Application of the ABEEM/MM model in studying the properties of the water clusters (H2O)n (n= 7- 1O)

ABEEM/MM model has been applied to compute the various properties characterizing water clusters (H2O)n(n = 7-10), such as optimized geometries, the hydrogen bonds number, cluster interaction energies, stabilities, ABEEM charge distributions, dipole moments, structural parameters, and so on, and to describe the transition reflected by the hexamer region from two-dimensional (from dimer to pentamer) to three-dimensional structures (for clusters larger than the hexamer).     

Application of the ABEEM/MM model in studying the properties of the water clusters (H2O) n (n=7−10)

ABEEM/MM model has been applied to compute the various properties characterizing water clusters (H₂O) _n (n = 7?10), such as optimized geometries, the hydrogen bonds number, cluster interaction energies, stabilities, ABEEM charge distributions, dipole moments, structural parameters, and so on, and to describe the transition reflected by the hexamer region from two-dimensional (from dimer to pentamer) to three-dimensional structures (for clusters larger than the hexamer).     

Application of the ABEEM/MM model in studying the properties of the water clusters (H2O) n ( n =7?10)

ABEEM/MM model has been applied to compute the various properties characterizing water clusters (H₂O) _n (n = 7−10), such as optimized geometries, the hydrogen bonds number, cluster interaction energies, stabilities, ABEEM charge distributions, dipole moments, structural parameters, and so on, and to describe the transition reflected by the hexamer region from two-dimensional (from dimer to pentamer) to three-dimensional structures (for clusters larger than the hexamer). Supported by the National Natural Science Foundation of China (Grant No. 20373021)     

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.     

Study of water clusters in the n = 2–34 size regime, based on the ABEEM/MM model

Various properties of water clusters in the n = 2–34 size regime with the change of cluster size have been systemically explored based on the newly developed flexible-body and charge-fluctuating ABEEM/MM water potential model. The ABEEM/MM water model is to take ABEEM charges of all atoms, bonds, and lone-pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The computed correlating properties characterizing water clusters (H₂O) _n (n = 2–34) include optimal structures, structural parameters, ABEEM charge distributions, binding energies, hydrogen bonds, dipole moments, and so on. The study of optimal structures shows that the ABEEM/MM model can correctly predict the following important structural features, such as the transition from two-dimensional (from dimer to pentamer) to three-dimensional (for clusters larger than the hexamer) structures at hexamer region, the transition from cubes to cages at dodecamer (H₂O)₁₂, the transition from all-surface (all water molecules on the surface of the cluster) to one water-centered (one water molecule at the center of the cluster, fully solvated) structures at (H₂O)₁₇, the transition from one to two internal molecules in the cage at (H₂O)₃₃, and so on. The first three structural transitions are in good agreement with those obtained from previous work, while the fourth transition is different from that identified by Hartke. Subsequently, a systematic investigation of structural parameters, ABEEM charges, energetic properties, and dipole moments of water clusters with increasing cluster size can provide important reference for describing the objective trait of hydrogen bonds in water cluster system, and also provide a strong impetus toward understanding how the water clusters approach the bulk limit.     

Sr2+和Ba2+水分子体系结构和结合能的从头算和ABEEM/MM研究

应用从头算方法和ABEEM/MM浮动电荷分子力场, 研究了水合碱土离子团簇Sr²⁺/Ba²⁺(H₂O)_n (n=1-6), 构建了离子-水相互作用的ABEEM/MM势能函数, 获得了水合离子团簇的稳定结构, 计算了结合能. 计算结果表明, ABEEM/MM方法的结果和从头算方法的结果有很好的一致性. 进一步应用ABEEM/MM对Sr²⁺和Ba²⁺水溶液进行了分子动力学模拟. 对Sr²⁺水溶液, 得到的Sr²⁺-水中氧原子的径向分布函数的第一和第二最高峰分别位于0.257和0.464 nm处, 第一和第二水合层的配位水分子数分别为9.2和11.4; 对Ba²⁺水溶液, 得到的Ba²⁺与水中氧原子的径向分布函数的第一和第二最高峰分别位于0.269和0.467 nm处, 第一和第二水合层的配位水分子数分别为9.9和12.4. 这与实验值或其它理论模拟结果有较好的一致性. 对比外层的水分子, 金属离子的极化作用使得溶液中第一水合层中水分子的O―H键长增长, HOH键角减小.     

Site-specific addition of D(2)O to the (H(2)O)(6)(-) "hydrated electron" cluster: isomer interconversion and substitution at the double H-bond acceptor (AA) electron-binding site

We report the results of an experimental study designed to establish whether, once formed, one of the isomer classes of the hydrated electron clusters, (H(2)O)(n)(-), can interconvert with others when a water molecule is added by condensation. This is accomplished in an Ar-cluster mediated approach where a single intact D(2)O molecule is collisionally incorporated into argon-solvated water hexamer anions, creating the isotopically labeled D(2)O.(H(2)O)(6)(-).Ar(n) heptamer anion. Photoelectron and infrared predissociation spectroscopies are employed both to characterize the isomers generated in the condensation event and to track the position that the D(2)O label adopts within these isomeric structures. Despite the fact that the water hexamer anion precursor clusters initially exist in the isomer I form, incorporation of D(2)O produces mostly isomers I' and II in the labeled heptamer, which bind the electron more (I') or less (II) strongly than does the isomer I class. Isomers I and I' are known to feature electron binding primarily onto a single water molecule that resides in an AA (A = H-bond acceptor) site in the network. Surprisingly, the D(2)O molecule can displace this special electron-binding H(2)O molecule such that the anionic cluster retains the high binding arrangement. In the more weakly binding isomer II clusters, the D(2)O molecule fractionates preferentially to sites that give rise to the vibrational signature of isomer II.     

Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.     

水合氢离子团簇从头算和ABEEM/MM的理论研究

应用高水平的从头计算方法和ABEEM/MM模型, 研究了水合氢离子团簇H3O＋(H2O)n (n＝1～6), 优化得到了低能构象, 探讨了其结合能和稳定性, 显示出H3O＋(H2O)3局域结构的优势存在．对H3O＋(H2O)6VIa团簇的ABEEM电荷分布进行分析, 表明第一水合层水分子与水合氢离子之间的氢键相互作用要明显强于与第二水层水分子的氢键相互作用. 研究结果表明, ABEEM/MM方法计算的结果和从头算得到的结果存在很好的一致性.     

Ab initio determination of the ionization potentials of water clusters (H2O)n (n = 2-6)

High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic ionization potentials of several water clusters: dimer, trimer, tetramer, pentamer, hexamer book, hexamer ring, hexamer cage, and hexamer prism. The present results establish reference values at a level not reported before for these systems, calibrating different computational strategies and helping to discard less reliable theoretical and experimental data. The systematic study with the increasing size of the water cluster allows obtaining some clues on the structure and reductive properties of liquid water.     

氟化氢团簇(HF)_n(n=2～8)拓扑性区别氢键构型的图论列举法和量子化学计算法研究

利用提出的图论程序列举出氟化氢团簇(HF)_n(n=2~8)所有可能存在的拓扑性区别氢键构型,通过精密调查获得有可能存在的拓扑性区别构型,发现了满足HF团簇稳定性的若干条件,在这些条件的基础上编写FORTRAN程序和Python语言执行程序,再用画图软件包Graph Viz2.37自动画出对应的有向图或条件性有向图.以对应的有向图作理论框架,分别利用从头算法Moller-Plesset(MP2)二级微扰方法和密度泛函理论(DFT)方法 B3LYP计算水平的6-31G**(d,p)基组对氟化氢团簇(HF)_n(n=3~7)所有拓扑性区别条件性有向图对应的初始结构进行结构优化并作振动频率分析,获得氟化氢团簇(HF)_n(n=2~7)的最稳定构型,发现了氟化氢团簇的五聚体(HF)_5、六聚体(HF)_6和七聚体(HF)_7等一些新的稳定结构.     

原子-键电负性均衡方法融合进分子力场(ABEEM/MM)应用于蛋白质分子(Crambin)模拟

建立应用于多肽和蛋白质模拟的ABEEM/MM浮动电荷力场.利用该模型和参数,对实际蛋白质分子Crambin(植物种子中的一种小的蛋白质)进行模拟,得到了满意的结果,为其更广泛的应用开辟了道路.     

A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.     

Theoretical study on the hydration of hydrogen peroxide in terms of ab initio method and atom-bond electronegativity equalization method fused into molecular mechanics

In this paper, the interaction between hydrogen peroxide (HP) and water were systemically studied by atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) and ab initio method. The results show that the optimized geometries, interaction energies and dipole moments of hydrated HP clusters HP(H₂O) _n (n = 1–6) calculated by ABEEM/MM model are fairly consistent with the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ results. The ABEEM/MM results indicate that n = 4 is the transition state structure from 2D planar structure to 3D network structure. The variations of the average hydrogen bond length with the increasing number of water molecules given by ABEEM/MM model agree well with those of ab initio studies. Moreover, the radial distribution functions (RDFs) of water molecule around HP in HP aqueous solution have been analyzed in detail. It can be confirmed that HP is a good proton donor and poor proton acceptor in aqueous solution by analysis of the RDFs.     

从头算和ABEEMσπ/MM对(CH_3OH)_n(n=3～12)和[Na(CH_3OH)_n]~+(n=3～6)体系的研究

采用从头算方法(ab initio)和原子-键电负性均衡浮动电荷分子力场方法(ABEEMσπ/MM),对甲醇团簇(CH_3OH)n(n=3~12)和[Na(CH_3OH)_n]~+(n=3~6)体系的结构、电荷分布和结合能进行研究.依据从头算结果构建上述体系的ABEEMσπ/MM浮动电荷势能函数,并确定相关参数.结果表明,ABEEMσπ/MM所获得的结构和结合能等均优于OPLS/AA力场,并与从头算结果相符,其中键长的平均绝对偏差(AAD)小于0.004 nm,键长、键角和结合能的相对均方根偏差(RRMSD)分别小于3.8%,1.7%和6.8%;电荷分布与从头算结果的线性相关系数均大于0.99.     

Comparison of the growth patterns of Si(n) and Ge(n) clusters (n = 25-33)

We performed an unbiased search for low-energy structures of medium-sized neutral Si n and Ge n clusters ( n = 25-33) using a genetic algorithm (GA) coupled with tight-binding interatomic potentials. Structural candidates obtained from our GA search were further optimized by first-principles calculations using density functional theory (DFT). Our approach reproduces well the lowest-energy structures of Si n and Ge n clusters of n = 25-29 compared to previous studies, showing the accuracy and reliability of our approach. In the present study, we pay more attention to determine low-lying isomers of Si n and Ge n ( n = 29-33) and study the growth patterns of these clusters. The B3LYP calculations suggest that the growth pattern of Si n ( n = 25-33) clusters undergoes a transition from prolate to cage at n = 31, while this transition appears at n = 26 from the PBE-calculated results. In the size range of 25-33, the corresponding Ge n clusters hold the prolate growth pattern. The relative stabilities and different structural motifs of Si n and Ge n ( n = 25-33) clusters were studied, and the changes of small cluster structures, when acting as building blocks of large clusters, were also discussed.     

Theoretical Study on Co^3＋ in Aqueous Solution in Terms of ABEEM/MM Model

A detailed theoretical investigation on Co^3＋ hydration in aqueous solution has been carded out by means of molecular dynamics （MD） simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics （ABEEM/MM）. The effective Co^3＋ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co^3＋（aq.） solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties （radial distribution function, angular distribution function and solvation energy） obtained for Co^3＋ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model.