Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Progress on phthalocyanine-conjugated Ag and Au nanoparticles: Synthesis,characterization, and photo-physicochemical properties

Phthalocyanine (Pc) complexes are an important class of dyes with numerous (e.g., biological, photophysical, and analytical) applications. Among the methods used to improve the properties of these complexes, one should mention the introduction of different substituents, variation of the central metal ion, ligand exchange, and conjugation to nanomaterials (e.g., carbon-based nanomaterials and metal nanoparticles (NPs)). This work briefly reviews Pc complex conjugation to Ag and Au NPs, highlights the different NP shapes, and discusses the diversity of conjugation approaches. Moreover, the use of UV–Vis spectroscopy, powder X-ray diffraction, X-ray photoelectron spectroscopy, transmission electron microscopy, atomic force microscopy, dynamic light scattering and Fourier transform infrared spectroscopy to characterize Pc-NP hybrids is summarized. The effect of conjugation on Pc photo-physicochemical properties (fluorescence, singlet oxygen generation, triplet state formation, and optical limiting behavior) is discussed, and future perspectives for the synthesis and applications of new hybrids are provided.     

Surface modification of low density polyethylene (LDPE) film by low pressure O2 plasma treatment

In this work, low pressure glow discharge O₂ plasma has been used to increase wettability in a LDPE film in order to improve adhesion properties and make it useful for technical applications. Surface energy values have been estimated using contact angle measurements for different exposure times and different test liquids. In addition, plasma-treated samples have been subjected to an aging process to determine the durability of the plasma treatment. Characterization of the surface changes due to the plasma treatment has been carried out by means of Fourier transformed infrared spectroscopy (FTIR) to determine the presence of polar species such as carbonyl, carboxyl and hydroxyl groups. In addition to this, atomic force microscopy (AFM) analysis has been used to evaluate changes in surface morphology and roughness. Furthermore, and considering the semicrystalline nature of the LDPE film, a calorimetric study using differential scanning calorimetry (DSC) has been carried out to determine changes in crystallinity and degradation temperatures induced by the plasma treatment. The results show that low pressure O₂ plasma improves wettability in LDPE films and no significant changes can be observed at longer exposure times. Nevertheless, we can observe that short exposure times to low pressure O₂ plasma promote the formation of some polar species on the exposed surface and longer exposure times cause slight abrasion on LDPE films as observed by the little increase in surface roughness.     

Adiabatic Potential Energy Surface of the 1,2,3-Trifluorobenzene Cation-Radical

Ab initio study of the adiabatic potential energy surface (PES) for 1,2,3-trifluorobenzene cation-radical was carried out by the ROHF, UHF, MCSCF, MP2, and DFT (B3LYP) methods with the 6-31G* basis set. The PES in question is a pseudorotation surface at all calculation levels. The pseudorotation barrier height does not exceed 3.2 kcal/mol, suggesting a possibility for its manifestations in experimental EPR spectra.     

Performance of hollow-fiber flow field-flow fractionation in protein separation

Since hollow-fiber flow field-flow fractionation (HF FIFFF) utilizes a cylindrical channel made of a hollow-fiber membrane, which is inexpensive and simple in channel assembly and thus disposable, interests are increasing as a potential separation device in cells, proteins, and macromolecules. In this study, performance of HF FIFFF of proteins is described by examining the influence of flow rate conditions and length of fiber (polyacrylonitrile or PAN in this work) on sample recovery as well as experimental plate heights. The interfiber reproducibility in terms of separation time and recovery was also studied. Experiments showed that sample recovery was consistent regardless of the length of fiber when the effective field strength (equivalent to the mean flow velocity at the fiber wall) and the channel void time were adjusted to be equivalent for channels of various fiber lengths. This supported that the majority of sample loss in HF FIFFF separation of apoferritin and their aggregates may occur before the migration process. It is finally demonstrated that HF FIFFF can be applied for characterizing the reduction in Stokes' size of low density lipoproteins from blood plasma samples obtained from patients having coronary artery disease and from healthy donors.     

Theoretical Study on the Reaction Mechanism of Ketene CH2CO with Isocyanate NCO Radical

The bimolecular single collision reaction potential energy surface of an isocyanate NCO radical with a ketene CH2CO molecule was investigated by means of B3LYP and QCISD（T） methods. The computed results indicate that two possible reaction channels exist on the surface. One is an addition-elimination reaction process, in which the CH2CO molecule is attacked by the nitrogen atom at its methylene carbon atom to lead to the formation of the intermediate OCNCH2CO followed by a C-C rupture channel to the products CH2NCO＋CO. The other is a direct hydrogen abstraction channel from CHzCO by the NCO radical to afford the products HCCO＋HNCO. Because of a higher barrier in the hydrogen abstraction reaction than in the addition-elimination reaction, the direct hydrogen abstraction pathway can only be considered as a secondary reaction channel in the reaction kinetics of NCO＋ CH2CO. The predicted results are in good agreement with previous experimental and theoretical investigations.     

磷酸三乙酯改性HZSM-5沸石的活性及理论研究

采用XRD表征了水蒸气和磷联合改性的HZSM-5沸石分子筛的结构．通过NH3-TPD和N2吸附脱附研究了样品的酸性和比表面．采用正庚烷的裂化反应研究了样品的裂化活性，研究结果表明，磷改性样品与母体样品相比，经过水蒸气处理后显示出较高的酸量和正庚烷裂化活性．上述结果首次用模型簇和计算量子化学方法进行了解释．采用Gaussian94软件包和PM3半经验量子化学方法对模型簇进行了全优化和频率分析．计算结果显示磷改性后样品的脱铝补硅反应热大于母体样品脱铝补硅反应热，从而显示出磷对骨架的稳定化作用．     

一代树状碳硅烷液晶的光化学研究－－端基含12个4－丁氧基氮苯介晶基元

研究了新的含12个丁氧基偶氮苯介晶基元的五代树状碳硅烷液晶D1及偶氮苯介 晶基元化合物M5在氯仿、四氢呋喃、N，N－二甲基甲酰胺、乙醇和苯等溶剂中的量 子产率、反－顺光异构化、光回复异构、反／顺异构组分比、热回复异构及活化能 。D1和M5的光致变色速率常数为10~(-1)s~(-1)，而含同一偶氮基元的光致变色液 晶聚硅氧烷的光致变色速率常数为10~(-8)s~(-1)，因此，液晶树状物D1的光响应 速度比后者快10~7倍。     

第三组分Et2Mg对二茂锆/铝氧烷体系催化乙烯聚合反应的影响

研究发现在二茂锆-铝氧烷催化体系中添加少量Et2Mg能够明显促进在低Al/Zr摩尔比条件下乙烯高聚.以MAO作为助催化剂,Al/Zr/Mg摩尔比为1012时,得到高聚物,粘均分子量(Mv)为1.37×105,催化活性为2.83×104g聚合物/mol(Zr)h.而在同样的反应条件下,Cp2ZrCl2-MAO和-EAO二组份催化体系在如此低的Al/Zr摩尔比条件下无催化活性或以很低的催化活性生成低碳烯烃.对于这类三组份烯烃高聚催化体系的研究目前仍在进行中,以期得到有效的低Al/Zr比乙烯高聚茂金属催化体系.     

interaction of nitro compounds with radicals: a quantum chemical study

Photoreduction of nitro compounds is accompanied by formation of various radical products that can react with the starting nitro compound, thus causing deviation of the decomposition kinetics from the first-order kinetics with respect to the nitro compound. The results of quantum chemical modeling of the reactions of nitro compounds with radicals and the pathways of further transformations of radical adducts formed in the reactions are presented. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 202–206, February, 2006.