石英玻璃高温分子动力学模拟中的势函数

根据石英玻璃高温下的分子动力学研究, 分析了势函数中多体势在高温应用下的局限性, 认为离子型对势在模拟石英玻璃高温结构方面优于多体势. 在原子电荷转移方面, 计算并分析了Si和O原子电荷大小对计算原子自扩散系数的影响, 发现用原子电荷转移较少的Morse势函数计算的原子自扩散激活温度比BKS势函数计算的低, 而且在同一温度下, 自扩散系数的计算值也随着原子电荷的减小而增大, 因此, 较小的原子电荷转移应该有利于石英玻璃在高温下的动力学性能的研究.     

约束条件下的硬球流体

利用密度泛函理论和分子动力学方法,对处于两平行硬墙之间的硬球流体的密度分布进行了计算通过比较两种方法的结果,发现在墙之间距离较大时,Rosenfeld密度泛函理论的结果与分子动力学模拟的结果符合很好;当两堵墙间的距离很小时,这两个结果之间存在明显的不一致.另外,还研究了约束条件下密度分布的结构.     

HMX/TATB复合材料弹性性能的MD模拟

用分子动力学(MD)方法COMPASS力场, 分别在正则系综(NVT)和等温等压系综(NPT)下, 模拟计算了著名常用高能炸药HMX(环四甲撑四硝胺)与著名钝感炸药TATB (1,3,5-三氨基-2,4,6三硝基苯)所构成的混合体系在室温时的弹性性能和结合能. 结果表明, 在NVT和NPT两种系综下模拟所得结果呈平行一致的趋势; 与纯HMX相比, HMX/TATB复合材料的拉伸模量、体模量和剪切模量均有所下降; 在NVT系综下, 还完成了HMX/TATB混合体系的不同温度的MD模拟. 发现当温度在245～345 K范围时, 体系的刚性和弹性变化很小; 但当温度达到395 K时, 材料的刚性减弱, 柔性增强.     

利用浮动电荷力场对N-甲基乙酰胺水溶液的分子动力学模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对N-甲基乙酰胺(NMA)分子的水溶液体系进行了分子动力学模拟. 与经典的力场模型相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理体现了分子中的电荷分布. 相对其它极化力场模型, 该模型具有计算量较小的特点. 在该模型下对NMA纯溶液和其水溶液体系进行了分子动力学模拟, 得到的径向分布函数、汽化热和偶极矩等物理量与实验值和其它极化力场方法符合很好, 合理描述了溶质与溶剂之间的静电极化和分子内的电荷转移.     

有机π共轭配体溶剂化效应与分子间相互作用的理论研究

采用可极化的连续介质模型(PCM), 运用密度泛函理论(DFT), 在B3LYP/6-31+G^**水平下研究了溶剂极性对有机π共轭配体N,N'-Bis-(3-pyridyl)ethylene-bis-urea(BPEBU)中syn-anti构象的分子几何和电子结构的影响, 并借助分子动力学模拟的方法, 采用明确溶剂模型研究了溶质-溶剂分子间的相互作用. 密度泛函理论计算结果表明, 随着溶剂极性的增强, BPEBU中尿素基上的CO键和N-H键以及吡啶环上的C-N键被明显极化, 使羰基氧原子和吡啶氮原子的电负性明显增强, 尿素基的N-H键上氢原子的正电荷也显著增加. 分子动力学模拟统计的结果表明, 在极性较强的乙醇溶液中, 有明确的O…H-O, N…H-O和N-H…O等3种氢键作用存在, 而在丙酮溶液中, 只有N…H-O一种氢键作用存在, 而且与乙醇溶液中的N…H-O作用相比要弱些. 另外, 采用密度泛函理论方法结合连续/明确的混合溶剂模型, 优化得到了溶质-溶剂三聚体的超分子簇结构, 与分子动力学模拟的第一溶剂层中的超分子结构相比, 两者定性一致.     

软胶体粒子形成束晶的动力学模拟

利用广义指数模型描述软胶体粒子, 结合分子动力学模拟研究软胶体粒子形成束晶的动力学过程. 通过等温压缩和等密度降温2个不同的过程, 研究了束晶形成过程中结构变化特征和动力学路径对结构的影响规律. 研究发现, 与蒙特卡洛模拟结果相比, 分子动力学模拟得到的结构随着密度的变化有明显的迟滞现象, 这是由于考虑了真实的动力学因素引起的差异. 此外, 在相同温度和压力下通过不同的动力学路径得到的相结构不完全相同, 这是由于动力学形成过程会对相结构产生很大的影响.     

分子动力学模拟纳米尺寸限制体系下氩溶液中I2的振动能量弛豫

利用平衡态分子动力学方法(EMD)模拟了纳米尺寸限制球壳内I2在Ar溶液中的振动能量转移.计算并讨论了I2振动能量弛豫时间T1随球壳半径、溶剂密度的变化规律.通过分子间相互作用分析,在原子、分子水平上,揭示了随着球壳半径的减小,T1呈逐渐增大趋势的原因.结果表明,球壳的几何限制效应和表面作用对受限溶液密度分布的影响较大,从而导致溶质振动弛豫的显著变化.此外,非限制体系模拟显示,非平衡态分子动力学(NEMD)方法可以得到与平衡态分子动力学方法较一致的振动能量弛豫时间T1.     

分子动力学模拟纳米尺寸限制体系下氩溶液中I2的振动能量弛豫

利用平衡态分子动力学方法(EMD)模拟了纳米尺寸限制球壳内I2在Ar溶液中的振动能量转移. 计算并讨论了I2振动能量弛豫时间T1随球壳半径、溶剂密度的变化规律. 通过分子间相互作用分析, 在原子、分子水平上, 揭示了随着球壳半径的减小, T1呈逐渐增大趋势的原因. 结果表明, 球壳的几何限制效应和表面作用对受限溶液密度分布的影响较大, 从而导致溶质振动弛豫的显著变化. 此外, 非限制体系模拟显示, 非平衡态分子动力学(NEMD)方法可以得到与平衡态分子动力学方法较一致的振动能量弛豫时间T1.     

线性响应理论及谱密度

介绍处理近平衡体系的量子统计理论——线性响应理论。导出弱电磁场作用下任意力学量的系综平均值。以电偶极矩吸收外电场的谱密度为例，用分子动力学模拟液态水的红外光谱，结果与实验值符合。     

流体系统模拟中邻区列表算法的优化理论

分子动力学模拟中邻区列表算法的效率依赖于其参数的选择. 作者提供了一种选择最优化参数的计算方法, 通过分别使用自由粒子近似和扩散近似对所需模拟的时间进行计算, 再对两种近似计算进行比较. 结果表明, 在密度较低或者皮肤半径较小的情况下需要采用自由粒子近似, 而当密度较高或者皮肤半径较大的情况下则需要采用扩散近似. 该方法的结果与Lennard-Jones流体系统的模拟结果符合得很好.     

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.     

Local and nonlocal contributions to molecular first-order hyperpolarizability: a Hirshfeld partitioning analysis

Based on first-principles calculations, a decomposition scheme is proposed to investigate the molecular site-specific first-order hyperpolarizability (β) responses by means of Hirshfeld population analysis and finite field method. For a molecule, its β is decomposed into local and nonlocal contributions of individual atoms or groups. The former describes the response within the atomic sphere, while the latter describes the contributions from interatomic charge transfer. This scheme is then applied to six prototypical donor-acceptor (D-A) or D-π-A molecules for which the local and nonlocal hyperpolarizabilities are evaluated based on their MP2 density. Both the local and nonlocal parts exhibit site-specific characteristics, but vary differently with molecular structures. The local part depends mainly on the atomic attributes such as electronegativity and charge state, as well as its location in the molecule, while the nonlocal part relates to the ability and distance of charge delocalization within the molecule, increasing rapidly with molecular size. The proposed decomposition scheme provides a way to distinguish atomic or group contributions to molecular hyperpolarizabilities, which is useful in the molecular design for organic nonlinear optical materials.     

The extent of molecular orientation at liquid/vapor interface of pyridine and its alkyl derivatives by molecular dynamics simulation

In this paper, molecular dynamics simulation was performed to investigate the liquid∕vapor interfacial structure of neat polar liquids. Large-scale ensembles of liquid pyridine and its alkyl derivatives, 4-methylpyridine and 4-ethylpyridine, were simulated by classical molecular dynamics at 298 K. For the liquid system of low polarity, the surface density profile of the atoms meet exactly at the middle of interfacial region, and atoms of hydrophobic nature can be hardly discriminated from hydrophilic ones in either vapor or liquid sides. For a liquid system of high polarity, the density profile of atoms with different nature is highly discriminated all over the interfacial region, and as the polarity increases, a dense region of atomic density is clearly developed in the subsurface region. The recognized bivariate method was also used to study the molecular orientational distribution quantitatively. Orientational analysis of the three liquid systems indicates that the pyridine ring plane in the outmost surface tends to be vertical. Its tendency in the innermost interfacial region is parallel. The orientational states available to 4-ethylpyridine and pyridine are discriminated by predicting the possibility of a bisector-wise tumbling for the ring plane in pyridine and a side-wise tumbling in 4-ethylpyridine. The orientational distribution maps explain the trend of experimental surface tension and surface entropy. As the dipole moment of these liquids increases with the alkyl chain length, the surface structural profile changes from a regular definite one to a surface of complex atomic structure involving a dense phase near the interface. The development of dense region in alkyl derivatives is the result of segregation of molecules due to the alkyl group, which is captured and discriminated by molecular dynamics simulation even when the length of a short alkyl chain is increased by one carbon atom.     

Interface structure of silicon nanocrystals embedded in an amorphous silica matrix

We performed molecular dynamics simulations of the atomic structure of silicon nanocrystals embedded in a stoichiometric amorphous silica matrix. The atom–atom interactions are described by a combination of well-assessed potentials for bulk silicon and SiO₂, plus a mixing term to allow adjusting the charge transfer at the interface between Si and silica. For the free-standing Si nanocrystals, we find that the spherical structure is favoured with respect to the faceted one, up to at least a diameter of 6 nm. Correspondingly, the surface layer shows a higher diffusivity than the bulk. When embedded in the silica matrix, nanocrystals are under severe mechanical stress which is released by the combined formation of porosity at the interface and of bridging Si–O–Si bonds, whose density increases with the nanocrystal size. Vibrational frequencies specific to the interface bonding are identified and discussed.     

The ellipsoidal Gaussian basis in molecular orbital theory

The ellipsoidal Gaussian basis function used in a minimal valence atomic orbital representation is compared with the double-zeta spherical Gaussian basis orbital representation for some seventeen molecules made up of first row atoms and hydrogen. Except for acetylene the double-zeta basis gives consistently better total electronic energies and generally better property values than the optimized ellipsoidal single zeta basis. Difference molecular density contour maps comparing the two basis sets, as well as other one-electron property values, indicate that the ellipsoidal basis exaggerates the transfer of charge from the atomic regions to the interatomic and lone pair regions of molecules. Apparently, the forced complete elliptization of the valence atomic orbital in the single-zeta representation does not allow the basis set sufficient flexibility to simultaneously represent both the basically spherical atomic part of these orbitals and the non-spherical molecular bond formation. Other properties and aspects of the ellipsoidal Gaussian basis are also discussed.     

Interatomic voids in analysis of computer model structures of liquids and glasses

To analyze the structure of noncrystalline systems (liquids, glasses), it is suggested that the functions to be calculated should include not only the conventional atom-atom radial distribution function and structural factor, but also the same functions for a system of points representing the centers of interatomic voids. The points are located at the nodes of Voronoi polyhedra or, which is equivalent, at the centers of the spheres circumscribed around the Delaunay simplices. The system of points (system {D}) is unambiguously defined by the atomic coordinates and conveys additional information on the structure of the system because each interatomic void is determined by the relative positions of several atoms. Using a homogeneous noncrystalline packing model of atoms and inhomogeneous models derived from it as an example, we demonstrate that system {D} is sensitive to the structural features on medium scales and may be used along with the conventional atom-atom functions to study structural correlations other than short-range order correlations.     

Molecular simulation of the interlayer structure and the mobility of alkyl chains in HDTMA+/montmorillonite hybrids

Molecular simulation techniques are used to find the basal spacing of organoclay on the basis of the energy minimum, using the canonical NVT ensemble. Then, the interlayer structure and mobility of alkyl chains are explored based on the interlayer atomic density profiles. Besides the basic lateral-monolayer arrangement, lateral-bilayer accompanied by partial a pseudo-trilayer and a transition structure between the two basic lateral models are observed. The later provides an excellent explanation about the reflection at 16 angstroms on XRD patterns in the literature. The atomic density profiles reveal that nitrogen atoms show stronger layering behavior than carbon atoms do. Our simulation demonstrates that the molecular mobility of the confined alkyl chains decreases from lateral-monolayer to lateral-bilayer with the increase of the intercalated surfactant. This is in accordance with the suggestion deduced from experiments. Furthermore, our simulation indicates that the mobility of the alkyl chains strongly depends on the surfactant arrangement rather than the surfactant packing density.     

桥基原子对金属—金属作用的影响

本文借助EHMO法得到的Mulliken集居数和经验公式,讨论了过渡金属原子簇分子构型的稳定性和桥基与金属原子形成的平面距离D对其稳定性的影响。指出可用D值与实验上得到的距离d值的差别,判断过渡金属原子簇化合物金属—金属作用的强弱。     

Chemical fragments in real space: definitions, properties, and energetic decompositions

The physical and chemical meaning of real space molecular fragments resulting from arbitrary partitions of the density is reviewed under a common unifying formalism. Both fuzzy (interpenetrating) and non-fuzzy (exhaustive) decompositions are treated on an equal basis. Density decompositions are consistently generalized to compatible density matrix partitions by using Li and Parr's ideas (Li and Parr J Chem Phys 1986, 84, 1704), and these are carried onto an energy partition. It is argued that the merits of a given decomposition should be judged against both the charge and the energetic image it provides. Atomic partitions are used to show how the interacting quantum atoms approach (IQA) allows us to cope with the most important energy cancellations of quantum chemistry. Binding results from a trade-off between atomic (or fragment) energy deformations with respect to a reference and interatomic (interfragment) interactions. Deformation energies are divided into charge transfer and redistribution terms and their relative roles are analyzed. A number of systems are compared against the fuzziness of different density decompositions. The results consistently show that fuzzy partitions tend to give low atomic net charges and enhanced covalency, while exhaustive partitions generate larger net charges and smaller covalencies, across a wide range of bonding regimes.