应用ABEEM/MM模型研究水分子团簇(H2O)n (n=11～16)的性质

应用ABEEM/MM 模型计算了较大的水分子团簇(H2O)n (n=11~16)的各种性质,如：优化的几何构型, 氢键个数, 结合能, 稳定性, ABEEM 电荷分布, 偶极矩, 以及结构参数、平均氢键个数和强度, 增加的团簇结合能等.结果表明,从立方体结构到笼状结构的过渡出现在n=12的水分子团簇中,随着类似于笼状结构特点的不断增强,五元环的富集程度有所增加.     

应用ABEEM/MM力场模型研究水分子团簇(H2O)n(n=7～35)的性质

应用ABEEM/MM模型研究和计算了水分子团簇(H2O)n(n=7～35)的各种性质,如:优化的几何构型,氢键个数,结合能,稳定性,ABEEM电荷分布,偶极矩,以及结构参数、平均氢键个数和强度、团簇的递增结合能等,并描述了六聚水区域中所反映的从二维结构(从二聚水到五聚水)到三维结构(n>6的水分子团簇)的过渡,又进一步地预测了从立方体结构到笼状结构的过渡出现在n=12的水分子团簇中,随着类似于笼状结构特点的不断增强,五元环的富集程度有所增加.以上研究不仅系统研究和分析了水团簇的各种性质,而且对比Ab initio研究和实验结果,进一步验证了ABEEM/MM模型的合理性以及参数的正确性和可转移性.     

硅氧团簇(SiO2)nO2H4的密度泛函理论研究

提出硅氧团簇(SiO2)nO2H4的两种新构型: 基于笼状结构和环状结构的构型, 并与链状构型相比较, 用密度泛函理论的B3LYP方法在6-31G(d)基组水平上计算了三种构型n=2～22(n取偶数)的几何结构、平均结合能、能隙以及能量的二次差分. 分析计算结果发现, 笼状构型不但在n=4和8处存在幻数团簇(实验上已经观察到), 而且预测在n=14处也存在类似的幻数团簇; 此外, 与(SiO2)n团簇不同的是, (SiO2)nO2H4团簇的环状构型的稳定性从n=4开始大于链状构型, 意味着水的加成对硅氧团簇的稳定性有着重要的影响.     

乙醇-水分子团簇C2H5OH(H2O)n (n=1-9)稳定结构的量子化学研究

采用密度泛函理论B3LYP方法, 在B3LYP/6-311++G(2d,2p)//B3LYP/6-311++G(d,p)基组水平上对乙醇-水分子团簇(C₂H₅OH(H₂O)_n (n=1-9))的各种性质进行研究, 如: 优化的几何构型、结构参数、氢键、结合能、平均氢键强度、自然键轨道(NBO)电荷分布、团簇的生长规律等. 结果表明, 从二维(2-D)环状结构到三维(3-D)笼状结构的过渡出现在n=5的乙醇-水分子团簇中. 此外, 利用团簇结合能的二阶差分、形成能、能隙等性质, 发现在n=6时乙醇-水分子团簇的最低能量结构稳定性较好, 可能为幻数结构. 最后, 为了进一步探讨氢键本质, 将C₂H₅OH(H₂O)_n (n=2-9)最低能量结构的各种性质与纯水分子团簇(H₂O)_n (n=3-10)比较, 结果表明前者与后者中的水分子之间氢键相似.     

(BN)_n团簇的结构和稳定性

用HF方法、密度泛函理论的B3LYP以及微扰理论的MP2方法 ,在 6 3 1G(d)基组水平上 ,对 (BN) n(n =1～ 16)团簇的各种可能结构进行了优化 .讨论了环状与笼状稳定团簇的几何构型、自然键轨道 (NBO)、振动频率、结合能、核独立化学位移 (NICS)和能量二次差分 ,得到了 (BN) n(n =1～ 16)团簇结构的稳定性信息 .比较了HF ,B3LYP以及MP2三种理论方法对(BN) n 团簇的适应性所表现出的差异 .     

单笼形水分子簇中心水分子对类型关系

随机产生单笼形水分子簇(H2O)n(n=8~36),经分类统计后发现,在笼形水分子簇中,其1221,1212,2121和2112四类氢键的个数与水分子和氢键总数之间有定量关系,且1212类氢键的个数与2121类的氢键始终相等.如果笼形水分子簇中某一类氢键数已知,则它的其余三类氢键的个数也随即确定.     

大气环境中的水分子团簇分布和H+(H2O)n(n=4～16)离子的解离

报道了用质谱学方法首次测得的大气中各种水的团簇分布情况.表明在室内大气环境下,水主要是以几个至几十个水分子所组成的分子团簇的形式存在,且团簇的分布与空气湿度,即水在空气中的分压有关.实验中,除观测到空气中也存在前人已报道过的具有笼状结构的H+(H2O)21外,还观测到其他几种较稳定结构的水的团簇,即H+(H2O)4,H+(H2O)10和H+(H2O)15.实验中所测得的水分子团簇分布结果与使用的离子源以及质量分析器种类无关.我们还用碰撞诱导解离(CID)的方法研究了H+(H2O)n(n=4～16)离子的碰撞解离产物,结果表明,对于H+(H2O)n(n=4～16)的离子,其较稳定的离子的碰撞解离产物均为H+(H2O)n(n=4～6).我们还进一步研究了H+(H2O)10离子的碰撞解离产物与碰撞气体(即Ar气)密度的关系,得到了碰撞气体密度与碰撞解离产物分布的关系.     

水分子团簇分子力场方法的比较研究

采用传统水分子力场模型(SPC, TIPnP(n=3-5))和极化模型(POL3, AMOEBA, SPC-FQ, TIP4P-FQ)对水分子二聚体团簇性质进行了比较和研究. 以从头计算和实验数据为依据, 分析水分子在外场作用下体系的静电极化, 电荷转移和分子结构变化. 通过水分子二聚体结合能和各分解能量项评价极化静电势能在双分子结合能中的地位和作用, 以及各水分子力场的适用性. 通过水分子团簇多体相互作用能的计算,展示不同极化水分子力场定量计算极化能量的实际能力. 通过对力场模型结果的对比和分析, 为进一步发展极化力场模型, 并应用到其他体系提供借鉴和依据.     

(Mg3N2)n(n=1～4)团簇结构与性质的密度泛函研究

用密度泛函理论(DFT)的杂化密度泛函B3LYP方法在6-31G*基组水平上对(Mg3N2)n(n=1～4)团簇各种可能的构型进行几何结构优化,预测了各团簇的最稳定结构.并对最稳定结构的振动特性、成键特性、电荷特性和稳定性等进行了理论分析.结果表明:(Mg3N2)n=1～4团簇易形成笼状结构,其最稳定构型中N原子配位数以3、4较多见;团簇主要由Mg-N键组成,Mg-N键长为0.194～0.218nm,Mg-Mg 键长为0.262～0.298 nm;N原子的平均自然电荷为-2.06 e,Mg原子的平均自然电荷为 1.37 e;(Mg3N2)2团簇有相对较高的动力学稳定性.     

(BN)n团簇的结构和稳定性

用HF方法、密度泛函理论的B3LYP以及微扰理论的MP2方法，在6—31G(d)基组 水平上，对(BN)n(n=1-16)团簇的各种可能结构进行了优化．讨论了环状与笼状稳 定团簇的几何构型、自然键轨道(NBO）、振动频率、结合能、核独立化学位移 (NICS)和能量二次差分，得到了(BN)n(n＝1-16)团簇结构的稳定性信息．比较了 HF，B3LYP以及MP2三种理论方法对(BN)n团簇的适应性所表现出的差异．     

The spectroscopic signature of the "all-surface" to "internally solvated" structural transition in water clusters in the n = 17-21 size regime

The existence of a transitional size regime where preferential stabilization alternates between "all-surface" (all atoms on the surface of a cluster) and "internally solvated" (one water molecule at the center of the cluster, fully solvated) configurations with the addition or the removal of a single water molecule, predicted earlier with the flexible, polarizable (many-body) Thole-type model interaction potential (TTM2-F), has been confirmed from electronic structure calculations for (H2O)n, n = 17-21. The onset of the appearance of the first "interior" configuration in water clusters occurs for n = 17. The observed structural alternation between interior (n = 17, 19, 21) and all-surface (n = 18, 20) global minima in the n = 17-21 cluster regime is accompanied by a corresponding spectroscopic signature, namely, the undulation in the position of the most redshifted OH stretching vibrations according to the trend: interior configurations exhibit more redshifted OH stretching vibrations than all-surface ones. These most redshifted OH stretching vibrations form distinct groups in the intramolecular region of the spectra and correspond to localized vibrations of donor OH stretches that are connected to neighbors via "strong" (water dimer-like) hydrogen bonds and belong to a water molecule with a "free" OH stretch.     

Geometry Optimization of Ba2+(H2O)n Clusters Using a Fast Hybrid Global Optimization Algorithm

A global optimization called fast hybrid global optimization algorithm was proposed based on genetic algorithm, fast simulated algorithm and conjugated gradient algorithm. We employ it to search the global minimum energy structures of Ba²⁺(H₂O)_n clusters for n = 1–30 within the TIP4P model. The results show that Ba²⁺(H₂O)_n clusters have the n+0 structure while n = 1–8. When n is in the range 9 ≤ n ≤ 18, the number of water molecules in the first shell around the barium ion is 8 and the other water molecules arrange in the outer shell. In the global minimum structure of Ba²⁺(H₂O)₁₉, the number of the first shell water molecules adds up to 9, and the value is kept until n = 30. According to the computational results, a conclusion that hydration numbers for Ba²⁺ is 9 can be drawn, which is in agreement with the result by a Monte Carlo simulation.     

Larger water clusters with edges and corners on their way to ice: structural trends elucidated with an improved parallel evolutionary algorithm

For the difficult task of finding global minimum energy structures for molecular clusters of nontrivial size, we present a highly efficient parallel implementation of an evolutionary algorithm. By completely abandoning the traditional concept of generations and by replacing it with a less rigid pool concept, we have managed to eliminate serial bottlenecks completely and can operate the algorithm efficiently on an arbitrary number of parallel processes. Nevertheless, our new algorithm still realizes all of the main features of our old, successful implementation. First tests of the new algorithm are shown for the highly demanding problem of water clusters modeled by a potential with flexible, polarizable monomers (TTM2-F). For this problem, our new algorithm not only reproduces all of the global minima proposed previously in considerably less CPU time but also leads to improved proposals in several cases. These, in turn, qualitatively change our earlier predictions concerning the transitions from all-surface structures to cages with a single interior molecule, and from one to two interior molecules. Furthermore, we compare preliminary results up to n = 105 with locally optimized cuts from several ice modifications. This comparison indicates that relaxed ice structures may start to be competitive already at cluster sizes above n = 90.     

Global potential energy minima of C60(H2O)n clusters

Likely candidates for the global potential energy minima of C60(H2O)n clusters with n < or = 21 are found using basin-hopping global optimization. The potential energy surfaces are constructed using the TIP4P intermolecular potential for the water molecules, a Lennard-Jones water-fullerene potential, and a water-fullerene polarization potential, which depends on the first few nonvanishing C60 multipole polarizabilities. This combination produces a rather hydrophobic water-fullerene interaction. As a consequence, the water component of the lowest C60(H2O)n minima is quite closely related to low-lying minima of the corresponding TIP4P (H2O)n clusters. In most cases, the geometrical substructure of the water molecules in the C60(H2O)n global minimum coincides with that of the corresponding free water cluster. Exceptions occur when the interaction with C60 induces a change in geometry. This qualitative picture does not change significantly if we use the TIP3P model for the water-water interaction. Structures such as C60@(H2O)60, in which the water molecules surround the C60 fullerene, correspond to local minima with much higher potential energies. For such a structure to become the global minimum, the magnitude of the water-fullerene interaction must be increased to an unphysical value.     

H·(H2O)n clusters: microsolvation of the hydrogen atom via molecular ab initio gradient embedded genetic algorithm (GEGA)

A new version of the ab initio gradient embedded genetic algorithm (GEGA) program for finding the global minima on the potential energy surface (PES) of mixed clusters formed by molecules and atoms is reported. The performance of the algorithm is demonstrated on the neutral H·(H(2)O)(n) (n = 1-4) clusters, that is, a radical H atom solvated in 1-4 water molecules. These clusters are of a fundamental interest. The solvated hydrogen atom forms during photochemical events in water, or during scavenging of solvated electrons by acids, and transiently exists in biological systems and possibly in inclusion complexes in the deep ocean and in the ice shield of earth. The processes associated with its existence are intriguingly complex, however, and have been the subject of decades-long debates. Using GEGA, we explicate the apparently extreme structural diversity in the H·(H(2)O)(n) (n = 1-4) clusters. All considered clusters have four basic structural types: type I, where the H radical is weakly coordinated to the oxygen atom of one of the water molecules; type II, where H is weakly coordinated to a H atom of one of the water molecules; type III, consisting of H(2), the OH radical, and n - 1 H(2)O molecules; and type IV, consisting of H(3)O and n - 1 H(2)O. There are myriads of isomers of all four types. The lowest energy species of types I and II are the isoenergetic global minima. H·(H(2)O)(n) clusters appear to be a challenging case for GEGA because they have many shallow minima close in energy some of which are significantly less stable than the global minimum. Additionally, the global minima themselves have high structural degeneracy, they are only weakly bound, and they are prone to dissociation. GEGA performed exceptionally well in finding both the global and the low-energy local minima that were subsequently confirmed at higher levels of theory.     

Nonstandard cages in the formation process of methane clathrate: stability, structure, and spectroscopic implications from first-principles

Endohedral CH(4)@(H(2)O)(n) (n = 16, 18, 20, 22, 24) clusters with standard and nonstandard cage configurations containing four-, five-, six-, seven-membered rings were generated by spiral algorithm and were systematically explored using DFT-D methods. The geometries of all isomers were optimized in vacuum and aqueous solution. In vacuum, encapsulation of methane molecules can stabilize the hollow (H(2)O)(n) cage by 2.31~5.44 kcal/mol; but the endohedral CH(4)@(H(2)O)(n) cages are still less stable than the pure (H(2)O)(n) clusters. Aqueous environment could promote the stabilities of the hollow (H(2)O)(n) cages as well as the CH(4)@(H(2)O)(n) clusters, and the CH(4)@(H(2)O)(n) clusters possess larger stabilization energies with regard to the pure (H(2)O)(n) clusters except for n = 24. The lowest energy structures of the CH(4)@(H(2)O)(20) and CH(4)@(H(2)O)(24) cages are identical to the building units in the crystalline sI clathrate hydrate. All of the low-energy cages (including both regular and irregular ones) have large structural similarity and can be connected by "dimer-insertion" operation and Stone-Wales transformation. Our calculation also showed that in the range of cluster size n = 16-24, the relative energies of cage isomers tend to decrease with increasing number of the adjacent pentagons in the oxygen skeleton structures. In addition to the regular endohedral CH(4)@(H(2)O)(20) and CH(4)@(H(2)O)(24) cage structures, some nonstandard CH(4)@(H(2)O)(n) (n = 18, 20, 22, 24) cages have lower energies and might appear during nucleation process of methane hydrate. For the methane molecules in these low-energy cage isomers, we found that the C-H symmetric stretching frequencies show a red-shift trend and the (13)C NMR chemical shifts generally move toward negative values as the cavity size increases. These theoretical results are comparable to the available experimental data and might help experimental identification of the endohedral water cages during nucleation.     

用密度泛函方法研究质子化苯基丙酮-水团簇

The structure and growth trend of the protonated acetophenone-water clusters have been investigated using the DFT-B3LYP method combined with the standard 6-31+G(d,p) basis set. In order to obtain more accurate single-point energy the B3LYP/6-311++G(3df,2p) method was adapted. The results show that the formation of H+C8H8O-H2O is a barrierless reaction process and the equilibrium distance between the proton and the O atom in C8H8O molecule is 1.015 A. For H+C8H8O-(H2O)n(n=1,2,3) clusters, the proton lies between the acetophenone molecule C8H8O and the water molecule H2O. The distance between the proton and the O atom of the C8H8O molecule increased from n=1 to n=3; C8H8O-H+-H2O can be regarded as an solvation shell. For H+C8H8O (H2O)n (n=4,5,6,7,8) clusters, the proton lies between the two H2O molecules forming a H5O2+ structure, C8H8O-H5O2+ is an important structure, which the other H2O molecules will attack from different sides.     

Protonated clathrate cages enclosing neutral water molecules: (H+)(H2O)21 and (H+)(H2O)28

This paper describes a systematic study on the clathrate structure of (H+)(H2O)21 using tandem mass spectrometry, vibrational predissociation spectroscopy, Monte Carlo simulations, and density functional theory calculations. We produced (H+)(H2O)n from a continuous corona-discharged supersonic expansion and observed three anomalies simultaneously at the cluster temperature near 150 K, including (1) the peak at n=21 is more intense than its neighboring ions in the mass spectrum, (2) the size-dependent dissociation fractions show a distinct drop for the 21-mer, and (3) the infrared spectrum of (H+)(H2O)21 exhibits only a single feature at 3699 cm(-1), corresponding to the free-OH stretching of three-coordinated water molecules. Interestingly, the anomalies appear or disappear together with cluster temperature, indicating close correlation of these three observations. The observations, together with Monte Carlo simulations and density functional theory calculations, corroborate the notion for the formation of a distorted pentagonal dodecahedral (5(12)) cage with a H2O molecule in the cage and a H3O+ ion on the surface for this "magic number" water cluster ion. The dodecahedral cage melts at higher temperatures, as evidenced by the emergence of a free-OH stretching feature at 3717 cm(-1) for the two-coordinated water in (H+)(H2O)21 produced in a warmer molecular beam. Extension of this study to larger clusters strongly suggests that the experimentally observed isomer of (H+)(H2O)28 is most likely to consist of a distorted protonated pentakaidecahedral (5(12)6(3)) cage enclosing two neutral water molecules.     

A theoretical investigation on optimal structures of ethane clusters (C2H6)n with n ≤ 25 and their building-up principle

Geometry optimization of ethane clusters (C(2)H(6))(n) in the range of n ≤ 25 is carried out with a Morse potential. A heuristic method based on perturbations of geometries is used to locate global minima of the clusters. The following perturbations are carried out: (1) the molecule or group with the highest energy is moved to the interior of a cluster, (2) it is moved to stable positions on the surface of a cluster, and (3) orientations of one and two molecules are randomly modified. The geometry obtained after each perturbation is optimized by a quasi-Newton method. The global minimum of the dimer is consistent with that previously reported. The putative global minima of the clusters with 3 ≤ n ≤ 25 are first proposed and their building-up principle is discussed.     

Dielectric studies of water clusters in cyclodextrins: Relevance to the transition between slow and fast forms of thrombin

Cyclodextrins are useful models in the study of hydrogen bonded water clusters. In alpha-cyclodextrin hexahydrate (alpha-CD.6H2O), water molecules are ordered and occupy well-defined positions whereas in the larger beta-cyclodextrin dodecahydrate (beta-CD.12H2O), there is considerable disorder with water molecules freely arranged over several possible sites. Here it is shown that beta-CD exhibits substantial structural flexibility and proton mobility compared with alpha-CD which is relatively very rigid and exhibits negligible short-range protonic conduction. These properties are directly controlled by the effective dielectric constant of the molecule, which is determined by the rotational freedom of water molecules in the hydrogen bond network. This model may be relevant to proteins where water clusters of this kind are found on the protein surface and occasionally in the protein interior. The case of thrombin, an allosteric enzyme incorporating a network of 20 internal hydrogen bonded water molecules, is discussed.