Ion transmission in an electrospray ionization-mass spectrometry interface using an S-lens

We present the design and performance of an in-house built electrospray ionization-mass spectrometry (ESI-MS) interface equipped with an S-lens ion guide. The ion source was designed specifically for our ion beam experiments to investigate the chemical reactivity and deposition of the clusters and nanoparticles. It includes standard ESI-MS interface components, such as nanoelectrospray, ion transfer capillary, and the S-lens. A custom design enables systematic optimization of all relevant factors influencing ion formation and transfer through the interface. By varying the ESI voltage and flow rate, we determined the optimal operating conditions for selected silica emitters. A comparison of the pulled silica emitters with different tip inner diameters reveals that the total ion current is highest for the largest tip, whereas a tip with the smallest diameter exhibited the highest transmission efficiency through the ESI-MS interface. Ion transmission through the transfer capillary is strongly limited by its length, but the loss of ions can be reduced by increasing the capillary voltage and temperature. The S-lens was characterized over a wide range of RF frequencies and amplitudes. Maximum ion current was detected at RF amplitudes greater than 50 V peak-to-peak (p/p) and frequencies above 750 kHz, with a stable ion transmission region of about 20%. A factor of 2.6 increase in total ion current is observed for 650 kHz as RF amplitudes reach 400 V p/p. Higher RF amplitudes also focus the ions into a narrow beam, which mitigates their losses when passing through the ion guide.     

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.     

电场下离子型聚合物复合囊泡结构变化的分子动力学模拟

利用粗粒化分子动力学模拟研究了电场作用下离子型聚合物复合囊泡形变与破裂的过程.定量分析了囊泡破裂过程中的结构变化,包括囊泡的形变程度、破裂速度、组分分布以及破裂后的结构.研究表明,电场强度较弱时,囊泡表面所吸附的聚电解质首先脱落,囊泡由球形结构转变为椭球结构.随着电场强度增大,离聚物的离子侧基发生重新排布,囊泡表面电荷的有序结构被破坏,导致囊泡的结构无法维持而破裂,囊泡塌缩,分裂形成离聚物团簇,并进一步破裂为小尺寸的离聚物聚集体,均匀分散于溶液中.本文利用分子动力学模拟明确了电场中离子型高分子复合囊泡破裂过程的分子机理,为药物释放技术的优化及发展提供了理论支持.     

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。     

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。     

Controlled protein adsorption on a silica microparticle

In the present study, controlled protein adsorption on a rigid silica microparticle is investigated numerically using classical Langmuir and two-state models under electrokinetic flow conditions. The instantaneous particle locations are simulated along a straight microchannel using an arbitrary Lagrangian−Eulerian framework in the finite element method for the electrophoretic motion of the charged particle. Within the scope of the parametric study, the strength of the external electric field (E), particle diameter (D_p), the zeta potential of the particle (ζ_p), and the location of the microparticle away from the channel wall (H) are systematically varied. The results are also compared to the data of pressure-driven flow having a parabolic flow profile at the inlet whose maximum magnitude is set to the particle's electrophoretic velocity magnitude. The validation studies reveal that the code developed for the particle motion in the present simulations agrees well with the experimental results. It is observed that protein adsorption can be controlled using electrokinetic phenomena. The plug-like flow profile in electrokinetics is beneficial for a microparticle at every spatial location in the microchannel, whereas it is not valid for the pressure-driven flow. The electric field strength and the zeta potential of the particle accelerate the protein adsorption. The wall shear stress and shear rate are good indicators to predict the adsorption process for electrokinetic flow.     

ABC三嵌段共聚物胶束从多间隔结构到多核结构转变的Monte Carlo模拟

采用Monte Carlo模拟方法研究了疏水-亲水-疏水(H-P-H)型ABC三嵌段共聚物在B嵌段的选择性溶剂中的自组装行为. 模拟结果表明, 通过调节A嵌段和C嵌段的疏水性和二者之间的不相容性, 体系中可以形成多种形貌各异的胶束. 根据胶束中疏水核结构的特点, 这些胶束大体上可以被分为多核型胶束和多间隔型胶束两种类型. 通过增强疏水嵌段的疏水性或降低A嵌段和C嵌段间的不相容性, H-P-H型ABC三嵌段共聚物胶束能够发生从多核型胶束向多间隔型胶束的转变. 进一步分析胶束中聚合物的链构象等微观结构信息发现, A嵌段和C嵌段间的排斥作用和疏水作用之间存在竞争关系, 而这种竞争关系是影响体系中形成多核型胶束还是多间隔型胶束的决定性因素.     

质子水合结构的振动态密度分析

使用基于多态经验价键模型的分子动力学模拟, 对水溶液中质子的水合结构及其在质子传递过程中的动力学过程进行了研究. 在价键模型的方法下, 质子的水合结构主要以H₉O₄⁺(Eigen)以及过渡态的H₅O₂⁺(Zundel)结构形态存在, 且在这两种结构中以Eigen的形态表现明显. 通过对质子传递过程中不同水合结构的态密度频谱分析, 发现一个在2000~3000 cm^-1范围内的明显连续的宽吸收谱带, 主要归因于Eigen结构的贡献, 这些特征峰的出现与水合氢离子第一溶剂化层内的强氢键作用密切相关. 对于Zundel的结构, 在1760 cm^-1处出现一个较为明显的肩峰, 归属为质子传递模式的特征振动. 通过对质子水合结构态密度频谱的分析, 可望增强对于稀酸溶液红外光谱中的连续宽吸收带以及质子传递的微观动力学过程的理解.     

高通量虚拟筛选CDK2/Cyclin A2靶点抑制剂

CDK2/Cyclin A2复合蛋白的异常表达与乳腺癌、 口腔癌、 食管鳞状细胞癌的发生密切相关. CDK2/ Cyclin A2复合蛋白的活性位点不同于CDK2单体. 至今临床上尚无靶向此复合蛋白的药物分子. 针对CDK2/Cyclin A2复合蛋白, 以实验报道的10个抑制剂分子构建药效团模型, 通过药物体外药代动力学（ADME）、 Docking、 聚类分析、 毒性预测, 从DrugBank, ChEMBL和TCM@Taiwan 3个数据库约90万组数据中进行高通量虚拟筛选, 进一步进行MD模拟、 MM/PBSA结合自由能计算、 能量分解和平均非共价作用(aNCI)分析, 筛选出3个抑制效果优于阳性实验药Roscovitine的先导分子: DrugBank-2004, DrugBank-583和ChEMBL-7122. 与CDK2蛋白相比, CDK2/Cyclin A2复合蛋白结合位点空间变大, 先导分子与Lys33, Asp86, Lys129和Asp145残基之间的排斥作用有所降低, 导致结合自由能更大.     

H-ZSM-5分子筛不同孔道处的酸位在甲醇制烯烃反应中的催化作用

甲醇制烯烃(MTO)作为一条由煤、天然气和生物质等含碳资源制备重要有机化学品的非石油路线,近年来备受关注.作为MTO催化剂,分子筛的骨架拓扑结构和酸性质对于其催化活性、反应路径和产物分布等具有重要的影响.H-ZSM-5分子筛是一种典型的MTO反应催化剂,酸位可以分布在MFI拓扑结构的直孔道、正弦孔道和交叉位点处.虽然目前已普遍认可MTO反应遵循芳烃/烯烃双循环烃池机理,分子筛的催化性能与其骨架中酸中心的位置相关,但对于H-ZSM-5分子筛不同孔道位置处的酸中心在甲醇制烯烃反应中的催化作用仍缺乏足够认识.本文采用密度泛函理论计算和分子动力学模拟方法,对H-ZSM-5分子筛不同孔道处(包括正弦孔道、直孔道和交叉腔)酸位中心上的MTO反应网络(包括芳烃循环、烯烃循环和芳构化)及甲醇原料和烯烃/芳烃产物的扩散行为进行了比较研究.结果表明,与正弦孔道和直孔道相比,芳烃循环和芳构化反应在交叉腔的酸中心上因具有较低的能垒而更易进行.相比之下,在正弦孔道和直孔道中,多甲基苯的生成受到显著限制,而烯烃循环却可以在三种酸中心(正弦孔道、直孔道和交叉腔)上以相近的能垒和相似的几率进行.芳烃循环生成乙烯和丙烯的几率相近,而烯烃循坏产物以丙烯和较高的烯烃产物为主.落位于H-ZSM-5交叉腔的酸中心能促进芳烃中间体如多甲基苯的生成,推动芳烃循环,提高乙烯选择性,而正弦孔道和直孔道中的酸中心则能增强烯烃循环,生成较多的丙烯和较高的烯烃产物.因此,H-ZSM-5分子筛对MTO的催化性能(包括活性和产物选择性等),可以通过有目的地调节酸中心在分子筛骨架中的位置分布(即铝落位)而得到有效调变和提升.本文阐明了H-ZSM-5分子筛酸中心在MTO反应中的催化作用与其骨架中的落位之间的有机联系,为高效甲醇转化分子筛催化剂的设计和性能提升提供了参考思路.