Rapid separation and binding configuration prediction of the components in Danshen decoction to endothelin A receptor using affinity chromatography and molecular dynamics simulation

As a famous traditional Chinese formula, Danshen Decoction has the potential to relieve the pain of pulmonary arterial hypertension patients, however, the functional components remain unknown. Herein, we reported a method to screen the functional components in Danshen Decoction targeting endothelin receptor A, an accepted target for the treatment of the disease. The receptor was functionalized on the macroporous silica gel through an epidermal growth factor receptor fusion tag and its covalent inhibitor. Using the affinity gel as the stationary phase, the bioactive compound was identified as salvianolic acid B by mass spectrometry. The binding kinetic parameter (dissociation rate constants k_d) of salvianolic acid B with the receptor was determined via peak profiling. Using the specific ligands of the receptor as probes, the binding configuration prediction of salvianolic acid B with the receptor was performed by molecular dynamics simulation. Our results indicated that salvianolic acid B is a potential bioactive compound in Danshen Decoction targeting the receptor. This work showed that receptor chromatography in combination with molecular dynamics simulation is applicable to predicting the binding kinetics and configuration of a ligand to a receptor, providing crucial insight for the rational design of drugs that recognize functional proteins.     

铁脂质体/水分配系数测定及影响因素考察

基于PAF-301分子模型通过Li 掺杂或B取代等模式设计了几种新型多孔芳香骨架(PAFs)材料, 采用量子力学和分子力学方法对新材料的储氢性能进行研究. 由量子力学计算得到了不同分子片段与H₂之间的结合能, 并结合DDEC方法计算了各分子片段的原子电荷分布. 利用巨正则蒙特卡洛(GCMC)模拟方法计算了77和298 K下H₂在不同PAFs材料中的吸附平衡性质. 结果表明, H₂直接与苯环的结合能较低, 但掺杂Li 原子能够提高H₂与六元环的结合能, 同时Li 原子体现出较高的正电性质, B原子取代苯环中的两个C原子后, 使得原有C原子电负性增强; 77 K下PAF-301Li 具有最高的储氢性能, 而PAF-C₄B₂H₄-Li₂-Si 和PAF-C₄B₂H₄-Li₂-Ge体现出较好的常温储氢性能, 各种材料的常温储氢性能远低于其低温储氢性能. 通过77 K下H₂在PAFs材料中的等位能面分布和吸附平衡质心密度分布对H₂在PAFs 材料中的优先吸附位置进行分析, 发现在PAF-301 和PAF-301Li 骨架中, 由于中心能量较低的等位能区域范围较宽, H₂在其中存在四个明显的吸附高密度分布区域, 而其它三种PAFs晶胞中心能量较低的等位能区域范围较窄, 使得H₂在其中只存在两个明显的吸附高密度分布区域.     

分子动力学模拟研究[Bmim][PF6]+水+醇三元体系的微观结构和分子间相互作用

研究离子液体体系的微观结构和分子间相互作用具有重要意义. 本文对1-丁基-3-甲基咪唑六氟磷酸盐([Bmim][PF₆])+水+乙醇和[Bmim][PF₆]+水+异丙醇三元体系进行了分子模拟研究, 计算了径向分布函数和不同组成的水-醇混合溶剂与离子液体阴阳离子间的相互作用能, 并将其分解为库仑相互作用能和Lennard-Jones(LJ)势能. 在此基础上, 研究了溶液体系的微观结构、分子间相互作用和相行为. 结果表明, 水倾向于与离子液体阴离子和阳离子极性部分作用, 醇倾向于与阴离子和阳离子非极性部分作用; 库仑力主导阴离子-溶剂相互作用, 色散力主导阳离子-溶剂相互作用, 阴阳离子的缔合状态对色散力影响较小, 对库仑力的影响非常显著.     

稀土萃取分离过程软测量方法的研究

分析了稀土组分含量在线检测技术进展缓慢的原因,分析了稀土萃取分离过程机制,找出影响稀土组分含量检测的主要因素,确定辅助变量。利用从包钢稀土厂采集的数据通过newrb函数创建径向基网络来实现稀土组分含量的软测量。文中通过流程图详细阐述了建模方法,采用50组样本数据对所建立的模型进行计算机仿真验证,仿真结果证明了模型的可行性。     

甲烷部分氧化过程中强制振荡的动力学Monte Carlo模拟

为了有效控制动力学振荡行为以提高反应的转化率, 利用Monte Carlo 方法研究了甲烷催化部分氧化过程中的强制振荡行为, 探讨了原料气周期性变化对振荡动力学和转化率的影响. 研究表明原料气周期性变化不仅可以有效调控振荡的动力学行为, 产生如短周期振荡和双峰振荡等特殊动力学过程, 而且还可以提高反应的转化率. 当强制过程的周期从T/3 增大到2T(T为自发振荡过程的平均周期), 振荡过程从短周期振荡变化为双峰振荡. 对反应过程中CO的转化率进行了计算, 结果表明原料气周期性变化可以有效提高反应的转化率.振荡动力学的改变和转化率的提高主要是因为强制振荡过程使得催化剂表面发生了从氧化态向还原态的转变.     

不同孪晶界密度银纳米线拉伸形变行为的分子动力学模拟

采用分子动力学方法模拟了不同孪晶界密度银纳米线的拉伸形变行为, 分析了孪晶界密度对多晶银纳米线屈服强度、弹性模量和塑性变形机理的影响. 在弹性形变区域, 孪晶界的存在对杨氏模量变化的作用不明显. 在塑性形变阶段, 首先从表面边缘开始产生位错成核, 然后延伸并受阻于孪晶界. 在进一步拉伸载荷作用下, 孪晶界将作为位错源产生新的位错. 模拟结果表明, 银纳米线的强度与孪晶界和晶粒的尺寸有关. 孪晶界密度较小(即晶粒的长径比大于1)时, 此纳米线的屈服应力比单晶纳米线还要小, 只有当孪晶界密度较大时(即晶粒的长径比小于1), 孪晶界使得纳米线得到强化. 综合分析了孪晶界和晶粒尺寸对银纳米线的影响, 为构建高强度金属纳米线打下基础. 最后讨论了温度和拉伸速度对孪晶纳米线屈服应力所产生的影响, 随着温度的升高, 孪晶纳米线与单晶纳米线的屈服应力差先升高后趋于稳定; 当拉伸速度逐渐增大, 孪晶纳米线与单晶纳米线的屈服应力差先稳定后增大.     

Recent developments in computer vision-based analytical chemistry: A tutorial review

Chemical analysis based on colour changes recorded with imaging devices is gaining increasing interest. This is due to its several significant advantages, such as simplicity of use, and the fact that it is easily combinable with portable and widely distributed imaging devices, resulting in friendly analytical procedures in many areas that demand out-of-lab applications for in situ and real-time monitoring. This tutorial review covers computer vision-based analytical (CVAC) procedures and systems from 2005 to 2015, a period of time when 87.5% of the papers on this topic were published. The background regarding colour spaces and recent analytical system architectures of interest in analytical chemistry is presented in the form of a tutorial. Moreover, issues regarding images, such as the influence of illuminants, and the most relevant techniques for processing and analysing digital images are addressed. Some of the most relevant applications are then detailed, highlighting their main characteristics. Finally, our opinion about future perspectives is discussed.     

Monte Carlo simulation of full energy spectrum of electrons emitted from silicon in Auger electron spectroscopy

A Monte Carlo simulation including surface excitation, Auger electron‐ and secondary electron production has been performed to calculate the energy spectrum of electrons emitted from silicon in Auger electron spectroscopy (AES), covering the full energy range from the elastic peak down to the true‐secondary‐electron peak. The work aims to provide a more comprehensive understanding of the experimental AES spectrum by integrating the up‐to‐date knowledge of electron scattering and electronic excitation near the solid surface region. The Monte Carlo simulation model of beam–sample interaction includes the atomic ionization and relaxation for Auger electron production with Casnati's ionization cross section, surface plasmon excitation and bulk plasmon excitation as well as other bulk electronic excitation for inelastic scattering of electrons (including primary electrons, Auger electrons and secondary electrons) through a dielectric functional approach, cascade secondary electron production in electron inelastic scattering events, and electron elastic scattering with use of Mott's cross section. The simulated energy spectrum for Si sample describes very well the experimental AES EN(E) spectrum measured with a cylindrical mirror analyzer for primary energies ranging from 500 eV to 3000 eV. Surface excitation is found to affect strongly the loss peak shape and the intensities of the elastic peak and Auger peak, and weakly the low energy backscattering background, but it has less effect to high energy backscattering background and the Auger electron peak shape. Copyright © 2014 John Wiley & Sons, Ltd.     

MOLSIM: A modular molecular simulation software

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal‐organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three‐step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal‐organic frameworks (MOFs), QuickFF is used to determine force fields for MIL‐53(Al) and MOF‐5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.