XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC‐CI combined with dipped adcluster model

O1s core‐electron binding energies (CEBE) of the atomic oxygens on different Ag surfaces were investigated by the symmetry adapted cluster‐configuration interaction (SAC‐CI) method combined with the dipped adcluster model, in which the electron exchange between bulk metal and adsorbate is taken into account properly. Electrophilic and nucleophilic oxygens (O_elec and O_nuc) that might be important for olefin epoxidation in a low‐oxygen coverage condition were focused here. We consider the O1s CEBE as a key property to distinguish the surface oxygen states, and series of calculation was carried out by the Hartree–Fock, Density functional theory, and SAC/SAC‐CI methods. The experimental information and our SAC/SAC‐CI results indicate that O_elec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that O_nuc is the one on the reconstructed added‐row site of Ag(110) and that one‐ and two‐electron transfers occur, respectively, to the O_elec and O_nuc adclusters from the silver surface. © 2013 Wiley Periodicals, Inc.     

High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

Water PMF for predicting the properties of water molecules in protein binding site

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.     

Mechanistic Simulation Studies on Viscous-Elastic Polymer Flooding in Petroleum Reservoirs

Based on the theory and application developments of polymer flooding on enhancing oil recovery, an improved mathematical model has been developed to simulate the mechanism of viscous-elastic polymer flooding. IMPES method has been presented to solve the polymer flooding model considering the viscosifying effect of elasticity, the effect of decreasing residual oil and the degradation of polymer molecules. The validation of the model is approved by an experiment. A simulation example was carried out using the developed numerical simulator. The enhanced oil recovery mechanism was discussed for viscous-elastic polymer flooding, and corresponding influencing factors were also studied.     

Study and Modeling of Metal Oxide Solubilization in (w/o) Microemulsions

Water-in-oil (w/o) microemulsions are very appealing reaction media due to their ability to provide huge surface of contact between water-soluble and oil-soluble reactants. Their application as reaction media, including the preparation of nanoparticles, is, however, limited to water soluble precursors. In this study, we present a first step scheme in a two-step process for the preparation of metal oxide nanoparticles starting from their water-insoluble metal oxide bulk powder. This step involves solubilizing the metal oxide in the water pools of the microemulsion with the aid of a solubilizing agent. The variables affecting the solubilizing capacity of iron and copper oxides, as examples of important metal oxides, in single HCl-containing AOT/water/isooctane microemulsions were investigated. The effect of the following variables on the solubilization capacity is reported, namely, mixing time, surfactant concentration, water to surfactant mole ratio (R), and the nominal concentration of HCl in the water pool. At 300-rpm, time-invariant concentration of the metals in the microemulsions was achieved in about 6 hours. These values were quoted as the solubilization capacity of the metal oxide at the corresponding conditions. Solubilization capacity increased linearly with the surfactant concentration and R, and portrait a power function with the nominal concentration of HCl in the water pool. A mathematical model previously derived to describe nanoparticle uptake by single microemulsion accurately accounted for the effect of the aforementioned variables on the solubilization capacity.     

Effect of Rough Nanoparticle Orientation on DLVO Energy Interaction

This study investigated the effect of the orientation of rough nanoparticles on Derjaguin and Landau, Verwey and Overbeek (DLVO) energy interaction. Rippled sphere model was used to survey van der Waals attraction energy and repulsive double-layer interaction energy between nanoparticles. The effect of particle size, asperity size, number of asperities, and concentration was studied for different orientations. Spherical coordinates were used to evaluate the effect of changes in orientation under controlled conditions. Surface element integral method was used to calculate DLVO energy interactions between rough particles at specific orientations. The DLVO energy results show that a change in orientation significantly affected the stability of the nanoparticles. The stability of dispersion varied as the contact surface between nanoparticles changed.     

Study on Influencing Factors of Chemical Flooding for Heavy Oil

Alkali and alkali/surfactant displacing agents are designed for two kinds of heavy oil. Results of emulsifying capacity, dynamic interfacial tension (IFT) and water-wet core flooding tests show that, although alkaline/surfactant systems exhibit better capacity in emulsification and IFT reduction, oil recovery values of alkaline/surfactant flooding are lower than those of alkaline flooding. Glass-etched micromodel tests further demonstrate that, when alkaline solution penetrates into the oil phase, water streams break into ganglia coating oil film. Water ganglia may be entrapped by narrow throats, consequently presenting a water-oil alternating slug flow. Similar water ganglia also appears in alkaline/surfactant flooding, however, water channeling along the pore surface occurs subsequently, resulting in its relatively lower oil recovery.     

生物油模型化合物催化裂化制备芳香烃的实验研究

通过HZSM-5分子筛催化剂对生物油典型模型化合物(乙酸、愈创木酚、正庚烷和环己烷等)在550℃进行了催化裂化反应,研究模型化合物催化裂化特性和反应机理以及催化剂性质。结果表明,正庚烷和环己烷裂化产物主要是芳香烃(53%和91%,均为积分面积分数),对于此类不含氧的模型化合物,催化裂化反应过程更容易进行;随着催化剂用量的增加,可以有效增加乙酸裂化产物中芳香烃含量(12%到90%,均为积分面积分数);愈创木酚结构比较复杂,HZSM-5催化剂主要脱除了甲氧基,催化剂用量的增加可以使芳香烃类稳定物质更容易形成。     

上湾煤及其惰质组富集物的结构表征与模型构建

对神东上湾煤(SDR)及其岩相分离所得惰质组富集物(SDI)分别进行核磁(¹³C-NMR)、红外光谱(FT-IR)和X射线光电子能谱(XPS)表征,得到煤结构单元信息,与元素分析数据相结合构建了SDR和SDI的结构模型,用ACD/CNMR predictor软件计算结构模型的 ¹³C化学位移。结果表明,SDR芳香结构主要是缩合程度为2的萘,SDI主要是菲和萘,SDI较SDR结构芳香度较高,两个结构中氧主要以羰基氧和羟基氧的形式存在,氮主要以吡咯和吡啶形式存在,两个结构模型计算得到核磁谱图与实验谱图吻合较好,结构式分别为C₁₈₁H₁₃₆N₂O₂₄和C₁₈₆H₁₄₈N₂O₂₂。