可快速计算水团簇三体作用强度的新方法

将水分子视为由2个O—H键偶极构成, 再将水分子间的三体作用视为长程诱导作用和短程校正之和, 使用Thole模型计算长程诱导作用, 通过同时考虑不同水分子间的置换和同一个水分子中2个键偶极间的置换计算短程校正, 从而提出了一个可快速计算水团簇三体作用强度的新方法. 根据已报道的12347个水三聚体的结构和CCSD(T)三体作用能, 确定了该方法所需参数. 将该方法和所确定的参数应用于67个水团簇体系, 计算这些体系的三体作用能, 并与CCSD(T), MP2, M06-2X方法的计算结果进行比较. 结果表明, 相对于CCSD(T)方法的总三体作用能, 本文方法的均方根偏差(RMSD)仅为3.32 kJ/mol, 平均相对偏差(MRD)仅为2.43%; 对较大水团簇体系, 该方法计算精度稍优于MP2方法, 明显优于M06-2X方法, 并且更快捷高效.     

含酰胺和尿嘧啶的氢键复合物的三体效应

采用包含BSSE校正的MP2/aug-cc-pVTZ方法对酰胺、二肽、尿嘧啶和水分子形成的氢键复合物的三体效应进行了研究,分析了三体作用能对体系总作用能的贡献.结果表明,在这些氢键复合物中,三体作用能占体系总作用能的10%~20%,三体作用属于近程作用,因此在分子模拟中至少应考虑近处的三体效应.     

基于神经网络势与增强采样的气相水团簇成核过程研究※

由于气相分子密度低, 对气相成核过程的理论模拟往往需要很大的计算量. 为了提高模拟效率, 本工作将神经网络势与增强采样技术结合, 并以水团簇成核为例进行了研究. 采用密度泛函理论方法对不同尺寸的水团簇进行了能量和力的计算, 并由此训练出一套能较好描述水团簇体系相互作用的神经网络势. 将这个势应用于蒙特卡洛模拟并结合多种增强采样方法, 实现了在不同尺寸水团簇之间的随机行走, 由此可得到水团簇在特定条件下的概率分布以及吉布斯自由能. 通过后续的蒙特卡洛模拟结合伞形采样和变分过渡态理论, 可以进一步计算出不同水团簇的水分子蒸发速率. 观察到了四聚体到五聚体的自由能和蒸发速率的突变现象. 结构分析表明虽然五聚体的最低能量构型是二维环状结构, 但是在有限温度下五聚体中三维氢键网络已经开始形成. 这导致了在四聚体过渡到五聚体时的异常. 本工作提供的第一性原理精度下对气相水团簇成核进行研究的方法可以推广到更为复杂的多组分体系, 为研究大气颗粒物形成机理奠定了基础.     

水团簇构象稳定性起源和本质的密度泛函理论与量子分子动力学研究

寻找确定分子体系构象稳定性的关键因素是至关重要的, 但即使对最简单的分子, 其稳定性的起源和本质仍存在很大的争议. 本文以水团簇为例, 采用量子分子动力学产生185个八聚水分子团簇模型, 并运用基于密度泛函理论的两个能量分解方法寻找其稳定性的决定因素. 我们发现不同水团簇的稳定性与其立体排斥能和交换相关能成良好的线性关系.本文还采用双变量模型模拟水团簇的稳定性, 取得了更好的结果(相关系数大于0.99). 本工作对揭示包括水分子团簇在内的通过弱相互作用组成的分子络合物的稳定性起源和本质提供了有益启示.     

平面五元水分子簇的量子化学研究

选用Gaussian03的B3LYP/6-31G(d,p)、DMol3的BLYP/DNP和deMon的BLYP/TZVP等方法计算了甲烷水合物(结构-1)中平面五元水分子簇的结合能和氢键能,作了基组重叠误差(BSSE)和色散能(dispersion)的修正,估算了次级相互作用的贡献.在DMol3程序中使用了大型数值基组DNP,将基组重叠误差降至最低.在Gaussi-an03的B3LYP/6-31G(d,p)计算中,采用平衡法(Counterpoise)校正基组重叠误差.两种计算方法给出了一致的结果,证实了在使用6-31G(d,p)基组时,一对水分子在平衡距离的基组重叠误差高达8 kJ/mol.为估算色散能的贡献,使用了新近发展的包含色散能的密度泛函的DFT程序deMon计算了五元水分子簇.用多种方法计算出了经基组重叠误差和色散能修正的五元水分子簇的分子间结合能和氢键能的较为精确的势能超曲面,为甲烷和其他气体水合物的分子动力学模拟提供了依据.     

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.     

水分子在高岭石中插层行为的量子化学研究

采用密度泛函理论B3LYP方法,在B3LYP/6-31G(d)理论水平上,构建高岭石的层间团簇模型Si6Al6O42H42(层间距为0.844 0和1.000 0nm),并对高岭石层间及其与n(n=1～3)个水分子相互作用的团簇的各种性质进行研究,如优化的几何构型、电子密度、氢键、能量、NBO电荷分布、振动频率等.结果表明,随着水分子个数n(n=1～3)的增加,体系的能量逐渐降低.水分子通过多种类型的氢键插层于高岭石层间,其中水分子间的氢键强度最强,其次是水分子与铝氧层之间形成的氢键,再次是水分子与硅氧层之间的氢键;层间距随着插层分子的增多而增大,但高岭石层间的活性位点依然存在,且位置较插层前没有明显变化.     

微观作用力对肽自组装过程中结构演化的影响:分子模拟研究

本文通过全原子分子动力学研究了典型的自组装芳香二肽分子(z-FF)自组装过程的微观结构演化,探索了肽分子间以及肽分子与溶剂水分子的微观作用力在自组装各个阶段的作用.模拟结果显示,尽管π-π堆积作用占分子间作用能的比重不高,但其在自组装初期对分子聚集起到的驱动力的贡献大于非π-π堆积作用力.肽分子与溶剂水分子形成的氢键数量随着组装进程而减少,总体呈现去溶剂化效应,但同时伴随着多次再溶剂化过程.水化层中的水分子存在两种特殊的“水桥”形式,即“单分子水桥”和“水团簇水桥”,其在水化层水分子中占比在30%～70%之间涨落.水桥的涨落伴随着肽分子结构重排,在自组装各个阶段(相分离、成核、生长和纤维交联)起着重要作用.     

17O-核磁共振法研究不同处理方法对液态水缔合结构的影响

水作为人类重要的生产要素,参与了卷烟生产的多个环节。水在自然条件下以分子簇的形式存在,多种处理方式可以改变水分子团簇的大小。本文以¹⁷O-核磁共振法为水分子团簇的表征手段,以自来水为水源,考察了氢气、远红外辐射陶瓷球、反渗透、磁场四种处理方法对水分子簇的影响。结果表明:四种处理方式均能使一定量水分子由氢键结合态变为自由态,从而使水分子簇变小。不同处理方法对液态水缔合结构的影响大小排序为氢气处理>远红外陶瓷球处理>反渗透处理>磁场处理。同时,对氢气处理效果的时效性进行了考察,随着放置时间增加,部分自由态水分子再次转变为氢键结合态,水分子簇尺寸变大,但三天后仍保留了一定处理效果。本研究表明氢气处理为四种处理方式中最优的水处理方式,具有提升烟草行业生产用水品质的潜在应用价值。     

限制在疏水板中的新的六边形-四边形三层冰结构

对限制在两个光滑的疏水板间的水进行了分子动力学模拟,观察到了两种晶体结构,都满足冰规则．在1GPa的压强和1．0nm的板间距下获得的新的冰相是平坦的六边形-四边形三层冰．在此结构中,靠近板的两层（外层）中的水分子形成六边形环,中间层的水分子形成四边形环．对于外层的水分子,其四个氢键中的三个在同一层中,另一个氢键与中间层连接．对于中间层的水分子,四个氢键中的两个在同。层中,而另外两个氢键与两个不同的外层相连．虽然三层的形状不同,但其面密度却接近相等．另一种结构是在0．8nm的板问距和100MPa的侧向压下获得的平坦的六边形双层冰．模拟中的相变既有一阶相变,也有连续相变．     

Computational study of glycine–(water)3 complex by density functional method

Glycine–(water)₃ complexes have been studied by means of B3LYP density functional method using 6-311++G* basis set. In the complex considered here, the three water molecule are either attached to the carboxylic group or bridge between the amino group and carboxylic group of glycine. Four such complexes are studied. Relaxation energies, two-, three- and four-body interaction energies are obtained by applying many-body analysis to know their role in binding energy of the complex. The results are compared with recent work on glycine–(water)₃ complex with group as proton donor [A. Chaudhari, P.K. Sahu, S.L. Lee, J. Chem. Phys. 120 (2004) 170]. In the most stable structure of glycine–(water)₃ complex, the three water molecules are attached to the carboxylic group of glycine and it is 5.3 kcal/mol lower in energy than that of the most stable structure reported earlier. The three-body term from water–water–water interaction in the most stable in this work and that reported earlier is unique since the distances between the water molecules are almost same. The two-body term from water–water interaction has significant contribution to the total two-body term when the distance between water molecules is less than 3 Å.     

Monte Carlo liquid water simulation with four-body interactions included

A four-body interaction potential for water molecules is derived. The new terms are combined with previously developed two- and three-body potential terms and applied in a Metropolis—Monte Carlo simulation at 298 K for an (N, V, T) ensemble with 512 water molecules. Improvements, relative to the results using only two-body, or two- and three-body interactions, are reported for the correlation function g(OO), for the X-ray and neutron-beam scattering intensities, and for the enthalpy.     

Stokes-Einstein relations for a square-well fluid

A Stokes-Einstein relation, relating the shear viscosity eta to the self-diffusion coefficient D, is constructed for a classical fluid subject to an effective two-body intermolecular force, derived from a square-well potential, undergoing dynamics as described by a Smoluchowski equation for pair diffusion. The time correlation functions for eta and 1D are separated into contributions from delta function, hard-sphere forces, and from delta function, square-well soft forces. Furthermore, D is separated into its two- and three-body time correlation functions, and eta into its two- to four-body terms. D shows activated diffusion, as in Arrhenius behavior, and on the level of two-body dynamics, the Deta product adheres to the Stokes-Einstein relation, subject to a small correction for potential softness. Three-body time correlation functions increase D, whereas three- and four-body correlation functions in eta are partially offsetting. The deviation of Deta product from the Stokes-Einstein law arises from the three-body time correlations functions in D.     

Cooperative effects in extended hydrogen bonded systems involving O?H groups. Ab initio studies of the cyclic S4 water tetramer

The additional energy stabilization due to cooperative effects was calculated in extended hydrogen bonded systems O? H ?O? H ?O? H with unidirectional (homodromic) orientation of the O? H groups. Ab initio restricted Hartree Fock, MP2 and MP3 calculations with geometry optimization and BSSE correction have been performed using the GAUSSIAN 83 program package for the ground states of the linear water dimer with C_s symmetry and the cyclic water tetramer with S₄ symmetry. The latter represents the smallest possible, experimentally observed cooperative structure. A new definition for a cooperativity parameter is proposed. The definition is based on the two-body, non-neighbour interaction energy, plus three- and four-body contributions, including one-body deformation terms in relation to the total interaction energy of the water tetramer. The advantage of this definition is its independence of the reference system, which is necessary in complicated molecular systems with an undefined number of hydrogen bonds, such as disordered or flip-flop systems. According to this definition the energy gain based on cooperativity in the S₄ water tetramer is 29% with the MP3/6-31G** approximation, (30% with HF/4-31G* and 46% with HF/3-21G). The largest contribution of 18% is due to the three-body term on the MP3/6-31G** level, followed by the two-body, non-neighbour term with 11%. The four-body term and the deformation term are in the order of 1% and cancel each other because they have opposite sign.     

A computational study of microsolvation effect on ethylene glycol by density functional method

This study focuses on the conformational analysis of ethylene glycol-(water)n (n=1-3) complex by using density functional theory method and the basis set 6-311++G*. Different conformers are reported and the basis set superposition error corrected total energy is -306.767 5171, -383.221 3135, and -459.694 1528 for lowest energy conformer with 1, 2, and 3 water molecules, respectively, with corresponding binding energy -7.75, -15.43, and -36.28 kcal/mol. On applying many-body analysis it has been found that relaxation energy, two-body, three-body energy have significant contribution to the binding energy for ethylene glycol-(water)3 complex whereas four-body energies are negligible. The most stable conformers of ethylene glycol-(water)n complex are the cyclic structures in which water molecules bridge between the two hydroxyl group of ethylene glycol.     

Four-body interaction energy for compressed solid krypton from quantum theory

The importance of the four-body contribution in compressed solid krypton was first evaluated using the many-body expansion method and the coupled cluster theory with full single and double excitations plus perturbative treatment of triples. All different four-atom clusters existing in the first- and second-nearest neighbor shells of face-centered cubic krypton were considered, and both self-consistent-field Hartree-Fock and correlation parts of the four-body interaction were accurately determined from the ambient conditions up to eightfold volume compression. We find that the four-body interaction energy is negative at compression ratio lower than 2, where the dispersive forces play a dominant role. With increasing the compression, the four-body contribution becomes repulsive and significantly cancels the over-softening effects of the three-body potential. The obtained equation of state (EOS) was compared with the experiments and the density-functional theory calculations. It shows that combination of the four-body effects with two- and three-body interactions leads to an excellent agreement with EOS measurements throughout the whole experimental range 0-130 GPa, and extends the prediction to 300 GPa.     

A study of the additivity of interactions in cation-water systems

The mono- to tetra-hydrates and hexahydrates of Na⁺, Mg²⁺ and Al³⁺ have been taken as examples to investigate to what extend the interactions in water-metal complexes can be replaced by sums of water-water and water-ion two-body interactions. It is found that the quality of the approximation of pairwise additivity of the interaction energies decreases with increasing charge of the ion and also with the number of water molecules in the hydrates. For cations with a charge of more than two the pair approximation can be expected to significantly influence the results of computer simulations of electrolyte solutions.     

Cyclic and ladder hydrogen bonded cyanamide oligomers: a density functional theory and many-body analysis approach

This work reports hydrogen bonding interaction in cyclic and ladder oligomers using density functional theory method. Many-body analysis technique has been used to study the nature of interactions between different molecules and their contribution to the binding energy of a respective hydrogen bonded oligomers. Hydrogen bonds in cyclic trimer to pentamer are stronger than those in corresponding ladder structures. Cyanamide monomer shows the lowest energy at B3LYP/aug-cc-pvdz level among different methods used here with the same basis set. The geometrical parameters for cyanamide monomer obtained at B3LYP/aug-cc-pvdz level are in excellent agreement with the experimental determinations. Cyclic structures are more stable than the ladder. In cyclic oligomers not only total two-body energies, but higher body energies also contribute significantly to the binding energy of a respective complex whereas in ladder, only total two-body energies contribute significantly and higher-body energies are almost negligible for cyanamide trimer to pentamer.     

Hydration and dewetting near fluorinated superhydrophobic plates

The water dynamics near nanoscale fluorinated (CF(3)(CF(2))(7)(CH(2))(2)SiH(3)) monolayers (plates) as well as possible dewetting transitions in-between two such plates have been studied with molecular dynamics simulations in this paper. A "weak water depletion" is found near the single fluorinated surface, with an average water density in the first solvation shells 6-8% lower than its hydrogenated counterpart. The fluorinated molecules are also found to be water impermeable, consistent with experimental findings. More surprisingly, a dewetting transition is found in the interplate region with a critical distance D(c) of 10 A (3-4 water diameters) for double plates with 8 x 8 molecules each (plate size approximately 4 nm x 4 nm). This transition, although occurring on a microscopic length scale, is reminiscent of a first-order phase transition from liquid to vapor. The unusual superhydrophobicity of fluorocarbons is found to be related to their larger size (or surface area) as compared to hydrocarbons, which "dilutes" their physical interactions with water. The water-plate interaction profile shows that the fluorinated carbons have a 10-12% weaker water-plate interaction than their hydrogenated counterparts in the nearest solvation shell, even though the fluorocarbons do have a stronger electrostatic interaction with water due to their larger partial charges. However, the van der Waals interactions dominate the water-plate interaction within the nearest shell, with up to 90% contributions to the total interaction energy, and fluorocarbons have a noticeably weaker (by 10-15%) van der Waals interaction with water in the nearest shell than do hydrocarbons. Both the slightly weaker water-plate interaction and larger surface area contribute to the stronger dewetting transition in the current fluorinated carbon plates.