氧分子在Pt低指数面上的吸附和解离

应用原子和表面簇合物相互作用的5参数Morse势方法(简称5-MP)构造推广的LEPS势对O₂-Pt分子体系进行了系统的研究, 获得了O₂分子在Pt的2个低指数面(111)和(110)重构面上的吸附几何、结合能和振动频率等临界点性质; 计算结果显示O₂在Pt(111)面上难解离, 且存在超氧化吸附态, 同时, 应用表面分子解离限和晶面解离距的概念分析了(111)面上的解离机理; 并根据分子指纹性质, 将O₂在Pt(110)缺行重构面上出现的振动频率860, 930, 1250 cm^－1进行了合理的指派.     

O2和CN在铜活化闪锌矿(110)表面的吸附

采用基于密度泛函理论(DFT)的平面波赝势法模拟了O₂和CN分子在铜活化闪锌矿(110)表面的吸附. 结果表明: 铜活化后闪锌矿表面的铜原子3d轨道处于费米能级附近, 增强了闪锌矿表面的活性. 未活化闪锌矿表面不能吸附O₂, 活化后闪锌矿表面的铜原子和硫原子提供电子填入氧的反键π_2p^*轨道从而形成吸附键. CN分子吸附模拟表明, 铜活化增强了CN分子与闪锌矿表面的吸附作用. Cu原子d轨道与C原子反键p轨道作用形成反馈π键, 同时C原子s轨道与Cu原子sp轨道作用形成共价键; CN分子中N原子与闪锌矿表面S原子发生相互作用.     

卤素及卤素离子的电子结构

卤素离子的质子亲和势是随卤素原子在元素周期表中的位置从上到下按F-,Cl-,Br-,I-依次降低.但人们熟知的卤素原子电负性却按F,Cl,Br,I依次减小,或者说卤素原子的电正性随上述顺序依次增大,对应于卤原子价轨道np的能量按F,Cl,Br,I依次升高;这个结果意味着卤素阴离子的电子给予能力,或者说它们的质子亲和势似乎应该随F-,Cl-,Br-,I-依次增大.这样就出现了两个完全相反的质子亲和势顺序.为了对这一结果作出解释,我们分别采用Kohn-Sham密度泛函理论(在SAOP/TZ2P和OLYP/TZ2P计算水平上),以及采用从头计算理论(在HF/TZ2P水平)中的分子轨道模型对卤素离子及卤素原子进行了详尽的理论分析.同时我们对在Hartree-Fock理论框架下轨道能量和质子亲和势的变化趋势之间存在的内在矛盾进行了阐述.研究表明质子亲和势按F-,Cl-,Br-,I-依次降低的原因是由于当卤素原子X得到一个电子成为卤素阴离子X-后,价轨道np的能量将会升高,从而表现出异常的不稳定性.更关键的是,这种由于库仑排斥造成的卤素离子价轨道的不稳定性对于本身半径比较小的氟原子尤为突出,但随着卤素的半径增大,这种不稳定效应逐渐减弱.结果较强的HOMO(F-)-LUMO(H+)轨道相互作用导致F-的质子亲和势大于其他体积较大的卤素离子.以上的定性分子轨道分析表明考虑净电荷对轨道能量的影响是十分重要的.这不仅清楚地解释了采用Kohn-Sham密度泛函理论可以得到正确的质子亲和势变化趋势,即F-Cl-Br-I-,而且还能解释为何在从头计算的Hartree-Fock分子轨道理论框架下,虽然X-的价轨道np能量随F-,Cl-,Br-,I-递减,似乎应该得到不正确的质子亲和势变化趋势,但实际上得到质子亲和势顺序仍然是正确的.之所以所有的分子轨道模型下都有同样的HOMO-LUMO相互作用能及质子亲和势顺序,其原因是电荷效应,即在HF,OLYP和SAOP计算中,卤素原子与卤素离子的价轨道能量差都是升高的.通过这些理论分析得到的结论有助于理解诸如亲核取代反应(SN2)以及碱催化的消去反应(E2)等基本有机化学反应的微观机理.     

基态XO~（n＋）（X=Ru,Rh,Pd;n=0,1）的势能函数和第一垂直电离势

运用原子分子反应静力学原理推导出XOn+(X=Ru,Rh,Pd;n=0,1)的基态电子状态及离解极限.运用密度泛函的B3P86方法和LANL2DZ赝势基组及aug-cc-pVTZ全电子基组,对XOn+X=Ru,Rh,Pd;n=0,1)体系进行计算,获得了这些分子及其离子基态的Murrell-Sorbie解析势能函数.同时计算了XOn+(X=Ru,Rh,Pd;n=0,1)的光谱数据,计算了XO(X=Ru,Rh,Pd)中性分子的第一垂直电离势.     

甲硫醇在Cu(111)表面的解离吸附: 密度泛函理论研究

采用基于密度泛函理论的第一性原理方法和平板模型研究了CH₃SH分子在Cu(111)表面的吸附反应.系统地计算了S原子在不同位置以不同方式吸附的一系列构型, 第一次得到未解离的CH₃SH分子在Cu(111)表面顶位上的稳定吸附构型,该构型吸附属于弱的化学吸附, 吸附能为0.39 eV. 计算同时发现在热力学上解离结构比未解离结构更加稳定. 解离的CH₃S吸附在桥位和中空位之间, 吸附能为0.75-0.77 eV. 计算分析了未解离吸附到解离吸附的两条反应路径, 最小能量路径的能垒为0.57 eV. 计算结果还表明S―H键断裂后的H原子并不是以H₂分子的形式从表面解吸附而是以与表面成键的形式存在. 通过比较S原子在独立的CH₃SH分子和吸附状态下的局域态密度, 发现S―H键断裂后S原子和表面的键合强于未断裂时S原子和表面的键合.     

超支化聚合反应的多尺度模拟

超支化聚合物具有与树枝状大分子相似的物理和化学性质,其具有合成简单、分子量分布宽等突出特点,超支化聚合物分子的结构形成取决于聚合反应过程,本文介绍了超支化聚合反应模拟研究的最新进展.首先介绍了八位置键涨落粗粒化格子模型在超支化聚合反应模拟中的应用,该方法考虑了聚合物分子空间位阻效应、分子内成环和反应点活性等影响因素,从而可以模拟不同类型的超支化聚合反应;为了定量描述单体和聚合物分子结构,研究者进一步发展了杂化多尺度超支化聚合反应模拟方法,该方法通过玻尔兹曼反演迭代方法获取单体和聚合物特异性粗粒化力场,然后通过粗粒化分子动力学方法结合反应性Monte Carlo方法对特异性超支化聚合反应进行定量模拟.多尺度聚合反应模拟不仅可以精确计算超支化聚合物分子量、多分散性指数和支化度等一般性聚合物参数,还可以获取分子成环率、超支化大分子构象等重要分子结构信息,在超支化聚合反应基础研究与预测方面具有重要应用价值.     

磷脂微滴囊泡化的介观模拟

发展了一种非显示溶剂的粗粒化三粒子磷脂模型,该模型明确反映磷脂分子的双尾结构．模型分别采用变形的MIE作用势和Harmonic作用势描述分子间非成键和分子内成键相互作用,粗粒化力场参数通过拟合DPPC双分子层的结构和力学性质获得．该粗粒化模型成功重现了磷脂分子从随机初始态到双分子层和从盘状结构到囊泡的形成过程．应用该模型系统研究了球形和柱形磷脂微滴囊泡化的过程,结果表明此模型能有效地模拟介观尺度下复杂磷脂囊泡的形成及演化．     

考虑相关能效应的过渡态计算方法

提出了一种在X_a方法基础上,同时包含电子相关效应和考虑电子自相互作用的过渡态计算方法.由此计算的一系列原子电离势的结果表明,相关能对电离势的计算结果有很大影响,其数值为—0.41eV～0.94eV.引入相关能效应使计算结果明显趋于合理.此计算模型兼有简便和合理的特点,且能适用于分子体系的计算.     

基于遗传算法的Caco-2细胞穿透系数的研究

采用遗传算法研究了一系列药物分子的Caco-2细胞表观穿透系数(lgP_eff)和分子结构之间的关系. 基于51个化合物构成的训练集, 计算得到了一组效果较好的定量构效关系(QSAR)模型. 这些模型不仅具有较好的回归能力, 还能对预测集中的分子进行较好的预测. 在计算得到的精华种群中, 共有4个分子参数具有较高的出现频率, 它们分别是lgD(表观酯水分配系数)、r_gyr(回旋半径)、Shadow-Xlength(分子在X维上的投影长度)以及N_HBD(氢键给体数目).     

用平均场近似研究液晶分子结构与清亮点的关系

液晶的平均场理论假设每个液晶分子都是处在其它周围所有分子的平均作用势场中, 而不考虑该分子与周围各个分子之间的单独关联, 一个分子所感受到的分子场就是所有其它分子给予这个分子的作用场对位置和对取向的平均值. 当周围分子不是完全有序排列时, 其混乱程度可以用序参量S表示(S≤1), 中央一个分子受的势能为－Sg(θ). 其中g(θ)是在排列整齐的平均场中该分子的势能函数的负值. 在此基础上, 可以解一个关于序参量和温度的积分方程, 求出清亮点. 本文采用Gay-Berne势模拟液晶分子的双体势, 用分子力学UFF方法优化液晶分子(二环辛烷和硼笼的衍生物)的单体和双体的构型和能量, 从而获得Gay-Berne势的参数, 得到液晶的清亮点. 计算结果与实验基本一致.     

Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling char-acteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlationfunction curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature T_g=120±10 K, which is in good agreement with experimental results 110±1 K.     

用流动电位法表征纳滤膜的结构及性能

利用测量流动电位的方法考察了纳滤膜的表面电学性能对纳滤膜的截留性能的影响.首先,采用不同功能层材料制备了复合纳滤(NF)膜,考察功能层的交联时间、单体结构等对表面电性能的影响,研究纳滤膜对不同无机盐的选择截留性能与表面电性能的关系.通过流动电位法测定纳滤膜的表面电学参数,如流动电位(ΔE)、zeta电位(ζ)和表面电荷密度(σd).实验表明,这些电学参数的变化与功能层交联时间和纳滤膜截留率的变化一致,在交联时间为45 s时,3种电学参数的绝对值均最大,而纳滤膜对无机盐的截留率也最大.复合纳滤膜zeta电位的绝对值(|ζ|)按照Na2SO4>MgSO4>MgCl2变化,同截留率的变化相同.带侧基单体交联后得到的纳滤膜的表面电性能参数的绝对值小于不带侧基单体的.因此,流动电位法可用于研究复合纳滤膜的截留机理和功能层结构.     

An anisotropic coarse‐grained model based on Gay–Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model

In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay–Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay–Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness (), area per lipid ( ) and volume per lipid ( ). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model. © 2015 Wiley Periodicals, Inc.     

Substitution effects in <Emphasis Type="Italic">N</Emphasis>-pyrazole and <Emphasis Type="Italic">N</Emphasis>-imidazole derivatives along the periodic table

A theoretical study of the monosubstitution effects of all the atoms of the second and third row of the periodic table on the pyrazole and imidazole rings has been carried out by means of B3LYP/6-31+G(d,p) DFT calculations. The geometric and electronic properties, calculated using the atoms in molecules methodology, electrostatic potential, and frontier orbitals have been analyzed. Some of the results have been rationalized based on the electronegativity of the substituents. In addition, the different parameters obtained have been compared with aromaticity indexes (HOMA and NICS). A comparison with the results obtained for the corresponding N-pyrrole derivatives has been carried out.     

Molecular dynamics simulation study on the phase behavior of the Gay-Berne model with a terminal dipole and a flexible tail

To study the effect of the alkyl tail and the terminal dipole on the stability of the liquid crystalline phase of mesogens, we have carried out molecular dynamics simulations for 1CB(4-methyl-4'-cyanobiphenyl) and 5CB(4-n-pentyl-4'-cyanobiphenyl) by using a coarse-grained model. In the coarse-grained model, a 5CB molecule is divided into the rigid part of 1CB moiety, which is represented by an ellipsoid, and the remaining flexible part which is represented by a chain of united atoms. The nonbonded potential between coarse-grained segments is represented by the generalized Gay-Berne (GB) potential and the potential parameters are determined by directly comparing the GB potential with the atomistic potentials averaged over the rotation of the mesogen around its axis. In addition, a dipole moment is placed at one end of the ellipsoid opposite to the flexible tail. The ordered state obtained in the polar 5CB model was assigned as the nematic phase, and the experimental static and dynamical properties were reproduced well by using this coarse-grained model. Both the dipole-dipole interactions and the thermal fluctuation of the flexible tail increase the positional disorder in the director direction, and stabilize the nematic phase. Thus, the nematic phase in the polar 5CB is induced by a cooperative effect of the flexible tail and the terminal dipole. It is noted that a local bilayer structure with head-to-head association is formed in the nematic phase, as experimentally observed by x-ray diffraction measurements.     

RF ion carpets: The electric field,the effective potential,operational parameters and an analysis of stability

Analytical solutions for the electric field of radiofrequency (RF) carpets are presented. The formulas have been applied to calculate the effective repulsive potential with the Dehmelt model. The resulting formulas have been used to investigate operational conditions such as the average distance of ions from the carpet in the presence of an attractive static electric field.The equations of motion of ions in the electric fields have been integrated using the developed formulas to determine the parameter space for carpet operation. The operational parameters have been reduced to three dimensionless parameters and a stability analysis is carried out in these terms.     

About using the approximate fields to calculate the electrostatic potential distribution of membrane channels

By the example of gramicidine channel, a comparative analysis of different approximate representations (heavy atoms, polar protons, near-by atoms) of AMBER force field has been carried out to calculate the electrostatic potential distribution of ionic channels in biological membranes. The results obtained are compared with the potential computed in a full-atom representation. The use of approximate representations is shown to lead to estimated errors of the potential.     

Electric properties of molecules confined by the spherical harmonic potential

The harmonic oscillator potential is very often used in quantum chemical studies of electric properties to model the effect of spatial confinement. In the vast majority of works, the harmonic potential of cylindrical symmetry was applied. Thus far, its spherical counterpart was used mainly to describe properties of spatially restricted atomic systems. Therefore, our main goal was to study the molecular electric properties in the presence of the spherically symmetric harmonic oscillator potential and to characterize the impact of the relative position of the considered molecules and spherical confinement on these properties. Moreover, we analyzed how the topology of confining environment affects the dipole moment and (hyper)polarizability, by comparing the results obtained in the spherical and cylindrical harmonic potential. Based on the conducted research, it was found that the position of the molecules relative to the spherical confinement strongly influences their electric properties. The observed trends of changes in the electric properties, caused by increasing the confinement strength, vary significantly. Moreover, it was shown that in the vast majority of cases, significant differences in the values of electric properties, obtained in the cylindrical and spherical confinement of a given strength, occur.     

Improved methods for semiempirical solvation models

We present improved algorithms for the SMx (x = 1, 1a, 2, 3) solvation models presented previously [see the overview in C. J. Cramer and D. G. Truhlar, J. Comp.-Aided Mol. Design, 6 , 629 (1992)]. These models estimate the free energy of solvation by augmenting a semiempirical Hartree-Fock calculation on the solute with the generalized Born (GB) model for electric polarization of the solvent and a surface tension term based on solvent-accessible surface area. This article presents three improvements in the algorithms used to carry out such calculations, namely (1) an analytical accessible surface area algorithm, (2) a more efficient radial integration scheme for the dielectric screening computation in the GB model, and (3) a damping algorithm for updating the GB contribution to the Fock update during the iterations to achieve a self-consistent field. Improvements (1) and (2) decrease the computer time, and improvement (3) leads to more stable convergence. Improvement (2) removes a small systematic numerical error that was explicitly absorbed into the parameterization in the SMx models. Therefore, we have adjusted the parameters for one of the previous models to yield essentially identical performance as was obtained originally while simultaneously taking advantage of improvement (2). The resulting model is called SM2.1. The fact that we obtain similar results after removing the systematic quadrature bias attests to the robustness of the original parameterization. © 1995 by John Wiley & Sons, Inc.     

Streaming potential across cation-exchange membranes in methanol-water electrolyte solutions

Streaming potential measurements across charged membranes separating two equal solutions have been carried out. Two cation-exchange membranes with different cross-linked and swelling properties (Ionics and Nafion membranes) and methanol-water electrolyte solutions of KCl have been used in the experiments. The obtained results show that the streaming potential is higher for the Ionics membrane and that the values depend on the methanol content of the solutions. A different behavior is found in the dependence of the streaming potential on the methanol percentage for each membrane. The study of the relaxation times in the decay of electrokinetic steady states of streaming potential has been carried out from the time dependence of the streaming potential when the pressure difference through the membrane is suppressed. The results show the existence of two different parts or partial relaxations, mechanical and electric. A different behavior of the mechanical relaxation time with the methanol percentage has been found for the two membranes, but any significant difference between their electric relaxation times. These differences have been explained in terms of the different degree of swelling of the membranes used.