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Water Clusters (water + cluster)
Selected AbstractsSpectral Signatures of the Pentagonal Water Cluster in BacteriorhodopsinCHEMPHYSCHEM, Issue 18 2008Marcel Baer Computed QM/MM IR spectra of the water molecules in the Schiff base region of bacteriorhodopsin (see figure) confirm a dangling bond at about 3600 cm,1. A broad experimental IR absorption band at 2800 cm,1 is assigned to a coupling of the Schiff base NH and the OH stretch of a ligand water molecule. [source] Ion,Molecule Reactions in Helium Nanodroplets Doped with C60 and Water Clusters,ANGEWANDTE CHEMIE, Issue 47 2009Stephan Denifl Dr. Weltraumchemie: Die Bindung zwischen C60+ und (H2O)4 in einem geladenen Komplex aus C60 und dem H2O-Tetramer in Heliumnanotröpfchen (siehe Bild) ist überraschend schwach. Doppelt geladene C602+ -Intermediate könnten durch Ladungstransfer mit He+ entstehen; sie können Ion-Molekül-Reaktionen auslösen, die bei der Molekülsynthese in interstellaren Wolken und im Sonnennebel eine Rolle spielen könnten. [source] ChemInform Abstract: Single-Molecule Precipitation of Transition Metal(I) Chlorides in Water Clusters.CHEMINFORM, Issue 18 2002Brigitte S. Fox Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Ab Initio Molecular Dynamics Studies of Ionic Dissolution and Precipitation of Sodium Chloride and Silver Chloride in Water Clusters, NaCl(H2O)n and AgCl(H2O)n, n = 6, 10, and 14CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2006Chi-Kit Siu Dr. Abstract An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H2O)n and AgCl(H2O)n with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H2O)n is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ,mol,1), are identifiable on the free energy profiles of NaCl(H2O)n for n = 10 and 14 at 300 K, with the Na+/Cl, pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ,mol,1). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H2O)n clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure. [source] Hydrogen-Bond Networks in Water Clusters (H2O)20: An Exhaustive Quantum-Chemical AnalysisCHEMPHYSCHEM, Issue 2 2010Andrei 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] Extended Car,Parrinello molecular dynamics and electronic g -tensors study of benzosemiquinone radical anion,MAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2005James R. Asher Abstract Car-Parrinello molecular dynamics simulations of benzoquinone and benzosemiquinone radical anion in both aqueous solution and the gas phase have been carried out at ambient conditions. Hydrogen bonding is considerably more extensive to the anionic than to the neutral aqueous system. In addition to the conventional hydrogen bonding to the carbonyl oxygen atoms, T-stacked hydrogen bonding to the , -system is statistically and energetically significant for the semiquinone anion but not for the neutral quinone. EPR g -tensors have been calculated at DFT level for snapshots taken at regular intervals from the gas-phase and solution semiquinone anion trajectories. Different criteria for extraction of semiquinone/water clusters from the solution trajectory give insight into the effects of different interactions on the g -tensor, as does correlation of the g -tensor with statistically significant hydrogen-bond configurations identified along the trajectories. Comparison of gas-phase and solution results indicates opposite directions of direct electronic and indirect structural influences of hydrogen bonding on g -tensors. Short-time oscillations in gx along the trajectory are due mainly to CO bond vibrations. Copyright © 2005 John Wiley & Sons, Ltd. [source] Sulfur Dioxide and Water: Structures and Energies of the Hydrated Species SO2·nH2O, [HSO3],·nH2O, [SO3H],·nH2O, and H2SO3·nH2O (n = 0,8)EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 10 2009Ralf Steudel Abstract The structures of a large number of hydrates of sulfur dioxide (SO2·nH2O), of the sulfonate ion ([HSO3],·nH2O), of the tautomeric hydrogensulfite anion ([SO3H],·nH2O), and of sulfurous acid (H2SO3·nH2O) with up to eight water molecules attached to these species have been optimized at the B3LYP/6-31G(2df,p) level of theory (DFT). The calculated vibrational frequencies allow the definite assignment of certain characteristic modes, and in this way a convincing interpretation of published spectra of aqueous SO2 as well as of SO2 adsorbed on very cold ice crystals has been achieved for the first time. Single-point calculations at the G3X(MP2) level of theory were used to calculate the binding energies of the water molecules in SO2·nH2O as well as the relative stabilities of the isomeric anionic species [HSO3],·nH2O and [SO3H],·nH2O. Generally, the water molecules tend to stick together forming clusters, whereas the particular sulfur-containing molecule remains at the surface of the water cluster, but it is always strongly hydrogen-bonded. Only when there are more than six water molecules are the anions more or less completely surrounded by water molecules. DFT calculations erroneously predict that the gaseous hydrated sulfonate ions are more stable than the isomeric hydrogensulfite ions, even when hydrated with six water molecules. However, if these hydrated species are calculated as being embedded in a polar continuum simulating the aqueous phase, the hydrogensulfite ions are more stable than the sulfonate ions, in agreement with various spectroscopic observations on aqueous sulfite solutions. On the other hand, at the higher G3X(MP2) level, the gaseous hydrated hydrogensulfite anions are more stable than the corresponding sulfonate ions only if the number of water molecules is larger than four, whereas for the weakly hydrated anions the order of relative energies is reversed. The possible implications of these results for the enzymatic oxidation of "sulfite ions" ([HSO3], and [SO3H],) by sulfite oxidase are discussed. The conversion of SO2·6H2O into its isomer H2SO3·5H2O is predicted to be exothermic (,H°298 = ,56.1 kJ,mol,1) and exergonic (,G°298 = ,22.5 kJ,mol,1). (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] A Role for Internal Water Molecules in Proton Affinity Changes in the Schiff Base and Asp85 for One-way Proton Transfer in Bacteriorhodopsin,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Joel E. Morgan Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M. [source] An ice-like water hexamer with symmetry in the hydrogen-bonded structure of 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene dihydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010Huan Xu An ice-like hexameric water cluster, stabilized by the flexible bis-imidazolyl compound 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene (Fbix), is found in the trigonal R crystal structure of the title compound, C14H10F4N4·2H2O or Fbix·2H2O. The Fbix molecule lies about an inversion centre with one water molecule in the asymmetric unit in a general position. A cyclic chair-like hexameric water cluster with symmetry is generated with a hydrogen-bonded O...O distance within the hexamer of 2.786,(3),Å. The Fbix molecule adopts a trans conformation, where the imidazole ring makes a dihedral angle of 70.24,(11)° with the central tetrafluorinated aromatic ring. Each water hexamer is connected by six Fbix molecules through intermolecular O,H...N hydrogen bonds [N...O = 2.868,(3),Å] to yield a three-dimensional supramolecular network with primitive cubic (pcu) topology. Large voids in each single pcu network lead to fourfold interpenetrated aggregates of Fbix·2H2O. [source] Poly[[diaqua(,3 -3-nitrophthalato)calcium(II)] monohydrate]ACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Ming-Lin Guo The title 3-nitrophthalate,calcium coordination polymer, {[Ca(C8H3NO6)(H2O)2]·H2O}n, crystallizes as a one-dimensional framework. The CaII centre has a distorted pentagonal,bipyramidal geometry, being seven-coordinated by five O atoms from three different 3-nitrophthalate groups and by two water molecules, resulting in a one-dimensional zigzag chain along the a -axis direction by the interconnection of the four O atoms from the two carboxylate groups. There is a D3 water cluster composed of the coordinated and the solvent water molecules within such chains. Adjacent chains are aggregated into two-dimensional layers via hydrogen bonds in the c -axis direction. The whole three-dimensional structure is further stabilized by weak O,H...O hydrogen bonds between the O atoms of the nitro group and the water molecules. [source] Structural Investigation of the Binding of 5-Substituted Swainsonine Analogues to Golgi ,-Mannosidase IICHEMBIOCHEM, Issue 5 2010Douglas A. Kuntz Dr. Abstract Golgi ,-mannosidase II (GMII) is a key enzyme in the N-glycosylation pathway and is a potential target for cancer chemotherapy. The natural product swainsonine is a potent inhibitor of GMII. In this paper we characterize the binding of 5,-substituted swainsonine analogues to the soluble catalytic domain of Drosophila GMII by X-ray crystallography. These inhibitors enjoy an advantage over previously reported GMII inhibitors in that they did not significantly decrease the inhibitory potential of the swainsonine head-group. The phenyl groups of these analogues occupy a portion of the binding site not previously seen to be populated with either substrate analogues or other inhibitors and they form novel hydrophobic interactions. They displace a well-organized water cluster, but the presence of a C(10) carbonyl allows the reestablishment of important hydrogen bonds. Already approximately tenfold more active against the Golgi enzyme than the lysosomal enzyme, these inhibitors offer the potential of being extended into the N-acetylglucosamine binding site of GMII for the creation of even more potent and selective GMII inhibitors. [source] Crystal Structure Analysis and in Silico pKa Calculations Suggest Strong pKa Shifts of Ligands as Driving Force for High-Affinity Binding to TGTCHEMBIOCHEM, Issue 4 2009Tina Ritschel Abstract Expandedlin -benzoguanines exhibit binding affinities to tRNA-guanine transglycosylase (TGT) in the low-nanomolar range. A significant pKa shift is observed for the inhibitors moving from aqueous solution to protein environment. The protonation of the inhibitor facilitates a charge-assisted hydrogen bond in the protein,ligand complex. A novel ligand series is presented to inhibit tRNA-guanine transglycosylase (TGT), a protein with a significant role in the pathogenicity mechanism of Shigella flexneri, the causative agent of Shigellosis. The enzyme exchanges guanine in the wobble position of tRNAAsn,Asp,His,Tyr against a modified base. To prevent the base-exchange reaction, several series of inhibitors have already been designed, synthesized, and tested. One aim of previous studies was to address a hydrophobic pocket with different side chains attached to the parent skeletons. Disappointingly, no significant increase in binding affinity could be observed that could be explained by the disruption of a conserved water cluster. The ligand series examined in this study are based on the known scaffold lin -benzoguanine. Different side chains were introduced leading to 2-amino- lin -benzoguanines, which address a different pocket of the protein and avoid disruption of the water cluster. With the introduction of an amino group in the 2-position, a dramatic increase in binding affinity can be experienced. To explain this significant gain in binding affinity, Poisson,Boltzmann calculations were performed to explore pKa changes of ligand functional groups upon protein binding, they can differ significantly on going from aqueous solution to protein environment. For all complexes, a permanent protonation of the newly designed ligands is suggested, leading to a charge-assisted hydrogen bond in the protein,ligand complex. This increased strength in hydrogen bonding takes beneficial effect on binding affinity of the ligands, resulting in low-nanomolar binders. Crystal structures and docking emphasize the importance of the newly created charge-assisted hydrogen bond. A detailed analysis of the crystal structures in complex with substituted 2-amino- lin -benzoguanines indicate pronounced disorder of the attached side chains addressing the ribose 33 binding pocket. Docking suggests multiple orientations of these side chains. Obviously, an entropic advantage of the residual mobility experienced by these ligands in the bound state is beneficial and reveals an overall improved protein binding. [source] Ab Initio Molecular Dynamics Studies of Ionic Dissolution and Precipitation of Sodium Chloride and Silver Chloride in Water Clusters, NaCl(H2O)n and AgCl(H2O)n, n = 6, 10, and 14CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2006Chi-Kit Siu Dr. Abstract An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H2O)n and AgCl(H2O)n with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H2O)n is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ,mol,1), are identifiable on the free energy profiles of NaCl(H2O)n for n = 10 and 14 at 300 K, with the Na+/Cl, pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ,mol,1). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H2O)n clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure. [source] How Does a Membrane Protein Achieve a Vectorial Proton Transfer Via Water Molecules?CHEMPHYSCHEM, Issue 18 2008Steffen Wolf Abstract We present a detailed mechanism for the proton transfer from a protein-bound protonated water cluster to the bulk water directed by protein side chains in the membrane protein bacteriorhodopsin. We use a combined approach of time-resolved Fourier transform infrared spectroscopy, molecular dynamics simulations, and X-ray structure analysis to elucidate the functional role of a hydrogen bond between Ser193 and Glu204. These two residues seal the internal protonated water cluster from the bulk water and the protein surface. During the photocycle of bacteriorhodopsin, a transient protonation of Glu204 leads to a breaking of this hydrogen bond. This breaking opens the gate to the extracellular bulk water, leading to a subsequent proton release from the protonated water cluster. We show in detail how the protein achieves vectorial proton transfer via protonated water clusters in contrast to random proton transfer in liquid water. [source] From 1D Polymeric Chain to Two-fold Parallel Interpenetration of (4,4) Net: Synthesis and Characterization of Two New Copper(II) Complexes Derived from Highly Polydentate Aminopolycarboxylate LigandCHINESE JOURNAL OF CHEMISTRY, Issue 7 2008Ya-Pan WU Abstract Two new copper(II) polymers, {[Cu2(egta)(bpe)(H2O)2]·H2O}n (1) and {[Cu2(egta)(bipy)(H2O)2]·5H2O}n(2), [H4egta=3,12-bis(carboxymethyl)-6,9-dioxa-3,12-diazatetradecanedioic acid, bpe=1,2-bis(4-pyridyl)ethane, bipy4,4,-bipyridyl] have been synthesized and structurally characterized by single-crystal X-ray diffraction, elemental analysis, IR spectra and TG analysis. The structure determination reveals that both 1 and 2 crystallize in a monoclinic system, space group P21/c. Complex 1 exhibits a two-fold parallel interpenetration of (4,4) net framework consisting of 1D zigzag chains interlocked together through hydrogen bonding interaction. However, the meso-helix chains of 2 are packed to form 2D supramolecular structures. Interestingly, in 2, the host frameworks encapsulate a unique pentamer water cluster and are further connected into 1D tapes by water-water hydrogen bonding interaction. Magnetic measurements reveal that there is a weak ferromagnetic interaction between the adjacent Cu(II) ions in 1. [source] Efficiency of nested Markov chain Monte Carlo for polarizable potentials and perturbed HamiltoniansINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Florent Calvo Abstract Nested Markov chain Monte Carlo is a rigorous way to enhance sampling of a given energy landscape using an auxiliary, approximate potential energy surface. Its practical efficiency mainly depends on how cheap and how different are the auxiliary potential with respect to the reference system. In this article, a combined efficiency index is proposed and assessed for two important families of energy surfaces. As illustrated for water clusters, many-body polarizable potentials can be approximated by simplifying the polarization contribution and keeping only the two-body terms. In small systems, neglecting polarization entirely is also acceptable. When the reference potential energy is obtained from diagonalization of a quantum mechanical Hamiltonian, a first-order perturbation scheme can be used to estimate the energy difference occuring on a Monte Carlo move. Our results indicate that this perturbation approximation performs well provided that the number of steps between successive diagonalization is adjusted beforehand. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2342,2346, 2010 [source] Proton collisions with the water dimer at keV energiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2009O. Quinet Abstract Proton collisions with the water dimer are studied using a nonadiabatic, direct, time-dependent approach called electron nuclear dynamics (END). Fragmentation of the water dimer in collisions with protons at energies of 5.0, 1.0 keV and 200 eV is the primary aim of this initial study of water clusters using END. We report on the initial fragmentation dynamic, that is, for times less than 200 fs. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Relation between macroscopic and microscopic dielectric relaxation times in water dynamicsISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2003Vladimir I. Arkhipov A simplified derivation for the ratio of macroscopic to microscopic relaxation times of polar liquids is based on the Mori-Zwanzig projection-operator technique, with added statistical assumptions. We obtain several useful forms for the lifetime ratio, which we apply to the dynamics of liquid water. Our theoretical single-molecule relaxation times agree with the second Debye relaxation times as measured by frequency-domain dielectric spectroscopy of water and alcohols. From the theory, fast relaxation modes couple to the Debye relaxation time, ,d, through very large water clusters, and their temperature dependence is similar to that of ,d. Slower modes are localized to smaller water clusters and exhibit weaker temperature dependence. This is exemplified by the lifetime ratios measured by time-domain dielectric spectroscopy and optical Kerr effect spectroscopy, respectively. [source] Gas permeation related to the moisture sorption in films of glassy hydrophilic polymersJOURNAL OF APPLIED POLYMER SCIENCE, Issue 6 2010F.L. Laksmana Abstract The purpose of this article is to elucidate the effect of integral sorption of moisture on gas permeation in glassy hydrophilic polymers. The oxygen and the simultaneous moisture sorption into various hydroxypropyl methylcellulose (HPMC) films were measured under a wide range of relative humidities using sorption analyzer equipment. Correspondingly, the oxygen permeability at different ambient conditions was measured using an oxygen detector. The solubility of oxygen in the HPMC film was found to be affected by the amount of water and therefore by the water state. At low moisture content, the water molecules are present as bound water, which promotes the sorption of oxygen in the HPMC films. At moisture content higher than 5%, water clusters are rapidly formed, which increase the affinity of HPMC polymer towards water rather than towards oxygen molecules, resulting in a decrease of oxygen solubility in the polymer. This was found to be the governing factor for the reduction in the oxygen permeability in glassy HPMC films at high water activity. This proposes a specific interaction between moisture sorption and oxygen transport in coating films like HPMC, which is of important aspect in the coating design and formulation. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010 [source] Fast fragments: The development of a parallel effective fragment potential methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2004Heather M. Netzloff Abstract The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute plus some number of solvent molecules, if desired, and an "effective fragment" region that contains the remaining solvent molecules. Interactions introduced with this fragment region (for example, Coulomb and polarization interactions) are added as one-electron terms to the total system Hamiltonian. As larger systems and dynamics are just starting to be studied with the EFP method, more needs to be done to decrease the calculation time of the method. This article considers parallelization of both the EFP fragment-fragment and mixed quantum mechanics (QM)-EFP interaction energy and gradient computation within the GAMESS suite of programs. The iteratively self-consistent polarization term is treated with a new algorithm that makes use of nonblocking communication to obtain better scalability. Results show that reasonable speedup is achieved with a variety of sizes of water clusters and number of processors. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1926,1935, 2004 [source] Direct analysis of lipids in mouse brain using electrospray droplet impact/SIMSJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 4 2010Daiki Asakawa Abstract Electrospray droplet impact (EDI)/secondary ion mass spectrometry (SIMS) is a new desorption/ionization technique for mass spectrometry in which highly charged water clusters produced from the atmospheric-pressure electrospray are accelerated in vacuum by 10 kV and impact the sample deposited on the metal substrate. EDI/SIMS was shown to enhance intact molecular ion formation dramatically compared to conventional SIMS. EDI/SIMS has been successfully applied to the analysis of mouse brain without any sample preparation. Five types of lipids, i.e. phosphatidylcholine (PC), phosphatidylserine, phosphatidylinositol (PI), galactocerebroside (GC) and sulfatide (ST), were readily detected from mouse brain section. In addition, by EDI/SIMS, six different regions of the mouse brain (cerebral cortex, corpus callosum, striatum, medulla oblongata, cerebellar cortex and cerebellar medulla) were examined. While GCs and STs were found to be rich in white matter, PIs were rich in gray matter. Copyright © 2010 John Wiley & Sons, Ltd. [source] Mesoscopic Morphology of Proton-Conducting Polyelectrolyte Membranes of Nafion® Type: A Self-Consistent Mean Field SimulationMACROMOLECULAR THEORY AND SIMULATIONS, Issue 2 2006Dmitry Y. Galperin Abstract Summary: A SCMF simulation is presented for a coarse-grained model of Nafion®. Based on a number of simplifying assumptions, this study predicts distinct morphological changes in the material upon alteration of temperature and water content. We found that the hydration level corresponding to the microphase segregation depends on the temperature of the system. Spherical clusters constituting the hydrophilic microphase of the membrane at relatively low water content (but above the transition point) grow in size, coalesce and form a network of channels responsible for the ionic transport at higher hydration levels. This hydrophilic phase is shielded from the hydrophobic matrix by the sidechains of Nafion®, their end-groups being turned towards the water clusters. The results obtained are similar to those reported from dissipative particle dynamics studies and support the "cluster-network" model for the low hydration levels and the "sponge" model at higher hydration levels. The simulation approach chosen proved to be effective for the mesoscopic structure analysis of the heterogeneous polymeric material. Schematic representation of the structure of Nafion®-water blends. [source] Monitoring chloramines and bromamines in a humid environment using selected ion flow tube mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 12 2010Wan-Ping Hu The selectivity and sensitivity of selected ion flow tube mass spectrometry (SIFT-MS) for individual breath analysis of haloamines has been improved by heating the flow tube in a commercial instrument to around 106°C. Data is presented showing the marked reduction in the number density of water clusters of product ions of common breath metabolites that are isobaric with the product ions from monochloramine and monobromamine that are used to monitor the haloamine concentrations. These results have direct relevance to the real-time monitoring of chloramines in drinking water, swimming pools and food processing plants. However, once the isobaric overlaps from water cluster ions are reduced at the higher temperatures, there is no conclusive evidence showing the presence of haloamines on single breath exhalations in the mid parts per trillion range from examination of the breaths of volunteers. Copyright © 2010 John Wiley & Sons, Ltd. [source] Poly[[diaqua(,3 -2,2-dimethylmalonato)cadmium(II)] tetrahydrate]ACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2009Ming-Lin Guo In the title complex, {[Cd(C5H6O4)(H2O)2]·4H2O}n, the dimethylmalonate,cadmium metal,organic framework co-exists with an extended structure of water molecules, which resembles a sodalite-type framework. In the asymmetric unit, there are five independent solvent water molecules, two of which are in special positions. The Cd atoms are eight-coordinated in a distorted square-antiprismatic geometry by six O atoms of three different dimethylmalonate groups and by two water molecules, and form a two-dimensional honeycomb layer parallel to the bc plane. Two such layers sandwich the hydrogen-bonded water layer, which has a sodalite-type structure with truncated sodalite units composed of coordinated and solvent water molecules. This work is the first example of a dimethylmalonate cadmium complex containing truncated sodalite-type water clusters. [source] Ab Initio Molecular Dynamics Studies of Ionic Dissolution and Precipitation of Sodium Chloride and Silver Chloride in Water Clusters, NaCl(H2O)n and AgCl(H2O)n, n = 6, 10, and 14CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2006Chi-Kit Siu Dr. Abstract An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H2O)n and AgCl(H2O)n with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H2O)n is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ,mol,1), are identifiable on the free energy profiles of NaCl(H2O)n for n = 10 and 14 at 300 K, with the Na+/Cl, pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ,mol,1). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H2O)n clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure. [source] Hydrogen-Bond Networks in Water Clusters (H2O)20: An Exhaustive Quantum-Chemical AnalysisCHEMPHYSCHEM, Issue 2 2010Andrei 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] How Does a Membrane Protein Achieve a Vectorial Proton Transfer Via Water Molecules?CHEMPHYSCHEM, Issue 18 2008Steffen Wolf Abstract We present a detailed mechanism for the proton transfer from a protein-bound protonated water cluster to the bulk water directed by protein side chains in the membrane protein bacteriorhodopsin. We use a combined approach of time-resolved Fourier transform infrared spectroscopy, molecular dynamics simulations, and X-ray structure analysis to elucidate the functional role of a hydrogen bond between Ser193 and Glu204. These two residues seal the internal protonated water cluster from the bulk water and the protein surface. During the photocycle of bacteriorhodopsin, a transient protonation of Glu204 leads to a breaking of this hydrogen bond. This breaking opens the gate to the extracellular bulk water, leading to a subsequent proton release from the protonated water cluster. We show in detail how the protein achieves vectorial proton transfer via protonated water clusters in contrast to random proton transfer in liquid water. [source] | |||||||||||||||||||||||||