采用分子动力学方法研究氯化钠水溶液的微观结构

溶液的微观结构对溶液的宏观性质具有决定性影响,团簇的存在和溶液不均性的认知是该领域研究的重要进展之一,也是关注的热点.为了考察溶液的微观结构,本文采用分子动力学方法对浓度适中的氯化钠水溶液进行了模拟,获得了各原子(离子)间的径向分布函数和溶液的瞬态图像.通过对比分析Na~+-Cl~-和Cl~--Na~+的径向分布函数,并结合已有研究结果,表明该径向分布函数上第三峰也来源于离子对,发现氯化钠水溶液存在着第三种离子对;上述径向分布函数上的三个峰分别与直接接触离子对、部分间隔离子对和完全间隔离子对相对应,并给出了这三种离子对的瞬态图像.三个时刻下系统瞬态图像的分析结果表明,溶液中存在水分子连续分布的区域和由离子与水分子共同构成的离子团簇.各瞬态图像中水分子连续分布的最大区域的平均尺寸至少为1.43 nm,溶液中部分间隔离子对的比例最大,约为0.68.在同时考虑直接接触离子对和部分间隔离子对时,三个时刻中最大团簇尺度的平均值为1.44 nm,该值约为部分间隔离子对最概然尺寸的3倍;团簇尺寸随团簇中离子数的增加而增大,在团簇中离子数较大时,满足无规行走(自由连接链)模型的结果.这些说明氯化钠水溶...     

基于路径积分分子动力学与热力学积分方法的高压氢自由能计算

在相图研究中, 严格计算一个真实系统在特定温度、压强下的自由能是近年来该领域理论方法发展的前沿. 自Mermin提出有限温度密度泛函理论后, 在电子结构层面, 弱关联系统中人们就其在对自由能贡献的描述已相对完善, 但在原子核运动的描述上, 热运动与量子运动的非简谐项却总被忽视. 本文将路径积分分子动力学与热力学积分结合, 对300 GPa下氢晶体Cmca 结构中原子核热涨落与量子涨落对自由能的影响进行了分析. 发现在100 K核量子涨落非简谐项的贡献约为15 meV每原子, 远大于不同结构间静态焓的差别. 该研究提醒人们简谐近似在核量子效应描述中可能存在的不准确性(即使在低温下). 同时, 我们采取的方法 也为人们进行自由能的准确计算提供了一个简单有效的手段.     

Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

Kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP molecules. An important factor characterizing the processivity of the kinesin motor is its dissociation from the microtubule. Here, using all-atom molecular dynamics simulations, we studied the dissociation process of the kinesin head in weak-microtubule-binding or ADP state from tubulin on the basis of the available high-resolution structural data for the head and tubulin. By analyzing the simulated snapshots of the structure of the head-tubulin complex we provided detailed structural and dynamic information for the dissociation process. We found that the dissociation of the head along different directions relative to the tubulin exhibits very different dynamic behaviors. Moreover, the potential forms or energy landscapes of the interaction between the head and tubulin along different directions were determined. The studies have important implications for the detailed molecular mechanism of the dissociation of the kinesin motor and thus are critical to the mechanism of its processivity.     

Atomic-scale simulations of material behaviors and tribology properties for BCC metal film

This work has two main purposes:(i) introducing the basic concepts of molecular dynamics analysis to material scientists and engineers, and(ii) providing a better understanding of instrumented indentation measurements, presenting an example of nanoindentation and scratch test simulations. To reach these purposes, three-dimensional molecular dynamics(MD) simulations of nanoindentation and scratch test technique were carried out for generic thin films that present BCC crystalline structures. Structures were oriented in the plane(100) and placed on FCC diamond substrates. A pair wise potential was employed to simulate the interaction between atoms of each layer and a repulsive radial potential was used to represent a spherical tip indenting the sample. Mechanical properties of this generic material were obtained by varying the indentation depth and dissociation energy. The load-unload curves and coefficient of friction were found for each test; on the other hand, dissociation energy was varied showing a better mechanical response for films that present grater dissociation energy. Structural change evolution was observed presenting vacancies and slips as the depth was varied.     

Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD–PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.     

Molecular dynamics study on water self-diffusion in aqueous mixtures of methanol,ethylene glycol and glycerol: investigations from the point of view of hydrogen bonding

Molecular dynamics simulations have been performed to investigate the aqueous binary mixtures of alcohols, including methanol, ethylene glycol (EG) and glycerol of molalities ranging from 1 to 5 m at the temperatures of 273, 288 and 298 K, respectively. The primary purpose of this paper is to investigate the mechanism of water self-diffusion in water-alcohol mixtures from the point of view of hydrogen bonding. The effects of temperature and concentration on water self-diffusion coefficient are evaluated quantitatively in this work. Temperature and concentration to some extent affect the hydrogen bonding statistics and dynamics of the binary mixtures. It is shown that the self-diffusion coefficient of water molecules decreases as the concentration increases or the temperature decreases. Moreover, calculations of mean square displacements of water molecules initially with different number n of H-bonds indicate that the water self-diffusion coefficient decreases as n increases. We also studied the aggregation of alcohol molecules by the hydrophobic alkyl groups. The largest cluster size of the alkyl groups clearly increases as the concentration increases, implying the emergence of a closely connected network of water and alcohols. The clusters of water and alcohol that interacted could block the movement of water molecules in binary mixtures. These findings provide insight into the mechanisms of water self-diffusion in aqueous binary mixtures of methanol, EG and glycerol.     

用分子动力学模拟甲烷水合物热激法分解

用分子动力学模拟方法研究甲烷水合物热激法分解，系统地研究注入340 K液态水的结构Ⅰ型甲烷水合物的分解机理.模拟显示水合物表层水分子与高温液态水分子接触获得热能，分子运动激烈，摆脱水分子间的氢键束缚，笼状结构被破坏.甲烷分子获得热能从笼中挣脱，向外体系扩散.热能通过分子碰撞从外层传递给内层水分子，水合物逐层分解.对比注入277K液态水体系模拟结果，得出热激法促进水合物分解. 关键词： 甲烷水合物 分子动力学模拟 热激法     

二聚物在Cu表面上的扩散和解离研究

利用分子动力学模拟统计了几种不同温度下三种不同二聚物(Cu₂, Ag₂和Pd₂)在铜衬底(100), (111)表面上的扩散和解离行为, 探讨同质和异质二聚物在Cu表面上扩散和解离的特点; 采用分子动力学中的静态计算方法计算了这三种二聚物在扩散和解离过程中的能量势垒, 并与动力学模拟、二聚物与衬底的结合能等结果进行了比较, 探讨二聚物扩散和解离过程与扩散势垒、结合能、表面性质和温度等的关系. 原子间相互作用采用半经验EAM势. 结果表明: 同质和异质二聚物在各个不同表面上的扩散势垒、解离势垒有一定的规律, 并和二聚物与衬底的结合性质有关; 二聚物是否易解离与衬底表面的结构以及二聚物与衬底的结合性质关系密切; 二聚物解离前协同扩散的快慢与二聚物和衬底的结合性质以及二聚物在表面的扩散和解离势垒密切相关.     

一元溶剂体系HNBP结晶形貌的理论研究

本文计算了苯、甲苯、氯苯、苯甲醚4种溶剂作用下HNBP的晶面层与溶剂层的相互作用能,并对附着能进行了修正,预测了不同溶剂作用下HNBP的晶体形貌.结果表明加入不同的溶剂后,HNBP晶体的重要晶面与溶剂都呈吸引作用.苯溶剂使晶体形貌呈长形柱体状,纵横比为8.54;甲苯溶剂使晶体形貌呈片状,纵横比为7.38;氯苯溶剂使晶体形貌呈现出长方体状,纵横比为4.53;苯甲醚溶剂使晶体形貌呈菱柱状,纵横比为4.15.     

双原子分子振动能谱与离解能的精确研究

代数方法(AM)的建立解决了实验方法和精确量子力学理论方法难以获得双原子分子的包含最高振动能级在内的所有高阶振动能级的精确数值这一问题.基于LeRoy与Bernstein的工作,孙卫国等又建立了精确计算双原子分子离解能的新解析表达式.应用新公式和代数方法(AM),研究了一些双原子分子部分电子态的振动能谱和分子离解能,获得了与实验值符合非常好的理论结果.该方法在理论上提供了获得双原子分子完全振动能谱和精确分子离解能的物理新方法.     

金属Ni纳米线凝固行为的分子动力学模拟

采用EAM镶嵌原子作用势，通过经典的分子动力学模拟方法研究了不同冷却速度下的金属Ni纳米线的凝固行为，并给出了纳米线在凝固区域的结构演变过程.利用键对分析技术研究了在不同冷却速度下体系中的原子团簇在降温过程中的变化情况.研究表明，纳米线的凝固起始于表面原子，并且随着冷却速度的降低，Ni纳米线的微观结构从非晶态过渡到多壳螺旋结构，最终达到稳定的面心立方结构.多壳螺旋结构同时具有确定的结晶温度和长程无序、短程有序的非晶结构的特征. 关键词： 纳米线 凝固行为 分子动力学 键对分析     

利用扩展系综法计算水的自由能

利用扩展系综法得到了正则系综下水的TIP4P模型的自由能值为-21．485±0．035kJ/mol， 并与其他方法所得的结果作了比较.提出了选择该方法中关键参数(平衡因子)的有效方法， 并讨论了该方法的可移植性. 关键词： 自由能 TIP4P水模型 扩展系综 分子动力学模拟 水分子团     

双原子离子部分电子态的离解能的精确研究

本文使用孙卫国提出的基于微扰理论的代数方法(AM),研究了双原子离子F2+的X2Πg,CO + 的X2Σ+, O2+的A2Πu ,BeH +的X1Σ+ 四个电子态的离解能,然后使用最近提出的新公式计算了这些电子态的离解能,并分别与离解能的实验值进行了比较．研究结果表明：使用新公式得到的分子离解能与实验值更加接近;同时AM和新公式相结合的理论方法也适用于双原子离子体系。     

双原子离子部分电子态的离解能的精确研究

本文使用基于微扰理论的代数方法(AM),研究了双原子离子F2+的X2Ⅱg,CO+的X2∑+,O2+的A2Ⅱu,BeH+的X1∑+四个电子态的离解能,然后使用最近提出的新公式计算了这些电子态的离解能,并分别与离解能的实验值进行了比较.研究结果表明:使用新公式得到的分子离解能与实验值更加接近;同时AM和新公式相结合的理论方法也适用于双原子离子体系.     

高能量短脉冲激光作用水分子的动力学模拟

基于高能量短脉冲激光作用水分子实验的复杂性,需用采取一种比较准确且较为方便的方法来预测实验结果是必要的.本文采用分子动力学方法(Molecular Dynamics)对高能量密度短脉冲激光加载下的超临界水分子进行热力学分析及结构研究.结果表明,随着能量快速加入加载区域,水分子系统的温度迅速提高.同时,由于分子迅速向四周扩散,在加载区域产生空泡.其中,只有25.5%的能量用以提高水分子系统的动能(温度),其余的能量都用于增大水分子系统的势能(水分子间距).伴随着温度的提高,水分子热运动加快,有序程度逐渐减弱,O—H间距增加,水分子间的氢键作用减弱,分子极性降低.分子动力学模拟方法研究短脉冲高能量激光对水分子的作用,对水下激光微加工研究有一定指导意义.     

Molecular dynamics study on the dissociation of methane hydrate via inorganic salts

Hydrate plugging is a hidden threat to the safe exploitation of oil and gas. Inorganic salts are widely used as thermodynamic inhibitors to effectively prevent the hydrate formation. This study uses a molecular dynamics method to explore the mechanism of the hydrate dissociation via inorganic salts on the micro-scale. We simulated the dissociating process of methane hydrate under different concentration series of NaCl, KCl and CaCl₂ solutions at 273 K, and analysed the changes of ionic structure, transport parameters and kinetic energy in the system of inorganic salt/hydrate. The simulation results successfully revealed the step-by-step dissociation of hydrate, and the differences in dissociation rates among the different inhibitors. The energy needed for hydrate dissociation alters for different inorganic solutions; the energy reaches maximum when KCl is the inhibitor, and lowest when the concentration of CaCl₂ exceeds 30% w/w. We calculated the coordination numbers of all components, including oxygen atoms, cations and anions, and also their diffusion coefficients; analysed the effects of the three inorganic salts on the simulated hydrate structure and its transport; in addition, investigated the mechanism of hydrate dissociation via inorganic salts.     

Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution

Besides our previous experimental discovery(Zhao Y R, et al. 2015 Langmuir, 31, 12975) that acetonitrile(ACN)can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK(KI4K) in aqueous solution,further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures.To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross-β sheet structure, and a proto-fibril of KI4 K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding(H-bonding) interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations.     

棱形石墨烯纳米孔道内离子传输性能的分子动力学模拟

纳米通道的尺寸、结构和表面化学对其内部溶液的分布结构和输运性质有着重大影响.本文研究了一种全新的菱形石墨烯纳米通道.这种理想的通道与最近被广泛研究的金属有机框架材料(MOF)的内部结构类似,有着与传统的碳纳米管截然不同的内部结构.本文使用分子动力学模拟的方法研究在不同尺寸的菱形石墨烯纳米通道内的KCl溶液的性质,并将其与同尺寸的单壁碳纳米管进行了比较.研究结果表明在小孔道内(<20?)其内部的溶液结构呈现若干个密度极高的聚集区域,即出现了结晶化的趋势．这一研究结果,将为MOF的结构设计提供思路,从而有望实现类似于生物离子通道的高选择性和高传输能力.     

Semi-classical explanation for the dissociation control of H_2~+

A semi-classical model is utilized to explain the dissociation control of the hydrogen molecular ion(H+2). By analyzing the curve of the dissociation asymmetry parameter as a function of the time delay between the exciting and steering pulses, we find that the dissociation control is dependent not only on the peak intensity and direction of the electric field of the steering pulse, but also on the peak intensity of the exciting pulse.     

D_2~+强场解离的电子局域化随激光波长的非线性变化

研究了周期量级激光脉冲的波长变化对氘分子离子D_2~+强场解离过程中电子局域化的影响.通过求解波恩,奥本海默近似下关于核波包演化的双能级含时薛定谔方程,发现电子局域化的不对称性对激光波长有反常的依赖关系.电子局域程度随着波长的增加呈现增强的趋势,但在某些波长范围内电子局域化出现了显著的衰减.导致电子局域化程度被削弱的直接原因是在某些波长下不同振动态的电子局域化对脉冲载波包络相位的响应出现了反相抵消.分析表明,当波长发生变化时,决定电子局域化的核运动和电子运动在外场作用下出现不一致的运动响应,最终导致了电子局域化的非线性变化.