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.     

Density functional theory based molecular-dynamics study of aqueous iodide solvation

We study the solvation of iodide in water using density functional theory based molecular-dynamics simulations. Detailed analysis of the structural and dynamical properties of the first solvation shell is presented, showing a disruptive influence of the ion on the local water structure. Iodide-water hydrogen bonding is weak, compared to water-water hydrogen bonds. This effective repulsive ion-water interaction leads to the formation of a quite unstructured solvation shell. The dynamics of water molecules surrounding the iodide is relatively fast. The intramolecular structural and electronical properties of water molecules around the ion are not affected.     

Nature of the aqueous hydroxide ion probed by X-ray absorption spectroscopy

X-ray absorption spectra of aqueous 4 and 6 M potassium hydroxide solutions have been measured near the oxygen K edge. Upon addition of KOH to water, a new spectral feature (532.5 eV) emerges at energies well below the liquid water pre-edge feature (535 eV) and is attributed to OH- ions. In addition to spectral changes explicitly due to absorption by solvated OH- ions, calculated XA spectra indicate that first-solvation-shell water molecules exhibit an absorption spectrum that is unique from that of bulk liquid water. It is suggested that this spectral change results primarily from direct electronic perturbation of the unoccupied molecular orbitals of first-shell water molecules and only secondarily from geometric distortion of the local hydrogen bond network within the first hydration shell. Both the experimental and the calculated XA spectra indicate that the nature of the interaction between the OH- ion and the solvating water molecules is fundamentally different than the corresponding interactions of aqueous halide anions with respect to this direct orbital distortion. Analysis of the Mulliken charge populations suggests that the origin of this difference is a disparity in the charge asymmetry between the hydrogen atoms of the solvating water molecules. The charge asymmetry is induced both by electric field effects due to the presence of the anion and by charge transfer from the respective ions. The computational results also indicate that the OH- ion exists with a predominately "hyper-coordinated" solvation shell and that the OH- ion does not readily donate hydrogen bonds to the surrounding water molecules.     

Probing the transition from hydrophilic to hydrophobic solvation with atomic scale resolution

Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L(1,3) edge EXAFS at 50 ps time delay points to the formation of an expanded water cavity around the iodine atom, in good agreement with classical and quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. These also show that while the hydrogen atoms pointed toward iodide, they predominantly point toward the bulk solvent in the case of iodine, suggesting a hydrophobic behavior. This is further confirmed by quantum chemical (QC) calculations of I(-)/I(0)(H(2)O)(n=1-4) clusters. The L(1) edge sub-picosecond spectra point to the existence of a transient species that is not present at 50 ps. The QC calculations and the QM/MM MD simulations identify this transient species as an I(0)(OH(2)) complex inside the cavity. The simulations show that upon electron abstraction most of the water molecules move away from iodine, while one comes closer to form the complex that lives for 3-4 ps. This time is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform an H-bond network. Only then is the interaction with the solvation shell strong enough to pull the water molecule of the complex toward the bulk solvent. Overall, much of the behavior at early times is determined by the reorientational dynamics of water molecules and the formation of a complete network of hydrogen bonded molecules in the first solvation shell.     

Binding of molecular hydrogen to halide anions: A computational exploration of eco-friendly materials for hydrogen storage

Using density functional theory calculations, we investigate the structures of the complexes derived from the interaction of molecular hydrogen to halide anions. The bromide anion can bind up to seven hydrogen molecules while both fluoride and chloride anions form stable complexes with up to six hydrogen molecules. According to the results of QTAIM analyses, closed shell interactions are operative in these complexes.     

Chloride ion conduction without water coordination in the pore of ClC protein

In the present work, we have found by an atomistic molecular dynamics simulation that hydrogen atoms originating from the residues of a prokaryotic ClC protein (EcClC) stabilize the chloride ion without water molecules in the pore of ClC protein. When the chloride ion conduction is simulated by pulling a chloride ion along the pore axis, the free energy barrier for chloride ion conduction is calculated to be low (4 kcal/mol), although the chloride ion is stripped of its hydration shell as it passes through the dehydrated pore region. The calculation of the number of hydrogen atoms surrounding the chloride ion reveals that water molecules hydrating the chloride ion are replaced by polar and non‐polar hydrogen atoms protruding from the protein residues. From the analysis of the pair interaction energy between the chloride ion and these hydrogen atoms, it is realized that the hydrogen atoms from the protein residues stabilize the chloride ion at the dehydrated region instead of water molecules, by which the energetic penalty for detaching water molecules from the permeating ion is compensated. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

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.     

A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: structural, electronic, and dynamical properties

The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.     

Infrared spectroscopy of anionic hydrated fluorobenzenes

We investigate the structural motifs of anionic hydrated fluorobenzenes by infrared photodissociation spectroscopy and density functional theory. Our calculations show that all fluorobenzene anions under investigation are strongly distorted from the neutral planar molecular geometries. In the anions, different F atoms are no longer equivalent, providing structurally different binding sites for water molecules and giving rise to a multitude of low-lying isomers. The absorption bands for hexa- and pentafluorobenzene show that only one isomer for the respective monohydrate complexes is populated in our experiment. For C6F6.-H2O, we can assign these bands to an isomer where water forms a weak double ionic hydrogen bond with two F atoms in the ion, in accord with the results of Bowen et al. [J. Chem. Phys. 127, 014312 (2007), following paper.] The spectroscopic motif of the binary complexes changes slightly with decreasing fluorination of the aromatic anion. For dihydrated hexafluorobenzene anions, several isomers are populated in our experiments, some of which may be due to hydrogen bonding between water molecules.     

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.     

Synthesis and Structural Characterization of [Mn（phen）2（H2O）2]（OAc）2.6H2O

1 INTRODUCTION Water oxidation to oxygen gas by photo- synthetic apparatus of green plants and cyano- bacteria is the origin of this gas in the atmosphere. The water oxidation center is a tetranuclear, oxide- bridged manganese cluster with O,N-based peri- pheral ligation by amino acid side-chain group[1, 2]. The binding of aqua to the Mn site may be impor- tant to the oxidation of aqua for producing dioxygen. 1,10-Phenanthroline has been adopted to simulate coordination sphere of manga…     

Tetraaquabis(pyridine)metal(II) saccharinate tetrahydrate, [M(H2O)4(py)2](sac)2·4H2O; M = Co,Ni. Crystal structure determination

The crystal structure determination of the title compounds showed that they are isomorphous, revealing the general formula [M(H₂O)₄(py)₂](sac)₂·4H₂O. Their structures are built up of [M(H₂O)₄(py)₂]²⁺ cations, saccharinato anions and non-coordinated water molecules. The metal atom lies on the inversion center and is octahedrally coordinated by four water oxygens and two pyridine nitrogen atoms. The crystal structure packing is achieved through the hydrogen bonds of O_w⋯O_w, O_w⋯O and O_w⋯N type. Coordinated water molecules are hydrogen bonded to non-coordinated ones at the same time participating in hydrogen bonding with carbonyl oxygen and nitrogen atom from the saccharinato anions. Non-coordinated water molecules participate in hydrogen bonding with the oxygen atoms belonging to the saccharinato CO and SO₂ groups. The hydrogen bond network between the oxygen atoms belonging to the SO₂ group of the saccharinato anions and one of the non-coordinated water molecules (OW3) constructs the centrosymmetric cavity in the structure.     

Syntheses and crystal structures of three cesium salts: Cesium 5-sulfosalicylate, cesium 3,5-dinitrosalicylate and cesium 2,4-dinitrophenoxide monohydrate

In an attempt to probe a potential template role of the large alkali-metal cation cesium in organization of biorelevant ligands, 5-sulfosalicylate, 3,5-dinitrosalicylate and 2,4-dinitrophenol complexes of cesium were prepared and structurally investigated. The structures of cesium 5-sulfosalicylate, cesium 3,5-dinitrosalicylate and cesium 2,4-dinitrophenoxide monohydrate have been determined through X-ray diffraction analysis. The 5-sulfosalicylate anion has lost the proton at the −SO₃H group while the 3,5-dinitrosalicylate anion at −COOH group but both retains the usual intermolecular hydrogen bond between phenolic and carboxylic oxygen. In cesium 2,4-dinitrophenoxide monohydrate, the Cs⁺ cation is 12-coordinate by O atoms in anions and water molecules while the metal atoms in cesium 5-sulfosalicylate and cesium 3,5-dinitrosalicylate have coordination numbers 10 and 11, respectively, with an irregular coordination sphere made up exclusively of oxygen atoms. Even more in cesium 2,4-dinitrophenoxide monohydrate, the water molecules are in rare triply bridging positions between these cations. Both complexes have layer structures containing the cations and polar groups of the ligands in core domains sandwiched by the aromatic rings above and below. The organization of all layer structures appears to be governed mainly by steric effects and electrostatic forces with very little directional influence of the cations.     

Diffusion Monte Carlo simulations on uracil-water using an anisotropic atom-atom potential model

We have developed an anisotropic atom-atom intermolecular potential model for the interaction of uracil with water. The potential consists of a distributed multipole analysis (DMA) model for the electrostatic energy, and a 6-exp potential to represent the repulsion-dispersion term. The repulsion-dispersion potential parameters are adjusted to yield good agreement with accurate ab initio data on the minima and transition states of the uracil-water complex. We have used this potential in diffusion Monte Carlo simulations of uracil-water, uracil-(water)2 and uracil-(water)3. The uracil-water simulations show that the theoretically based potential gives a qualitatively different picture of uracil hydration than that provided by a standard isotropic atom-atom point charge model, which is shown to underestimate the delocalized motion of the water hydrogen atoms. Plots of the vibrational probability density of the hydrogen atoms show the delocalized motion of the water hydrogen atoms that are not involved in hydrogen bonding.     

Fumed silica synthesis: influence of small molecules on the particle formation process

Burning silicon tetrachloride in an oxygen‐hydrogen flame produces fumed silica. This process is known for at least 50 years [1‐5], but some important details are still uncertain. We would like to study several starting steps of fumed silica synthesis on the way from molecules to products. To do this we have performed quantum‐level simulations of protoparticle and primary particle formation, from silicon dioxide molecules. Additionally, we have simulated the behavior of silica clusters in the presence of small molecules like water and hydrochloric acid. The reaction of silicon dioxide molecules leads to a silica cluster, which is covered with chemicaly highly active sites of one‐coordinated oxygen atoms and three‐coordinated silicon atoms. These clusters interact together and produce silica bulk like quartz glass. Reaction with water terminates the silica particle surface and leads to a complicated structure of the particle surfaces. The hydroxyl shell protects the particle body against the increase in particle size, but leads to aggregate and agglomerate formation.     

Dirubidium hexaaquacobalt(II) tetrakis(hydrogen phthalate) tetrahydrate and coordination modes of the hydrogen phthalate anion

The title compound, Rb₂[Co(H₂O)₆](C₈H₅O₄)₄·4H₂O, consists of nearly regular octahedral [Co(H₂O)₆]²⁺ cations with the Co^II cations on the inversion centre (special position 2a), Rb⁺ cations, hydrogen phthalate (Hpht⁻) anions and disordered water molecules. The Rb⁺ cation is surrounded by nine O atoms from Hpht⁻ anions and water molecules, with a strongly deformed pentagonal–bipyramidal geometry and one apex split into three positions. The crystal packing is governed by numerous hydrogen bonds involving all water molecules and Hpht⁻ anions. In this way, layers parallel to the ab plane are formed, with the aromatic rings of the Hpht⁻ anions esentially directed along the c axis. While Hpht⁻ anions form the outer part of the layers, disordered water molecules and Rb⁺ cations alternate with [Co(H₂O)₆]²⁺ cations in the inner parts. The only interactions between the layers are van der Waals forces between the atoms of the aromatic rings. A search of the Cambridge Structural Database for coordination modes and types of hydrogen‐bonding interaction of the Hpht⁻ anion showed that, when uncoordinated Hpht⁻ anions are present, compounds with intermolecular hydrogen bonds are more numerous than compounds with intramolecular hydrogen bonds. For coordinated Hpht⁻ anions, chelating and bridging anions are almost equally common, while monodentate anions are relatively scarce. The same coordination modes appear for Hpht⁻ anions with or without intramolecular hydrogen bonds, although intramolecular hydrogen bonds are less common.     

Thermal motion from monte carlo simulations of aqueous ionic solutions

The statistical pattern recognition procedure of Marchese and Beveridge for the analysis of Monte Carlo simulations of aqueous ionic solutions [J. Am. Chem. Soc. 106 , 3713 (1984)] has been extended to include average hydrogen positions as well as oxygen positions. In addition, thermal ellipsoids have been calculated for each atom and displayed graphically. Application of this procedure to the analysis of a dilute aqueous solution of Zn⁺⁺ reveals an octahedral arrangement of water molecules within the ion's first hydration shell. The thermal ellipsoids show that most of the water motion is manifest in the hydrogen atoms.     

Hydration processes of electrolyte anions and cations on pt(111), Ir(111), Ru(001) and Au(111) surfaces: coadsorption of water molecules with electrolyte ions

Water adsorption on Pt( 111) and Ru(001) treated with oxygen, hydrogen chloride and sodium atom at 20 K has been studied by Fourier transform infrared spectroscopy, scanning tunneling microscopy and surface X-ray diffraction. Water molecules chemisorb predominantly on the sites of the electronegative additives, forming hydrogen bonds. Three types of hydration water molecules coordinate to an adsorbed Na atom through an oxygen lone pair. In contrast, water molecules adsorb on electrode surfaces in a simple way in solution. In 1 mM CuSO4 + 0.5 M H2SO4 solution on an Au(111) electrode surface, water molecules coadsorb not only with sulfuric acid anions through hydrogen bonding but also with copper, over wide potential ranges. In the first stage of underpotential deposition (UPD), each anion is accommodated by six copper hexagon (honeycomb) atoms on which water molecules dominate. At any UPD stage water molecules interact with both the copper atom and sulfuric acid anions on the Au(111) surface. Water molecules also coadsorb with CO molecules on the surface of 2 x 2-2CO-Ru(001). All of the hydration water molecules chemisorb weakly on the surfaces. There appears to be a correlation between the orientation of hydrogen bonding water molecules and the electrode potential.     

The interaction between trapped electron and water molecules in one interior structure of water tetramer anion

Using aug-cc-pVDZ basis sets supplemented with diffused bond functions, the (H₂O)₄⁻ isomer of the water tetramer anion in Ci-symmetry was optimized at the MP2 level. The excess electron was enveloped directly by the four hydrogen atoms of two inside water molecules, forming an interior structure. This study shows four hydrogen atoms of two outside water molecules also have important interaction with the trapped electron. We described the interactions between individual water molecule (including both inside and outside) and the trapped electron. The influence of the trapped electron on the surrounded second layer molecules was also put forward.