26 resultados para WATER-MOLECULES
Resumo:
A semi-phenomenological molecular model is presented, which is capable of describing with the use of analytical formulae, the wideband dielectric(1) and far-infrared spectra of ordinary and heavy water. In the model the vector of a dipole moment is presented as a sum of two components. The absolute value of the first one is constant; the second one changes harmonically with time. The key aspect of this work is consideration of FIR spectra due to the second component. In the context of the modified hybrid model presented in the work, reorientation of the dipoles in the rectangular potential well is considered, as a result of which the librational (near 700 cm (-1)) and translational (near 200 cm (-1)) absorption bands and the microwave Debye relaxation spectrum arise. It is shown that the time-dependent part of a dipole moment contributes most to the translational band, the relevant mechanism is taken to be stretching vibration of the H-bonded molecules. Previous linear-response molecular models were unsuccessful in describing this band (in heavy water) in terms of the complex dielectric permittivity. The spatial and time scales characteristic of water are estimated. (C) 2002 Elsevier Science B.V. All rights reserved.
Resumo:
A nonlinear equation of motion is found for the dimer comprising two charged H2O molecules. The THz dielectric response to nonharmonic vibration of a nonrigid dipole, forming the hydrogen bond (HB), is found in the direction transverse to this bond. An explicit expression is derived for the autocorrelator that governs the spectrum generated by transverse vibration (TV) of such a dipole. This expression is obtained by analytical solution of the truncated set of recurrence equations. The far infrared (FIR) spectra of ice at the temperature - 7 degrees C are calculated. The wideband, in the wavenumber (frequency) v range 0... 100.0 cm(-1), spectra are obtained for liquid water at room temperature and for supercooled water at -5.6 degrees C. All spectra are represented in terms of the complex permittivity epsilon(v) and the absorption coefficient alpha(v). The obtained analytical formula for epsilon comprises the term epsilon(perpendicular to) pertinent to the studied TV mechanism with three additional terms Delta epsilon(q), Delta epsilon(mu), and epsilon(or) arising, respectively, from: elastic harmonic vibration of charged molecules along the H-bond; elastic reorientation of HB permanent dipoles; and rather free libration of permanent dipoles in 'defects' of water/ice structure. The suggested TV-dielectric relaxation mechanism allows us: (a) to remove the THz 'deficit' of loss epsilon" inherent in previous theoretical studies; (b) to explain the THz loss and absorption spectra in supercooled (SC) water; and (c) to describe, in agreement with the experiment, the low- and high-frequency tails of the two bands of ice H2O located in the range 10...300 cm(-1). Specific THz dielectric properties of SC water are ascribed to association of water molecules, revealed in our study by transverse vibration of HB charged molecules. (C) 2006 Published by Elsevier B.V.
Resumo:
The light emission spectrum from a scanning tunnelling microscope (LESTM) is investigated as a function of relative humidity and shown to provide a novel and sensitive means for probing the growth and properties of a water meniscus on the nanometre scale. An empirical model of the light emission process is formulated and applied successfully to replicate the decay in light intensity and spectral changes observed with increasing relative humidity. The modelling indicates a progressive water filling of the tip-sample junction with increasing humidity or, more pertinently, of the volume of the localized surface plasmons responsible for light emission; it also accounts for the effect of asymmetry in structuring of the water molecules with respect to the polarity of the applied bias. This is juxtaposed with the case of a non-polar liquid in the tip-sample nanocavity where no polarity dependence of the light emission is observed. In contrast to the discrete detection of the presence/absence of a water bridge in other scanning probe experiments through measurement of the feedback parameter for instrument control, LESTM offers a means of continuously monitoring the development of the water bridge with sub-nanometre sensitivity. The results are relevant to applications such as dip-pen nanolithography and electrochemical scanning probe microscopy.
Resumo:
The structural interactions of biological macromolecules, their biochemical activities and, ultimately, the metabolic function of cellular systems are dependent upon weak inter- and intra-molecular forces such as hydrogen bonds, Van der Waals forces, and the hydrophobic effect. Water molecules, and those of hydrophobic substances such as hydrocarbons, can take part in and/or modify these interactions and thereby determine the operational and structural stability of the microbial cell and its macromolecular systems. We explain how the cytosol, plasma membrane and the extracellular solution form a material and energetic continuum; and discuss the behavior of hydrophobic substances of extracellular origin as they migrate into the plasma membrane and into the cell's interior. The adverse effects of substances with a log P octanol-water =2, that partition into the hydrophobic domains of biological macromolecules, are discussed in relation to microbial cell function; and we speculate whether the cellular stress that they induce is symmetrical or asymmetrical in nature. In the context of the microbial environment, we take a situational-functional approach to consider how hydrophobic stressors interact with the microbial cell, and what types of evasion tactics microbes can employ to minimize their inhibitory activities. Finally, we discuss the ecological implications of hydrocarbon-induced cellular stress for microbial systems.
Resumo:
Low-energy electron-impact hydrogen loss due to dissociative electron attachment (DEA) to the uracil and thymine molecules in a water cluster environment is investigated theoretically. Only the A'-resonance contribution, describing the near-threshold behavior of DEA, is incorporated. Calculations are based on the nonlocal complex potential theory and the multiple scattering theory, and are performed for a model target with basic properties of uracil and thymine, surrounded by five water molecules. The DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster. This growth is due to two effects: the increase of the resonance lifetime and the negative shift in the resonance position due to interaction of the intermediate negative ion with the surrounding water molecules. A similar effect was earlier found in DEA to chlorofluorocarbons.
Resumo:
We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster. (C) 2014 AIP Publishing LLC.
Resumo:
The structure and properties of the interfaces between the room temperature ionic liquid dimethylimidazolium chloride ([dmim]Cl) and different Lennard-Jones fluids and between ionic liquid and water have been studied by molecular dynamics simulations, and compared to the ionic liquid-vapour interface. Two contrasting types of interface were investigated, thermodynamically stable interfaces between ionic liquid and vapour and between ionic liquid and Lennard-Jones fluids, and diffusing interfaces between miscible phases of different compositions involving water. The density profiles of different species through the interface are presented. The cations and water molecules near the former type of interface are aligned relative to the surface, but no orientational preference was found near or in the broad diffusing interface. The ionic liquid has a negative electrostatic potential relative to vapour or Lennard-Jones fluid, but is more positive than pure water. This contrast is explained in terms of the relative importance of orientation and concentration differences in the two types of interface.
Coordination environment of [UO2Br4](2-) in ionic liquids and crystal structure of [Bmim](2)[UO2Br4]
Resumo:
The complex formed by the reaction of the uranyl ion, UO22+, with bromide ions in the ionic liquids 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([Bmiml[Tf2N]) and methyl-tributylammonium bis(trifluoromethylsulfonyl)imide ([MeBu3N][Tf2N]) has been investigated by UV-Vis and U L-III-edge EXAFS spectroscopy and compared to the crystal structure of [Bmim](2)[UO2Br4]. The solid state reveals a classical tetragonal bipyramid geometry for [UO2Br4](2-) with hydrogen bonds between the Bmim(+) and the coordinated bromides. The UV-Vis spectroscopy reveals the quantitative formation of [UO2Br4](2-) when a stoichiometric amount of bromide ions is added to UO2(CF3SO3)(2) in both Tf2N-based ionic liquids. The absorption spectrum also suggests a D-4h symmetry for [UO2Br4](2-) in ionic liquids, as previously observed for the [UO2Cl4](2-) congener. EXAFS analysis supports this conclusion and demonstrates that the [UO2Br4](2-) coordination polyhedron is maintained in the ionic liquids without any coordinating solvent or water molecules. The mean U-O and U-Br distances in the solutions, determined by EXAFS, are, respectively, 1.766(2) and 2.821(2)angstrom in [Bmim][Tf2N], and, respectively, 1.768(2) and 2.827(2) angstrom, in [MeBu3N][Tf2N]. Similar results are obtained in both ionic liquids indicating no significant influence of the ionic liquid cation either on the complexation reaction or on the structure of the uranyl species. (C) 2009 Elsevier Ltd. All rights reserved.
Resumo:
Five new compounds in the system (NH4)Cl/HgCl2/H2O have been obtained as colourless single crystals, (NH4)Hg5Cl11, (NH4)(2)Hg3Cl8(H2O), (NH4)(4)Hg3Cl10(H2O)(2), (NH4)(2)HgCl4(H2O), and (NH4)(10)Hg3Cl16. In all of these, as in HgCl2 itself, (almost) linear HgCl2 molecules persist with Hg-Cl distances varying from 229 to 236 pm. In (NH4)(10)Hg3Cl16 there are also tetrahedra [HgCl4] with d(Hg-Cl) = 247 pm present. If larger Hg-Cl distances (of up to 340 pm) are considered as belonging to the coordination sphere of Hg-II, the structures may be described as consisting of isolated octahedra and tetrahedra as in (NH4)(10)Hg3Cl16, edge-connected chains as in (NH4)(2)HgCl4(H2O), edge-connected chains and layers of octahedra as in (NH4)(4)Hg3Cl10(H2O)(2), corrugated layers of edge-connected octahedra as in (NH4)(2)Hg3Cl8(H2O), and, finally, a three-dimensional network of connected six- and seven-coordinate Hg-Cl polyhedra as in (NH4)Hg5Cl11. The water molecules are never attached to Hg-II. The (NH4)(+) cations, and sometimes Cl- anions, play a role for electroneutrality only.
Resumo:
Lanthanide(III) complexes of p-nitrobenzenesulfonic acid, Ln(p-NBSA)(3), m-nitrobenzenesulfonic acid, Ln(m-NBSA)(3), and 2,4-nitrobenzenesulfonic acid, Ln(2,4-NBSA)(3), were prepared, characterized and examined as catalyst for the nitration of benzene, toluene, xylenes, naphthalene, bromobenzene and chlorobenzene. The initial screening of the catalysts showed that lanthanum(III) complexes were more effective than the corresponding ytterbium(III) complexes, and that catalysts containing the bulky 2,4-NBSA ligand were less effective than the catalyst containing p-NBSA (nosylate) or m-NBSA ligands. Examination of a series of Ln(p-NBSA)(3) and Ln(m-NBSA)(3) catalysts revealed that there is a clear correlation between the ionic radii of the lanthanide(III) ions and the yields of nitration, with the lighter lanthanides being more effective. The X-ray single crystal structure of Yb(m-NBSA)(3).6H(2)O shows that two m-NBSA ligands are directly bound to the metal centre while the third ligand is not located in the first coordination sphere, but it is hydrogen bonded to one of the water molecules which is coordinated to ytterbium(III). NMR studies suggest that this structure is preserved under the conditions used in the nitration reaction. The structure of Yb(m-NBSA)(3) is markedly different from the structure of the well-known ytterbium(III) triflate catalyst. The coordination of the nitrobenzenesulfonate counterion to the lanthanide(III) ion suggests that steric effects might play an important role in determining the efficiency of these novel nitration catalysts. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004).
Resumo:
The liquid structures of thin films of aqueous solutions of 0, 7, 19, 50, and 100 mol % isopropanol above O/Al-terminated gamma-alumina surfaces have been investigated by means of classical molecular dynamics simulations. The structuring effect of the oxide oil the liquid mixtures is strong and heavily dependent on the local structure of the oxide. Two distinct re-ions are found oil the oxide Surface characterized by the degree of coordination of Al atoms. Above octahedral Al atoms, water and isopropanol molecules adsorb via the oxygen atoms to maximize the electrostatic interaction, whereas above tetrahedral Al sites the solvent molecules adsorb via hydrogen atoms with the oxygen atoms away front the surface. More mobility is found in the second layer compared with the first; however, its structure is still influenced significantly by the orientation of molecules in the first adsorbed layer. Qualitatively, the displacement of water from the surface by the adsorption of isopropanol occurs with 2.6 Water molecules lost for every alcohol molecule present based on the effective surface areas of the two species calculated from the pure simulations.
Resumo:
We present a study on the transport properties through conductivity (s), viscosity (?), and self-diffusion coefficient (D) measurements of two pure protic ionic liquids—pyrrolidinium hydrogen sulfate, [Pyrr][HSO4], and pyrrolidinium trifluoroacetate, [Pyrr][CF3COO]—and their mixtures with water over the whole composition range at 298.15 K and atmospheric pressure. Based on these experimental results, transport mobilities of ions have been then investigated in each case through the Stokes–Einstein equation. From this, the proton conduction in these PILs follows a combination of Grotthuss and vehicle-type mechanisms, which depends also on the water composition in solution. In each case, the displacement of the NMR peak attributed to the labile proton on the pyrrolidinium cation with the PILs concentration in aqueous solution indicates that this proton is located between the cation and the anion for a water weight fraction lower than 8%. In other words, for such compositions, it appears that this labile proton is not solvated by water molecules. However, for higher water content, the labile protons are in solution as H3O+. This water weight fraction appears to be the solvation limit of the H+ ions by water molecules in these two PILs solutions. However, [Pyrr][HSO4] and [Pyrr][CF3COO] PILs present opposed comportment in aqueous solution. In the case of [Pyrr][CF3COO], ?, s, D, and the attractive potential, Epot, between ions indicate clearly that the diffusion of each ion is similar. In other words, these ions are tightly bound together as ion pairs, reflecting in fact the importance of the hydrophobicity of the trifluoroacetate anion, whereas, in the case of the [Pyrr][HSO4], the strong H-bond between the HSO4– anion and water promotes a drastic change in the viscosity of the aqueous solution, as well as on the conductivity which is up to 187 mS·cm–1 for water weight fraction close to 60% at 298 K.
Resumo:
Signal Transducers and Activators of Transcription (STAT) proteins are a group of latent cytoplasmic transcription factors involved in cytokine signaling. STAT3 is a member of the STAT family and is expressed at elevated levels in a large number of diverse human cancers and is now a validated target for anticancer drug discovery.. Understanding the dynamics of the STAT3 dimer interface, accounting for both protein-DNA and protein-protein interactions, with respect to the dynamics of the latent unphosphorylated STAT3 monomer, is important for designing potential small-molecule inhibitors of the activated dimer. Molecular dynamics (MD) simulations have been used to study the activated STAT3 homodimer:DNA complex and the latent unphosphorylated STAT3 monomer in an explicit water environment. Analysis of the data obtained from MD simulations over a 50 ns time frame has suggested how the transcription factor interacts with DNA, the nature of the conformational changes, and ways in which function may be affected. Examination of the dimer interface, focusing on the protein-DNA interactions, including involvement of water molecules, has revealed the key residues contributing to the recognition events involved in STAT3 protein-DNA interactions. This has shown that the majority of mutations in the DNA-binding domain are found at the protein-DNA interface. These mutations have been mapped in detail and related to specific protein-DNA contacts. Their structural stability is described, together with an analysis of the model as a starting-point for the discovery of novel small-molecule STAT3 inhibitors.
Resumo:
The flexibility of the metal-organic framework Cu-2(OH)(C8H3O7S)(H2O)center dot 2H(2)O (Cu-SIP-3) toward reversible single-crystal to single-crystal transformations is demonstrated using in situ diffraction methods at variable temperature. At temperatures below a dehydration-induced phase transition (T < 370 K) the structure is confirmed as being hydrated. In the temperature range where the transition takes place (370 K < T < 405 K) no discrete, sharp Bragg peaks can be seen in the single-crystal X-ray diffraction pattern, indicating significant loss of long-range order. At temperatures higher than 405 K, the Bragg peaks return and the structure can be refined as dehydrated Cu-SIP-3. The loss of guest water molecules can be followed at temperatures below the phase transition giving insight into the mechanism of the dehydration. Addition of nitric oxide gas to the material above the gating opening pressure of 275 mbar also leads to loss of Bragg scattering in the diffraction pattern.
Resumo:
Ice Ih is comprised of orientationally disordered water molecules giving rise to positional disorder of the hydrogen atoms in the hydrogen bonded network of the lattice. Here we arrive at a first principles determination of the surface energy of ice Ih and suggest that the surface of ice is significantly more proton ordered than the bulk. We predict that the proton order-disorder transition, which occurs in the bulk at similar to 72 K, will not occur at the surface at any temperature below surface melting. An order parameter which defines the surface energy of ice Ih surfaces is also identified.