DMSO溶剂中有机化合物pKa的定量构效关系研究

应用物质结构-性质关系(QSPR, quantitative structure-property relationships)方法研究了DMSO溶剂中45个有机化合物的pKa数值与电拓扑状态指数之间的定量关系, 并建立如下模型: pKa＝－1.545×E2＋0.633×E4－0.737×E5＋0.973×E6－4.048×E7－1.456×E8＋0.628×E9＋28.650. R＝0.991, S＝0.828. “逐一剔除”交叉验证的结果证明模型具有良好的稳定性和较强的预测能力. 研究结果表明电拓扑状态指数能够有效地预测有机化合物的pKa值.     

手性有机酸保留指数的手性指数及原子类型电拓扑指数模型

基于手性碳原子的取代基次序规则,提出分子手性指数(wj),结合原子类型电拓扑指数(En)研究18种手性羟基酸和氨基酸的薄层色谱保留指数(RM)的定量关系(QSRR).经最佳变量子集回归建立最佳四元数学模型,传统的相关系数(R2)为0.969,留一法(LOO)的交互验证系数(Q2)为0.943,结果证明具有良好的稳健性及预测能力.根据进入该模型的4个结构参数(wj,E13,E16,E17)可知,影响手性有机酸保留指数的主要因素是分子的二维结构特征(如襒O,—OH,—NH2)和分子的手性特征.综上所述,新建wj及En对手性有机酸的保留指数表征具有合理性与有效性,为预测手性有机酸的保留指数提供一种有效方法.     

用拓扑指数和神经网络研究有机污染物的生物富集因子

在修正Randic的分子连接性指数和连接矩阵的基础上, 定义新型分子连接性指数(mF), 并计算了239种有机污染物的分子连接性指数(mF). 用其1F构建了239种有机污染物生物富集因子(lgBCF)的QSAR模型, 该模型判定系数(R2)及逐一剔除法(LOO)的交互验证系数(Q2)分别为0.747和0.742. 而用1F和4个电性距离矢量(Mk)构建的五元QSAR模型的R2及Q2分别为0.829和0.819. 结果表明, 从统计学的角度, 该模型具有高度的稳定性及良好预测能力. 从此模型可知, 有机污染物BCF的主要影响因素是—C—, ＞C—, —O—, —S—, —X等分子结构碎片以及分子的柔韧性、折叠程度等空间因素. 将5个结构参数作为人工神经网络的输入层结点, 采用5∶26∶1的网络结构, 利用BP算法, 获得了一个令人满意的QSAR模型, 其R2和标准偏差s分别为0.987和0.157, 表明lgBCF与这5个参数具有良好的非线性关系. 从上可见, 新建的连接性指数1F以及电性距离矢量与有机物的生物富集因子具有良好的相关性, 可望在物质构效关系研究中获得广泛的应用.     

有机污染物的生物富集因子与拓扑指数的数学模型

依据价连接性指数(xi)、电性拓扑态指数(ej)及电性距离矢量(mk)构建239种有机污染物生物富集因子(FBC)的6参数QSFR(定量结构-生物富集因子相关性)模型, 不仅相关程度高, 而且所用自变量数少. 该模型的传统相关系数(R2)为0.821, LOO(levae-one-out)交互验证系数(Q2)为0.809, 证明具有良好的稳健性及预测能力. 根据进入该模型的6个参数可知, 影响有机污染物FBC的主要结构基团是: —C—、>C—、—O—、—X、—NH2以及分子的柔韧性、折叠程度等空间因素. 可以认为在生物富集过程中,“诱导契合机理”也发挥一定作用. 对自变量集进行正交变换, 既不影响模型的相关性, 又能降低其自相关性.     

Intercalation of a nonionic surfactant (C10E3) bilayer into a Na-montmorillonite clay

A nonionic surfactant, triethylene glycol mono-n-decyl ether (C(10)E(3)), characterized by its lamellar phase state, was introduced in the interlayer of a Na-montmorillonite clay at several concentrations. The synthesized organoclays were characterized by small-angle X-ray scattering in conjunction with Fourier transform infrared spectroscopy and adsorption isotherms. Experiments showed that a bilayer of C(10)E(3) was intercalated into the interlayer space of the naturally exchanged Na-montmorillonite, resulting in the aggregation of the lyotropic liquid crystal state in the lamellar phase. This behavior strongly differs from previous observations of confinement of nonionic surfactants in clays where the expansion of the interlayer space was limited to two monolayers parallel to the silicate surface and cationic surfactants in clays where the intercalation of organic compounds is introduced into the clay galleries through ion exchange. The confinement of a bilayer of C(10)E(3) nonionic surfactant in clays offers new perspectives for the realization of hybrid nanomaterials, since the synthesized organoclays preserve the electrostatic characteristics of the clays, thus allowing further ion exchange while presenting at the same time a hydrophobic surface and a maximum opening of the interlayer space for the adsorption of neutral organic molecules of important size with functional properties.     

电性拓扑态指数预测PCDFs光解半衰期

以电性拓扑态指数(E-state indices)为参数, 应用偏最小二乘法(PLS)对48种多氯代二苯并呋喃(PCDFs)在云杉(Picea abies)针叶和飞灰表面的光解半衰期(t_1/2)进行模拟分析, 分别获得5变量和4变量定量结构-性质相关(QSPR)模型. 模型交叉验证相关系数(Q_cum²)分别为0.758和0.701, 标准偏差(SD)分别为0.047和0.049, 模型具有较高的预测能力和可靠性. 随着氯原子取代数目的增多, PCDFs与活性氢供体接触的“位阻效应”增大, PCDFs分子中苯环的静电荷密度随之降低, 以致高氯代PCDFs较难发生光解作用.     

有机物对蝴蝶幼虫麻醉活性与结构参数的关系

应用量子化学HF/3-21G从头算法得到了20种有机分子的优势构象,利用HF/3-21G和分子图形学技术获得其电子结构参数和几何结构参数,并将这些参数与有机物对蝴蝶幼虫的麻醉活性相关联.结果表明,有机物麻醉活性与分子的范德华体积、分子最低空轨道能和分子偶极矩之间存在良好的多元线性相关性,成功地建立有机物对蝴蝶幼虫麻醉活性的构效关系式.     

Analysis of Affinity Energy Between Biphenyl Dioxygenase and Polychlorinated Biphenyls Using Molecular Docking

Molecular docking was used to calculate the affinity energy between biphenyl dioxygenases(BphA),including 1ULJ,1WQL,2YFJ,2YFL,2GBX,2XSH,2B4P,3GZX,and 3GZY(selected from the Protein Data Bank)and 209 polychlorinated biphenyl(PCB)congeners.The relationships between the calculated affinity energy and the persistent organic pollutant characteristics(migration,octanol-air partition coefficients,lgKOA;persistence,half-life,lgt1/2;toxicity,half-maximal inhibitory concentration,IgIC50;bioaccumulation,bioconcentration factor,lgBCF)of the PCBs were studied to mderstand the BphA mediated degradation of PCBs.The effect of substituent characteristics on the affinity energy was explored through full factorial experimental design.The affinities of nine kinds of BphA proteins on PCBs ranked as follows:2GBX>2YFJ>2YFL>3GZX>2XSH>3GZY>2E4P>1 WQL>1ULJ.The relationships between the calculated affinity energy and the molecular weight,lgKOA,lgBCF,and lgt1/2 of the PCBs were statistically signiflcant(p<0.01),whereas the relationship with the lgIC50 of PCBs was not statistically significant(p>0.05).PCBs were more difficult to degrade following an increase in the free energy of binding.Correlation analysis showed that the average affinity energy values of PCBs gradually increased as the number of chlorine atoms increased,regardless of the substituent position.The substituents at the ortho-positions interacted mainly through a second-order interaction,whereas those at the para-positions did not participate via a second-order interaction.     

偏最小二乘和量子化学参数预测酯类物质的闪点

基于化合物定量结构与性质的关系,对其中88个酯类化合物进行了B3LYP/6-31G*水平上的结构优化,并在优化结构基础上进行了量子化学结构参数的计算。应用偏最小二乘(PLS)方法对酯类化合物闪点温度这个理化性质与量子化学参数进行了关联。结果表明,分子热力学自由能(ΔG)结合偶极距(μ)可以很好地表达酯类化合物闪点温度与量子化学参数间的定量关系。所建立的QSPR模型具有较强的稳健性和预测能力。     

脂肪醇的生物毒性与结构参数的相关性研究

应用量子化学从头算HF/3-21G方法得到了14种脂肪醇分子的优势构象,利用HF/3-21G法和分子图形学技术获得其电子结构、几何结构参数和连接性指数,并将这些参数与脂肪醇对番茄和红蜘蛛的毒性相关联.结果表明,脂肪醇对番茄的生物毒性与一阶分子连接性指数1X和羟基电荷QOH之间存在良好的二元线性相关性,而脂肪醇对红蜘蛛的生物毒性与一阶分子连接性指数1X和分子最高已占轨道能EH之间存在良好的二元线性相关性,成功地建立脂肪醇对番茄和红蜘蛛毒性的构效关系式.     

Absorption and Fluorescence Emission Spectra of Molecules Containing Azo and/or Oxadiazole Units

The ground state structures of a series of organic molecules containing azo and/or oxadiazole units were obtained by means of density functional theory B3LYP/6-31G(d) method. The first singlet excited state structures were optimized by virtue of singlet-excitation configuration interaction CIS/6-31G(d) method. The absorption and fluorescence emission spectra were then evaluated via the time-dependent density functional theory B3LYP and PBE1PBE methods with 6-311++G(3df,2p) basis set. The calculation results show that compared with those of their parent molecules A-H, B-H, C-H, D-H, the absorption and emission wavelength values of all the derivatives show red shifts. The derivatives containing both the oxadiazole and methoxyl units are good candidates for longer absorption wavelength materials. The effects of azo, oxadiazole, and methoxyl units on the absorption and emission wavelength were discussed.     

Evolution of packing parameters in the structural changes of silica mesoporous crystals: cage-type, 2D cylindrical, bicontinuous diamond and gyroid, and lamellar

Cage-type, two-dimensional (2D) cylindrical hexagonal (C), bicontinuous diamond (D), bicontinuous gyroid (G), and one-dimensional (1D) lamellar (L) structures of silica mesoporous crystals (SMCs) were obtained by using the anionic surfactant N-stearoyl-l-glutamic acid (C(18)GluA) as a template in the presence of the nonionic surfactant C(16)(EO)(10) (Brij-56). The mesostructures were controlled by the organic/inorganic interface curvature change induced by Brij-56. A synthesis-field diagram showed that the mesostructure changed in the sequence cage-type → C → intergrowth of C and D → intergrowth of C and G → D → G → L with increase of the amount of Brij-56. Mixed micelles were formed by the anionic and nonionic surfactants, the packing parameter g of which increased with increasing the addition amount of nonionic surfactant and the reaction temperature. The local g parameter was obtained from electron crystallography reconstruction results by calculating mean curvatures and Gaussian curvatures from the equi-electrostatic potential surface. The intergrowth of C and D and two kinds of intergrowth of C and G are also discussed.     

Influence of temperature and headgroup size on condensed-phase patterns in langmuir monolayers of some oxyethylenated nonionic surfactants

The surface phase behavior in Langmuir monolayers of some oxyethylenated nonionic surfactants of the general formula C16En, with n = 1, 2, 3, and 4, at the air-water interface has been studied by film balance and Brewster angle microscopy (BAM) over a wide range of temperatures. The C16E4 monolayers cannot show any indicative features of phase transition because of strong dipolar as well as hydration-induced repulsive interactions between the bulky headgroups. On the other hand, the monolayers of C16E1, C16E2, and C16E3 show a sharp cusp point followed by a pronounced plateau region in their respective isotherms with subsequent formation of a variety of structures in the two-phase coexistence region between the liquid expanded (LE) and liquid condensed (LC) phases at different temperatures. As usually observed, the domains of C16E1, which bears only one ethylene oxide (EO) unit in the headgroup, are circular at lower temperatures while fractal at higher temperatures. On the other hand, those for C16E2 and C16E3 are initially found to be irregular structures, which attain increasingly compact shape with increasing temperature, and finally become circular when the subphase temperature is 26 and 15 degrees C for C16E2 and C16E3, respectively. It is concluded that a higher degree of dehydration around the headgroup region appreciably reduces the headgroup size, which imparts to the molecules an increase in hydrophobicity, thereby a closer molecular packing. Consequently, the line tension of the interface increases, showing compact structures at higher temperatures. Since C16E1 bears only one EO unit in its headgroup, the dehydration effect cannot appreciably raise its hydrophobicity to overcome the increases in thermal motion and chain flexibility of the molecules. Rather, increases in subphase temperature result in a decrease in the line tension of the interface, giving fractal structures at higher temperatures.     

Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

To promote accuracy of the atom‐bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc‐Zn, Y‐Cd, and Lu‐Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO‐3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy. © 2014 Wiley Periodicals, Inc.