Water Structure (water + structure)

Distribution by Scientific Domains

Selected Abstracts

Structural and dynamic properties of water around acetylcholinesterase

Richard H. Henchman
AChE, acetylcholinsterase; ARC/TAP, averaged residue coordinate/time-averaged position Abstract Structural and dynamic properties of water molecules around acetylcholinesterase are examined from a 10-nsec molecular dynamics simulation to help understand how the protein alters water properties. Water structure is broken down into hydration sites constructed from the water density <3.6 from the protein surface. These sites are characterized according to occupancy, number of water neighbors, hydrogen bonds, dipole moment, and residence time. The site description provides a convenient means to describe the extent and localization of these properties. Determining the network of paths that waters follow from site to site and measuring the rate of flow of waters from the sites to the bulk make it possible to quantitatively study the time scales and paths that water molecules follow as they move around the protein. [source]

Carbon Nanotubes and Nanofluidic Transport

Jason Knowles Holt
Abstract Recent strides have been made in both the modeling and measurement of fluid flow on the nanoscale. Carbon nanotubes, with their atomic dimensions and atomic smoothness, are ideal materials for studying such flows. This Progress Report describes recent modeling and experimental advances concerning fluid transport in carbon nanotubes. The varied flow characteristics predicted by molecular dynamics are described, as are the roles of defects and chirality on transport. Analytical models are increasingly being used to describe nanofluidic transport by relaxing many of the assumptions commonly used to describe bulk water. Recent experimental studies examine the size dependence of flow enhancements through carbon nanotubes and use varied spectroscopies to probe water structure and dynamics in these systems. Carbon nanotubes are finding increasing applications in biology, from protein filters to platforms for cell interrogation. [source]

Thermal analysis of polymer,water interactions and their relation to gas hydrate inhibition

Manika Varma-Nair
Abstract Gas hydrates formed in oil production pipelines are crystalline solids where hydrocarbon gas molecules such as methane, propane, and their mixtures are trapped in a cagelike structure by hydrogen-bonded water molecules to form undesirable plugs. Methanol and glycol are currently used to prevent these plugs via thermodynamic inhibition. Small amounts of water-soluble polymers may provide an alternate approach for preventing gas hydrates. In this study, we expand the fundamental understanding of water,polymer systems with differential scanning calorimetry. Nonfreezable bound water was used to quantify polymer,water interactions and relate them to the chemical structure for a series of polymers, including acrylamides, cyclic lactams, and n -vinyl amides. For good interactions, the water structure needs to be stabilized through hydrophobic interactions. An increased hydrophobicity of the pendant group also appears to favor polymer performance as a gas hydrate inhibitor. Good inhibitors, such as poly(diethyl acrylamide) and poly(N -vinyl caprolactam), also show higher heat capacities, which indicate higher hydrophobicity, than poor performers such as polyzwitterions, in which hydrophilicity dominated. The phase behavior and thermodynamic properties of dilute polymer solutions were also evaluated through measurements of the heat of demixing and lower critical solution temperature. 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 2642,2653, 2007 [source]

Raman spectra indicative of unusual water structure in crystals formed from a room-temperature ionic liquid

Hiroko Miki
Abstract Formation of crystals with unusual water structure has been found to take place in an ionic liquid 1-butyl-3-methylimidazolium tetrachloroferrate (bmim[FeCl4]). The Raman spectrum of a crystal formed in bmim[FeCl4] showed two prominent Raman bands ascribed to H2O. Another crystal formed in bmim[FeCl4] exposed to D2O atmosphere showed Raman bands of H2O, HOD and D2O. These findings indicate that an unusually high concentration of water is contained in the crystals. The observed Raman bands of the HOH, HOD and DOD bending modes are unusually narrow, implying an unknown unique structure of water. Copyright 2006 John Wiley & Sons, Ltd. [source]

Molecular Dynamics Simulations of the Orientation and Reorientational Dynamics of Water and Polypyrrole Rings as a Function of the Oxidation State of the Polymer

Jose J. Lpez Cascales
Abstract Summary: Polypyrrole is one of the most widely-studied conducting polymers due to its steady electrochemical response and good chemical stability in different solvents, including organic and inorganic ones. In this work, we provide for the first time valuable information in atomic detail concerning the steady and dynamic properties of pyrrole rings as a function of the oxidation state of the polymer. The study was carried out by Classical molecular dynamics simulation, where the system was modelled by 256 polypyrrole chains of 10 pyrrole rings each. Water was explicitly introduced in our simulations. Besides the uncharged or reduced state, two steady oxidation states of the polymer have been simulated by introducing a net charge (+1) on 85 and 256 of the polypyrrole chains. To balance the charges emerging in these oxidised states, 85 and 256 chloride ions (Cl,1) respectively, were introduced into the system. From an analysis of the simulated trajectories, the orientation and relaxation times of water and pyrrole rings were evaluated for the different oxidation states of the polymer across the polypyrrole/water interface. The calculated densities for different oxidation states describe the swelling or shrinking process during electrochemical oxidation or reduction respectively. The rotational relaxation times calculated for the polypyrrole rings decrease with increasing oxidation of the polymer, which is in a good agreement with experimental electrochemical data. Almost no variation in pyrrole ring orientation was measured for the different oxidation states of the polymer, even compared with polypyrrole bulk. As regards the water structure in the vicinity of the polypyrrole/water interface, both the orientation and orientation relaxation time were strongly affected by the presence of charges in the polymer. Thus, the water dipole was strongly orientated in the vicinity of the water/polypyrrole interface and its orientational relaxation time increased by one order of magnitude compared with bulk water, even when only one-third of the total polymer chains were oxidised. The results attained in this work were validated with experimental results, when they were available. Polypyrrole ring orientation and water orientation at the polypyrrole/water interface. (a) 256 rPPy and (b)171 rPPy,+,85 oPPy. [source]

The controlled release behavior and pH- and thermo-sensitivity of alginate/poly(vinyl alcohol) blended hydrogels

Win-Chun Jao
Abstract Poly(vinyl alcohol) (PVA) was blended with sodium alginate (Alg) in various ratios and crosslinked with calcium chloride and made into hydrogel membranes. The dependence of the swelling behavior of these Alg-Ca/PVA hydrogels on pH was investigated. The temperature-dependent swelling behavior of the semi-interpenetrating network (semi-IPN) hydrogels was examined at temperatures from 2 to 45C and the enthalpy of mixing (,Hmix) was determined at various temperatures. The molecular structure of the hydrogels was studied by infrared spectroscopy and their water structure in the semi-IPN hydrogels was measured by differential scanning calorimetry (DSC). The influence of Ca2+ content on the network structure of Alg-Ca/PVA hydrogels was investigated in terms of the compressive elastic modulus, effective crosslinking density, and the polymer,solvent interaction parameter based on the Flory theory. The loading of alizarin red S (ARS) followed the Langmuir isotherm mechanism and the release kinetics of ARS from the Alg-Ca/PVA hydrogels followed the Fickian diffusion mechanism. Copyright 2008 John Wiley & Sons, Ltd. [source]

Structure of the ThDP-dependent enzyme benzaldehyde lyase refined to 1.65, resolution

Andy Maraite
Benzaldehyde lyase (BAL; EC is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6, using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005), FEBS J.272, 6067,6076]. In this communication of parallel studies, BAL was crystallized in an alternative space group (P212121) and its structure refined to a resolution of 1.65,, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface. [source]

Water transport in crosslinked 2-hydroxyethyl methacrylate

K. F. Chou
Water transport in crosslinked 2-hydroxyethyl methacrylate (HEMA) was investigated. Crosslinked HEMA was irradiated by gamma ray in vacuum for this study. The sorption data of de-ionized water transport in crosslinked HEMA subjected to various gamma ray dosages are in excellent agreement with Harmon's model which accounts for Case I, Case II, as well as the anomalous transport processes. The diffusion coefficient for Case I transport and velocity for Case II transport satisfy the Arrhenius equation for all dosages. The transport process was exothermic and the equilibrium-swelling ratio satisfied the van't Hoff plot. The pH value of de-ionized water after the sorption/de-sorption treatment of the irradiated crosslinked HEMA specimen was analyzed. The transmittance of irradiated crosslinked HEMA treated by de-ionized water was also studied. The effect of irradiation on the polymer chains was revealed by the measurement of glass transition temperature and the quantitative determination of water structures in crosslinked HEMA hydrogel. The UV cut-off wavelength of crosslinked HEMA shifted to longer wavelength side with increasing irradiation dosage, but the trend of transmittance after water treatment was opposite. The effect of specimen thickness on water transport was also studied. [source]

Hydrogen-Bond Networks in Water Clusters (H2O)20: An Exhaustive Quantum-Chemical Analysis

CHEMPHYSCHEM, Issue 2 2010
Andrei M. Tokmachev Dr.
Abstract Water aggregates allow for numerous configurations due to different distributions of hydrogen bonds. The total number of possible hydrogen-bond networks is very large even for medium-sized systems. We demonstrate that targeted ultra-fast methods of quantum chemistry make an exhaustive analysis of all configurations possible. The cage of (H2O)20 in the form of the pentagonal dodecahedron is a common motif in water structures. We calculated the spatial and electronic structure of all hydrogen-bond configurations for three systems: idealized cage (H2O)20 and defect cages with one or two hydrogen bonds broken. More than 3 million configurations studied provide unique data on the structure and properties of water clusters. We performed a thorough analysis of the results with the emphasis on the cooperativity in water systems and the structure-property relations. [source]