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     

中介尺度Au纳米团簇熔化的分子动力学模拟

采用分子动力学模拟技术，研究了原子个数为16～8628的 Au纳米团簇的熔化过程.采用 Johnson的EAM (embedded atom method) 模型,模拟结果表明，金属纳米团簇存在一中介尺度区域.对Au纳米团簇而言，当原子个数N >456时，团簇的热力学性质与团簇尺寸呈线性关系，熔化首先从表面开始，逐步向中心区域推进，且满足Tmb－Tmc(N)＝aN(－1/3)的关系.另外，计算了中介区域的团簇的尺寸、熔化温度、表面能、熵、焓等热力学量以及均方根位移（RMSD）等动力学量，为研究纳米团簇提供定量数据.     

纳米镍团簇表面性质及能量的分子动力学研究

在单分散金属纳米粒子制备过程中,金属烧结现象需要尽量避免。烧结与诸多因素有关,其中金属纳米粒子的表面性质和能量对烧结作用有着重要影响。本工作利用分子动力学,以4种不同粒径的金属Ni纳米团簇为研究对象,在COMPASS力场下对不同温度下其表面积、扩散性质、表面能以及比表面能等进行了计算。结果显示,随着温度从300K升至1000K,纳米团簇的表面积稍微增加了约5%,表面层扩散系数显著增加了约3个数量级,表面能量升高了约15%,同时表面层与体相的能量差明显增加了近3倍。比表面能定义为增加单位表面积所引起的表面能的增量。计算结果表明,700K时团簇的比表面能比镍熔点处的表面张力高出约3个数量级,预示着团簇烧结具有强大的推动力。比表面能随温度升高以及粒径增大而下降,与热力学原理相一致。     

小尺寸金属团簇熔化过程的分子动力学模拟

运用分子动力学方法模拟了小尺寸金属团簇的熔化过程, 原子之间的作用采用嵌入原子法(EAM)模型, 计算了均方根键长涨落δ随温度的变化, 以及升温过程中团簇热容的变化. 包含55、56个原子的面心立方(FCC)结构Au团簇的熔化过程是基本相同的. 而同样结构和数目Cu团簇的熔化过程却呈现出不同的趋势. Cu55、Cu56在模拟过程中都出现了FCC结构到二十面体结构的转变. 但由于表面多出了一个原子, Cu56的热容曲线比Cu55多了一个峰, 体系出现了预熔化现象. 这表明小尺寸团簇的固液转变的过程与团簇的原子类型、几何结构和原子数目密切相关.     

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。     

钯团簇碰撞沉积钯/银基板的分子动力学模拟

运用分子动力学模拟方法研究了常温下较大的钯团簇以不同初始速度撞击不同硬度基板的微观过程,着重分析了沉积形貌的变化、团簇的嵌入深度和原子的扩散程度、基板碰撞接触区域的温度演变以及碰撞过程中团簇与基板间的能量转化,获得了沉积过程中变形形貌、结构特征及能量转化随团簇尺寸、初始速度及基板材质的变化规律.并进一步探究了第二颗团簇以不同时刻沉积时前一团簇的变形形貌及基板接触区域温度变化的特点,发现短时间间隔下第二颗团簇的沉积更有利于团簇与基板的结合.     

团簇研究中的原子间势函数

原子间势函数在团簇结构和性质的理论研究中十分重要.本文将模拟团簇原子间相互作用的势函数划分成三类,对各类势函数的发展状况进行了综述;并对原子间势函数与最优化方法和分子动力学相结合,在团簇结构和性能研究中的应用和发展方向进行了讨论.     

（AgI）n团簇熔化行为的分子动力学模拟

用遗传算法结合经验势搜索了 (AgI)n(n=3-15) 团簇的可能稳定结构,并用微正则分子动力学方法研究了它们的熔化行为.(AgI)n 团簇的稳定结构主要以四叫元环和六元环相接的笼状结构为主.大多数(AgI)n会在一个较大的温度范围内随温度升高结构不断扭曲,原子间距涨落及动能涨落不断增大,直到在某个温度下熔化,结构变得完全无序.(AgI)6 的结构具有很高的对称性,熔化发生在一个较窄的温度范围.对于(AgI)5,会在熔化前较大的温度范围内发生最稳定结构与能量较高的环状异构体之间的转化,并可能出现负热容现象.     

(AgI)n团簇熔化行为的分子动力学模拟

用遗传算法结合经验势搜索了(AgI)n(n=3-15)团簇的可能稳定结构, 并用微正则分子动力学方法研究了它们的熔化行为. (AgI)n团簇的稳定结构主要以四元环和六元环相接的笼状结构为主. 大多数(AgI)n会在一个较大的温度范围内随温度升高结构不断扭曲, 原子间距涨落及动能涨落不断增大, 直到在某个温度下熔化, 结构变得完全无序. (AgI)6的结构具有很高的对称性, 熔化发生在一个较窄的温度范围. 对于(AgI)5, 会在熔化前较大的温度范围内发生最稳定结构与能量较高的环状异构体之间的转化, 并可能出现负热容现象.     

TNT高温热解及含碳团簇形成的反应分子动力学模拟

ReaxFF-MD模拟三硝基甲苯(TNT)高温热解显示增加了伦敦耗散力项(Elg)的ReaxFF/lg势函数在含能材料平衡密度计算方面具有优越性.产物识别分析得出TNT热解的主要产物为NO2、NO、H2O、N2、CO2、CO、OH以及HONO,且最终产物为H2O、N2和CO2.使用ReaxFF势函数模拟同样过程进行比较性分析显示,在主要产物和最终产物方面与ReaxFF/lg作用结果具有一致性,但在化学反应动力学方面表现出一些差异.orthoNO2键断裂和C―NO2→C―ONO重排布-断裂形成NO2和NO是TNT热解的主要初级反应,且前者产生速率大于后者,NO2和NO形成后很快参与次级反应并最终形成N2.高温热解中形成OH等小分子会促进H2O的形成.环上基团相互反应或直接脱落后,主环间C―C键才发生断裂,但温度升高会加快主环断裂,并进一步分解形成CO2,这也是高温条件下CO2分布产生波动的一个重要原因.并且当晶胞中的TNT分子几乎完全分解时,系统的势能开始明显衰减.与温度相比,密度对热解中最大含碳团簇形成的影响更明显.并且,模拟结果显示,在TNT完全分解前已经出现含碳中间体的聚合现象.此项工作表明使用ReaxFF/lg反应力场研究TNT高温热解可以提供具体的动力学和化学方面的信息,并有助于理解含能材料的爆轰问题并可进行安全评估.     

Molecular dynamics implementation in MSINDO: study of silicon clusters

Born-Oppenheimer molecular dynamics is implemented in the semiempirical self-consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Si(n) clusters (n = 5-7). The melting behavior of the Si(7) cluster is investigated and the MSINDO results are compared to previous high-level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si(45) and Si(60) clusters. New Si(45) and Si(60) structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.     

H2 adsorption on Ag‐nanocluster/single‐walled carbon nanotube composites: A molecular dynamics study on the effects of nanocluster size,diameter, and chirality of nanotube

The H₂ physisorption on Ag_N (with N = 32, 108, 256, 500, and 864)/carbon nanotube (CNT; in armchair and zigzag structures with diameters between 0.54 and 2.98 nm) composites were studied by molecular dynamic simulation to investigate the effect of nanocluster size, diameter, and chirality of nanotube on the adsorption phenomena. The calculations indicate that the effects of nanocluster properties are more important than those of the nanotube, in such a way that increase of nanocluster size, decreases the H₂ adsorption. Also, the diameter and chirality of CNTs have considerable influence on the adsorption phenomena. As the diameter of nanotube is increased, the amount of adsorption is decreased. Moreover, H₂ molecules have more tendencies to those nanoclusters located on the armchair nanotubes than the zigzag ones. Another important result is the reversibility of H₂ adsorption on these materials in which the structure of composite in vacuum and after reduction of H₂ pressure to zero, is not changed, considerably. © 2015 Wiley Periodicals, Inc.     

Tetracyclines adsorption onto alumina: A comparative experimental and molecular dynamics simulation study

Using alumina (Al₂O₃) as the adsorbent, a static adsorption experiment was carried out in this study. It comprehensively evaluated the factors including Al₂O₃ dosage, adsorption temperature, and pH that influence the adsorption capability of three tetracyclines (TCs), namely, tetracycline hydrochloride (TC), chlortetracycline hydrochloride (CTC) and oxytetracycline hydrochloride (OTC). The results demonstrate that the adsorption efficiency increases with Al₂O₃ dosage. In addition, low-acid or natural solution is benefit for the adsorption. The adsorption behavior is more reasonably described with the Freundlich isotherm, and fits well with the pseudo-second-order kinetic model (R²?>?0.999). The results of molecular dynamics (MD) simulation show that the structures of TCs deformed during the combining process. The values of binding energy of TCs follow the order as: CTC (88.45?kcal/mol)?>?OTC (73.54?kcal/mol)?>?TC (54.28?kcal/mol). The MD simulation results agree well with the adsorption experimental results, which indicates that the MD simulation is reliable and reasonable. The MD simulation will provide theoretical knowledge in understanding the adsorption mechanism and environmental behavior of TCs.     

Molecular dynamics study on lattice defects and heat capacity of LiCr1/6Mn11/6O4-d

Heat capacity of spinel LiCr_1/6Mn_11/6O_4-d (d=0, 0.0184)was measured between 5 and 300 K. Both compounds showed no anomaly in the measured temperature range, especially around the room temperature where a structural phase transition is reported for the parent compound LiMn₂O₄. The non-stoichiometric compound LiCr_1/6Mn_11/6O_3.9816 has greater heat capacity than that of the stoichiometric LiCr_1/6Mn_11/6O₄. Molecular dynamics study on the vibrational property of LiMn₂O_4-d revealed that the lattice defects in the non-stoichiometric compound increase the low frequency phonons compared with the stoichiometric compound. It should be related to the greater heat capacity of the non-stoichiometric compound LiCr_1/6Mn_11/6O_3.9816. This revised version was published online in August 2006 with corrections to the Cover Date.     

麋鹿朊蛋白结构稳定性的分子动力学研究

朊蛋白病是一种致命且具有高度传染性的神经退行性疾病.糜鹿是目前已经报道的哺乳类动物中较易发生朊蛋白病的物种之一.作者使用分子动力学和操控式分子动力学模拟相结合的方法对糜鹿正常朊蛋白的结构稳定性进行了研究.发现了麋鹿朊蛋白结构中的不稳定结构域分布以及热动力学性质,揭示了糜鹿朊蛋白稳定性的分子结构基础以及力学特征.     

Molecular dynamics simulation of surface morphology and thermodynamic properties of polyaniline nanostructured film

To develop predictive models in nanostructured films, there is an ongoing research to validate molecular dynamics (MD) simulation results with experimental data. The morphology and surface topography of polyaniline (PANI) nanostructured film coated on a TiO₂ nanocrystalline surface were investigated by scanning electron microscopy and atomic force microscopy, respectively. The atomistic model of the simulated PANI was generated using energy minimization with a condensed‐phase optimized molecular potential for atomistic studies force field function to reach a thermodynamic equilibrium state. Various parameters of PANI such as density, energy, cavity size, and free volume distributions are calculated. MD simulation has also been used to obtain specific volume (V) as a function of temperature (T). It is demonstrated that this V–T curve can be used to determinate glass transition temperature T_g, reliably. Although experimental data available for the PANI film are very limited, simulation results such as density and T_g are in good agreement with the experimental values reported in the literature. Comparison of the surface topography of PANI demonstrates a reasonable trend between atomic force microscopy image analysis and the MD simulation results at various temperatures. Copyright © 2014 John Wiley & Sons, Ltd.     

Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties

Clusters of a solute and a few solvent molecules obtained from molecular dynamics (MD) are a powerful tool to study solvation effects by advanced quantum chemical (QC) methods. For spectroscopic properties strongly dependent on the solvation, however, a large number of clusters are needed for a good convergence. In this work, a parallel variable selection (PVS) method is proposed that in some cases efficiently reduces the number of clusters needed for the averaging. The mass, charge, or atomic density MD distributions are used as a secondary variable to preselect the most probable cluster geometries used for averaging of solute spectral properties. When applied to nuclear magnetic resonance chemical shift of a model alcohol, the method allowed one to significantly reduce the total computational time, by a factor of 10. Even larger savings were achieved for the modeling of Raman and Raman optical activity spectra of (S)‐lactamide molecule dissolved in water. The results thus suggest that the PVS method can be generally used for simulations of spectroscopic properties of solvated molecules and makes multiscale MD/QC computations more affordable. © 2012 Wiley Periodicals, Inc.     

Properties of polystyrene and polymethyl methacrylate copolymers of polyhedral oligomeric silsesquioxanes: A molecular dynamics study

Molecular dynamics simulations were carried out on copolymers of both styrene and methyl methacrylate with polyhedral oligomeric silsesquioxane (POSS) derivatives to identify the origin of the property changes imparted upon the chemical incorporation of POSS. Simulations were carried out on these hybrid copolymers and the parent homopolymers to elucidate the effect of the T₈, T₁₀, and T₁₂ POSS cages. These POSS comonomers were derivatized with a single polymerizable function and 7, 9, and 11 nonpolymerizable hydrocarbon moieties, respectively. Glass transition temperatures (T_g) were computed from specific volume versus temperature plots. The packing of POSS units around the polymer backbone was analyzed via their radial distribution functions. The effect of POSS on polymer motion was analyzed through the mean square displacement function. The improvements in the elastic moduli upon incorporation of POSS were computed by employing the static deformation method. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 234–248, 2006     

Thermal analysis via molecular dynamics simulation

Thermal analysis by classical molecular dynamics simulations is discussed on hand of heat capacity of crystals of 9600 atoms. The differences between quantum mechanical and classical mechanical calculations are shown. Anharmonicity is proven to be an important factor. Finally, it is found that defects contribute to an increase in heat capacity before melting. The energy of conformational gauche defects within the crystal is only about 10% due to internal rotation. The other energy must be generated by cooperative strain. The conclusion is that the next generation of faster computers may permit wider use of molecular dynamics simulations in support of the interpretation of thermal analysis.Dedicated to Professor Bernhard Wunderlich on the occasion of his 65th birthday