钯团簇形成和增长机理的Monte Carlo研究

利用Monte Carlo（MC）方法和Lennard-Jones加Axilord-Teller （LJ＋AT）势能函数,研究了气相中钯团簇的形成过程和增长机理.发现具有二十面体结构的Pd13团簇可以在气相中自发形成,较大的团簇通过在Pd13二十面体结构的表面添加原子组成四面体的方式形成.通过分析团簇结构和能量之间的关系,发现除了Pd13和Pd55以外,Pd19和Pd39团簇也具有五次对称性,都是比较稳定的结构.     

铝原子Bernal多面体团簇的理论研究

将遗传算法用于铝原子团簇的构型计算.运用这种方法,从任意构型开始,较好地计算了6、8、9、10个铝原子组成的原子团簇的能量最低时的构型,发现这四种铝原子团簇的能量最低构型分别取四种Bernal多面体排列.并对得到的四种构型用密度泛函方法（DFT）进行量子化学计算,结果表明，这类构型是势能面上的极小值点,可以稳定存在.     

Li和Al掺杂的MgO(001)表面负载W_3O_9团簇的构型与电子结构

采用基于第一性原理的分子动力学和量子力学相结合的方法,对W3O9团簇在经Li和Al原子掺杂的MgO(001)表面的负载构型、稳定性以及体系的电子结构进行了系统研究.结果表明,当掺杂发生在表层时,杂质原子的类型对W3O9团簇的负载构型有显著影响.对于缺电子的Li掺杂,负载后W3O9团簇环状构型并不稳定,转化为链状结构;而Al原子的掺杂则使得MgO(001)表面电子富余,此时W3O9团簇存在平躺和垂直两种吸附方式,二者能量稳定性相近,其中前者存在同时与三个W原子成键的帽氧结构.当掺杂发生在次表层时,两种掺杂体系W3O9的负载构型相似,团簇仍保持环状结构并倾向于采用垂直方式沉积在表面上.与Li掺杂体系相比,富电子的Al掺杂可显著增强W3O9与MgO(001)表面之间的结合能力,负载后有较多电子从表面转移到团簇中特定的W原子上,这将对W3O9团簇的催化性能产生显著影响.     

Pdn(n=2～13)团簇的密度泛函理论研究

采用密度泛函理论B3LYP方法计算并讨论钯原子团簇Pdn(n=2～13)结构模型.通过对钯原子团簇进行几何构型优化和振动频率计算,找出团簇总能量最低的同分异构体.由于Jahn-Teller效应的存在,团簇的最稳定结构采取对称性较低的几何构型.在钯原子数相同时,往往存在多个能量极为相近的稳定构型.单位原子平均静态极化率呈奇偶变化.     

(TiNi)_x(x=2~4)团簇结构和电子结构

从团簇角度对TiNi形状记忆合金进行了量子化学从头算研究。设计并优化了等原子比(TiNi)x(x=2~4)簇的多种可能几何结构,并对较稳定构型进行电子结构的分析。结果表明,等原子比的(TiNi)n团簇以TiNi成键为主要分子骨架,小团簇有较多能量接近的异构体,TiTi成键对能量降低有较大贡献。     

定向Monte Carlo格点搜索算法用于氧化铝团簇(Al2O3)n (n=1~50)的结构搜索

氧化铝纳米团簇在众多技术应用中日益受到重视, 找到其最优结构对进一步的研究非常重要. 本工作提出了一种定向Monte Carlo格点搜索算法用于搜索不同氧化铝晶体(α, θ和δ)内的不同尺寸的氧化铝纳米团簇的结构, 并对结构进行了分析比较. 通过定向移动策略, 定向Monte Carlo格点搜索中每一步都是“有效”移动, 极大地增加了搜索效率. 研究结果发现α氧化铝团簇形成一种多层结构, θ和δ氧化铝团簇形成一种单层薄膜结构. θ和δ氧化铝团簇的二阶能量差分存在奇偶震荡, 偶数尺寸的氧化铝团簇具有相对更高的稳定性. 通过相对能量比较发现相同尺寸下θ和δ氧化铝团簇薄膜结构比α氧化铝团簇结构更稳定, 在对这种薄膜进行第一性原理计算后进一步验证这种薄膜具有良好的稳定性和抗氧化性.     

团簇Ti4 P的反应活性研究

为了得到团簇Ti4P参与化学反应时反应活性最好的结构模型,对团簇Ti4P分析时依据密度泛函理论,并在B3LYP和BP86杂化泛函和Lan12dz赝势基组分别进行分析研究.首先从能量角度分析团簇Ti4P的稳定性,得到构型1(4)即四重态构型中能量最低的戴帽三角锥构型稳定性最好,3(2)即二重态构型中能量最高的戴帽三角锥构...     

双二十面体Agn(n=19, 23, 24, 25)团簇低能稳态构型的TS搜索

采用基于NEB的MEP的LST/QST方法, 发展了一种不依赖团簇初始结构而得到其低能稳态构型的过渡态搜索方法, 预测和分析了孤立与铰链双二十面体Ag_n (n=13, 19, 23, 24, 25)的低能稳态构型. 证实Ag₁₃-I_h的低能稳态构型是一个含有五角双锥碎片的Ag₁₃-C₂扁平层状结构, 而Ag₁₉-D_5h的低能稳态构型则是在13原子二十面体上添加6原子组成Ag₁₉-C₁球形结构. 并且揭示Ag₂₃-D_3h, Ag₂₄-D_2h, Ag₂₅-D_5d与Ag_n (n=17～22)团簇一样, 其低能稳态构型也含有一个13原子的变形二十面体核心.     

丙酮团簇的多光子电离解离与结构计算

用355nm激光多光子电离解离飞行时间质谱观测到在超声分子束中形成的最多为12个分子的团簇离子及其碎片.用密度泛函方法对n=2～5的丙酮团簇结构进行计算,给出了优化构型及其基态能量.结果表明,两个丙酮分子组成团簇时稳定结构为近似垂直构型.3～5个丙酮分子组成团簇时以环状结构最稳定.     

TiO2(110)表面负载W3O10团簇构型和电子结构的理论研究

采用基于第一性原理的分子动力学和量子力学相结合的方法, 对非化学计量比富氧型钨氧化物团簇W₃O₁₀在TiO₂(110)表面负载的构型和电子结构进行了系统研究. 研究结果表明, 热力学最稳定的负载构型为W₃O₁₀团簇通过端氧原子和W原子形成四根Ti-O键和两根W-O键吸附在TiO₂(110)表面. 负载W₃O₁₀团簇后, 有较多电子从TiO₂表面转移到团簇上, TiO₂表面不再保持半导体性质, 相应地, 表面功函上升. 比较负载前后团簇的稳定性可知, 可以通过沉积在合适的固体表面来稳定气相中的不稳定构型.     

Parallel random tunneling algorithm for structural optimization of Lennard-Jones clusters up to N=330

A random tunneling algorithm (RTA) is derived from the terminal repeller unconstrained subenergy tunneling (TRUST) algorithm, and the parallelization of the RTA is implemented with an island parallel paradigm. Combined with the techniques of angular moving, the parallel random tunneling algorithm (PRTA) is applied to the optimization of Lennard-Jones (LJ) atomic clusters, and all the global minima of LJ clusters with size up to 200 are successfully located. For the optimization of larger cluster, a PRTA with an improved seeding technique is developed and successfully applied to the optimization of LJ151-LJ309. Furthermore, the optimized structures of LJ309-330 with the PRTA, which have not been studied before, are also provided.     

Clever and efficient method for searching optimal geometries of lennard-jones clusters

An unbiased algorithm for determining global minima of Lennard-Jones (LJ) clusters is proposed in the present study. In the algorithm, a global minimum is searched by using two operators: one modifies a cluster configuration by moving atoms to the most stable positions on the surface of a cluster and the other gives a perturbation on a cluster configuration by moving atoms near the center of mass of a cluster. The moved atoms are selected by employing contribution of the atoms to the potential energy of a cluster. It was possible to find new global minima for LJ506, LJ521, LJ536, LJ537, LJ538, and LJ541 together with putative global minima of LJ clusters of 10-561 atoms reported in the literature. This indicates that the present method is clever and efficient for cluster geometry optimization.     

Global optimization of Lennard-Jones clusters by a parallel fast annealing evolutionary algorithm

A parallel fast annealing evolutionary algorithm (PFAEA) was presented and applied to optimize Lennard-Jones (LJ) clusters. All the lowest known minima up to LJ(116) with both icosahedral and nonicosahedral structure, including the truncated octahedron of LJ(38), central fcc tetrahedron of LJ(98), the Marks' decahedron of LJ(75)(-)(77), and LJ(102)(-)(104), were located successfully by the unbiased algorithm. PFAEA is a parallel version of fast annealing evolutionary algorithm (FAEA) that combines the aspect of population in genetic algorithm and annealing algorithm with a very fast annealing schedule. A master-slave paradigm is used to parallelize FAEA to improve the efficiency. The performance of PFAEA is studied, and the scaling of execution time with the cluster size is approximately cubic, which is important for larger scale energy minimization systems.     

A dynamic lattice searching method with constructed core for optimization of large Lennard-Jones clusters

A variation of the previous dynamic lattice searching (DLS) method, named as DLS with constructed core (DLSc), was proposed for structural optimization of Lennard-Jones (LJ) clusters. In the new method, the starting random structure is generated with an icosahedron or a decahedron as a core. For a cluster with n shells, the atoms in the inner n - 2 shells are set as a fixed core, and the remaining atoms in the outer 2 shells are optimized by DLS. With applications of DLSc to optimization of LJ100-200 and LJ660-670, it was found that all the putative global minima can be obtained by using the DLSc method, and the method was proved to be high efficient compared with the previous DLS, because the searching space is reduced by the use of the fixed core. However, although DLSc is still an unbiased approach for smaller LJ clusters, it turned out to be biased for large ones. Further works are still needed to make it to be a more general method for cluster optimization problem.     

Global minimum structure searches via particle swarm optimization

Novel implementation of the evolutionary approach known as particle swarm optimization (PSO) capable of finding the global minimum of the potential energy surface of atomic assemblies is reported. This is the first time the PSO technique has been used to perform global optimization of minimum structure search for chemical systems. Significant improvements have been introduced to the original PSO algorithm to increase its efficiency and reliability and adapt it to chemical systems. The developed software has successfully found the lowest-energy structures of the LJ(26) Lennard-Jones cluster, anionic silicon hydride Si(2)H(5) (-), and triply hydrated hydroxide ion OH(-) (H(2)O)(3). It requires relatively small population sizes and demonstrates fast convergence. Efficiency of PSO has been compared with simulated annealing, and the gradient embedded genetic algorithm.     

A dynamic lattice searching method with interior operation for unbiased optimization of large Lennard-Jones clusters

For improving the efficiency of dynamic lattice searching (DLS) method for unbiased optimization of large Lennard-Jones (LJ) clusters, a variant of the interior operation (IO) proposed by Takeuchi was combined with DLS. The method is named as DLS-IO. In the method, the IO moves outer atoms with higher energy toward the coordinates center, i.e., (0, 0, 0), of a cluster and a local minimization (LM) follows each IO. This makes the interior atoms more compact and the outer atoms more uniformly distributed with lower potential energy. Therefore, the starting structure for DLS operations is closer to the global optimum compared with the randomly generated structures. On the other hand, a method to identify the central atom is proposed for the central vacancy problem. Optimizations of LJ(500), LJ(561), LJ(660), LJ(665), and LJ(670) were investigated with the DLS-IO, and the structural transition during the optimization was analyzed. It was found that the method is efficient and unbiased for optimization of large LJ clusters, and it may be a promising approach to be universally used for structural optimizations.     

A doubly nudged elastic band method for finding transition states

A modification of the nudged elastic band (NEB) method is presented that enables stable optimizations to be run using both the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) quasi-Newton and slow-response quenched velocity Verlet minimizers. The performance of this new "doubly nudged" DNEB method is analyzed in conjunction with both minimizers and compared with previous NEB formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to 2 orders of magnitude. Applications to permutational rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an updated algorithm for constructing complicated multi-step pathways using successive DNEB runs.     

PDECO: Parallel differential evolution for clusters optimization

The optimization of the atomic and molecular clusters with a large number of atoms is a very challenging topic. This article proposes a parallel differential evolution (DE) optimization scheme for large‐scale clusters. It combines a modified DE algorithm with improved genetic operators and a parallel strategy with a migration operator to address the problems of numerous local optima and large computational demanding. Results of Lennard–Jones (LJ) clusters and Gupta‐potential Co clusters show the performance of the algorithm surpasses those in previous researches in terms of successful rate, convergent speed, and global searching ability. The overall performance for large or challenging LJ clusters is enhanced significantly. The average number of local minimizations per hit of the global minima for Co clusters is only about 3–4% of that in previous methods. Some global optima for Co are also updated. We then apply the algorithm to optimize the Pt clusters with Gupta potential from the size 3 to 130 and analyze their electronic properties by density functional theory calculation. The clusters with 13, 38, 54, 75, 108, and 125 atoms are extremely stable and can be taken as the magic numbers for Pt systems. It is interesting that the more stable structures, especially magic‐number ones, tend to have a larger energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital. It is also found that the clusters are gradually close to the metal bulk from the size N > 80 and Pt₃₈ is expected to be more active than Pt₇₅ in catalytic reaction. © 2013 Wiley Periodicals, Inc.     

Approximation of the Dymond-Rigby-Smith potential function using the Lennard-Jones form

Due to the mathematical similarities between the Dymond-Rigby-Smith (DRS) function with the conventional Lennard-Jones (LJ) functions, modification to the LJ indices is made herein in order to approximate the DRS energy curve. It is herein shown that the LJ(9-6) potential approximates well the DRS curve for interatomic distance shorter than the equilibrium distance. For interatomic distance longer than the equilibrium distance, a pair of LJ indices, based on the equal mean stretching energy, was found to give very good agreement with the DRS curve. Modification to the conventional LJ functions for describing the DRS energy, rather than the replacement of the LJ potentials with DRF function, allows numerous computational chemistry softwares to quantify the DRS energy with minimal hard-coding of their algorithms.     

Comparison of double-ended transition state search methods

While a variety of double-ended transition state search methods have been developed, their relative performance in characterizing complex multistep pathways between structurally disparate molecular conformations remains unclear. Three such methods (doubly-nudged elastic band, a string method, and a growing string method) are compared for a series of benchmarks ranging from permutational isomerizations of the seven-atom Lennard-Jones cluster (LJ(7)) to highly cooperative LJ(38) and LJ(75) rearrangements, and the folding pathways of two peptides. A database of short paths between LJ(13) local minima is used to explore the effects of parameters and suggest reasonable default values. Each double-ended method was employed within the framework of a missing connection network flow algorithm to construct more complicated multistep pathways. We find that in our implementation none of the three methods definitively outperforms the others, and that their relative effectiveness is strongly system and parameter dependent.