Molecular mechanics and dynamics of biomolecules using a solvent continuum model

An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001     

High temperature corrosion behaviour of M(Co,Ni)CrAIY-coatings on high temperature materials-microanalytical investigations

In our former investigations, the phenomenon high temperature corrosion (HTC) was described exemplarily on selected materialcoating combinations for blades of stationary gas turbines, mainly in the temperature region of up to 750° C. To answer the question, in which manner higher gas inlet and/or higher material surface temperature would influence the HTC behaviour, a special analytical technique—the integral layer profile analysis—was introduced to ameliorate concentration profile methods. By examining IN 738 LC specimens with CoCrAlY plasma spray coating, stressed by hot gas at 900° C, the limits of this system are shown by explaining the corrosion mechanism; the method is also used for other systems, e.g. U 520 with NiCrAlY coating at 750° C.     

Solar Light Induced Photocatalytic Degradation of Pollutants over Titania Pillared Zirconium Phosphate and Titanium Phosphate

Titania pillared zirconium phosphate (ZrP) and titanium phosphate (TiP) were prepared by intercalating Ti (IV) isopropoxide sol in the interlayers of the mono sodium form of the corresponding metal phosphate. The sol-intercalated samples were activated at various temperatures and characterized by XRD, UV–vis DRS, FTIR, BET-surface area, BJH-pore size distribution and acid sites measurement. Basal spacing and surface area analyses revealed that highest amount of pillaring has taken place with 2 and 4 wt.% titania loading for ZrP and TiP, respectively. The photocatalytic degradation of 4-nitrophenol (4-NP), phenol, methylene blue (MB) and hexavalent chromium (Cr (VI)) was studied in aqueous solution over the neat as well as pillared materials under solar irradiation. Catalytic activity tests revealed that hexavalent chromium (Cr (VI)) and 4-nitrophenol (4-NP) were completely degraded under acidic conditions, whereas, the same was observed in almost neutral conditions for phenol and methylene blue (MB) over 0.6 g/L of catalyst.

Contents of heavy metals in lotus seed from REEs mining area

At rare earth mining area, the pollution of heavy metals has been paid little attention. In lotus seeds and soil samples sampled from a typical rare earth elements mining area were detected the contents of eight kinds of heavy metals (Cr, Mn, Cu, Zn, As, Cd, Hg and Pb) to investigate the pollution from rare earth elements mining by ICP-MS (Inductively Coupled Plasma Mass Spectrometry). The results showed that the contents of the heavy metals Cr, Mn, Cu, Zn, As, Cd, Hg and Pb in lotus seeds were 0.25, 86.94, 8.32, 19.76, 0.13, 0.08, 0.01, and 0.20 μg/g in lotus seeds, respectively, and corresponding contents in soil were 27.68, 168.71, 20.23, 47.16, 1.83, 0.13, 0.04, and 23.15 μg/g. These data showed that the contents of heavy metals in lotus seeds from REEs mining area are no higher than reference area and meet national food safety standards of China.     

Synthesis of activated carbon foams with high specific surface area using polyurethane elastomer templates for effective removal of methylene blue

Carbon foams have gained significant attention due to their tuneable properties that enable a wide range of applications including catalysis, energy storage and wastewater treatment. Novel synthesis pathways enable novel applications via yielding complex, hierarchical material structure. In this work, activated carbon foams (ACFs) were produced from waste polyurethane elastomer templates using different synthesis pathways, including a novel one-step method. Uniquely, the produced foams exhibited complex structure and contained carbon microspheres. The ACFs were synthesized by impregnating the elastomers in an acidified sucrose solution followed by direct activation using CO₂ at 1000 ℃. Different pyrolysis and activation conditions were investigated. The ACFs were characterized by a high specific surface area (S_BET) of 2172 m²/g and an enhanced pore volume of 1.08 cm³/g. Computer tomography and morphological studies revealed an inhomogeneous porous structure and the presence of numerous carbon spheres of varying sizes embedded in the porous network of the three-dimensional carbon foam. X-ray diffraction (XRD) and Raman spectroscopy indicated that the obtained carbon foam was amorphous and of turbostratic structure. Moreover, the activation process enhanced the surface of the carbon foam, making it more hydrophilic via altering pore size distribution and introducing oxygen functional groups. In equilibrium, the adsorption of methylene blue on ACF followed the Langmuir isotherm model with a maximum adsorption capacity of 592 mg/g. Based on these results, the produced ACFs have potential applications as adsorbents, catalyst support and electrode material in energy storage systems.     

化合物分子表面积计算方法的研究

化合物的分子表面积是重要的物理化学性质参数．根据不同的应用领域及数学方法,提出了多种分子表面积算法[1-10],由此产生了“分子表面积法”,各方法的有效性在各具体应用领域都已被验证．本文将统计方法中的随机变量引入计算化合物分子表面积体系,由分子模型化技术得到化合物分子的原子坐标,不考虑化合物分子中原子的相互作用及分子间近似,直接计算分子表面积．使用该方法可以计算“净”分子表面积、“溶剂可及表面积”、甚至分子结构片段,分子结构中有交叉重叠片段及存在“空洞”的各种分子表面积,该算法及程序较简捷,适应范围广,计算结果较为满意．     

Oxidation kinetics of timahdit and tarfaya moroccan oil shales

Organic matter evolution and kinetics of combustion of Tarfaya and Timahdit oil shales have been examined by thermogravimetry (TG) and by differential thermal analysis (DTA). An agreement is observed between both techniques where it was found that combustion of organic matter occurs in two steps. Kissinger's method applied on experimental results gives an activation energy of the same magnitude for the first step of both oil shales (103 kJ mol^–1) whereas the second is 148 kJ mol^–1 for Timahdit and 118 kJ mol^–1 for Tarfaya.The changes in specific surface area during thermal combustion of Timahdit and Tarfaya oil shales have been studied by thermogravimetric gas sorption balance and correlated with experimental results obtained on TG/DTA in air. For Timahdit oil shale oxidation products, specific surface areas calculated from nitrogen adsorption data shows a slight increase during the temperature domain of 280 to 430°C and after this temperature, they increase sharply. However, data obtained with Tarfaya oil shales shows a significant increase at the temperature of maximum oxidation of the first stage of combustion of organic matter.This revised version was published online in November 2005 with corrections to the Cover Date.     

Evaluation of the enantiomeric selectivity in the chiral ligand-exchange chromatography of amino acids by a computational model

The chromatographic resolution of enantiomeric amino acids is accomplished on a reversed phase column using aqueous mobile phase containing the chiral reagent N,N-dimethyl-S-phenylalanine-Cu(II). The separation is a result of the whole interaction between the diastereomeric complex surface and the mixed stationary phase realized by the dynamic coating of the RP-18 carbon chains layer. The elution order seems to be related to the different water coordination capability on copper ion in the formation of the mixed ternary complexes.     

FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.