Clustering of chemical databases by means of the projection of maximum overlapping sets similarity measurements onto multidimensional spaces

In this paper, we propose a new method for clustering of chemical databases based on the representation of measurements of structural similarity onto multidimensional spaces. The proposed method permits the tuning of the clustering process through the selection of the dimension of the projection space, the normal vectors and the sensibility of the projection process. The structural similarity of each element regarding to the database elements is projected onto the defined spaces generating clusters that represent the characteristics and diversity of the database and whose size and characteristics can be easily adjusted.     

Scaling in second-order electron correlation calculations using systematic sequences of even-tempered basis sets

Improved results can often be obtained from second-order Rayleigh-Schrödinger perturbation calculations of electron correlation energies using large basis sets by introducing a scaling factor in the zero-order Hamiltonian. The scaling parameter may be determined from full third-order calculations using a smaller basis set. This scaling procedure can be applied in a systematic fashion by employing a sequence of even-tempered basis sets. Calculations illustrating this approach for the beryllium atom and the neon atom are presented. The scaling procedure is also employed in conjunction with a universal systematic sequence of basis functions. Calculations illustrating this Correlation energy — Mang-body perturbation theory.Work supported in part by S.R.C. Research Grant GR/B/4738.6.S.R.C. Advanced Fellow.     

Electron-density-dependent fused-sphere surfaces derived from pseudopotential calculations

Fused-sphere surfaces can be used to mimic a molecular boundary associated with a constant value of the electron density. The simplest of such fused-sphere models are constructed by using the atomic radii for the spherical isodensity surfaces of individual atoms. In this work, we discuss the extension of this model to molecules containing atoms beyond the second row. In these many- electron systems, the computation of electron densities is usually simplified by adopting a pseudopotential (or effective-core potential) approach. Here, we discuss the performance of large- and small-core pseudo-potential calculations as a tool to derive atomic radii. Our results provide an optimum set of variable radii that can be used to build fused-sphere surfaces. This continuum of surfaces provides a simple approximation to the low-electron-density regions around molecules with heavy atoms.     

New methods for data analysis of isothermal titration calorimetry

Heat divided by ligand concentration vs. heat, similar to the Scatchard plot, was introduced to obtain the equilibrium constant (K) and the enthalpy of binding (DH) using isothermal titration calorimetry data. Values of K and DH obtained by this linear pseudo-Scatchard plot for a system with a set of independent binding sites (such as binding fluoride ions on urease and monosaccharide methyl a-D-mannopyranoside on concavalin A) were remarkably like that obtained from a normal fitting Wiseman method and other our technical methods. On applying this graphical method to study the binding of copper ion on myelin basic protein (MBP), a concave downward curve obtained was consistent with the positive cooperativity in the binding. A graphical fitting by simple method for determination of thermodynamic parameters was also introduced. This method is general, without any assumption and restriction made in previous method. This general method was applied to the product inhibition study of adenosine deaminase. This revised version was published online in July 2006 with corrections to the Cover Date.     

Tetrakis(thiadiazolo)porphyrazines. 3. Acid-base Properties and Stability of Tetrakis-3,4-(1,2,5-thiadiazolo)porphyrazine in Sulfuric Acid Solutions

AM1 calculations gave the proton affinities of different types of donor sites in tetrakis-3,4-(1,2,5-thiadiazolo)porphyrazine, H₂{[SN₂)₄PA}, and protonation of the meso-nitrogen atoms was found to be favored. A spectrometric study showed that the basicity of the meso-nitrogen atoms of the porphyrazine macrocycle is strongly diminished and these atoms in CF₃CO₂H are involved in an incomplete acid-base interaction (ABI) to give acid solvates, while a complete ABI (protonation) is found only in the presence of sulfuric acid. The basicity constants of the meso-nitrogen atoms were determined spectrophotometrically in CF₃CO₂H-H₂SO₄. The kinetics of decomposition of the macrocyclic chromophore in concentrated sulfuric acid was studied and a possible mechanism for this process was proposed.__________Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 278–287, February, 2005.     

Surface modification of soft-glass capillaries for gas chromatography by treatment with water vapour

“Leaching” or “etching” by strong mineral acids seems to be a necessary pretreatment step for the most commonly used deactivation procedures of glass capillaries by reaction with either polyethylene glycol or silylation reagents. The acidic sites which are formed on the surface during this acid treatment cannot be completely removed by the subsequent deactivation process. This drawback can be overcome by performing the leaching with water vapour, resulting in an accumulation of cations at the surface and a decrease in the number of silanol groups. Capillaries of this type show excellent properties for the chromatography of strongly basic compounds. After the wash-out of the alkaline surface layer, the acidity of the support is suited for the chromatography of strongly basic as well as strongly acidic compounds. Due to a lack of reactive acidic sites, special deactivation procedures have to be applied to capillaries produced in this way.     

A novel nomenclature of polycyclic aromatic hydrocarbons without using graph centre

In this paper, we develop a novel adjacency matrix, He-matrix, corresponding to the dualist graph. Without using the graph center concept, we advance a novel nomenclature of polycyclic aromatic hydrocarbons. Further, we derive some distinguishing theorems about PAH molecules and present some results of our automatic derivatization and automatic classification counting of fused PAH molecules.     

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.     

离子交换-双氧水氧化法制备纳米CeO2晶体

以99.995% Ce(NO₃)₃和强碱性阴离子交换树脂为原料，采用离子交换-双氧水氧化法合成制备出纳米CeO₂晶体。并就离子交换反应中的Ce³⁺浓度、树脂加入速度和离子交换温度及H₂O₂加入速度等条件对CeO₂粒径的影响进行了探讨，得出了离子交换-双氧水氧化法制备纳米CeO₂晶体的最佳工艺条件。FTIR、TEM分析表明，离子交换法无需对合成的Ce(OH)₃溶胶进行洗涤即可去除NO₃^-、CO₃^2-等阴离子杂质，并用H₂O₂将该溶胶氧化，经真空干燥可制得粒径分布均匀，平均晶粒尺寸约3 nm，高纯度的CeO₂粉体。     

呋喃-乙酸分子间相互作用的量子化学研究

用密度泛函理论B3LYP方法选取6-311＋＋G(d,p)基组对呋喃-乙酸复合物进行了量子化学计算研究, 通过在相同水平下的频率振动分析发现了该势能面上6个极小值点, 其最稳定构型对应一强O…H—O型氢键, 其结合能在消除基组重叠误差后为－20.87 kJ•mol^－1. 通过自然键轨道(NBO)分析, 研究了电荷转移及轨道相互作用. 通过自洽反应场(SCRF)理论中的Onsager 溶剂模型在介电常数分别为1.0, 2.247, 4.9, 7.58, 10.36, 20.7, 32.63, 38.2, 46.7, 78.39的不同溶剂环境下重新优化呋喃与乙酸势能面上最稳定构型A, 研究了溶剂对呋喃-乙酸复合物几何构型、电荷分布、偶极矩以及结合能的影响. 发现溶剂化作用增大了呋喃与乙酸分子间的结合能, 导致O…H距离减小, H—O振动频率红移. 当溶液介电常数在1.0～32.63范围时, 溶剂效应十分显著, 当介电常数大于32.63后, 溶剂化作用几乎达到了极限.