of mild steel in acidic medium at 1000 ?ppm concentration with an inhibition efficiency of 89.75% and corrosion rate of 2.392 mpy. The mixed type behavior of the inhibitor is identified from Tafel polarization studies. Electrochemical impedance spectroscopy (EIS) measurements suggest that the corrosion inhibition process is kinetically controlled. adsorption and kinetic behavior of the inhibitor also have been studied. Surface manifestations were followed using FESEM and AFM techniques. DFT calculations and Monte Carlo simulations were also carried out to corroborate the experimental results with theoretical outputs and succeeded to a great extent.     

A detailed insight into the optimization of plate and frame heat exchanger design by comparing old and new generation metaheuristics algorithms

The voluminous utilization and application of plate and frame heat exchangers (PFHE) in many industries has accelerated the consumer and designer both to optimize exchanger total cost. Over the last few years, several old and new generation algorithms were employed and exploited to optimize PFHE cost. This study explores the application and performance of three new-generation algorithms Big Bang-Big Crunch (BBBC), Grey Wolf Optimizer (GWO), and Water Evaporation Optimization (WEO) in designing optimally PFHE. Besides, this study also compares the performance of three well-established old generations algorithms namely genetic algorithm (genetics and natural selection), particle swarm optimization (animals behaviour), and differential evolution (population-based) with the above three new algorithms in the optimization of PFHE.Seven design factors are chosen for PFHE optimization: exchanger length on hot and cold sides, height and thickness of fin, length of the fin-strip, fin frequency, and the number of hot side layers. The applicability of the suggested algorithms is assessed using a case study based on published research. Though DE performs the best in this study of design optimization concerning total cost and computational time, the three new-generation meta-heuristic algorithms BBBC, GWO, and WEO also provide the novel scope of application in heat exchanger design optimization and successfully finding the cost of the heat exchanger. According to this study, capital costs increase by 19.5% for BBBC, 24% for GWO, and 7.6% for GWO, but operational costs fall by 9.5% for BBBC and GWO when compared to the best performing algorithm (DE). On the other hand, WEO shows an increase of 32.6% in operational costs. Aside from that, a full analysis of the computing time for each algorithm is also provided. The DE has the quickest run time of 0.09 ?s, while the PSO takes the longest at 33.97 ?s. The rest of the algorithms have nearly identical values. As a result, a good comparison is established in this study, offering an excellent platform for designers and customers to make selections. Additionally, the three new generations algorithms mentioned here were not used earlier for optimization of PFHE and the comparative study illustrates that each of them possesses eat potential for cost optimization and also solving other complex problems.     

基础理论纵贯化学学科:吉林大学“统计力学与分子模拟”课程建设*

化学的基础理论的演进不断重塑着化学学科。传统的教学体系所依据的理论范式落后于现代化学理论的发展。吉林大学化学学院面向本科学生开设了“统计力学与分子模拟”课程。针对吉林大学本科学生的特点,精心安排了教学内容,通盘考虑知识体系的衔接,优化了教学方法。同时,淬炼了课程中的思政元素,从而在思想、道德、知识等3个方面进一步提升学生的综合素质。     

Synthesis and antimicrobial bioassays of 1,3,4-thiadiazole sulfone derivatives containing amide moiety: A study based on molecular dynamics (MD) simulations,MM/GBSA,and molecular docking

The backbone structure (1,3,4-thiadiazole sulfone derivatives containing amide moiety) of target compounds was determined by modification and optimization of the theoretical design based on commercial chemical carboxin, including molecular docking, scaffold hopping, ligand expansion, etc.In this paper, 23 target compounds were synthesized by the combination of theoretical design and chemical synthesis, and characterized by ¹H NMR, ¹³C NMR and HR MS. Addtionally, the antibacterical bioassay showed that most target compounds performed excellent inhibition on Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas oryzae pv. oryzae (Xoo) in vitro. Meanwhile, molecular docking, molecular dynamics (MD) simulations, and studies on ligand/protein (carboxin/2FBW and 4n/2FBW) complex systems were displayed, and the interaction patterns of ligand/protein complex system were predicted by molecular docking. Besides, the ligand/protein complex system was subject to MD simulation. The analysis of molecular dynamics such as RMSD values suggested that compound/2FBW complexes were stable. MM/GBSA (Molecular mechanics generalized born surface area) dynamic binding affinity results revealed that the active residues (TYR58, HIS26, ARG43, SER39, etc.) played an essential part in the binding of the compound(s) to form a stable low-energy ligand/protein complex, while the MD trajectories demonstrated that the interactions of drugs with 2FBW affected the tertiary structure and increased the stability of protein. Besides, compound 4n also showed control efficacies (curative and protective) on Xoo in vivo, where the curative efficacy was 35.91% and the protective efficacy was 18.97%. In a word, this study showed that 1,3,4-thiadiazole sulfone derivatives containing amide moiety designed based on the structure of carboxin were promising agricultural antibacterial agents, featuring certain stability of binding affinity to proteins and carboxin.     

Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling,Molecular Docking,and Molecular Dynamics Simulation

Six phthalate acid esters(PAEs) priority pollutants[dimethyl phthalate(DMP), diethyl phthalate(DEP), dibutyl phthalate (DBP or DNBP), di-n-octyl phthalate(DNOP), di 2-ethyl hexyl phthalate(DEHP), and butyl benzyl phthalate(BBP)] were opted as the research object. PAE-degrading esterase CarEW(PDB ID:1C7I) isolated from Bacillus subtilis acting as a template and an iterative saturation mutation strategy was adopted to modify key amino acids to attain efficient PAE-degrading esterase substitutes with a reasonable structure constructed by homology modeling method. Present study designed a total of 285 unit-site and multi-site substitutions of PAE-degrading esterase using the homology modeling method. Among them, 207 PAE-degrading esterase substitutions, which contained the 6-site PAE-degrading esterase substitute 1C7I-6-9 with 84.21% enhancement intensity of degradation ability revealed better degradability to all the 6 PAEs after modification. Moreover, molecular dynamics simulation based on the Taguchi method reported the optimal external application environment for PAE-degrading esterase substitutes as follows:pH=6, T=35℃, the rhamnolipid concentration was 50 mg/L, the molar ratio of nitrogen to phosphorus(N:P) was 10:1, the concentration of H₂O₂ was 50 mg/L, and the voltage gradient was 1.5 V/cm. The degradation ability of PAE-degrading esterase substitutes was found to be elevated by 13.04% as compared to that of the blank control under the optimal condition. Moreover, 11 highly efficient PAE-degrading esterase substitutes with thermal stability were designed.     

Bioassay-guided isolation of human carboxylesterase 2 inhibitory and antioxidant constituents from Laportea bulbifera: Inhibition interactions and molecular mechanism

Laportea bulbifera (Sieb. et. Zucc.) Wedd has long been utilized in Traditional Chinese Medicines (TCM) for the treatment of rheumatoid arthritis. However, the study of systematic anti-inflammatory chemical constituents in L. bulbifera has never been reported. Thus, bioassay-guided isolation for its roots part led to 46 compounds, including 38 phenolic derivatives. Their structures were determined on the basis of ¹H and ¹³C NMR and MS spectra. All compounds were isolated from L. bulbifera for the first time except for 13 compounds. Most of the compounds showed good COX-2 inhibitory activity (IC₅₀: 0.13–3.94 μM) and DPPH radical-scavenging activity (IC₅₀: 1.57–9.55 μM). Four compounds (4, 17, 35, and 43) with different skeletons showed preferential COX-2 over COX-1 inhibition with selective indices ranging from 12 to 171. High content active compounds are important for elucidating the basis of the active substance of TCM. Compound 4 (COX-2, IC₅₀ 0.24 μM), a high content compound, represented one of the best selective COX-2 inhibitors. Another high content active compound (35) with a different skeleton might have different mechanism. Further study for the inhibition kinetics against COX-2 indicated compounds 4 and 35 were noncompetitive and competitive COX-2 inhibitors, respectively. Moreover, molecular docking and molecular dynamics simulation data further indicated that compound 4 could bind in the cavity of COX-2 and interacted with key residues VAL-538, PHE-142, and GLY-225 of COX-2 through hydrogen bonds. The results indicated that L. bulbifera roots could be applied as antioxidant and anti-inflammatory agents due to their potent selective COX-2 inhibitory and antioxidant activity of phenolic compounds.