EPR谱图模拟软件EasySpin的图形用户界面设计

EasySpin是一款较为流行的电子顺磁共振（EPR）谱图模拟和拟合软件,LabVIEW是一种图形化编程语言开发环境．本文介绍了一款使用LabVIEW为EasySpin设计的图形用户界面LV-EasySpin．LV-EasySpin提供了一种直观的操作方法来实现连续波EPR多组分波谱的可视化模拟和拟合．本文辅以各种模式下的实例进行说明,阐述了LV-EasySpin的设计思路与实现方案,最终希望具有简洁、易操作界面的LV-EasySpin可以降低用户使用EasySpin分析EPR谱图的难度．     

Polymer-mediated and ultrasound-assisted crystallization of ropivacaine: Crystal growth and morphology modulation

The objective of this research was to modify the crystal shape and size of poorly water-soluble drug ropivacaine, and to reveal the effects of polymeric additive and ultrasound on crystal nucleation and growth. Ropivacaine often grow as needle-like crystals extended along the a-axis and the shape was hardly controllable by altering solvent types and operating conditions for the crystallization process. We found that ropivacaine crystallized as block-like crystals when polyvinylpyrrolidone (PVP) was used. The control over crystal morphology by the additive was related to crystallization temperature, solute concentration, additive concentration, and molecular weight. SEM and AFM analyses were performed providing insights into crystal growth pattern and cavities on the surface induced by the polymeric additive. In ultrasound-assisted crystallization, the impacts of ultrasonic time, ultrasonic power, and additive concentration were investigated. The particles precipitated at extended ultrasonic time exhibited plate-like crystals with shorter aspect ratio. Combined use of polymeric additive and ultrasound led to rice-shaped crystals, which the average particle size was further decreased. The induction time measurement and single crystal growth experiments were carried out. The results suggested that PVP worked as strong nucleation and growth inhibitor. Molecular dynamics simulation was performed to explore the action mechanism of the polymer. The interaction energies between PVP and crystal faces were calculated, and mobility of the additive with different chain length in crystal-solution system was evaluated by mean square displacement. Based on the study, a possible mechanism for the morphological evolution of ropivacaine crystals assisted by PVP and ultrasound was proposed.     

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。     

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.     

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.     

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.     

The evolution of numerical methods for predicting the distribution of surfactant in the bubble-scale dynamics of foams

Many numerical methods now exist to simulate the structure and dynamics of surface-tension-dominated aqueous foams at the level of the individual films and the liquid structures where they meet. We review these methods, focusing in particular on bubble-scale simulations of foam rheology. We highlight methods that allow the distribution of surfactant during flow to be taken into account.     

基于虚拟现实的分子对接教学软件*

由于其强大的沉浸性和交互性等特征,虚拟现实技术在教育教学方面有着独特的优势。基于分子建模工具和虚拟现实技术构建了一种关于分子对接的教学软件,该软件将语音讲解、动画演示、分子可视化、交互操作等内容有机整合在虚拟现实环境中,从理论知识讲解和VR实验操作2个方面展开,深入浅出地讲解了分子对接的知识点,达到辅助教学的目的。     

正溴丁烷合成虚拟仿真系统的设计与辅助实验教学研究*

介绍了正溴丁烷合成虚拟仿真系统的设计与功能,并结合具体的教学实践和研究结果的对比分析,提出了虚实结合的混合式教学模式,这种教学模式能有效解决传统实验教学过程中实验预习效果差、过程性评价难的教学痛点。     

双活性磺酸基蔗渣木聚糖对羟基苯甲酸酯的合成及活性模拟

以蔗渣木聚糖(BX)为主要原料、氨基三磺酸钠为酯化剂,在一步酯化合成磺酸基蔗渣木聚糖酯的基础上,利用磺酸基蔗渣木聚糖酯和对羟基苯甲酸进行二步酯化反应,合成了磺酸基蔗渣木聚糖对羟基苯甲酸酯,并考察了反应条件对酯化反应的影响,通过单因素实验确定了第二步酯化反应较佳的合成工艺条件.蔗渣木聚糖酯化改性前后的样品分别用FT-IR,DG-DTG和XRD进行了表征,并对该双酯化衍生物的分子进行了优化与活性模拟.结果表明:FT-IR证明双酯化产物含有磺酸基团和对羟基苯甲酸酯基团,TG-DTG分析表明该双酯化衍生物的热稳定性提高,XRD说明发生双酯化改性后分子排列的规整性提高,结晶度增加;活性模拟实现了磺酸基蔗渣木聚糖对羟基苯甲酸酯与艾滋病毒的对接.