Molecular simulation analysis and X-ray absorption measurement of Ca2+, K+ and Cl- ions in solution

This paper presents recent advances in the use of molecular simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy, which enable us to understand solvated ions in solution. We report and discuss the EXAFS spectra and related properties governing solvation processes of different ions in water and methanol. Molecular dynamics (MD) trajectories are coupled to electron scattering simulations to generate the MD-EXAFS spectra, which are found to be in very good agreement with the corresponding experimental measurements. From these simulated spectra, the ion-oxygen distances for the first hydration shell are in agreement with experiment within 0.05-0.1 A. The ionic species studied range from monovalent to divalent, positive and negative: K+, Ca2+, and Cl-. This work demonstrates that the combination of MD-EXAFS and the corresponding experimental measurement provides a powerful tool in the analysis of the solvation structure of aqueous ionic solutions. We also investigate the value of electronic structure analysis of small aqueous clusters as a benchmark to the empirical potentials. In a novel computational approach, we determine the Debye-Waller factors for Ca2+, K+, and Cl- in water by combining the harmonic analysis of data obtained from electronic structure calculations on finite ion-water clusters, providing excellent agreement with the experimental values, and discuss how they compare with results from a harmonic classical statistical mechanical analysis of an empirical potential.     

Exploring the capabilities of X-ray absorption spectroscopy for determining the structure of electrolyte solutions: computed spectra for Cr(3+) or Rh(3+) in water based on molecular dynamics

Extended X-ray absorption fine structure (EXAFS) spectra of Cr(3+) and Rh(3+) in aqueous solution are analyzed and compared with computed spectra derived from structural results obtained by molecular dynamics (MD) simulation. This procedure quantifies the reliability of the EXAFS structural determination when applied to ions in solution. It provides guidelines for interpreting experimental spectra of octahedrally coordinated metal cations in aqueous solution. A set of relationships among Debye-Waller factors is proposed on the basis of MD results to reduce the number of independent fit parameters. The determination of the second hydration shell is examined. Calculated XANES spectra compare well with experimental ones. Indeed, the splitting observed on the main peak of the Rh K-edge was anticipated by the calculations. Simulated spectra from MD structures of increasing cluster size show a relationship between the second hydration shell and features of the XANES region at energies just above the edge. The combination of quantum and statistical calculations with the XANES spectrum is found to be very fruitful to get insight into the quantitative estimation of structural properties of electrolyte solutions.     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

Importance of multiple-scattering phenomena in XAS structural determinations of [Ni(CN)4]2- in condensed phases

A quantitative analysis of the XAS spectra of the tetracyanonickelate complex [Ni(CN)4]2- has been carried out. The simultaneous study of the EXAFS and XANES regions yielded complementary information regarding the geometric and electronic structures of the complex. XANES spectra were modeled by applying recently developed self-consistent, full multiple-scattering algorithms in the FEFF8 code (version 8 x 34). XANES spectra for clusters of different sizes (from 9 to 125 atoms) were computed and compared with experimental spectra. This region of the spectra was proportional to a broadened Ni p-density of states diagram above the Fermi level. Although the main features of the XANES spectra were reasonably reproduced by computations, the weak dependence of the theoretical spectra on cluster size contrasts with the close similarity between the experimental spectra of the solid and solution systems. Because of the special geometry of the complex, calculations with polarized light parallel and perpendicular to the molecular plane were carried out, yielding a reasonable reproduction of the experimental data from another report for cluster sizes equal to or higher than 45 atoms. The highly symmetric square planar structure of the complex was found to be responsible for the unusual amplitude of the multiple-scattering (MS) contributions to the EXAFS spectra. Spectra in this region were fitted using the FEFFIT EXAFS analysis program, taking into account only the MS paths that simultaneously have both a high amplitude, as calculated with the ab initio code FEFF, and a small Debye-Waller factor, as estimated by the independent-vibration approximation model. Fitting results yielded very similar structures for the Ni2+ complex in the solid state and in solution, though the larger Debye-Waller factors found for the solid suggest higher static disorder in this state.     

Hydration of simple amides. FTIR spectra of HDO and theoretical studies

The hydration of formamide (F), N-methylformamide (NMF), N,N-dimethylformamide (DMF), acetamide (A), N-methylacetamide (NMA), and N,N-dimethylacetamide (DMA) has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure has been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To facilitate the interpretation of obtained spectral results, DFT calculations of aqueous amide clusters were performed. Molecular dynamics (MD) simulation for the cis and trans forms of NMA was also carried out for the SPC model of water. Infrared spectra reveal that only two to three water molecules from the surrounding of the amides are statistically affected, from among ca. 30 molecules present in the first hydration sphere. The structural-energetic characteristic of these solute-affected water molecules differs only slightly from that in the bulk and corresponds to the clathrate-like hydrogen-bonded cage typical for hydrophobic hydration, with the possible exception of F. MD simulations confirm such organization of water molecules in the first hydration sphere of NMA and indicate a practical lack of orientation and energetic effects beyond this sphere. The geometry of hydrogen-bonded water molecules in the first hydration sphere is very similar to that in the bulk phase, but MD simulations have affirmed subtle differences recognized by the spectral method and enabled their understanding. The spectral data and simulations results are highly compatible. In the case of F, NMF, and A, there is a visible spectral effect of water interactions with N-H groups, which have destabilizing influence on the amides hydration shell. There is no spectral sign of such interaction for NMA as the solute. The energetic stability of water H-bonds in the amide hydration sphere and in the bulk fulfills the order: NMA > DMA > A > NMF > bulk > DMF > F. Microscopic parameters of water organization around the amides obtained from the spectra, which have been used in the hydration model based on volumetric data, confirm the more hydrophobic character of the first three amides in this sequence. The increased stability of the hydration sphere of NMA relative to DMA and of NMF relative to DMF seems to have its origin in different geometries, and so the stability, of water cages containing the amides.     

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.     

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions

In this paper we have developed an effective computational procedure for the structural and dynamical investigation of ions in aqueous solutions. Quantum mechanical potential energy surfaces for the interaction of a transition metal ion with a water molecule have been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective ion-water interactions have been fitted by suitable analytical potentials, and have been utilized in molecular dynamics (MD) simulations to obtain structural and dynamical properties of the ionic aqueous solutions. This procedure has been successfully applied to the Co2+-H2O open-shell system and, for the first time, Co-oxygen and Co-hydrogen pair potential functions have been determined and employed in MD simulations. The reliability of the whole procedure has been assessed by applying it also to the Zn2+ and Ni2+ aqueous solutions, and the structural and dynamical properties of the three systems have been calculated by means of MD simulations and have been found to be in very good agreement with experimental results. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to extended X-ray absorption fine structure (EXAFS) experiments.     

Be2+ hydration in concentrated aqueous solutions of BeCl2

Neutron diffraction experiments were carried out on concentrated aqueous solutions of beryllium chloride at three concentrations: 1.5, 3, and 6 molal. By working with a specific ("null") mixture of heavy water (D2O) and water (H2O), information on the local structure around Be2+ ions was extracted directly. For all three BeCl2 solutions, the results show that the Be2+ ion has a well-defined 4-fold coordination shell that is dominated by oxygen atoms. There is also a relatively small probability (10-15%) that there are direct contacts between Be2+ and Cl- at a distance of approximately 2.2 angstroms. The oxygen atoms of the highly structured Be2+ first hydration shell are found to be situated at 2.6 angstroms apart, and form a pyramidal structure, in agreement with recent MD simulation results. The Cl- ions have approximately seven oxygen atoms (water molecules) in their hydration shells sited at 3.2 angstroms.     

浓度及冷冻-解冻处理对CuCl_2水溶液中Cu~(2+)区域结构的影响

应用扩展X射线吸收精细结构(EXAFS)光谱研究了CuCl2水溶液中Cu2+的区域环境结构,通过测定CuCl2水溶液在不同浓度条件下及冷冻-解冻(FT)处理前后CuK边EXAFS吸收谱,研究了浓度及冷冻-解冻处理对Cu2+第一配位层结构的影响.EXAFS实验结果表明,CuCl2水溶液中Cu2+第一配位层距离中心原子Cu最近邻原子为O原子,配位数介于3.0-4.3之间,Cu—O键长在0.192-0.198nm之间,这种结构与Cu2+的Jahn-Teller效应有关.不同浓度的CuCl2水溶液中Cu2+的区域环境结构有很大不同,随着CuCl2水溶液浓度的升高,Cu2+第一配位层配位数减小,Cu—O键伸长.结构参数拟合结果证实冷冻-解冻处理对Cu2+的区域环境结构有影响,CuCl2溶液经冷冻-解冻处理后,Cu2+第一配位层配位数变大,热无序度增加.     

浓度及冷冻鄄解冻处理对CuCl2水溶液中Cu2+区域结构的影响

应用扩展X射线吸收精细结构(EXAFS)光谱研究了CuCl2水溶液中Cu2+的区域环境结构, 通过测定CuCl2水溶液在不同浓度条件下及冷冻-解冻(FT)处理前后Cu K边EXAFS 吸收谱, 研究了浓度及冷冻-解冻处理对Cu2+第一配位层结构的影响. EXAFS实验结果表明, CuCl2水溶液中Cu2+第一配位层距离中心原子Cu最近邻原子为O原子, 配位数介于3.0-4.3之间, Cu—O键长在0.192-0.198 nm 之间, 这种结构与Cu2+的Jahn-Teller效应有关. 不同浓度的CuCl2水溶液中Cu2+的区域环境结构有很大不同, 随着CuCl2水溶液浓度的升高, Cu2+第一配位层配位数减小, Cu—O键伸长. 结构参数拟合结果证实冷冻-解冻处理对Cu2+的区域环境结构有影响, CuCl2溶液经冷冻-解冻处理后, Cu2+第一配位层配位数变大, 热无序度增加.     

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.     

Hydrogen Bonding in Liquid Water and in the Hydration Shell of Salts

A near‐IR spectral study on pure water and aqueous salt solutions is used to investigate stoichiometric concentrations of different types of hydrogen‐bonded water species in liquid water and in water comprising the hydration shell of salts. Analysis of the thermodynamics of hydrogen‐bond formation signifies that hydrogen‐bond making and breaking processes are dominated by enthalpy with non‐negligible heat capacity effects, as revealed by the temperature dependence of standard molar enthalpies of hydrogen‐bond formation and from analysis of the linear enthalpy–entropy compensation effects. A generalized method is proposed for the simultaneous calculation of the spectrum of water in the hydration shell and hydration number of solutes. Resolved spectra of water in the hydration shell of different salts clearly differentiate hydrogen bonding of water in the hydration shell around cations and anions. A comparison of resolved liquid water spectra and resolved hydration‐shell spectra of ions highlights that the ordering of absorption frequencies of different kinds of hydrogen‐bonded water species is also preserved in the bound state with significant changes in band position, band width, and band intensity because of the polarization of water molecules in the vicinity of ions.     

Electronic structure, statistical mechanical simulations, and EXAFS spectroscopy of aqueous potassium

We investigate the solvation structure of aqueous potassium ions, using a combination of electronic structure calculations, statistical mechanical simulations with a derived polarizable empirical potential and experimental measurement of the extended X-ray absorption fine structure (EXAFS) spectra. The potassium K-edge (at 3,608 eV) EXAFS spectra were acquired on the bending magnet of sector 20 at the Advanced Photon Source, at ambient conditions and for the concentrations of 1 and 4 m KCl. We focus on the coordination distances and the degree of disorder of the first hydration shell as determined by electronic structure calculations, molecular dynamics simulations and experimental measurement. Finally, we characterize the changes of the structure in the first hydration shell with increasing temperature as predicted by molecular simulation     

Experimental evidence for a variable first coordination shell of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea solution

A combined extended X-ray absorption fine structure (EXAFS) and large angle X-ray scattering (LAXS) investigation has been performed to evaluate the coordination structure of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea (dmpu) solutions. This approach has singled out the existence of a flexible coordination shell around the cadmium(II) ion in aqueous and dimethyl sulfoxide solutions, whereas a regular octahedral complex is detected in dmpu. The EXAFS and LAXS techniques provide different values of the Cd-O first shell distance (2.27(1) A and 2.302(5) A, respectively) for the hydrated and dimethyl sulfoxide solvated complexes, and this discrepancy is originated by the simultaneous presence of hexa- and heptacoordinated complexes in solution, giving rise to a broad distribution of distances around the ion. These findings demonstrate that, in solution, the cadmium(II) ion forms quite flexible hydration and dimethyl sulfoxide solvate complexes undergoing a solvent exchange with unusually stable seven-coordinated intermediate complexes, and therefore the mean ion-solvent distance is longer in solution than in the solid state. In the dmpu solution, due to the bulkiness of the solvent molecules, the octahedral cadmium(II) solvate is extremely crowded and it is not possible for a seventh ligand to enter the inner-coordination shell. This investigation shows that the combined analysis of the EXAFS and LAXS data allows a reliable determination of the structural properties of electrolyte solutions, also in the presence of flexible coordination shell with a variable number of coordinating molecules.     

Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution

We report molecular dynamics (MD) simulations of three protein-water systems (ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1), from which we compute the dielectric properties of the solutions. Since two of the proteins studied have a net charge, we develop the necessary theory to account for the presence of charged species in a form suitable for computer simulations. In order to ensure convergence of the time correlation functions needed for the analysis, the minimum length of the MD simulations was 20 ns. The system sizes (box length, number of waters) were chosen so that the resulting protein concentrations are comparable to experimental conditions. A dielectric component analysis was carried out to analyze the contributions from protein and water to the frequency-dependent dielectric susceptibility chi(omega) of the solutions. Additionally, an even finer decomposition into protein, two solvation shells, and the remaining water (bulk water) was carried out. The results of these dielectric decompositions were used to study protein solvation at mesoscopic resolution, i.e., in terms of protein, first and second solvation layers, and bulk water. This study, therefore, complements the structural and dynamical analyses at molecular resolution that are presented in the companion paper. The dielectric component contributions from the second shell and bulk water are very similar in all three systems. We find that the proteins influence the dielectric properties of water even beyond the second solvation shell, in agreement with what was observed for the mean residence times of water molecules in protein solutions. By contrast, the protein contributions, as well as the contributions of the first solvation shell, are system specific. Most importantly, the protein and the first water shell around ubiquitin and apo-calbindin are anticorrelated, whereas the first water shell around the SH2 domain is positively correlated.