The reaction force. A scalar property to characterize reaction mechanisms

The reaction force is a global property of a chemical reaction that arises when applying the Hellmann–Feynmann theorem to the potential energy surface that links reactants, products and transition states. In the present work, the reaction force is defined rigorously from the cartesian components coming out from all forces exerted over each atom of a molecular system during the chemical reaction; it is demonstrated that the reaction force is a scalar property. An erratum to this article can be found at     

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Energetic analyses of chair and boat conformations of maleimide substituted cyclohexane derivatives

An analysis of the conformational preferences of two maleimide substituted cyclohexane derivatives proposed as scaffolds for HIV-1 fusion inhibitors is presented. Hybrid Low Mode-Monte Carlo (1:1) conformational searches using seven different force fields were performed in combination with the GBSA(water) solvent model. Low energy structures identified in this way were subjected to geometry optimization on the B3LYP/6-31G** surface. Solvent effects were included in the quantum calculation using the self-consistent reaction field model for water. Quantum results indicate that the 1,3,5-maleimide functionalized 1,3,5-methyl cyclohexane is more stable in the boat conformation, whereas 1,3,5-maleimide functionalized cyclohexane adopts the expected chair conformation with equatorial arms. None of the force fields studied was able to predict the unexpected preference for the boat conformation of 1,3,5-maleimide functionalized 1,3,5-methyl cyclohexane. Comparison of low energy and experimental structures was also performed.     

The mechanism of double proton transfer in dimers of uracil and 2-thiouracil--the reaction force perspective

The intermolecular double proton transfer in dimers of uracil and 2-thiouracil is studied through density functional theory calculations. The reaction force framework provides the basis for characterizing the mechanism that in all cases has been associated to a dynamic balance between polarization and charge transfer effects. It has been found that the barriers for proton transfer depend upon the nature of the acceptor atoms and its position within the seminal monomer. Actually, the change in the nature of the hydrogen bonds connecting the two monomers along the reaction coordinate may favor or disfavor the double-proton transfer.     

醛酮类化合物的分子力场参数推导及热力学性质计算

针对醛酮类分子, 基于第一原理的量子化学计算结果开发了准确、可迁移的全原子力场. 利用所得到的力场, 采用分子动力学和蒙特卡罗方法对醛酮类分子的气相分子结构、振动频率、构象能和凝聚相液体性质(密度和蒸发焓), 以及流体的多种热力学性质包括气液相平衡和临界性质, 与涨落相关的等压热容, 传递性质如剪切粘度等进行了计算和预测. 计算结果表明, 该力场可准确地反映气相分子的结构、振动频率、构象能和凝聚相液体密度和蒸发焓等性质, 并准确地预测一系列醛酮类分子的多种热力学性质. 所开发的醛酮类分子力场函数形式简单, 并具有良好的可迁移性和准确性, 在应用范围和计算精度上都有明显的改善和提高.     

鞘氨醇与DPPC, DPPE单层膜的热力学特性及形态观察

鞘氨醇(sphingosine)是生物体内合成鞘脂的母体化合物, 是生物膜中的重要组分之一. 通过分析表面压力和平均分子面积(π-A)等温线数据分别研究了鞘氨醇与二棕榈酰基磷脂酰胆碱(DPPC)和二棕榈酰基磷脂酰乙醇胺(DPPE)二元组分单层膜的热力学特性, 并在恒定膜压下制备不同摩尔比例的混合脂膜用原子力显微镜进行观测. 实验结果表明: (1)鞘氨醇与DPPC组成的系统中, XD-Sph＝0.2, 0.4, 0.6时, 过量分子面积与过量吉布斯自由能在所研究的表面压力下表现为负值, 而当XD-Sph＝0.8时, 表现为正值; (2)鞘氨醇与DPPE组成的系统中, 当表面压力 π＜25 mN•m－1时, 过量分子面积与过量吉布斯自由能在所研究的组分比例下表现为负值, 当π≥25 mN•m－1时为正值. 混合单层膜的分子面积与表面吉布斯自由能决定了分子间的相互作用, 当为负值时分子间相互作用表现为吸引力, 出现凝聚现象; 为正值时分子间相互作用表现为排斥力, 促使单层膜出现相分离现象. 过量吉布斯自由能值越小, 单层膜的热稳定性越高. 弹性系数曲线分析和AFM图片观测进一步验证了理论分析的结果.     

Sol–gel synthesis,preparation and characterization of photoactive TIO<Subscript>2</Subscript> with ultrasound treatment

Titania was prepared by the sol–gel method from titanium isopropoxide with ultrasound influence (USI) by different pH (acetic acid (AA) or diethyl amine (DEA). Samples were represented in powder and films forms. The TiO₂ was characterized by X-ray diffraction (XRD), FTIR. XRD shows that TiO₂ prepared with diethyl amine has only the anatase phase, however the samples prepared with acetic acid–anatase and rutile phases both could be detected. Ultrasound influence increases the anatase content in comparison with its missing. Photo electromotive force (Photo EMF) datas of TiO₂ films were received in a three-electrode wet cell. It was found that the photo activity depended on the conditions of synthesis crystalline phases. Photo EMF for the TiO₂ films on the nickel electrode is 1.5 mV (TiO₂ with acetic acid conditions), 6.8 mV (TiO₂ with diethyl amine conditions) 8.0 mV (TiO₂ with acetic acid + USI conditions), 22.0 mV (TiO₂ with diethyl amine +USI conditions).     

牛血清白蛋白与十二烷基硫酸钠作用的机理

利用电动势法得到了牛血清白蛋白(BSA)与十二烷基硫酸钠(SDS)相互作用的结合等温线. 通过四阶导数紫外光谱法和荧光光谱法研究了相互作用过程中芳香族氨基酸残基微环境极性的变化. 通过研究发现, 随着SDS浓度的逐渐增大, SDS在BSA上的平均结合数(v)逐渐增大, 色氨酸(Trp)残基所处微环境的极性在减弱后保持基本不变, 酪氨酸残基所处微环境的极性在明显增强后稍有减弱, 苯丙氨酸残基所处微环境的极性略有增强. 结果表明, 当v由0增大到14时, SDS主要结合在BSA的Trp-213附近并逐渐形成聚集体, 从而诱导BSA由结构域ⅡA 开始逐渐展开. 此后, SDS呈正协同作用的特点与BSA 结合, v急剧增大. 当v约为302 时, SDS在BSA上的结合基本达到饱和, BSA的构象趋于稳定.     

温敏性微凝胶的研究技术

温敏性微凝胶因具有尺寸小、对温度的变化响应速度快、渗透性好等优点,所以在许多领域显示出良好的应用前景.温敏性微凝胶的应用性能取决于由其结构所决定的物理化学性能.为了深入了解温敏性微凝胶的结构与性能关系,研究人员利用不同技术手段进行了广泛研究.本文主要综述了显微技术、示差扫描量热技术、光散射技术、中子散射技术、核磁共振及荧光光谱等在温敏性微凝胶结构与性能研究中的应用、主要研究结果,并对微凝胶未来的研究方向提出了一些建议.