Mode-coupling study on the dynamics of hydrophobic hydration II: Aqueous solutions of benzene and rare gases

The dynamic properties of both the solute and solvent of the aqueous solution of benzene, xenon and neon are calculated by the mode-coupling theory for molecular liquids based on the interaction-site model. The B-coefficients of the reorientational relaxation and the translational diffusion of the solvent are evaluated from their dependence on the concentration of the solute, and the reorientational relaxation time of water within the hydration shell is estimated based on the two-state model. The reorientational relaxation times of water in the bulk and within the hydration shell, that of solute, and the translational diffusion coefficients of solute and solvent, are calculated at 0-30 degrees C. The temperature dependence of these dynamic properties is in qualitative agreement with that of NMR experiment reported by Nakahara et al. (M. Nakahara, C. Wakai, Y. Yoshimoto and N. Matubayasi, J. Phys. Chem., 1996, 100, 1345-1349, ref. 36), although the agreement of the absolute values is not so good. The B-coefficients of the reorientational relaxation times for benzene, xenon and neon solution are correlated with the hydration number and the partial molar volume of the solute. The proportionality with the latter is better than that with the former. These results support the mechanism that the retardation of the mobility of water is caused by the cavity formation of the solute, as previously suggested by us (T. Yamaguchi, T. Matsuoka and S. Koda, J. Chem. Phys., 2004, 120, 7590-7601, ref. 34), rather than the conventional one that the rigid hydration structure formed around the hydrophobic solute reduces the mobility of water.     

Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations

We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics.     

脉冲激光溅射下固液界面生长的碳纳米管及其机理初探

以脉冲激光束直接溅射浸在水中的单质碳样品，发现在固液界面也能产生的碳纳米管，实验还发现碳纳米管的形成与样品的结构有密切的关联：石墨的层状结构越完整，碳纳米管的形成越容易，而且石墨层面相对于激光束的取向也会显著地影响碳的生成。     

显微镜图像分析研究聚丙烯/尼龙1010共混物相结构及其性能

用扫描电子显微镜图像分析研究了聚丙烯/聚酰胺1010共混物及其部分相容体系的相形态结构,计算了表征相结构和尺寸的结构参数,如分散相的平均直径、平均弦长和分散相的质心相关距等.并分别讨论了聚丙烯/聚酰胺1010共混物及其部分相容体系的相形态以及其结构参数与共混物组成的关系.测定了聚合物及其共混物体系的力学性能,讨论了共混物组成与力学性能的关系.聚丙烯/聚酰胺1010共混物的拉伸模量与组成的关系较为复杂,但其部分相容体系的拉伸模量与组成呈线性关系.聚丙烯/聚酰胺1010及其共混物体系的屈服强度与共混物组成均呈线性关系.表征相结构的两相平均弦长比(l-1/-l2)与组成以及共混物体系力学性能与组成的关系,二者相似.同时讨论了体系力学性能随相尺寸等的变化规律.     

理论化学与下世纪“化学学科重组”前瞻

本文展望了理论化学的发展趋势并预言了下个世纪“化学学科的重组”。作者建议了现代化学的定义：化学是研究从原子,分子片,分子,超分子,生物大分子到分子的各种不同尺度和不同程度的聚集态的合成和反应,分离和分析,结构和形态,物理性能和生物活性及其规律和应用的科学． 根据这个定义,从化学的研究对象不同,在２１ 世纪化学分支学科可能发生重组,因此化学可以划分为如下八个层次：１） 原子层次的化学; ２） 分子片层次的化学; ３） 分子层次的化学; ４） 超分子层次的化学; ５）生物与分子层次的化学; ６） 宏观聚集态化学; ７） 介观聚集态化学和８） 复杂分子体系的化学     

Role of electrostatic forces in cluster formation in a dry ionomer

This simulation study investigates the dependence of the structure of dry Nafion-like ionomers on the electrostatic interactions between the components of the molecules. In order to speed equilibration, a procedure was adopted which involved detaching the side chains from the backbone and cutting the backbone into segments, and then reassembling the macromolecule by means of a strong imposed attractive force between the cut ends of the backbone, and between the nonionic ends of the side chains and the midpoints of the backbone segments. Parameters varied in this study include the dielectric constant, the free volume, side chain length, and strength of head group interactions. A series of coarse-grained mesoscale simulations shows the morphology to depend sensitively on the ratio of the strength of the dipole-dipole interactions between the side-chain acidic end groups to the strength of the other electrostatic components of the Hamiltonian. Examples of the two differing morphologies proposed by Gierke and co-workers [J. Polym. Sci., Polym. Phys. Ed. 19, 1687 (1981); Macromolecules 15, 101 (1982); J. Membr. Sci. 13, 307 (1982)] and by Gebel [Fuel Cells 5, 261 (2005); Macromolecules 37, 7772 (2004)] emerge from our simulations.     

坚膜反应对染印法空白片性能的影响

本文研究了在染印法空白片的各种坚膜条件下媒染层的物理机械性能和染印性能,包括媒染层的断裂强度、空白片的膨胀度、染色密度和线格清晰度。铬矾坚膜的效果用媒染层中铬的含量和媒染层经水萃取后所得交联物含量来表示。在此基础上计算出用铬矾坚膜的媒染层的交联密度。为排除空白片中乳剂层的干扰,采用了单独处理媒染层的方法。得到了在本实验中获得空白片最佳清晰度和最佳物理机械性能的条件,并对媒染层中主要物质分子间的相互关系进行了探讨。     

Effects of T-tubules on dielectric spectra of skeletal muscle simulated by boundary element method with two-dimensional models

In order to investigate the origin of large intensity the alpha-relaxation in skeletal muscles observed in dielectric measurements with extracellular electrode methods, effects of the interfacial polarization in the T-tubules on dielectric spectra were evaluated with the boundary-element method using two-dimensional models in which the structure of the T-tubules were represented explicitly. Each model consisted of a circular inclusion surrounded by a thin shell corresponding to the sarcolemma. The T-tubules were represented by simplified two types of invagination of the shell: straight invagination along the radial directions, and branched one. Each of the models was subjected to two kinds of calculations relevant to experiments with the extracellular and the intracellular electrode methods. Electrical interactions between the cells were omitted in the calculations. Both calculations showed that the dielectric spectra of the models contained two relaxation terms. The low-frequency relaxation term assigned to the alpha-relaxation depended on the structure of the T-tubules. Values of the relaxation frequency of the alpha-relaxation obtained from the two types of calculations agreed with each other. At the low-frequency limit, the permittivity obtained from the extracellular-electrode-type calculations varied in proportion to the capacitance obtained from the intracellular-electrode-type ones. These results were consistent with conventional lumped and distributed circuit models for the T-tubules. This confirms that the interfacial polarization in the T-tubules in a single muscle cell is not sufficient to explain the experimental results in which the intensity of the alpha-relaxation in the extracellular-electrode-type experiments exceeded the intensity expected from the results of the intracellular-electrode-type experiments. The high-frequency relaxation term that was assigned to the beta-relaxation was also affected by the T-tubule structure in the calculations relevant to the extracellular-electrode-type experiments.     

Thermodynamic conformational analysis and structural stability of the nicotinic analgesic ABT-594

This work presents a theoretical study of the nicotinic analgesic ABT-594. We describe its neutral (precursor) and protonated (active) forms in vacuum and aqueous solution at the MP2/cc-pVDZ level. A conformational analysis is performed on the two torsional angles describing the orientation of the azetidinyl group and the azetidinylmethoxy moiety. To account for entropic effects, a thermostatistical study of conformational populations at physiological temperature is carried out. In the neutral form, conformer I is found as the most populated in vacuum and solution. Here, the nitrogen of the azetidinyl group is far from the electron pairs of the oxygen and the pyridinic nitrogen. In the protonated form, conformer VIII is the most stable in vacuum and solution. Now, the additional proton on the azetidinyl group is oriented toward the electron lone pairs of oxygen. The structural stability of conformers I and VIII is considered through the atoms in molecules theory. The conformer I, in the neutral forms, is stabilized by an intramolecular hydrogen bond. The preference of conformer VIII in the protonated forms is explained by the higher strength of its intramolecular hydrogen bond over the cation-pi interaction found in conformer I. The effect of the interaction energy with the receptor on the conformational preferences of protonated ABT-594 is simulated. The result is that the population of conformers associated to the rotation of the azetidinyl group increases. So, the molecule can easily adopt the optimal internitrogen separation for interaction with the receptor.     

A Monte Carlo simulation of a knotted linear chain system as an elementary network fragment

We present the results of the Monte Carlo simulations of the dynamics of the linear chain system. The chains were constructed on a simple cubic lattice. The simulations were carried out by means of the classical Metropolis sampling method with the excluded volume effect present. No other interactions were introduced into the system (athermal polymer case). The linear chains in the system were constructed in such a way that there were knots at certain positions. Also, some chains were threaded through the knots forming the topological constraints in the system. The system under consideration underwent a series of micromodifications during the simulation run. Then the trajectory was analysed and the dynamics of the system was described by means of the autocorrelation functions. The short-time dynamics enabled us to investigate whether or not the knotted constraints affect the local dynamics of the chains. Also the long-time dynamics of the system can be useful in the characterizations of the dynamical properties of the fragments of the networks.     

Liesegang pattern formation in kappa-carrageenan gel

We report a new class of the spatial pattern formation process in which the gel plays essential roles. The system studied here is the solution of kappa-carrageenan in which potassium chloride is diffused. The solution transforms into the gel state with the diffusion of potassium chloride. Then the stripe pattern, which is perpendicular to the direction of the diffusion of potassium chloride, appears within the gel. The pattern thus formed in the gel is studied as a function of the concentration of the solution of potassium chloride. We find that the dense region of the stripe pattern consists of the liquid crystalline gel, whereas the dilute region is the amorphous gel. The transition from the amorphous gel to the liquid crystalline gel, hence, occurs in the gel state of kappa-carrageenan. The gel behaves as a pattern-forming substance as well as the supporting medium of the pattern in this system. The period and the thickness of the layers of liquid crystalline gel are analyzed. Both the period and the thickness of the layers are found to depend strongly on the concentration of the solution of potassium chloride.     

阵列凹坑结构分布与水滴黏附性质的关系

以新鲜玫瑰花花瓣正面为模板, 采用模板印刷法制备具有微米级阵列凹坑和纳米级沟壑结构的聚二甲基硅氧烷(PDMS)薄膜, 通过对该薄膜逐级拉伸改变其微观结构的分布; 采用场发射扫描电子显微镜(SEM)和原子力显微镜(AFM)观察了不同拉伸程度下薄膜表面微观结构的变化, 采用高敏感性微电力学天平测试了样品表面微观结构变化过程中水滴的黏附力, 分析了其微观结构分布与水滴黏附性质的关系; 采用接触角测量仪表征不同拉伸条件下薄膜的浸润性. 结果表明, 随着PDMS薄膜被逐次拉伸, 单位面积内的凹坑结构数目减少, 且凹坑逐渐分离, 凹坑的深度逐渐降低, 水滴更容易浸入到凹坑结构中, 因此水滴与薄膜的黏附力急剧增大; 随着薄膜进一步拉伸, 纳米级沟壑结构会随着凹坑的拉伸而不断伸展, 纳米级沟壑结构的面积增加, 纳米沟壑结构诱捕的空气量逐渐上升, 导致水滴与薄膜表面的接触面积降低, 使得水滴与薄膜的黏附力下降; 继续拉伸PDMS薄膜, 纳米级沟壑结构进一步伸展, 水滴逐渐浸入纳米级沟壑结构中, 水滴与薄膜的黏附力缓慢增大, 当水滴完全进入到纳米级沟壑中时, 水滴与薄膜的黏附力达到极大值, 此时继续拉伸PDMS薄膜, 纳米级沟壑结构随着拉伸程度的增加继续伸展, 水滴与薄膜的接触面积稍有减少, 黏附力将有所下降, 直至薄膜被完全破坏. 由此可见, 微米级凹坑结构和纳米级褶皱结构的分布是影响PDMS薄膜对水滴黏附性质的主要因素.     

Coarse-grained polyethylene: Including cross terms in bonded interactions and introducing anisotropy into the model for the orthorhombic crystal

Our previous paper (E.A. Zubova, I.A. Strelnikov, N.K. Balabaev, A.V. Savin, M.A. Mazo, and L.I. Manevich, Polym. Sci., Ser. A 59 (1) (2017)) addressed the simplest coarse-grained model of polyethylene and alkanes. The CH₂ group in this united-atom model is replaced with a bead. In the framework of the model, nonbonded interactions are described by the Lennard-Jones potential (6–12), whereas the potential for bonded interactions accounts for the bonds between beads and for coarse grained angles and dihedral angles but not for the cross terms between them. We found the area of geometrical parameters of the model where all the three known crystalline phases of polyethylene are stable at low temperatures. We parametrized the force field of the model using the dynamic properties of the system, namely, the inelastic neutron scattering spectrum of the orthorhombic phase of polyethylene. However, the simplest model underestimates the value of the elastic modulus along the chains of the crystal by a factor of two. The derived setting angle of the molecules also differs appreciably from the experimental data. Moreover, the acoustic dispersion curves for the modes with the wave vector directed along the chain axis deviate from the experimental data at low frequencies. In the present study, we included the cross terms into the bonded interactions. This made it possible to reproduce the experimental elastic modulus along the chains of the crystal and to decrease the frequency range for the optical skeletal dispersion curve to proper values. As for the beads, we separated force centers for the bonded and nonbonded interactions, which enabled us to reproduce the optical skeletal curve and to bring the anisotropy of interchain interactions in line with the experiment. However, the model fails to reproduce the balance of interactions between the neighboring chains in the crystal. For this, a different form of the potential energy of van der Waals interactions seems to be needed.     

基于随机扩散理论的气相色谱分离模拟

色谱分离过程中的粒子扩散问题是色谱动力学研究的基础,深入理解粒子的扩散行为对优化分离操作条件、提升色谱性能和开发新型色谱柱尤为关键.现有的模拟方法多集中于局部过程的热力学研究,而整体的扩散分离过程报道并不多见.为此,该文基于微尺度受限空间内随机扩散的方法,通过动态追踪粒子的运动轨迹,实现粒子在气相色谱开管柱内的扩散全过...     

Predicting the infrared transition intensities in the Ar-HF complex: the key role of the dipole moment surface accuracy

The method proposed earlier for the generation of the full-dimensional energy surface for van der Waals complexes [P. Jankowski, J. Chem. Phys. 121, 1655 (2004)] is used to obtain a fulldimensional dipole moment surface for the atom-diatom complex in calculations based on the coupled-cluster with single, double, and noniterative triple excitation approach and the aug-cc-pVQZ basis sets. This surface has been employed to calculate transition intensities of the infrared spectra of Ar-HF. Special attention has been paid to study the problem of relative intensities of the different bands which have not been properly predicted within the long-range models of the dipole moment [A. E. Thornley and J. M. Hutson, J. Chem. Phys. 101, 5578 (1994)]. The intensities calculated with the present dipole moment surface agree very well with the experimental data, which indicate that the short-range interactions significantly affect the dipole moment surface and the calculated intensities. To investigate the role of the accuracy of the dipole moment surface on infrared transition intensities in atom-diatom complexes, four models of increasing complexity are studied. Their performance is shown to strongly depend on the region of the interaction energy surface probed by the initial and final states of the individual transitions.     

Precise construction on the structure of zeolite microcapsules

In this paper, the precise construction on the structure of silicalite-1 microcapsules (S1) was specifically described. The interior carbon modifications and the outside mesoporous functionalizations were successfully conducted and each sample was characterized in detail. It was found that the carbon networks could be formed inside the zeolite microcapsules via the pretreatment of sugar injections. The uniformity of the distinct microcapsule could be regulated by adjusting the sugar concentrations. With the encapsulated Pt species inside the MSSs, the nano-particles could be dispersed well within the carbon network. On the other hand, during the fabrication of the mesoporous materials outside the microcapsules, the template and the acidity of the system could play an important role in determining the morphology of S1. Besides, the PDDA modification on the shell of S1 could help the combination of the meso-layer and the shell of S1 at nano-scale. The thickness of the outside mesopore could be modulated through the controlling of the silica content.     

Simple quantum-mechanical model of the elementary event of organic nucleophilic substitution reactions in the condensed phase

A semiempirical model is proposed for the elementary event of nucleophilic S_N2 substitution in alkyl halides. An analysis was made of the factors which determine the activation energies of the processes, i.e., the energy of approach of the reagents, the energy of extension of the chemical bonds, the energy of reorganization of the medium, and the equilibrium energy of the elementary event. The contributions from the first three energy parameters are commensurable, and the energy of approach has a predominant role. The role of the equilibrium energy, determined by the solvation energy of the reacting ions and the energy of the formed and broken chemical bonds, involves the creation of thermally neutral conditions for the reactions. The effective potential surfaces of the repulsive interaction between the halide ions and the methyl halides were constructed in terms of the model. The tunneling factor and the kinetic isotope effect for the lightest reacting particle in the reaction series (the fluoride ion) were also determined.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 21, No. 4, pp. 417–424, July–August, 1985.     

Intrinsic optical bistability of thin films of linear molecular aggregates: the two-exciton approximation

We generalize our recent work on the optical bistability of thin films of molecular aggregates [J. A. Klugkist et al., J. Chem. Phys. 127, 164705 (2007)] by accounting for the optical transitions from the one-exciton manifold to the two-exciton manifold as well as the exciton-exciton annihilation of the two-exciton states via a high-lying molecular vibronic term. We also include the relaxation from the vibronic level back to both the one-exciton manifold and the ground state. By selecting the dominant optical transitions between the ground state, the one-exciton manifold, and the two-exciton manifold, we reduce the problem to four levels, enabling us to describe the nonlinear optical response of the film. The one- and two-exciton states are obtained by diagonalizing a Frenkel Hamiltonian with an uncorrelated on-site (diagonal) disorder. The optical dynamics is described by means of the density matrix equations coupled to the electromagnetic field in the film. We show that the one- to two-exciton transitions followed by a fast exciton-exciton annihilation promote the occurrence of bistability and reduce the switching intensity. We provide estimates of pertinent parameters for actual materials and conclude that the effect can be realized.     

关于热力学自发过程及其判据的讨论

文章指出现有各种自发过程的判据都是在指定的约束条件下才能应用,缺乏普适性是自发过程定义多样化的引发原因。在无约束条件下将热力学第一定律代入总熵判据得出并分析讨论了总熵判据的另一种形式,结合自发过程的特点总结出了热力学变化过程中能量变化的本质,给出了自发过程的通用定义。进一步指出原总熵判据只能分辨可逆与不可逆,不能分辨自发与非自发。文章给出的总熵判据的另一种形式——封闭系统任意过程的做功能力判据具有分辨自发与非自发的能力。通过理论研讨和实际应用表明,做功能力判据与总熵判据完全等价,在相应约束条件下可还原为当前热力学中各类方向判据。填补了常见的变温过程和变压过程在以前的教科书中无自发和非自发判据的空白。以前教科书中由于自发过程定义和解释的混乱而出现的一些疑难问题,在通用定义和做功能力判据面前都能得到满意的解答。