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Journal of Molecular Liquids (v.129, #1-2)
Ion association of alkaline and alkaline-earth metal perchlorates in acetonitrile by Pamela Eberspächer; Erwin Wismeth; Richard Buchner; Josef Barthel (pp. 3-12).
In this contribution results of a joint investigation by dielectric and infrared spectroscopy into the ion association of LiClO4, NaClO4, Mg(ClO4)2 and Ca(ClO4)2 in acetonitrile solutions at 25 °C are presented. All electrolytes exhibit multi-step ion association. Whereas the alkali salts only form solvent-shared (SIP) and contact ion pairs (CIP), a significant amount of neutral triple ions M(ClO4)2 ( T0) is additionally observed for the earth–alkali salts. For Ca(ClO4)2 there are also indications for the formation of [Ca2ClO4]3+ triples ( T+).Also discussed are effective solvation numbers derived from the acetonitrile relaxation.
Keywords: Dielectric relaxation; Infrared spectroscopy; Ion association; Solvation number; Acetonitrile; Perchlorates
A FTIR study of ion-solvent interactions in N,N-dimethylacetamide by Dmytro M. Verbovy; Thomas G. Smagala; Marcin A. Brynda; W. Ronald Fawcett (pp. 13-17).
FTIR spectroscopy has been used to study ion solvation in electrolyte solutions in N,N-dimethylacetamide (DMA). Principal component analysis was used to analyze the dependence of absorption on electrolyte concentration. Results are reported for NaI, LiI, and LiBr. By comparing the effects of the electrolytes in a given region of the spectrum, one is able to distinguish sites for cation solvation in DMA from those for anion solvation. The present data are compared with those obtained earlier for N,N-dimethylformamide.
Keywords: N,N-dimethylacetamide; FTIR
Solvation structure of metal ions in nitrogen-donating solvents by Yasuhiro Inada; Yasuhiro Niwa; Kuniko Iwata; Shigenobu Funahashi; Hitoshi Ohtaki; Masaharu Nomura (pp. 18-24).
The solvation structure of the Mn(II), Fe(II), Co(II), Ni(II), and Zn(II) ions has been determined in various nitrogen-donating solvents of n-propylamine (PA), trimethylenediamine (TA), ethylenediamine (EN), pyridine (PY), 2-methylpyridine (2MPY), 4-methylpyridine (4MPY), and acetonitrile (AN) by the X-ray absorption spectroscopy. The 6-coordinate octahedral structure has been observed for all the ions except for the species of Zn(II) in PA and 2MPY. The mixed formation of 4- and 6-coordinate species is found for Zn(II) in TA, of which the electron donicity is compared with that of PA. A similar mixed formation of solvated species has been observed for the Co(II) ion in PA. The M–N bond distances vary in the order Mn(II)>Fe(II)>Co(II)>Ni(II)
Keywords: Solvation structure; XAFS; Nitrogen-donating solvents; Electron donating ability; Solvent bulkiness
Microheterogeneity of ethanol–water binary mixtures observed at the cluster level by Akihiro Wakisaka; Kazuo Matsuura (pp. 25-32).
The microscopic structures in ethanol–water binary mixtures were examined by analyzing the mass spectra of clusters generated through fragmentation of liquid droplets. From the effects of temperature and mixing ratios on the cluster structures, we have demonstrated that the ethanol–water binary mixtures have microscopic phase separation at the cluster level in wide mixing ratios: 10 vol.%<[EtOH]<90 vol.%. In this region, ethanol-rich clusters whose molecular composition is independent of the mixing ratio were observed at lower temperatures, and the ethanol-rich clusters interacted with water molecules with increasing temperature. Furthermore, we would like to present the mechanism for the formation of ethanol-rich clusters, induced by the contact with water molecules.
Keywords: Microheterogeneity; Cluster; Phase separation; Ethanol; Mixture
Functionalization of carbon nanotubes with oligonucleotide in solutions — Production of nanotube chips by Zoltán Kónya; Krisztián Niesz; Imre Kiricsi; Sándor Botka; Zsófia Keresztes; Erika Kálmán (pp. 33-38).
Multiwall carbon nanotubes were synthesized using the catalytic chemical vapor deposition (CVD) technique followed by an oxidative purification process. The nanotube modified by functional groups were connected by pre-synthesized oligonucleotides in solution. The material thus obtained was characterized by various microscopic methods. The preparation of nanotube chips is discussed.
Keywords: Multiwall carbon nanotubes; Oligonucleotides; Nanotube chip
NMR relaxation in the double clathrate hydrate tetrahydrofuran/hydrogen sulfide by Thomas R. Keβler; Manfred D. Zeidler (pp. 39-43).
Nuclear magnetic proton relaxation times T1 are reported for the double clathrate hydrate tetrahydrofuran/hydrogen sulfide in the temperature range 4–285 K at frequencies 60 and 300 MHz. The guest molecules contained alternatively light and heavy hydrogen isotopes. This permitted the molecular motion of both guests to be studied separately. Data analysis of tetrahydrofuran shows that between 15 and 120 K isotropic rotation with activation energy of 5 kJ/mol occurs. Data analysis of hydrogen sulfide points to strong interactions with the cage wall, less at lower than at higher temperature resulting in two different activation energies of 0.3 kJ/mol below and 3 kJ/mol above 26 K.
Keywords: Tetrahydrofuran; NMR relaxation; Hydrogen sulfide; Clathrate
Internal diffusive and collective motions in proteins studied by neutron scattering by M.-C. Bellissent-Funel (pp. 44-48).
It is well known that water plays a major role in the stability and catalytic function of proteins. Both the effect of hydration water on the dynamics of proteins and the effect of proteins on the dynamics of water have been studied using inelastic neutron scattering. Dynamic neutron scattering is the most direct probe of diffusive and collective protein dynamics on the picosecond–nanosecond timescale. We present here results for C-phycocyanin, which is a globular protein important for photosynthesis. It can be obtained in protonated and deuterated forms. Diffusive motions have been studied using the protonated C-phycocyanin protein. The collective dynamics has been investigated using the fully deuterated C-phycocyanin protein. Comparison is made with results of molecular dynamics simulation.
Keywords: Proteins; Water; Neutron scattering
Anomaly of the basicity of water in mixed solvents by Hitoshi Ohtaki; Yasuhiro Niwa; Kazuhiko Ozutsumi; Michael Probst; Barbara Mroz; Fernando Rull Perez; Javier Alvarez; Silvia Bolado (pp. 49-56).
Intermolecular interactions between water and N, N-dimethylformamide (DMF) in their mixtures were investigated by Raman spectroscopic and X-ray diffraction methods and by molecular orbital calculations. The Raman spectroscopic and X-ray diffraction measurements indicated the formation of water-DMF associates or clusters in the mixtures. Theoretical calculations for the electron density of H2O-HOH-OH2,▪ of electron density on the oxygen atom of the water molecule in the DMF-HOH-DMF associate due to the accumulation of electrons transferred from DMF to the oxygen atom of the terminal water molecule. The increase resulted in a larger donicity of the terminal H2O compared to normal water. Although the donor number DN of the water molecule in the DMF-H2O-DMF associate was not determinable, it was estimated to be DN ∼30 from the behavior of the preferential solvation of the cobalt(II) ion in water-DMF mixtures.
Keywords: Basicity; Solvation; Isosolvation point; Water-DMF mixtures
X-ray diffraction study of water confined in activated carbon pores over a temperature range of 228–298 K by Toshio Yamaguchi; Hitoshi Hashi; Shigeharu Kittaka (pp. 57-62).
The structure and properties of water confined in activated carbon (AC) pores of an average diameter 20 Å have been investigated over a temperature range between 298 K and 228 K by adsorption isotherms, differential scanning calorimetry (DSC), and large-angle X-ray diffraction. The adsorption isotherm at 298 K has shown the V-type one, in which the adsorption of water takes place at a relative pressure ( p/ p0)∼0.4, increasing rapidly with an increase in the relative pressure to a saturated value at p/ p0=1. The DSC data of water in AC at p/ p0=1.0 have shown three steps of vitrification of water, suggesting different pore sizes of AC. The X-ray diffraction data on confined water at p/ p0=1.0 have revealed that the ice-like tetrahedral network of water is slightly perturbed from bulk water structure, but not to such an extent as found for water confined in hydrophilic pores of MCM-41 previously reported [P. Smirnov, T. Yamaguchi, S. Kittaka, S. Takahara, Y. Kuroda, J. Phys. Chem. B 104 (2000) 5498]. With decreasing temperature, the hydrogen bonded network of water was enhanced, and at 243 K hexagonal ice Ih was partially formed in the AC pores, in contrast with cubic ice Ic formed in hydrophilic pores (diameter 100 Å) of silica. The microscopic structure of supercooled water confined in hydrophobic AC pores is compared with those in hydrophilic MCM-41 pores.
Keywords: Confined water; Activated carbon pore; X-ray diffraction; Adsorption isotherm; Differential scanning calorimetry
Ion pairing in aqueous calcium chloride solution: Molecular dynamics simulation and diffraction studies by Tünde Megyes; Imre Bakó; Szabolcs Bálint; Tamás Grósz; Tamás Radnai (pp. 63-74).
X-ray and neutron diffraction and molecular dynamics simulation studies were performed on 2.5 and 4.0 M aqueous solutions of calcium chloride. The aim of the work, beyond the determination of the solution structure, was to discuss the capability of each method to detect ion pair formation. It has been found that the diffraction methods are performing very well in the determination of Ca2+–O distances: the obtained values fell in the range 2.43–2.46 Å. Further on, by applying the X-ray diffraction method ion pairs could be observed in the case of higher concentrated solution, but for neutron diffraction study, the most adequate isotope substitution method has to be chosen with care in order to be able to describe ion pairs in solution. The results of diffraction studies were compared to molecular dynamics simulation results; the latter ones were found to be in general accordance with the experimental findings. The smaller discrepancies between the simulation and the experimental results are coming from small differences in the ion–water and ion–ion distances, and they may be due to the potential model applied in the simulation and to the experimental uncertainties.
Keywords: Calcium ion; Hydration; Solution structure; Diffraction; Simulation
Structural and dielectric properties of 1,4-dioxane – water mixtures by Gudrun Ahn-Ercan; Hartmut Krienke; Georg Schmeer (pp. 75-79).
Pure 1,4-dioxane and 1,4-dioxane – water mixtures are investigated in the framework of Monte Carlo (MC) simulations on the molecular Born–Oppenheimer (BO) level with classical interaction site models (ISM). Our proposed ISM for 1,4-dioxane [H. Krienke, G. Ahn Ercan, J. Barthel J.Mol.Liq. 109, 115 (2004)], the chair formation DXC and the twisted boat formation DXT, is used as well as the SPC/E model for water. Dielectric constants are calculated within the Monte Carlo simulations and by integral equation theories.
Keywords: 1,4-dioxane; ISM molecules; Monte Carlo simulation; Water; Mixtures
Molecular dynamics simulations of aqueous RbBr-solutions over the entire solubility range at room temperature by Ildikó Harsányi; László Pusztai; Jean-Christophe Soetens; Philippe A. Bopp (pp. 80-85).
We report a comparison of the structures of a series of aqueous rubidium bromide solutions at concentrations from 0.955 mol/l to 4.89 mol/l and at room temperature as obtained from classical molecular dynamics computer simulations. The structures are analyzed in terms of the atom–atom radial distribution functions obtained from the simulation trajectories. Neutron weighted total scattering functions, as calculated from simulations, qualitatively follow the experimental trends as the concentration changes. Apart from structural features, self-diffusion coefficients of the ions and the solvent have also been calculated.
Keywords: PACS; 61.25.-f; 61.43.Mv; 61.43.BnAqueous solutions; Microscopic structure; Molecular dynamics simulation
Molecular dynamics simulation of GM1 gangliosides embedded in a phospholipid membrane by Marcello Sega; Pál Jedlovszky; Renzo Vallauri (pp. 86-91).
Molecular dynamics simulation of the hydrated phospholipid membrane built up by the unsaturated dioleylphosphatidylcholine (DOPC) molecules, containing a GM1 ganglioside molecule in each of its two layers has been performed. The system can be regarded as a model of the infinitely dilute solution of gangliosides in a phospholipid membrane, and can serve as a reference system for future studies of mixed membranes of finite concentration.It is found that the GM1 ganglioside molecule, the headgroup of which is bearing a negative charge can form charge pairs with the positively charged choline group of the zwitterionic head of the DOPC molecules. This charge pair can involve either 1 or 2 nearest neighbour DOPC molecules. The observed lifetime of such a charge pair is in the order of a few nanoseconds, whereas the lifetime of a bifurcated charge pairing formed with two DOPC molecules is considerably shorter, being in the order of a few hundred picoseconds. The dipole vector of the polar headgroup of the DOPC molecules charge paired to GM1, represented by the vector pointing from their P to N atom (PN vector) prefers to point straight to the centre of the negative charge located at the C atom of the negatively charged carboxylic (COO−) group of the GM1 molecule.
Keywords: Dioleoylphosphatidylcholine; GM1; Rafts; Glycolipids
MD simulations of proton transport along a model Nafion surface decorated with sulfonate groups by Supaporn Dokmaisrijan; Eckhard Spohr (pp. 92-100).
We analyse the proton distributions in slab simulations of models of characteristic aqueous pores in polymer electrolyte membranes utilized in low temperature hydrogen and direct methanol fuel cells. In particular we calculate density profiles across the interfacial region and density distributions parallel to the interface for aqueous systems near nonpolar surfaces covered with static or tethered sulfonate groups. Three different model descriptions have been used, two based on a previously employed fluxional empirical valence bond model, and one using rigid ion and water models. The goal is to identify common characteristics, which are to first approximation independent of the particular choice of the details of the interaction and geometrical model. We observe that lateral (diffusive) proton motion shows only small barriers for reasonable choices of the arrangement of SO3− groups and that there is a significant coupling between lateral motion and motion perpendicular to the pore surface. We provide structural evidence that previously proposed surface and bulk transport mechanisms in a polymer electrolyte are not distinct mechanisms. Instead we conclude that the simulations are consistent with a common structural diffusion mechanism, modified by the topology of the landscape around the sulfonate groups.
Keywords: Molecular dynamics; Proton transfer; Polymer electrolyte membranes
Relation between hydrogen bonding and intramolecular motions in liquid and supercritical methanol by Jean-Michel Andanson; Philippe A. Bopp; Jean-Christophe Soetens (pp. 101-107).
Molecular dynamics (MD) simulations of liquid and supercritical methanol have been performed using a well known flexible 3-sites model. The analysis of the hydrogen bond network has been carried out using first standard geometric criteria on dimers. We then analyzed the effect of hydrogen bonds on single-molecule properties by studying the vibrational and librational motions of a molecule in terms of specific autocorrelation functions and their Fourier transforms. This approach led to an alternative definition of the hydrogen bond, based on molecular properties that can be compared directly with results from molecular spectroscopies (infrared and Raman). It is found that geometric and “spectroscopic� criteria lead to consistent average results over a wide range of thermodynamics conditions while individual molecular results can be different.
Keywords: Molecular dynamics; Autocorrelation functions; Spectroscopies; Hydrogen bonding
Reverse Monte Carlo analysis of small-angle scattering data on colloids and nanoparticles by Gergely Tóth (pp. 108-114).
Applications of Reverse Monte Carlo-type simulations are summarized for understanding the inter-particle structure of colloids and nanoparticles. Results are shown for simple spherical polymer latex, for micelles and for a catalyst containing nanoparticles. Different methodological extensions of the traditional Reverse Monte Carlo simulations are developed in order to get reliable interpretation of small-angle scattering data and they are compared: the traditional Reverse Monte Carlo technique, a method for polydisperse spheres, a combination of direct minimization and Reverse Monte Carlo procedures, and a method for particles with arbitrary shape and without analytical particle form factor.
Keywords: Reverse Monte Carlo simulation; Colloids; Inter-particle structure; Modelling
Structural changes in liquid selenium with increasing temperature by Pál Jóvári; László Pusztai (pp. 115-119).
Structural models of liquid selenium, containing up to 20,000 atoms, have been constructed by means of Reverse Monte Carlo modelling. The models are consistent with a set of X-ray diffraction results obtained at elevated temperatures and pressures. Based on the characteristics of these models we suggest that the general view of the liquid as a collection of chain-like molecules, especially close to the critical point, is probably inappropriate. Instead, near-critical (metallic) fluid Se could be considered as an atomic liquid where first neighbor orientational correlations strongly resemble those found in the solid forms of selenium.
Keywords: PACS; 61.25.-f; 61.43.Mv; 61.43.BnLiquid selenium; Reverse Monte Carlo modelling
On the re-engineered TIP4P water models for the prediction of vapor–liquid equilibrium by Ariel A. Chialvo; Albert Bartók; András Baranyai (pp. 120-124).
We perform extensive Gibbs Ensemble Monte Carlo simulations to study the capability of some recently re-parameterizations of the original TIP4P model intended to predict accurately the vapor–liquid coexistence envelope of water, its critical point, and its temperature dependence for the vapor pressure and second virial coefficient, and complement this analysis with the characterization of some specific crystalline faces of ice. We also disclose some trends between the resulting dipole moment of the models and the Lennard–Jones parameters, the location of the negative charge, as well as the estimated critical temperature. Finally, we discuss the inability of these models to predict accurately and simultaneously the melting temperature and the temperature of maximum density.
Keywords: Gibbs Ensemble Monte Carlo; Water models; Ices; Melting point; Density maximum