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.     

制备方法对MoO_3／ZrO_2结构的影响及MoO_3／ZrO_2固体超强酸的结构特征 Ⅰ．ZrO_2的形态与样品比表面的研究

ＸＲＤ，ＤＴＡ，比表面测定等结果表明，制备方法对ＭｏＯ３／ＺｒＯ２结构有决定性影响．仲钼酸铵浸渍仅经干燥的Ｚｒ（ＯＨ）４再经高温焙烧所得团体超强酸ＭｏＯ３／ＺｒＯ２（Ⅰ）与浸渍晶态ＺｒＯ２所得部分氧化催化剂ＭｏＯ３／ＺｒＯ２（Ⅱ）的载体形态有明显不同．（１）ＭｏＯ３／ＺｒＯ２（Ⅰ）的比表面数倍于ＭｏＯ３／ＺｒＯ２（Ⅱ）；（２）ＭｏＯ３含量增加时，ＭｏＯ３／ＺｒＯ２（Ⅰ）的比表面逐步增大至一极大值再缓缓下降，而ＭｏＯ３／ＺｒＯ２（Ⅱ）的比表面随ＭｏＯ３含量增加而单调下降；（３）在ＭｏＯ３／ＺｒＯ２（Ⅰ）中，ＺｒＯ２以介稳四方相存在，而在ＭｏＯ３／ＺｒＯ２（Ⅱ）中则是稳定的单斜相．在此基础上研究了事先引入的活性组分在载体织构形成过程中的作用，包括延迟ＺｒＯ２晶化，阻碍晶粒长大及与之相关的相变等，并讨论了ＭｏＯ３／ＺｒＯ２（Ⅰ）中ＭｏＯ３最佳含量的科学含义．     

Effects of Calcination on the Physical and Photocatalytic Properties of TiO<Subscript>2</Subscript> Powders Prepared by Sol–Gel Template Method

TiO₂ powders were prepared by sol–gel template method and calcined under different conditions. XRD, BET and TEM were used to characterize the TiO₂ powders obtained. The photocatalytic activity of TiO₂ was investigated by the degradation of methyl orange. It was found that TiO₂ powder has the highest photocatalytic activity at a calcination temperature of 673 K. The effects of physical properties such as surface area, crystallinity and crystal phase on the photocatalytic activity of TiO₂ were discussed.     

含Co纳米介孔分子筛的制备与表征

用两步水热法合成出了含Co介孔分子筛,采用XRD,FT-IR,TPR,AFM,BET,B JH等方法对样品的物化性能进行了表征.结果表明合成出了纳米级具有介孔结构的CoMCM-41.样品在550℃焙烧可以将模板剂有效去除而不影响孔结构.所得CoMCM-41比表面积大于500 m2/g,平均孔径分布为3.57 nm,粒径分布在20~40 nm范围内.     

Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density

The aim of our study is the development of a method for calculating the interface of dimerization of protein-protein complexes based on simplified medium-resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent-Accessible Surface Area (SASA) of macromolecules could be applied to medium-resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 A crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side-chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side-chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins.     

A New Orthorhombic Phase of ZrW1.6Mo0.4O8 at Ambient Pressure

IntroductionZr W2 O8presents a few models of structures.The first report was made by Graham etal.[1] andconfirmed by Chang et al.[2 ] in the pseudobinaryphase diagram of a Zr O2 - WO3 system atatmospheric pressure.Cubic zirconium tungstate,Zr W2 O8,possesses the acentric P2 13 structure( αform,a=0 .91 5 75 nm at 2 93K) [3 ] and istransformed to the disordered centric Pa3structure(β form,a =0 .91 371 nm,at 483 K) [3 ] .Theprecise transition temperature ofα toβ form is448K determined …     

碱性水蒸气处理的ZSM-5沸石酸性质及孔结构的影响

 采用XRD，NH3－TPD，比表面积和孔结构测定等研究了在不同温度下用含10％NH3的水蒸气处理时HZSM－5沸石n（Si）／n（Al）＝25）酸性质及孔结构的变化规律．结果表明，随着处理温度的提高，HZSM－5的结构未发生明显的变化；样品的总酸量下降很快，但弱酸分布量相对提高，而强酸分布量相对下降；提高处理温度，样品的比表面积和微孔体积减小，二次孔或中孔体积及外表面积有增大的趋势．     

高比表面积窄孔分布氧化铝的制备研究 Ⅰ.沉淀条件的影响

 以硫酸铝液为原料，以氨水、氢氧化钠和铝酸钠为碱沉淀剂，采用pH摆动法制备了高比表面积、大孔径、窄孔分布、大孔体积氧化铝，考察了沉淀剂、沉淀温度及沉淀时酸侧pH值对氧化铝物性的影响，并对pH摆动法与等pH沉淀法的结果进行了比较．结果表明，通过改变制备参数可以获得高比表面积、大孔体积的氧化铝，当沉淀温度为70℃，pH摆动3或4次时，氧化铝的孔体积可高达1．0ml／g，比表面积仍大于300m2／g．用pH摆动法制得的样品比用等pH沉淀法制得的样品容易酸溶，对挤压成型有利．不同样品在酸溶液中的分散性表明，用氨水沉淀剂可获得相对较小的沉淀粒子．改变沉淀时酸侧的pH值，可导致沉淀粒子的结构发生变化．     

Optimization of the electrophoretic deposition of YBa2Cu3O7−x superconducting large area coatings

Large area coatings (>10cm²) of the high temperature superconductor YBa₂Cu₃O_7–x (x = 0.1 – 0.2) (YBCO) have been prepared by scale up an electrophoretic deposition technique using silver sheets and Si-wafers coated with Ag or Au as substrates. Several parameters, like the kind of the solvent, the applied voltage, the distance between the electrodes, the initial concentration of the suspension and the temperature during the electrophoresis were investigated in order to attain high deposition rates, as well as uniform YBCO coatings with the proper stoichiometry. To obtain a strongly adherent and dense coating a subsequent appropriate sintering and annealing procedure has been developed. The coatings obtained were characterized for their stoichiometry and superconducting properties by X-ray diffraction (XRD), Raman spectroscopy and magnetic measurements. The homogeneity and thickness of the films and the average grain size of the deposited particles have been investigated by optical and scanning electron microscopy (SEM).