Structure and dynamics of high-spin Ru in aqueous solution: Ab initio QM/MM molecular dynamics simulation

The structural and dynamical properties of high-spin Ru²⁺ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru²⁺. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru²⁺ and the 6-31G^∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru²⁺–O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru²⁺ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.     

Be2+在水、甲醇和乙醇中结构性质的从头算分子动力学模拟

采用Car-Parrinello分子动力学(CPMD)方法分别研究了Be²⁺在水、甲醇和乙醇中的溶剂结构性质, 并对Be²⁺的第一溶剂壳结构的实验及理论结果进行了比较. 所得第一溶剂壳结构与已报道的实验和理论结果较为一致. 对径向分布函数、配位数以及角度分布等进行了详细的分析. 结果表明: 在水、甲醇和乙醇中, Be²⁺第一溶剂壳为稳定理想的四面体结构. 在本文的模拟时间尺度内,没有观察到第一溶剂壳中的分子与第二溶剂壳中的分子进行交换, 进一步证明Be²⁺第一溶剂壳为稳定的四配位结构. 根据计算得到的空间分布函数, Be²⁺在溶剂分子的等高面上主要集中分布在溶剂分子接受氢键的方向. 根据氧原子在Be²⁺周围的分布, 壳层分子主要集中分布在Be²⁺周围的四个区域, 进一步证实溶剂壳为四面体对称.     

Car-Parrinello molecular dynamics simulation of Fe 3+ (aq)

The optimized geometry and energetic properties of Fe(D2O)n 3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe 3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell...second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.     

Structure and dynamics of the hydration shells of the Al3+ ion

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 degrees C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12 s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis. Water transfers into and out of the second solvation shell were observed to occur on a picosecond time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating water molecules (20 ps). Limited simulations with 128 water molecules (7 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region.     

First and Second Hydration Shell of Ni2+ Studied by Molecular Dynamics Simulations

Molecular dynamics simulations of a Ni²⁺ ion in water have been carried out to investigate the structure and dynamics of water molecules around the nickel, extending the analysis to the second hydration shell. The structural parameters as well as the motions of water molecules in various sub-structures of the solution have been evaluated giving a detailed picture of the motional modes of water molecules     

Hydration of the ions Al3+ and Cu2+. An ab initio SCF study

Ab initio calculations are reported for the systems Al(H₂O)_n³⁺ and Cu(H₂O)_n²⁺ with n up to 7. The calculated binding energies increase monotically up to n = 6, with equal binding energies for n = 6 and 7 for the Al³⁺ cation. An estimate of the enthalpy of hydration of Al³⁺ is given, based on model calculations with one or two water molecules from the second solvation shell. An SN1 (dissociative) mechanism for the exchange of the water molecules from the first hydration shell of Al³⁺ appears energetically favorable if the leaving molecule remains in the second hydration shell.     

Solute�CSolvent Interactions in Aqueous Glycylglycine�CCuCl2 Solutions: Acoustical and Molecular Dynamics Perspective

Acoustical and molecular dynamics studies were carried out to understand the various interactions present in glycylglycine?CCuCl₂ aqueous solutions. Amongst these interactions, hydrogen bonding and solute?Csolvent interactions have been highlighted in this study. The radial distribution function (RDF) was used to investigate solution structure and hydration parameters. Binding of Cu²⁺ with various polar peptide atoms reveals the nature and degree of binding. The formation of complex clusters between glycylglycine and water molecules increases the relaxation time. The first hydration shell considerably influences the structure of the second shell, facilitating the formation of an ordered hydrogen bonded network. Both experimental and theoretical results have proved to be efficient in analyzing the behavior of molecules and to give a clear idea on molecular interactions in solutions.     

Equatorial and apical solvent shells of the UO2 2+ ion

First principles molecular dynamics simulations of the hydration shells surrounding UO(2)(2+) ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree with very well-known results from x-ray data. The average U=O bond length was found to be 1.77 A. The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O-U-O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44 A (2.46 A, 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U-O radial distribution function at 4.59 A. The equatorial second shell contained ten water molecules hydrogen bonded to the five first shell molecules. Above and below the UO(2)(2+) ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO(2)(2+), oriented in such a way as to have their protons pointed toward the cation. While the number of apical waters varied greatly, an average of five to six waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.     

The Structural Features of the Hydrated Ferrous Ion Clusters: [Fe(H2O) n ]2+ (n?=?1–19)

The low-lying structures of the hydrated ferrous ion clusters [Fe(H₂O) _n ]²⁺ (n?=?1?C19) were extensively searched at the level of the density functional theory. The results show that the first hydration shell consists of six water molecules, and the second hydration shell contains seven water molecules. Furthermore, it is found that all the lowest-energy states of [Fe(H₂O) _n ]²⁺ (n?=?1?C19) clusters are spin quintet states. These lowest-energy states keep well even at finite temperatures. The analyses of the successive water binding energy and natural charges population on ferrous ion clearly show that the influence of ferrous ion on the surrounding water molecules goes beyond the second hydration shell.     

Hydrated germanium (II): Irregular structural and dynamical properties revealed by a quantum mechanical charge field molecular dynamics study

Structural and dynamical properties of Ge (II) in aqueous solution have been investigated using the novel ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism. The first and second hydration shells were treated by ab initio quantum mechanics at restricted Hartree–Fock (RHF) level using the cc‐pVDZ‐PP basis set for Ge (II) and Dunning double‐ζ plus polarization basis sets for O and H. Besides ligand exchange processes and mean ligand residence times to observe dynamics, tilt‐ and theta‐angle distributions along with an advanced structural parameter, namely radial and angular distribution functions (RAD) for different regions were also evaluated. The combined radial and angular distribution depicted through surface plot and contour map is presented to provide a detailed insight into the density distribution of water molecules around the Ge²⁺ ion. A strongly distorted hydration structure with two trigonal pyramidal substructures within the first hydration shell is observed, which demonstrates the lone‐pair influence and provides a new basis for the interpretation of the catalytic and pharmacological properties of germanium coordination compounds. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Speciation of the curium(III) ion in aqueous solution: a combined study by quantum chemistry and molecular dynamics simulation

The structures of aquo complexes of the curium(III) ion have been systematically studied using quantum chemical and molecular dynamics (MD) methods. The first hydration shell of the Cm3+ ion has been calculated using density functional theory (DFT), with and without inclusion of the conductor-like polarizable continuum medium (CPCM) model of solvation. The calculated results indicate that the primary hydration number of Cm3+ is nine, with a Cm-O bond distance of 2.47-2.48 A. The calculated bond distances and the hydration number are in excellent agreement with available experimental data. The inclusion of a complete second hydration shell of Cm3+ has been investigated using both DFT and MD methods. The presence of the second hydration shell has significant effects on the primary coordination sphere, suggesting that the explicit inclusion of second-shell effects is important for understanding the nature of the first shell. The calculated results indicate that 21 water molecules can be coordinated in the second hydration shell of the Cm3+ ion. MD simulations within the hydrated-ion model suggest that the second-shell water molecules exchange with the bulk solvent with a lifetime of 161 ps.     

A molecular dynamics study on Rh3+ hydration: development and application of a first principles hydrated ion–water interaction potential

The Rh³⁺ aquaion exhibits one of the largest residence times of water molecules in the first hydration shell. The extreme stability of this hexahydrated ion in water solutions makes Rh³⁺ an extremely suitable candidate to be studied using the hydrated ion model. According to this approach, the representative cationic entity in aqueous solution is the ion plus its first hydration shell (i.e. the hydrated ion) and not the bare ion. Our group has successfully applied that concept in the framework of classical statistical simulations based on first principles ion–water interaction potentials. The methodology is now applied to the [Rh(H₂O)₆]³⁺ case based on a previous generalization in which some of the contributions were found to be transferable among the cases already studied (Cr³⁺, Al³⁺, Mg²⁺, Be²⁺). In this contribution a flexible hydrate model is presented, in which rigid first-shell water molecules have rotational and translational degrees of freedom, allowing for internal dynamics of the hydrated ion entity. The potential presented is thoroughly tested by means of a set of molecular dynamics simulations. Structural, dynamical, energetic and spectroscopic information is retrieved from the simulations, allowing the estimation of properties such as ion hydration energy, vibrational spectra of the intermolecular modes, cation mobility, rotational dynamics of the hydrated ion and first-shell water molecules and residence times of the second-shell water molecules. Extension of the Ewald sum to terms r^–4, r^–6 and r^–7 is presented and applied to systems of different size ([Rh(H₂O)₆]³⁺+(n–6)H₂O, n=50, 100, 200, 500, 1000 and 2500) and cutoff radii.Contribution to the Jacopo Tomasi Honorary Issue     

Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution

Structural and dynamical properties of the TiO(2+) ion in aqueous solution have been investigated by using the new ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism, which does not require any other potential functions except those for solvent-solvent interactions. Both first and second hydration shell have been treated at Hartree-Fock (HF) quantum mechanical level. A Ti-O bond distance of 1.5 A was observed for the [Ti=O](2+) ion. The first hydration shell of the ion shows a varying coordination number ranging from 5 to 7, five being the dominant one and representing one axial and four equatorial water molecules directly coordinated to Ti, which are located at 2.3 A and 2.1 A, respectively. The flexibility in the coordination number reflects the fast exchange processes, which occur only at the oxo atom, where water ligands are weakly bound through hydrogen bonds. Considering the first shell hydration, the composition of the TiO(2+) hydrate can be characterized as [(H(2)O)(0.7)(H(2)O)(4) (eq)(H(2)O)(ax)](2+). The second shell consists in average of 12 water molecules located at a mean distance of 4.4 A. Several other structural parameters such as radial and angular distribution functions and coordination number distributions were analyzed to fully characterize the hydration structure of the TiO(2+) ion in aqueous solution. For the dynamics of the TiO(2+) ion, different sets of dynamical parameters such as Ti=O, Ti-O(eq), and Ti-O(ax) stretching frequencies and ligands' mean residence times were evaluated. During the simulation time of 15 ps, 3 water exchange processes in the first shell were observed at the oxo atom, corresponding to a mean residence time of 3.6 ps. The ligands' mean residence time for the second shell was determined as 3.5 ps.     

Structure and dynamics of Au+ ion in aqueous solution: ab initio QM/MM MD simulations

Structure and dynamics of hydrated Au(+) have been investigated by means of molecular dynamics simulations based on ab initio quantum mechanical molecular mechanical forces at Hartree-Fock level for the treatment of the first hydration shell. The outer region of the system was described using a newly constructed classical three-body corrected potential. The structure was evaluated in terms of radial and angular distribution functions and coordination number distributions. Water exchange processes between coordination shells and bulk indicate a very labile structure of the first hydration shell whose average coordination number of 4.7 is a mixture of 3-, 4-, 5-, 6-, and 7-coordinated species. Fast water exchange reactions between first and second hydration shell occur, and the second hydration shell is exceptionally large. Therefore, the mean residence time of water molecules in the first hydration shell (5.6 ps/7.5 ps for t*= 0.5 ps/2.0 ps) is shorter than that in the second shell (9.4 ps/21.2 ps for t*= 0.5 ps/2.0 ps), leading to a quite specific picture of a "structure-breaking" effect.     

Structure and dynamics of the [Zn(NH3)(H2O)5]2+ complex in aqueous solution obtained by an ab initio QM/MM molecular dynamics study

A model complex of the hexahydrated zinc(ii) cation with one water substituted by ammonia in aqueous solution has been studied by hybrid ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) at the double-zeta Hartree-Fock (HF) quantum mechanical level. The first solvation shell, consisting of 5 + 1 ligand(s) at mean distances of 2.2 and 2.1 A, respectively, from the Zn(ii) ion, was found to remain stable with respect to exchange processes within the simulation time. The labile second shell consists on average of approximately 19 water molecules. For structural elucidation of the pentaaquozinc(ii) amine complex in aqueous solution several data sets such as radial distribution functions (RDF), coordination number distributions (CND) and different angular distributions (ADF, tilt and theta angle) were employed. Dynamics were characterised by the ligands' mean residence time (MRT), ion-ligand stretching frequencies and the vibrational and librational motions of water ligands. The labile second shell's MRT value decreases upon introduction of one NH(3) ligand to 7.2 ps from the 10.5 ps observed for the hexaaquozinc(ii) complex.     

Structural and dynamical properties of the Hg2+ aqua ion: a molecular dynamics study

Molecular dynamics simulations of the Hg2+ ion in aqueous solution have been carried out using an effective two-body potential derived from quantum mechanical calculations. A stable heptacoordinated structure of the Hg2+ first hydration shell has been observed and confirmed by extended X-ray absorption fine structure (EXAFS) experimental data. The structural properties of the Hg2+ hydration shells have been investigated using radial and angular distribution functions, while the dynamical behavior has been discussed in terms of reorientational correlation functions, mean residence times of water molecules in the first and second hydration shells, and self-diffusion coefficients. The effect of water-water interactions on the Hg2+ hydration properties has been evaluated using the SPC/E and TIP5P water models.     

Hydration Structure and Dynamic Properties of the Square Planar Pt(II) Aquaion Compared to the Pd(II) Case

This work examines, by means of classical Molecular Dynamics simulations, the hydration of a square planar hydrate, [Pt(H₂O)₄]²⁺, focussing the attention on the structure and dynamics adopted by water molecules in the regions above and underneath the molecular plane. Results obtained are compared with those previously derived for the case of the [Pd(H₂O)₄]²⁺ where the concept of meso-shell was introduced to define this axial region [Martínez et al. (J Phys Chem B 108:15851, 2004)]. Specific ab initio intermolecular potentials describing the interaction between the ion and the solvent have been developed following the statistical implementation of the hydrated ion concept for the case of a planar aquaion. A meso-shell is characterized by a peak in the Pt–O RDF centered at 2.95 Å which integrates to two water molecules; the mean residence time for these molecules is in the range 1–7 ps. The vibrational frequency associated to the dynamic variable defined from the distance meso-shell water molecule-cation is used to quantify the linkage degree of the water molecule in this shell. The meso-shell in Pt(II) is more labile than in the Pd(II) case, whereas the first and second hydration shells of both cations are highly similar. The observed differences in meso-shell are discussed in relation with the mechanistic interpretation of the solvent exchange at the first hydration shell.     

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.     

Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations

We have analyzed a set of molecular dynamics (MD) trajectories of maltose in vacuum and water for solute imposed structuring on the solvent. To do this, we used a novel technique to calculate water probability densities to locate the areas in which the solvent is most populated in the maltose solution. We found that only the layer of water within the first maltose hydration shell has a probability density 50% and greater than that of bulk water. On investigating this water layer using Voronoi polyhedra (VP) analysis it was seen that only the waters adjacent to the hydrophobic (CH and CH₂) groups are more structured than bulk water. We found that in a maltose solution of approximately 1.0 g/cm³ the solute does not disrupt the structure of the surrounding water beyond the first hydration shell. Next we performed a 700‐ps MD simulation of a maltohexaose strand in a box of 4096 SPC/E waters. The water probability density calculations and the VP analysis of the maltohexaose solution show that the larger amylose repeat unit decreases the solvent configurational entropy of the water beyond the first hydration shell. Analysis of this trajectory reveals that the helical conformation of the maltohexaose strand is preserved via bridging intermolecular water hydrogen bonds, indicating that a single amylose helical turn in water is preserved by hydrophilic and not hydrophobic interactions. Using VP analysis we present a method to accurately determine the number of water molecules in the first hydration shell of dissolved solutes. In the case of maltose, there are 40 water molecules in this shell, while for maltohexaose the number is 98. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 445–456, 2001