苯与铂化学吸附作用及其溶剂效应的量子化学研究

采用Gaussian98程序密度泛函方法全优化计算了考虑水溶剂效应下苯与铂化学吸附作用的位能曲线,得到的位能曲线呈单调下降,苯与铂的吸附是自发过程.计算得到无水和有水溶剂作用时的吸附作用能分别为-149.6535和-202.1635kJ/mol;有水溶剂作用时吸附作用能被降低,展示出明显的水溶剂效应.计算还发现,铂可在苯环上发生吸附转移,在无水和有水溶剂效应下,铂转移的活化能分别为61.2537和70.8356kJ/mol.     

双背景法扣除溶剂水峰及蛋白质热变性的研究

研究蛋白质水溶液的红外光谱(IR)谱时,由于溶剂水的强吸收与蛋白质的吸收峰会发生严重重叠,极大地干扰对蛋白质吸收峰的识别、定性、定量和结构分析.尝试利用杂化光谱法扣除溶剂水峰.采用双背景方法,用空白ATR晶体(背景样品1)与ATR水层(背景样品2)合成了单光束杂化背景谱,通过控制对背景样品1和背景样品2的扫描次数,合成...     

溶剂化效应对阴离子型天冬氨酸在HA (110)表面吸附行为影响的密度泛函理论研究

本工作用密度泛函理论研究了溶剂化效应对阴离子型天冬氨酸(Aspartic acid, ASP)在羟基磷灰石(110)表面[HA (110)]表面的吸附影响.通过分析相互作用能,态密度,布居电荷,差分电荷密度发现阴离子型天冬氨酸在真空条件下(Vacuum)与HA (110)表面主要形成"monodenate" Ca-O和"bridge bidenate" O-Ca-O相互作用,在隐形溶剂水分子(COSMO Water, CW)中也存在上述两种相互作用;在水环境条件下(Water Environment, WE),主要在天冬氨酸的羧基,水分子和HA表面的PO_4之间形成"water-bridge"氢键;在水层条件下(Water Layer, WL),主要形成"bridge bidenate" O-Ca-O相互作用,"water-bridge"氢键以及天冬氨酸中氨基与水分子形成的氢键.而且,研究发现ASP-HA (110)-Vacuum模型中吸附能最大,其次是ASP-HA (110)-WL模型,然后是ASP-HA (110)-CW模型,吸附能最小的模型是ASP-HA (110)-WE.研究结果表明在隐形溶剂水分子条件下, ASP在HA (110)表面吸附相对于真空条件下有所减小.当ASP中羧基在被水分子包围的水环境条件下,由于水分子阻碍了Ca-O静电相互作用,所以吸附达到最低.在水层条件下, HA (110)表面有一层水分子,但是未完全阻挡ASP中羧基时,羧基仍然可以与HA (110)表面的Ca原子形成Ca-O相互作用,此时吸附相对于水环境大大增大,但对于真空条件仍然有所减小.研究结果有望为氨基酸在不同溶剂中的应用提供有价值的理论指导.     

Cl-在α-Al2O3表面吸附的驰豫方式和溶剂化模型选择

采用基于密度泛函理论的第一性原理方法,研究了模型弛豫方式和隐式溶剂化模型的使用对α-Al₂O₃(0001)表面初始结构和Cl~-在表面吸附行为的影响.结果表明,在VASPsol方法模拟的水溶液环境下,全弛豫的α-Al₂O₃(0001)模型最上侧两个原子层的层间距变化量分别为-66.0%和+7.7%,更接近于实验值的-51%、+16%. Cl~-在液相表面上有着更低的吸附能,更容易与表面发生相互作用.相对于全弛豫的方法,固定底层6层原子的方式对α-Al₂O₃(0001)的表面结构、Cl~-在表面的吸附能、吸附距离以及表面原子bader电荷的变化量均造成了一定的影响.此工作将为α-Al₂O₃(0001)表面的点蚀研究提供可参照的前期结果和部分参数设置依据.     

基于溶剂化效应的BDE-15分子振动光谱增强特征振动研究

利用密度泛函与自洽反应场理论在B3LYP/6-31+G(d)水平下分别计算气态及24种不同极性溶剂中4,4’-二溴二苯醚(4,4’-dibrominated diphenyl ethers, BDE-15)的分子振动光谱(红外光谱、拉曼光谱),以气态分子振动光谱为基准,筛选出对溶剂极性敏感的特征振动作为指标构建溶剂对BDE-15振动光谱溶剂化效应指标体系,探究溶剂对BDE-15分子振动频率、红外/拉曼峰强溶剂化效应及综合效应,并寻求显著增强BDE-15分子特征振动频移/强度的溶剂。研究表明：从分子振动频率角度,溶剂极性敏感的(频移>1 cm-1)分子特征振动均为伸缩振和面外弯曲振,但24种溶剂对BDE-15分子振动频率溶剂化效应并不显著;从分子振动峰强角度,24种溶剂对BDE-15分子振动光谱峰强的增强效应主要发生在红外光谱的中低频区及拉曼光谱的高频区,其中起显著增强(红外/拉曼效应指标值分别大于6与5)的溶剂为醇类、乙腈、二甲亚砜、硝基苯;不同极性溶剂对BDE-15拉曼峰强溶剂化效应及综合效应指标值均表现出随溶剂介电常数增长由线性到对数的增长趋势,而红外峰强只保留低介电常数溶剂时的线性关系。利用上述BDE-15分子振动光谱峰强增强方法对BDE-153,BDE-154和BDE-209进行验证,醇类、乙腈、二甲亚砜、硝基苯对三者的振动光谱红外/拉曼峰强的效应指标值分别大于6与5,且最大峰强增倍数皆大于33,说明所建BDE-15分子振动光谱增强特征振动方法有助于进一步开展基于分子振动光谱的PBDEs同系物间辨识研究。     

半胱胺单分子膜结构的表面增强拉曼散射研究(英文)

在金属电极表面所形成的有机分子的单分子膜或薄膜对于基础研究和实际应用都有着极其重要的意义。以化学吸附形式在金电极表面所形成的半胱胺单分子膜,常常用于蛋白质等生物大分子在金属表面进行吸附的连接层,以避免这些生物大分子在金属表面直接吸附而造成的变性、失活现象的发生。本文报道了我们采用表面增强拉曼散射光谱方法研究在金电极表面吸附的半胱胺单分子膜的结构特征。研究结果表明,在金电极表面所形成的半胱胺单分子膜中,半胱胺分子主要的构型为扭转构型。在与金表面的相互作用中,由于除巯基的结合作用以外,还存在半胱胺分子中端基氨基和金表面较强的亲和性,使得以扭转构型吸附在金表面的半胱胺单分子膜相当稳定。这是金电极表面的半胱胺单分子膜结构的主要行征。当考察外加电势对此单分子膜结构的影响时,可以发现有关扭转构型的特征谱峰其相对强度随着电位负移而减小。这一结构随电位的变化关系可以通过表面电势的变化对氨基氮原子上孤对电子与金属表面间相互作用的影响来加以阐释。     

MLIMCL：基于机器学习的隐式溶剂蒙特卡罗方法

对于分子结构的优化和预测,蒙特卡罗(MC)是很重要的计算工具. 当溶剂效应被显式的考虑时,由于水分子和电离子的自由度很大,蒙特卡罗方法变得非常昂贵. 相对而言,基于隐式溶剂的蒙特卡罗方法可以通过对溶剂效应平均场的近似来大大降低计算成本,同时还能保持目标分子在原子水平上的细节. 目前两种最流行的隐式溶剂模型是泊松-波兹曼模型和通用化波恩模型. 通用化波恩模型是泊松-波兹曼模型的近似,但在模拟计算时间上要快得多. 本文通过结合两种隐式溶剂模型在准确性和效率方面的优势,开发了一种基于机器学习的隐式溶剂蒙特卡罗方法. 具体而言,蒙特卡罗方法通过机器学习既保留了泊松-波兹曼模型的精度,又达到了通用化波恩模型的速度,从而能快速准确地获取模拟计算中每一步的静电溶解自由能. 本文采用苯-水系统和蛋白质-水系统来验证我们的蒙特卡罗方法. 实验证明蒙特卡罗方法在分子结构优化和预测的速度和准确性方面具有很大优势.     

核黄素在不同极性溶剂中的光谱特性研究

实验测得核黄素在水、二甲基亚砜(DMSO)和三氯甲烷三种不同极性溶剂中的稳态吸收光谱、荧光光谱和时间分辨荧光光谱,研究了溶剂对核黄素光谱性质的影响。实验结果表明,在不同极性的溶剂中,核黄素的吸收峰位置几乎不变,而荧光光谱峰值随着溶剂极性的增大而出现红移。这是由于溶质分子的电子激发及溶剂化效应引起的电子重新分布导致它在极性溶剂中第一激发单重态能级的变化。在时间分辨荧光光谱实验中,核黄素在水溶液中荧光寿命也高于在其他两种溶剂中,荧光寿命的延长可归因于核黄素与氢键对体溶剂之间的分子间氢键相互作用。应用Gaussian09软件,采用密度泛函理论和含时密度泛函理论,结合基于密度的溶剂化模型,对不同极性溶剂中的核黄素分子进行基态和激发态优化和计算。通过前线分子轨道分析,核黄素的受激跃迁属于苯环和含氮杂环上的π电子向苯环及C N,C O共轭双键的反键轨道π*的跃迁。分子偶极矩的计算结果表明,核黄素分子的第一激发态偶极矩大于基态偶极矩,偶极矩的增大,导致溶质与溶剂分子之间的相互作用的增大。而溶剂分子与溶质分子基态和激发态的相互作用程度不同,使得吸收峰和荧光峰出现不同变化情况。极性越大的溶剂越有利于对激发态的稳定作用,使激发态能量降低,相应的发射波长发生红移。最后,通过分子表面静电势和弱相互作用分析,在水溶剂中考虑氢键作用对核黄素分子光谱的影响。多聚体结构的理论吸收和发射峰值更接近实验结果,说明多聚体结构合理。水分子二聚体与核黄素形成的环状结构,有利于提高核黄素分子的刚性,有利于荧光的发射,减少非辐射跃迁的几率,荧光寿命延长。     

溶液酸碱性对异构体氨基酸单分子膜影响的表面增强拉曼光谱研究

利用表面增强拉曼(SERS)光谱技术研究比较了在粗糙化银电极表面吸附的亮氨酸与异亮氨酸自组装单层膜结构以及溶液酸碱性对分子吸附作用的影响。研究表明在粗糙化银电极表面两种氨基酸分子主要是以COO-为作用位点进行吸附的。进一步的研究也揭示溶液pH值的变化没有显著改变两种氨基酸分子在银电极表面以去质子化羧基吸附为主的特征,但对于羧基吸附作用的影响程度及其变化规律是迥异的,对氨基的影响也有一定的差异。     

不同尺度的蛋白质在纯石墨烯及氧化石墨烯表面的吸附比较（英文）

本文运用分子动力学模拟的方法,系统地比较了不同大小的蛋白质在石墨烯及其氧化物表面的吸附稳定性和构象变化.结果表明在含氧官能团的静电作用的协助下,GO的吸附稳定性要强于PG:由少量残基组成的多肽在PG和GO表面其α螺旋结构都发生变化,蛋白片段在PG表面部分α螺旋被破坏,在GO表面保持完好,而完整的球状蛋白在PG和GO表面结构都没发生明显变化,尤其是GO,体现出良好的生物相容性.GO作为吸附底物在纳米生物技术领域显示出良好的应用前景.     

Where do ions solvate?

We study a simple model of ionic solvation inside a water cluster. The cluster is modeled as a spherical dielectric continuum. It is found that unpolarizable ions always prefer the bulk solvation. On the other hand, for polarizable ions, there exists a critical value of polarization above which surface solvation becomes energetically favorablefor large enough water clusters.     

生物分子结合水的结构与动力学研究进展

生物结合水在维护生物大分子的结构、稳定性以及调控动力学性质和生理功能等方面起着决定性的作用.从分子水平上理解生物结合水分子的结构与性质及其影响生物结构和功能的本质与规律,是揭示生物大分子生理功能机理的关键.目前生物结合水的结构与动力学相关研究尚处于初步阶段.本文从三个方面介绍当前生物结合水的相关研究及其进展:首先介绍结合水对蛋白质折叠、质子给予与迁移、配体结合与药物设计以及变构效应等生物结构和功能的影响;然后介绍生物分子周围的水分子结构研究情况;最后从时间尺度、动力学属性、生物分子与水分子之间的动力学耦合作用、蛋白质表面结合水次扩散运动等角度介绍生物分子水合动力学的研究进展,并归纳出一些目前尚待进一步解决的科学问题.     

Image systems for the reaction field inside spheroidal dielectric objects and applications

Charges inside a dielectric object embedded in a dissimilar dielectric medium polarize the surrounding medium, which in turn makes a contribution, called the reaction field, to the electric field inside the object. In this work, we develop complete image systems for the reaction field inside a prolate or oblate spheroidal dielectric object embedded in an infinite dissimilar dielectric medium. In either case, an image system consists of a point image and a symmetric surface image over an exterior confocal spheroid that passes through the point image. As an application, the point image is applied into the generalized image charge solvation model (GICSM) and is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulation as references. The results indicate that, for both the prolate and oblate cases, the single point image charge approximation for the reaction field inside the dielectric cavity of the model is good enough for the GICSM to faithfully reproduce typical static and dynamic properties of the liquid water at least when the spheroidal cavity has relatively small eccentricity.     

Reaction kinetics and solubility in water‐organic binary solutions are governed by similar solvation equilibria

The solvation effects observed in water‐organic solutions were studied by combining data for reaction kinetics and dissolution equilibria by means of a linear free‐energy (similarity) analysis. Kinetic data for the pH‐independent hydrolysis of (4‐methoxyphenyl)‐2,2‐dichloroacetate measured in this work and solubility data for naphthalene, and other substrates of low polarity, in aqueous binary mixtures of methanol, ethanol, acetonitrile, dimethyl sulfoxide (DMSO), and 1,4‐dioxane were used. Linear similarity relationships were discovered for these data over the full range of solvent compositions studied. To gain insight into the similarities observed between these different phenomena, molecular dynamics simulations were carried out for naphthalene and an ester in water–acetonitrile solutions. The results revealed considerable preferential solvation of these substrates by the co‐solvent. Linear relationships between the experimental data and the mole fractions of acetonitrile in the solvation shells of substrates were found. Surprisingly, a linear relationship was found between the mole fractions of acetonitrile in the solvation shells of the ester and naphthalene. This linearity indicated that a similar solvation mechanism governs even such different phenomena as dissolution and reaction kinetics. The relationships between the experimental data and the results of the molecular dynamics calculations found in this work explained the solvent effect observed in water‐organic solutions on the molecular level. Copyright © 2015 John Wiley & Sons, Ltd.     

Solvation energy of multiply charged anions and dielectric constant for finite system: a microscopic theory based bottom-up and top-down approach

This is the first time a microscopic theory-based bottom-up approach has been implemented to derive an analytical expression for the solvation energy for a finite (N) system, including the bulk. This bottom-up approach provides the information on solvation energies of anionic solutes in finite-size clusters, including the bulk (N = ∞), from the knowledge of the detachment energies for the system containing a few numbers of solvent molecules. However, in the case of dielectric constant, a microscopic theory-based top-down approach has been prescribed to derive an analytical expression for the static dielectric constant for the finite system. In this approach, the knowledge of the dielectric constant for the bulk provides a scheme to obtain the same quantity for a wide numbers of solvent molecules. As an illustrative example, the hydrated doubly charged anions, SO^?2 ₄.NH₂O and C₂O^?2 ₄.NH₂O, have been considered, and the calculated bulk solvation energy for the SO^?2 ₄.NH₂O system is found to be in very good agreement (within 5%) with the available experimental result. However, the same quantity calculated based on the Born model is found to be largely deviating (32%) from the experimental result. The calculated results of the dielectric constant for these two systems support the linear theory of dielectric constant.     

Kinetic sonication effects in aqueous acetonitrile solutions. Reaction rate levelling by ultrasound

The kinetics of the pH-independent hydrolysis of 4-methoxyphenyl dichloroacetate were investigated with and without ultrasonic irradiation in acetonitrile–water binary mixtures containing 0.008 to 35 wt.% of acetonitrile and the kinetic sonication effects (k_son/k_non) were calculated. Molecular dynamics (MD) simulations of the structure of the solutions were performed with ethyl acetate as the model ester. The ester is preferentially solvated by acetonitrile. The excess of acetonitrile over water in the solvation shell grows fast with an increase in the co-solvent content in the bulk solution. In parallel, the formation of a second solvation shell rich in acetonitrile takes place. Significant kinetic sonication effects for the hydrolysis were explained with facile destruction of the diffuse second solvation shell followed by a rearrangement of the remaining solvent layer under sonication. The rate levelling effect of ultrasound was discussed. In an aqueous-organic binary solvent, independent of the solvent composition, the ultrasonic irradiation evokes changes in the reaction medium which result in an almost identical solvation state of the reagent thus leading to the reaction rate levelling.     

Hydration of clays at the molecular scale: the promising perspective of classical density functional theory

We report here how the hydration of complex surfaces can be efficiently studied, thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophyllite clay. After presenting the most recent advances, we show that the strength of this implicit method is that: (1) it is in quantitative or semi-quantitative agreement with reference all-atom simulations (molecular dynamics here) for both the solvation structure and energetics, and (2) the computational cost is two to three orders of magnitude less than in explicit methods. The method remains imperfect in that it locally overestimates the polarisation of water close to hydrophylic sites of the clay. The high numerical efficiency of the method is illustrated and exploited to carry out a systematic study of the electrostatic and van der Waals components of the surface–solvent interactions within the most popular force field for clays, CLAYFF. Hydration structure and energetics are found to weakly depend upon the electrostatics. We conclude on the consequences of such findings on future force-field development.     

双酚A在氧化石墨烯表面吸附的分子动力学模拟

双酚A(bisphenol A,BPA)是一种内分泌干扰物,会对机体多方面产生不良影响,包括生殖系统、神经系统、胚胎发育等.因此,在水环境中如何检测和去除BPA显得尤为重要.实验研究表明,氧化石墨烯(graphene oxide,GO)对BPA具有优异的吸附去除性能,但在分子层面的吸附机制尚不清楚.分子动力学模拟,能提供BPA在GO表面的动态吸附过程以及吸附构象等详细信息,可以弥补实验的不足.本文利用GROMACS分子动力学模拟软件,系统模拟了BPA在含GO的水溶液中的吸附过程,并计算了吸附自由能.结果显示:所有的BPA均被吸附在GO两侧,通过分析BPA的吸附构象以及与GO的相互作用,发现π-π疏水作用对吸附起主导作用,且显示出很好的稳定性,而静电和氢键作用增加了GO的吸附能力.通过自由能计算,BPA在GO表面的结合能达30 k J/mol,远大于水分子的5 k J/mol.这些结果进一步证实GO对BPA具有很强的吸附能力以及GO作为吸附剂在水溶液中去除BPA的可行性.     

Solvent density mode instability in non-polar solutions

We analyse the origin of the multiple long time scales associated with the long time decay observed in non-polar solvation dynamics by linear stability analysis of solvent density modes where the effects of compressibility and solvent structure are systematically incorporated. The coupling of the solute-solvent interactions at both ground and excited states of the solute with the compressibility and solvent structure is found to have important effects on the time scales. The present theory suggests that the relatively longer time constant is controlled by the solvent compressibility, while the solvent structure at the nearest-neighbour length scale dominates the shorter time constant.      

Selective nonspecific solvation under dielectric saturation and fluorescence spectra of dye solutions in binary solvents

The influence of selective nonspecific solvation on the fluorescence spectra of three substitutedN-methylphthalimides in a binary solvent system consisting of a nonpolar (n-heptane) and a polar (pyridine) component has been studied under conditions close to dielectric saturation. The substantially nonlinearity of the effect is confirmation that the spectral shifts of fluorescence bands depend on the number of polar solvent molecules involved in solvating the dye molecule. The measured fluorescence spectral shifts determined by substituting one nonpolar solvent molecula with a polar one in the proximity of the dye molecule agree quantitatively with the forecasts of the previously proposed semiempirical theory which describes this nonlinear solvation phenomenon.