Achiral and chiral separations using MEKC,polyelectrolyte multilayer coatings,and mixed mode separation techniques with molecular micelles

Mixed mode (MM) separation using a combination of MEKC and polyelectrolyte multilayer (PEM) coatings is herein reported for the separation of achiral and chiral analytes. Many analytes are difficult to separate by MEKC and PEM coatings alone. Therefore, the implementation of a MM separation provides several advantages for overcoming the limitations of these well‐established methods. In this study, it was observed that achiral separations using MEKC and PEM coatings individually resulted in partial resolution of eight very similar aryl ketones when the molecular micelle (sodium poly(N‐undecanoyl‐L ‐glycinate)) concentration was varied from 0.25 to 1.00% w/v and the bilayer number varied from 2 to 4. However, when MM separation was introduced, baseline resolution was achieved for all eight analytes. In the case of chiral separations, temazepam, aminoglutethimide, benzoin, benzoin methyl ether, and coumachlor were separated using the three separation techniques. For chiral separations, the chiral molecular micelle, sodium poly(N‐undecanoyl‐L ‐leucylvalinate), was employed at concentrations of 0.25–1.50% w/v for both MEKC and PEM coatings. Overall, the results revealed partial separation with MEKC and PEM coatings individually. However, MM separation enabled baseline separation of each chiral mixture. The separation of achiral and chiral compounds from different compound classes demonstrates the versatility of this MM approach.     

Drug efficiency indices for improvement of molecular docking scoring functions

A dataset of protein‐drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as ΔG/W (Wiener index), ΔG/NoC (number of carbons), and ΔG/P (partition coefficient), improve the correlation between experimental and calculated values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Surface diffusion in reversed-phase liquid chromatography

More than 40 years ago, Giddings pointed out in “Dynamics of Chromatography” that surface diffusion should become an important research topic in the kinetics of chromatographic phenomena. However, few studies on surface diffusion in adsorbents used in chromatography were published since then. Most scientists use ordinary rate equations to study mass transfer kinetics in chromatography. They take no account of surface diffusion and overlook the significant contributions of this mass transfer process to chromatographic behavior and to column efficiency at high mobile phase flow rate. Only recently did the significance of surface diffusion in separation processes begin to be recognized in connection with the development of new techniques of fast flow, high efficiency chromatography. In this review, we revisit the reports on experimental data on surface diffusion and introduce a surface-restricted molecular diffusion model, derived as a first approximation for the mechanism of surface diffusion, on the basis of the absolute rate theory. We also explain how this model accounts for many intrinsic characteristics of surface diffusion that cannot properly be explained by the conventional models of surface diffusion.     

QM/MM Study on Enzymatic Mechanism in Sinigrin Biosynthesis

As the major and abundant type of glucosinolates (GL) in plants, sinigrin has potential functions in promoting health and insect defense. The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds, which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase (SOT). However, due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL, little is known about this sulfonation process. Fortunately, the crystal structure of SOT 18 from Arabidopsis thaliana (AtSOT18) containing the substance (sinigrin) similar to 3-methylthiopropyl GL has been determined. To understand the enzymatic mechanism, we employed molecular dynamics (MD) simulation and quantum mechanics combined with molecular mechanics (QM/MM) methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18. The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism. Moreover, Lys93, Thr96, Thr97, Tyr130, His155, and two enzyme peptide chains (Pro92-Lys93 and Gln95-Thr96-Thr97) play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry. Particularly, His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process. The presently proposed concerted dissociative mechanism explains the role of AtSOT18 in sinigrin biosynthesis, and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.     

含1,3,4-噁二唑的喹啉衍生物的合成、抗AChE活性及分子对接研究

为研发新型乙酰胆碱酯酶抑制剂,本文通过碘介导环化反应合成了一系列含1,3,4-噁二唑的喹啉衍生物,并通过熔点和核磁共振确定了其结构。在1 μmol/mL浓度下,对这些衍生物抗乙酰胆碱酯酶活性进行了初步的生物测定。结果表明,化合物4b和4j具有中等的抑制活性,抑制率分别为79.18%和78.46%。初步的构效关系表明,在目标化合物的1,3,4-噁二唑环上引入杂环可以其提高其活性。分子对接研究表明,化合物4b和4j和乙酰胆碱酯酶的催化活性中心部位显著结合。     

Synthesis and application of multi-walled carbon nanotubes-molecularly imprinted sol-gel composite material for on-line solid-phase extraction and high-performance liquid chromatography determination of trace Sudan IV

A novel composite material of multi-walled carbon nanotubes (MWNTs)-Sudan IV molecularly imprinted polymers (MIPs) was prepared by surface molecular imprinting technique in combination with sol-gel technology. The MWNTs-MIPs were evaluated by scanning electron micrograph (SEM), Fourier transform infrared spectroscopy (FT-IR), and adsorption experiments. The results showed that the MWNTs-MIPs exhibited good selective recognition to Sudan IV. The maximum saturated binding capacity (Q_max) is 63.2 μmol g⁻¹. Applied as sorbent, the MWNTs-MIPs were used for the determination of trace Sudan IV in chilli powder by on-line solid-phase extraction-high-performance liquid chromatography (SPE-HPLC). The results showed that an enrichment factor of 741 was achieved with a loading flow rate of 1.0 mL min⁻¹ for sampling 50 mL. The MWNTs-MIPs provided a fast and convenience determination platform for Sudan IV in real samples.     

Precise and global identification of phospholipid molecular species by an Orbitrap mass spectrometer and automated search engine Lipid Search

In the present research, we have established a new lipidomics approach for the comprehensive and precise identification of molecular species in a crude lipid mixture using a LTQ Orbitrap mass spectrometer (MS) and reverse-phase liquid chromatography (RPLC) combination with our newly developed lipid search engine “Lipid Search”. LTQ Orbitrap provides high mass accuracy MS spectra by Fourier-transform (FT) mass spectrometer mode and can perform rapid MSⁿ by ion trap (IT) mass spectrometer mode. In this study, the negative ion mode was selected to detect fragment ions from phospholipids, such as fatty acid anions, by MS2 or MS3. We selected the specific detection approach by neutral loss survey-dependent MS3, for the identification of molecular species of phosphatidylcholine, sphingomyelin and phosphatidylserine. Identification of molecular species was performed by using both the high mass accuracy of the mass spectrometric data obtained from FT mode and structural data obtained from fragments in IT mode. Some alkylacyl and alkenylacyl species have the same m/z value as molecular-related ions and fragment ions, thus, direct acid hydrolysis analysis was performed to identify alkylacyl and alkenylacyl species, and then the RPLC–LTQ Orbitrap method was applied. As a result, 290 species from mouse liver and 248 species from mouse brain were identified within six different classes of phospholipid, only those in manually detected and confirmed. Most of all manually detected mass peaks were also automatically detected by “Lipid Search”. Adding to differences in molecular species in different classes of phospholipids, many characteristic differences in molecular species were detected in mouse liver and brain. More variable number of saturated and monounsaturated fatty acid-containing molecular species were detected in mouse brain than liver.     

天然无序蛋白质:序列-结构-功能的新关系

天然无序蛋白质是一类新发现的蛋白质,它们在天然条件下没有确定的三维结构,却具有正常的生物学功能,广泛参与信号传递、DNA转录、细胞分裂和蛋白质聚集等重要的生理与病理过程.无序蛋白质的发现是对传统的蛋白质"序列-结构-功能"范式的挑战.在这篇综述里,我们首先回顾了蛋白质的传统范式以及无序蛋白质的发现过程,然后介绍无序蛋白质在结构、序列、功能等方面的特征与相互作用,并以分子识别过程为例,进一步阐述目前国际上对无序蛋白质所具有优势的一些认识与观点.我们还分析了无序蛋白质研究在生命科学和医学等领域的应用前景,并介绍了国内在无序蛋白质领域的研究现状.     

PdO0,±1, PdH0,±1及PdOH分子结构和电子性质的从头计算

利用多种从头计算方法对PdO0,±1, PdH0,±1以及PdOH的结构和电子性质进行了理论研究. 优化了PdO分子两个能量相近的态(3∏和3∑-), 结果表明PdO 的3∏态较3∑-态更为稳定, 在单双激发耦合簇理论(CCSD)水平下3∑-态的总能量比3∏态的高出0.286 eV. 在结构优化的基础上计算了PdO以及PdH的绝热电离能(AIE)和电子亲和能(AEA), 计算结果与实验值符合得很好. PdOH的基态为Cs对称性的角型结构Pd—OH(2A'态), 另外还优化得到两个2A'态的亚稳结构, 分别对应于Pd—OH和O—Pd—H, CCSD水平下两个亚稳态的总能量较基态分别高0.405和2.284 eV, 优化得到了连接这两个2A'态的过渡态, 并计算了相应的反应能垒.