Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.     

Optimization of the process variables for the synthesis of cardanol-based novolac-type phenolic resin using response surface methodology

Models capable of predicting the maximum extent of conversion (p) of cardanol-based novolac-type phenolic resin, have been developed using response surface methodology to determine the optimum reaction conditions. Three-dimensional response surface and their contour plot were drawn. The maximum extent of conversion (98.93%) was predicted when the cardanol was condensed with formaldehyde (molar ratio 1:0.652) at 119.84 °C for a time period of 3 h with the catalyst (e.g., citric acid) concentration of 1.988% of total volume of cardanol and formaldehyde. The pH of the reaction mixture was maintained at 3.0. These predicted values for optimum process conditions were in good agreement with experimental data.     

Synthese und Geruch von (Z)-Dehydro-homo-β-santalol

Summary Guided by molecular modeling studies, the synthesis of the title compound is described. The organoleptic evaluation proved the predicted real sandal like odour of (Z)-dehydro-homo--santalol.

Aus den Diplomarbeiten von C.P. (1991), I.P. und B.Ö. (1992), Universität Wien     

新型氮杂2-β萘基苯并噁唑分子设计与光物理性质的研究

为了寻找新的有效光敏材料，设计了一系列新型氮杂2-β萘基苯并恶唑分子，用改进的PPP-SCF-CI方法，对设计分子的第一激发单线态，三线态，振子强度和跃迁矩等光物理性质进行了较为详细的研究，筛选出了一些新型的具有特殊光物理特性的分子，并预测了有可能产生新型氮杂2-β萘基苯并恶唑分子类光敏感功能材料的取代基部位。     

Novel type of heterogenized CuCl2 catalytic systems for oxidative carbonylation of methanol

A novel type of heterogenized CuCl₂ catalysts was designed for the oxidative carbonylation of methanol to dimethyl carbonate (DMC) taking account of the plausible reaction mechanism and intermediates. To prevent severe corrosion of the reaction equipment materials due to Cl^– while keeping the catalytic activity of the homogeneous CuCl₂ catalyst, we adopted, as supports (or ligands) of CuCl₂, four polymers, bearing a 2,2-bipyridine (bpy) or pyridine (py) unit, namely, poly(2,2-bipyridine-5,5-diyl) (Pbpy), poly(pyridine-2,5-diyl) (Ppy), poly(N,N-bisphenylene-2,2-bipyridine-4,4-dicarboxylic amide) (Bpya), and poly(4-methyl-4-vinyl-2,2-bipyridine) (Pvbpy), together with one chelate compound, 8-quinolinol. The catalytic activity, stability of heterogenized CuCl₂ and their corrosivities to stainless steels were examined in the liquid-phase reaction of the oxidative carbonylation of methanol. These polymer-supported catalysts showed considerable catalytic activity and stability for the DMC synthesis. In particular, the Pbpy-CuCl₂ and Ppy-CuCl₂ catalysts exhibited high DMC yields and selectivity comparable to those of the homogeneous CuCl₂ catalyst. This high activity appears to be associated with the presence of the -conjugated system in the polymers, which affect the redox reactions of Cu involved in the catalytic reaction. All of the polymer-supported CuCl₂ catalysts could be easily recycled after filtration, and the initial catalytic activity was maintained after three times of use. The corrosive characters of the catalysts were closely related to CuCl₂ leaching from the supports, which reflects the ability of supports to coordinate Cu. These experimental results suggest that both the electronic structure and the coordination ability of the polymer supports are key factors for the development of an effective catalytic system.     

Chemometric approach in optimization of micellar liquid chromatographic separation of some halogenated phenols

Simultaneous optimization of separation quality and analysis time of the micellar liquid chromatography of nine chlorophenol isomers was investigated. The effect on retention of three experimental parameters was studied using multivariate analysis. The factors studied were the concentration of sodium dodecyl sulfate, propanol content and pH of the mobile phase. The experiments were performed according to the face-centred cube central composite design and the inverse form of the experimental retention times for analytes were fitted to the polynomial models. The results of the analysis of variance showed that the models obtained explain greater than 99% of the variance observed in the chromatograms. Good predictive ability of the models was verified as high values of the statistics R² and F were obtained for the linear relationship between predicted cross-validated and experimental values of the dependent variable. The study showed that the use of Pareto-optimality method, an approach from multi-criteria decision-making, allows the selection of the best possible combinations of separation and analysis time in micellar liquid chromatography of chlorophenols.     

Physico-chemical characterization of nanofiltration membranes.

This study presents a methodology for an in-depth characterization of six representative commercial nanofiltration membranes. Laboratory-made polyethersulfone membranes are included for reference. Besides the physical characterization [molecular weight cut-off (MWCO), surface charge, roughness and hydrophobicity], the membranes are also studied for their chemical composition [attenuated total reflectance Fourier spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS)] and porosity [positron annihilation spectroscopy (PAS)]. The chemical characterization indicates that all membranes are composed of at least two different layers. The presence of an additional third layer is proved and studied for membranes with a polyamide top layer. PAS experiments, in combination with FIB (focused ion beam) images, show that these membranes also have a thinner and a less porous skin layer (upper part of the top layer). In the skin layer, two different pore sizes are observed for all commercial membranes: a pore size of 1.25-1.55 angstroms as well as a pore size of 3.20-3.95 angstroms (both depending on the membrane type). Thus, the pore size distribution in nanofiltration membranes is bimodal, in contrast to the generally accepted log-normal distribution. Although the pore sizes are rather similar for all commercial membranes, their pore volume fraction and hence their porosity differ significantly.     

模糊正交法用于石墨炉探针原子化测定铋条件的研究

模糊正交法是通过把正交试验结果模糊化,然后用模糊数学的理论和方法来处理实验数据。与常规正交设计相比,能在同样实验工作量的情况下获得更多的信息。本文采用模糊正交法对元素Bi的测定条件进行优化,并将其同常规正交设计方差分析的结果进行了比较,并提出一个综合评价参数,对建立的分析方法进行了综合评价。     

Unnatural multidentate metal ligating α-amino acids

A family of penta- and hexadentate metal ligating α-amino acids, suitably protected for Fmoc solid-phase chemistry, has been prepared. These residues incorporate the mono-amides of ethanolaminetriacetic acid, ethylenediaminetriacetic acid, and ethylenediaminetetraacetic acid as side chains. Side chains are tethered varying distances (n) from the Cα-carbon to allow metal binding events to occur at distinct distances from the peptide backbone. These residues are designed to allow the facile installation of metal chelates along a peptide backbone.     

地锦草总黄酮最佳提取分离工艺的研究

采用四因素三水平的正交实验方法,对地锦草总黄酮的最佳提取工艺进行了探索.采用乙酸乙酯萃取、酸碱沉淀、铅盐沉淀3种方法,对其最佳分离工艺进行了探索.正交实验结果表明:温浸法中四因素对地锦草黄酮的影响顺序为乙醇浓度>样液比>提取温度>提取时间.通过实验得到了地锦草总黄酮的最佳提取工艺:以10倍体积的50%的乙醇水溶液在80℃浸提1 h.地锦草总黄酮的最佳分离方法为酸碱沉淀法.这些数据为中药地锦草的开发和应用提供了科学依据.