Bioactive Fluorenes. Part II. Unprecedented biologically active thiazole derivatives based-2,7-dichlorofluorene as competent DHFR inhibitors: Design,synthesis, and molecular docking approaches

In this study, a new series of (4-(2,7-dichloro-9H-fluoren-4-yl)thiazol-yl)acetamide derivatives was synthesized, and the new heterocycles were completely characterized, evaluated for their antimicrobial activity, and screened for cytotoxic activity against human lung carcinoma (A-549) and human breast carcinoma (MCF-7) cell lines. A molecular docking study was undertaken to identify the possible mode of action of the synthesized compounds, which suggested binding interactions with the dihydrofolate reductase (DHFR) active sites.Most of the synthesized compounds displayed meaningful activity against A-549 and MCF-7 cell lines when compared to 5-fluorouracil (5-FU), which was used as a reference drug. Furthermore, some of the prepared compounds exhibited potent antibacterial and antifungal activities. The highly pronounced biological activities of the compounds under investigation offer such species as promising future drug prospects which may find applications in the fields of biological and medicinal sciences.     

A study on the phase transformation behaviour of Cu-20wt.Sn alloy produced using powder metallurgy method: Experimental and molecular dynamics modelling

In this study, Cu-20wt.Sn alloy was produced by powder metallurgy (PM) method by using high purity element powders. The phases in the microstructure of the produced alloy were determined by XRD study. The phase transformation behaviour of the alloy was investigated by DSC and modelling method. Moreover, the Cu-20wt.Sn alloy system was modelled with molecular dynamics (MD) simulation based on modified Embedded Atom Method (MEAM). The radial distribution function (RDF) was calculated to determine the structural properties of system during the phase transformations. The experimental results showed that the transformation ($\alpha +\delta$) → ($\alpha +\gamma$) occur at temperature above 500°C. The simulation results showed that the phase transformation $\alpha +\delta \to \alpha +\gamma$ occurs at 550°C temperature. Our simulation results are in reasonable agreement with the experimental data.     

Computational study of the formation of aluminum-graphene nanocrystallites

The molecular dynamics method is used to study the formation of the Al/graphene nanocomposite in the structural grains of different size under the action of internal stresses. The behavior of graphene sheets inside an individual structural grain as well as in the process of two Al grains containing graphene are joined is investigated. The motion of graphene films, starting from the middle of the aluminum matrix, ends with their location at the crystallite boundaries. Graphene moves in the Al matrix along closely packed planes. In this case, graphene sheets acquire curvature. An intergrowth of graphene sheets is also observed. A contact between two Al-C nanocrystallites through a graphene interlayer is created. The self-diffusion coefficients of atoms and the partial potential energies increased with decreasing nanocrystallite size. The angular distribution of the nearest geometric neighbors and the distribution of distances to the nearest neighbors are determined using the construction of Voronoi polyhedra.     

Molecular insight for the role of key residues of calreticulin in its binding activities: A computational study

Calreticulin (CRT) is localized to and has functions in multiple cellular compartments, including the cell surface, the endoplasmic reticulum, and the extracellular matrix. Mutagenesis studies have identified several residues on a concave β-sheet surface of CRT critical for CRT binding to carbohydrate and other proteins/peptides. How the mutations of these key residues in CRT affect the conformation and dynamics of CRT, further influencing CRT binding to carbohydrates and other proteins to signal the important biological activities remain unknown. In this study, we investigated the effect of three key point mutations (C105A, C137A and W319A) on CRT conformation and dynamics via atomistic molecular dynamics simulations. Results show that these three key residues mutations induced the changes of CRT local backbone flexibility and secondary structure of CRT N-domain, which could further affect CRT’s binding activity. C137A mutation led to dramatic decrease of the overall size of CRT due to the P-domain fold back to the globular domain and formed new inter-domain contacts, which can cause blockage of CRT’s binding with other large substrates. Furthermore, for CRT concave β-strand surface patch containing lectin binding site, CRT C105A, C137A and W319A point mutation resulted in the changes in solvent accessible surface area, key residues’ side chain atom positions and dynamical correlated motions between residues. All these changes could directly affect CRT binding behavior. Results of this study provide molecular and structural insights into understanding the role of key residues of CRT in its binding behavior.     

Investigation on thermal conductivity of graphene/Si heterostructure with different defect ratios and sizes

The thermal conductivity (TC) of graphene/Si heterostructures with different defect ratios and sizes was investigated using the molecular dynamics method. As the defect ratio of heterostructure increased, the TC decreased first sharply and then slowly under a high temperature stage. The TC of heterostructure also showed a significant size effect. This phenomenon was explained by phonon dispersion and flip competition. The phonon density of states for the graphene heterostructure with different defect ratios and sizes was obtained to understand the thermal transport mechanism. Analysis showed that with the increase in the defect ratio and when the flexural modes of the heterostructure became weak, the longitudinal and transverse modes gradually dominated the phonon transport. This phenomenon can be explained that the Si atom vibration was harder in the vertical plane than that of graphene. The vibration mode hindered the heat carrier of graphene and affected heat transport to the heterostructure.     

Molecular dynamic study of temperature dependence of mechanical properties and plastic inception of CoCrCuFeNi high-entropy alloy

Molecular dynamics simulations are performed to study mechanical characteristics and homogeneous plastic inception of CoCrCuFeNi high-entropy alloy at various temperatures under uniaxial tension. It is found that the elastic modulus and ultimate tensile strength increase with temperature decreasing. A notable softening effect is observed at the elastic deformation stage caused by the decrease of the interatomic force gradient. Extrinsic stacking faults and deformation twins are extensively observed, which are formed via intrinsic stacking faults overlap.     

乙基苯胺的转动光谱及分子结构

本文使用傅里叶变换微波谱仪研究了乙基苯胺类物质(邻乙基苯胺，间乙基苯胺，对乙基苯胺)的分子结构. 由于此类分子含氮原子(I¹⁴N=1)，因此跃迁谱线中都呈现出核四级裂分. 通过比较实验测定得到的分子结构，可总结苯胺环上不同位置乙基的取代对氨基及分子整体结构的影响.     

Tensile properties of microtubules: A study by nonlinear molecular structural mechanics modelling

A nonlinear molecular structural mechanics (MSM) model is proposed in this paper for studying the tensile properties of microtubules (MTs). In the nonlinear MSM models, the interactions between tubulin monomers in MTs are treated as nonlinear axial and torsional springs, whose stiffness coefficients are extracted from all-atom molecular dynamics simulations. The Young's modulus and fracture properties of MTs under tension extracted from the present nonlinear MSM models are found to agree well with the existing simulation and experiment results, which shows the efficiency and accuracy of the proposed nonlinear MSM models. In addition, the nonlinear MSM models are also extended to investigate the tensile properties including Young's modulus and fracture strain of MTs possessing lattice defects. The results obtained from nonlinear MSM models are utilized to develop a predictive equation for quickly predicting the tensile properties of MTs with different lattice defect levels.     

基于Discovery Studio软件的本科生创新实验项目设计*——卡托普利与血管紧张素转化酶的分子对接

基于Discovery Studio软件高质量的分子三维结构可视化功能和分子对接模拟模块,设计了卡托普利与血管紧张素转化酶的分子对接实验,让学生通过分子对接模拟过程,掌握药物分子结构特征,理解构效关系特征,认识酶抑制剂和靶蛋白的作用机制,了解药物研究新手段。     

分子模拟实验课程建设的探索与实践

We put forward the idea of building a molecular simulation experiment course. After two-year teaching practice, we write the experiment textbook which not only covers the classic experimental projects, but also includes the frontier hot issues, and open exploration experiment. This article summarizes the teaching requirements, basic content, assessment methods, the initial achievements made so far and the prospects for the future.