溴化钾团簇相变的分子动力学研究

众所周知，团簇的尺寸介于原子或分子与大块物质之间。由于它有较大的表面／体积比而有独特的物理化学性质。团簇在成核，晶体生长，材料科学和纳米器件加工等领域起了至关重要的作用。近年来，计算机模拟已成为物理，化学，生物，天文，地质等领域的重要研究工具。计算机模拟不仅可以     

RbCl熔解的分子动力学模拟研究

采用等压分子动力学模拟方法，研究了从晶相到液相不同温度下ＲｂＣｌ体系的结构和性质，等压模拟咄等容怀致的平衡性质和结构特征，键序参数计算，不计及导热过程情形下，体系在振荡驰豫时间量级内完成熔化过程，由于不需要密度数据，等压模拟有望发展成为材料设计中的一种手段。     

Order and Phase Behavior of a Cylinder Forming Diblock Copolymers and Nano‐Particles Mixture in Confinement: A Molecular Dynamics Study

We study a coarse grained model of cylinder forming diblock copolymers and nano‐particles (NPs) mixture confined between Lennard–Jones hard walls. Two models for non‐selective interactions between monomers and NPs are applied. In the case of purely repulsive interactions between NPs and monomers (athermal case) strong segregation of NPs at the film surfaces and the formation of droplets of particles inside the copolymer film can be observed. For weakly attractive interactions between NPs and monomers (thermal case) formation of droplets of particles disappears and segregation on the film surfaces depend on temperature. The uptake of NPs by the copolymer film in the thermal case displays a non‐monotonic dependence on temperature which can be qualitatively explained by a mean‐field model. In both cases of non‐selective interactions NPs are preferentially localized at the interface between the microphase domains.

     

氟化钾团簇的相变、成核和重结晶的分子动力学模拟

我们利用Born-Mayer-Huggins相互作用势函数对(KF)_N(N=108，256，500和864)团簇进行了分子动力学(MD)模拟。为了避免周期性边界条件对相变、成核和重结晶的干扰作用，对体系采用了自由边界。基于MD模拟结果，对团簇的熔化温度、熔化焓、扩散系数、成核速率、固液界面自由能、临界核大小等进行了计算和讨论。在对(KF)₈₆₄双晶团簇的热退火模拟中，观察到了固态的重结晶和晶粒的生长。经典的成核理论成功地解释了(KF)₈₆₄双晶团簇的重结晶MD模拟结果。     

Light-Triggered Transformation of Molecular Baskets into Organic Nanoparticles

Discovering novel and functional photoresponsive materials is of interest for improving controlled release of molecules and scavenging toxic compounds for cleaning our environment or designing chemosensors. In this study, we report on the photoinduced decarboxylation of basket 1 ⁶⁻, containing three glutamic acids at its rim. This concave compound is, in an aqueous environment (30 mm phosphate buffer at pH 7.0), monomeric (¹H NMR DOSY, DLS) with glutamic acid residues randomly oriented about its rim (¹H NMR and MM-OPLS3). The irradiation (300 nm) of 1 ⁶⁻ leads to the exclusive removal of its α-carboxylates to give amphiphilic 2 ³⁻ possessing γ-carboxylates. The photochemical transformation is a consecutive reaction with mono- and bis-decarboxylated products observed with ¹H NMR spectroscopy and ESI mass spectrometry. Amphiphilic 2 ³⁻ is a preorganized molecule (MM-OPLS3) that, in water, aggregates into organic nanoparticles (ca. 50–200 nm in diameter; DLS, TEM and cryo-TEM) having a critical aggregation concentration of 12 μm (UV/Vis). As the transition of monomeric 1 ⁶⁻ into nanoparticulate 2 ³⁻ is triggered with light, we reasoned that stimuli-responsive formation of the soft material lends itself to nanotechnology applications such as controlled release or scavenging of targeted compounds.     

覆盖的氩原子簇过热的分子动力学模拟(英)

通过分子动力学模拟研究了覆盖较高熔点的原子的氩原子簇．原子族由177个氩原子和72个覆盖原子组成．覆盖原子的势能参数ε比氩原子大50％，该原子簇比纯氩原子簇熔点过热2K．模拟结果表明，覆盖的原子簇过热的原因是：在达到熔点之前，体系缺少氩原子构成的自由表面，仍然是覆盖原子的有序表面．     

Melting Behaviour of Shell-symmetric Aluminum Nanoparticles: Molecular Dynamics Simulation

Molecular dynamics simulations with embedded atom method potential were carried out for Al nanoparticles of 561 atoms in three structures: icosahedron, decahedron, and truncated octahedron. The total potential energy and specfic heat capacity were calculated to estimate the melting temperatures. The melting point is 540±10 K for the icosahedral structure,500±10 K for the decahedral structure, and 520±10 K for the truncated octahedral structure.With the results of mean square displacement, the bond order parameters and radius of gyration are consistent with the variation of total potential energy and specific heat capacity. The relaxation time and stretching parameters in the Kohlraush-William-Watts relaxation law were obtained by fitting the mean square displacement. The results show that the relationship between the relaxation time and the temperatures is in agreement with standard Arrhenius relation in the high temperature range.     

由CBr4分子动力学研究观察到的可能的新相

通过分子动力学模拟考察并分析了１０８个分子组成的分子簇相变的结构、能量和动力学行为。结果表明，分子簇经历了由低温单斜相到新相的转变，该相变包含平动和转动相变。     

受限于不同螺旋性的纳米碳管中水的分子动力学模拟

近年来将纳米碱米碳管引入到与生命过程息息相关的离子通道膜的研究逐渐成 为热点，而其中的关键就是要了解受限于膜孔道（碳管）中水分子的行为。采用分 子动力学模拟在300 K和1.01 * 10~5 Pa下对受限于（6，6）armchair型和（10， 0）zigzag型纳米碳管中的水进行了研究，得到了水分子在碳管中的局部密度分布 等静态性质以及水分子在碳管中的传递等动态性质，并对不同势能模型的模拟结果 作了比较。结果表明选择不同的势能模型并没有改变此体系的固有性质，即水分子 不仅能够进入到憎水性的（6，6）碳管中而且能形成一条稳定的由氢键相连的纵列 （single file），而且在管中以纵列的形式进行同歇传递。此外，碳管螺旋性对 受限水的静态性质影响不大但对动态性质则有一定程度的影响，水分子在（10，0 ）zigzag型碳管中的传递能力要强于在（6，6）armchair型碳管中的能力。     

Effects of Cationic Structure on Cellulose Dissolution in Ionic Liquids: A Molecular Dynamics Study

In recent years, great progress has been made in the dissolution of cellulose with ionic liquids (ILs). However, the mechanism of cellulose dissolution, especially the role the IL cation played in the dissolution process, has not been clearly understood. Herein, the mixtures of cellulose with a series of imidazolium‐based chloride ionic liquids and 1‐butyl‐3‐methyl pyridinium chloride ([C₄mpy]Cl) were simulated to study the effect that varying the heterocyclic structure and alkyl chain length of the IL cation has on the dissolution of cellulose. It was shown that the dissolution of cellulose in [C₄mpy]Cl is better than that in [C₄mim]Cl. For imidazolium‐based ILs, the shorter the alkyl chain is, the higher the solubility will be. In addition, an all‐atom force field for 1‐allyl‐3‐methyl imidazolium cation ([Amim]⁺) was developed, for the first time, to investigate the effect the electron‐withdrawing group within the alkyl chain of the IL cation has on the dissolution of cellulose. It was found that the interaction energy between [Amim]⁺ and cellulose was greater than that between [C₃mim]⁺ and cellulose, indicating that the presence of electron‐withdrawing group in alkyl chain of the cation enhanced the interaction between the cation and cellulose due to the increase of electronegativity of the cations. These findings are used to assess the cationic effect on the dissolution of cellulose in ILs. They are also expected to be important for rational design of novel ILs for efficient dissolution of cellulose.     

诺氟沙星-DNA复合物的分子动力学模拟

采用分子模建的方法构建了诺氟沙星-DNA复合物的初始结构, 通过2 ns的分子动力学(MD)模拟研究表明: 诺氟沙星能够和双螺旋d[ATATCGATAT]₂形成稳定的复合物, 药物分子可紧密结合在DNA的小沟区域, 并且能够与DNA的鸟嘌呤碱基形成两个稳定的氢键. 在分子水平上提供了诺氟沙星直接与双螺旋DNA相互作用的结构及复合物的动态变化情况.     

Effect of Vacancy Defects on the Young's Modulus and Fracture Strength of Graphene: A Molecular Dynamics Study

The Young's modulus of graphene with various rectangular and circular vacancy defects is investigated by molecular dynamics simulation. By comparing with the results calculated from an effective spring model, it is demonstrated that the Young's modulus of graphene is largely correlated to the size of vacancy defects perpendicular to the stretching direction. And a linear reduction of Young's modulus with the increasing concentration of mono‐atomic‐vacancy defects (i.e., the slope of ?0.03) is also observed. The fracture behavior of graphene, including the fracture strength, crack initiation and propagation are then studied by the molecular dynamics simulation, the effective spring model, and the quantized fracture mechanics. The blunting effect of vacancy edges is demonstrated, and the characterized crack tip radius of 4.44 Å is observed.     

嵌入纳米Fe颗粒的Fe液凝固过程的分子动力学模拟

采用Sutton-Chen 势函数及分子动力学(MD)方法对嵌入了Fe纳米团簇(半径从0.4-1.8 nm)的Fe液凝固过程进行了模拟. 模拟结果表明只有当嵌入的纳米团簇半径超过0.82 nm才能降低凝固时所需要的临界过冷度(ΔT^*), 起到诱导凝固的作用. 同时采用原子键型指数法(CTIM-2)对样本在凝固过程中的原子结构进行了标定, 通过观察微观结构演变发现当嵌入纳米团簇能够作为凝固核心时, 体系按照hcp-fcc 交叉形核的方式长大. 同时还发现嵌入纳米团簇对体系凝固过程晶核的生长方向及凝固的最终构型存在“结构遗传效应”.     

异型碳纳米管储氢性能的分子动力学模拟研究

采用分子动力学(MD)方法对三种理想的Y型碳纳米管[记为Y(4,4), Y(6,6), Y(10,0)]和三种L型碳纳米管[记为L(9,0), L(6,6), L(10,0)]之储氢性能进行了模拟研究, 并与相应的直线型碳纳米管的储氢能力进行了比较, 同时考察了温度、碳纳米管的直径和螺旋性以及缺陷的位置和大小对异型碳纳米管储氢性能的影响. 结果表明, 在室温和低温条件下, 异型碳纳米管的储氢量高于直线型碳纳米管的储氢量, 且其储氢量大小随温度的降低和碳管直径的增大而增加, 椅式碳纳米管的储氢性能优于齿式碳纳米管, 而缺陷的位置和大小对异型碳管之储氢性能的影响则因碳管的形貌和直径的大小不同而存在差异.     

分子动力学研究V82A和L90M变异对HIV PR-IDV复合物的影响

为了说明V82A和L90M变异对蛋白酶(PR)和茚地那韦(IDV)复合物的影响,进行了5.5ns的MD模拟.用MM-PBSA方法计算了体系的结合自由能,计算和实验结果一致.分解自由能为不同能量项说明,这两个变异引起熵的贡献变化大于焓的贡献变化.分解自由能到每个残基说明Wild,V82A和L90M具有相似的结合模式,结合能的贡献主要来源于A28/A28',I50/I50'和I84/I84'这六个残基组,详细分析了Wild和IDV的结合模式,对比分析了V82A和L90M变异引起结合模式的细小变化.V82A变异引起结合模式的变化是由于变异后位阻减小导致的.L90M变异引起D25和L90间的作用增强并引起结合模式的细小变化.研究结果有助于更好地理解变异对抑制剂和HIV-1PR结合模式的影响,并可以用来帮助设计更高效的PR抑制剂.     

自组装的分子动力学模拟

简要回顾了近年来国内外分子动力学模拟自组装的研究,对已报道的建模方法、可视化表现以及相关应用略作概述,并以此为基础对自组装过程的分子动力学模拟研究所面临的问题和尚需深入的内容进行了讨论。基于自组装、相变和涨落的固有联系,提出了以研究波动为手段,和以频率相关热容为研究对象的探索方向。希望能够为分子动力学模拟推动自组装研究提供有益的参考。     

Properties of Polyvinyl Alcohol Oligomers: A Molecular Dynamics Study

MD studies of liquid isopropyl alcohol and melts of short poly(vinyl alcohol) (PVA) oligomers are described. The specific volume was found to depend inversely on the number N of repeat units. If the chain length is enhanced, the viscosity of the PVA melt increases and the peaks in the radial distribution function become sharper. Additional peaks that appear in melts of PVA chains are of pure intramolecular origin. The calculated radius of gyration was found to depend on the number of formula units via . The orientation correlation functions showed that all molecular vectors of PVA melts with chain lengths N = 1, 2, 3 relax completely within a few nanoseconds. The relaxation times for the O H bond vector as obtained via the Kohlrausch‐Williams‐Watts expression showed an exponential dependence on the number of repeat units.

     

Effect of Size and Temperature on Water Dynamics inside Carbon Nano-Tubes Studied by Molecular Dynamics Simulation

Water transport inside carbon nano-tubes (CNTs) has attracted considerable attention due to its nano-fluidic properties, its importance in nonporous systems, and the wide range of applications in membrane desalination and biological medicine. Recent studies show an enhancement of water diffusion inside nano-channels depending on the size of the nano-confinement. However, the underlying mechanism of this enhancement is not well understood yet. In this study, we performed Molecular Dynamics (MD) simulations to study water flow inside CNT systems. The length of CNTs considered in this study is 20 nm, but their diameters vary from 1 to 10 nm. The simulations are conducted at temperatures ranging from 260 K to 320 K. We observe that water molecules are arranged into coaxial water tubular sheets. The number of these tubular sheets depends on the CNT size. Further analysis reveals that the diffusion of water molecules along the CNT axis deviates from the Arrhenius temperature dependence. The non-Arrhenius relationship results from a fragile liquid-like water component persisting at low temperatures with fragility higher than that of the bulk water.     

Influence of Substitutional Defects in ZIF-8 Membranes on Reverse Osmosis Desalination: A Molecular Dynamics Study

In this study, molecular dynamics simulation is used to investigate the effects of water-based substitutional defects in zeolitic imidazolate frameworks (ZIF)-8 membranes on their reverse osmosis (RO) desalination performance. ZIF-8 unit cells containing up to three defect sites are used to construct the membranes. These substitutional defects can either be Zn defects or linker defects. The RO desalination performance of the membranes is assessed in terms of the water flux and ion rejection rate. The effects of defects on the interactions between the ZIF-8 membranes and NaCl are investigated and explained with respect to the radial distribution function (RDF) and ion density distribution. The results show that ion adsorption on the membranes occurs at either the nitrogen atoms or the defect sites. Complete NaCl rejection can be achieved by introducing defects to change the size of the pores. It has also been discovered that the presence of linker defects increases membrane hydrophilicity. Overall, molecular dynamics simulations have been used in this study to show that water-based substitutional defects in a ZIF-8 structure reduce the water flux and influence its hydrophilicity and ion adsorption performance, which is useful in predicting the type and number of defect sites per unit cell required for RO applications. Of the seven ZIF-8 structures tested, pristine ZIF-8 exhibits the best RO desalination performance.     

HIV-1整合酶链转移抑制剂的3D-QSAR、分子对接和分子动力学模拟研究

为了获得高活性、结构新颖的整合酶链转移(INST)抑制剂,本文采用Co MFA和Co MSIA两种方法对32个萘啶类INST抑制剂进行了三维定量构效关系研究,并建立了相关模型,其交叉验证系数分别为q~2=0. 809和q~2=0. 816,拟合验证系数分别为r~2=0. 998和r~2=0. 981,表明所建立的模型是可靠的且具有一定的预测能力。利用分子对接探讨小分子化合物与INST蛋白的相互作用模式,结果表明,萘啶类化合物主要通过疏水作用和氢键作用与INSTIs蛋白结合。最后通过分子动力学模拟进一步验证对接结果发现,对接的结合模式与分子动力学模拟得到的结果是一致的。本研究获得的综合模型和推论可以为开发有效的HIV INSTIs提供重要的理论信息。