WorldWideScience

Sample records for water molecule orientations

  1. Water molecules orientation in surface layer

    Science.gov (United States)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  2. Molecular Water Lilies: Orienting Single Molecules in a Polymer Film by Solvent Vapor Annealing

    CERN Document Server

    Wuersch, Dominik; Eder, Theresa; Aggarwal, A Vikas; Idelson, Alissa; Hoeger, Sigurd; Lupton, John M; Vogelsang, Jan

    2016-01-01

    The microscopic orientation and position of photoactive molecules is crucial to the operation of optoelectronic devices such as OLEDs and solar cells. Here, we introduce a shape-persistent macrocyclic molecule as an excellent fluorescent probe to simply measure (i) its orientation by rotating the excitation polarization and recording the strength of modulation in photoluminescence (PL), and (ii) its position in a film by analyzing the overall PL brightness at the molecular level. The unique shape, the absorption and the fluorescence properties of this probe yields information on molecular orientation and position. We control orientation and positioning of the probe in a polymer film by solvent vapor annealing (SVA). During the SVA process the molecules accumulate at the polymer/air interface, where they adopt a flat conformation, much like water lilies on the surface of a pond. The results are significant for OLED fabrication and single-molecule spectroscopy (SMS) in general.

  3. Hydroxyl and water molecule orientations in trypsin: Comparison to molecular dynamics structures

    Energy Technology Data Exchange (ETDEWEB)

    McDowell, R.S.; Kossiakoff, A.A. [Genentech, Inc., South San Francisco, CA (United States)

    1994-12-31

    A comparison is presented of experimentally observed hydroxyl and water hydrogens in trypsin determined from neutron density maps with the results of a 140ps molecular dynamics (MD) simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogens. Neutron densities, derived from 2.1{Angstrom} D{sub 2}O-H{sub 2}O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogens. Most of the simulated hydroxyl orientations are within a standard deviation of the experimentally-observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a {open_quote}standard{close_quote} rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2{Angstrom} density map based on the hydrogen atom distributions from the simulation. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule. A method is presented for comparing the discrete observations sampled in a dynamics trajectory with the time- averaged data obtained from X-ray or neutron diffraction studies. This method is particularly useful for statically-disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy.

  4. Electron impact double ionization of single oriented water molecules: evidence of the role of the two-step mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Dal Cappello, C; Champion, C [Universite Paul Verlaine-Metz, LPMC, Institut de Physique, 1 bd Arago, 57078 Metz Cedex 3 (France); Kada, I; Mansouri, A, E-mail: cappello@univ-metz.fr [Universite Ferhat Abbas, LPQSD, Departement de physique, 19000 Setif (Algeria)

    2011-04-01

    Double ionization of single oriented water molecules is here investigated within a theoretical approach based on the second Born approximation. The initial wave function describing the two active electrons is taken from a single-centre description previously used with success for describing the single ionization process whereas the final state wave function describing the two ejected electrons is the approximate BBK wave function. Secondary electron angular distributions for an incident energy close to 600 eV are then reported for particular kinematical conditions and compared to their first Born homologous. Strong similarities are observed in terms of maxima localization as well as identification of the main mechanisms involved in the double ionization. On the contrary, for particular kinematical conditions we demonstrate that the first-order treatment is unable to explain the observations contrary to the second-order approximation which points out pure TS2 contributions.

  5. Molecule-oriented programming in Java

    NARCIS (Netherlands)

    Bergstra, J.A.

    2002-01-01

    Molecule-oriented programming is introduced as a programming style carrying some perspective for Java. A sequence of examples is provided. Supporting the development of the molecule-oriented programming style several matters are introduced and developed: profile classes allowing the representation

  6. Molecule-oriented programming in Java

    NARCIS (Netherlands)

    Bergstra, J.A.

    2002-01-01

    Molecule-oriented programming is introduced as a programming style carrying some perspective for Java. A sequence of examples is provided. Supporting the development of the molecule-oriented programming style several matters are introduced and developed: profile classes allowing the representation o

  7. Absolute Orientation of Molecules with Competing Hydrophilic Head Groups at the Air/Water Interface Probed with Sum Frequency Generation Vibrational Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    Feng Wang; Zhi Huang; Zhifeng Cui; Hongfei Wang

    2009-01-01

    The constructive or destructive spectral interference between the molecular groups oriented up and down at the interface in the sum-frequency generation (SFG) spectra provides a direct measurement of the absolute orientation of these molecular groups. This simple approach can be employed to interrogate absolute molecular orientations other than using the complex absolute phase measurement in the SFG studies. We used the -CN group in the p-cyanophenol (PCP) molecule as the internal phase standard, and we measured the phases of the SFG fields of the -CN groups in the 3,5-dimethyl-4-hydroxy-benzonitrile (35DMHBN)and 2,6-dimethyl-4-hydroxy-benzonitrile (26DMHBN) at the air/water interface by measuring the SFG spectra of the aqueous surfaces of the mixtures of the PCP, 35DMHBN, and 26DMHBN solutions. The results showed that the 35DMHBN had its -CN group pointing into the aqueous phase; while the 26DMHBN, similar to the PCP, had its -CN group pointing away from the aqueous phase. The tilt angles of the -CN group for both the 35DMHBN and 26DMHBN molecules at the air/water interface were around 25°-45° from the interface normal. These results provided insights on the understanding of the detailed balance of the competing factors, such as solvation of the polar head groups, hydrogen bonding and hydrophobic effects, etc., on influencing the absolute molecular orientation at the air/water interface.

  8. Field-free orientation of molecules

    DEFF Research Database (Denmark)

    Machholm, Mette; Henriksen, Niels Engholm

    2001-01-01

    The excitation of angular motion, in particular, the creation of a wave packet in the angular degrees of freedom via short-pulse, off-resonant excitation with respect to rotational transitions, was examined. The key result was that field-free time-dependent orientation for a molecule like LiH can...

  9. When water molecules meet air

    OpenAIRE

    Hsie, Cho-Shuen; Campen, R. Kramer; Verde, Ana Vila; Bolhuis, Peter; Nienhuys, Han-Kwang; Bonn, Mischa

    2012-01-01

    About 70% of our planet is covered in water. Most of that water exists as water in the bulk – the neighbors of water molecules are other water molecules – and only a small fraction of molecules are at the air-water interface. Despite the small relative abundance of interfacial water, it is of the utmost importance: it governs the chemistry involving the surface of oceans and seawater aerosols, or the small water droplets forming clouds. Reactions at the air-water interface are directly releva...

  10. Orientation of KRb molecules in a switched electrostatic field

    Institute of Scientific and Technical Information of China (English)

    Huang Yun-Xia; Xu Shu-Wu; Yang Xiao-Hua

    2013-01-01

    We theoretically investigate the orientation of the cold KRb molecules induced in a switched electrostatic field by numerically solving the full time-dependent Schr(o)dinger equation.The results show that the periodic field-free molecular orientation can be realized for the KRb molecules by rapidly switching off the electrostatic field.Meanwhile,by varying the switching times of the electrostatic field,the adiabatic and nonadiabatic interactions of the molecules with the applied field can be realized.Moreover,the influences of the electrostatic field strength and the rotational temperature to the degree of the molecular orientation are studied.The investigations show that increasing the electrostatic field will increase the degree of the molecular orientation,both in the constant-field regime and in the field-free regime,while the increasing of the rotational temperature of the cold molecules will greatly decrease the degree of the molecular orientation.

  11. Orientation of the pigment molecules in the chloroplast

    NARCIS (Netherlands)

    Goedheer, J.C.

    1955-01-01

    Dichroism, absorption anisotropy, and anomal dispersion of birefringence were measured in the big lamellate chloroplasts of Mougeotia. The results of these measurements indicate a certain orientation of the chlorophyll molecules, and to a smaller extent, of the carotenoids in the chloroplast. In sp

  12. Molecule scattering from solid surfaces : Orientation and surface corrugation effects

    NARCIS (Netherlands)

    Vicanek, M; Schlatholter, T; Heiland, W

    1997-01-01

    Various effects connected with orientation and surface corrugation in molecule scattering from solid surfaces are investigated by means of classical trajectories simulations for H-2 impinging on Pd(110). Primary excitation of the projectiles is modeled according to the situation in molecular beam ex

  13. Nano-sensing of the orientation of fluorescing molecules with active coated nano-particles

    DEFF Research Database (Denmark)

    Arslanagic, Samel; Ziolkowski, Richard W.

    2015-01-01

    The potential of using active coated nano-particles to determine the orientation of fluorescing molecules is reported. By treating each fluorescing molecule as an electric Hertzian dipole, single and multiple fluorescing molecules emitting coherently and incoherently in various orientations...

  14. Controlling the Orientation and Alignment of Reagent Molecules by a Polarized Laser

    Institute of Scientific and Technical Information of China (English)

    丛书林; 韩克利; 楼南泉

    2003-01-01

    The expressions used for controlling the alignment and orientation of reagent molecules are derived. The problem to the control of the orientation and alignment of reagent molecules by the polarization direction and propagation direction of laser is discussed.

  15. Orientational dependence of electronic stopping of molecule and cluster ions

    Science.gov (United States)

    Jensen, J.; Mikkelsen, H. H.; Sigmund, P.

    1994-04-01

    The electronic energy deposited by a fast molecule or cluster penetrating through matter is estimated on the basis of a multipole expansion of the Coulomb interaction between the projectile and the target electrons. The treatment is directed at distant collisions, and the primary purpose has been to gain an impression of the dependence of the electronic energy loss on the orientation of the projectile relative to the beam direction. With this qualitative goal in mind, and considering that the total charge of a moving cluster can be quite high, we chose Bohr's classical-oscillator model of the target atom as the theoretical basis. The energy loss versus impact parameter consists of the familiar monopole term which applies to a point charge, plus a number of multipole terms, the leading one of which is found to be a monopole-quadrupole term. In the energy loss averaged over all orientations, that term vanishes, and the leading nonvanishing term then becomes the quadrupole-quadrupole term which reflects the properties of expressions in the literature based on Bethe theory. It is concluded that for anisotropic molecules, the directional dependence of electronic energy loss is more pronounced than what could be expected from published proximity factors. Explicit examples refer to a diatomic molecule.

  16. Classical interaction model for the water molecule.

    Science.gov (United States)

    Baranyai, András; Bartók, Albert

    2007-05-14

    The authors propose a new classical model for the water molecule. The geometry of the molecule is built on the rigid TIP5P model and has the experimental gas phase dipole moment of water created by four equal point charges. The model preserves its rigidity but the size of the charges increases or decreases following the electric field created by the rest of the molecules. The polarization is expressed by an electric field dependent nonlinear polarization function. The increasing dipole of the molecule slightly increases the size of the water molecule expressed by the oxygen-centered sigma parameter of the Lennard-Jones interaction. After refining the adjustable parameters, the authors performed Monte Carlo simulations to check the ability of the new model in the ice, liquid, and gas phases. They determined the density and internal energy of several ice polymorphs, liquid water, and gaseous water and calculated the heat capacity, the isothermal compressibility, the isobar heat expansion coefficients, and the dielectric constant of ambient water. They also determined the pair-correlation functions of ambient water and calculated the energy of the water dimer. The accuracy of theirs results was satisfactory.

  17. Evidence of water molecules--a statistical evaluation of water molecules based on electron density.

    Science.gov (United States)

    Nittinger, Eva; Schneider, Nadine; Lange, Gudrun; Rarey, Matthias

    2015-04-27

    Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we introduce a new measurement of electron density around an individual atom enabling the automatic quantification of experimental support. On the basis of this measurement, we present an analysis of water molecules with a detailed profile of geometric and structural features. This data, which is freely available, can be applied to not only modeling and validation of new water models in structural biology but also in molecular design.

  18. Modelling proton transfer in water molecule chains

    CERN Document Server

    Korzhimanov, Artem; Shutova, Tatiana; Samuelsson, Goran

    2011-01-01

    The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better understood in terms of simplified model problems. Here we have tested, analytically and numerically, a model describing the classical proton hopping process in molecular water chains. In order to capture the main features of the proton hopping process in such molecular chains, we use a simplified model for our analysis. In particular, our discrete model describes a 1D chain of water molecules situated in an external protein channel structure, and each water molecule is allowed to oscillate around its equilibrium point in this system, while the protons are allowed to move along the line of neighboring oxygen atoms. The occurrence and properties of nonlinear solitary transport structures, allowing for much faster proton transport, are discussed, and the possible implications of...

  19. Orientational Order of C60 Molecules in Low-dimensional Lattices

    Institute of Scientific and Technical Information of China (English)

    Hou Jianguo

    2002-01-01

    The orientational order is an important concept of the materials composed of large molecules or clusters. Using high-resolution scanning tunneling microscopy, we have studied the orientational order of two kinds of typical low-dimensional C60 lattices: two-dimensional molecules array and C60(111) multi-layer film surface. Due to the change of the crystal field, their orientational orders are distinctly different from those in bulk system, and some unique phenomena appear.

  20. Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

    NARCIS (Netherlands)

    Y.L.A. Rezus; H.J. Bakker

    2008-01-01

    We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at

  1. Neglected Outcomes of Customer Orientation in Urban Public Water ...

    African Journals Online (AJOL)

    Neglected Outcomes of Customer Orientation in Urban Public Water Utilities in Uganda and Tanzania. ... a positive correlation between customer orientation and customer satisfaction ... Keywords · Customer orientation · Service quality · DEA ...

  2. Measurement of the orientation of buffer-gas-cooled, electrostatically-guided ammonia molecules

    Science.gov (United States)

    Steer, Edward W.; Petralia, Lorenzo S.; Western, Colin M.; Heazlewood, Brianna R.; Softley, Timothy P.

    2017-02-01

    The extent to which the spatial orientation of internally and translationally cold ammonia molecules can be controlled as molecules pass out of a quadrupole guide and through different electric field regions is examined. Ammonia molecules are collisionally cooled in a buffer gas cell, and are subsequently guided by a three-bend electrostatic quadrupole into a detection chamber. The orientation of ammonia molecules is probed using (2 + 1) resonance-enhanced multiphoton ionisation (REMPI), with the laser polarisation axis aligned both parallel and perpendicular to the time-of-flight axis. Even with the presence of a near-zero field region, the ammonia REMPI spectra indicate some retention of orientation. Monte Carlo simulations propagating the time-dependent Schrödinger equation in a full basis set including the hyperfine interaction enable the orientation of ammonia molecules to be calculated - with respect to both the local field direction and a space-fixed axis - as the molecules pass through different electric field regions. The simulations indicate that the orientation of ∼95% of ammonia molecules in JK =11 could be achieved with the application of a small bias voltage (17 V) to the mesh separating the quadrupole and detection regions. Following the recent combination of the buffer gas cell and quadrupole guide apparatus with a linear Paul ion trap, this result could enable one to examine the influence of molecular orientation on ion-molecule reaction dynamics and kinetics.

  3. Elastic electron scattering from CH sub 3 I molecules oriented in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Volkmer, M.; Meier, C.; Mihill, A.; Fink, M.; Boewering, N. (Fakultaet fuer Physik, Universitaet Bielefeld, D-4800 Bielefeld 1 (Germany))

    1992-04-13

    A novel experiment on elastic electron scattering from free, spatially oriented molecules has been performed. CH{sub 3}I molecules state selected by an electrostatic hexapole lens were oriented in a homogeneous electric field. The differential scattering cross sections were measured at an electron energy of 1 keV in the angular range of 4{degree}--14{degree} with the orientation switched on and off. From these data the orientation-dependent contribution to the molecular interference was determined. The results show a distinct oscillatory pattern as a function of momentum transfer as predicted by theory.

  4. Imposed Orientation of Dye Molecules by Liquid Crystals and an Electric Field.

    Science.gov (United States)

    Sadlej-Sosnowska, Nina

    1980-01-01

    Describes experiments using dye solutions in liquid crystals in which polar molecules are oriented in an electrical field and devices are constructed to change their color in response to an electric signal. (CS)

  5. Photoelectron angular distributions from strong-field ionization of oriented molecules

    DEFF Research Database (Denmark)

    Holmegaard, Lotte; Hansen, Jonas Lerche; Kalhøj, Line;

    2010-01-01

    perpendicular to the fixed permanent dipole moment, which are absent for randomly oriented molecules. Furthermore, for benzonitrile oriented in three dimensions, striking suppression of electron emission in the fixed molecular plane appears. Our theoretical analysis, based on tunnelling ionization theory, shows...... ionization, which is limited to species and processes where ionization leads to fragmentation. An alternative is to fix the molecular frame before ionization. The only demonstrations of such spatial orientation involved aligned small linear nonpolar molecules. Here we extend these techniques to the general...... class of polar molecules. Carbonylsulphide and benzonitrile molecules, fixed in space by combined laser and electrostatic fields, are ionized with intense, circularly polarized 30-fs laser pulses. For carbonylsulphide and benzonitrile oriented in one dimension, the MFPADs exhibit pronounced anisotropies...

  6. Libration of strongly-oriented polar molecules inside a superfluid

    CERN Document Server

    Lemeshko, Mikhail

    2016-01-01

    We study a polar molecule immersed into a superfluid environment, such as a helium nanodroplet or a Bose-Einstein condensate, in the presence of an intense electrostatic field. We show that coupling of the molecular pendular motion, induced by the field, to the fluctuating bath leads to formation of pendulons -- spherical harmonic librators dressed by a field of many-particle excitations. We study the behavior of the pendulon in a broad range of molecule-bath and molecule-field interaction strengths, and reveal that its spectrum features series of instabilities which are absent in the field-free case of the angulon quasiparticle. Furthermore, we show that an external field allows to finetune the positions of these instabilities in the molecular rotational spectrum. This opens the door to detailed experimental studies of redistribution of orbital angular momentum in many-particle systems.

  7. Simultaneous measurement of orientational and spectral dynamics of single molecules in nanostructured host-guest materials.

    Science.gov (United States)

    Jung, Christophe; Hellriegel, Christian; Platschek, Barbara; Wöhrle, Dieter; Bein, Thomas; Michaelis, Jens; Bräuchle, Christoph

    2007-05-02

    Nanostructured host-guest materials are important for various applications in nanoscience, and therefore, a thorough understanding of the dynamics of the guest molecules within the host matrix is needed. To this aim we used single-molecule fluorescence techniques to simultaneously examine the spectral and the orientational behavior of single molecules in nanostructured porous host materials. Two types of host-guest systems have been investigated. First, oxazine-1 dye molecules were fixed rigidly in the channels of microporous AlPO4-5 crystals. Second, it was shown that terrylenediimide (TDI) dye molecules move in the mesoporous network of an uncalcined M41S thin film. In the first sample both spectral fluctuations ( approximately 5 nm) and rare spectral jumps (>10 nm) of the emission maximum were observed. However, the orientation of the emission dipole of the dye molecules remained constant. In contrast, the second system showed orientational dynamics as well as substantially more spectral dynamics. In this system the molecules were found to move between different regions in the host. The typical motion of the TDI molecules in the pores of M41S was not continuous but characterized by jumps between specific sites. Moreover, the spectral and orientational dynamics were correlated and arose directly from the different environments that were being explored by the mobile molecule.

  8. The spontaneous synchronized dance of pairs of water molecules

    Energy Technology Data Exchange (ETDEWEB)

    Roncaratti, Luiz F. [Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia (Italy); Instituto de Física, Universidade de Brasília, 70910-900 Brasília (Brazil); Cappelletti, David, E-mail: david.cappelletti@unipg.it; Pirani, Fernando [Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia (Italy)

    2014-03-28

    Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupled pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions.

  9. Spatial and Orientational Structure of the Hydration Shell of Benzene in Sub- and Supercritical Water.

    Science.gov (United States)

    Choudhary, Ashu; Chandra, Amalendu

    2015-07-09

    The spatial and orientational structure of the solvation shell of benzene in sub- and supercritical water are investigated by means of molecular dynamics simulations. The present study reveals different local organization of water molecules at different parts of the solute. The π-hydrogen-bonding between benzene and water along the axial direction is found to exist even at supercritical conditions although to a reduced extent. The coordination number of benzene decreases substantially on increase of temperature and decrease of density. While the π-hydrogen-bonded part in the axial region shows a slight expansion, the hydrophobically solvated part in the equatorial plane shows an opposite behavior as the temperature is increased from normal to the supercritical temperature. Two other distribution functions, namely the radial/angular and spatial orientational functions (SOFs) are calculated to explore the spatially resolved angular preferences of water molecules around the benzene solute. Water molecules located axial to the benzene are found to have strong inward orientation toward the solute, however an opposite behavior is found in the equatorial region. Although at supercritical conditions, the orientational distributions of water molecules are broadened, the preferential orientations in the axial and equatorial regions remain similar to that under ambient condition on average.

  10. Single molecule optical measurements of orientation and rotations of biological macromolecules

    Science.gov (United States)

    Shroder, Deborah Y.; Lippert, Lisa G.; Goldman, Yale E.

    2016-12-01

    Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.

  11. Diffusion of oriented single molecules with switchable mobility in networks of long unidimensional nanochannels.

    Science.gov (United States)

    Jung, Christophe; Kirstein, Johanna; Platschek, Barbara; Bein, Thomas; Budde, Michael; Frank, Irmgard; Müllen, Klaus; Michaelis, Jens; Bräuchle, Christoph

    2008-02-06

    Single dye molecules incorporated into a mesoporous matrix can act as highly sensitive reporters of their environment. Here, we use single TDI molecules incorporated as guests into hexagonal mesoporous films containing highly structured domains. The dye molecules allow us to map the size of these domains which can extend to over 100 microm. Investigation of the translational and orientational dynamics via single molecule fluorescence techniques gives structural as well as dynamical information about the host material. In an air atmosphere, the guest molecules show no movement but perfect orientation along the pore direction. The diffusion of the TDI molecules can be induced by placing the mesoporous film in a saturated atmosphere of chloroform. In single molecule measurements with very high positioning accuracy (down to 2-3 nm) the movement of molecules could be observed even between neighboring channels. This reveals the presence of defects like dead ends closing the pores or small openings in the silica walls between neighboring channels, where molecules can change from one channel to the next. A statistical analysis demonstrates that the diffusion of TDI in the mesoporous film cannot be described with a 1D-random diffusion but is more complicated due to the presence of adsorption sites in which the TDI molecules can be occasionally trapped.

  12. Origins of Water Molecules in the Photosystem II Crystal Structure.

    Science.gov (United States)

    Sakashita, Naoki; Watanabe, Hiroshi C; Ikeda, Takuya; Saito, Keisuke; Ishikita, Hiroshi

    2017-06-20

    The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl(-)2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.

  13. Two dimensional NMR of liquids and oriented molecules

    Energy Technology Data Exchange (ETDEWEB)

    Gochin, M.

    1987-02-01

    Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of /sup 13/C and /sup 1/H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface.

  14. Photoelectron angular distributions from strong-field ionization of oriented molecules

    CERN Document Server

    Holmegaard, Lotte; Kalhøj, Line; Kragh, Sofie Louise; Stapelfeldt, Henrik; Filsinger, Frank; Küpper, Jochen; Meijer, Gerard; Dimitrovski, Darko; Abu-samha, Mahmoud; Martiny, Christian P J; Madsen, Lars Bojer

    2010-01-01

    The combination of photoelectron spectroscopy and ultrafast light sources is on track to set new standards for detailed interrogation of dynamics and reactivity of molecules. A crucial prerequisite for further progress is the ability to not only detect the electron kinetic energy, as done in traditional photoelectron spectroscopy, but also the photoelectron angular distributions (PADs) in the molecular frame. Here carbonylsulfide (OCS) and benzonitrile molecules, fixed in space by combined laser and electrostatic fields, are ionized with intense, circularly polarized, 30 femtosecond laser pulses. For 1-dimensionally oriented OCS the molecular frame PADs exhibit pronounced anisotropies, perpendicular to the fixed permanent dipole moment, that are absent in PADs from randomly oriented molecules. For 3-dimensionally oriented benzonitrile additional striking structures appear due to suppression of electron emission in nodal planes of the fixed electronic orbitals. Our theoretical analysis, relying on tunneling io...

  15. Pulse train induced rotational excitation and orientation of a polar molecule.

    Science.gov (United States)

    Tyagi, Ashish; Arya, Urvashi; Vidhani, Bhavna; Prasad, Vinod

    2014-08-14

    We investigate theoretically the rotational excitation and field free molecular orientation of polar HBr molecule, interacting with train of ultrashort laser pulses. By adjusting the number of pulses, pulse period and the intensity of the pulse, one can suppress a population while simultaneously enhancing the desired population in particular rotational state. We have used train of laser pulses of different shaped pulse envelopes. The dynamics and orientation of molecules in the presence of pulse train of different shapes is studied and explained. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Ionization of oriented carbonyl-sulfide molecules by intense circularly polarized laser pulses

    CERN Document Server

    Dimitrovski, Darko; Madsen, Lars Bojer; Filsinger, Frank; Meijer, Gerard; Küpper, Jochen; Holmegaard, Lotte; Kalhøj, Line; Nielsen, Jens H; Stapelfeldt, Henrik

    2010-01-01

    We present combined experimental and theoretical results on strong-field ionization of oriented carbonyl-sulphide molecules by circularly-polarized laser pulses. The obtained molecular frame photoelectron angular distributions show pronounced asymmetries perpendicular to the direction of the molecular electric dipole moment. These findings are explained by a tunneling model invoking the laser-induced Stark shifts associated with the dipoles and polarizabilities of the molecule and its unrelaxed cation.

  17. Theoretical study of determining orientation and alignment of symmetric top molecule using laser-induced fluorescence

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    General expressions used for extracting the orientation and alignment parameters of a symmetric top molecule from laser-induced fluorescence (LIF) intensity are derived by employing the density matrix approach. The molecular orientation and alignment are described by molecular state multipoles. Excitation and detection are circularly and linearly polarized lights, respectively. In general cases, the LIF intensity is a complex function of the initial molecular state multipoles, the dynamic factors and the excitation-detection geometrical factors. It contains a population, ten orientation and fourteen alignment multipoles. The problem of how to extract the initial molecular state multipoles from the resolved LIF intensity is discussed.

  18. A New Method for Determining Dipole Moment Orientation of Single Molecules

    Institute of Scientific and Technical Information of China (English)

    WANG Chen; LIU Li; WANG Gui-Ying; XU Zhi-Zhan

    2004-01-01

    @@ A new imaging method is proposed to determine the three-dimensional dipole moment orientation of single fluorophore. Far-field microscopy can provide orientational information projected in the sample plane, while total internal reflection fluorescence microscopy (TIRFM) can offer the knowledge perpendicular to the surface because longitudinal electric-field components can be generated in total internal reflection geometry. By comparing fluorescence intensities measured with far-field epi-fluorescence microscopy and TIRFM, the exact information of single-fluorescent-molecule orientation is extracted. Detailed analysis of the method is given with a numerical example.

  19. Differential cross sections for the ionization of oriented H2 molecules by electron-impact

    Energy Technology Data Exchange (ETDEWEB)

    Colgan, James P [Los Alamos National Laboratory; Pindzola, M S [AUBURN UNIV; Kaiser, C [UNIV MANCHESTER; Madison, D H [MISSOURI INST.; Robicheaux, F [AUBURN UNIV; Balance, J [ROLLINS COLLEGE

    2008-01-01

    A nonperturbative close-coupling technique is used to calculate differential cross sections for the electron-impact ionization of H{sub 2} at an energy of 35.4 eV. Our approach allows cross sections for any orientation of the molecule with respect to the incident electron beam to be analyzed. New features in the resulting cross sections are found compared with the case where the molecular orientation is averaged, and also with cross sections for He at equivalent electron kinematics. When averaged over all possible molecular orientations, good agreement is found with recent experimental results.

  20. Structure and dynamics of water molecules confined in triglyceride oils.

    Science.gov (United States)

    Groot, Carien C M; Velikov, Krassimir P; Bakker, Huib J

    2016-10-26

    Though it is commonly known that a small amount of water can be present in triglyceride oil, a molecular picture of how water molecules organize in the oil phase is lacking. We investigate the hydrogen-bond configuration and dynamics of water in triacetin, tributyrin and trioctanoin using linear infrared and time-resolved two-dimensional infrared (2DIR) spectroscopy of the water hydroxyl stretch vibration. We identify water molecules with a single strong hydrogen bond to the triglyceride, water molecules with two weaker hydrogen bonds to the triglycerides, and water clusters. These species do not interconvert on the 20 ps timescale of the experiment, as evidenced by the absence of cross-peaks in the 2DIR spectrum. The vibrational response of water molecules with a single strong hydrogen bond to the triglyceride depends strongly on the excitation frequency, revealing the presence of different subspecies of singly-bound water molecules that correspond to different hydrogen-bond locations. In contrast, the water molecules with two weaker hydrogen bonds to the triglyceride correspond to a single, specific hydrogen-bond configuration; these molecules likely bridge the carbonyl groups of adjacent triglyceride molecules, which can have considerable influence on liquid triglyceride properties.

  1. Mixed-field orientation of a thermal ensemble of linear polar molecules

    CERN Document Server

    Omiste, Juan J

    2013-01-01

    We present a theoretical study of the impact of an electrostatic field combined with nonresonant linearly polarized laser pulses on the rotational dynamics of a thermal ensemble of linear molecules. We solve the time-dependent Schr\\"odinger equation within the rigid rotor approximation for several rotational states. Using the carbonyl sulfide (OCS) molecule as a prototype, the mixed-field orientation of a thermal sample is analyzed in detail for experimentally accessible static field strengths and laser pulses. We demonstrate that for the characteristic field configuration used in current mixed-field orientation experiments, a significant orientation is obtained for rotational temperatures below 0.7K or using stronger dc fields.

  2. Adiabatic mixed-field orientation of ground-state-selected carbonyl sulfide molecules

    CERN Document Server

    Kienitz, Jens S; Mullins, Terry; Długołęcki, Karol; González-Férez, Rosario; Küpper, Jochen

    2016-01-01

    We experimentally demonstrated strong adiabatic mixed-field orientation of carbonyl sulfide molecules (OCS) in their absolute ground state of $\\text{N}_{\\text{up}}/\\text{N}_{\\text{tot}}=0.882$. OCS was oriented in combined non-resonant laser and static electric fields inside a two-plate velocity map imaging spectrometer. The transition from non-adiabatic to adiabatic orientation for the rotational ground state was studied by varying the applied laser and static electric field. Above static electric field strengths of 10~kV/cm and laser intensities of $10^{11} \\text{W/cm}^2$ the observed degree of orientation reached a plateau. These results are in good agreement with computational solutions of the time-dependent Schr\\"odinger equation.

  3. Orientation of azobenzene molecules in polymer films induced by all-optical poling

    Institute of Scientific and Technical Information of China (English)

    Xiaoxia Zhong(钟晓霞); Shouyu Luo(罗售余); Xiuqin Yu(虞秀琴); Qu Li(李劬); Yingli Chen(陈英礼); Yu Sui(隋郁); Jie Yin(印杰)

    2003-01-01

    A model of the alignment of azobenzene molecules in polymer film induced by all-optical poling is proposedand verified by experiment. We found that when the writing beams of frequencies ω and 2ω are both linearlypolarized with their polarization directions parallel to each other, azobenzene molecules tend to reorientto the direction perpendicular to the writing beams polarization. At the end of the writing process, moremolecules orient to the direction perpendicular to the writing beams polarization than those which orientto the parallel direction. The alignment of molecules parallel or perpendicular to the polarization of thewriting beams is characteristic of polarity or no polarity, respectively. The alignment of molecules alongthe polarization of writing beams results in the second order nonlinearity in the polymer film. Accordingto the model, a new method to improve the optical poling efficiency is put forward.

  4. Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

    Science.gov (United States)

    Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio

    2017-08-01

    We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

  5. Free enthalpies of replacing water molecules in protein binding pockets

    Science.gov (United States)

    Riniker, Sereina; Barandun, Luzi J.; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F.

    2012-12-01

    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

  6. Switching orientation of adsorbed molecules: Reverse domino on a metal surface

    Science.gov (United States)

    Braatz, C. R.; Esat, T.; Wagner, C.; Temirov, R.; Tautz, F. S.; Jakob, P.

    2016-01-01

    A thus far unknown phase of 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA) on Ag(111), characterized by an all perpendicular orientation of the planar molecules and bound to the Ag substrate through the carboxyl oxygen atoms has been identified using infrared absorption spectroscopy and scanning tunneling microscopy. Its formation process requires second layer NTCDA to squeeze into empty spaces between relaxed monolayer NTCDA molecules. Remarkably, this process causes initially parallel oriented NTCDA to likewise adopt the new, highly inclined adsorption geometry. According to our SPA-LEED and STM findings, the new phase displays a distinct long range order and shows a pronounced tendency to form 1D rows or narrow islands. We suggest that extra NTCDA preferentially transforms into the upright configuration close to existing islands and attaches to them, i.e. the transformation process proceeds in a directed and recurrent manner (reverse domino scenario). Identical processing starting with a compressed NTCDA/Ag(111) monolayer leads to a purely parallel oriented bilayer, that is, the NTCDA monolayer phase is retained and merely acts as a passive template for bilayer NTCDA. The new vertical NTCDA phase represents an unusual molecular system with π-orbitals oriented parallel to a metal surface. A substantially reduced coupling of these orbitals to Ag(111) electronic levels is conjectured, which will have a major impact on intermolecular couplings and electronically excited state lifetimes.

  7. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

    DEFF Research Database (Denmark)

    Rønnest, A. K.; Peters, Günther H.J.; Hansen, Flemming Yssing;

    2016-01-01

    the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic...... compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have...... potential within phospholipid membranes imply an enormous electric field of 108-109 V m-1, which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential...

  8. Rotational state selection and orientation of diatomic and asymmetric top molecules via the electric hexapole technique

    Science.gov (United States)

    Hain, Toby Douglas

    2000-11-01

    The hexapole rotational state selection of 2∏ Ω diatomic and asymmetric top molecules is investigated. Classical molecular trajectory simulations are shown to reproduce experimental focusing spectra in these large classes of molecules. Deviations from linear Stark effects introduce significant effects in the focusing behavior of both the 2∏ and asymmetric rotor species. The laboratory frame distributions of orientations of the state-selected molecules are quantified by quantum mechanical orientational probability distribution functions (opdf's). Chapter 1 introduces preliminary data for the hexapole focusing of hydroxyl radicals and shows the deviation of the structured focusing curves from the first-order Stark effect. In Chapter 2, the focusing theory is developed for 2∏ diatomics, and the focusing spectra presented in Chapter 1 are analyzed using the theory. The Λ-doublet splitting is found to be the important parameter for simulating the measured focusing spectra. The high field limit opdf's are calculated, and highly anisotropic orientational distributions for the selected states are shown. Chapter 3 shows the laboratory orientation of 2∏ molecules is tunable via the electric field strength of an orienting field for post- hexapole selected rotational states. A laser induced fluorescence experiment is detailed allowing experimental validation of the theoretical opdf's. Chapter 4 explores the scattering of hexapole selected OD rotational states with various target gases. Elastic scattering cross sections are reported for OD + M (M = He, Ar, H2O, CO2, NH3, and CH3F). Hexapole focusing and the subsequent orientation of asymmetric rotors are the subjects of Chapter 5. Matrix treatments are used to calculate the field-free and Stark energies exactly. Perturbation and intermediate Stark effect approximations are compared to the exact matrix method, yielding several general rules useful in analyzing and predicting experimental focusing spectra. The theory

  9. On the Several Molecules and Nanostructures of Water

    OpenAIRE

    Cynthia Kolb Whitney

    2012-01-01

    This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are in...

  10. Bayesian orientation estimate and structure information from sparse single-molecule x-ray diffraction images.

    Science.gov (United States)

    Walczak, Michał; Grubmüller, Helmut

    2014-08-01

    We developed a Bayesian method to extract macromolecular structure information from sparse single-molecule x-ray free-electron laser diffraction images. The method addresses two possible scenarios. First, using a "seed" structural model, the molecular orientation is determined for each of the provided diffraction images, which are then averaged in three-dimensional reciprocal space. Subsequently, the real space electron density is determined using a relaxed averaged alternating reflections algorithm. In the second approach, the probability that the "seed" model fits to the given set of diffraction images as a whole is determined and used to distinguish between proposed structures. We show that for a given x-ray intensity, unexpectedly, the achievable resolution increases with molecular mass such that structure determination should be more challenging for small molecules than for larger ones. For a sufficiently large number of recorded photons (>200) per diffraction image an M^{1/6} scaling is seen. Using synthetic diffraction data for a small glutathione molecule as a challenging test case, successful determination of electron density was demonstrated for 20000 diffraction patterns with random orientations and an average of 82 elastically scattered and recorded photons per image, also in the presence of up to 50% background noise. The second scenario is exemplified and assessed for three biomolecules of different sizes. In all cases, determining the probability of a structure given set of diffraction patterns allowed successful discrimination between different conformations of the test molecules. A structure model of the glutathione tripeptide was refined in a Monte Carlo simulation from a random starting conformation. Further, effective distinguishing between three differently arranged immunoglobulin domains of a titin molecule and also different states of a ribosome in a tRNA translocation process was demonstrated. These results show that the proposed method is

  11. Green chemistry oriented organic synthesis in water.

    Science.gov (United States)

    Simon, Marc-Olivier; Li, Chao-Jun

    2012-02-21

    The use of water as solvent features many benefits such as improving reactivities and selectivities, simplifying the workup procedures, enabling the recycling of the catalyst and allowing mild reaction conditions and protecting-group free synthesis in addition to being benign itself. In addition, exploring organic chemistry in water can lead to uncommon reactivities and selectivities complementing the organic chemists' synthetic toolbox in organic solvents. Studying chemistry in water also allows insight to be gained into Nature's way of chemical synthesis. However, using water as solvent is not always green. This tutorial review briefly discusses organic synthesis in water with a Green Chemistry perspective.

  12. On the Several Molecules and Nanostructures of Water

    Directory of Open Access Journals (Sweden)

    Cynthia Kolb Whitney

    2012-01-01

    Full Text Available This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown’s gas, and cold fusion.

  13. On equilibrium structures of the water molecule

    Science.gov (United States)

    Császár, Attila G.; Czakó, Gábor; Furtenbacher, Tibor; Tennyson, Jonathan; Szalay, Viktor; Shirin, Sergei V.; Zobov, Nikolai F.; Polyansky, Oleg L.

    2005-06-01

    Equilibrium structures are fundamental entities in molecular sciences. They can be inferred from experimental data by complicated inverse procedures which often rely on several assumptions, including the Born-Oppenheimer approximation. Theory provides a direct route to equilibrium geometries. A recent high-quality ab initio semiglobal adiabatic potential-energy surface (PES) of the electronic ground state of water, reported by Polyansky et al. [Polyansky et al.Science 299, 539 (2003)] and called CVRQD here, is analyzed in this respect. The equilibrium geometries resulting from this direct route are deemed to be of higher accuracy than those that can be determined by analyzing experimental data. Detailed investigation of the effect of the breakdown of the Born-Oppenheimer approximation suggests that the concept of an isotope-independent equilibrium structure holds to about 3×10-5Å and 0.02° for water. The mass-independent [Born-Oppenheimer (BO)] equilibrium bond length and bond angle on the ground electronic state PES of water is reBO=0.95782Å and θeBO=104.485°, respectively. The related mass-dependent (adiabatic) equilibrium bond length and bond angle of H2O16 is read=0.95785Å and θead=104.500°, respectively, while those of D2O16 are read=0.95783Å and θead=104.490°. Pure ab initio prediction of J =1 and 2 rotational levels on the vibrational ground state by the CVRQD PESs is accurate to better than 0.002cm-1 for all isotopologs of water considered. Elaborate adjustment of the CVRQD PESs to reproduce all observed rovibrational transitions to better than 0.05cm-1 (or the lower ones to better than 0.0035cm-1) does not result in noticeable changes in the adiabatic equilibrium structure parameters. The expectation values of the ground vibrational state rotational constants of the water isotopologs, computed in the Eckart frame using the CVRQD PESs and atomic masses, deviate from the experimentally measured ones only marginally, especially for A0 and B0. The

  14. Time-resolved dynamics of odd and even harmonic emission from oriented asymmetric molecules

    Science.gov (United States)

    Zhang, Bing; Yu, Shujuan; Chen, Yanjun; Jiang, Xiangqian; Sun, Xiudong

    2015-11-01

    We study the time-resolved dynamics of high-order harmonic generation (HHG) from oriented asymmetric molecules in intense laser fields theoretically. Previous studies have shown that the odd-even HHG spectra of asymmetric molecules don't show the striking two-center-interference-induced minimum, as the symmetric molecules do, due to the symmetry breaking. Surprisingly, with considering only the short-trajectory contribution, an apparent groove with small amplitudes is observed in the HHG time-frequency distribution, which implies that the harmonic emission is strongly suppressed in a specific time-frequency region. The position of this groove is sensitive to the molecular parameters and the orientation. Our analyses on this origin of the groove reveal different time-frequency properties of odd versus even signals, where the interplay of intramolecular interference and the permanent-dipole effect plays an important role. We show that the even-odd ratio often used in high-harmonic spectroscopy can be influenced significantly by the interference effect.

  15. Adsorption mechanism of water molecule on goethite (010) surface

    Science.gov (United States)

    Xiu, Fangyuan; Zhou, Long; Xia, Shuwei; Yu, Liangmin

    2016-12-01

    Goethite widely exists among ocean sediments; it plays an important role in fixing heavy metals and adsorbing organic contaminants. So the understanding of the adsorbing process of water molecule on its surface will be very helpful to further reveal such environmental friendly processes. The configuration, electronic properties and interaction energy of water molecules adsorbed on pnma goethite (010) surface were investigated in detail by using density functional theory on 6-31G (d,p) basis set and projector- augment wave (PAW) method. The mechanism of the interaction between goethite surface and H2O was proposed. Despite the differences in total energy, there are four possible types of water molecule adsorption configurations on goethite (010) surface (Aa, Ab, Ba, Bb), forming coordination bond with surface Fe atom. Results of theoretical modeling indicate that the dissociation process of adsorbed water is an endothermic reaction with high activation energy. The dissociation of adsorbed water molecule is a proton transportation process between water's O atoms and surface. PDOS results indicate that the bonding between H2O and (010) surface is due to the overlapping of water's 2p orbitals and Fe's 3d orbitals. These results clarify the mechanism on how adsorbed water is dissociated on the surface of goethite and potentially provide useful information of the surface chemistry of goethite.

  16. The elliptical oscillations of the protons of water molecules

    Directory of Open Access Journals (Sweden)

    Николай Тимофеевич Малафаев

    2017-01-01

    Full Text Available The analysis of elliptical oscillations of the protons of water molecules by means of a dual-frequency pendulum model is carried out. The vibrational mode is determined, for which the average angles of pendulum deviation are consistent with the corners of bends of hydrogen bonds in water. The possibility of occurrence of elliptical and ellipse-like rotation of protons in the liquid water around the axis of molecules bonds in a non-uniform in the angle field of intermolecular forces is proved

  17. Theoretical description of mixed-field orientation of asymmetric top molecules: a time-dependent study

    CERN Document Server

    Omiste, Juan J

    2016-01-01

    We present a theoretical study of the mixed-field-orientation of asymmetric top molecules in tilted static electric field and non-resonant linearly polarized laser pulse by solving the time-dependent Schr\\"odinger equation. Within this framework, we compute the mixed-field orientation of a state selected molecular beam of benzonitrile (C$_7$H$_5$N) and compare with the experimental observations [J. L. Hansen et al., Phys. Rev. A 83, 023406 (2011)], and with our previous time-independent descriptions [J. J. Omiste et al., Phys. Chem. Chem. Phys. 13, 18815 (2011)]. For an excited rotational state, we investigate the field-dressed dynamics for several field configurations as those used in the mixed-field experiments. The non-adiabatic phenomena and their consequences on the rotational dynamics are analyzed in detail.

  18. Comment on "A New Method for Determining Dipole Moment Orientation of Single Molecules"

    Institute of Scientific and Technical Information of China (English)

    Martin Vacha; Masahiro Kotani

    2004-01-01

    @@ In a recent issue of Chinese Physics Letters, Wang et al.[1] proposed a method for determining orientation of transition dipole moments of single molecules. The suggested method is based on differences in electric field profile in fluorescence microscope produced by excitation light in epi-fluorescence illumination and total internal reflection illumination configurations, respectively. Here, we wish to draw attention to the fact that the same method based on identical physical principles has been already proposed and experimentally demonstrated by us in a publication which appeared more than one year before Wang's paper.

  19. Anisotropic diffusion of water molecules in hydroxyapatite nanopores

    Science.gov (United States)

    Prakash, Muthuramalingam; Lemaire, Thibault; Caruel, Matthieu; Lewerenz, Marius; de Leeuw, Nora H.; Di Tommaso, Devis; Naili, Salah

    2017-07-01

    New insights into the dynamical properties of water in hydroxyapatite (HAP) nanopores, a model system for the fluid flow within nanosize spaces inside the collagen-apatite structure of bone, were obtained from molecular dynamics simulations of liquid water confined between two parallel HAP surfaces of different sizes (20 Å ≤ H ≤ 240 Å). Calculations were conducted using a core-shell interatomic potential for HAP together with the extended simple point charge model for water. This force field gives an activation energy for water diffusion within HAP nanopores that is in excellent agreement with available experimental data. The dynamical properties of water within the HAP nanopores were quantified in terms of the second-order water diffusion tensor. Results indicate that water diffuses anisotropically within the HAP nanopores, with the solvent molecules moving parallel to the surface twice as fast as the perpendicular direction. This unusual dynamic behaviour is linked to the strong polarizing effect of calcium ions, and the synergic interactions between the water molecules in the first hydration layer of HAP with the calcium, hydroxyl, and phosphate ions, which facilitates the flow of water molecules in the directions parallel to the HAP surface.

  20. Transport behavior of water molecules through two-dimensional nanopores

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Chongqin; Li, Hui; Meng, Sheng, E-mail: smeng@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2014-11-14

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  1. Transport behavior of water molecules through two-dimensional nanopores

    Science.gov (United States)

    Zhu, Chongqin; Li, Hui; Meng, Sheng

    2014-11-01

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  2. Vibrational states of a water molecule in a nano-cavity of beryl crystal lattice

    Energy Technology Data Exchange (ETDEWEB)

    Zhukova, Elena S., E-mail: zhukovaelenka@gmail.com; Gorshunov, Boris P. [Moscow Institute of Physics and Technology, 9 Institutskiy per., 141700 Dolgoprudny, Moscow Region (Russian Federation); 1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); A.M. Prokhorov General Physics Institute, Russian Academy of Sciences, Vavilova Street 38, 119991 Moscow (Russian Federation); Torgashev, Victor I. [Faculty of Physics, Southern Federal University, 5 Zorge St., 344090 Rostov-on-Don (Russian Federation); Lebedev, Vladimir V. [Moscow Institute of Physics and Technology, 9 Institutskiy per., 141700 Dolgoprudny, Moscow Region (Russian Federation); Landau Institute for Theoretical Physics, Russian Academy of Sciences, Akademika Semenova av., 1-A, 142432 Chernogolovka, Moscow Region (Russian Federation); Shakurov, Gil' man S. [Kazan Physical-Technical Institute, Russian Academy of Sciences, 10/7 Sibirsky Trakt, 420029 Kazan (Russian Federation); Kremer, Reinhard K. [Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, 70569 Stuttgart (Germany); Pestrjakov, Efim V. [Institute of Laser Physics, Russian Academy of Sciences, 13/3 Ac. Lavrentyev' s Prosp., 630090 Novosibirsk (Russian Federation); Thomas, Victor G.; Fursenko, Dimitry A. [Institute of Geology and Mineralogy, Russian Academy of Sciences, 3 Ac. Koptyug' s Prosp., 630090 Novosibirsk (Russian Federation); Prokhorov, Anatoly S. [Moscow Institute of Physics and Technology, 9 Institutskiy per., 141700 Dolgoprudny, Moscow Region (Russian Federation); A.M. Prokhorov General Physics Institute, Russian Academy of Sciences, Vavilova Street 38, 119991 Moscow (Russian Federation); Dressel, Martin [1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany)

    2014-06-14

    Low-energy excitations of a single water molecule are studied when confined within a nano-size cavity formed by the ionic crystal lattice. Optical spectra are measured of manganese doped beryl single crystal Mn:Be{sub 3}Al{sub 2}Si{sub 6}O{sub 18}, that contains water molecules individually isolated in 0.51 nm diameter voids within the crystal lattice. Two types of orientation are distinguished: water-I molecules have their dipole moments aligned perpendicular to the c axis and dipole moments of water-II molecules are parallel to the c-axis. The optical conductivity σ(ν) and permittivity ε{sup ′}(ν) spectra are recorded in terahertz and infrared ranges, at frequencies from several wavenumbers up to ν = 7000 cm{sup −1}, at temperatures 5–300 K and for two polarizations, when the electric vector E of the radiation is parallel and perpendicular to the c-axis. Comparative experiments on as-grown and on dehydrated samples allow to identify the spectra of σ(ν) and ε{sup ′}(ν) caused exclusively by water molecules. In the infrared range, well-known internal modes ν{sub 1}, ν{sub 2}, and ν{sub 3} of the H{sub 2}O molecule are observed for both polarizations, indicating the presence of water-I and water-II molecules in the crystal. Spectra recorded below 1000 cm{sup −1} reveal a rich set of highly anisotropic features in the low-energy response of H{sub 2}O molecule in a crystalline nano-cavity. While for E∥c only two absorption peaks are detected, at ∼90 cm{sup −1} and ∼160 cm{sup −1}, several absorption bands are discovered for E⊥c, each consisting of narrower resonances. The bands are assigned to librational (400–500 cm{sup −1}) and translational (150–200 cm{sup −1}) vibrations of water-I molecule that is weakly coupled to the nano-cavity “walls.” A model is presented that explains the “fine structure” of the bands by a splitting of the energy levels due to quantum tunneling between the minima in a six-well potential

  3. Vibrational states of a water molecule in a nano-cavity of beryl crystal lattice.

    Science.gov (United States)

    Zhukova, Elena S; Torgashev, Victor I; Gorshunov, Boris P; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Prokhorov, Anatoly S; Dressel, Martin

    2014-06-14

    Low-energy excitations of a single water molecule are studied when confined within a nano-size cavity formed by the ionic crystal lattice. Optical spectra are measured of manganese doped beryl single crystal Mn:Be3Al2Si6O18, that contains water molecules individually isolated in 0.51 nm diameter voids within the crystal lattice. Two types of orientation are distinguished: water-I molecules have their dipole moments aligned perpendicular to the c axis and dipole moments of water-II molecules are parallel to the c-axis. The optical conductivity σ(ν) and permittivity ɛ'(ν) spectra are recorded in terahertz and infrared ranges, at frequencies from several wavenumbers up to ν = 7000 cm(-1), at temperatures 5-300 K and for two polarizations, when the electric vector E of the radiation is parallel and perpendicular to the c-axis. Comparative experiments on as-grown and on dehydrated samples allow to identify the spectra of σ(ν) and ɛ'(ν) caused exclusively by water molecules. In the infrared range, well-known internal modes ν1, ν2, and ν3 of the H2O molecule are observed for both polarizations, indicating the presence of water-I and water-II molecules in the crystal. Spectra recorded below 1000 cm(-1) reveal a rich set of highly anisotropic features in the low-energy response of H2O molecule in a crystalline nano-cavity. While for E∥c only two absorption peaks are detected, at ~90 cm(-1) and ~160 cm(-1), several absorption bands are discovered for E⊥c, each consisting of narrower resonances. The bands are assigned to librational (400-500 cm(-1)) and translational (150-200 cm(-1)) vibrations of water-I molecule that is weakly coupled to the nano-cavity "walls." A model is presented that explains the "fine structure" of the bands by a splitting of the energy levels due to quantum tunneling between the minima in a six-well potential relief felt by a molecule within the cavity.

  4. Structures of water molecules in carbon nanotubes under electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji; Yasuoka, Kenji, E-mail: yasuoka@mech.keio.ac.jp [Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522 (Japan)

    2015-03-28

    Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.

  5. Orientation-dependent ionization yields from strong-field ionization of fixed-in-space linear and asymmetric top molecules

    DEFF Research Database (Denmark)

    Hansen, Jonas Lerche; Holmegaard, Lotte; Nielsen, Jens Hedegaard

    2012-01-01

    The yield of strong-field ionization, by a linearly polarized probe pulse, is studied experimentally and theoretically as a function of the relative orientation between the laser field and the molecule. Experimentally, carbonyl sulphide (OCS), benzonitrile and naphthalene molecules are aligned in...

  6. Development of a strain visualization system for microstructures using single fluorescent molecule tracking on a three-dimensional orientation microscope

    Science.gov (United States)

    Yoshida, Shintaro; Yoshiki, Keisuke; Namazu, Takahiro; Araki, Nozomu; Hashimoto, Mamoru; Kurihara, Makoto; Hashimoto, Nobuyuki; Inoue, Shozo

    2011-09-01

    We propose a technique that employs single fluorescent molecules for visualizing the distribution of strain induced in microstructures. We sprayed single-molecule tracers on microstructures by ultrasonic atomization and traced the position and orientation of the tracers by a single-molecule detection technique with a three-dimensional (3D) orientation microscope, which consists of a conventional fluorescent microscope and a polarization-mode converter. By using 3D spline interpolation, we visualized the surface geometry of a microelectromechanical (MEMS) device. We tracked the 3D position and orientation of tracers attached to a supporting beam of the MEMS mirror. The surface declination angles calculated from the orientation of the tracers were in agreement with the tilt angle obtained from the 3D position of the tracers.

  7. Fingerprints of charge exchange between He2+ and water molecules

    NARCIS (Netherlands)

    Bodewits, D.; Tielens, A.G.G.M.; Morgenstern, R.W.H.; Hoekstra, R.A.

    We have measured state selective cross sections for single and double charge exchange of He2+ and water molecules at velocities of 500-1000 km/s. The cross sections for single electron capture into the HeII(2p) state are much larger than those for double electron capture into the HeI(1s2p) state.

  8. Continuum simulations of water flow past fullerene molecules

    DEFF Research Database (Denmark)

    Popadic, A.; Praprotnik, M.; Koumoutsakos, P.;

    2015-01-01

    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as ...

  9. On the polarity of buckminsterfullerene with a water molecule inside

    NARCIS (Netherlands)

    Ensing, B.; Costanzo, F.; Silvestrelli, P.L.

    2012-01-01

    Since the recent achievement of Kurotobi and Murata to capture a water molecule in a C60 fullerene (Science2011, 333, 613), there has been a debate about the properties of this H2O@C60 complex. In particular, the polarity of the complex, which is thought to be underlying the easy separation of H2O@C

  10. Modeling Water Shortage Management Using an Object-Oriented Approach

    Science.gov (United States)

    Wang, J.; Senarath, S.; Brion, L.; Niedzialek, J.; Novoa, R.; Obeysekera, J.

    2007-12-01

    As a result of the increasing global population and the resulting urbanization, water shortage issues have received increased attention throughout the world . Water supply has not been able to keep up with increased demand for water, especially during times of drought. The use of an object-oriented (OO) approach coupled with efficient mathematical models is an effective tool in addressing discrepancies between water supply and demand. Object-oriented modeling has been proven powerful and efficient in simulating natural behavior. This research presents a way to model water shortage management using the OO approach. Three groups of conceptual components using the OO approach are designed for the management model. The first group encompasses evaluation of natural behaviors and possible related management options. This evaluation includes assessing any discrepancy that might exist between water demand and supply. The second group is for decision making which includes the determination of water use cutback amount and duration using established criteria. The third group is for implementation of the management options which are restrictions of water usage at a local or regional scale. The loop is closed through a feedback mechanism where continuity in the time domain is established. Like many other regions, drought management is very important in south Florida. The Regional Simulation Model (RSM) is a finite volume, fully integrated hydrologic model used by the South Florida Water Management District to evaluate regional response to various planning alternatives including drought management. A trigger module was developed for RSM that encapsulates the OO approach to water shortage management. Rigorous testing of the module was performed using historical south Florida conditions. Keywords: Object-oriented, modeling, water shortage management, trigger module, Regional Simulation Model

  11. Orientation-dependent ionization yields from strong-field ionization of fixed-in-space linear and asymmetric top molecules

    CERN Document Server

    Hansen, Jonas L; Nielsen, Jens H; Stapelfeldt, Henrik; Dimitrovski, Darko; Madsen, Lars Bojer

    2011-01-01

    The yield of strong-field ionization, by a linearly polarized probe pulse, is studied experimentally and theoretically, as a function of the relative orientation between the laser field and the molecule. Experimentally, carbonyl sulfide, benzonitrile and naphthalene molecules are aligned in one or three dimensions before being singly ionized by a 30 fs laser pulse centered at 800 nm. Theoretically, we address the behaviour of these three molecules. We consider the degree of alignment and orientation and model the angular dependence of the total ionization yield by molecular tunneling theory accounting for the Stark shift of the energy level of the ionizing orbital. For naphthalene and benzonitrile the orientational dependence of the ionization yield agrees well with the calculated results, in particular the observation that ionization is maximized when the probe laser is polarized along the most polarizable axis. For OCS the observation of maximum ionization yield when the probe is perpendicular to the intern...

  12. The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging.

    Science.gov (United States)

    Backlund, Mikael P; Lew, Matthew D; Backer, Adam S; Sahl, Steffen J; Moerner, W E

    2014-03-17

    Numerous methods for determining the orientation of single-molecule transition dipole moments from microscopic images of the molecular fluorescence have been developed in recent years. At the same time, techniques that rely on nanometer-level accuracy in the determination of molecular position, such as single-molecule super-resolution imaging, have proven immensely successful in their ability to access unprecedented levels of detail and resolution previously hidden by the optical diffraction limit. However, the level of accuracy in the determination of position is threatened by insufficient treatment of molecular orientation. Here we review a number of methods for measuring molecular orientation using fluorescence microscopy, focusing on approaches that are most compatible with position estimation and single-molecule super-resolution imaging. We highlight recent methods based on quadrated pupil imaging and on double-helix point spread function microscopy and apply them to the study of fluorophore mobility on immunolabeled microtubules.

  13. Orientation dependence of the differential cross section in elastic electron scattering from CH{sub 3}I molecules

    Energy Technology Data Exchange (ETDEWEB)

    Volkmer, M.; Meier, C.; Lieschke, J.; Mihill, A.; Fink, M.; Boewering, N. [Fakultaet fuer Physik, Universitaet Bielefeld, D-33501 Bielefeld (Germany)]|[Center for Advanced Microstructures and Devices, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)]|[Physics Department, University of Texas at Austin, Austin, Texas 78712 (United States)

    1996-03-01

    The elastic differential electron cross section of CH{sub 3}I molecules, state selected with an electrostatic hexapole and oriented in an electric field by the linear Stark effect, was measured as a function of the transferred momentum at electron energies of 700, 1000, and 1250 eV. The molecular-state ensemble was oriented with a preferential direction of the molecular symmetry axis parallel or antiparallel to the electron beam. By switching the orientation on and off, the orientation-dependent interference contribution {bar {ital M}}, normalized to the differential cross section of unoriented molecules, was determined, independently of a model, for scattering angles of 4{degree}{endash}15{degree}. The results, which can be divided into pure orientation and alignment parts, display different dependences on the electron energy and the degree of orientation. Model calculations based on the independent atom model (IAM) were carried out for the state mixture present in the scattering region. They reproduce the orientation contributions fairly well, but show some deviations for the stronger alignment contributions. Assuming the validity of the IAM, a Legendre expansion analysis was carried out to extract the leading Legendre moments characterizing the oriented molecular-state ensemble. {copyright} {ital 1996 The American Physical Society.}

  14. Electrostatic deflection of a molecular beam of massive neutral particles: Fully field-oriented polar molecules within superfluid nanodroplets

    CERN Document Server

    Merthe, Daniel J

    2016-01-01

    Electric deflection measurements on liquid helium nanodroplets doped with individual polar molecules demonstrate that the cold superfluid matrix enables full orientation of the molecular dipole along the external field. This translates into a deflection force which is increased enormously by comparison with typical deflection experiments, and it becomes possible to measurably deflect neutral doped droplets with masses of tens to hundreds of thousands of Daltons. This approach permits preparation and study of continuous fluxes of fully oriented polar molecules and is broadly and generally applicable, including to complex and biological molecules. It is shown that the dipole moments of internally cryogenically cold molecules can be directly determined from a deflection measurement on the doped nanodroplet beam.

  15. Variational path integral molecular dynamics study of a water molecule

    Science.gov (United States)

    Miura, Shinichi

    2013-08-01

    In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.

  16. Dissociative Electron Attachment to Polyatomic Molecules - I : Water

    CERN Document Server

    Ram, N Bhargava; Krishnakumar, E

    2010-01-01

    Using the velocity map imaging technique, we studied and characterized the process of Dissociative Electron Attachment (DEA) in polyatomic molecules like Water, Hydrogen Sulphide, Ammonia, Methane, Formic Acid and Propyl Amine. We present the details of these studies in a series of 5 articles. In the first article here, we discuss the DEA process in gas phase water ($H_{2}O$ and $D_{2}O$) molecules. Electrons of 6.5 eV, 8.5 eV and 12 eV are captured by water molecules in neutral ground state to form $H_{2}O^{-*}$ ($D_{2}O^{-*}$) resonant states which dissociate into an anion fragment and one or more neutrals. Kinetic energy and angular distributions of the fragment anions $H^{-}$($D^{-}$) and $O^{-}$ produced from the three negative ion resonant states in the entire $2\\pi$ scattering range are obtained. Unique angular distribution patterns are observed at the 8.5 eV and 11.8 eV resonances showing dissociation dynamics beyond the axial recoil approximation.

  17. Effect of aligning pulse train on the orientation and alignment of a molecule in presence of orienting pulse

    Science.gov (United States)

    Tyagi, Ashish; Maan, Anjali; Ahlawat, Dharamvir Singh; Prasad, Vinod

    2017-02-01

    Field-free molecular alignment is studied theoretically in presence of orienting laser pulse and a delayed Infrared laser (IRL) pulse train. The pulse shapes taken are sine square (sin2) and square. The degree of alignment can be significantly enhanced by the combination of orienting pulse and IRL pulse train compared with only IRL pulse train. Special emphasis is laid on time delay between orienting and aligning pulse, the width and shape of the pulse train. By adjusting the time delay, width and intensity of coupling laser one can suppress a population of particular state while simultaneously enhancing the population of desired states.

  18. Geometry-dependent distributed polarizability models for the water molecule

    Energy Technology Data Exchange (ETDEWEB)

    Loboda, Oleksandr; Ingrosso, Francesca; Ruiz-López, Manuel F.; Millot, Claude [Université de Lorraine, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506 (France); CNRS, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506 (France); Szalewicz, Krzysztof [Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716 (United States)

    2016-01-21

    Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successively occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.

  19. Identification of a wagging vibrational mode of water molecules at the water/vapor interface.

    Science.gov (United States)

    Perry, Angela; Neipert, Christine; Ridley, Christina; Space, Brian; Moore, Preston B

    2005-05-01

    An improved time correlation function description of sum frequency generation (SFG) spectroscopy was applied to theoretically describe the water/vapor interface. The resulting spectra compare favorably in shape and relative magnitude to extant experimental results in the O-H stretching region of water. Further, the SFG spectra show a well-defined intermolecular mode at 875 cm(-1) that has significant intensity. The resonance is due to a wagging mode localized on a single water molecule. It represents a well-defined population of water molecules at the interface that, along with the free O-H modes, represent the dominant interfacial species.

  20. Synthesis and properties of water-soluble asterisk molecules.

    Science.gov (United States)

    Menger, Fredric M; Azov, Vladimir A

    2002-09-18

    An asterisk is comprised of six semirigid arms projecting from a benzene nucleus. In the case at hand, asterisks were synthesized with one, two, or three aromatic rings (connected by sulfur atoms) in each of the six arms. A phosphomonoester at the termini of each arm solubilized the asterisks in water. The colloidal properties of these amphiphilic molecules were investigated by UV-vis and fluorescence spectroscopy, calorimetry, light scattering, surface tensiometry, and pulse-gradient spin-echo NMR. Solubility, solubilization, metal binding, and micelle "seeding" experiments were also carried out. Chain-conformation and supramolecular assembly into remarkable molecular "scrolls" were investigated by X-ray analysis and electron microscopy, respectively. One of the more interesting properties of the asterisks is that they remain monomeric in water despite having as many as 19 hydrophobic aromatic rings exposed to the water. The reasons for this behavior, and the possibility of exploiting it for constructing enzyme models free from aggregation equilibria, are discussed.

  1. Effect of aligning pulse train on the orientation and alignment of a molecule in presence of orienting pulse.

    Science.gov (United States)

    Tyagi, Ashish; Maan, Anjali; Ahlawat, Dharamvir Singh; Prasad, Vinod

    2017-02-15

    Field-free molecular alignment is studied theoretically in presence of orienting laser pulse and a delayed Infrared laser (IRL) pulse train. The pulse shapes taken are sine square (sin(2)) and square. The degree of alignment can be significantly enhanced by the combination of orienting pulse and IRL pulse train compared with only IRL pulse train. Special emphasis is laid on time delay between orienting and aligning pulse, the width and shape of the pulse train. By adjusting the time delay, width and intensity of coupling laser one can suppress a population of particular state while simultaneously enhancing the population of desired states. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Theoretical description of circular dichroism in photoelectron angular distributions of randomly oriented chiral molecules after multi-photon photoionization

    CERN Document Server

    Goetz, R E; Nikoobakht, B; Berger, R; Koch, C P

    2016-01-01

    Photoelectron circular dichroism refers to the forward/backward asymmetry in the photoelectron angular distribution with respect to the propagation axis of circularly polarized light. It has recently been demonstrated in femtosecond multi-photon photoionization experiments with randomly oriented camphor and fenchone molecules [C. Lux et al., Angew. Chem. Int. Ed. 51, 5001 (2012);C. S. Lehmann et al., J. Chem. Phys. 139, 234307 (2013)]. A theoretical framework describing this process as (2+1) resonantly enhanced multi-photon ionization is constructed, which consists of two-photon photoselection from randomly oriented molecules and successive one-photon ionisation of the photoselected molecules. It combines perturbation theory for the light-matter interaction with ab initio calculations for the two-photon absorption and a single-center expansion of the photoelectron wavefunction in terms of hydrogenic continuum functions. It is verified that the model correctly reproduces the basic symmetry behavior expected un...

  3. Hydrogen bonding characterization in water and small molecules

    Science.gov (United States)

    Silvestrelli, Pier Luigi

    2017-06-01

    The prototypical hydrogen bond in water dimer and hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by first-principles calculations based on density functional theory, considering not only a standard generalized gradient approximation functional but also, for the water dimer, hybrid and van der Waals corrected functionals. We compute structural, energetic, and electrostatic (induced molecular dipole moments) properties. In particular, hydrogen bonds are characterized in terms of differential electron density distributions and profiles, and of the shifts of the centres of maximally localized Wannier functions. The information from the latter quantities can be conveyed to a single geometric bonding parameter that appears to be correlated with the Mayer bond order parameter and can be taken as an estimate of the covalent contribution to the hydrogen bond. By considering the water trimer, the cyclic water hexamer, and the hexagonal phase of ice, we also elucidate the importance of cooperative/anticooperative effects in hydrogen-bonding formation.

  4. Electric dipole moments of nanosolvated acid molecules in water clusters

    CERN Document Server

    Guggemos, Nicholas; Kresin, Vitaly V

    2015-01-01

    The electric dipole moments of $(H_{2}O)_{n}DCl$ ($n=3-9$) clusters have been measured by the beam deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at $n\\approx5-6$. This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters, and generally to the essential role played by motional effects in determining the response of fluxional nanoscale sy...

  5. Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules.

    Science.gov (United States)

    Choi, Hyunsung; Chang, Hyun Joon; Lee, Myeongsang; Na, Sungsoo

    2017-02-04

    In biological systems, structural confinements of amyloid fibrils can be mediated by the role of water molecules. However, the underlying effect of the dynamic behavior of water molecules on structural stabilities of amyloid fibrils is still unclear. By performing molecular dynamics simulations, we investigate the dynamic features and the effect of interior water molecules on conformations and mechanical characteristics of various amyloid fibrils. We find that a specific mechanism induced by the dynamic properties of interior water molecules can affect diffusion of water molecules inside amyloid fibrils, inducing their different structural stabilities. The conformation of amyloid fibrils induced by interior water molecules show the fibrils' different mechanical features. We elucidate the role of confined and movable interior water molecules in structural stabilities of various amyloid fibrils. Our results offer insights not only in further understanding of mechanical features of amyloids as mediated by water molecules, but also in the fine-tuning of the functional abilities of amyloid fibrils for applications.

  6. Continuum simulations of water flow past fullerene molecules

    Science.gov (United States)

    Popadić, A.; Praprotnik, M.; Koumoutsakos, P.; Walther, J. H.

    2015-09-01

    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.

  7. Conformation and Orientation of Phospholipid Molecule in Pure Phospholipid Monolayer During Compressing

    Institute of Scientific and Technical Information of China (English)

    XUE Weilan; WANG Dan; ZENG Zuoxiang; GAO Xuechao

    2013-01-01

    On the basis of energy conservation law and surface pressure isotherm,the conformation energy changes of dipalmitoylphosphatidylcholine(DPPC)and dipalmitoylphosphatidylglycerol(DPPG)in pure phospholipid monolayer at the air/water interface during compression are derived.The optimized conformations of phospholipids at absolute freedom state are simulated by Gaussian 98 software.Based on following assumptions:(1)the conformation energy change is mainly caused by the rotation of one special bond;(2)the atoms of glycerol near the water surface are active;(3)the rotation is motivated by hydrogen-bond action;(4)the rotation of bond is inertial,one simplified track of conformational change is suggested and the conformations of DPPC and DPPG at different states are determined by the plots of conformation energy change vs.dihedral angle.The thickness of the simulated phospholipid monolayer is consistent with published experimental result.According to molecular areas at different states,the molecular orientations in the compressing process are also developed.

  8. Molecular dynamics study of water molecule diffusion in oil-paper insulation materials

    Science.gov (United States)

    Liao, Rui-Jin; Zhu, Meng-Zhao; Yang, Li-Jun; Zhou, Xin; Gong, Chun-Yan

    2011-03-01

    Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

  9. Ionization of one- and three-dimensionally-oriented asymmetric-top molecules by intense circularly polarized femtosecond laser pulses

    DEFF Research Database (Denmark)

    Hansen, Jonas Lerche; Holmegaard, Lotte; Kalhøj, Line;

    2011-01-01

    are quantum-state selected using a deflector and three-dimensionally (3D) aligned and oriented adiabatically using an elliptically polarized laser pulse in combination with a static electric field. A characteristic splitting in the molecular frame photoelectron momentum distribution reveals the position......We present a combined experimental and theoretical study on strong-field ionization of a three-dimensionally-oriented asymmetric top molecule, benzonitrile (C7H5N), by circularly polarized, nonresonant femtosecond laser pulses. Prior to the interaction with the strong field, the molecules...... of the nodal planes of the molecular orbitals from which ionization occurs. The experimental results are supported by a theoretical tunneling model that includes and quantifies the splitting in the momentum distribution. The focus of the present article is to understand strong-field ionization from 3D...

  10. Sticking of molecules on non-porous amorphous water ice

    CERN Document Server

    He, Jiao; Vidali, Gianfranco

    2016-01-01

    Accurate modeling of physical and chemical processes in the interstellar medium requires detailed knowledge of how atoms and molecule adsorb on dust grains. However, the sticking coefficient, a number between 0 and 1 that measures the first step in the interaction of a particle with a surface, is usually assumed in simulations of ISM environments to be either 0.5 or 1. Here we report on the determination of the sticking coefficient of H$_2$, D$_2$, N$_2$, O$_2$, CO, CH$_4$, and CO$_2$ on non-porous amorphous solid water (np-ASW). The sticking coefficient was measured over a wide range of surface temperatures using a highly collimated molecular beam. We showed that the standard way of measuring the sticking coefficient --- the King-Wells method --- leads to the underestimation of trapping events in which there is incomplete energy accommodation of the molecule on the surface. Surface scattering experiments with the use of a pulsed molecular beam are used instead to measure the sticking coefficient. Based on th...

  11. Insight into STM image contrast of n-tetradecane and n-hexadecane molecules on highly oriented pyrolytic graphite

    Science.gov (United States)

    Zhao, Miao; Jiang, Peng; Deng, Ke; Yu, Ai-Fang; Hao, Yan-Zhong; Xie, Si-Shen; Sun, Jie-Lin

    2011-02-01

    Two-dimensional ordered patterns of n-tetradecane (n-C14H30) and n-hexadecane (n-C16H34) molecules at liquid/graphite interface have been directly imaged using scanning tunneling microscope (STM) under ambient conditions. STM images reveal that the two different kinds of molecules self-organize into ordered lamellar structures in which alkane chains of the molecules extend along one of three equivalent lattice axes of highly oriented pyrolytic graphite (HOPG) basal plane. For n-C14H30 molecules, the molecular axes are observed to tilt by 60° with respect to inter-lamellar trough lines and the carbon backbones of the alkane chains are perpendicular to the HOPG basal plane in an all-trans conformation. However, for n-C16H34 molecules, the molecular axes are perpendicular to lamellar borders (90°) and the planes of the all-trans carbon skeletons are parallel to the graphite basal plane. The results clearly indicate that outmost hydrogen atoms of the alkane chains dominate atom-scaled features of the STM images. That is, in the case of long-chain alkane molecules, topographic effects dominantly determine STM image contrast of the methylene regions of the alkane chains that are adsorbed on HOPG.

  12. Distribution of binding energies of a water molecule in the water liquid-vapor interface

    Energy Technology Data Exchange (ETDEWEB)

    Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV

    2008-01-01

    Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

  13. Quantum-state selection, alignment, and orientation of large molecules using static electric and laser fields

    DEFF Research Database (Denmark)

    Filsinger, Frank; Küpper, Jochen; Meijer, Gerard;

    2009-01-01

    Supersonic beams of polar molecules are deflected using inhomogeneous electric fields. The quantum-state selectivity of the deflection is used to spatially separate molecules according to their quantum state. A detailed analysis of the deflection and the obtained quantum-state selection is presen...

  14. Laser-induced 3D alignment and orientation of quantum state-selected molecules

    DEFF Research Database (Denmark)

    Nevo, Iftach; Holmegaard, Lotte; Nielsen, Jens H.;

    2009-01-01

    A strong inhomogeneous static electric field is used to spatially disperse a rotationally cold supersonic beam of 2,6-difluoroiodobenzene molecules according to their rotational quantum state. The molecules in the lowest-lying rotational states are selected and used as targets for 3-dimensional a...

  15. Ultralong-Range Rb-KRb Rydberg Molecules: Selected Aspects of Electronic Structure, Orientation and Alignment

    Science.gov (United States)

    Aguilera-Fernández, Javier; Sadeghpour, H. R.; Schmelcher, Peter; González-Férez, Rosario

    2015-09-01

    We investigate the structure and features of an ultralong-range triatomic Rydberg molecule formed by a Rb Rydberg atom and a KRb diatomic molecule. In our numerical description, we perform a realistic treatment of the internal rotational motion of the diatomic molecule, and take into account the Rb(n, l ≥ 3) Rydberg degenerate manifold and the energetically closest neighboring levels with principal quantum numbers n' > n and orbital quantum number l ≤ 2. We focus here on the adiabatic electronic potentials evolving from the Rb(n,l ≥ 3) and Rb(n = 26, l = 2) manifolds. The directional properties of the KRb diatomic molecule within the Rb-KRb triatomic Rydberg molecule are also analyzed in detail.

  16. Ultralong-Range Rb-KRb Rydberg Molecules: Selected Aspects of Electronic Structure, Orientation and Alignment

    CERN Document Server

    Aguilera-Fernández, Javier; Schmelcher, Peter; González-Férez, Rosario

    2015-01-01

    We investigate the structure and features of an ultralong-range triatomic Rydberg molecule formed by a Rb Rydberg atom and a KRb diatomic molecule. In our numerical description, we perform a realistic treatment of the internal rotational motion of the diatomic molecule, and take into account the Rb($n, l\\ge 3$) Rydberg degenerate manifold and the energetically closest neighboring levels with principal quantum numbers $n'>n$ and orbital quantum number $l\\le2$. We focus here on the adiabatic electronic potentials evolving from the Rb($n, l\\ge 3$) and Rb($n=26, l=2$) manifolds. The directional properties of the KRb diatomic molecule within the Rb-KRb triatomic Rydberg molecule are also analyzed in detail.

  17. Concentration of nitrogen molecules needed by nitrogen nanobubbles existing in bulk water

    Institute of Scientific and Technical Information of China (English)

    张萌; 涂育松; 方海平

    2013-01-01

    This paper investigates the stability of nitrogen nanobubbles under dif-ferent concentrations of nitrogen molecules by molecular dynamics simulations. It is found that the stability of nanobubbles is very sensitive to the concentration of nitrogen molecules in water. A sharp transition between disperse states and assemble states of nitrogen molecules is observed when the concentration of nitrogen molecules is changed. The relevant critical concentration of nitrogen molecules needed by the existing nitrogen nanobubbles is analyzed.

  18. Quantum Tunneling of Water in Beryl: A New State of the Water Molecule.

    Science.gov (United States)

    Kolesnikov, Alexander I; Reiter, George F; Choudhury, Narayani; Prisk, Timothy R; Mamontov, Eugene; Podlesnyak, Andrey; Ehlers, George; Seel, Andrew G; Wesolowski, David J; Anovitz, Lawrence M

    2016-04-22

    Using neutron scattering and ab initio simulations, we document the discovery of a new "quantum tunneling state" of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. In addition, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

  19. Double ionization of the hydrogen sulfide molecule by electron impact: Influence of the target orientation on multiple differential cross sections

    Energy Technology Data Exchange (ETDEWEB)

    Imadouchene, N. [Laboratoire de Mécanique, Structures et Energétique Université Mouloud Mammeri de Tizi-Ouzou, B.P. 17, Tizi-Ouzou 15000 (Algeria); Aouchiche, H., E-mail: h_aouchiche@yahoo.fr [Laboratoire de Mécanique, Structures et Energétique Université Mouloud Mammeri de Tizi-Ouzou, B.P. 17, Tizi-Ouzou 15000 (Algeria); Champion, C. [Centre d’Etudes Nucléaires de Bordeaux Gradignan, Université Bordeaux, CNRS/IN2P3, Boîte Postale 120, Gradignan 33175 (France)

    2016-07-15

    Highlights: • The double ionization of the H{sub 2}S molecule is here theoretically studied. • The orientation dependence of the differential cross sections is scrutinized. • The specific double ionizing mechanisms are clearly identified. - Abstract: Multiple differential cross sections of double ionization of hydrogen sulfide molecule impacted by electrons are here investigated within the first Born approximation. In the initial state, the incident electron is represented by a plane wave function whereas the target is described by means of a single-center molecular wave function. In the final state, the two ejected electrons are described by Coulomb wave functions coupled by the Gamow factor, whereas the scattered electron is described by a plane wave. In this work, we analyze the role played by the molecular target orientation in the double ionization of the four outermost orbitals, namely 2b{sub 1}, 5a{sub 1}, 2b{sub 2} and 4a{sub 1} in considering the particular case of two electrons ejected from the same orbital. The contribution of each final state to the double ionization process is studied in terms of shape and magnitude for specific molecular orientations and for each molecular orbital we identified the mechanisms involved in the double ionization process, namely, the Shake-Off and the Two-Step 1.

  20. Fabrication of novel microstructures based on orientation-dependent adsorption of surfactant molecules in a TMAH solution

    Science.gov (United States)

    Pal, Prem; Sato, K.; Gosalvez, M. A.; Tang, B.; Hida, H.; Shikida, M.

    2011-01-01

    In this work, the orientation-dependent adsorption of surfactant molecules on the silicon surface during etching in surfactant-added tetramethylammonium hydroxide (TMAH) is investigated. Triton X-100 (C14H22O(C2H4O)n, n = 9-10) and 25 wt% TMAH are used as surfactant and main etchant, respectively. The crystallographic planes affected by the surfactant molecules are determined by analyzing the etching behavior of different mask patterns on Si{1 0 0} wafers and silicon hemispheres in pure and surfactant-added TMAH. Taken together, the shapes of the etched profiles and the analysis of the hemispherical etch rates confirm that thick and dense adsorbed surfactant layers are typically formed on both the exact and vicinal Si{1 1 0} surfaces. In addition, the results indicate that the adsorbed surfactant layer behaves as a permeable mask, partially slowing down the etch rate of the affected surface orientation/s and thus enforcing their appearance on the etching front. The peculiar etching properties of surfactant-added and surfactant-free TMAH are then utilized for the fabrication of advanced micromechanical structures with new shapes on Si{1 0 0} wafers and polydimethylsiloxane based on complex Si{1 0 0} molds.

  1. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    Science.gov (United States)

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  2. Imaging Molecular Structure through Femtosecond Photoelectron Diffraction on Aligned and Oriented Gas-Phase Molecules

    CERN Document Server

    Boll, R; Adolph, M; Anielski, D; Aquila, A; Bari, S; Bomme, C; Bostedt, C; Bozek, J D; Chapman, H N; Christensen, L; Coffee, R; Coppola, N; De, S; Decleva, P; Epp, S W; Erk, B; Filsinger, F; Foucar, L; Gorkhover, T; Gumprecht, L; Hoemke, A; Holmegaard, L; Johnsson, P; Kienitz, J S; Kierspel, T; Krasniqi, F; Kuehnel, K -U; Maurer, J; Messerschmidt, M; Moshammer, R; Mueller, Nele L M; Rudek, B; Savelyev, E; Schlichting, I; Schmidt, C; Scholz, F; Schorb, S; Schulz, J; Seltmann, J; Stener, M; Stern, S; Techert, S; Thogersen, J; Trippel, S; Viefhaus, J; Vrakking, M; Stapelfeldt, H; Kuepper, J; Ullrich, J; Rudenko, A; Rolles, D

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray Free-Electron Laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C8H5F) and dissociating, laseraligned 1,4-dibromobenzene (C6H4Br2) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  3. Rapid and accurate prediction and scoring of water molecules in protein binding sites.

    Directory of Open Access Journals (Sweden)

    Gregory A Ross

    Full Text Available Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

  4. The equivalent potential of water molecules for electronic structure of lysine

    Institute of Scientific and Technical Information of China (English)

    LI ChunJie; ZHENG HaoPing; WANG XueMei

    2007-01-01

    In order to get more reliable electronic structures of proteins in aqueous solution,it is necessary to construct a potential of water molecules for protein's electronic structure calculation.The lysine is a hydrophilic amino acid.It is positively charged (Lys+) in neutral water solution.The first-principles,all-electron,ab initio calculations,based on the density functional theory,have been performed to construct such an equivalent potential of water molecules for lysine (Lys+).The process consists of three parts.First,the electronic structure of the cluster containing Lys+ and water molecules is calculated.By adjusting the positions of water molecules,the geometric structure of the cluster having minimum total energy is determined.Then,based on the structure,the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method.Finally,the electronic structure of Lys+ with the potential of dipoles is calculated.The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules.Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained.The major effect of water molecules on lysine's electronic structure is raising the occupied eigenvalues about 0.5032 eV,and broadening energy gap 89%.The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.

  5. The equivalent potential of water molecules for electronic structure of lysine

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In order to get more reliable electronic structures of proteins in aqueous solution, it is necessary to construct a potential of water molecules for protein’s electronic structure calculation. The lysine is a hydrophilic amino acid. It is positively charged (Lys+) in neutral water solution. The first-principles, all-electron, ab initio calcula-tions, based on the density functional theory, have been performed to construct such an equivalent potential of water molecules for lysine (Lys+). The process consists of three parts. First, the electronic structure of the cluster containing Lys+ and water molecules is calculated. By adjusting the positions of water molecules, the geometric structure of the cluster having minimum total energy is determined. Then, based on the structure, the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of Lys+ with the potential of dipoles is calculated. The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained. The major effect of water molecules on lysine’s electronic structure is raising the occupied eigenvalues about 0.5032 eV, and broadening energy gap 89%. The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.

  6. Theoretical description of circular dichroism in photoelectron angular distributions of randomly oriented chiral molecules after multi-photon photoionization

    Science.gov (United States)

    Goetz, R. E.; Isaev, T. A.; Nikoobakht, B.; Berger, R.; Koch, C. P.

    2017-01-01

    Photoelectron circular dichroism refers to the forward/backward asymmetry in the photoelectron angular distribution with respect to the propagation axis of circularly polarized light. It has recently been demonstrated in femtosecond multi-photon photoionization experiments with randomly oriented camphor and fenchone molecules [C. Lux et al., Angew. Chem., Int. Ed. 51, 4755 (2012) and C. S. Lehmann et al., J. Chem. Phys. 139, 234307 (2013)]. A theoretical framework describing this process as (2+1) resonantly enhanced multi-photon ionization is constructed, which consists of two-photon photoselection from randomly oriented molecules and successive one-photon ionization of the photoselected molecules. It combines perturbation theory for the light-matter interaction with ab initio calculations for the two-photon absorption and a single-center expansion of the photoelectron wavefunction in terms of hydrogenic continuum functions. It is verified that the model correctly reproduces the basic symmetry behavior expected under exchange of handedness and light helicity. When applied to fenchone and camphor, semi-quantitative agreement with the experimental data is found, for which a sufficient d wave character of the electronically excited intermediate state is crucial.

  7. Electron capture by bare ions on water molecules

    Science.gov (United States)

    Rivarola, Roberto; Montenegro, Pablo; Monti, Juan; Fojón, Omar

    2016-05-01

    Single electron capture from water molecules by impact of bare ions is theoretically investigated at intermediate and high collision energies. This reaction is of fundamental importance to determine the deposition of energy in biological matter irradiated with ion beams (hadrontherapy), dominating other ionizing processes of the target at low-intermediate impact velocities and giving principal contributions to the energetic region where electronic stopping power maximizes. The dynamics of the interaction between the aggregates is described within the one active-electron continuum distorted wave-eikonal initial state theory. The orbitals of the target in the ground state are represented using the approximate self-consistent complete neglect of differential orbitals (SC-CNDO) model. The contribution of different molecular orbitals on the partial cross sections to selected n-principal quantum number projectile states is discriminated as well as the collaboration of these n-states on total cross sections. The latter ones are dominated by capture to n=1 states at high enough energies decreasing their contribution as n increases.

  8. Theoretical description of the mixed-field orientation of asymmetric-top molecules: A time-dependent study

    Science.gov (United States)

    Omiste, Juan J.; González-Férez, Rosario

    2016-12-01

    We present a theoretical study of the mixed-field-orientation of asymmetric-top molecules in tilted static electric field and nonresonant linearly polarized laser pulse by solving the time-dependent Schrödinger equation. Within this framework, we compute the mixed-field orientation of a state-selected molecular beam of benzonitrile (C7H5N ) and compare with the experimental observations [J. L. Hansen et al., Phys. Rev. A 83, 023406 (2011), 10.1103/PhysRevA.83.023406] and with our previous time-independent descriptions [J. J. Omiste et al., Phys. Chem. Chem. Phys. 13, 18815 (2011), 10.1039/c1cp21195a]. For an excited rotational state, we investigate the field-dressed dynamics for several field configurations as those used in the mixed-field experiments. The nonadiabatic phenomena and their consequences on the rotational dynamics are analyzed in detail.

  9. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules

    OpenAIRE

    Boll, Rebecca; Rouzée, Arnaud; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; Sankar,; Decleva, Piero; Epp, Sascha W.; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Adolph, Marcus; Gumprecht, Lars; Hömke, André

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump–probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C8H5F) and dissociating, laser-aligned 1,4-dibromobenzene (C6H4Br2) molecules and discuss them in the larger context of photoelectron diffrac...

  10. A Services-Oriented Architecture for Water Observations Data

    Science.gov (United States)

    Maidment, D. R.; Zaslavsky, I.; Valentine, D.; Tarboton, D. G.; Whitenack, T.; Whiteaker, T.; Hooper, R.; Kirschtel, D.

    2009-04-01

    Water observations data are time series of measurements made at point locations of water level, flow, and quality and corresponding data for climatic observations at point locations such as gaged precipitation and weather variables. A services-oriented architecture has been built for such information for the United States that has three components: hydrologic information servers, hydrologic information clients, and a centralized metadata cataloging system. These are connected using web services for observations data and metadata defined by an XML-based language called WaterML. A Hydrologic Information Server can be built by storing observations data in a relational database schema in the CUAHSI Observations Data Model, in which case, web services access to the data and metadata is automatically provided by query functions for WaterML that are wrapped around the relational database within a web server. A Hydrologic Information Server can also be constructed by custom-programming an interface to an existing water agency web site so that responds to the same queries by producing data in WaterML as do the CUAHSI Observations Data Model based servers. A Hydrologic Information Client is one which can interpret and ingest WaterML metadata and data. We have two client applications for Excel and ArcGIS and have shown how WaterML web services can be ingested into programming environments such as Matlab and Visual Basic. HIS Central, maintained at the San Diego Supercomputer Center is a repository of observational metadata for WaterML web services which presently indexes 342 million data measured at 1.75 million locations. This is the largest catalog water observational data for the United States presently in existence. As more observation networks join what we term "CUAHSI Water Data Federation", and the system accommodates a growing number of sites, measured parameters, applications, and users, rapid and reliable access to large heterogeneous hydrologic data repositories

  11. Imaging Molecular Structure through Femtosecond Photoelectron Diffraction on Aligned and Oriented Gas-Phase Molecules

    DEFF Research Database (Denmark)

    Boll, Rebecca; Rouzee, Arnaud; Adolph, Marcus

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray Free-Electron Laser. We present results of two experiments aimed at measuring photoelectron angular...

  12. Ionization of oriented carbonyl sulfide molecules by intense circularly polarized laser pulses

    DEFF Research Database (Denmark)

    Dimitrovski, Darko; Abu-Samha, Mahmoud; Madsen, Lars Bojer;

    2011-01-01

    of the molecular electric dipole moment. These findings are explained by a tunneling model invoking the laser-induced Stark shifts associated with the dipoles and polarizabilities of the molecule and its unrelaxed cation. The focus of the present article is to understand the strong-field ionization of one...

  13. Simulations of the flipping images and microparameters of molecular orientations in liquids according to the molecule string model

    Institute of Scientific and Technical Information of China (English)

    Wang Li-Na; Zhao Xing-Yu; Zhang Li-Li; Huang Yi-Neng

    2012-01-01

    The relaxation dynamics of liquids is one of the fundamental problems in liquid physics,and it is also one of the key issues to understand the glass transition mechanism.It will undoubtedly provide enlightenment on understanding and calculating the relaxation dynamics if the molecular orientation flipping images and relevant microparameters of liquids are studied.In this paper,we first give five microparameters to describe the individual molecular string (MS) relaxation based on the dynamical Hamiltonian of the MS model,and then simulate the images of individual MS ensemble,and at the same time calculate the parameters of the equilibrium state.The results show that the main molecular orientation flipping image in liquids (including supercooled liquid) is similar to the random walk.In addition,two pairs of the parameters are equal,and one can be ignored compared with the other.This conclusion will effectively reduce the difficulties in calculating the individual MS relaxation based on the single-molecule orientation flipping rate of the general Glauber type,and the computer simulation time of interaction MS relaxation.Moreover,the conclusion is of reference significance for solving and simulating the multi-state MS model.

  14. Adsorption of Small Molecules at Water--Hexane and Water--Membrane Interfaces

    Science.gov (United States)

    Wilson, Michael A.

    1996-03-01

    The interaction of solutes with aqueous interfaces plays a significant role in a variety of physical processes, including general anesthesia and atmospheric chemistry. We present molecular dynamics results for the transfer of several small solutes across water liquid--vapor, water--hexane and water--GMO bilayer membrane interfaces. (A. Pohorille and M. A. Wilson, J. Chem. Phys. (in press, 1995).)^, (A. Pohorille, P. CIeplak, and M. A. Wilson, Chem. Phys. (in press, 1995).) The free energies of transferring small polar molecules across the interface exhibit fairly deep minima while those of nonpolar molecules do not. This is due to a balance between nonelectrostatic contributions --- primarily the work required to create a cavity large enough to accommodate the solute --- and the solute--solvent electrostatic interactions.^1 The surface excess of solute is calculated and compared with experimental results from the Gibbs adsorption isotherm. The interfacial solubilities correlate with measured anesthetic potencies of these compounds, implying that the binding sites for anesthetics are located near the water--membrane interface.

  15. Competitive Adsorption of Naphthenic Acids and Polyaromatic Molecules at a Toluene-Water Interface.

    Science.gov (United States)

    Teklebrhan, Robel B; Jian, Cuiying; Choi, Phillip; Xu, Zhenghe; Sjöblom, Johan

    2016-12-22

    The early-stage competitive co-adsorption of interfacially active naphthenic acids (NAs) and polyaromatic (PA) molecules to a toluene-water interface from the bulk toluene phase was studied using molecular dynamics (MD) simulation. The NA molecules studied had the same polar functional group but different cycloaliphatic nonpolar tails, and a perylene bisimide (PBI)-based molecule was used as a representative PA compound. The results from our simulations suggest that the size and structural features of NA molecules greatly influence the interfacial activity of PA molecules and partitioning of NA molecules at the toluene-water interface. At low concentrations of PA (∼2.3 wt %) and NA (∼0.4 wt %) molecules, NA molecules containing large cycloaliphatic rings (e.g., four rings) or with a very long aliphatic tail (e.g., carbon chain length of 14) were observed to impede the migration of PA molecules to the interface, whereas small NA molecules containing two cycloaliphatic rings had little effect on the adsorption of PA molecules at the toluene-water interface. At high NA concentrations, the adsorption of PA molecules (∼5.75-17.25 wt %) was greatly hindered by the presence of small NA molecules (∼1.6-4.8 wt %) due to the solvation of PA nanoaggregates in the bulk. Adsorption mechanisms of PA and NA molecules at toluene-water interfaces were clarified through a detailed analysis on the interactions among different species in the system. The results obtained from this work provide insights into designing appropriate chemical demulsifiers or co-demulsifiers for breaking water-in-oil emulsions of great industrial applications.

  16. Subdivision of phase space for anisotropically interacting water molecules

    Science.gov (United States)

    Epifanov, S. Yu.; Vigasin, A. A.

    An efficient numerical algorithm is employed which enables one to perform multidimensional integrations of complicated integrands. Temperature dependence of the second virial coefficient for water is reproduced using the Matsuoka Clementi Yoshimine intermolecular water water potential. Metastable states are shown to occupy significant domain in the water dimer phase space.

  17. Experimental Study of Water Cluster Molecules with Relevance to Mesospheric Clouds

    Science.gov (United States)

    Robertson, Scott; Sternovsky, Zoltan; Horanyi, Mihaly

    2000-10-01

    We have begun an experimental investigation of the properties of the water cluster molecules responsible for clouds occurring in the polar mesopause. These clusters disturb the charge balance in the ionosphere by attaching electrons which then creates localized reductions in the electron density. A supersonic nozzle sprays a mixture of water vapor and argon into vacuum and the expansion leads to condensation of clusters with 4 to 11 water molecules. Initial measurements are of the collision cross section of these molecules with neutral gas. The cross sections have a minimum at six waters consistent with the tighter molecular arrangement predicted for this cluster number. Additional measurements are underway for charging processes.

  18. Molecular orientation and lattice ordering of C60 molecules on the polar FeO/Pt(111) surface

    Science.gov (United States)

    Qin, Zhihui; Liu, Cunding; Chen, Jian; Guo, Qinmin; Yu, Yinghui; Cao, Gengyu

    2012-01-01

    C60 molecules assemble into close packing layer under the domination of the intermolecular interaction when deposited onto Pt(111)-supported FeO layer kept at 400 K. From corresponding high resolution scanning tunneling microscopy (STM) image, a kind of C60 molecular orientational ordering stabilized by the intermolecular interaction is revealed as C60/FeO(111)-(√133 × √133) R17.5° structure and determined from the commensurability between the C60 nearest-neighbor distance and the lattice of the underlying oxygen layer. Moreover, due to the inhomogeneously distributed work function of the underlying FeO layer, the C60 molecular electronic state is periodically modulated resulting in a bright-dim STM contrast. In addition, one coincidence lattice ordering is determined as 8 × 8 superstructure with respect to the C60 primitive cell, which overlays a 3 × 3 moiré cell of the underlying FeO layer.

  19. The DPSIR Framework and a Pressure-Oriented Water Quality Monitoring Approach to Ecological River Restoration

    Directory of Open Access Journals (Sweden)

    Björn Frostell

    2012-09-01

    Full Text Available Without monitoring anthropogenic pressures on the water environment, it is difficult to set realistic river restoration targets in relation to water quality. Therefore a more holistic approach is needed to systematically explore the links between socio-economic drivers and observed water quality-related impacts on river ecosystems. Using the DPSIR (Drivers-Pressures-State of the Environment-Impacts-Responses framework, this study linked ecological river restoration with the socio-economic sector, with the focus on promoting a pressure-oriented water quality monitoring system. Based on the European Water Framework Directive (WFD and relevant literature, it was found that most water quality-related indicators employed today are state/impacts-oriented, while very few are pressure-oriented. As a response, we call for more attention to a DPR (Drivers-Pressures-Responses framework in developing an industrial ecology-based pressure-oriented water quality monitoring system for aiding ecological river restoration planning. This approach is characterized in general by accounting for material-related flows throughout the socio-economic sector in relation to river ecosystem degradation. Then the obtained information would help decision makers take appropriate measures to alleviate various significant human-induced wastes and emissions at their sources. We believe that such a pressure-oriented monitoring system will substantially complement traditional state/impacts-oriented environmental and ecological monitoring and help develop more proactive planning and decision-making processes for specific river restoration projects and general water quality management.

  20. Implication of Crystal Water Molecules in Inhibitor Binding at ALR2 Active Site

    Directory of Open Access Journals (Sweden)

    Hymavati

    2012-01-01

    Full Text Available Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecule. The solvent environment around such biomolecule controls their structure and plays important role in protein-ligand interactions. An understanding of the nature and role of these water molecules in the active site of a protein could greatly increase the efficiency of rational drug design approaches. We have performed the comparative crystal structure analysis of aldose reductase to understand the role of crystal water in protein-ligand interaction. Molecular dynamics simulation has shown the versatile nature of water molecules in bridge H bonding during interaction. Occupancy and life time of water molecules depend on the type of cocrystallized ligand present in the structure. The information may be useful in rational approach to customize the ligand, and thereby longer occupancy and life time for bridge H-bonding.

  1. Coupling between diffusion and orientation of pentacene molecules on an organic surface

    Science.gov (United States)

    Rotter, Paul; Lechner, Barbara A. J.; Morherr, Antonia; Chisnall, David M.; Ward, David J.; Jardine, Andrew P.; Ellis, John; Allison, William; Eckhardt, Bruno; Witte, Gregor

    2016-04-01

    The realization of efficient organic electronic devices requires the controlled preparation of molecular thin films and heterostructures. As top-down structuring methods such as lithography cannot be applied to van der Waals bound materials, surface diffusion becomes a structure-determining factor that requires microscopic understanding. Scanning probe techniques provide atomic resolution, but are limited to observations of slow movements, and therefore constrained to low temperatures. In contrast, the helium-3 spin-echo (HeSE) technique achieves spatial and time resolution on the nm and ps scale, respectively, thus enabling measurements at elevated temperatures. Here we use HeSE to unveil the intricate motion of pentacene admolecules diffusing on a chemisorbed monolayer of pentacene on Cu(110) that serves as a stable, well-ordered organic model surface. We find that pentacene moves along rails parallel and perpendicular to the surface molecules. The experimental data are explained by admolecule rotation that enables a switching between diffusion directions, which extends our molecular level understanding of diffusion in complex organic systems.

  2. First Principles Study on the Interaction Mechanisms of Water Molecules on TiO₂ Nanotubes.

    Science.gov (United States)

    Dai, Jianhong; Song, Yan

    2016-12-16

    The adsorption properties of water molecules on TiO₂ nanotubes (TiO₂NT) and the interaction mechanisms between water molecules are studied by first principles calculations. The adsorption preferences of water molecules in molecular or dissociated states on clean and H-terminated TiO₂NT are evaluated. Adsorption of OH clusters on (0, 6) and (9, 0) TiO₂ nanotubes are first studied. The smallest adsorption energies are -1.163 eV and -1.383 eV, respectively, by examining five different adsorption sites on each type of tube. Eight and six adsorption sites were considered for OH adsorbtion on the H terminated (0, 6) and (9, 0) nanotubes. Water molecules are reformed with the smallest adsorption energy of -4.796 eV on the former and of -5.013 eV on the latter nanotube, respectively. For the adsorption of a single water molecule on TiO₂NT, the molecular state shows the strongest adsorption preference with an adsorption energy of -0.660 eV. The adsorption of multiple (two and three) water molecules on TiO₂NT is also studied. The calculated results show that the interactions between water molecules greatly affect their adsorption properties. Competition occurs between the molecular and dissociated states. The electronic structures are calculated to clarify the interaction mechanisms between water molecules and TiO₂NT. The bonding interactions between H from water and oxygen from TiO₂NT may be the reason for the dissociation of water on TiO₂NT.

  3. Density dependence of hydrogen bonding and the translational-orientational structural order in supercritical water: a molecular dynamics study.

    Science.gov (United States)

    Ma, Haibo; Ma, Jing

    2011-08-07

    Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.

  4. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  5. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  6. Unraveling the Sc(3+) Hydration Geometry: The Strange Case of the Far-Coordinated Water Molecule.

    Science.gov (United States)

    Migliorati, Valentina; D'Angelo, Paola

    2016-07-05

    The hydration structure and dynamics of Sc(3+) in aqueous solution have been investigated using a combined approach based on quantum mechanical (QM) calculations, molecular dynamics (MD) simulations, and extended X-ray absorption fine structure (EXAFS) spectroscopy. An effective Sc-water two-body potential has been generated from QM calculations and then used in the MD simulation of Sc(3+) in water, and the reliability of the entire procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The outstanding outcome of this work is that the Sc(3+) ion forms a well-defined capped square antiprism (SAP) complex in aqueous solution, where the eight water molecules closest to the ion are located at the vertexes of a SAP polyhedron, while the ninth water molecule occupying the capping position is unusually found at a very long distance from the ion. This far-coordinated water molecule possesses a degree of structure comparable with the other first shell molecules surrounding the ion at much shorter distances, and its presence gave us the unique opportunity to easily identify the geometry of the Sc(3+) coordination polyhedron. Despite very strong ion-water interactions, the Sc(3+) hydration shell is very labile, as the far-coordinated ligand allows first shell water molecules to easily exchange their positions both inside the solvation shell and with the rest of the solvent molecules.

  7. Affinity transformation from hydrophilicity to hydrophobicity of water molecules on the basis of adsorption of water in graphitic nanopores.

    Science.gov (United States)

    Ohba, Tomonori; Kanoh, Hirofumi; Kaneko, Katsumi

    2004-02-11

    The interaction of water with hydrophobic surfaces is quite important in a variety of chemical and biochemical phenomena. The coexistence of water and oil can be realized by introduction of surfactants. In the case of water vapor adsorption on graphitic nanopores, plenty of water can be adsorbed in graphitic nanopores without surfactants, although the graphitic surface is not hydrophilic. Why are water molecules adsorbed in hydrophobic nanopores remarkably? This work can give an explicit insight to water adsorption in hydrophobic graphite nanopores using experimental and theoretical approaches. Water molecules are associated with each other to form the cluster of 1 nm in size, leading to a significant stabilization of the cluster in the graphitic nanopores. This mechanism can be widely applied to interfacial phenomena relating to coexistence of water and nanostructural materials of hydrophobicity.

  8. Heterogeneity of the state and functionality of water molecules sorbed in an amorphous sugar matrix.

    Science.gov (United States)

    Imamura, Koreyoshi; Kagotani, Ryo; Nomura, Mayo; Kinugawa, Kohshi; Nakanishi, Kazuhiro

    2012-04-01

    An amorphous matrix, comprised of sugar molecules, is frequently used in the pharmaceutical industry. An amorphous sugar matrix exhibits high hygroscopicity, and it has been established that the sorbed water lowers the glass transition temperature T(g) of the amorphous sugar matrix. It is naturally expected that the random allocation and configuration of sugar molecules would result in heterogeneity of states for sorbed water. However, most analyses of the behavior of water, when sorbed to an amorphous sugar matrix, have implicitly assumed that all of the sorbed water molecules are in a single state. In this study, the states of water molecules sorbed in an amorphous sugar matrix were analyzed by Fourier-transform IR spectroscopy and a Fourier self-deconvolution technique. When sorbed water molecules were classified into five states, according to the extent to which they are restricted, three of the states resulted in a lowering of T(g) of an amorphous sugar matrix, while the other two were independent of the plasticization of the matrix. This finding provides an explanation for the paradoxical fact that compression at several hundreds of MPa significantly decreases the equilibrium water content at a given RH, while the T(g) remains unchanged.

  9. Frictional energy barrier and blocking temperature in water molecules and carbon nanotubes system

    Science.gov (United States)

    Zhang, Jianwei; Li, Jiaxi; Li, Wenfeng

    2015-03-01

    Water transport through hydrophobic channels of single-walled carbon nanotubes has attracted a lot interests, especially, various potential applications of SWCNTs have been proposed for designing novel nanofluidic devices. By adopting Molecular dynamics method, we investigated mechanics and statistics properties of water molecules escaping from a confined single-walled carbon nanotube. From our numerical MD simulations and statistical model, we determined the friction energy barrier of water molecules in (10.10) SWCNT is 9.88 kcal/mol, and which is the minimal energy for flowing a water molecules in CNT. By only using friction energy barrier and relaxation time parameter, our model can fit all different situations MD simulation results. In order to describing the frictional lock behavior of water molecules, we introduced a new blocking temperature, below this temperature (391K for our system), water is locked in CNT due to friction energy barrier. We found that the blocking temperature is closely related to system response time, and it also shows a linear behavior to frictional energy barrier. Furthermore, we found several other interesting statistics results when a water molecules leaving SWCNTs. This work was supported by NSFC No. 11274240 and NO. 51471119.

  10. Quasiphase Transition in a Single File of Water Molecules Encapsulated in (6,5) Carbon Nanotubes Observed by Temperature-Dependent Photoluminescence Spectroscopy

    Science.gov (United States)

    Ma, Xuedan; Cambré, Sofie; Wenseleers, Wim; Doorn, Stephen K.; Htoon, Han

    2017-01-01

    Molecules confined inside single-walled carbon nanotubes (SWCNTs) behave quite differently from their bulk analogues. In this Letter we present temperature-dependent (4.2 K up to room temperature) photoluminescence (PL) spectra of water-filled and empty single-chirality (6,5) SWCNTs. Superimposed on a linear temperature-dependent PL spectral shift of the empty SWCNTs, an additional stepwise PL spectral shift of the water-filled SWCNTs is observed at ˜150 K . With the empty SWCNTs serving as an ideal reference system, we assign this shift to temperature-induced changes occurring in the single-file chain of water molecules encapsulated in the tubes. Our molecular dynamics simulations further support the occurrence of a quasiphase transition of the orientational order of the water dipoles in the single-file chain.

  11. An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.

    Science.gov (United States)

    Debler, Erik W; Müller, Roger; Hilvert, Donald; Wilson, Ian A

    2009-11-03

    Design of catalysts featuring multiple functional groups is a desirable, yet formidable goal. Antibody 13G5, which accelerates the cleavage of unactivated benzisoxazoles, is one of few artificial enzymes that harness an acid and a base to achieve efficient proton transfer. X-ray structures of the Fab-hapten complexes of wild-type 13G5 and active-site variants now afford detailed insights into its mechanism. The parent antibody preorganizes Asp(H35) and Glu(L34) to abstract a proton from substrate and to orient a water molecule for leaving group stabilization, respectively. Remodeling the environment of the hydrogen bond donor with a compensatory network of ordered waters, as seen in the Glu(L34) to alanine mutant, leads to an impressive 10(9)-fold rate acceleration over the nonenzymatic reaction with acetate, illustrating the utility of buried water molecules in bifunctional catalysis. Generalization of these design principles may aid in creation of catalysts for other important chemical transformations.

  12. Influence of Molecular Oxygen on Ortho-Para Conversion of Water Molecules

    Science.gov (United States)

    Valiev, R. R.; Minaev, B. F.

    2017-07-01

    The mechanism of influence of molecular oxygen on the probability of ortho-para conversion of water molecules and its relation to water magnetization are considered within the framework of the concept of paramagnetic spin catalysis. Matrix elements of the hyperfine ortho-para interaction via the Fermi contact mechanism are calculated, as well as the Maliken spin densities on water protons in H2O and O2 collisional complexes. The mechanism of penetration of the electron spin density into the water molecule due to partial spin transfer from paramagnetic oxygen is considered. The probability of ortho-para conversion of the water molecules is estimated by the quantum chemistry methods. The results obtained show that effective ortho-para conversion of the water molecules is possible during the existence of water-oxygen dimers. An external magnetic field affects the ortho-para conversion rate given that the wave functions of nuclear spin sublevels of the water protons are mixed in the complex with oxygen.

  13. Probing the orientations of coordination complex molecules onto the surface of ZnO nanoparticles by means of surface enhanced Raman scattering, UV–vis and DFT methods

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, Om; Gautam, Priyanka; Singh, Ranjan K., E-mail: ranjanksingh65@rediffmail.com

    2015-09-15

    Graphical abstract: - Highlights: • The adsorption geometry of three complex molecules onto the surface of ZnO nanoparticles is investigated by Raman, SERS and UV–vis techniques. • All the three complex molecules are adsorbed in flat-on geometry. • On the adsorption onto the ZnO NPs, the fluorescence background of Raman spectra of Zn complex is quenched. - Abstract: The surface enhanced Raman scattering (SERS) is a highly surface sensitive technique to study inter-surface properties of biological, organic, and inorganic materials. It is a precise technique to determine the adsorption geometry/orientation of the molecules as the intensity enhancement of the SERS bands depends on the adsorption geometry/orientation of molecules on SERS substrate. In the present work, Ni, Cu and Zn complexes of (Z)-N′(1,3,4-thiadiazol-2-yl) acetimidate were synthesized and adsorbed on ZnO nanoparticles. The surface enhanced Raman scattering (SERS), UV–vis and DFT techniques were applied to investigate the possible adsorption geometries of the complexes on ZnO. Consequently, it was found that the orientation of all three complex molecules is flat-on onto the surface of ZnO nanoparticles. The fluorescence background of Raman spectra of Zn complex is quenched and its geometry is isomerized after the adsorption onto the surface of ZnO nanoparticles. The adsorbed Cu complex on ZnO NPs absorbed UV radiations efficiently.

  14. Dynamics of water molecules in the active-site cavity of human cytochromes P450

    DEFF Research Database (Denmark)

    Rydberg, Patrik; Rod, Thomas Holm; Olsen, Lars;

    2007-01-01

    have quite big cavities, with 41 water molecules on average in 2C8 and 54-58 in 2C9 and 3A4, giving a water volume of 1500-2100 A3. The two crystal structures of 2C9 differ quite appreciably, whereas those of 3A4 are quite similar. The active-site cavity is connected to the surroundings by three to six......We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot...

  15. Incipient ferroelectricity of water molecules confined to nano-channels of beryl

    Science.gov (United States)

    Gorshunov, B. P.; Torgashev, V. I.; Zhukova, E. S.; Thomas, V. G.; Belyanchikov, M. A.; Kadlec, C.; Kadlec, F.; Savinov, M.; Ostapchuk, T.; Petzelt, J.; Prokleška, J.; Tomas, P. V.; Pestrjakov, E. V.; Fursenko, D. A.; Shakurov, G. S.; Prokhorov, A. S.; Gorelik, V. S.; Kadyrov, L. S.; Uskov, V. V.; Kremer, R. K.; Dressel, M.

    2016-09-01

    Water is characterized by large molecular electric dipole moments and strong interactions between molecules; however, hydrogen bonds screen the dipole-dipole coupling and suppress the ferroelectric order. The situation changes drastically when water is confined: in this case ordering of the molecular dipoles has been predicted, but never unambiguously detected experimentally. In the present study we place separate H2O molecules in the structural channels of a beryl single crystal so that they are located far enough to prevent hydrogen bonding, but close enough to keep the dipole-dipole interaction, resulting in incipient ferroelectricity in the water molecular subsystem. We observe a ferroelectric soft mode that causes Curie-Weiss behaviour of the static permittivity, which saturates below 10 K due to quantum fluctuations. The ferroelectricity of water molecules may play a key role in the functioning of biological systems and find applications in fuel and memory cells, light emitters and other nanoscale electronic devices.

  16. Incipient ferroelectricity of water molecules confined to nano-channels of beryl.

    Science.gov (United States)

    Gorshunov, B P; Torgashev, V I; Zhukova, E S; Thomas, V G; Belyanchikov, M A; Kadlec, C; Kadlec, F; Savinov, M; Ostapchuk, T; Petzelt, J; Prokleška, J; Tomas, P V; Pestrjakov, E V; Fursenko, D A; Shakurov, G S; Prokhorov, A S; Gorelik, V S; Kadyrov, L S; Uskov, V V; Kremer, R K; Dressel, M

    2016-09-30

    Water is characterized by large molecular electric dipole moments and strong interactions between molecules; however, hydrogen bonds screen the dipole-dipole coupling and suppress the ferroelectric order. The situation changes drastically when water is confined: in this case ordering of the molecular dipoles has been predicted, but never unambiguously detected experimentally. In the present study we place separate H2O molecules in the structural channels of a beryl single crystal so that they are located far enough to prevent hydrogen bonding, but close enough to keep the dipole-dipole interaction, resulting in incipient ferroelectricity in the water molecular subsystem. We observe a ferroelectric soft mode that causes Curie-Weiss behaviour of the static permittivity, which saturates below 10 K due to quantum fluctuations. The ferroelectricity of water molecules may play a key role in the functioning of biological systems and find applications in fuel and memory cells, light emitters and other nanoscale electronic devices.

  17. Quasielastic neutron scattering investigation of motion of water molecules in n-propyl alcohol-water mixture

    OpenAIRE

    Nakada, Masaru; Maruyama, Kenji; Yamamuro, Osamu; MISAWA, Masakatsu

    2009-01-01

    The dynamics of water molecules in the n-propyl alcohol-water mixtures is investigated by using quasielastic neutron scattering measurements. The dynamic structure factor S(Q,E) obtained from incoherent scattering of hydrogen atoms of water is fitted with jump diffusion and relaxing cage models. The diffusion constant obtained from the relaxing cage model, which gives better fitting with S(Q,E), shows better agreement to the experimental value than that of jump diffusion model. The dependence...

  18. Giant pumping of single-file water molecules in a carbon nanotube.

    Science.gov (United States)

    Wang, Y; Zhao, Y J; Huang, J P

    2011-11-17

    Achieving a fast, unidirectional flow of single-file water molecules (UFSWM) across nanochannels is important for membrane-based water purification or seawater desalination. For this purpose, electro-osmosis methods are recognized as a very promising approach and have been extensively discussed in the literature. Utilizing molecular dynamics simulations, here we propose a design for pumping water molecules in a single-walled carbon nanotube in the presence of a linearly gradient electric (GE) field. Such a GE field is inspired by GE fields generated from charged ions located adjacent to biological membrane water nanochannels that can conduct water in and out of cells and can be experimentally achieved by using the charged tip of an atomic force microscope. As a result, the maximum speed of the UFSWM can be 1 or 2 orders of magnitude larger than that in a uniform electric (UE) field. Also, inverse transportation of water molecules does not exist in case of the GE field but can appear for the UE field. Thus, the GE field yields a much more efficient UFSWM than the UE field. The giant pumping ability as revealed is attributed to the nonzero net electrostatic force acting on each water molecule confined in the nanotube. These observations have significance for the design of nanoscale devices for readily achieving controllable UFSWM at high speed.

  19. Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12.

    Science.gov (United States)

    Ueno-Noto, Kaori; Takano, Keiko

    2016-10-05

    Water molecules inside biomolecules constitute integral parts of their structure and participate in the functions of the proteins. Some of the X-ray crystallographic data are insufficient for analyzing a series of ligand-protein complexes in the same condition. We theoretically investigated antibody binding abilities of saccharide ligands and the effects of the inner water molecules of ligand-antibody complexes. Classical molecular dynamics and quantum chemical simulations using a model with possible water molecules inside the protein were performed with saccharide ligands and Human Immunodeficiency Virus 1 neutralizing antibody 2G12 complexes to estimate how inner water molecules of the protein affect the dynamics of the complexes as well as the ligand-antibody interaction. Our results indicate the fact that d-fructose's strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligand's conformation and relative position in the active site. © 2016 Wiley Periodicals, Inc.

  20. Molecules, water, and radiant energy: new clues for the origin of life.

    Science.gov (United States)

    Pollack, Gerald H; Figueroa, Xavier; Zhao, Qing

    2009-03-27

    We here examine the putative first step in the origin of life: the coalescence of dispersed molecules into a more condensed, organized state. Fresh evidence implies that the driving energy for this coalescence may come in a manner more direct than previously thought. The sun's radiant energy separates charge in water, and this free charge demonstrably induces condensation. This condensation mechanism puts water as a central protagonist in life rather than as an incidental participant, and thereby helps explain why life requires water.

  1. Oriented and vectorial immobilization of linear M13 dsDNA between interdigitated electrodes--towards single molecule DNA nanostructures.

    Science.gov (United States)

    Hölzel, Ralph; Gajovic-Eichelmann, Nenad; Bier, Frank F

    2003-05-01

    The ability to control molecules at a resolution well below that offered by photolithography has gained much interest recently. DNA is a promising candidate for this task since it offers excellent specificity in base-pairing combined with addressability at the nanometer scale. New applications in biosensing, e.g. interaction analysis at the single molecule level, or nanobiotechnology, e.g. ultradense DNA microarrays, have been devised that rely on stretched DNA bridges. The basic technology required is the ability to deposit spatially defined, stretched DNA-bridges between anchoring structures on surfaces. In this paper we present two techniques for spanning 2 microm long dsDNA bridges between neighboring interdigitated electrodes (IDEs). The extended DNA used was linearized M13 dsDNA (M13mp18 7231 bp, ca. 2.5 microm length), either unmodified, or with chemical modifications at both ends. The first approach is based on the dielectrophoretic (DEP) concentration and alignment of linearized wild-type dsDNA. IDEs with 1.7 microm spacing are driven with an AC voltage around 1 MHz leading to field strengths in the order of 1 MV m(-1). The dsDNA is polarized and linearized by the force field and accumulates in the gap between two neighboring electrodes. This process is reversible and was visualized by fluorescence staining of M13 DNA using PicoGreen, as intercalating dye. The resulting dsDNA bridges and their orientation are discernible under the fluorescence microscope using fluorescent particles of different color. The particles are tagged with sequence specific peptide nucleic acid (PNA) probes that bind to the DNA double strand at specific sites. The second approach is based on asymmetric electrochemical modification of a gold IDE with 2.0 microm spacings followed by spontaneous or stimulated deposition of a chemically modified M13-DNA. One side of the IDE was selectively coated with streptavidin by electropolymerization of a novel hydrophilic conductive polymer in

  2. Interaction of water molecules with hexagonal 2D systems. A DFT study

    Science.gov (United States)

    Rojas, Ángela; Rey, Rafael

    Over the years water sources have been contaminated with many chemical agents, becoming issues that affect health of the world population. The advances of the nanoscience and nanotechnology in the development new materials constitute an alternative for design molecular filters with great efficiencies and low cost for water treatment and purification. In the nanoscale, the process of filtration or separation of inorganic and organic pollutants from water requires to study interactions of these atoms or molecules with different nano-materials. Specifically, it is necessary to understand the role of these interactions in physical and chemical properties of the nano-materials. In this work, the main interest is to do a theoretical study of interaction between water molecules and 2D graphene-like systems, such as silicene (h-Si) or germanene (h-Ge). Using Density Functional Theory we calculate total energy curves as function of separation between of water molecules and 2D systems. Different spatial configurations of water molecules relative to 2D systems are considered. Structural relaxation effects and changes of electronic charge density also are reported. Universidad Nacional de Colombia.

  3. Nanoscale charge localization induced by random orientations of organic molecules in hybrid perovskite CH3NH3PbI3

    Science.gov (United States)

    Ma, Jie; Wang, Lin-Wang

    2015-03-01

    Perovskite-based solar cells have achieved high solar-energy conversion efficiencies and attracted wide attentions nowadays. Despite the rapid progress in solar-cell devices, many fundamental issues of the hybrid perovskites have not been fully understood. Experimentally, it is well known that in CH3NH3PbI3, the organic molecules CH3NH3 are randomly orientated at the room temperature, but the impact of the random molecular orientation has not been investigated. Using linear-scaling ab-initiomethods, we have calculated the electronic structures of the tetragonal phase of CH3NH3PbI3 with randomly orientated organic molecules in large supercells up to ~20,000 atoms. Due to the dipole moment of the organic molecule, the random orientation creates a novel system with long-range potential fluctuations unlike alloys or other conventional disordered systems. We find that the charge densities of the conduction-band minimum and the valence-band maximum are localized separately in nanoscales due to the potential fluctuations. The charge localization causes electron-hole separation and reduces carrier recombination rates, which may contribute to the long carrier lifetime observed in experiments. We have also proposed a model to explain the charge localization.

  4. Derivative fluorimetry analysis of new cluster structures formed by ethanol and Water molecules

    Institute of Scientific and Technical Information of China (English)

    Bin Wu; Ying Liu; Caiqin Han; Xiaosen Luo; Jian Lu; Xiaowu Ni

    2009-01-01

    The ultraviolet (UV) light excited fluorescence spectra of ethanol-water mixture with different concentra-tions are investigated by derivative fluorimetry. It is found that there are 8 types of luminescent cluster molecules, formed by ethanol and water molecules in different ways, existing in the solution. The peak wavelengths of all these clusters' fluorescence spectra are measured and their contents are obtained by measuring the peak values in the second derivative fluorescence spectra. The spectra corresponding to the 8 types of clusters are obtained by Gaussian decomposition. It is found that two kinds of cluster molecules whose peak wavelengths are 330 and 345 nm have an optimal excitation wavelength located at (236±3) nm. This research contributes to the study of ethanol-water cluster structures and their physical and chemical characteristics.

  5. Depletion of water molecules during ethanol wet-bonding with etch and rinse dental adhesives

    Energy Technology Data Exchange (ETDEWEB)

    Gregoire, Genevieve, E-mail: gregoire@cict.fr [Department of Biomaterials, Faculty of Odontology, University Toulouse III, 31062, Toulouse (France); Sharrock, Patrick [Medical and Spatial Imaging Laboratory, University Toulouse III, Ave. Pompidou, 81104, Castres (France); Delannee, Mathieu [Department of Biomaterials, Faculty of Odontology, University Toulouse III, 31062, Toulouse (France); Delisle, Marie-Bernadette [Faculty of Medicine, University Toulouse III, 31062, Toulouse (France)

    2013-01-01

    The treatment of demineralized dentin with ethanol has been proposed as a way to improve hydrophobic monomer penetration into otherwise water saturated collagen fibrils. The ethanol rinse is expected to preserve the fibrils from collapsing while optimizing resin constituent infiltration for better long term adhesion. The physico-chemical investigations of demineralized dentin confirmed objectively these working hypotheses. Namely, Differential Scanning Calorimetry (DSC) measurements of the melting point of water molecules pointed to the presence of free and bound water states. Unfreezable water was the main type of water remaining following a rinsing step with absolute ethanol. Two different liquid water phases were also observed by Magic Angle Spinning (MAS) solid state Nuclear magnetic Resonance (NMR) spectroscopy. Infrared spectra of ethanol treated specimens illustrated differences with the fully hydrated specimens concerning the polar carbonyl vibrations. Optical microscopy observations as well as scanning electron microscopy showed an improved dentin-adhesive interface with ethanol wet bonding. The results indicate that water can be confined to strongly bound structural molecules when excess water is removed with ethanol prior to adhesive application. This should preserve collagen from hydrolysis upon aging of the hybrid layer. - Highlights: Black-Right-Pointing-Pointer Non-freezable water exists in demineralized dentine. Black-Right-Pointing-Pointer Free water can be removed by ethanol rinse of the demineralized collagen. Black-Right-Pointing-Pointer Ethanol wet bonding leads to a homogeneous hybrid layer free of defects.

  6. Local lateral environment of the molecules at the surface of DMSO-water mixtures

    Science.gov (United States)

    Fábián, Balázs; Idrissi, Abdenacer; Marekha, Bogdan; Jedlovszky, Pál

    2016-10-01

    Molecular dynamics simulations of the liquid-vapour interface of dimethyl sulphoxide (DMSO)-water mixtures of 11 different compositions, including two neat systems are performed on the canonical (N, V, T) ensemble at 298 K. The molecules constituting the surface layer of these systems are selected by means of the identification of the truly interfacial molecules (ITIM) method, and their local lateral environment at the liquid surface is investigated by performing Voronoi analysis. The obtained results reveal that both molecules prefer to be in a mixed local environment, consisting of both kinds of molecules, at the liquid surface, and this preference is even stronger here than in the bulk liquid phase. Neat-like patches, in which a molecule is surrounded by like neighbours, are not found. However, vacancies that are surrounded solely by water molecules are observed at the liquid surface. Our results show that strongly hydrogen bonded DMSO·H2O complexes, known to exist in the bulk phase of these mixtures, are absent from the liquid surface.

  7. Proton transfer in hydrogen-bonded network of phenol molecules: intracluster formation of water.

    Science.gov (United States)

    Lengyel, Jozef; Gorejová, Radka; Herman, Zdeněk; Fárník, Michal

    2013-11-07

    Electron ionization and time-of-flight mass spectrometry was used to investigate the phenol clusters (PhOH)n of different size from single molecule to large clusters: in coexpansion with He, the dimers n = 2 are mostly generated; in Ar, large species of n ≥ 10 also occur. Besides [(PhOH)n](+•) cluster ion series, hydrated phenol cluster ions [(PhOH)n·xH2O](+•) with up to x = 3 water molecules and dehydrated phenol clusters [(PhOH)n-H2O](+•) were observed. The hydrated phenol series exhibits minima and maxima that are interpreted as evidence for proton transfer between the hydrogen bonded cluster ions of cyclic structures. The proton transfer leads to a water generation within the clusters, and subsequent elimination of the diphenyl ether molecule(s) from the cluster yields the hydrated phenol cluster ions. Alternatively, a water molecule release yields a series of dehydrated phenols, among which the diphenyl ether ion [PhOPh](+•) (n = 2) constitutes the maximum.

  8. Collision Dynamics and Solvation of Water Molecules in a Liquid Methanol Film

    CERN Document Server

    Thomson, Erik S; Andersson, Patrik U; Marković, Nikola; Pettersson, Jan B C; 10.1021/jz200929y

    2011-01-01

    Environmental molecular beam experiments are used to examine water interactions with liquid methanol films at temperatures from 170 K to 190 K. We find that water molecules with 0.32 eV incident kinetic energy are efficiently trapped by the liquid methanol. The scattering process is characterized by an efficient loss of energy to surface modes with a minor component of the incident beam that is inelastically scattered. Thermal desorption of water molecules has a well characterized Arrhenius form with an activation energy of 0.47{\\pm}0.11 eV and pre-exponential factor of 4.6 {\\times} 10^(15{\\pm}3) s^(-1). We also observe a temperature dependent incorporation of incident water into the methanol layer. The implication for fundamental studies and environmental applications is that even an alcohol as simple as methanol can exhibit complex and temperature dependent surfactant behavior.

  9. Near-Field Birefringence Response of Liquid Crystal Molecules in Thickness Direction of Liquid Crystal Thin Film Orientated by Shear Force

    Institute of Scientific and Technical Information of China (English)

    Jing QIN; Norihiro UMEDA

    2007-01-01

    Information of molecular orientation in nematic liquid crystal (LC) is attractive and important for applications in the field of display devices. We demonstrate a novel method using a birefringence scanning near-field optical microscope (Bi-SNOM) with a probe which is inserted into the LC thin film to detect the molecular orientation from its birefringence responses in the thickness direction of the LC thin film. The probe is laterally vibrated when going forward into the LC thin film, and the retardation and azimuth angle are recorded as the probe going down. Firstly, the thickness of the LC thin film is measured by the shear force detection. Since the shear force acts as a stimulation to reorientate the LC molecules above the substrate surface, we can detect the molecular orientation caused by a polyimide alignment substrate and the effect to molecular orientation caused by vibration of fibre probe. As a result, the orientation profiling of the LC film in depth direction is obtained in both the cases that the direction of probe vibrating is vertical/parallel to the rubbing direction of the alignment film.Furthermore, the thickness of completely orientated layers just above the substrate surface can also be obtained by either vibrating probe or no-vibrating probe. Ultimately, the LC thin film can be modelled in thickness direction from all the results using this method.

  10. Molecules, Water, and Radiant Energy: New Clues for the Origin of Life

    OpenAIRE

    Qing Zhao; Gerald H. Pollack; Xavier Figueroa

    2009-01-01

    We here examine the putative first step in the origin of life: the coalescence of dispersed molecules into a more condensed, organized state. Fresh evidence implies that the driving energy for this coalescence may come in a manner more direct than previously thought. The sun’s radiant energy separates charge in water, and this free charge demonstrably induces condensation. This condensation mechanism puts water as a central protagonist in life rather than as an incidental participant, and the...

  11. Identification of intrinsic catalytic activity for electrochemical reduction of water molecules to generate hydrogen

    KAUST Repository

    Shinagawa, Tatsuya

    2015-01-01

    Insufficient hydronium ion activities at near-neutral pH and under unbuffered conditions induce diffusion-limited currents for hydrogen evolution, followed by a reaction with water molecules to generate hydrogen at elevated potentials. The observed constant current behaviors at near neutral pH reflect the intrinsic electrocatalytic reactivity of the metal electrodes for water reduction. This journal is © the Owner Societies.

  12. An interpretation of the enhancement of the water dipole moment due to the presence of other water molecules.

    Science.gov (United States)

    Kemp, Daniel D; Gordon, Mark S

    2008-06-05

    The dipole moment of the gas phase water monomer is 1.85 D. When solvated in bulk water, the dipole moment of an individual water molecule is observed to be enhanced to the much larger value of 2.9 +/- 0.6 D. To understand the origin of this dipole moment enhancement, the effective fragment potential (EFP) method is used to solvate an ab initio water molecule to predict the dipole moments for various cluster sizes. The dipole moment as a function of cluster size, nH 2O, is investigated [for n = 6-20 (even n), 26, 32, 41, and 50]. Localized charge distributions are used in conjunction with localized molecular orbitals to interpret the dipole moment enhancement. These calculations suggest that the enhancement of the dipole moment originates from the decrease of the angle between the dipole vectors of the lone pairs on oxygen as the number of hydrogen bonds to that oxygen increases. Thus, the decreased angle, and the consequent increase in water dipole moment, is most likely to occur in environments with a larger number of hydrogen bonds, such as the center of a cluster of water molecules.

  13. Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.

    Science.gov (United States)

    Poornima, C S; Dean, P M

    1995-12-01

    Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of 'binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

  14. Continuum Navier-Stokes modelling of water ow past fullerene molecules

    DEFF Research Database (Denmark)

    Walther, J. H.; Popadic, A.; Koumoutsakos, P.;

    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as ...

  15. Calculating pure rotational transitions of water molecule with a simple Lanczos method

    Indian Academy of Sciences (India)

    Pranab Sarkar

    2001-04-01

    We have calculated pure rotational transitions of water molecule from a kinetic energy operator (KEO) with the -axis perpendicular to the molecular plane. We have used rotational basis functions which are linear combinations of symmetric top functions so that all matrix elements are real. The calculated spectra agree well with the observed values.

  16. Proton Migration in Clusters Consisting of Protonated Pyridine Solvated by Water Molecules.

    Science.gov (United States)

    Berthias, Francis; Feketeová, Linda; Chermette, Henry; Forquet, Valérian; Morell, Christophe; Abdoul-Carime, Hassan; Farizon, Bernadette; Farizon, Michel; Märk, Tilmann D

    2015-10-26

    Proton transfer (PT) from protonated pyridine to water molecules is observed after excitation of microhydrated protonated pyridine (Py) clusters PyH(+) (H2 O)n (n=0-5) is induced by a single collision with an Ar atom at high incident velocity (95×10(3)  m s(-1) ). Besides the fragmentation channel associated with the evaporation of water molecules, the charged-fragment mass spectrum shows competition between the production of the PyH(+) ion (or its corresponding charged fragments) and the production of H(+) (H2 O) or H(+) (H2 O)2 ions. The increase in the production of protonated water fragments as a function of the number of H2 O molecules in the parent cluster ion as well sd the observation of a stable H(+) (H2 O)2 fragment, even in the case of the dissociation of PyH(+) (H2 O)2 , are evidence of the crucial role of PT in the relaxation process, even for a small number of solvating water molecules.

  17. Partition Coefficients of Organic Molecules in Squalane and Water/Ethanol Mixtures by Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Lundsgaard, Rasmus; Kontogeorgis, Georgios; Economou, Ioannis G.

    2011-01-01

    coefficient can be estimated for both a small hydrophilic and a hydrophobic organic molecules between squalane (used here to mimic low density poly ethylene) and water/ethanol solutes using thermodynamic integration to calculate the free energy of solvation. Molecular dynamics simulations are performed, using...

  18. Construction of diverse supramolecular assemblies of dimetal subunits differing in coordinated water molecules via strong hydrogen bonding interactions: Synthesis, crystal structures and spectroscopic properties

    Indian Academy of Sciences (India)

    Sadhika Khullar; Sanjay K Mandal

    2014-09-01

    Three new supramolecular assemblies (constructed through strong hydrogen bonding) of [Co2(bpta)2(adc)(H2O)4](ClO4)2.2H2O (1), [Cu2(bpta)2(fum)(H2O)2](ClO4)2 (2) and [Cu2(bpta)2(tdc)(H2O) (ClO4)](ClO4).3H2O (3), which are synthesised by one pot self-assembly of the metal salt, bpta ligand and the corresponding dicarboxylate under the same reaction conditions, are reported (where adc = acetylene dicarboxylate, fum = fumarate, tdc = 2,5-thiophenedicarboxylate and bpta = N,N'-bis(2-pyridylmethyl)-tertbutylamine). These compounds have varying degrees of coordinatedwater molecules per dimetal subunits (four for 1, two for 2 and one for 3, respectively). Furthermore, the orientation of the coordinated water molecules in 1 and 2, with respect to the mono (carboxylato)-bridged dimetal subunit, is different (cis and trans, respectively). On the other hand, there is a coordinated perchlorate ion in 3 making the two metal centers inequivalent. Unlike 1 and 3, there are no lattice water molecules in 2. This difference in the dimetal subunit in 1-3 and the presence or absence of the lattice water molecules are the keys to forming the diverse supramolecular assemblies. In 1 and 3, the involvement of lattice water molecules in the construction of such assemblies is distinctly different. In case of 2, the formation of supramolecular assembly depends on the coordinated water molecule (trans to each other) and thus a ladder shaped supramolecular assembly is the result. The strength of hydrogen bonding observed in the networks of 1-3 is indicated in the O…O distances (2.596 Å to 3.160 Å) and the OH…O angles 124° to 176°. All are characterised by elemental analysis, FTIR spectroscopy and single crystal X-ray diffraction studies.

  19. Polarisation-dependence of anomalous scattering in brominated DNA and RNA molecules, and importance of crystal orientation in SAD and MAD phasing.

    Energy Technology Data Exchange (ETDEWEB)

    Sanishvili, R.; Besnard, C.; Camus, F.; Fleurant, M.; Pattison, P.; Bricogne, G.; Schiltz, M.; Biosciences Division; Ecole Polytechnique Federale de Lausanne; ESRF; Global Phasing Ltd.

    2007-01-01

    In this paper the anisotropy of anomalous scattering at the Br K-absorption edge in brominated nucleotides is investigated, and it is shown that this effect can give rise to a marked directional dependence of the anomalous signal strength in X-ray diffraction data. This implies that choosing the correct orientation for crystals of such molecules can be a crucial determinant of success or failure when using single- and multiple-wavelength anomalous diffraction (SAD or MAD) methods to solve their structure. In particular, polarized absorption spectra on an oriented crystal of a brominated DNA molecule were measured, and were used to determine the orientation that yields a maximum anomalous signal in the diffraction data. Out of several SAD data sets, only those collected at or near that optimal orientation allowed interpretable electron density maps to be obtained. The findings of this study have implications for instrumental choices in experimental stations at synchrotron beamlines, as well as for the development of data collection strategy programs.

  20. Interactions of carbon nanotubes with the nitromethane-water mixture governing selective adsorption of energetic molecules from aqueous solution.

    Science.gov (United States)

    Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Kang, Ying; Ge, Zhongxue

    2015-03-14

    The structure and dynamics of the nitromethane-water (NM-WT) binary mixture surrounding single walled carbon nanotubes (SWNTs) have been investigated by molecular dynamics simulations. The simulation trajectories show that the NM molecules can be selectively adsorbed both outside the surface and inside the cavity of SWNTs mainly dominated by van der Waals attractions because SWNTs have a higher binding affinity for NM than WT. The binding energies of SWNTs with NM and WT obtained from electronic structure calculations at the M06-2X/6-31+G* level are 15.31 and 5.51 kcal mol(-1), respectively. Compared with the SWNT exterior, the selective adsorption of NM is preferentially occurred in the SWNT interior due to the hydrophobic interactions and the dipole-dipole interactions, which induces the decrease of the hydrogen-bond number of NM with WT and ordered structures of NM with preferred intermolecular orientation in the SWNT cavity. Furthermore, the selective adsorption dynamics of NM from the aqueous solution is regardless of the chirality and radius of SWNTs. The SWNT radius plays a negligible role in the mass density distributions of NM outside the SWNTs, while the mass density of NM in the SWNT interior decreases gradually as the SWNT radius increases. The structural arrangements and intermolecular orientations of NM in the SWNT cavity are greatly dependent on the SWNT radius due to the size effect.

  1. Conserved water molecules in family 1 glycosidases: a DXMS and molecular dynamics study.

    Science.gov (United States)

    Teze, David; Hendrickx, Johann; Dion, Michel; Tellier, Charles; Woods, Virgil L; Tran, Vinh; Sanejouand, Yves-Henri

    2013-08-27

    By taking advantage of the wealth of structural data available for family 1 glycoside hydrolases, a study of the conservation of internal water molecules found in this ubiquitous family of enzymes was undertaken. Strikingly, seven water molecules are observed in more than 90% of the known structures. To gain insight into their possible function, the water dynamics inside Thermus thermophilus β-glycosidase was probed using deuterium exchange mass spectroscopy, allowing the pinpointing of peptide L117-A125, which exchanges most of its amide hydrogens quickly in spite of the fact that it is for the most part buried in the crystal structure. To help interpret this result, a molecular dynamics simulation was performed whose analysis suggests that two water channels are involved in the process. The longest one (∼16 Å) extends between the protein surface and W120, whose side chain interacts with E164 (the acid-base residue involved in the catalytic mechanism), whereas the other channel allows for the exchange with the bulk of the highly conserved water molecules belonging to the hydration shell of D121, a deeply buried residue. Our simulation also shows that another chain of highly conserved water molecules, going from the protein surface to the bottom of the active site cleft close to the nucleophile residue involved in the catalytic mechanism, is able to exchange with the bulk on the nanosecond time scale. It is tempting to speculate that at least one of these three water channels could be involved in the function of family 1 glycoside hydrolases.

  2. Polarization induced water molecule dissociation below the first-order electronic-phase transition temperature.

    Science.gov (United States)

    Das Arulsamy, Andrew; Kregar, Zlatko; Eleršič, Kristina; Modic, Martina; Subramani, Uma Shankar

    2011-09-01

    Hydrogen produced from the photocatalytic splitting of water is one of the reliable alternatives to replace the polluting fossil and the radioactive nuclear fuels. Here, we provide unequivocal evidence for the existence of blue- and red-shifting O-H covalent bonds within a single water molecule adsorbed on the MgO surface as a result of asymmetric displacement polarizabilities. The adsorbed H-O-H on MgO gives rise to one weaker H-O bond, while the other O-H covalent bond from the same adsorbed water molecule compensates this effect with a stronger bond. The weaker bond (nearest to the surface), the interlayer tunneling electrons and the silver substrate are shown to be the causes for the smallest dissociative activation energy on the MgO monolayer. The origin that is responsible to initiate the splitting mechanism is proven to be due to the changes in the polarizability of an adsorbed water molecule, which are further supported by the temperature-dependent static dielectric constant measurements for water below the first-order electronic-phase transition temperature.

  3. Polarization induced water molecule dissociation below the first-order electronic-phase transition temperature

    CERN Document Server

    Arulsamy, Andrew Das; Elersic, Kristina; Modic, Martina; Subramani, Uma Shankar

    2011-01-01

    Hydrogen produced from the photocatalytic splitting of water is one of the reliable alternatives to replace the polluting fossil and the radioactive nuclear fuels. Here, we provide unequivocal evidence for the existence of blue- and red-shifting O$-$H covalent bonds within a single water molecule adsorbed on MgO surface as a result of asymmetric displacement polarizabilities. The adsorbed H-O-H on MgO gives rise to one weaker H-O bond, while the other O-H covalent bond from the same adsorbed water molecule compensates this effect with a stronger bond. The weaker bond (nearest to the surface), the interlayer tunneling electrons and the silver substrate are shown to be the causes for the smallest dissociative activation energy on MgO monolayer. The origin that is responsible to initiate the splitting mechanism is proven to be due to the changes in the polarizability of an adsorbed water molecule, which are further supported by the temperature-dependent static dielectric constant measurements for water below the...

  4. Understanding the role of ions and water molecules in the NaCl dissolution process

    CERN Document Server

    Klimeš, Jiří; Michaelides, Angelos

    2013-01-01

    The dissolution of NaCl in water is one of the most common everyday processes, yet it remains poorly understood at the molecular level. Here we report the results of an extensive density functional theory study in which the initial stages of NaCl dissolution have been examined at low water coverages. Our specific approach is to study how the energetic cost of moving an ion or a pair of ions to a less coordinated site at the surface of various NaCl crystals varies with the number of water molecules adsorbed on the surface. This "microsolvation" approach allows us to study the dependence of the defect energies on the number of water molecules in the cluster and thus to establish when and where dissolution becomes favorable. Moreover, this approach allows us to understand the roles of the individual ions and water molecules in the dissolution process. Consistent with previous work we identify a clear preference for dissolution of Cl ions over Na ions. However, the detailed information obtained here leads to the ...

  5. Neuroscience of water molecules: a salute to professor Linus Carl Pauling.

    Science.gov (United States)

    Nakada, Tsutomu

    2009-04-01

    More than 35 years ago double Nobel laureate Linus Carl Pauling published a powerful model of the molecular mechanism of general anesthesia, generally referred to as the hydrate-microcrystal (aqueous-phase) theory. This hypothesis, based on the molecular behavior of water molecules, did not receive serious attention during Pauling's life time, when scientific tools for examining complex systems such as the brain were still in their infancy. The situation has since drastically changed, and, now, in the twenty first century, many scientific tools are available for examining different types of complex systems. The discovery of aquaporin-4, a subtype of water channel abundantly expressed in glial systems, further highlighted the concept that the dynamics of water molecules in the cerebral cortex play an important role in important physiological brain functions including consciousness and information processing.

  6. Molecules, Water, and Radiant Energy: New Clues for the Origin of Life

    Directory of Open Access Journals (Sweden)

    Qing Zhao

    2009-03-01

    Full Text Available We here examine the putative first step in the origin of life: the coalescence of dispersed molecules into a more condensed, organized state. Fresh evidence implies that the driving energy for this coalescence may come in a manner more direct than previously thought. The sun’s radiant energy separates charge in water, and this free charge demonstrably induces condensation. This condensation mechanism puts water as a central protagonist in life rather than as an incidental participant, and thereby helps explain why life requires water.

  7. Specific Na+ and K+ Cation Effects on the Interfacial Water Molecules at the Air/Aqueous Salt Solution Interfaces Probed with Non-resonant Second Harmonic Generation (SHG)

    CERN Document Server

    Bian, Hong-tao; Guo, Yuan; Wang, Hong-fei

    2008-01-01

    Here we report the polarization dependent non-resonant second harmonic generation (SHG) measurement of the interfacial water molecules at the aqueous solution of the following salts: NaF, NaCl, NaBr, KF, KCl, and KBr. Through quantitative polarization analysis of the SHG data,the orientational parameter D value and the relative surface density of the interfacial water molecules at these aqueous solution surfaces were determined. From these results we found that addition of each of the six salts caused increase of the thickness of the interfacial water layer at the surfaces to a certain extent. Noticeably, both the cations and the anions contributed to the changes, and the abilities to increase the thickness of the interfacial water layer were in the following order: KBr > NaBr > KCl > NaCl ~ NaF > KF. Since these changes can not be factorized into individual anion and cation contributions, there are possible ion pairing or association effects, especially for the NaF case. We also found that the orientational ...

  8. Formation of prebiotic molecules in liquid water environments on the surface of Titan

    Science.gov (United States)

    Neish, Catherine Dorothy

    Saturn's moon Titan represents a unique locale for studying prebiotic chemistry. Reactions occurring in its thick nitrogen-methane atmosphere produce a wide variety of carbon, hydrogen, and nitrogen containing organic molecules. If these molecules are exposed to liquid water, they may react further to produce oxygen-containing species, a key step in the formation of terrestrial biomolecules. On average, Titan's surface is too cold for liquid water. However, models indicate that melting caused by impacts and/or cryovolcanism may lead to its episodic availability. One possible cryovolcanic dome, Ganesa Macula, was identified in early observations by the Cassini spacecraft. In this work, I estimate the height and morphology of this feature using a synthetic aperture radar (SAR) image. I then use a thermal conduction code to calculate the freezing timescale for an initially liquid dome, yielding freezing timescales of ~10^2 - 10^5 years. To determine how far aqueous organic chemistry can proceed in liquid water environments on Titan, I measure the rate coefficients of Titan analogue organic molecules ("tholins") with low temperature aqueous solutions to produce oxygenated species. These reactions display first-order kinetics with half- lives between 0.4 and 7 days at 273 K (in water) and between 0.3 and 14 days at 253 K (in 13 wt. % ammonia-water). Tholin hydrolysis in aqueous solutions is thus very fast compared to the freezing timescales of impact melts and volcanic sites on Titan, which take hundreds to thousands of years to freeze. The fast incorporation of oxygen, along with new chemistry made available by the introduction of ammonia, may lead to the formation of molecules of prebiotic interest in these transient liquid water environments. This chemistry makes impact craters and cryovolcanoes important targets for future missions to Titan.

  9. The role of riparian vegetation density, channel orientation and water velocity in determining river temperature dynamics

    Science.gov (United States)

    Garner, Grace; Malcolm, Iain A.; Sadler, Jonathan P.; Hannah, David M.

    2017-10-01

    A simulation experiment was used to understand the importance of riparian vegetation density, channel orientation and flow velocity for stream energy budgets and river temperature dynamics. Water temperature and meteorological observations were obtained in addition to hemispherical photographs along a ∼1 km reach of the Girnock Burn, a tributary of the Aberdeenshire Dee, Scotland. Data from nine hemispherical images (representing different uniform canopy density scenarios) were used to parameterise a deterministic net radiation model and simulate radiative fluxes. For each vegetation scenario, the effects of eight channel orientations were investigated by changing the position of north at 45° intervals in each hemispheric image. Simulated radiative fluxes and observed turbulent fluxes drove a high-resolution water temperature model of the reach. Simulations were performed under low and high water velocity scenarios. Both velocity scenarios yielded decreases in mean (≥1.6 °C) and maximum (≥3.0 °C) temperature as canopy density increased. Slow-flowing water resided longer within the reach, which enhanced heat accumulation and dissipation, and drove higher maximum and lower minimum temperatures. Intermediate levels of shade produced highly variable energy flux and water temperature dynamics depending on the channel orientation and thus the time of day when the channel was shaded. We demonstrate that in many reaches relatively sparse but strategically located vegetation could produce substantial reductions in maximum temperature and suggest that these criteria are used to inform future river management.

  10. Design and Dynamic Characterization of an Orientation Insensitive Microwave Water-Cut Sensor

    KAUST Repository

    Karimi, Muhammad Akram

    2017-06-12

    Modern reservoir management in oil and gas industry relies on accurate water fraction measurement which is produced as a by-product with oil. This paper presents a novel and contactless water fraction (also known as water-cut) measurement technique which is independent of geometric distribution of oil and water inside the pipe. The sensor is based on a modified T-resonator implemented directly on the pipe\\'s outer surface and whose resonance frequency decreases by increasing the water content in oil. The E-fields have been made to rotate and distribute well inside the pipe, despite having narrow and curved ground plane. It makes the sensor\\'s reading dependent only on the water fraction and not on the mixture distribution inside the pipe. That is why, the presented design does not require any flow conditioner to homogenize the oil/water mixture unlike many commercial water-cut (WC) sensors. The presented sensor has been realized by using extremely low-cost methods of screen printing and reusable 3-D printed mask. Complete characterization of the proposed WC sensor, both in horizontal and vertical orientations, has been carried out in an industrial flow loop. Excellent repeatability of the sensor\\'s response has been observed in \\'dispersed bubble\\' as well as in \\'stratified wavy\\' flow regimes. The performance test of the sensor confirms that the water fraction measurement is independent of the flow pattern, flow rate or orientation. The measured performance results of the sensor show full range accuracy of $± $2%-3% while tested under random orientations and wide range of flow rates.

  11. Rotational excitation of water by hydrogen molecules: comparison of results from classical and quantum mechanics.

    Science.gov (United States)

    Faure, Alexandre; Wiesenfeld, Laurent; Wernli, Michael; Valiron, Pierre

    2006-06-07

    Quasiclassical trajectory calculations are carried out for rotational excitation of water by hydrogen molecules. State-to-state rate coefficients are determined at 100 K and are compared to available quantum results. A good agreement between classical and quantum rates is observed for downward transitions, with an average accuracy of classical results better than a factor of 2. It is thus found that the ambiguities described by Faure and Wiesenfeld [J. Chem. Phys. 121, 6771 (2004)] can be solved in the particular case of waterlike asymmetric-top molecules.

  12. Monte Carlo simulation of several biologically relevant molecules and zwitterions in water

    Science.gov (United States)

    Patuwo, Michael Y.; Bettens, Ryan P. A.

    2012-02-01

    In this work, we study the hydration free energies of butane, zwitterionic alanine, valine, serine, threonine, and asparagine, and two neuraminidase inhibitors by means of Monte Carlo (MC) simulation. The solute molecule, represented in the form of distributed multipoles and modified 6-12 potential, was varied from a non-interacting 'ghost' molecule to its full potential functions in TIP4P water. Intermediate systems with soft-core solute-solvent interaction potentials are simulated separately and then subjected to Bennett's Acceptance ratio (BAR) for the free energy calculation. Hydration shells surrounding the solute particles were used to assess the quality of potential functions.

  13. Structure and orientation changes of omega- and gamma-gliadins at the air-water interface: a PM-IRRAS spectroscopy and Brewster angle microscopy study.

    Science.gov (United States)

    Banc, Amélie; Desbat, Bernard; Renard, Denis; Popineau, Yves; Mangavel, Cécile; Navailles, Laurence

    2007-12-18

    Microscopic and molecular structures of omega- and gamma-gliadin monolayers at the air-water interface were studied under compression by three complementary techniques: compression isotherms, polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and Brewster angle microscopy (BAM). For high molecular areas, gliadin films are homogeneous, and a flat orientation of secondary structures relative to the interface is observed. With increasing compression, the nature and orientation of secondary structures changed to minimize the interfacial area. The gamma-gliadin film is the most stable at the air-water interface; its interfacial volume is constant with increasing compression, contrary to omega-gliadin films whose molecules are forced out of the interface. gamma-Gliadin stability at a high level of compression is interpreted by a stacking model.

  14. Single molecule fluorescence image patterns linked to dipole orientation and axial position: application to myosin cross-bridges in muscle fibers.

    Directory of Open Access Journals (Sweden)

    Thomas P Burghardt

    Full Text Available BACKGROUND: Photoactivatable fluorescent probes developed specifically for single molecule detection extend advantages of single molecule imaging to high probe density regions of cells and tissues. They perform in the native biomolecule environment and have been used to detect both probe position and orientation. METHODS AND FINDINGS: Fluorescence emission from a single photoactivated probe captured in an oil immersion, high numerical aperture objective, produces a spatial pattern on the detector that is a linear combination of 6 independent and distinct spatial basis patterns with weighting coefficients specifying emission dipole orientation. Basis patterns are tabulated for single photoactivated probes labeling myosin cross-bridges in a permeabilized muscle fiber undergoing total internal reflection illumination. Emitter proximity to the glass/aqueous interface at the coverslip implies the dipole near-field and dipole power normalization are significant affecters of the basis patterns. Other characteristics of the basis patterns are contributed by field polarization rotation with transmission through the microscope optics and refraction by the filter set. Pattern recognition utilized the generalized linear model, maximum likelihood fitting, for Poisson distributed uncertainties. This fitting method is more appropriate for treating low signal level photon counting data than χ(2 minimization. CONCLUSIONS: Results indicate that emission dipole orientation is measurable from the intensity image except for the ambiguity under dipole inversion. The advantage over an alternative method comparing two measured polarized emission intensities using an analyzing polarizer is that information in the intensity spatial distribution provides more constraints on fitted parameters and a single image provides all the information needed. Axial distance dependence in the emission pattern is also exploited to measure relative probe position near focus. Single

  15. Field dependence and orientation of upside-down posture in water.

    Science.gov (United States)

    Counil, Lou

    2015-02-01

    Sensory information from the environment is used for body orientation and maintaining posture for effective movement, and the effects of specific senses on orientation and posture can be tested by removing input. In the present study, field dependence was used to evaluate the importance of vision in the perception of verticality when an upside-down posture was adopted under water. Eleven female synchronized swimmers at the French national level were participants. These swimmers were assessed for field dependence and all of them attempted to orient to the vertical with different types of sensory disturbance (eyes closed, opaque goggles, noiseless environment). Kinematic analyses of body inclination were conducted under the different conditions of sensory disturbance. Participants who were more field-dependent aligned their posture more accurately with the gravitational vertical than those who were more field-independent when the tactile afferents from the thighs are blocked.

  16. Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

    KAUST Repository

    Yoon, Seyoon

    2013-01-01

    The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current knowledge of the refined structure. The MD simulations provide detailed information on the position and mobility of the hydrogen and oxygen of interlayer water, as well as its self-diffusion coefficient, through the interlayer of 14 Å tobermorite. Comparison of the MD simulation results at 100 and 300 K demonstrates that water molecules in the interlayer maintain their structure but change their mobility. The dominant configuration and self-diffusion coefficient of interlayer water are obtained in this study. Copyright © 2013 Japan Concrete Institute.

  17. Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation

    KAUST Repository

    Adhikari, Aniruddha

    2016-10-10

    Lipid/water interaction is essential for many biological processes. The water structure at the nonionic lipid interface remains little known, and there is no scope of a priori prediction of water orientation at nonionic interfaces, either. Here, we report our study combining advanced nonlinear spectroscopy and molecular dynamics simulation on the water orientation at the ceramide/water interface. We measured χ spectrum in the OH stretch region of ceramide/isotopically diluted water interface using heterodyne-detected vibrational sum-frequency generation spectroscopy and found that the interfacial water prefers an overall hydrogen-up orientation. Molecular dynamics simulation indicates that this preferred hydrogen-up orientation of water is determined by a delicate balance between hydrogen-up and hydrogen-down orientation induced by lipid-water and intralipid hydrogen bonds. This mechanism also suggests that water orientation at neutral lipid interfaces depends highly on the chemical structure of the lipid headgroup, in contrast to the charged lipid interfaces where the net water orientation is determined solely by the charge of the lipid headgroup.

  18. Parameterization of ammonia and water content of atmospheric droplets with fixed number of sulfuric acid molecules

    Science.gov (United States)

    Napari, I.; Makkonen, R.; Kulmala, M.; Vehkamäki, H.

    2006-12-01

    We present a parameterization for numbers of water and ammonia molecules in an equilibrium droplet with fixed number of sulfuric acid molecules at known relative humidity, ammonia mixing ratio and temperature. The radius of the droplet is also parameterized. The parameterizations are based on macroscopic model of solution droplets and up-to-date thermodynamics. The binary parameterizations are valid for temperatures 190-330 K and relative humidities 1-99%. The ternary parameterization can be used at temperatures 240-300 K, relative humidities 5-95%, and ammonia mixing ratios 10 - 4 -100 ppt. In both cases the parameterizations are valid for droplets containing up to 10 11 sulfuric acid molecules. The droplet composition is always between the limits of pure ammonium bisulfate and pure ammonium sulfate.

  19. Temperature dependence of local solubility of hydrophobic molecules in the liquid-vapor interface of water.

    Science.gov (United States)

    Abe, Kiharu; Sumi, Tomonari; Koga, Kenichiro

    2014-11-14

    One important aspect of the hydrophobic effect is that solubility of small, nonpolar molecules in liquid water decreases with increasing temperature. We investigate here how the characteristic temperature dependence in liquid water persists or changes in the vicinity of the liquid-vapor interface. From the molecular dynamics simulation and the test-particle insertion method, the local solubility Σ of methane in the liquid-vapor interface of water as well as Σ of nonpolar solutes in the interface of simple liquids are calculated as a function of the distance z from the interface. We then examine the temperature dependence of Σ under two conditions: variation of Σ at fixed position z and that at fixed local solvent density around the solute molecule. It is found that the temperature dependence of Σ at fixed z depends on the position z and the system, whereas Σ at fixed local density decreases with increasing temperature for all the model solutions at any fixed density between vapor and liquid phases. The monotonic decrease of Σ under the fixed-density condition in the liquid-vapor interface is in accord with what we know for the solubility of nonpolar molecules in bulk liquid water under the fixed-volume condition but it is much robust since the solvent density to be fixed can be anything between the coexisting vapor and liquid phases. A unique feature found in the water interface is that there is a minimum in the local solubility profile Σ(z) on the liquid side of the interface. We find that with decreasing temperature the minimum of Σ grows and at the same time the first peak in the oscillatory density profile of water develops. It is likely that the minimum of Σ is due to the layering structure of the free interface of water.

  20. Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory

    Science.gov (United States)

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

    2016-09-01

    Thermodynamic properties of water molecules around single- and double-stranded DNAs (ssDNAs and dsDNAs) with different sequences were investigated using grid inhomogeneous solvation theory. Free energies of water molecules solvating the minor groove of dsDNAs are lower than those near ssDNAs, while water molecules should be released during the formation of dsDNA. Free energies of water molecules around dsDNA are lower than those around ssDNA even in the second and third hydration shells. Our findings will help to clarify the role of water molecules in the formation of dsDNA from ssDNAs, thus facilitating the designs of drugs or nanomaterials using DNA.

  1. Water molecule network and active site flexibility of apo protein tyrosine phosphatase 1B

    DEFF Research Database (Denmark)

    Pedersen, A.K.; Peters, Günther H.J.; Møller, K.B.;

    2004-01-01

    Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural information about the structure of PTP1B, including...... the conformation and flexibility of active-site residues as well as the water-molecule network, is a key issue in understanding ligand binding and enzyme kinetics and in structure-based drug design. A 1.95 Angstrom apo PTP1B structure has been obtained, showing four highly coordinated water molecules in the active...... of PTP1B and form a novel basis for structure-based inhibitor design....

  2. Calculation of FDCS for the low and intermediate energy ionization of water molecules

    Science.gov (United States)

    Purohit, G.; Singh, P.; Dom, A.; Patidar, V.

    2015-09-01

    Triply differential cross sections for the electron induced ionization of the 3a1 and 1b1 orbitals of the water molecule are calculated within the distorted wave Born approximation. The distorted wave functions are numerically calculated by modelling both the initial and the final channels whereas single-center Slater type wave functions are used for describing the molecular target. A good agreement with the existing experimental data is obtained.

  3. PERMEABILITY OF STERLET SPERM MEMBRANES (ACIPENSER RUTHENUS L., 1758 FOR WATER MOLECULES

    Directory of Open Access Journals (Sweden)

    A. Puhovkin

    2016-03-01

    Full Text Available Purpose. The literature analysis of the results cryopreservation of different fish species highlights a variation of many parameters, in particular the sperm survival rate during the freezing and unfreezing process. The survival capability of spermatozoa may be called the main parameter, which indentifies the efficiency of the entire process of low temperature freezing of reproductive products. Therefore, the goal of this work was to investigate and find the causes of different degrees of fish sperm cryoimmunity, in particular that of starlet, which is a valuable of sturgeon (Acipenser species. We also studies the possibility to find the optimum ways to improve the efficiency of the survival rate of the defrosted spermatozoa of different fish species for their further use to produce viable offspring. Methodology. The determination of sterlet sperm membrane permeability was performed after carrying out all necessary manipulations with brood males which included: prespawning incubation, hormonal stimulation, determination of sperm maturity degree, obtaining the sperm by stripping. The measurement of sperm membrane permeability for water molecules was performed based on the technique, which had been used earlier to measure carp sperm permeability, but taking account the specific peculiarities inherent to sterlet sperm. Findings. Based on the performed measurements, we determined the sterlet sperm membrane permeability for water molecules with the use of photometric method. The received experimental data show the highest degree of sterlet sperm membrane permeability for water molecules as compared to carp sperm membrane permeability. Originality. As a result of this experiment, we determined for the first time the absolute value of sterlet sperm membrane permeability for water molecules with the use of photometric method as well as compared the results with those obtained during our work with the carp sperm. Practical value. The data obtained during

  4. Diagrammatic perturbation theory applied to the ground state of the water molecule

    Science.gov (United States)

    Silver, D. M.; Wilson, S.

    1977-01-01

    The diagrammatic many-body perturbation theory is applied to the ground state of the water molecule within the algebraic approximation. Using four different basis sets, the total energy, the equilibrium OH bond length, and the equilibrium HOH bond angle are examined. The latter is found to be a particularly sensitive test of the convergence of perturbation expansions. Certain third-order results, which incorporate all two-, three-, and four-body effects, show evidence of good convergence properties.

  5. Mathematical Modeling to Study the Dynamics of A Diatomic Molecule N2 in Water

    CERN Document Server

    Sharma, Nitin

    2010-01-01

    In the present work an attempt has been made to study the dynamics of a diatomic molecule N2 in water. The proposed model consists of Langevin stochastic differential equation whose solution is obtained through Euler's method. The proposed work has been concluded by studying the behavior of statistical parameters like variance in position, variance in velocity and covariance between position and velocity. This model incorporates the important parameters like acceleration, intermolecular force, frictional force and random force.

  6. Investigation of the Hydantoin Monomer and its Interaction with Water Molecules

    Science.gov (United States)

    Gruet, Sébastien; Perez, Cristobal; Schnell, Melanie

    2017-06-01

    Hydantoin (Imidazolidine-2,4-dione, C_3H_4N_2O_2) is a five-membered heterocyclic compound of astrobiological interest. This molecule has been detected in carbonaceous chondrites [1], and its formation can rise from the presence of glycolic acid and urea, two prebiotic molecules [2]. The hydrolysis of hydantoin under acidic conditions can also produce glycine [3], an amino acid actively searched for in the interstellar medium. Spectroscopic data of hydantoin is very limited and mostly dedicated to the solid phase. The high resolution study in gas phase is restricted to the work recently published by Ozeki et al. reporting the pure rotational spectra of the ground state and two vibrational states of the molecule in the millimeter-wave region (90-370 GHz)[4]. Using chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy, we recorded the jet-cooled rotational spectra of hydantoin with water between 2 to 8 GHz. We observed the ground state of hydantoin monomer and several water complexes with one or two water molecules. All the observed species exhibit a hyperfine structure due to the two nitrogen atoms present in the molecule, which were fully resolved and analyzed. Additional experiments with a ^{18}O enriched water sample were realized to determine the oxygen-atom positions of the water monomers. These experiments yielded accurate structural information on the preferred water binding sites. The observed complexes and the interactions that hold them together, mainly strong directional hydrogen bonds, will be presented and discussed. [1] Shimoyama, A. and Ogasawara, R., Orig. Life Evol. Biosph., 32, 165-179, 2002. DOI:10.1023/A:1016015319112. [2] Menor-Salván, C. and Marín-Yaseli, M.R., Chem. Soc. Rev., 41(16), 5404-5415, 2012. DOI:10.1039/c2cs35060b. [3] De Marcellus P., Bertrand M., Nuevo M., Westall F. and Le Sergeant d'Hendecourt L., Astrobiology. 11(9), 847-854, 2011. DOI:10.1089/ast.2011.0677. [4] Ozeki, H., Miyahara R., Ihara H., Todaka S., Kobayashi

  7. Effects of water molecules of Ar-Cs MHD disk generator operated with strong MHD interaction

    Energy Technology Data Exchange (ETDEWEB)

    Ishikawa, M.; Kosugi, A.; Inui, Y.; Kabashima, S.

    1998-07-01

    Effects of water molecule impurity are studied on performance of a disk type MHD generator operated with Ar-Cs weakly ionized plasma. To reveal phenomena for a wide range of operation conditions, time-dependent one-dimensional analyses are carried out, where an up-wind, second order Chakravarthy TVD scheme is applied for the gasdynamics, while a Galerkin FEM is used for the electrodynamics. A simplified model is used for the water molecule impurity, where total effects of nonelastic collision between electrons and water molecules are estimated by the collision loss factor of electrons and also the electron momentum-transfer collision frequency is taken into account. The collision loss factor of electrons and the electron momentum-transfer collision frequency are taken from references, and the loss factor is assumed to be 700 independently of the electron temperature. On the Fuji-1 facilities at Tokyo Institute Technology, Japan, series of experiment A4105 were carried out with the Disk F-4 generator. Ar was heated with the heat-exchanger heated by the natural gas-air combustion and the metal cesium was used as the seeding material, while SCM maintained the magnetic field of 4.7 T at the center of disk and the very strong MHD interaction was realized. The thermal input was about 3 MW, the electrical output was about 500 kW with the enthalpy extraction ratio of about 17%. The numerical analyses have shown that the water molecule enhances the ionization instability at the low voltage loading because of insufficient Joule heating for electrons. The generator performance is degraded and the strong MHD interaction between the unstable plasma and the flow field induces slow and fast moving shock waves, leading to the very complicated flow field. The fast and slow moving shocks collide with each other, merge into a sharp shock moving downward, and then the shock front moves back slightly to maintain the pressure balance, collides again with another weak moving shock, and

  8. Effects of inlet momentum and orientation on the hydraulic performance of water storage tanks

    Science.gov (United States)

    Xavier, Manoel Lucas Machado; Janzen, Johannes Gérson

    2017-09-01

    The influence of inlet momentum and inlet orientation on hydraulic performance of cylindrical water process tanks were investigated using a factorial design strategy. The hydraulic performance of the tanks was assessed with a computational fluid dynamics (CFD) model, which calculated the flow fields and the residence time distribution (RTD). RTDs were used to quantify the tanks hydraulic performance using hydraulic indexes that represent short-circuiting, mixing, and moment. These indexes were later associated with the effluent fraction of disinfectant (inlet and outlet disinfectant ratio). For small depth-to-diameter ratios, the inlet orientation and the inlet momentum were the most important factors regarding the hydraulic indexes and the effluent fraction of disinfectant, respectively. A poor correlation was obtained between the hydraulic indexes and the effluent fraction of disinfectant, indicating that they are not good predictors for water quality. For large depth-to-diameter ratios, the inlet orientation had the most significant effect on both the hydraulic indexes and effluent fraction of disinfectant. The short-circuiting and mixing indexes presented a good correlation with water quality for this case.

  9. Effect of Adsorbed Alcohol Layers on the Behavior of Water Molecules Confined in a Graphene Nanoslit: A Molecular Dynamics Study.

    Science.gov (United States)

    Gao, Qingwei; Zhu, Yudan; Ruan, Yang; Zhang, Yumeng; Zhu, Wei; Lu, Xiaohua; Lu, Linghong

    2017-09-11

    With the rapid development of a two-dimensional (2D) nanomaterial, the confined liquid binary mixture has attracted increasing attention, which has significant potential in membrane separation. Alcohol/water is one of the most common systems in liquid-liquid separation. As one of the most focused systems, recent studies have found that ethanol molecules were preferentially adsorbed on the inner surface of the pore wall and formed an adsorbed ethanol layer under 2D nanoconfinement. To evaluate the effect of the alcohol adsorption layer on the mobility of water molecules, molecular simulations were performed to investigate four types of alcohol/water binary mixtures confined under a 20 Å graphene slit. Residence times of the water molecules covering the alcohol layer were in the order of methanol/water molecules and the surrounding water molecules could induce a small degree of damage to the H-bond network of the water molecules covering the alcohol layer, resulting in the long residence time of the water molecules.

  10. Developing Economic Arrangements for Water Resources Management : The potential of stakeholder oriented Water Valuation

    NARCIS (Netherlands)

    Hermans, L.M.; Halsema, van G.E.; Renault, D.

    2006-01-01

    As water is increasingly recognized as a scarce resource, the use of economic arrangements for water resources management seems increasingly promising. Experiences show that economic arrangements can contribute to a more efficient use of water resources but only if specific conditions are met, relat

  11. Gravitactic orientation of Euglena gracilis – a sensitive endpoint for ecotoxicological assessment of water pollutants

    Directory of Open Access Journals (Sweden)

    Aziz eUllah

    2013-12-01

    Full Text Available Pollution of aquatic environments with natural and anthropogenically produced substances is one of the major environmental problems of the world. In many countries the decreasing quantity of water coupled with its increasing usage in multiple sectors has adversely affected water quality and caused problems of water pollution. Polluted water has been a main cause of adverse effects on plants, animals and humans throughout the world. Physicochemical analysis of water, which is a common method used for quality assessment of water, alone may not be enough as it cannot evaluate the impact on living organisms. Therefore, bioassessment of water and wastewater quality is considered to be essential to reflect the ultimate effects on living organisms. Many organisms like bacteria, algae, fish, invertebrates and protozoan are used as bioassay organisms for assessment of water quality. This review article elucidates the use of Euglena gracilis, a freshwater motile flagellate of the phylum Euglenophyta, as a suitable organism in ecotoxicological studies with special emphasis on its gravitactic orientation as a sensitive end point in ecotoxicological assessment of water pollutants.

  12. Magnetic orientation of nontronite clay in aqueous dispersions and its effect on water diffusion.

    Science.gov (United States)

    Abrahamsson, Christoffer; Nordstierna, Lars; Nordin, Matias; Dvinskikh, Sergey V; Nydén, Magnus

    2015-01-01

    The diffusion rate of water in dilute clay dispersions depends on particle concentration, size, shape, aggregation and water-particle interactions. As nontronite clay particles magnetically align parallel to the magnetic field, directional self-diffusion anisotropy can be created within such dispersion. Here we study water diffusion in exfoliated nontronite clay dispersions by diffusion NMR and time-dependant 1H-NMR-imaging profiles. The dispersion clay concentration was varied between 0.3 and 0.7 vol%. After magnetic alignment of the clay particles in these dispersions a maximum difference of 20% was measured between the parallel and perpendicular self-diffusion coefficients in the dispersion with 0.7 vol% clay. A method was developed to measure water diffusion within the dispersion in the absence of a magnetic field (random clay orientation) as this is not possible with standard diffusion NMR. However, no significant difference in self-diffusion coefficient between random and aligned dispersions could be observed.

  13. Are there Helium-like Protonic States of Individual Water Molecules in Liquid H2O?

    CERN Document Server

    Mueller-Herold, Ulrich

    2015-01-01

    Are there indications that individual H2O molecules in liquid water can loose their bent structure, i.e. that the protons give up their rigid angular correlation and behave largely uncorrelated, similar to electrons in the ground-state of helium? In agreement with the two-state picture of liquid water this would allow for the thermal coexistence of tetraedrically coordinated and spherical water molecules in the liquid. In the Hooke-Calogero model of a confined triatomic of XY2-type it is shown that energetically low-lying zero orbital-momentum states, which are bent if unconfined can change to helium-like shape under increasing confinement strength f. For the respective states this occurs at different values for f. It turns out that at f = 2.79 a bent and a helium-like state can thermally coexist. In order to characterize more precisely 'helium-like' angular correlation a maximum entropy estimate for the marginal correlation of electrons in the helium ground state is given. KEY WORDS: Liquid water, molecular ...

  14. Modeling the Release Kinetics of Poorly Water-Soluble Drug Molecules from Liposomal Nanocarriers

    Directory of Open Access Journals (Sweden)

    Stephan Loew

    2011-01-01

    Full Text Available Liposomes are frequently used as pharmaceutical nanocarriers to deliver poorly water-soluble drugs such as temoporfin, cyclosporine A, amphotericin B, and paclitaxel to their target site. Optimal drug delivery depends on understanding the release kinetics of the drug molecules from the host liposomes during the journey to the target site and at the target site. Transfer of drugs in model systems consisting of donor liposomes and acceptor liposomes is known from experimental work to typically exhibit a first-order kinetics with a simple exponential behavior. In some cases, a fast component in the initial transfer is present, in other cases the transfer is sigmoidal. We present and analyze a theoretical model for the transfer that accounts for two physical mechanisms, collisions between liposomes and diffusion of the drug molecules through the aqueous phase. Starting with the detailed distribution of drug molecules among the individual liposomes, we specify the conditions that lead to an apparent first-order kinetic behavior. We also discuss possible implications on the transfer kinetics of (1 high drug loading of donor liposomes, (2 attractive interactions between drug molecules within the liposomes, and (3 slow transfer of drugs between the inner and outer leaflets of the liposomes.

  15. Modeling the Release Kinetics of Poorly Water-Soluble Drug Molecules from Liposomal Nanocarriers

    Science.gov (United States)

    Loew, Stephan; Fahr, Alfred; May, Sylvio

    2011-01-01

    Liposomes are frequently used as pharmaceutical nanocarriers to deliver poorly water-soluble drugs such as temoporfin, cyclosporine A, amphotericin B, and paclitaxel to their target site. Optimal drug delivery depends on understanding the release kinetics of the drug molecules from the host liposomes during the journey to the target site and at the target site. Transfer of drugs in model systems consisting of donor liposomes and acceptor liposomes is known from experimental work to typically exhibit a first-order kinetics with a simple exponential behavior. In some cases, a fast component in the initial transfer is present, in other cases the transfer is sigmoidal. We present and analyze a theoretical model for the transfer that accounts for two physical mechanisms, collisions between liposomes and diffusion of the drug molecules through the aqueous phase. Starting with the detailed distribution of drug molecules among the individual liposomes, we specify the conditions that lead to an apparent first-order kinetic behavior. We also discuss possible implications on the transfer kinetics of (1) high drug loading of donor liposomes, (2) attractive interactions between drug molecules within the liposomes, and (3) slow transfer of drugs between the inner and outer leaflets of the liposomes. PMID:21773045

  16. Single-Molecule Imaging of DNAs with Sticky Ends at Water/Fused Silica Interface

    Energy Technology Data Exchange (ETDEWEB)

    Isailovic, Slavica [Iowa State Univ., Ames, IA (United States)

    2005-01-01

    Total internal reflection fluorescence microscopy (TIRFM) was used to study intermolecular interactions of DNAs with unpaired (sticky) ends of different lengths at water/fused silica interface at the single-molecule level. Evanescent field residence time, linear velocity and adsorption/desorption frequency were measured in a microchannel for individual DNA molecules from T7, Lambda, and PSP3 phages at various pH values. The longest residence times and the highest adsorption/desorption frequencies at the constant flow at pH 5.5 were found for PSP3 DNA, followed by lower values for Lambda DNA, and the lowest values for T7 DNA. Since T7, Lambda, and PSP3 DNA molecules contain none, twelve and nineteen unpaired bases, respectively, it was concluded that the affinity of DNAs for the surface increases with the length of the sticky ends. This confirms that hydrophobic and hydrogen-bonding interactions between sticky ends and fused-silica surface are driving forces for DNA adsorption at the fused-silica surface. Described single-molecule methodology and results therein can be valuable for investigation of interactions in liquid chromatography, as well as for design of DNA hybridization sensors and drug delivery systems.

  17. Metaphase I orientation of Robertsonian trivalents in the water-hyacinth grasshopper, Cornops aquaticum (Acrididae, Orthoptera

    Directory of Open Access Journals (Sweden)

    Pablo César Colombo

    2009-01-01

    Full Text Available Trivalents resulting from polymorphic Robertsonian rearrangements must have a regular orientation in metaphase I if the polymorphisms are to be maintained. It has been argued that redistribution of proximal and interstitial chiasmata to more distal positions is necessary for a convergent orientation, the only one that produces viable gametes. Cornops aquaticum is a South-American grasshopper that lives and feeds on water-hyacinths, and has three polymorphic Robertsonian rearrangements in its southernmost distribution area in Central Argentina and Uruguay. The orientation of trivalents in metaphase I, the formation of abnormal spermatids and the frequency and position of chiasmata in the trivalents, was analysed in a polymorphic population of C. aquaticus. In this study we observed a correlation between the number of trivalents with the frequency of abnormal spermatids; additionally, the number of chiasmata, especially proximal and interstitial ones, was strongly correlated with the frequency of the linear orientation. Therefore we confirmed our previous assumption, based on other evidence, that the chiasmata redistribution in fusion carriers is essential to the maintenance of the polymorphisms.

  18. Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis.

    Science.gov (United States)

    Koehler, Angela N; Shamji, Alykhan F; Schreiber, Stuart L

    2003-07-16

    Small molecule microarrays were screened to identify a small molecule ligand for Hap3p, a subunit of the yeast Hap2/3/4/5p transcription factor complex. The compound, named haptamide A, was determined to have a KD of 5.03 muM for binding to Hap3p using surface plasmon resonance analysis. Haptamide A also inhibited activation of a GDH1-lacZ reporter gene in a dose-dependent fashion. To explore structure-activity relationships, 11 derivatives of haptamide A were prepared using the same synthetic route that was developed for the original library synthesis. Analysis of dissociation constants and IC50 values for the reporter gene assay revealed a more potent inhibitor, haptamide B, with a KD of 330 nM. Whole-genome transcriptional profiling was used to compare effects of haptamide B with a hap3Delta yeast strain. Treatment with haptamide B, like the deletion mutant, reduced lactate-induced transcription of several genes from wild-type levels. Profiling the genetic "knockout" and the chemical genetic "knockdown" led to the identification of several genes that are regulated by Hap3p under nonfermentative conditions. These results demonstrate that a small molecule discovered using the small molecule microarray binding assay can permeate yeast cells and reach its target transcription factor protein in cells.

  19. Ab Initio Density Functional Theory Investigation of the Interaction between Carbon Nanotubes and Water Molecules during Water Desalination Process

    Directory of Open Access Journals (Sweden)

    Loay A. Elalfy

    2013-01-01

    Full Text Available Density functional theory calculations using B3LYP/3-21G level of theory have been implemented on 6 carbon nanotubes (CNTs structures (3 zigzag and 3 armchair CNTs to study the energetics of the reverse osmosis during water desalination process. Calculations of the band gap, interaction energy, highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity, hardness, and pressure of the system are discussed. The calculations showed that the water molecule that exists inside the CNT is about 2-3 Å away from its wall. The calculations have proven that the zigzag CNTs are more efficient for reverse osmosis water desalination process than armchair CNTs as the reverse osmosis process requires pressure of approximately 200 MPa for armchair CNTs, which is consistent with the values used in molecular dynamics simulations, while that needed when using zigzag CNTs was in the order of 60 MPa.

  20. Dynamical Orientation of Large Molecules on Oxide Surfaces and its Implications for Dye-Sensitized Solar Cells

    KAUST Repository

    Brennan, Thomas P.

    2013-11-12

    A dual experimental-computational approach utilizing near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory-molecular dynamics (DFT-MD) is presented for determining the orientation of a large adsorbate on an oxide substrate. A system of interest in the field of dye-sensitized solar cells is studied: an organic cyanoacrylic acid-based donor-π-acceptor dye (WN1) bound to anatase TiO2. Assessment of nitrogen K-edge NEXAFS spectra is supported by calculations of the electronic structure that indicate energetically discrete transitions associated with the two π systems of the C-N triple bond in the cyanoacrylic acid portion of the dye. Angle-resolved NEXAFS spectra are fitted to determine the orientation of these two orbital systems, and the results indicate an upright orientation of the adsorbed dye, 63 from the TiO2 surface plane. These experimental results are then compared to computational studies of the WN1 dye on an anatase (101) TiO2 slab. The ground state structure obtained from standard DFT optimization is less upright (45 from the surface) than the NEXAFS results. However, DFT-MD simulations, which provide a more realistic depiction of the dye at room temperature, exhibit excellent agreement - within 2 on average - with the angles determined via NEXAFS, demonstrating the importance of accounting for the dynamic nature of adsorbate-substrate interactions and DFT-MD\\'s powerful predictive abilities. © 2013 American Chemical Society.

  1. Interstellar ices as witnesses of star formation: selective deuteration of water and organic molecules unveiled

    CERN Document Server

    Cazaux, S; Spaans, M

    2011-01-01

    The environments where stars are born contain gas and dust grains covered by icy mantles. As the star forms and heats up its surroundings, the ices evaporate which leads to a very complex chemistry with high abundances of deuterated molecules. While formaldehyde and water are both ice constituents, deuterated formaldehyde is very abundant in comets and star forming regions, while deuterated water rarely is. Here, we explain this selective deuteration by following the formation and evolution of the ices as a cloud collapses to form a star. We show that the deuteration of formaldehyde is sensitive to the gas D/H ratio as the cloud undergoes gravitational collapse, while the deuteration of water strongly depends on the dust temperature at the time of ice formation.

  2. Calculations for ion-impact induced ionization and fragmentation of water molecules

    Science.gov (United States)

    Kirchner, Tom; Murakami, Mitsuko; Horbatsch, Marko; Jürgen Lüdde, Hans

    2012-10-01

    Charge-state correlated cross sections for single- and multiple-electron removal processes in proton-water-molecule collisions are calculated by using the non-perturbative basis generator method adapted for ion-molecule collisions [1,2]. A fragmentation model is then applied to calculate the yields of H2O^+, OH^+, H^+, and O^+ ions emerging after H2O^q+ formation [3]. A detailed comparison is made with experimental data from three groups covering the energy range from 20--5000 keV. It is found that multiple electron processes with qMurakami et al, Phys. Rev. A 85, 052704 (2012)[0pt] [3] M. Murakami et al, Phys. Rev. A 85, 052713 (2012)

  3. Covalent immobilization of oriented photosystem II on a nanostructured electrode for solar water oxidation.

    Science.gov (United States)

    Kato, Masaru; Cardona, Tanai; Rutherford, A William; Reisner, Erwin

    2013-07-24

    Photosystem II (PSII) offers a biological and sustainable route of photochemical water oxidation to O2 and can provide protons and electrons for the generation of solar fuels, such as H2. We present a rational strategy to electrostatically improve the orientation of PSII from a thermophilic cyanobacterium, Thermosynechococcus elongatus , on a nanostructured indium tin oxide (ITO) electrode and to covalently immobilize PSII on the electrode. The ITO electrode was modified with a self-assembled monolayer (SAM) of phosphonic acid ITO linkers with a dangling carboxylate moiety. The negatively charged carboxylate attracts the positive dipole on the electron acceptor side of PSII via Coulomb interactions. Covalent attachment of PSII in its electrostatically improved orientation to the SAM-modified ITO electrode was accomplished via an amide bond to further enhance red-light-driven, direct electron transfer and stability of the PSII hybrid photoelectrode.

  4. Influence of the water molecules near surface of viral protein on virus activation process

    Energy Technology Data Exchange (ETDEWEB)

    O, Shepelenko S; S, Salnikov A; V, Rak S; P, Goncharova E; B, Ryzhikov A, E-mail: shep@vector.nsc.r, E-mail: shep@ngs.r [Federal State Research Institution State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-being (FSRI SRC VB VECTOR) Koltsovo, Novosibirsk Region (Russian Federation)

    2009-06-01

    The infection of a cell with influenza virus comprises the stages of receptor binding to the cell membrane, endocytosis of virus particle, and fusion of the virus envelope and cell endosome membrane, which is determined by the conformational changes in hemagglutinin, a virus envelope protein, caused by pH decrease within the endosome. The pH value that induces conformation rearrangements of hemagglutinin molecule considerably varies for different influenza virus strains, first and foremost, due to the differences in amino acid structure of the corresponding proteins. The main goal of this study was to construct a model making it possible to assess the critical pH value characterizing the fusogenic activity of influenza virus hemagglutinin from the data on hemagglutinin structure and experimental verification of this model. Under this model, we assume that when the electrostatic force between interacting hemagglutinin molecules in the virus envelop exceeds a certain value, the hemagglutinin HA1 subunits are arranged so that they form a cavity sufficient for penetration of water molecules. This event leads to an irreversible hydration of the inner fragments of hemagglutinin molecule in a trimer and to the completion of conformational changes. The geometry of electrostatic field in hemagglutinin trimer was calculated taking into account the polarization effects near the interface of two dielectrics, aqueous medium and protein macromolecule. The critical pH values for the conformational changes in hemagglutinin were measured by the erythrocyte hemolysis induced by influenza virus particles when decreasing pH. The critical pH value conditionally separating the pH range into the regions with and without the conformational changes was calculated for several influenza virus H1N1 and H3N2 strains based on the data on the amino acid structure of the corresponding hemagglutinin molecules. Comparison of the theoretical and experimental values of critical pH values for

  5. Label‐Free Fluctuation Spectroscopy Based on Coherent Anti‐Stokes Raman Scattering from Bulk Water Molecules

    OpenAIRE

    Rabasovic, M. D.; Sisamakis, E.; Wennmalm, S.; Widengren, J.

    2016-01-01

    Abstract Nanoparticles (NPs) and molecules can be analyzed by inverse fluorescence correlation spectroscopy (iFCS) as they pass through an open detection volume, displacing fractions of the fluorescence‐emitting solution in which they are dissolved. iFCS does not require the NPs or molecules to be labeled. However, fluorophores in μm–mm concentrations are needed for the solution signal. Here, we instead use coherent anti‐Stokes Raman scattering (CARS) from plain water molecules as the signal ...

  6. Detection of water molecules in inert gas based plasma by the ratios of atomic spectral lines

    Science.gov (United States)

    Bernatskiy, A. V.; Ochkin, V. N.

    2017-01-01

    A new approach is considered to detect the water leaks in inert plasma-forming gas present in the reactor chamber. It is made up of the intensity ratio of D α and H α spectral lines in combination with O, Ar and Xe lines intensity. The concentrations of H2O, O, H and D particles have been measured with high sensitivity. At the D2 admixture pressure {{p}{{\\text{D}\\text{2}}}}   =  0.025 mbar, we used the acquisition time of 10 s to measure the rate of water molecules injected from the outside, Γ0  =  1.4 · 10-9 mbar · m3 · s-1, and the incoming water molecules to plasma, Γ  =  5 ·10-11 mbar · m3 · s-1. The scaling proves that at small D2 admixtures (10-4 mbar), the leaks with the rates Γ0  ≈  6 · 10-12 mbar · m3 · s-1 and Γ  ≈  2 · 10-13 mbar · m3 · s-1 can be detected and measured. The difference between Γ0 and Γ values is due to the high degree of H2O dissociation, which can be up to 97-98%.

  7. The Effect of Water Molecules on Mechanical Properties of Bamboo Microfibrils

    Science.gov (United States)

    Rahbar, Nima

    Bamboo fibers have higher strength-to-weight ratios than steel and concrete. The unique properties of bamboo fibers come from their natural composite structures that comprise mainly cellulose nanofibrils in a matrix of intertwined hemicellulose and lignin called lignin-carbohydrate complex (LCC). Here, we have utilized atomistic simulations to investigate the mechanical properties and mechanisms of interactions between these materials, in the presence of water molecules. Our results suggest that hemicellulose exhibits better mechanical properties and lignin shows greater tendency to adhere to cellulose nanofibrils. Consequently, the role of hemicellulose found to be enhancing the mechanical properties and lignin found to be providing the strength of bamboo fibers. The abundance of Hbonds in hemicellulose chains is responsible for improving the mechanical behavior of LCC. The strong van der Waals forces between lignin molecules and cellulose nanofibrils is responsible for higher adhesion energy between LCC/cellulose nanofibrils. We also found out that the amorphous regions of cellulose nanofibrils is the weakest interface in bamboo Microfibrils. In presence of water, the elastic modulus of lignin increases at low water content (less than 10 NSF CAREER Grant No. 1261284.

  8. Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study

    Science.gov (United States)

    Takahashi, Ohgi; Kirikoshi, Ryota

    2014-01-01

    Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-β-Asp, d-Asp, and d-β-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31 + G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace-Asp-Nme, where Ace = acetyl and Nme = NHCH3). The three water molecules act as catalysts by mediating ‘long-range’ proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.

  9. Water orientation and hydrogen-bond structure at the fluorite/water interface

    CERN Document Server

    Khatib, Rémi; Bonn, Mischa; Perez-Haro, María-José; Gaigeot, Marie-Pierre; Sulpizi1, Marialore

    2016-01-01

    Water in contact with mineral interfaces is important for a variety of different processes. Here, we present a combined theoretical-experimental study which provides a quantitative, molecular-level understanding of the ubiquitous and important flourite-water interface. Our results show that, at low pH, the surface is positively charged, causing a substantial degree of water ordering. The surface charge originates primarily from the dissolution of fluoride ions, rather than from adsorption of protons to the surface. At high pH we observe the presence of Ca-OH species pointing into the water. These OH groups interact remarkably weakly with the surrounding water, and are responsible for the free OH signature in the SFG spectrum, which can be explained from local electronic structure effects. The quantification of the surface termination, near-surface ion distribution and water arrangement is enabled by a combination of advanced phase-resolved Vibrational Sum Frequency Generation spectra of flourite-water interfa...

  10. Continuum Navier-Stokes modelling of water flow past fullerene molecules

    Science.gov (United States)

    Walther, J. H.; Popadic, A.; Koumoutsakos, P.; Praprotnik, M.

    2015-11-01

    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the computational cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.

  11. Water and oxygen induced degradation of small molecule organic solar cells

    DEFF Research Database (Denmark)

    Hermenau, Martin; Riede, Moritz; Leo, Karl

    2011-01-01

    Small molecule organic solar cells were studied with respect to water and oxygen induced degradation by mapping the spatial distribution of reaction products in order to elucidate the degradation patterns and failure mechanisms. The active layers consist of a 30 nm bulk heterojunction formed...... with isotopic labeling using H218O and 18O2 provided information on where and to what extent the atmosphere had reacted with the device. A comparison was made between the use of a humid (oxygen free) atmosphere, a dry oxygen atmosphere, and a dry (oxygen free) nitrogen atmosphere during testing of devices...

  12. Orientation of lizards in a Morris water-maze: roles of the sun compass and the parietal eye.

    Science.gov (United States)

    Foà, Augusto; Basaglia, Francesca; Beltrami, Giulia; Carnacina, Margherita; Moretto, Elisa; Bertolucci, Cristiano

    2009-09-15

    The present study examined for the first time whether a Morris water-maze can be used to explore compass and other orientation mechanisms in the ruin lizard Podarcis sicula. In the open field, during sunny days, lizards were individually trained to swim from the center of the water maze onto a hidden platform (the goal), positioned at the periphery of the maze in a single compass direction. The goal was invisible because it was placed just beneath the water surface and the water was rendered opaque. The results showed that lizards learn to swim directly towards the hidden goal under the sun in the absence of visual feature cues. We further examined whether the observed orientation response would be due to lizards learning the spatial position of the goal relative to the sun's azimuth, i.e. to the use of a time-compensated sun compass. Lizards reaching learning criteria were subjected to 6 h clock-shift (fast or slow), and tested for goal orientation in the Morris water-maze. Results demonstrated that the learned orientation response is mediated by a time-compensated sun compass. Further investigations provided direct evidence that in ruin lizards an intact parietal eye is required to perform goal orientation under the sun inside a Morris water-maze, and that other brain photoreceptors, like the pineal or deep brain photoreceptors, are not involved in orientation.

  13. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    Science.gov (United States)

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

  14. Detection of long-lived bound water molecules in complexes of human dihydrofolate reductase with methotrexate and NADPH.

    Science.gov (United States)

    Meiering, E M; Wagner, G

    1995-03-24

    The locations of long-lived bound water molecules in the binary complex of human dihydrofolate reductase (hDHFR) with methotrexate (MTX) and the ternary complex of hDHFR with MTX and NADPH have been investigated using 15N-resolved, three-dimensional ROESY-HMQC and NOESY-HSQC spectra acquired at 25 degrees C and 8 degrees C. NOEs with NH groups of the protein are detected for five bound water molecules in the binary complex and six bound water molecules in the ternary complex. Inspection of crystal structures of hDHFR reveals that the bound water molecules perform structural and functional roles in the complexes. Two water molecules located outside the active site, WatA and WatB, have similar NOEs in the binary and ternary complexes. These water molecules from multiple hydrogen bonds bridging loops and/or secondary structural elements in crystal structures of hDHFR and so stabilize the tertiary fold of the enzyme. Two water molecules in the active site, WatC and WatD, also have similar NOEs in both complexes. In crystal structures of hDHFR, WatC is involved in MTX binding by forming hydrogen bonds to the ligand and protein, while WatD stabilizes WatC by hydrogen bonding to it and the protein. A third active-site water molecule, WatE, has a markedly stronger NOE in the ternary complex than in the binary complex. Differences in the binding of WatE in the binary and ternary complexes are important for understanding the mechanism of DHFR, since this water molecule is believed to be involved in substrate protonation. Although the increased NOE intensity for WatE could be caused by a change in the position of water molecule, it may also be caused by an increase in its lifetime, since structural fluctuations in the active site are decreased upon cofactor binding. NOEs for one other water molecule, WatF, may be observed in the ternary complex but not the binary complex. WatF forms hydrogen bonds bridging the cofactor and the protein in crystal structures of hDHFR.

  15. Explicit Consideration of Water Molecules to Study Vibrational Circular DICHROÎSM of Monosaccharide's

    Science.gov (United States)

    Moussi, Sofiane; Ouamerali, Ourida

    2014-06-01

    Carbohydrates have multiples roles in biological systems. It has been found that the glycoside bond is fundamentally important in many aspects of chemistry and biology and forms the basis of carbohydrate chemistry. That means the stereochemical information, namely, glycosidic linkages α or β, gives an significant features of the carbohydrate glycosidation position of the glycosylic acceptor. For these reasons, much effort was made for the synthesis and analysis of the glycoside bond. Vibrational circular dichroism VCD has some advantages over conventional electronic circular dichroism (ECD) due to the applicability to all organic molecules and the reliability of ab initio quantum calculation. However, for a molecule with many chiral centers such as carbohydrates, determination of the absolute configuration tends to be difficult because the information from each stereochemical center is mixed and averaged over the spectrum. In the CH stretching region, only two VCD studies on carbohydrates have been reported and spectra--structure correlation, as determined for the glycoside band, remains to be investigated. T. Taniguchi and collaborators report that methyl glycosides exhibit a characteristic VCD peak, the sign of which solely reflects the C-1 absolute configuration. This work is a theoretical contribution to study the behaviour of VCD spectrum's of the monosaccharides when the water molecules are taken explicitly. This study is focused on six different monosaccharides in theirs absolute configuration R and S. We used the method of density functional theory DFT by means of the B3LYP hybrid functional and 6-31G * basis set.

  16. Effects of a Single Water Molecule on the Reaction Barrier of Interstellar CO2 Formation Reaction.

    Science.gov (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-08-25

    The mechanism by which CO2 is formed in the interstellar space remains a mystery. The most likely reaction is collision between CO and OH; however, previous theoretical works have shown that the activation barrier for CO2 formation is high enough to prevent the reaction at the low thermal conditions of space (∼10 K). The effects of single water molecule on the reaction barrier of CO2 formation from reaction between CO and OH have been investigated here by means of ab initio calculation. The barrier height along the lowest-energy pathway in the reaction between CO and OH in the absence of the H2O molecule was calculated to be 2.3 kcal/mol when CCSD(T) energy corrections are combined with the MP2 basis set limit. In the case of the hydrated (H2O-CO-OH) system, the inclusion of a single H2O molecule into the system significantly decreased the barrier height to 0.2 kcal/mol. This suggests that CO2 can be formed when CO and OH react in the presence of H2O, even under thermal conditions as low as 10 K.

  17. Energy deposition model based on electron scattering cross section data from water molecules

    Energy Technology Data Exchange (ETDEWEB)

    Munoz, A; Oiler, J C [Centra de Investigaciones Energeticas, Medioambientales y Tecnologicas (CIEMAT), Avenida Complutense 22, 28040 Madrid (Spain); Blanco, F [Departamento de Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid, Avenida Complutense s.n., 28040 Madrid (Spain); Gorfinkiel, J D [Department of Physiscs and Astronomy, The Open University, Walton Hall, Milton Keynes MK7 6AA (United Kingdom); Limao-Vieira, P [Departamento de Fisica, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Maira-Vidal, A; Borge, M J G; Tengblad, O [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas (CSIC), Serrano 113-bis, 28006 Madrid, Spam (Spain); Huerga, C; Tellez, M [Hospital Universitario La Paz, paseo de la Castellana 261, 28046 Madrid (Spain); Garcia, G [Instituto de Matematicas y Fisica Fundamental, Consejo Superior de Investigaciones CientifIcas (CSIC), Serrano 113-bis, 28006 Madrid (Spain)], E-mail: g.garcia@imaff.cfmac.csic.es

    2008-10-01

    A complete set of electrons scattering cross sections by water molecules over a broad energy range, from the me V to the Me V ranges, is presented in this study. These data have been obtained by combining experiments and calculations and cover most relevant processes, both elastic and inelastic, which can take place in the considered energy range. A new Monte Carlo simulation programme has been developed using as input parameter these cross sectional data as well as experimental energy loss spectra. The simulation procedure has been applied to obtain electron tracks and energy deposition plots in water when irradiated by a Ru-106 plaque as those used for brachytherapy of ocular tumours. Finally, the low energy electron tracks provided by the present model have been compared with those obtained with other codes available in the literature.

  18. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhigang [Wayne State Univ., Detroit, MI (United States); Case Western Reserve Univ., Cleveland, OH (United States); Harbor Hospital Baltimore, MD (United States); Wang, Yong [Wayne State Univ., Detroit, MI (United States); Yedidi, Ravikiran S. [Wayne State Univ., Detroit, MI (United States); National Institutes of Health, Bethesda, MD (United States); Dewdney, Tamaria G. [Wayne State Univ., Detroit, MI (United States); Reiter, Samuel J. [Wayne State Univ., Detroit, MI (United States); Brunzelle, Joseph S. [Northwestern Univ. Feinberg School of Medicine, Chicago, IL (United States); Kovari, Iulia A. [Wayne State Univ., Detroit, MI (United States); Kovari, Ladislau C. [Wayne State Univ., Detroit, MI (United States)

    2012-12-19

    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  19. Permeation of oxygen, water vapor, and limonene through printed and unprinted biaxially oriented polypropylene films.

    Science.gov (United States)

    Rubino, M; Tung, M A; Yada, S; Britt, I J

    2001-06-01

    Oriented polypropylene (OPP) and coated OPP (acrylic/OPP/PVDC) films were printed with two commercially available inks to investigate the influence of inks on water vapor and oxygen transmission rates. The permeation of an aroma compound (d-limonene) through coated OPP film printed with these inks was also evaluated at 35 degrees C and 100% relative humidity. The water vapor transmission rate increased significantly through OPP film printed with nitrocellulose-based ink. The oxygen transmission rate was significantly lower through both OPP and coated OPP films printed with the nitrocellulose ink. The effect of inks on limonene permeation was minor compared to the marked increase in permeation measured when the PVDC side of the coated film was exposed to the aroma, compared to the acrylic side. Scanning electron micrographs of coated film cross sections revealed changes in film structure upon exposure to limonene vapors, which were most pronounced when the PVDC side was exposed to limonene.

  20. Motivational orientation of persons managing community water supply and sanitation programmes: An empirical study.

    Directory of Open Access Journals (Sweden)

    Hayford Benjamin Kwashie

    2010-04-01

    Full Text Available This paper reports on an investigation into factors that determined the decisions of members of Water and Sanitation (Watsan Committees to participate in and commit themselves to management activities that would ensure the sustainability of water supply and sanitation programmes in their communities.The major finding was that the motivational orientation of the Watsan members was gradually shifting from purely normative to remunerative values. It implies that their continued membership and willingness to perform their management tasks satisfactorily, in future, would depend on how much satisfaction they derived from being members. These motivational factors are essential if the participation and commitment of local organizations to the entire programme management process is to be guaranteed.

  1. Finite-bias electronic transport of molecules in a water solution

    KAUST Repository

    Rungger, Ivan

    2010-06-04

    The effects of water wetting conditions on the transport properties of molecular nanojunctions are investigated theoretically by using a combination of empirical-potential molecular-dynamics and first-principles electronic-transport calculations. These are at the level of the nonequilibrium Green’s-function method implemented for self-interaction corrected density-functional theory. We find that water effectively produces electrostatic gating to the molecular junction with a gating potential determined by the time-averaged water dipole field. Such a field is large for the polar benzene-dithiol molecule, resulting in a transmission spectrum shifted by about 0.6 eV with respect to that of the dry junction. The situation is drastically different for carbon nanotubes (CNTs). In fact, because of their hydrophobic nature the gating is almost negligible so that the average transmission spectrum of wet Au/CNT/Au junctions is essentially the same as that in dry conditions. This suggests that CNTs can be used as molecular interconnects also in water-wet situations, for instance, as tips for scanning tunnel microscopy in solution or in biological sensors.

  2. [Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

    Science.gov (United States)

    Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

    2013-01-01

    To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

  3. Cation effects on rotational dynamics of anions and water molecules in alkali (Li+, Na+, K+, Cs+) thiocyanate (SCN-) aqueous solutions.

    Science.gov (United States)

    Bian, Hongtao; Chen, Hailong; Zhang, Qiang; Li, Jiebo; Wen, Xiewen; Zhuang, Wei; Zheng, Junrong

    2013-07-03

    Waiting time dependent rotational anisotropies of SCN(-) anions and water molecules in alkali thiocyanate (XSCN, X = Li, Na, K, Cs) aqueous solutions at various concentrations were measured with ultrafast infrared spectroscopy. It was found that cations can significantly affect the reorientational motions of both water molecules and SCN(-) anions. The dynamics are slower in a solution with a smaller cation. The reorientational time constants follow the order of Li(+) > Na(+) > K(+) ~/= Cs(+). The changes of rotational time constants of SCN(-) at various concentrations scale almost linearly with the changes of solution viscosity, but those of water molecules do not. In addition, the concentration-dependent amplitudes of dynamical changes are much more significant in the Li(+) and Na(+) solutions than those in the K(+) and Cs(+) solutions. Further investigations on the systems with the ultrafast vibrational energy exchange method and molecular dynamics simulations provide an explanation for the observations: the observed rotational dynamics are the balanced results of ion clustering and cation/anion/water direct interactions. In all the solutions at high concentrations (>5 M), substantial amounts of ions form clusters. The structural inhomogeneity in the solutions leads to distinct rotational dynamics of water and anions. The strong interactions of Li(+) and Na(+) because of their relatively large charge densities with water molecules and SCN(-) anions, in addition to the likely geometric confinements because of ion clustering, substantially slow down the rotations of SCN(-) anions and water molecules inside the ion clusters. The interactions of K(+) and Cs(+) with water or SCN(-) are much weaker. The rotations of water molecules inside ion clusters of K(+) and Cs(+) solutions are not significantly different from those of other water species so that the experimentally observed rotational relaxation dynamics are only slightly affected by the ion concentrations.

  4. Phase transition study of confined water molecules inside carbon nanotubes: hierarchical multiscale method from molecular dynamics simulation to ab initio calculation.

    Science.gov (United States)

    Javadian, Soheila; Taghavi, Fariba; Yari, Faramarz; Hashemianzadeh, Seyed Majid

    2012-09-01

    In this study, the mechanism of the temperature-dependent phase transition of confined water inside a (9,9) single-walled carbon nanotube (SWCNT) was studied using the hierarchical multi-scale modeling techniques of molecular dynamics (MD) and density functional theory (DFT). The MD calculations verify the formation of hexagonal ice nanotubes at the phase transition temperature T(c)=275K by a sharp change in the location of the oxygen atoms inside the SWCNT. Natural bond orbital (NBO) analysis provides evidence of considerable intermolecular charge transfer during the phase transition and verifies that the ice nanotube contains two different forms of hydrogen bonding due to confinement. Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) analyses were used to demonstrate the fundamental influence of intermolecular hydrogen bonding interactions on the formation and electronic structure of ice nanotubes. In addition, the NQR analysis revealed that the rearrangement of nano-confined water molecules during the phase transition could be detected directly by the orientation of ¹⁷O atom EFG tensor components related to the molecular frame axes. The effects of nanoscale confinements in ice nanotubes and water clusters were analyzed by experimentally observable NMR and NQR parameters. These findings showed a close relationship between the phase behavior and orientation of the electronic structure in nanoscale structures and demonstrate the usefulness of NBO and NQR parameters for detecting phase transition phenomena in nanoscale confining environments.

  5. Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2.

    Science.gov (United States)

    Modesto-Costa, Lucas; Uhl, Elmar; Borges, Itamar

    2015-11-15

    The first three valence transitions of the two nitromethane conformers (CH3NO2) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas-phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor-like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S-QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry-adapted-cluster CI (SAC-CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic-diagrammatic construction (ADC(2)) electronic structure methods were used. Gas-phase CASPT2, SAC-CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC-CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S-QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S-QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S-QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment.

  6. Molecular dynamics simulations of trehalose as a 'dynamic reducer' for solvent water molecules in the hydration shell.

    Science.gov (United States)

    Choi, Youngjin; Cho, Kum Won; Jeong, Karpjoo; Jung, Seunho

    2006-06-12

    Systematic computational work for a series of 13 disaccharides was performed to provide an atomic-level insight of unique biochemical role of the alpha,alpha-(1-->1)-linked glucopyranoside dimer over the other glycosidically linked sugars. Superior osmotic and cryoprotective abilities of trehalose were explained on the basis of conformational and hydration characteristics of the trehalose molecule. Analyses of the hydration number and radial distribution function of solvent water molecules showed that there was very little hydration adjacent to the glycosidic oxygen of trehalose and that the dynamic conformation of trehalose was less flexible than any of the other sugars due to this anisotropic hydration. The remarkable conformational rigidity that allowed trehalose to act as a sugar template was required for stable interactions with hydrogen-bonded water molecules. Trehalose made an average of 2.8 long-lived hydrogen bonds per each MD step, which was much larger than the average of 2.1 for the other sugars. The stable hydrogen-bond network is derived from the formation of long-lived water bridges at the expense of decreasing the dynamics of the water molecules. Evidence for this dynamic reduction of water by trehalose was also established based on each of the lowest translational diffusion coefficients and the lowest intermolecular coulombic energy of the water molecules around trehalose. Overall results indicate that trehalose functions as a 'dynamic reducer' for solvent water molecules based on its anisotropic hydration and conformational rigidity, suggesting that macroscopic solvent properties could be modulated by changes in the type of glycosidic linkages in sugar molecules.

  7. Rotations and vibrations of water molecule inside the fullerene cage: infrared study of H2O@C60

    Science.gov (United States)

    Room, Toomas; Shugai, A.; Nagel, U.; Mamone, S.; Krachmalnicoff, A.; Whitby, R. J.; Levitt, M. H.; Nishida, T.; Murata, Y.; Lei, Xuegong; Li, Yongjun; Turro, N. J.

    2015-03-01

    Water is the second molecule after hydrogen what has been trapped inside the cage of a C60 molecule by the molucular surgery method. We studied isolated water molecule isotopologs H2O, D2O, and HDO in the solid phase at cryogenic temperatures using IR spectroscopy. The water molecule rotation transitions were observed in the THz and vibration-rotation transitions in the mid-IR range. The slow conversion between para and ortho water allowed us to record the time evolution of spectra and to separate ortho and para absorption lines of water. The similarity of the rotation spectrum of caged water to water in the gas phase indicates that water is free to rotate in the C60 cage even at temperature as low as 3 K. However, spectral lines show a splitting of about 0.5 meV what is not compatible with the icosahedral symmetry of C60. Different models (e.g. crystal field effects in solid C60, C60 cage distortions) will be discussed. This work was supported by institutional research funding IUT23-3 of the Estonian Ministry of Education and Research.

  8. Rate-Enhancing Roles of Water Molecules in Methyltrioxorhenium-Catalyzed Olefin Epoxidation by Hydrogen Peroxide.

    Science.gov (United States)

    Goldsmith, Bryan R; Hwang, Taeho; Seritan, Stefan; Peters, Baron; Scott, Susannah L

    2015-08-01

    Olefin epoxidation catalyzed by methyltrioxorhenium (MTO, CH3ReO3) is strongly accelerated in the presence of H2O. The participation of H2O in each of the elementary steps of the catalytic cycle, involving the formation of the peroxo complexes (CH3ReO2(η(2)-O2), A, and CH3ReO(η(2)-O2)2(H2O), B), as well as in their subsequent epoxidation of cyclohexene, was examined in aqueous acetonitrile. Experimental measurements demonstrate that the epoxidation steps exhibit only weak [H2O] dependence, attributed by DFT calculations to hydrogen bonding between uncoordinated H2O and a peroxo ligand. The primary cause of the observed H2O acceleration is the strong co-catalytic effect of water on the rates at which A and B are regenerated and consequently on the relative abundances of the three interconverting Re-containing species at steady state. Proton transfer from weakly coordinated H2O2 to the oxo ligands of MTO and A, resulting in peroxo complex formation, is directly mediated by solvent H2O molecules. Computed activation parameters and kinetic isotope effects, in combination with proton-inventory experiments, suggest a proton shuttle involving one or (most favorably) two H2O molecules in the key ligand-exchange steps to form A and B from MTO and A, respectively.

  9. Electron impact ionization of water molecules in ice and liquid phases

    Energy Technology Data Exchange (ETDEWEB)

    Joshipura, K N [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120 (India); Gangopadhyay, Sumona [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120 (India); Limbachiya, C G [P S Science College, Kadi (N.G.) 382 715 (India); Vinodkumar, Minaxi [V P and R P T P Science College, Vallabh Vidyanagar-388 120 (India)

    2007-09-15

    Electron scattering processes in ice or water are known to occur in natural as well as man-made systems. But the processes are difficult to investigate in theory or in laboratory. We present our calculations on total ionization cross section (Q{sub ion}) for collisions of electrons with H{sub 2}O molecules in condensed matter (ice and liquid) forms, at impact energies from ionization threshold to 1000 eV, extendable to about 1 MeV. Our theoretical method determines the total inelastic cross section (Q{sub inel}) of electron impact on H{sub 2}O (ice), by starting with the complex scattering potential partial wave formalism. Reasonable approximations are invoked to project out the ionization cross section of H{sub 2}O molecule in ice (or liquid) form by using the Q{sub inel} as an input. Properties of the condensed phase H{sub 2}O are incorporated together with bulk screening effects in the scattering echanism. Due to medium effects, the present Q{sub ion} are found to be lower than the corresponding values for H{sub 2}O in free or gaseous state. Macroscopic cross sections and electron mean free paths for the bulk medium are also calculated. This study has potential applications in radiation biology as well as chemistry and in planetary science and astrophysics.

  10. Adsorption of ethyl xanthate on ZnS(110) surface in the presence of water molecules: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Long, Xianhao [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Chen, Jianhua, E-mail: jhchen@gxu.edu.cn [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Guangxi Colleges and University Key Laboratory of Minerals Engineering, 530004 (China); Chen, Ye, E-mail: fby18@126.com [College of Resources and Metallurgy, Guangxi University, Nanning 530004 (China)

    2016-05-01

    Graphical abstract: - Highlights: • Adsorption of water molecules decreases the reactivity of surface Zn atom. • Copper impurities decrease the band gap of ZnS surface. • Copper impurities enhance the adsorption of xanthate on the ZnS surface. • Water molecules have little influence on the properties of Cu-substituted ZnS surface. • The xanthate S atom can interact with the surface S atom of Cu-substituted ZnS surface. - Abstracts: The interaction of collector with the mineral surface plays a very important role in the froth flotation of sphalerite. The adsorptions occurred at the interface between the mineral surface and waters; however most of DFT simulations are performed in vacuum, without consideration of water effect. Semiconductor surface has an obvious proximity effect, which will greatly influence the surface reactivity. To understand the mechanism of xanthate interacting with sphalerite surface in the presence of water molecules, the ethyl xanthate molecule adsorption on un-activated and Cu-activated ZnS(110) surface in the absence and presence of water molecules were performed using the density functional theory (DFT) method. The calculated results show that the adsorption of water molecules dramatically changes the properties of ZnS surface, resulting in decreasing the reactivity of surface Zn atoms with xanthate. Copper activation of ZnS surface changes the surface properties, leading to the totally different adsorption behaviors of xanthate. The presence of waters has little influence on the properties of Cu-activated ZnS surface. The xanthate S atom can interact with the surface S atom of Cu-substituted ZnS surface, which would result in the formation of dixanthogen.

  11. Molecular theories and simulation of ions and polar molecules in water

    CERN Document Server

    Hummer, G; García, A; Hummer, Gerhard; Pratt, Lawrence R.; Garcia, Angel E.

    1998-01-01

    Recent developments in molecular theories and simulation of ions and polar molecules in water are reviewed. The hydration of imidazole and imidazolium solutes is used to exemplify the theoretical issues. The treatment of long-ranged electrostatic interactions in simulations is discussed extensively. It is argued that the Ewald approach is an easy way to get correct hydration free energies in the thermodynamic limit from molecular calculations; and that molecular simulations with Ewald interactions and periodic boundary conditions can also be more efficient than many common alternatives. The Ewald treatment permits a conclusive extrapolation to infinite system size. The picture that emerges from testing of simple models is that the most prominent failings of the simplest theories are associated with solvent proton conformations that lead to non-gaussian fluctuations of electrostatic potentials. Thus, the most favorable cases for the second-order perturbation theories are monoatomic positive ions. For polar and...

  12. Switching of the magnetocaloric effect of Mn(II) glycolate by water molecules.

    Science.gov (United States)

    Chen, Yan-Cong; Guo, Fu-Sheng; Liu, Jun-Liang; Leng, Ji-Dong; Vrábel, Peter; Orendáč, Martin; Prokleška, Jan; Sechovský, Vladimír; Tong, Ming-Liang

    2014-03-10

    The transformation of Mn(II) glycolates (glc) between the three-dimensional coordination polymer [Mn(glc)2]n (1) and discrete mononuclear phase [Mn(glc)2 (H2O)2] (2) can be reversibly switched by water molecules, which dramatically change the magnetocaloric effect (MCE) of Mn(II) glycolates from the maximum of 6.9 J kg(-1)  K(-1) in 1 to 60.3 J kg(-1)  K(-1) in 2. This case example reveals that the effect of magnetic coupling on MCE plays a dominant role over that of other factors such as magnetic density for 3d-type magnetic refrigerants.

  13. Hydration of gelatin molecules in glycerol-water solvent and phase diagram of gelatin organogels.

    Science.gov (United States)

    Sanwlani, Shilpa; Kumar, Pradip; Bohidar, H B

    2011-06-09

    We present a systematic investigation of hydration and gelation of the polypeptide gelatin in water-glycerol mixed solvent (glycerol solutions). Raman spectroscopy results indicated enhancement in water structure in glycerol solutions and the depletion of glycerol density close to hydration sheath of the protein molecule. Gelation concentration (c(g)) was observed to decrease from 1.92 to 1.15% (w/v) while the gelation temperature (T(g)) was observed to increase from 31.4 to 40.7 °C with increase in glycerol concentration. Data on hand established the formation of organogels having interconnected networks, and the universal gelation mechanism could be described through an anomalous percolation model. The viscosity of sol diverged as η ∼ (1 - c(g)/c)(-k) as c(g) was approached from below (c c(g)). It is important to note that values determined for critical exponents k and t were universal; that is, they did not depend on the microscopic details. The measured values were k = 0.38 ± 0.10 and t = 0.92 ± 0.17 whereas the percolation model predicts k = 0.7-1.3 and t = 1.9. Isothermal frequency sweep studies showed power-law dependence of gel storage modulus (G') and loss modulus (G'') on oscillation frequency ω given as G'(ω) ∼ ω(n') and G''(ω) ∼ ω(n''), and consistent with percolation model prediction it was found that n' ≈ n'' ≈ δ ≈ 0.73 close to gelation concentration. We propose a unique 3D phase diagram for the gelatin organogels. Circular dichroism data revealed that the gelatin molecules retained their biological activity in these solvents. Thus, it is shown that the thermomechanical properties of these organogels could be systematically tuned and customized as per application requirement.

  14. Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction

    Directory of Open Access Journals (Sweden)

    Jan Kučera

    2011-07-01

    Full Text Available The geometric and electronic structure of the metal–molecule interface in metal/molecule/metal junctions is of great interest since it affects the functionality of such units in possible nanoelectronic devices. We have investigated the interaction between water and a palladium monolayer of a Au(111/4-mercaptopyridine/Pd junction by means of DFT calculations. A relatively strong bond between water and the palladium monolayer of the Au/Mpy/Pd complex is observed via a one-fold bond between the oxygen atom of the water molecule and a Pd atom. An isolated H2O molecule adsorbs preferentially in a flat-lying geometry on top of a palladium atom that is at the same time also bound to the nitrogen atom of a Mpy molecule of the underlying self-assembled monolayer. The electronic structure of these Pd atoms is considerably modified which is reflected in a reduced local density of states at the Fermi energy. At higher coverages, water can be arranged in a hexagonal ice-like bilayer structure in analogy to water on bulk metal surfaces, but with a much stronger binding which is dominated by O–Pd bonds.

  15. An approach to water molecule dynamics associated with motion of catalytic moiety

    Science.gov (United States)

    Shimahara, Hideto; Sugimori, Kimikazu; Koyimatu, Muhmad; Nagao, Hidemi; Ohkubo, Tadayasu; Kobayashi, Yuji

    2013-02-01

    A water bridge composed of several water molecules between the catalytic moieties, His64 and the zinc-bound solvent, in human carbonic anhydrase II (hCAII) is disrupted when the inhibitor acetazolamide (ACZ) binds to the zinc ion, according to the crystallographic structure of the ACZ-hCAII complex. In this structure, the ACZ methyl group is far (˜10 Å) from the His64. However, this binding causes an 1H NMR chemical shift change (˜1 ppm) in His64 in solution. This suggests two alternative mechanisms: a) the ACZ methyl group may be closer to His64 in the complex in solution, compared to the crystal, or b) the disruption of the water bridge might cause the His64 to move or behave in a different manner. The binding of ACZ to the enzyme in solution was examined by observing the NMR signals of the 13C-labeled ACZ methyl group in the ACZ-hCAII complex. The 13C signals of the free and bound forms were detected. In the bound form, the signal for the acetamide group was pH dependent, whereas the sulfonamide group signal was pH independent. Some 13C-filtered NOE signals were observed, although none of the signals were related to the His64 chemical shift. Based on these observations, we suggest that the position or motion of His64 is associated with disruption of the water bridge in the ACZ-hCAII complex in solution, which could change the 1H chemical shift.

  16. Small molecule, big difference: the role of water in the crystallization of paclitaxel.

    Science.gov (United States)

    Vella-Zarb, Liana; Baisch, Ulrich; Dinnebier, Robert E

    2013-02-01

    Paclitaxel is an important antineoplastic drug, which is used widely in the treatment of many forms of cancer. The crystal structures of the anhydrous form and the hemihydrate were determined from laboratory X-ray powder diffraction data, whereas the dihydrate was solved from single-crystal synchrotron diffraction data. Intermolecular spaces allow for the inclusion of loosely bound water molecules, which are then lost easily upon heating. All three forms were found to crystallize in the orthorhombic spacegroup P2(1)2(1)2(1), with Z' = 2. The unit cell parameters were found to be a = 9.6530(3) Å, b = 28.1196(8) Å, c = 33.5378(14) Å, and V = 9103.5(5) Å for the anhydrous form (363 K); a = 9.6890(2) Å, b = 28.0760(4) Å, c = 33.6166(8) Å, and V = 9144.7(3) Å(3) for the hemihydrate (333 K); and a = 9.512(6) Å, b = 28.064(16) Å, c = 33.08(2) Å, and V = 8829.0(9) Å(3) for the dihydrate (120 K). Water loss occurs in two steps between 120 K ≤ t ≤ 363 K. The thermal stability of the hydrates and accompanying unit cell changes were observed in situ via temperature-resolved X-ray powder diffraction and thermogravimetric analysis.

  17. Lattice water molecules tuned spin-crossover for an iron(II) complex with thermal hysteresis.

    Science.gov (United States)

    Luo, Yang-Hui; Yang, Li-Jing; Liu, Qing-Ling; Ling, Yang; Wang, Wei; Sun, Bai-Wang

    2014-11-28

    A new iron(II) complex based on the 4,4'-dimethyl-2,2'-bipyridine ligand [Fe(4,4'-dmbpy)3(ClO4)(SCN)·3H2O (1·3H2O)] has been prepared and characterized. Structural studies and Hirshfeld surface analysis for complex 1·3H2O at three different temperatures (300, 240 and 130 K) are described. The UV-vis absorption spectrum of a water-free sample (1) in methanol solution and magnetic susceptibility measurements for solid-state samples 1·3H2O and 1 revealed that the removal of lattice water molecules from complex 1·3H2O changed the magnetic properties from the low-spin state (1·3H2O) to the complete spin-crossover (1) between 350-220 K with a thermal hysteresis of 7 K, and was accompanied by a colour change from brown to red.

  18. A proactive role of water molecules in acceptor recognition by Protein-O-fucosyltransferase 2

    Science.gov (United States)

    Valero-González, Jessika; Leonhard-Melief, Christina; Lira-Navarrete, Erandi; Jiménez-Osés, Gonzalo; Hernández-Ruiz, Cristina; Pallarés, María Carmen; Yruela, Inmaculada; Vasudevan, Deepika; Lostao, Anabel; Corzana, Francisco; Takeuchi, Hideyuki; Haltiwanger, Robert S.; Hurtado-Guerrero, Ramon

    2016-01-01

    Protein O-fucosyltransferase 2 (POFUT2) is an essential enzyme that fucosylates serine/threonine residues of folded thrombospondin type 1 repeats (TSRs). To date, the mechanism by which this enzyme recognizes very dissimilar TSRs remained unclear. By engineering of a fusion protein, we report the crystal structure of Caenorhabditis elegans POFUT2 (CePOFUT2) in complex with GDP and human TSR1 that suggests an inverting mechanism for fucose transfer assisted by a catalytic base, and shows that nearly half of the TSR1 is embraced by CePOFUT2. A small number of direct interactions and a large network of water molecules maintain the complex. Site-directed mutagenesis demonstrates that POFUT2 fucosylates threonine preferentially over serine and relies on folded TSRs containing the minimal consensus sequence CXX(S/T)C. Crystallographic and mutagenesis data together with atomic-level simulations uncover an unprecedented binding mechanism by which POFUT2 promiscuously recognizes the structural fingerprint of poorly homologous TSRs through a dynamic network of water-mediated interactions. PMID:26854667

  19. Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules.

    Science.gov (United States)

    Huggins, David J

    2012-11-21

    The structures of biomolecules and the strengths of association between them depend critically on interactions with water molecules. Thus, understanding these interactions is a prerequisite for understanding the structure and function of all biomolecules. Inhomogeneous fluid solvation theory provides a framework to derive thermodynamic properties of individual water molecules from a statistical mechanical analysis. In this work, two biomolecules are analysed to probe the distribution and thermodynamics of surrounding water molecules. The great majority of hydration sites are predicted to contribute favourably to the total free energy with respect to bulk water, though hydration sites close to non-polar regions of the solute do not contribute significantly. Analysis of a biomolecule with a positively and negatively charged functional group predicts that a charged species perturbs the free energy of water molecules to a distance of approximately 6.0 Å. Interestingly, short simulations are found to provide converged predictions if samples are taken with sufficient frequency, a finding that has the potential to significantly reduce the required computational cost of such analysis. In addition, the predicted thermodynamic properties of hydration sites with the potential for direct hydrogen bonding interactions are found to disagree significantly for two different water models. This study provides important information on how inhomogeneous fluid solvation theory can be employed to understand the structures and intermolecular interactions of biomolecules.

  20. Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models.

    Science.gov (United States)

    Bauer, Brad A; Zhong, Yang; Meninger, David J; Davis, Joseph E; Patel, Sandeep

    2011-04-01

    We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for

  1. Thermodynamic properties of water in the lattice gas model with consideration of the vibrational motions of molecules

    Science.gov (United States)

    Titov, S. V.; Tovbin, Yu. K.

    2016-11-01

    A molecular model developed earlier for a polar fluid within the lattice gas model is supplemented by considering the vibrational motions of molecules using water as an example. A combination of point dipole and Lennard-Jones potentials from SPC parametrization is chosen as the force field model for the molecule. The main thermodynamic properties of liquid water (density, internal energy, and entropy) are studied as functions of temperature. There is qualitative agreement between the calculation results and the experimental data. Ways of refining the molecular theory are discussed.

  2. Location and orientation of the N,N-diisopropylethylamine template molecule in the AlPO4-18 framework by X-ray synchrotron diffraction and molecular modelling

    Institute of Scientific and Technical Information of China (English)

    Christiana Zenonos; Dewi W. Lewis; Gopinathan Sankar

    2015-01-01

    Phase pure AlPO4 with the AlPO4-18 (AEI) structure was synthesised using N,N-diisopropylethyla-mine as a template. Using a combination of X-ray powder diffraction and computational methods, the location and orientation of the N,N-diisopropylethylamine molecules inside the cages of the AEI structure were determined. Thermogravimetric analysis confirmed that the number of template molecules per unit cell was consistent with the diffraction study. We unequivocally show that only one template molecule is present in each cage of the crystalline AEI material. Our work demon-strates that a combined approach enables accurate structure resolution of such complex materials.

  3. The effects of cold rolling orientation and water chemistry on stress corrosion cracking behavior of 316L stainless steel in simulated PWR water environments

    Science.gov (United States)

    Chen, Junjie; Lu, Zhanpeng; Xiao, Qian; Ru, Xiangkun; Han, Guangdong; Chen, Zhen; Zhou, Bangxin; Shoji, Tetsuo

    2016-04-01

    Stress corrosion cracking behaviors of one-directionally cold rolled 316L stainless steel specimens in T-L and L-T orientations were investigated in hydrogenated and deaerated PWR primary water environments at 310 °C. Transgranular cracking was observed during the in situ pre-cracking procedure and the crack growth rate was almost not affected by the specimen orientation. Locally intergranular stress corrosion cracks were found on the fracture surfaces of specimens in the hydrogenated PWR water. Extensive intergranular stress corrosion cracks were found on the fracture surfaces of specimens in deaerated PWR water. More extensive cracks were found in specimen T-L orientation with a higher crack growth rate than that in the specimen L-T orientation with a lower crack growth rate. Crack branching phenomenon found in specimen L-T orientation in deaerated PWR water was synergistically affected by the applied stress direction as well as the preferential oxidation path along the elongated grain boundaries, and the latter was dominant.

  4. Biology-oriented synthesis of a natural-product inspired oxepane collection yields a small-molecule activator of the Wnt-pathway.

    Science.gov (United States)

    Basu, Sudipta; Ellinger, Bernhard; Rizzo, Stefano; Deraeve, Céline; Schürmann, Markus; Preut, Hans; Arndt, Hans-Dieter; Waldmann, Herbert

    2011-04-26

    In Biology Oriented Synthesis the scaffolds of biologically relevant compound classes inspire the synthesis of focused compound collections enriched in bioactivity. This criterion is met by the structurally complex scaffolds of natural products (NPs) selected in evolution. The synthesis of NP-inspired compound collections approaching the complexity of NPs calls for the development of efficient synthetic methods. We have developed a one pot 4-7 step synthesis of mono-, bi-, and tricyclic oxepanes that resemble the core scaffolds of numerous NPs with diverse bioactivities. This sequence entails a ring-closing ene-yne metathesis reaction as key step and makes productive use of polymer-immobilized scavenger reagents. Biological profiling of a corresponding focused compound collection in a reporter gene assay monitoring for Wnt-signaling modulation revealed active Wntepanes. This unique class of small-molecule activators of the Wnt pathway modulates the van-Gogh-like receptor proteins (Vangl), which were previously identified in noncanonical Wnt signaling, and acts in synergy with the canonical activator protein (Wnt-3a).

  5. Association of Catechin Molecules in Water: Quantitative Binding Study and Complex Structure Analysis.

    Science.gov (United States)

    Ujihara, Tomomi; Hayashi, Nobuyuki

    2016-01-22

    Associations between catechin molecules were investigated by (1)H NMR titration experiments. Eight green tea catechins formed self-assembled dimers in water, and gallate-type catechins had a greater tendency to self-associate than non-gallate-type catechins. All eight catechins also associated as 1:1 heterodimer complexes. Investigation of complex formation of epigallocatechin-3-O-gallate (EGCg) and epigallocatechin (EGC) with the other catechins showed that the affinity between EGCg and 2,3-trans-gallate-type catechins was remarkably high, and the binding affinity of EGCg for ECg was also rather strong. In contrast, the non-gallate-type catechin EGC exhibited generally low binding affinity for other catechins. Structural analyses of the complexes by ROESY experiments and density functional theory calculations demonstrated that the higher binding abilities of gallate-type catechins are due to providing multiple intermolecular interactions that remain effective in an aqueous environment, such as aromatic/aromatic or CH/π interactions.

  6. NO Exchange for a Water Molecule Favorably Changes Iontophoretic Release of Ruthenium Complexes to the Skin

    Directory of Open Access Journals (Sweden)

    Danielle C. A. S. de Santana

    2017-01-01

    Full Text Available Ruthenium (Ru complexes have been studied as promising anticancer agents. Ru nitrosyl complex (Ru-NO is one which acts as a pro-drug for the release of nitric oxide (NO. The Ru-aqueous complex formed by the exchange of NO for a water molecule after NO release could also possess therapeutic effects. This study evaluates the influence of iontophoresis on enhancing the skin penetration of Ru-NO and Ru-aqueous and assesses its applicability as a tool in treating diverse skin diseases. Passive and iontophoretic (0.5 mA·cm−2 skin permeation of the complexes were performed for 4 h. The amount of Ru and NO in the stratum corneum (SC, viable epidermis (VE, and receptor solution was quantified while the influence of iontophoresis and irradiation on NO release from Ru-NO complex was also evaluated. Iontophoresis increased the amount of Ru-NO and Ru-aqueous recovered from the receptor solution by 15 and 400 times, respectively, as compared to passive permeation. Iontophoresis produced a higher accumulation of Ru-aqueous in the skin layers as compared to Ru-NO. At least 50% of Ru-NO penetrated the SC was stable after 4 h. The presence of Ru-NO in this skin layer suggests that further controlled release of NO can be achieved by photo-stimulation after iontophoresis.

  7. Alkyl Chain Length Dependent Structural and Orientational Transformations of Water at Alcohol-Water Interfaces and Its Relevance to Atmospheric Aerosols.

    Science.gov (United States)

    Mondal, Jahur A; Namboodiri, V; Mathi, P; Singh, Ajay K

    2017-04-06

    Although the hydrophobic size of an amphiphile plays a key role in various chemical, biological, and atmospheric processes, its effect at macroscopic aqueous interfaces (e.g., air-water, oil-water, cell membrane-water, etc.), which are ubiquitous in nature, is not well understood. Here we report the hydrophobic alkyl chain length dependent structural and orientational transformations of water at alcohol (CnH2n+1OH, n = 1-12)-water interfaces using interface-selective heterodyne-detected vibrational sum frequency generation (HD-VSFG) and Raman multivariate curve resolution (Raman-MCR) spectroscopic techniques. The HD-VSFG results reveal that short-chain alcohols (CnH2n+1OH, n alcohols (CnH2n+1OH, n > 4, i.e., beyond 1-butanol) make the interfacial water more strongly H-bonded and reversely orientated; the OH stretch band maximum appears at ∼3200 cm(-1), and the H atoms are pointed away from the bulk water, that is, "H-up" oriented. Interestingly, for the alcohol of intermediate chain length (CnH2n+1OH, n = 4, i.e, 1-butanol), the interface is quite unstable even after hours of its formation and the time-averaged result is qualitatively similar to that of the long-chain alcohols, indicating a structural/orientational crossover of interfacial water at the 1-butanol-water interface. pH-dependent HD-VSFG measurements (with H2O as well as isotopically diluted water, HOD) suggest that the structural/orientational transformation of water at the long-chain alcohol-water interface is associated with the adsorption of OH(-) anion at the interface. Vibrational mapping of the water structure in the hydration shell of OH(-) anion (obtained by Raman-MCR spectroscopy of NaOH in HOD) clearly shows that the water becomes strongly H-bonded (OH stretch max. ≈ 3200 cm(-1)) while hydrating the OH(-) anion. Altogether, it is conceivable that alcohols of different hydrophobic chain lengths that are present in the troposphere will differently affect the interfacial electrostatics and

  8. The δ18O of Atmospheric Water Vapour is Recorded in the Oxygen Isotope Ratios of Leaf water and Organic Molecules at High Relative Humidity

    Science.gov (United States)

    Lehmann, M. M.; Goldsmith, G. R.; Schmid, L.; Siegwolf, R. T.; Gessler, A.; Saurer, M.

    2016-12-01

    The oxygen stable isotope ratios (δ18O) of water and organic molecules in plants hold information about plant physiology, ecohydrology, and environmental conditions. For instance, the δ18O ratio of leaf water reflects both the δ18O ratios of water in the soil and in the atmosphere. This water, which is incorporated into organic molecules at the time of synthesis, thus serves to record the environment in which the plant was growing. However, how δ18O of atmospheric water vapour affects the δ18O ratio of organic molecules remains poorly understood. In order to investigate the effects of fog and rain (e.g. high atmospheric water availability) on δ18O ratios of leaf water and organic molecules, we exposed oak tree saplings (Quercus robur) in wet and dry soil treatments to 18O-depleted water vapour at ca. 90% relative humidity for 5 h. We harvested plant material over 24 h to trace the movement of the isotopic label in water and organics throughout the plant from the leaves to the stem. The atmospheric water vapour caused a strong 18O-depletion in leaf and xylem water, as well as in leaf carbohydrates, with the most negative ratios observed at the end of the fogging. Moreover, the label was clearly observed in twig and stem phloem carbohydrates following a short delay. A detailed compound-specific isotope analysis of the leaf carbohydrates revealed that the label caused an 18O-depletion in fructose, glucose, and sucrose. Quercitol, an oak-specific alditol, did not show 18O-depletion. Clear soil moisture treatment effects were only observed for twig phloem carbohydrates, with a stronger 18O-depletion in wet plants than in dry plants, suggesting retarded leaf-to-phloem sugar export in trees under drought. We demonstrate that labelling with 18O-depleted water is a potential tool to trace the movement and incorporation of oxygen stable isotopes in plants. We clearly show that changes in δ18O of atmospheric water vapour are quickly imprinted on leaf water and

  9. A planning-oriented sustainability assessment framework for peri-urban water management in developing countries.

    Science.gov (United States)

    Starkl, Markus; Brunner, Norbert; López, Eduardo; Martínez-Ruiz, José Luis

    2013-12-15

    DPSIR and the three-pillar model are well-established frameworks for sustainability assessment. This paper proposes a planning-oriented sustainability assessment framework (POSAF). It is informed by those frameworks but differs insofar as it puts more emphasis on a constructivist conception which recognises that sustainability needs to be defined anew for each planning problem. In finding such a consensus definition, POSAF uses participatory scenario analysis and participatory planning, technical feasibility study, participatory assessment, analysis of trade-offs and social networks in an unusual combination and for goals that differ from the original conceptions of these methods. POSAF was applied in a peri-urban area of Mexico City for the design of improved water service provision, integrating solid waste management. It supported consensus amongst users about the importance of environmental issues, informed planners about the values of stakeholders and users, detected local differences, and identified possible conflicts at an early stage of decision-making. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. A stereographic projection path integral study of the coupling between the orientation and the bending degrees of freedom of water.

    Science.gov (United States)

    Curotto, E; Freeman, David L; Doll, J D

    2008-05-28

    A Monte Carlo path integral method to study the coupling between the rotation and bending degrees of freedom for water is developed. It is demonstrated that soft internal degrees of freedom that are not stretching in nature can be mapped with stereographic projection coordinates. For water, the bending coordinate is orthogonal to the stereographic projection coordinates used to map its orientation. Methods are developed to compute the classical and quantum Jacobian terms so that the proper infinitely stiff spring constant limit is recovered in the classical limit, and so that the nonconstant nature of the Riemann Cartan curvature scalar is properly accounted in the quantum simulations. The theory is used to investigate the effects of the geometric coupling between the bending and the rotating degrees of freedom for the water monomer in an external field in the 250 to 500 K range. We detect no evidence of geometric coupling between the bending degree of freedom and the orientations.

  11. Effects of Oscillatory Shear on the Orientation of the Inverse Bicontinuous Cubic Phase in a Nonionic Surfactant/Water System.

    Science.gov (United States)

    Yamanoi, Mutsumi; Kawabata, Youhei; Kato, Tadashi

    2016-03-29

    The bicontinuous inverse cubic phase (V2 phase) formed in amphiphilic systems consists of bilayer networks with a long-range order. We have investigated effects of oscillatory shear on the orientation of the V2 phase with space group Ia3d formed in a nonionic surfactant (C12E2)/water system by using simultaneous measurements of rheology/small-angle X-ray scattering. It is shown that grain refining occurs by applying the large amplitude oscillatory shear (LAOS) with a strain amplitude (γ0) of ∼20, which gives the ratio of the loss modulus (G″) to the storage modulus (G') (G″/G' = tan δ) of ∼100. On the other hand, orientation of the cubic lattice occurs when the small amplitude (γ0 ≈ 0.0004) oscillatory shear (SAOS) in the linear regime is applied to the sample just after the LAOS. Interestingly, the orientation is strongly enhanced by the "medium amplitude" (γ0 ≈ 0.05) oscillatory shear ("MAOS") after the SAOS. When the MAOS is applied before applying the LAOS, orientation to a particular direction is not observed, indicating that the grain refining process by the LAOS is necessary for the orientation during the MAOS. The results of additional experiments show that the shear sequence "LAOS-MAOS" is effective for the orientation of the cubic lattice. When the LAOS and MAOS are applied to the sample alternatively, grain refining and orientation occur during the LAOS and MAOS, respectively, indicating reversibility of the orientation. It is shown that (i) the degree of the orientation is dependent on γ0 and the frequency (ω) of the MAOS and (ii) relatively higher orientation can be obtained for the combination of γ0 and ω, which gives tan δ = 2-3. The lattice constant does not change throughout all the shearing processes and is equal to that before shearing within the experimental errors, indicating that the shear melting does not occur. These results suggest a possibility to control the orientation of the cubic lattice only by changing the

  12. Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.

    Science.gov (United States)

    Luo, Zhoujie; Gao, Ya; Zhu, Tong; Zhang, John Zenghui; Xia, Fei

    2017-08-31

    Water molecules can serve as proton shuttles for proton transfer in the C-H bond insertion reactions catalyzed by transition metal complexes. Recently, the control experiments performed for C-H bond insertion of phenol and anisol by gold carbenes show that large discrepancy exists in the yields of hydrogenated and deuterated products. Thus, we conducted a detailed theoretical analysis on the function of water molecules in the C-H bond insertion reactions. The comparison of calculated results and control experiments indicates that the solution water molecules play a crucial role of proton shuttle in C-H bond insertion. In particular, it was found that the hydroxyl groups in phenols were capable of donating protons via water shuttles for the production of C-H products, which had a substantial influence on the yields of inserted products. The hydroxyl groups instead of C-H bonds in phenols function like "proton reservoirs" in the C-H bond insertion, which we call the "proton self-sufficient" (PSS) function of phenol. The PSS function of phenol indicates that the substrates with and without proton reservoirs will lead to different C-H bond insertion products.

  13. Dependence of crack growth kinetics on dendrite orientation and water chemistry for Alloy 182 weld metal in high-temperature water

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Zhanpeng, E-mail: zplu@shu.edu.cn [Institute of Materials Science, School of Materials Science and Engineering, Shanghai University, Shanghai 200072 (China); New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Chen, Junjie [Institute of Materials Science, School of Materials Science and Engineering, Shanghai University, Shanghai 200072 (China); Shoji, Tetsuo [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Meng, Fanjiang [Shanghai Nuclear Engineering Research & Design Institute, Shanghai 200233 (China)

    2015-03-15

    Highlights: • SCC paths along dendrite directions in both T–S and T–L specimens of Alloy 182. • Higher SCC growth rates in T–S orientation specimen than in T–L orientation specimen. • CGR increased with increasing dissolved oxygen. • Apparently negative da/dt curve by ACPD in hydrogen saturated water. - Abstract: Stress corrosion cracking growth rates of Alloy 182 weld metals in T–S and T–L orientations in 288 °C pure water with various dissolved oxygen and hydrogen concentrations were measured. Extensive inter-dendritic stress corrosion cracking paths on the side surfaces and fracture surfaces were observed. The crack growth path in the T–S orientation specimen was perpendicular to the applied loading direction, and parallel to the loading direction in the T–L specimen. Crack growth rates of the T–S specimen were significantly higher than those of the T–L specimen under the same test conditions. The crack growth rate decreased significantly with decreasing dissolved oxygen concentration. Adding dissolved hydrogen in water caused an apparent decrease of the alternating current potential drop signal during crack growth monitoring.

  14. Degradation of Bacterial Quorum Sensing Signaling Molecules by the Microscopic Yeast Trichosporon loubieri Isolated from Tropical Wetland Waters

    Directory of Open Access Journals (Sweden)

    Cheng-Siang Wong

    2013-09-01

    Full Text Available Proteobacteria produce N-acylhomoserine lactones as signaling molecules, which will bind to their cognate receptor and activate quorum sensing-mediated phenotypes in a population-dependent manner. Although quorum sensing signaling molecules can be degraded by bacteria or fungi, there is no reported work on the degradation of such molecules by basidiomycetous yeast. By using a minimal growth medium containing N-3-oxohexanoylhomoserine lactone as the sole source of carbon, a wetland water sample from Malaysia was enriched for microbial strains that can degrade N-acylhomoserine lactones, and consequently, a basidiomycetous yeast strain WW1C was isolated. Morphological phenotype and molecular analyses confirmed that WW1C was a strain of Trichosporon loubieri. We showed that WW1C degraded AHLs with N-acyl side chains ranging from 4 to 10 carbons in length, with or without oxo group substitutions at the C3 position. Re-lactonisation bioassays revealed that WW1C degraded AHLs via a lactonase activity. To the best of our knowledge, this is the first report of degradation of N-acyl-homoserine lactones and utilization of N-3-oxohexanoylhomoserine as carbon and nitrogen source for growth by basidiomycetous yeast from tropical wetland water; and the degradation of bacterial quorum sensing molecules by an eukaryotic yeast.

  15. Relativistic theory of incoherent scattering of a photon by water, hydrogen cyanide, glucose, protein molecules

    Science.gov (United States)

    Grimm, Shu-Ya Lisa

    We have developed a general method to calculate the incoherent scattering cross section for complex molecules for photon energy ranging from 1 keV to 130 keV. Within this energy range the binding energy of an electron in a biosystem is comparable to the energy of the incident photon, thus we need to take into account the effect of binding energy in calculations of the total scattering cross section. Also the energy acquired by the scattered electron is in the high energy range, and therefore we are required to use relativistic treatment in our calculations. In our Theory we show the derivation of incoherent scattering function. The calculation of the incoherent scattering function involves matrix elements between two molecular wave functions. With Sharma's analytical formula we are able to expand one of the wave functions to the center of the other wave function, enabling us to perform the calculation of incoherent scattering function for molecules which require multi-center integrals. We explain briefly how one obtains the wave function of a molecule in the Hartree-Fock self-consistent field approximation. Since there are no available molecular wave functions for large molecules such as glucose and Gly-Pro-Pro sequence protein (which are important molecules in biosystems) we develop and use the molecular wave functions using the overlap effect only for large molecules. We further apply the calculated incoherent scattering function to calculate the total incoherent scattering cross section for a molecule. We perform the calculations of incoherent scattering function and total incoherent scattering cross sections for H2O,/ HCN, Glucose, and Gly-Pro-Pro protein molecules. For H2O,/ HCN molecules we calculate the incoherent scattering function using both Hartree-Fock (HF) self-consistent field wave functions and overlap- effect-only wave functions. We further apply these two calculated incoherent scattering functions obtained by Hartree-Fock (HF) self-consistent field

  16. Self-assembly of neuroprotective carbazolium based small molecules at octane/water interface: A simulation investigation

    Science.gov (United States)

    Zolghadr, Amin Reza; Heydari Dokoohaki, Maryam

    2016-11-01

    The self-assembly of dibromocarbazole based small molecule (P7C3) and its analogues is studied at the octane/water interface by using molecular dynamics simulations. P7C3 protects newborn neurons from apoptotic cell death and enhances neurogenesis. The bromines on the carbazole appear particularly important, as the derivatives with dichloro and parent carbazole did not appear active at the concentrations tested. We are mainly focused on the question that why is dibromocarbazole derivative an effective neuroprotective drug, but not dichlorocarbazole or parent carbazole? It was found that P7C3 and P7C3-Cl were concentrated in the interfacial region, whereas the parent carbazole derivative were distributed throughout the water phase. The diffusion of P7C3 molecules in the interfacial region are higher than P7C3-Cl. This approach could use by experimentalist to evaluate the permeability of drug candidates prior to their synthesis.

  17. (e,3e) and (e,3-1e) differential cross sections for the double ionization of water molecule

    Energy Technology Data Exchange (ETDEWEB)

    Mansouri, A. [Laboratoire de Physique quantique et systemes dynamiques, Departement de Physique, Faculte des Sciences Universite Ferhat Abbas, Setif 19000 (Algeria); Dal Cappello, C., E-mail: cappello@univ-metz.f [Universite Paul Verlaine-Metz, Laboratoire de Physique Moleculaire et des Collisions, ICPMB (FR 2843), Institut de Physique, 1 rue Arago, 57078 Metz Cedex 3 (France); Kada, I. [Laboratoire de Physique quantique et systemes dynamiques, Departement de Physique, Faculte des Sciences Universite Ferhat Abbas, Setif 19000 (Algeria); Champion, C. [Universite Paul Verlaine-Metz, Laboratoire de Physique Moleculaire et des Collisions, ICPMB (FR 2843), Institut de Physique, 1 rue Arago, 57078 Metz Cedex 3 (France); Roy, A.C. [School of Mathematical Sciences, Ramakrishna Mission Vivekananda University, Belur Math 711202, West Bengal (India)

    2009-08-24

    We report new results for differential cross sections for the double ionization of water molecule by 1 keV electron impact. The present calculation is based on the first Born approximation. We describe the water molecule by a single centre wave function of Moccia. For the final state, an approximation of the well-known 3C wave function is used. An extensive study has been made by varying the angles of detection and the energies of each ejected electron. We have investigated the double ionization of each molecular state (1b{sub 1}, 3a{sub 1}, 1b{sub 2} and 2a{sub 1}) and identified the mechanisms of this process.

  18. Effects of a surface oriented travelling screen and water abstraction practices on downstream migrating Salmonidae smolts in a lowland stream

    DEFF Research Database (Denmark)

    Svendsen, Jon Christian; Aarestrup, Kim; Deacon, Michael G.

    2010-01-01

    Downstream migration of immature salmonids (smolts) may be associated with severe mortalities in anthropogenically altered channels. In Pacific salmon, several investigations have suggested the use of the dominating surface orientation of smolts to improve fish by-pass structures in large and deep...... hydroelectric reservoirs. The present study tested the use of a surface orientated travelling screen to guide Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.) smolts past a water abstraction site in a shallow lowland stream. The percentage of total discharge abstracted from the stream...... was included in the analyses. Indigenous migrating smolts were trapped, PIT tagged and subsequently released upstream of the water abstraction site. Releases shifted between a present or absent travelling screen. The migration success of the released smolts was evaluated using a trap situated downstream...

  19. Orientation hydrogen-bonding effect on vibronic spectra of isoquinoline in water solvent: Franck-Condon simulation and interpretation

    Science.gov (United States)

    Liu, Yu-Hui; Wang, Shi-Ming; Wang, Chen-Wen; Zhu, Chaoyuan; Han, Ke-Li; Lin, Sheng-Hsien

    2016-10-01

    The excited-state orientation hydrogen-bonding dynamics, and vibronic spectra of isoquinoline (IQ) and its cationic form IQc in water have been investigated at the time-dependent density functional theory quantum chemistry level plus Franck-Condon simulation and interpretation. The excited-state orientation hydrogen bond strengthening has been found in IQ:H2O complex due to the charge redistribution upon excitation; this is interpreted by simulated 1:1 mixed absorption spectra of free IQ and IQ:H2O complex having best agreement with experimental results. Conversely, the orientation hydrogen bond in IQc:H2O complex would be strongly weakening in the S1 state and this is interpreted by simulated absorption spectra of free IQc having best agreement with experimental results. By performing Franck-Condon simulation, it reveals that several important vibrational normal modes with frequencies about 1250 cm-1 involving the wagging motion of the hydrogen atoms are very sensitive to the formation of the orientation hydrogen bond for the IQ/IQc:H2O complex and this is confirmed by damped Franck-Condon simulation with free IQ/IQc in water. However, the emission spectra of the IQ and IQc in water have been found differently. Upon the excitation, the simulated fluorescence of IQ in water is dominated by the IQ:H2O complex; thus hydrogen bond between IQ and H2O is much easier to form in the S1 state. While the weakened hydrogen bond in IQc:H2O complex is probably cleaved upon the laser pulse because the simulated emission spectrum of the free IQc is in better agreement with the experimental results.

  20. Rehabilitation and improvement of Guilin urban water environment: function-oriented management.

    Science.gov (United States)

    Pei, Yuansheng; Zuo, Hua; Luan, Zhaokun; Gao, Sijia

    2013-07-01

    Economic development and population growth have deeply damaged the urban water environment of Guilin City, China. Main problems involved structural damage and functional deterioration of the urban waters. An integrated technical scheme was developed to rehabilitate the urban water environment and to enhance the waters' functions during 1998-2008. Improvement of waters' functions included water system reconstruction, water pollution control, water safety assurance, and aquatic ecological restoration. The water system was reconstructed to connect different waters and clean water supplies to the lakes. Moreover, water pollution was controlled to improve water quality by endogenous pollutant elimination and extraneous pollutant interception. In addition, ecological measures put in place serve to enhance water system functions and better benefit both nature and humans. The project has brought about sound ecological, economic and social benefits in Guilin City, which can potentially be extended to similar cities.

  1. Different catalytic effects of a single water molecule: the gas-phase reaction of formic acid with hydroxyl radical in water vapor.

    Science.gov (United States)

    Anglada, Josep M; Gonzalez, Javier

    2009-12-07

    The effect of a single water molecule on the reaction mechanism of the gas-phase reaction between formic acid and the hydroxyl radical was investigated with high-level quantum mechanical calculations using DFT-B3LYP, MP2 and CCSD(T) theoretical approaches in concert with the 6-311+G(2df,2p) and aug-cc-pVTZ basis sets. The reaction between HCOOH and HO has a very complex mechanism involving a proton-coupled electron transfer process (pcet), two hydrogen-atom transfer reactions (hat) and a double proton transfer process (dpt). The hydroxyl radical predominantly abstracts the acidic hydrogen of formic acid through a pcet mechanism. A single water molecule affects each one of these reaction mechanisms in different ways, depending on the way the water interacts. Very interesting is also the fact that our calculations predict that the participation of a single water molecule results in the abstraction of the formyl hydrogen of formic acid through a hydrogen atom transfer process (hat).

  2. Water-COOH Composite Structure with Enhanced Hydrophobicity Formed by Water Molecules Embedded into Carboxyl-Terminated Self-Assembled Monolayers.

    Science.gov (United States)

    Guo, Pan; Tu, Yusong; Yang, Jinrong; Wang, Chunlei; Sheng, Nan; Fang, Haiping

    2015-10-30

    By combining molecular dynamics simulations and quantum mechanics calculations, we show the formation of a composite structure composed of embedded water molecules and the COOH matrix on carboxyl-terminated self-assembled monolayers (COOH SAMs) with appropriate packing densities. This composite structure with an integrated hydrogen bond network inside reduces the hydrogen bonds with the water above. This explains the seeming contradiction on the stability of the surface water on COOH SAMs observed in experiments. The existence of the composite structure at appropriate packing densities results in the two-step distribution of contact angles of water droplets on COOH SAMs, around 0° and 35°, which compares favorably to the experimental measurements of contact angles collected from forty research articles over the past 25 years. These findings provide a molecular-level understanding of water on surfaces (including surfaces on biomolecules) with hydrophilic functional groups.

  3. Water-COOH Composite Structure with Enhanced Hydrophobicity Formed by Water Molecules Embedded into Carboxyl-Terminated Self-Assembled Monolayers

    Science.gov (United States)

    Guo, Pan; Tu, Yusong; Yang, Jinrong; Wang, Chunlei; Sheng, Nan; Fang, Haiping

    2015-10-01

    By combining molecular dynamics simulations and quantum mechanics calculations, we show the formation of a composite structure composed of embedded water molecules and the COOH matrix on carboxyl-terminated self-assembled monolayers (COOH SAMs) with appropriate packing densities. This composite structure with an integrated hydrogen bond network inside reduces the hydrogen bonds with the water above. This explains the seeming contradiction on the stability of the surface water on COOH SAMs observed in experiments. The existence of the composite structure at appropriate packing densities results in the two-step distribution of contact angles of water droplets on COOH SAMs, around 0° and 35°, which compares favorably to the experimental measurements of contact angles collected from forty research articles over the past 25 years. These findings provide a molecular-level understanding of water on surfaces (including surfaces on biomolecules) with hydrophilic functional groups.

  4. Effects of water molecules on the chemical stability of MAGeI3 perovskite explored from a theoretical viewpoint.

    Science.gov (United States)

    Sun, Ping-Ping; Chi, Wei-Jie; Li, Ze-Sheng

    2016-09-21

    The stability of perovskite in humid environments is one of the biggest obstacles for its potential applications in light harvesting and electroluminescent displays. Understanding the detailed degradation mechanism of MAGeI3 in moisture is a critical way to explore the practicability of MAGeI3 perovskite. In this study, we report a quantitative and systematic investigation of MAGeI3 degradation processes by exploring the effects of H2O molecules on the structural and electronic properties of the most stable MAGeI3(101) surface under various simulated environmental conditions with different water coverage based on first-principles calculations. The results show that H2O molecules can easily diffuse into the inner side of the perovskite and gradually corrode the structure as the number of H2O molecules increases. As a result of the interactions between perovskite and H2O molecules, a hydrated intermediate will be generated as the first step in the degradation mechanism; the perovskite will further decompose to HI and GeI2. In terms of one MAGeI3 molecule, it will be dissociated completely to GeI2 as a result of hydrolysis reactions with a minimum of 4H2O molecules. In addition, the degradation of the perovskite will also affect the electronic structure, causing a decrease in optical absorption across the visible region of the spectrum and a distinct deformation change in the crystal structure of the material. These findings further illustrate the degradation of the hydrolysis process of MAGeI3 perovskite in humid environments, which should be helpful to inspire experimentalists to take action to prolong the lifetimes of perovskite solar cells to achieve high conversion efficiency in their applications.

  5. Dissociation of water molecules upon keV H+- and Heq+-induced ionization

    NARCIS (Netherlands)

    Alvarado, F; Hoekstra, R; Schlatholter, T

    2005-01-01

    The interaction of keV H+, He+ and He2+, ions with gas-phase H2O molecules leads to formation of H2Oq+ ions which subsequently can undergo dissociation into various fragment species. From coincident determination of the fragmention kinetic energies, kinetic energy releases (KER) for the different di

  6. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

    DEFF Research Database (Denmark)

    Rønnest, A. K.; Peters, Günther H.J.; Hansen, Flemming Yssing

    2016-01-01

    in the gel phase and 17.5 molecules in the fluid phase, considerably smaller than inferred experimentally for 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) membranes but comparable to the number inferred for 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) membranes. Some of the properties...

  7. A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qiang [School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100 (China); Gao, Jun, E-mail: gaojun@sdu.edu.cn [Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070 (China); School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100 (China); Zhang, Dongju; Liu, Chengbu [School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100 (China)

    2015-04-01

    Highlights: • We theoretical studied peptide bond formation reaction mechanism with two water molecules. • The first water molecule can decrease the reaction barriers by forming hydrogen bonds. • The water molecule mediated three-proton transfer mechanism is the favorable mechanism. • Our calculation supports the two-step and eight membered ring mechanism. - Abstract: The ribosome is the macromolecular machine that catalyzes protein synthesis. The kinetic isotope effect analysis reported by Strobel group supports the two-step mechanism. However, the destination of the proton originating from the nucleophilic amine is uncertain. A computational simulation of different mechanisms including water molecules is carried out using the same reaction model and theoretical level. Formation the tetrahedral intermediate with proton transfer from nucleophilic nitrogen, is the rate-limiting step when two water molecules participate in peptide bond formation. The first water molecule forming hydrogen bonds with O9′ and H15′ in the A site can decrease the reaction barriers. Combined with results of the solvent isotope effects analysis, we conclude that the three-proton transfer mechanism in which water molecule mediate the proton shuttle between amino and carbon oxygen in rate-limiting step is the favorable mechanism. Our results will shield light on a better understand the reaction mechanism of ribosome.

  8. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

    Energy Technology Data Exchange (ETDEWEB)

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M.A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C. (Michigan); (NWU); (Kentucky)

    2010-11-15

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine {epsilon}-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine {epsilon}-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated {epsilon}-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.

  9. Texture and hydride orientation relationship of Zircaloy-4 fuel clad tube during its fabrication for pressurized heavy water reactors

    Science.gov (United States)

    Vaibhaw, Kumar; Rao, S. V. R.; Jha, S. K.; Saibaba, N.; Jayaraj, R. N.

    2008-12-01

    Zircaloy-4 material is used for cladding tube in pressurized heavy water reactors (PHWRs) of 220 MWe and 540 MWe capacity in India. These tubes are fabricated by using various combinations of thermo-mechanical processes to achieve desired mechanical and corrosion properties. Cladding tube develops crystallographic texture during its fabrication, which has significant influence on its in-reactor performance. Due to radiolytic decomposition of water Zircaloy-4 picks-up hydrogen. This hydrogen in excess of its maximum solubility in reactor operating condition (˜300 °C), precipitates as zirconium hydrides causing embrittlement of cladding tube. Hydride orientation in the radial direction of the tube limits the service life and lowers the fuel burn-up in reactor. The orientation of the hydride primarily depends on texture developed during fabrication. A correlation between hydride orientation ( F n) with the texture in the tube during its fabrication has been developed using a second order polynomial. The present work is aimed at quantification and correlation of texture evolved in Zircaloy-4 cladding tube using Kearn's f-parameter during its fabrication process.

  10. Texture and hydride orientation relationship of Zircaloy-4 fuel clad tube during its fabrication for pressurized heavy water reactors

    Energy Technology Data Exchange (ETDEWEB)

    Vaibhaw, Kumar [Nuclear Fuel Complex, ECIL Post, Hyderabad 500 062 (India)], E-mail: krvaibhaw@yahoo.co.in; Rao, S.V.R.; Jha, S.K.; Saibaba, N.; Jayaraj, R.N. [Nuclear Fuel Complex, ECIL Post, Hyderabad 500 062 (India)

    2008-12-15

    Zircaloy-4 material is used for cladding tube in pressurized heavy water reactors (PHWRs) of 220 MWe and 540 MWe capacity in India. These tubes are fabricated by using various combinations of thermo-mechanical processes to achieve desired mechanical and corrosion properties. Cladding tube develops crystallographic texture during its fabrication, which has significant influence on its in-reactor performance. Due to radiolytic decomposition of water Zircaloy-4 picks-up hydrogen. This hydrogen in excess of its maximum solubility in reactor operating condition ({approx}300 deg. C), precipitates as zirconium hydrides causing embrittlement of cladding tube. Hydride orientation in the radial direction of the tube limits the service life and lowers the fuel burn-up in reactor. The orientation of the hydride primarily depends on texture developed during fabrication. A correlation between hydride orientation (F{sub n}) with the texture in the tube during its fabrication has been developed using a second order polynomial. The present work is aimed at quantification and correlation of texture evolved in Zircaloy-4 cladding tube using Kearn's f-parameter during its fabrication process.

  11. Control-oriented modeling and real-time control for the ozone dosing process of drinking water treatment.

    Science.gov (United States)

    Wang, Dongsheng; Li, Shihua; Zhou, Xingpeng

    2013-03-01

    Ozonation is one of the most important steps during drinking water treatment. To improve the efficiency of ozonation and to stabilize the quality of the treated water, control-oriented modeling and a real-time control method for the ozone dosing process are developed in this study. Compared with existing ozonation models developed by bench-scale and pilot-scale batch experiments, the model reported herein is control-oriented and based on plant-scale batch experiments. A real-time control strategy for maintaining a constant ozone exposure is attempted to meet primary disinfection requirements. An internal model control scheme is proposed to maintain a constant ozone exposure by adjusting the ozone dosage. The proposed real-time control method can cope with changing water quality, water flow rate, and process operational conditions. Both simulations and experimental studies have been carried out and implemented for the ozone dosing process control system, and the results demonstrate the effectiveness and practicality of this real-time control method.

  12. sup 2 D NMR study of the dynamics of bound water molecules in dipalmitoyl-phosphatidylcholine-D sub 2 O system at a low water content

    CERN Document Server

    Takahashi, A; Takizawa, T

    2003-01-01

    We found two doublet signals A and B in sup 2 D-NMR of dipalmitoyl-phosphatidylcholine-D sub 2 O system at a low water content below the temperature of the onset of the main phase transition, i.e. in the beta'-crystalline (L subbeta sub ') phase. The splitting of each doublet becomes minimum at the onset of the transition. The signal A decreases in intensity with a slight increase of its splitting as the temperature increases further, accompanying the marked growth of the signal B in its intensity and splitting. These features of two doublets in the L subbeta sub ' phase and at higher temperatures have never been noticed. The signals A and B were ascribed to the tightly bound water and the loosely bound water, respectively. These assignments were confirmed by the theoretical calculations of the splitting of the doublet A for all possible number of the tightly bound water molecules. (author)

  13. Hydrogen migration within a water molecule: formation of HD+ upon irradiation of HOD with intense, ultrashort laser pulses

    Science.gov (United States)

    Mathur, Deepak; Dharmadhikari, Aditya K.; Dharmadhikari, Jayashree A.; Vasa, Parinda

    2017-08-01

    We have carried out velocity map imaging experiments on HOD molecules irradiated by 10 fs long pulses of intense (˜1 PW cm-2) laser light (800 nm). We have detected HD+ ions as a signature of unimolecular hydrogen migration within the water molecule; ion momentum maps measured at different laser polarizations yield evidence that such hydrogen migration occurs on ultrafast timescales. We have been able to utilize the momentum maps to deduce that (i) the HD+ ion that is formed is vibrationally excited, and (ii) that the electronic state of the precursor HOD2+ dication has an essentially linear geometrical structure with elongated O-H and O-D bonds. Our results are in agreement with expectations from ab initio quantum chemical computations of potential energy surfaces of the lowest-energy states of HOD, HOD+ and HOD2+.

  14. Charge-specific size-dependent separation of water-soluble organic molecules by fluorinated nanoporous networks

    Science.gov (United States)

    Byun, Jeehye; Patel, Hasmukh A.; Thirion, Damien; Yavuz, Cafer T.

    2016-11-01

    Molecular architecture in nanoscale spaces can lead to selective chemical interactions and separation of species with similar sizes and functionality. Substrate specific sorbent chemistry is well known through highly crystalline ordered structures such as zeolites, metal organic frameworks and widely available nanoporous carbons. Size and charge-dependent separation of aqueous molecular contaminants, on the contrary, have not been adequately developed. Here we report a charge-specific size-dependent separation of water-soluble molecules through an ultra-microporous polymeric network that features fluorines as the predominant surface functional groups. Treatment of similarly sized organic molecules with and without charges shows that fluorine interacts with charges favourably. Control experiments using similarly constructed frameworks with or without fluorines verify the fluorine-cation interactions. Lack of a σ-hole for fluorine atoms is suggested to be responsible for this distinct property, and future applications of this discovery, such as desalination and mixed matrix membranes, may be expected to follow.

  15. Cyclic State Orientation of Polar Molecules Produced by a Train of Half-Cycle Pulse Clusters of a Long Repetition Period

    Institute of Scientific and Technical Information of China (English)

    HUANG Yu-Xin; YANG Yu-Jun; WU Bin; GUO Fu-Ming; ZHU Qi-Ren

    2008-01-01

    @@ Using a variational method, we derive the optimal population distribution of angular momentum eigenstates for any given population range in a rotational wavepacket within the field-free cyclic state orientation framework.Correspondingly, we devise a train of half-cycle pulse clusters to purposively make the structure of the computed wavepacket approach the optimal population distribution, so that we can now utilize much more powerful means to realize an ideal orientation goal.

  16. Hydrogen bonding of single acetic acid with water molecules in dilute aqueous solutions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In separation processes,hydrogen bonding has a very significant effect on the efficiency of isolation of acetic acid (HOAc) from HOAc/H2O mixtures. This intermolecular interaction on aggregates composed of a single HOAc molecule and varying numbers of H2O molecules has been examined by using ab initio molecular dynamics simulations (AIMD) and quantum chemical calculations (QCC). Thermodynamic data in aqueous solution were obtained through the self-consistent reaction field calculations and the polarizable continuum model. The aggregation free energy of the aggregates in gas phase as well as in aqueous system shows that the 6-membered ring is the most favorable structure in both states. The relative stability of the ring structures inferred from the thermodynamic properties of the QCC is consistent with the ring distributions of the AIMD simulation. The study shows that in dilute aqueous solution of HOAc the more favorable molecular interaction is the hydrogen bonding between HOAc and H2O molecules,resulting in the separation of acetic acid from the HOAc/H2O mixtures with more difficulty than usual.

  17. Anisotropic dynamics of water ultraconfined in macroscopically oriented channels of single-crystal beryl: a multifrequency analysis.

    Science.gov (United States)

    Anovitz, Lawrence M; Mamontov, Eugene; ben Ishai, Paul; Kolesnikov, Alexander I

    2013-11-01

    The properties of fluids can be significantly altered by the geometry of their confining environments. While there has been significant work on the properties of such confined fluids, the properties of fluids under ultraconfinement, environments where, at least in one plane, the dimensions of the confining environment are similar to that of the confined molecule, have not been investigated. This paper investigates the dynamic properties of water in beryl (Be(3)Al(2)Si(6)O(18)), the structure of which contains approximately 5-Å-diam channels parallel to the c axis. Three techniques, inelastic neutron scattering, quasielastic neutron scattering, and dielectric spectroscopy, have been used to quantify these properties over a dynamic range covering approximately 16 orders of magnitude. Because beryl can be obtained in large single crystals we were able to quantify directional variations, perpendicular and parallel to the channel directions, in the dynamics of the confined fluid. These are significantly anisotropic and, somewhat counterintuitively, show that vibrations parallel to the c-axis channels are significantly more hindered than those perpendicular to the channels. The effective potential for vibrations in the c direction is harder than the potential in directions perpendicular to it. There is evidence of single-file diffusion of water molecules along the channels at higher temperatures, but below 150 K this diffusion is strongly suppressed. No such suppression, however, has been observed in the channel-perpendicular direction. Inelastic neutron scattering spectra include an intramolecular stretching O-H peak at ~465 meV. As this is nearly coincident with that known for free water molecules and approximately 30 meV higher than that in liquid water or ice, this suggests that there is no hydrogen bonding constraining vibrations between the channel water and the beryl structure. However, dielectric spectroscopic measurements at higher temperatures and lower

  18. Computational study of the interaction of indole-like molecules with water and hydrogen sulfide.

    Science.gov (United States)

    Cabaleiro-Lago, Enrique M; Rodríguez-Otero, Jesús; Peña-Gallego, Ángeles

    2011-10-01

    The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H···π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH(2) ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.

  19. Computational study of the interaction of indole-like molecules with water and hydrogen sulfide

    Science.gov (United States)

    Cabaleiro-Lago, Enrique M.; Rodríguez-Otero, Jesús; Peña-Gallego, Ángeles

    2011-10-01

    The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H...π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH2 ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.

  20. DFT studies of carbohydrate solvation: II. MD-DFTr of a super-molecule complex of glucose, explicit waters, and an implicit solvent (COSMO)

    Science.gov (United States)

    MD-DFTr studies are carried out on the super-molecule solvated complexes of glucose described in paper I. Included were ten explicit water molecules and an implicit solvation model, COSMO, superimposed upon the complex. Starting configurations were taken from DFTr optimized complexes resulting from ...

  1. Reactivity of ionic oxides through water molecules adsorption process; MgO-V sub 2 O sub 5 behaviour

    Energy Technology Data Exchange (ETDEWEB)

    Goni-Elizalde, S. (Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Instituto de Ciencias de la Construccion Eduardo Torroja); Garcia-Clavel, M.E. (Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Instituto de Edafologia)

    1991-03-01

    Crystalline V{sub 2}O{sub 5} reactivity is strongly dependent on both particle size and relative humidity surrounding the sample. To study the increase of reactivity of crystalline V{sub 2}O{sub 5} (grain size<0.05 mm), a mixture of MgO-V{sub 2}O{sub 5} (1:1) has been kept in a watervapour saturated atmosphere for different periods of time. X-ray diffraction is employed to follow the structural evolution of the mixture, the adsorption process of water molecules has been studied by infrared spectroscopy as well as by thermogravimetry. (author). 11 refs.; 5 figs.; 1 tab.

  2. Electron- and positron-induced ionization of water molecules: Theory versus experiment at the triply differential scale

    Science.gov (United States)

    Singh, P.; Purohit, G.; Champion, C.; Patidar, V.

    2014-03-01

    Triply differential cross sections for electron- and positron-induced ionization of the 3a1 orbital of the water molecule are calculated within the second-order distorted-wave Born approximation. In this context, distorted-wave functions are numerically calculated by modeling both the initial and the final channels whereas single-center Slater-type wave functions are used for describing the molecular target. A good agreement with the existing experimental data is observed. Differences in the trends of differential cross sections are observed for the electron- and positron-impact ionization.

  3. Infrared spectra of rubidium and cesium diaquatetrachloro-manganates. II. External vibrations of the water molecules

    Science.gov (United States)

    Stefov, Viktor; Šoptrajanov, Bojan; Petruševski, Vladimir

    1992-03-01

    Three bands of librational origin are found in the infrared spectra of Rb 2[MnCl 4 (H 2O) 2] and of its cesium analogue. On the basis of the behaviour on partial deuteration, the band having the lowest frequency can be attributed to a mode which is essentially rocking in character. The remaining two librations are the result of the partial mixing of the twisting and wagging modes. For the HDO molecules the out-of-plane ( oop) modes are mixed to a much higher degree, giving rise to modes which are best described as oop motions of the proton (H-motion) and the deuteron (D-motion) respectively.

  4. Flux controllable pumping of water molecules in a double-walled carb on nanotub e%通量可控的双壁碳纳米管水分子泵∗

    Institute of Scientific and Technical Information of China (English)

    曹平; 罗成林; 陈贵虎; 韩典荣; 朱兴凤; 戴亚飞

    2015-01-01

    A water pumping system model has been designed based on the double-walled carbon nanotube. In this system, the inner tube is fixed as the water channel, while the exterior one can move, similar to the piston motion along the axial direction, to create a pumping force. Molecular dynamics simulations confirm that both the water flux and the water dipole orientation are sensitive to the velocity of motions of the outer tube so that a controllable unidirectional water flow can be achieved in this system by varying the velocity. Its pumping ability comes mainly from the carbon–water van der Waals driving forces of the exterior tube. The piston motion of the outer tube changes the position of the vdW balance point, which not only leads to the increase of vdW force on the water molecules already residing in the inner tube, but also enlarges their accelerated distance. Meanwhile, the orientation of water molecules inside the inner tube is strongly coupled to the water flux, the probability of +dipole states attains unity at v=0.05 Å/ps, where the water flux reaches its maximum value (2.02 ns−1). Compared to the pump which is controlled by uniform electric field, the transmission efficiency of our mechanical pump is higher. This design may open a new way for water pumping in the field of nanodevices.%以双壁碳纳米管作为基本单元设计了一种新型纳米机械水泵,其内管固定作为水分子通道,外管做活塞式轴向运动。分子动力学计算表明,水分子净通量及管内水分子电偶极矩分布均与外管运动速率有强烈耦合效应。该设计可以实现水分子的高效单向运输,且输运效率可以通过外管活塞运动的速率进行调控。这些发现可为未来实用纳米分子泵器件的设计提供新的思路。

  5. GYY4137, a novel water-soluble, H2S-releasing molecule.

    Science.gov (United States)

    Rose, Peter; Dymock, Brian W; Moore, Philip K

    2015-01-01

    Hydrogen sulfide (H2S) is now recognized as the so called "third gasotransmitter" taking its place alongside nitric oxide and carbon monoxide. In recent years, H2S has been reported to exhibit a diverse range of pharmacological effects in biological systems. Much of this evidence is derived from a combination of conventional pharmacological and genetic approaches coupled with the use of chemical compounds such as sodium hydrosulfide, a rapid H2S releasing donor. Developments in the design of new drug entities which attempt to take into account physicochemical properties, targeting to specific cellular organelles, triggering of H2S release upon specific chemical reactions in the cell, and controlling the release of H2S over extended periods of time have been described. For most of these molecules, little or no work has been conducted to determine their biological activity or possible therapeutic effects. It is therefore not clear whether such molecules have therapeutic potential which highlights the need for further in vivo studies. One exception to the general rule is GYY4137 (morpholin-4-ium 4-methoxyphenyl(morpholino) phosphinodithioate), a slow releasing H2S donor, which has been evaluated for activity in a range of pharmacological models both in vitro and in vivo. GYY4137 was first reported to release H2S and exhibit vasodilator activity over 5 years ago and, to date, GYY4137 is becoming increasingly employed as a pharmacological "tool" to explore the biological functions of H2S.

  6. The key role of meteorites in the formation of relevant prebiotic molecules in a formamide/water environment

    Science.gov (United States)

    Rotelli, Luca; Trigo-Rodríguez, Josep M.; Moyano-Cambero, Carles E.; Carota, Eleonora; Botta, Lorenzo; di Mauro, Ernesto; Saladino, Raffaele

    2016-12-01

    We show that carbonaceous chondrite meteorites actively and selectively catalyze the formation of relevant prebiotic molecules from formamide in aqueous media. Specific catalytic behaviours are observed, depending on the origin and composition of the chondrites and on the type of water present in the system (activity: thermal > seawater > pure). We report the one-pot synthesis of all the natural nucleobases, of aminoacids and of eight carboxylic acids (forming, from pyruvic acid to citric acid, a continuous series encompassing a large part of the extant Krebs cycle). These data shape a general prebiotic scenario consisting of carbonaceous meteorites acting as catalysts and of a volcanic-like environment providing heat, thermal waters and formamide. This scenario also applies to the other solar system locations that experienced rich delivery of carbonaceous materials, and whose physical-chemical conditions could have allowed chemical evolution.

  7. The key role of meteorites in the formation of relevant prebiotic molecules in a formamide/water environment.

    Science.gov (United States)

    Rotelli, Luca; Trigo-Rodríguez, Josep M; Moyano-Cambero, Carles E; Carota, Eleonora; Botta, Lorenzo; Di Mauro, Ernesto; Saladino, Raffaele

    2016-12-13

    We show that carbonaceous chondrite meteorites actively and selectively catalyze the formation of relevant prebiotic molecules from formamide in aqueous media. Specific catalytic behaviours are observed, depending on the origin and composition of the chondrites and on the type of water present in the system (activity: thermal > seawater > pure). We report the one-pot synthesis of all the natural nucleobases, of aminoacids and of eight carboxylic acids (forming, from pyruvic acid to citric acid, a continuous series encompassing a large part of the extant Krebs cycle). These data shape a general prebiotic scenario consisting of carbonaceous meteorites acting as catalysts and of a volcanic-like environment providing heat, thermal waters and formamide. This scenario also applies to the other solar system locations that experienced rich delivery of carbonaceous materials, and whose physical-chemical conditions could have allowed chemical evolution.

  8. Size-dependent molecule-like to plasmonic transition in water-soluble glutathione stabilized gold nanomolecules

    Science.gov (United States)

    Kothalawala, Nuwan; Lee West, James, IV; Dass, Amala

    2013-12-01

    A size-dependent transition from molecule-like to plasmonic behaviour is demonstrated in the case of water soluble Au:SG nanomolecules. This was achieved using PAGE separation of smaller and larger nanomolecules, resulting in an unprecedented 26 bands, in a wide-range from 10's to 1000's of Au-atoms. PAGE separation of larger plasmonic nanomolecules is demonstrated for the first time. High resolution ESI-MS, with isotopic resolution, of smaller nanoparticles is reported, including the first time report of Au43(SG)26. This report will aid in the fundamental understanding of size-dependent properties of nanomolecules. The synthetic procedure employs a green approach with non-toxic chemicals and processes. The water solubility, non-toxicity and biocompatibility will lead to applications in biomedicine.A size-dependent transition from molecule-like to plasmonic behaviour is demonstrated in the case of water soluble Au:SG nanomolecules. This was achieved using PAGE separation of smaller and larger nanomolecules, resulting in an unprecedented 26 bands, in a wide-range from 10's to 1000's of Au-atoms. PAGE separation of larger plasmonic nanomolecules is demonstrated for the first time. High resolution ESI-MS, with isotopic resolution, of smaller nanoparticles is reported, including the first time report of Au43(SG)26. This report will aid in the fundamental understanding of size-dependent properties of nanomolecules. The synthetic procedure employs a green approach with non-toxic chemicals and processes. The water solubility, non-toxicity and biocompatibility will lead to applications in biomedicine. Electronic supplementary information (ESI) available: Detailed synthetic conditions, expanded MS, and optical spectra. This material is available free of charge via the Internet at http://pubs.acs.org. See DOI: 10.1039/c3nr03657j

  9. Proposed Photosynthesis Method for Producing Hydrogen from Dissociated Water Molecules Using Incident Near-Infrared Light

    Science.gov (United States)

    Li, Xingxing; Li, Zhenyu; Yang, Jinlong

    2014-01-01

    Highly efficient solar energy utilization is very desirable in photocatalytic water splitting. However, until now, the infrared part of the solar spectrum, which constitutes almost half of the solar energy, has not been used, resulting in significant loss in the efficiency of solar energy utilization. Here, we propose a new mechanism for water splitting in which near-infrared light can be used to produce hydrogen. This ability is a result of the unique electronic structure of the photocatalyst, in which the valence band and conduction band are distributed on two opposite surfaces with a large electrostatic potential difference produced by the intrinsic dipole of the photocatalyst. This surface potential difference, acting as an auxiliary booster for photoexcited electrons, can effectively reduce the photocatalyst's band gap required for water splitting in the infrared region. Our electronic structure and optical property calculations on a surface-functionalized hexagonal boron-nitride bilayer confirm the existence of such photocatalysts and verify the reaction mechanism.

  10. Effect of anodizing voltage on the sorption of water molecules on porous alumina

    Energy Technology Data Exchange (ETDEWEB)

    Vrublevsky, I., E-mail: vrublevsky@bsuir.edu.by [Belarusian State University of Informatics and Radioelectronics, Department of Micro and Nanoelectronics, 220013 Minsk (Belarus); Chernyakova, K. [Belarusian State University of Informatics and Radioelectronics, Department of Micro and Nanoelectronics, 220013 Minsk (Belarus); Bund, A.; Ispas, A.; Schmidt, U. [Fachgebiet Elektrochemie und Galvanotechnik, Technische Universitaet Ilmenau, 98693 Ilmenau (Germany)

    2012-05-01

    The amount of water adsorbed on different centers on the surface of oxalic acid alumina films is a function of the anodizing voltage. It is decreased with increasing the anodizing voltage from 20 up to 50 V, came up to maximum value at 20-30 V and slightly increased at voltages above 50 V. Water adsorption by oxide films formed at voltages below 50 V can be due to the negative surface charge that is present on the alumina surface. The negative surface charge disappears in the films formed at voltages higher than 50 V, and thus, the water is adsorbed on aluminum ions in a tetrahedral and octahedral environment. The correlation between anodizing conditions of aluminum in oxalic acid and the structure and composition of anodic alumina was established by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM), thermogravimetric and differential thermal analyses (TG/DTA).

  11. Nanometer range correlations between molecular orientations in liquids of molecules with perfect tetrahedral shape: CCl4, SiCl4, GeCl4, and SnCl4

    Science.gov (United States)

    Pothoczki, Sz.; Temleitner, L.; Jóvári, P.; Kohara, S.; Pusztai, L.

    2009-02-01

    Neutron and x-ray weighted total scattering structure factors of liquid carbon, silicon, germanium, and tin tetrachlorides, CCl4, SiCl4, GeCl4, and SnCl4, have been interpreted by means of reverse Monte Carlo modeling. For each material the two sets of diffraction data were modeled simultaneously, thus providing sets of particle coordinates that were consistent with two experimental structure factors within errors. From these particle configurations, partial radial distribution functions, as well as correlation functions characterizing mutual orientations of molecules as a function of distance between molecular centers were calculated. Via comparison with reference systems, obtained by hard sphere Monte Carlo simulations, we demonstrate that orientational correlations characterizing these liquids are much longer ranged than expected, particularly in carbon tetrachloride.

  12. Nanometer range correlations between molecular orientations in liquids of molecules with perfect tetrahedral shape: CCl(4), SiCl(4), GeCl(4), and SnCl(4).

    Science.gov (United States)

    Pothoczki, Sz; Temleitner, L; Jóvári, P; Kohara, S; Pusztai, L

    2009-02-14

    Neutron and x-ray weighted total scattering structure factors of liquid carbon, silicon, germanium, and tin tetrachlorides, CCl(4), SiCl(4), GeCl(4), and SnCl(4), have been interpreted by means of reverse Monte Carlo modeling. For each material the two sets of diffraction data were modeled simultaneously, thus providing sets of particle coordinates that were consistent with two experimental structure factors within errors. From these particle configurations, partial radial distribution functions, as well as correlation functions characterizing mutual orientations of molecules as a function of distance between molecular centers were calculated. Via comparison with reference systems, obtained by hard sphere Monte Carlo simulations, we demonstrate that orientational correlations characterizing these liquids are much longer ranged than expected, particularly in carbon tetrachloride.

  13. The effects of metabolite molecules produced by drinking water-isolated bacteria on their single and multispecies biofilms.

    Science.gov (United States)

    Simões, Lúcia Chaves; Simões, Manuel; Vieira, Maria João

    2011-08-01

    The elucidation of the mechanisms by which diverse species survive and interact in drinking water (DW) biofilm communities may allow the identification of new biofilm control strategies. The purpose of the present study was to investigate the effects of metabolite molecules produced by bacteria isolated from DW on biofilm formation. Six opportunistic bacteria, viz. Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp. isolated from a drinking water distribution systems (DWDS) were used to form single and multispecies biofilms in the presence and absence of crude cell-free supernatants produced by the partner bacteria. Biofilms were characterized in terms of mass and metabolic activity. Additionally, several physiological aspects regulating interspecies interactions (sessile growth rates, antimicrobial activity of cell-free supernatants, and production of iron chelators) were studied to identify bacterial species with biocontrol potential in DWDS. Biofilms of Methylobacterium sp. had the highest growth rate and M. mucogenicum biofilms the lowest. Only B. cepacia was able to produce extracellular iron-chelating molecules. A. calcoaceticus, B. cepacia, Methylobacterium sp. and M. mucogenicum biofilms were strongly inhibited by crude cell-free supernatants from the other bacteria. The crude cell-free supernatants of M. mucogenicum and S. capsulata demonstrated a high potential for inhibiting the growth of counterpart biofilms. Multispecies biofilm formation was strongly inhibited in the absence of A. calcoaceticus. Only crude cell-free supernatants produced by B. cepacia and A. calcoaceticus had no inhibitory effects on multispecies biofilm formation, while metabolite molecules of M. mucogenicum showed the most significant biocontrol potential.

  14. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis.

    Science.gov (United States)

    Pastor, M; Cruciani, G; Watson, K A

    1997-12-05

    Water present in a ligand binding site of a protein has been recognized to play a major role in ligand-protein interactions. To date, rational drug design techniques do not usually incorporate the effect of these water molecules into the design strategy. This work represents a new strategy for including water molecules into a three-dimensional quantitative structure-activity relationship analysis using a set of glucose analogue inhibitors of glycogen phosphorylase (GP). In this series, the structures of the ligand-enzyme complexes have been solved by X-ray crystallography, and the positions of the ligands and the water molecules at the ligand binding site are known. For the structure-activity analysis, some water molecules adjacent to the ligands were included into an assembly which encompasses both the inhibitor and the water involved in the ligand-enzyme interaction. The mobility of some water molecules at the ligand binding site of GP gives rise to differences in the ligand-water assembly which have been accounted for using a simulation study involving force-field energy calculations. The assembly of ligand plus water was used in a GRID/GOLPE analysis, and the models obtained compare favorably with equivalent models when water was excluded. Both models were analyzed in detail and compared with the crystallographic structures of the ligand-enzyme complexes in order to evaluate their ability to reproduce the experimental observations. The results demonstrate that incorporation of water molecules into the analysis improves the predictive ability of the models and makes them easier to interpret. The information obtained from interpretation of the models is in good agreement with the conclusions derived from the structural analysis of the complexes and offers valuable insights into new characteristics of the ligands which may be exploited for the design of more potent inhibitors.

  15. Missing Links in Global Water Governance: a Processes-Oriented Analysis

    Directory of Open Access Journals (Sweden)

    Claudia Pahl-Wostl

    2013-06-01

    Full Text Available Over the past decade, the policy and scholarly communities have increasingly recognized the need for governance of water-related issues at the global level. There has been major progress in the achievement of international goals related to the provision of basic water and some progress on sanitation services. However, the water challenge is much broader than securing supply. Doubts have been raised about the effectiveness of some of the existing governance processes, in the face of trends such as the unsustainable use of water resources, the increasing pressure imposed by climate change, or the implications of population growth for water use in food and energy production. Conflicts between different water uses and users are increasing, and the state of the aquatic environment is further declining. Inequity in access to basic water and sanitation services is still an issue. We argue that missing links in the trajectories of policy development are one major reason for the relative ineffectiveness of global water governance. To identify these critical links, a framework is used to examine how core governance processes are performed and linked. Special attention is given to the role of leadership, representativeness, legitimacy, and comprehensiveness, which we take to be critical characteristics of the processes that underpin effective trajectories of policy development and implementation. The relevance of the identified categories is illustrated with examples from three important policy arenas in global water governance: the effort to address access to water and sanitation, currently through the Millennium Development Goals; the controversy over large dams; and the links between climate change and water resources management. Exploratory analyses of successes and failures in each domain are used to identify implications and propose improvements for more effective and legitimate action.

  16. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car-Parrinello molecular dynamics study

    Science.gov (United States)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep

    2015-12-01

    The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car-Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  17. Maximum entropy analysis of NMR data of flexible multirotor molecules partially oriented in nematic solution: 2,2':5',2″-terthiophene, 2,2'- and 3,3'-dithiophene

    Science.gov (United States)

    Caldarelli, Stefano; Catalano, Donata; Di Bari, Lorenzo; Lumetti, Marco; Ciofalo, Maurizio; Alberto Veracini, Carlo

    1994-07-01

    The dipolar couplings observed by NMR spectroscopy of solutes in nematic solvents (LX-NMR) are used to build up the maximum entropy (ME) probability distribution function of the variables describing the orientational and internal motion of the molecule. The ME conformational distributions of 2,2'- and 3,3'-dithiophene and 2,2':5',2″-terthiophene (α-terthienyl)thus obtained are compared with the results of previous studies. The 2,2'- and 3,3'-dithiophene molecules exhibit equilibria among cisoid and transoid forms; the probability maxima correspond to planar and twisted conformers for 2,2'- or 3,3'-dithiophene, respectively, 2,2':5',2″-Terthiophene has two internal degrees of freedom; the ME approach indicates that the trans, trans and cis, trans planar conformations are the most probable. The correlation between the two intramolecular rotations is also discussed.

  18. Economic potential of market-oriented water storage decisions: Evidence from Australia

    Science.gov (United States)

    Brennan, Donna

    2010-08-01

    Significant reforms made to Australian irrigation property rights in recent years have enabled the development of an active seasonal water market. In contrast, decisions regarding the allocation of water across time are typically based on central decisions, with little or no opportunity offered to irrigators to manage risk by physically transferring their water access right between years by leaving it in the public dam. An empirical examination of the economics of water storage is presented using a case study of the Goulburn Valley, a major irrigation region in the state of Victoria. It is shown that, compared to the historically used, centrally determined storage policy, a market-based storage policy would store more water, on average, and would also allocate more water in periods of low rainfall. The analysis indicates that the costs associated with a recent prolonged drought were $100 million more than they would have been if water storage decisions had been guided by the market and prices were 3 times higher.

  19. Application of differential scanning calorimetry to measure the differential binding of ions, water and protons in the unfolding of DNA molecules.

    Science.gov (United States)

    Olsen, Chris M; Shikiya, Ronald; Ganugula, Rajkumar; Reiling-Steffensmeier, Calliste; Khutsishvili, Irine; Johnson, Sarah E; Marky, Luis A

    2016-05-01

    The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition. Copyright

  20. Organic Molecules and Water in the Inner Disks of T Tauri Stars

    Science.gov (United States)

    2011-05-11

    water emission properties in the full Spitzer spectrum (but see Section 4.2.2). By focusing on this wavelength region we can also optimize the...cores and comets are from references given in the text . (A color version of this figure is available in the online journal.) error bars corresponds to...because comets are made of icy material that was originally present in the Jupiter– Saturn region and in the outer solar nebula (the Kuiper Belt) during

  1. Protein-bound water molecule counting by resolution of (1)H spin-lattice relaxation mechanisms.

    OpenAIRE

    Kiihne, S; Bryant, R G

    2000-01-01

    Water proton spin-lattice relaxation is studied in dilute solutions of bovine serum albumin as a function of magnetic field strength, oxygen concentration, and solvent deuteration. In contrast to previous studies conducted at high protein concentrations, the observed relaxation dispersion is accurately Lorentzian with an effective correlation time of 41 +/- 3 ns when measured at low proton and low protein concentrations to minimize protein aggregation. Elimination of oxygen flattens the relax...

  2. Binding Energy of Molecules on Water Ice: Laboratory Measurements and Modeling

    CERN Document Server

    He, Jiao; Vidali, Gianfranco

    2016-01-01

    We measured the binding energy of N$_2$, CO, O$_2$, CH$_4$, and CO$_2$ on non-porous (compact) amorphous solid water (np-ASW), of N$_2$ and CO on porous amorphous solid water (p-ASW), and of NH$_3$ on crystalline water ice. We were able to measure binding energies down to a fraction of 1\\% of a layer, thus making these measurements more appropriate for astrochemistry than the existing values. We found that CO$_2$ forms clusters on np-ASW surface even at very low coverages. The binding energies of N$_2$, CO, O$_2$, and CH$_4$ decrease with coverage in the submonolayer regime. Their values at the low coverage limit are much higher than what is commonly used in gas-grain models. An empirical formula was used to describe the coverage dependence of the binding energies. We used the newly determined binding energy distributions in a simulation of gas-grain chemistry for cold cloud and hot core models. We found that owing to the higher value of desorption energy in the sub-monlayer regime a fraction of all these ice...

  3. Organic Molecules and Water in the Inner Disks of T Tauri Stars

    CERN Document Server

    Carr, John S

    2011-01-01

    We report high signal-to-noise Spitzer IRS spectra of a sample of eleven classical T Tauri stars. Molecular emission from rotational transitions of H2O and OH and ro-vibrational bands of simple organic molecules (CO2, HCN, C2H2) is common among the sources in the sample. The gas temperatures (200-800 K) and emitting areas we derive are consistent with the emission originating in a warm disk atmosphere in the inner planet formation region at radii < 2 AU. The H2O emission appears to form under a limited range of excitation conditions, as shown by the similarity in relative strengths of H2O features from star to star and the narrow range in derived temperature and column density. Emission from highly excited rotational levels of OH is present in all stars; the OH emission flux increases with the stellar accretion rate, and the OH/H2O flux ratio shows a relatively small scatter. We interpret these results as evidence for OH production via FUV photo-dissociation of H2O in the disk surface layers. No obvious ex...

  4. Effects of a movement and swimming program on water orientation skills and self-concept of kindergarten children with cerebral palsy.

    Science.gov (United States)

    Hutzler, Y; Chacham, A; Bergman, U; Reches, I

    1998-02-01

    In this study the effect of an experimental movement and swimming program of six months on motor function in the water measured by means of the Water Orientation Score and self-perception measured by means of the Martinek-Zaichkowsky Self-concept Scale was investigated. 23 children participated in the program, completing both tests prior to and after the intervention. An age-, sex-, and disability-matched control group of 23 children completed only the Self-concept Scale at pre- and posttest. Analysis indicated a significant improvement in Water Orientation Score of children in the trained group, but no effect on scores of the Self-concept Scale.

  5. Flow-alignment of bicellar lipid mixtures: orientations of probe molecules and membrane-associated biomacromolecules in lipid membranes studied with polarized light

    KAUST Repository

    Kogan, Maxim

    2011-01-01

    Bicelles are excellent membrane-mimicking hosts for a dynamic and structural study of solutes with NMR, but the magnetic fields required for their alignment are hard to apply to optical conditions. Here we demonstrate that bicellar mixtures can be aligned by shear forces in a Couette flow cell, to provide orientation of membrane-bound retinoic acid, pyrene and cytochrome c (cyt c) protein, conveniently studied with linear dichroism spectroscopy. © 2011 The Royal Society of Chemistry.

  6. Environmental assessment: Proposed construction of Refuge operational facilities, water management facilities, wildlife oriented interpretation/recreation development, road and water management facilities rehabilitation, and implementation of a vegetation control plan

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The proposed action consists of the construction of facilities for refuge operation, water management, and wildlife-oriented interpretation and recreation; the...

  7. Detailed Investigation Into a Single Water Molecule Entering Carbon Nanotubes%单个水分子与碳纳米管的离散-连续混合模型——水分子进入碳纳米管的条件及其相互作用力、速度和能量分布

    Institute of Scientific and Technical Information of China (English)

    R·安萨利; E·卡泽米; 海治

    2012-01-01

    研究水分子进入碳纳米管(CNT)时的物理特性.采用连续模型连同Lennard-Jones势函数,得到单壁面碳纳米管(SWCNT)与单个水分子之间的van der Waals力.水分子选择3种方位进入纳米管,其中水分子质心位于纳米管轴线上.对不同的纳米管半径和水分子进入方位,广泛地研究了相互作用力、能量和速度的分布.用分子动力学(MD)模拟得到的结果,来验证上述得到的相互作用力和能量分布.导出水分子进入纳米管时的可吸入半径,并详细地给出了有利于水分子进入纳米管半径的界限.计算单个水分子进入纳米管的速度,为不同进入方位的水分子,给出最大的入口速度和最大的管内速度.%The behavior of a water molecule while entering carbon nanotubes (CNTs) was studied. The Lennard-Jones potential function together with the continuum approximation was used to obtain the van der Waals interaction between a single-walled carbon nanotube (SWC-NT) and a single water molecule. Three orientations were chosen for water molecule as the centre of mass located on the axis of nanotube. Extensive studies on the variations of force, energy and velocity distributions were performed by varying the nanotube radius and the orientations of water molecule. The force and energy distributions were validated by those obtained from molecular dynamics (MD) simulations. The acceptance radius of nanotube for sucking the water molecule inside was derived also specified in which limit of radii, nanotube was favorable to absorb water molecule. The velocities of a single water molecule while entering nanotubes were calculated and maximum entrance and interior velocity for different orientations were assigned.

  8. Confined Water Determines Transport Properties of Guest Molecules in Narrow Pores.

    Science.gov (United States)

    Phan, Anh; Cole, David R; Weiß, R Gregor; Dzubiella, Joachim; Striolo, Alberto

    2016-08-23

    We computed the transport of methane through 1 nm wide slit-shaped pores carved out of solid substrates. Models for silica, magnesium oxide, and alumina were used as solid substrates. The pores were filled with water. The results show that the methane permeability through the hydrated pores is strongly dependent on the solid substrate. Detailed analysis of the simulated systems reveals that local properties of confined water, including its structure, and more importantly, evolution of solvation free energy and hydrogen bond structure are responsible for the pronounced differences observed. The simulations are extended to multicomponent systems representative of natural gas, containing methane, ethane, and H2S. The results show that all pores considered have high affinity for H2S, moderate affinity for methane, and low affinity for ethane. The H2S/methane transport selectivity through the hydrated alumina pore is comparable, or superior, to that reported for existing commercial membranes. A multiscale approach was then implemented to demonstrate that a Smoluchowski one-dimensional model is able to reproduce the molecular-level results for short pores when appropriate values for the local self-diffusion coefficients are used as input parameters. We propose that the model can be extended to predict methane transport through uniform hydrated pores of macroscopic length. When verified by experiments, our simulation results could have important implications in applications such as natural gas sweetening and predictions of methane migration through hydraulically fractured shale formations.

  9. Photo-electrochemical Oxidation of Organic C1 Molecules over WO3 Films in Aqueous Electrolyte: Competition Between Water Oxidation and C1 Oxidation.

    Science.gov (United States)

    Reichert, Robert; Zambrzycki, Christian; Jusys, Zenonas; Behm, R Jürgen

    2015-11-01

    To better understand organic-molecule-assisted photo-electrochemical water splitting, photo-electrochemistry and on-line mass spectrometry measurements are used to investigate the photo-electrochemical oxidation of the C1 molecules methanol, formaldehyde, and formic acid over WO3 film anodes in aqueous solution and its competition with O2 evolution from water oxidation O2 (+) and CO2 (+) ion currents show that water oxidation is strongly suppressed by the organic species. Photo-electro-oxidation of formic acid is dominated by formation of CO2 , whereas incomplete oxidation of formaldehyde and methanol prevails, with the selectivity for CO2 formation increasing with increasing potential and light intensity. The mechanistic implications for the photo-electro-oxidation of the organic molecules and its competition with water oxidation, which could be derived from this novel approach, are discussed.

  10. Water as probe molecule for midgap states in nanocrystalline strontium titanate by conventional and synchronous luminescence spectroscopy under ambient conditions

    Science.gov (United States)

    Taylor, Sean; Samokhvalov, Alexander

    2017-03-01

    Alkaline earth metal titanates are broad bandgap semiconductors with applications in electronic devices, as catalysts, photocatalysts, sorbents, and sensors. Strontium titanate SrTiO3 is of interest in electronic devices, sensors, in the photocatalytic hydrogen generation, as catalyst and sorbent. Both photocatalysis and operation of electronic devices rely upon the pathways of relaxation of excited charge in the semiconductor, including relaxation through the midgap states. We report characterization of nanocrystalline SrTiO3 at room temperature by "conventional" vs. synchronous luminescence spectroscopy and complementary methods. We determined energies of radiative transitions in the visible range through the two midgap states in the nanocrystalline SrTiO3. Further, adsorption and desorption of vapor of water as "probe molecule" for midgap states in the nanocrystalline SrTiO3 was studied, for the first time, by luminescence spectroscopy under ambient conditions. Emission of visible light from the nanocrystalline SrTiO3 is significantly increased upon desorption of water and decreased (quenched) upon adsorption of water vapor, due to interactions with the surface midgap states.

  11. Greenlandic water and sanitation-a context oriented analysis of system challenges towards local sustainable development.

    Science.gov (United States)

    Hendriksen, Kåre; Hoffmann, Birgitte

    2017-08-28

    Today, as Greenland focuses on more economic and cultural autonomy, the continued development of societal infrastructure systems is vital. At the same time, pressure is put on the systems by a lack of financial resources and locally based professional competences as well as new market-based forms of organization. Against this background, the article discusses the challenges facing Greenland's self-rule in relation to further develop the existing water and wastewater systems so that they can contribute to the sustainable development of Greenland. The article reviews the historical development of the water supply and wastewater system. This leads to an analysis of the sectorisation, which in recent decades has reorganized the Greenlandic infrastructures, and of how this process is influencing local sustainable development. The article discusses the socio-economic and human impacts and points to the need for developing the water and sanitation system to support not only hygiene and health, but also local sustainable development.

  12. The Research of Ecology-Oriented Reasonable Deployment of Water Resources at Shuangtaizi Estuary Wetland

    Institute of Scientific and Technical Information of China (English)

    LU Xiaofeng; WANG Tieliang; SU Fangli; ZHOU Linfei; LI Bo

    2011-01-01

    Shuangtaizi estuary wetland, the largest natural conservation district in China, and one of the best preserved, largest ecological lands with the most complete vegetation types in the world, is located in Panjin city, Liaoning Province. In rccent years,the degradation of Shuangtaizi estuary wetland is very serious. In order to rescue lives in the wetland and protect valuable natural resources, the information system of Shuangtaizi estuary wetland was built with ‘3S' technology, and the minimum, optimum, and maximum eco-environmental water requirements were calculated respectively. Furthermore, for restoring the ecological functions of wetland and preventing wetland degradation, the balance between supply and demand of water resource was analyzed, and an optimal allocation scheme of water resources was proposed based on three kinds of equilibrium.

  13. Theoretical investigation of hydrogen bonding between water and platinum(II): an atom in molecule (AIM) study

    Science.gov (United States)

    Li, Yan; Zhang, Guiqiu; Chen, Dezhan

    2012-02-01

    Recently, Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] [1] reported a hydrogen-bonding-like interaction between a water molecule and a d8 metal ion (PtII) based on neutron diffraction, and provided the first crystallographic evidence for this interaction. We studied the hydrogen bonding of the O-H ... Pt interaction theoretically using atoms in molecule (AIM) and natural bond orbital analysis (NBO) in the crystallographic geometries. The method used density functional theory (DFT) with the hybrid B3LYP function. For platinum atoms, we used the Los Alamos National Laboratory 2-Double-Zeta (LANL2DZ) basis set, and for the other atoms we used 6-311++G(d,p) basis sets. Criteria based on a topological analysis of the electron density were used in order to characterize the nature of interactions in the complexes. The main purpose of the present work is to provide an answer to the following questions: Why can a filled d orbital of square-planar d8 metal ions such as platinum(II) also act as hydrogen-bond acceptors? Can a study based on the electron charge density answer this question? A good correlation between the density at the intermolecular bond critical point and the energy interaction was found. The interaction is mainly closed-shell and there is some charge transfer in this system.

  14. Small molecule mixture analysis by heteronuclear NMR under spin diffusion conditions in the viscous DMSO-water solvent.

    Science.gov (United States)

    Lameiras, Pedro; Patis, Solène; Jakhlal, Jouda; Castex, Stéphanie; Clivio, Pascale; Nuzillard, Jean-Marc

    2017-02-13

    Spin diffusion in NMR occurs for small and medium-sized molecules when their tumbling rate reduces in solution so that magnetization exchange by longitudinal cross relaxation becomes highly efficient. Composite DMSO-water viscous solvents were used for the first time to access the individual NMR spectra of mixture components in spin diffusion conditions. The easy handling and high dissolution power of [D6]DMSO/H2O offers a wide range of potential applications for polar and apolar mixture analysis. In addition to 2D 1H-1H NOESY and 1H-13C HSQC-NOESY, 1H-15N HSQC-NOESY, 1D and 2D 1H-19F HOESY experiments were set up to offer new ways to individualize molecules within a mixture. This article reports the analysis of a polar mixture of four dipeptides dissolved in [D6]DMSO/H2O (7:3, v/v) and of a low polarity fluorinated dinucleotide dissolved in [D6]DMSO/H2O (8:2, v/v) by means of spin diffusion in NOESY, HOESY, and HSQC-NOESY experiments.

  15. Bond-selective fragmentation of water molecules with intense, ultrafast, carrier envelope phase stabilized laser pulses

    CERN Document Server

    Mathur, D; Dharmadhikari, J A; Dharmadhikari, A K

    2013-01-01

    Carrier envelope phase (CEP) stabilized pulses of intense 800 nm light of 5 fs duration are used to probe the dissociation dynamics of dications of isotopically-substituted water, HOD. HOD$^{2+}$ dissociates into either H$^+$ + OD$^+$ or D$^+$ + OH$^+$. The branching ratio for these two channels is CEP-dependent; the OD$^+$/OH$^+$ ratio (relative to that measured with CEP-unstabilized pulses) varies from 150% to over 300% at different CEP values, opening prospects of isotope-dependent control over molecular bond breakage. The kinetic energy released as HOD$^{2+}$ Coulomb explodes is also CEP-dependent. Formidable theoretical challenges are identified for proper insights into the overall dynamics which involve non-adiabatic field ionization from HOD to HOD$^+$ and, thence, to HOD$^{2+}$ via electron rescattering.

  16. Control of Hydrogen Generation from Water Molecules Dissociated by Activated Aluminum Particles Based on Fuzzy Logic

    Science.gov (United States)

    Maekawa, Koji; Takahara, Kenji; Kajiwara, Toshinori; Watanabe, Masao

    This paper proposes a control system to keep hydrogen generation by a reaction between water and activated aluminum particles at desired level. Because the activated aluminum particles are produced shredded aluminum sawdust, the characteristics of hydrogen generation vary depending on its samples. Therefore, the fuzzy control system to determine the quantum of the activated aluminum particles is designed based on the measured characteristics of hydrogen generation. Error form a desired value, error rate and dead time of the reaction are chosen as the labels of the proposed fuzzy membership functions. The reactor vessel that the activated aluminum particles are put into is developed to generate hydrogen continuously. Three types of aluminum particles of the characteristic are used for the experiments. The proposed system is confirmed to be useful for the control of hydrogen generation, coping with the effect of reacting characteristic changes according to the activated aluminum samples.

  17. Ubiquitous water-soluble molecules in aquatic plant exudates determine specific insect attraction.

    Directory of Open Access Journals (Sweden)

    Julien Sérandour

    Full Text Available Plants produce semio-chemicals that directly influence insect attraction and/or repulsion. Generally, this attraction is closely associated with herbivory and has been studied mainly under atmospheric conditions. On the other hand, the relationship between aquatic plants and insects has been little studied. To determine whether the roots of aquatic macrophytes release attractive chemical mixtures into the water, we studied the behaviour of mosquito larvae using olfactory experiments with root exudates. After testing the attraction on Culex and Aedes mosquito larvae, we chose to work with Coquillettidia species, which have a complex behaviour in nature and need to be attached to plant roots in order to obtain oxygen. This relationship is non-destructive and can be described as commensal behaviour. Commonly found compounds seemed to be involved in insect attraction since root exudates from different plants were all attractive. Moreover, chemical analysis allowed us to identify a certain number of commonly found, highly water-soluble, low-molecular-weight compounds, several of which (glycerol, uracil, thymine, uridine, thymidine were able to induce attraction when tested individually but at concentrations substantially higher than those found in nature. However, our principal findings demonstrated that these compounds appeared to act synergistically, since a mixture of these five compounds attracted larvae at natural concentrations (0.7 nM glycerol, <0.5 nM uracil, 0.6 nM thymine, 2.8 nM uridine, 86 nM thymidine, much lower than those found for each compound tested individually. These results provide strong evidence that a mixture of polyols (glycerol, pyrimidines (uracil, thymine, and nucleosides (uridine, thymidine functions as an efficient attractive signal in nature for Coquillettidia larvae. We therefore show for the first time, that such commonly found compounds may play an important role in plant-insect relationships in aquatic eco-systems.

  18. Control of the selectivity of the aquaporin water channel family by global orientational tuning

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Tajkhorshid, E.; Nollert, P.

    2002-01-01

    membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution...

  19. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2015-07-28

    Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

  20. Tehran Water Museum with the Performance-Oriented Approach to Bionic Architecture

    Directory of Open Access Journals (Sweden)

    Faeghe Farokhizad

    2017-01-01

    Full Text Available Form and function of architecture in nature, is a process that is perceived as instinctive as the development of internal growth and creation. The most basic level of commitment to life that reveals itself in the form of materials. Architecture form and shape to the beat and rhythm of the invisible life, in fact, it is a process which gives the project structure and the structure of the plan. Every living organism is driven by unchangeable force. Trying to become more efficient form and function. In the natural area is very important that "performance" is defined as the process and relationship and "form" is defined as a result of this process. Forms of interaction with nature that takes shape and naturally goes in the direction of performance to match its relationship with the wider environment and in the surrounding territory. Methods and new ideas can be learned from nature. Generally architecture is defined as to imagine, design, understanding and build according to circumstances. These problems may in itself was fully functional and to varying degrees, reflecting the economic, political and social project. In any case, it seems that the status quo is not simply satisfying. For this reason, we seek a new agreement that they "answer the question" is called. Therefore, in this study, based on architectural features permit, trying to establish a performance-oriented architecture, nature-based design and natural patterns to be defined by Vitruvius

  1. Vertically oriented Ti-Fe-O nanotube array films: toward a useful material architecture for solar spectrum water photoelectrolysis.

    Science.gov (United States)

    Mor, Gopal K; Prakasam, Haripriya E; Varghese, Oomman K; Shankar, Karthik; Grimes, Craig A

    2007-08-01

    In an effort to obtain a material architecture suitable for high-efficiency visible spectrum water photoelectrolysis, herein we report on the fabrication and visible spectrum (380-650 nm) photoelectrochemical properties of self-aligned, vertically oriented Ti-Fe-O nanotube array films. Ti-Fe metal films of variable composition, iron content ranging from 69% to 3.5%, co-sputtered onto FTO-coated glass are anodized in an ethylene glycol + NH4F electrolyte. The resulting amorphous samples are annealed in oxygen at 500 degrees C, resulting in nanotubes composed of a mixed Ti-Fe-O oxide. Some of the iron goes into the titanium lattice substituting titanium ions, and the rest either forms alpha-Fe2O3 crystallites or remains in the amorphous state. Depending upon the Fe content, the band gap of the resulting films ranges from about 380 to 570 nm. The Ti-Fe oxide nanotube array films are utilized in solar spectrum water photoelectrolysis, demonstrating 2 mA/cm2 under AM 1.5 illumination with a sustained, time-energy normalized hydrogen evolution rate by water splitting of 7.1 mL/W.hr in a 1 M KOH solution with a platinum counter electrode under an applied bias of 0.7 V. The surface morphology, structure, elemental analysis, optical, and photoelectrochemical properties of the Ti-Fe oxide nanotube array films are considered.

  2. Antiosteoporosis Activity of New Oriental Medicine Preparation (Kyungokgo Mixed with Water Extract of Hovenia dulcis on the Ovariectomized Mice

    Directory of Open Access Journals (Sweden)

    Yun-Ho Hwang

    2015-01-01

    Full Text Available Protective effect of new oriental medicine (Kyungokgo mixed with water extract of Hovenia dulcis, KOGHD was assessed on the bone loss induced mice by ovariectomy. In the in vivo experiments, antiosteoporosis effect of KOGHD was investigated using ovariectomized osteoporosis mice model. After 6 weeks of treatment, the mice were euthanized, and the effect of Kyungokgo (KOG and KOGHD on body weight, spleen weigh, thymus weight, uterine weight, serum biochemical indicators, bone weight and length, immune cell population, bone morphometric parameters, and histological stains was observed. Our results showed that KOGHD prevented the deterioration of trabecular microarchitecture caused by ovariectomy, which were accompanied by the lower levels of bone turnover markers and immune cell population as evidenced by the inhibition of RANKL-mediated osteoclast differentiation without cytotoxic effect on bone marrow derived macrophages (BMMs. Therefore, these results suggest that the Hovenia dulcis (HD supplementation in the KOG may also prevent and treat bone loss.

  3. Forming nanoparticles of water-soluble ionic molecules and embedding them into polymer and glass substrates

    Directory of Open Access Journals (Sweden)

    Stella Kiel

    2012-03-01

    Full Text Available This work describes a general method for the preparation of salt nanoparticles (NPs made from an aqueous solution of ionic compounds (NaCl, CuSO4 and KI. These nanoparticles were created by the application of ultrasonic waves to the aqueous solutions of these salts. When the sonication was carried out in the presence of a glass microscope slide, a parylene-coated glass slide, or a silicon wafer the ionic NPs were embedded in these substrates by a one-step, ultrasound-assisted procedure. Optimization of the coating process resulted in homogeneous distributions of nanocrystals, 30 nm in size, on the surfaces of the substrates. The morphology and structure of each of the coatings were characterized by physical and chemical methods, such as X-ray diffraction (XRD, scanning electron microscopy (SEM, atomic force microscopy (AFM, Raman spectroscopy and X-ray photoelectron spectroscopy (XPS. After 24 h of leaching into water the nanoparticles of the inorganic salts were still present on the slides, and complete leaching of nanoparticles occurred only after 96 h. A mechanism of the ultrasound-assisted coating is proposed.

  4. Greenlandic water and sanitation-a context oriented analysis of system challenges towards local sustainable development

    DEFF Research Database (Denmark)

    Hendriksen, Kåre; Hoffmann, Birgitte

    2017-01-01

    Today, as Greenland focuses on more economic and cultural autonomy, the continued development of societal infrastructure systems is vital. At the same time, pressure is put on the systems by a lack of financial resources and locally based professional competences as well as new market-based forms...... of organization. Against this background, the article discusses the challenges facing Greenland's self-rule in relation to further develop the existing water and wastewater systems so that they can contribute to the sustainable development of Greenland. The article reviews the historical development of the water...... supply and wastewater system. This leads to an analysis of the sectorisation, which in recent decades has reorganized the Greenlandic infrastructures, and of how this process is influencing local sustainable development. The article discusses the socio-economic and human impacts and points to the need...

  5. Aviation-oriented Micromachining Technology-Micro-ECM in Pure Water

    Institute of Scientific and Technical Information of China (English)

    Bao Huaiqian; Xu Jiawen; Li Ying

    2008-01-01

    This article proposes a precise and ecofriendly micromachining technology for aerospace application called electrochemical machining in pure water (PW-ECM). On the basis of the principles of water dissociation, a series of test setups and tests are devised and performed under different conditions. These tests explain the need for technological conditions realizing PW-ECM, and further explore the technological principles. The results from the tests demonstrate a successful removal of electrolytic slime by means of ultrasonic vibration of the workpiece. To ensure the stability and reliability of PW-ECM process, a new combined rnachining method of PW-ECM assisted with ultrasonic vibration (PW-ECM/USV) is devised. Trilateral and square cavities and holes as well as a group of English alphabets are worked out on a stainless steel plate. It is eonfirmed that PW-ECM will be probably an efficient new aviation precision machining method.

  6. Statistical thermodynamics of fluids with orientation-dependent interactions.

    NARCIS (Netherlands)

    Besseling, N.A.M.

    1993-01-01

    The aim of the present study was to develop a lattice theory for systems, homogeneous as well as heterogeneous, containing molecules with orientation- dependent interactions such as water. It was soon recognised that the so-called Bragg-Williams mean-field approximation is not capable of reproducing

  7. Double differential distribution of electron emission in the ionization of water molecules by fast bare oxygen ions

    Science.gov (United States)

    Bhattacharjee, Shamik; Biswas, Shubhadeep; Bagdia, Chandan; Roychowdhury, Madhusree; Nandi, Saikat; Misra, Deepankar; Monti, J. M.; Tachino, C. A.; Rivarola, R. D.; Champion, C.; Tribedi, Lokesh C.

    2016-03-01

    The doubly differential distributions of low-energy electron emission in the ionization of water molecules under the impact of fast bare oxygen ions with energy of 48 MeV are measured. The measured data are compared with two quantum-mechanical models, i.e. the post and prior versions of the continuum distorted wave-eikonal initial state (CDW-EIS) approximation, and the first-order Born approximation with initial and final wavefunctions verifying correct boundary conditions (CB1). An overall excellent qualitative agreement is found between the data and the CDW-EIS models whereas the CB1 model showed substantial deviation. However, the detailed angular distributions display some discrepancies with both CDW-EIS models. The single differential and total cross-sections exhibit good agreement with the CDW-EIS models. The present detailed data set could also be used as an input for modeling highly charged ion induced radiation damage in living tissues, whose most abundant component is water. Similar measurements are also carried out for a projectile energy of 60 MeV. However, since the double differential cross-section data show similar results the details are not provided here, except for the total ionization cross-sections results.

  8. Chemical interaction of water molecules with framework Al in acid zeolites: a periodic ab initio study on H-clinoptilolite.

    Science.gov (United States)

    Valdiviés-Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M

    2015-09-28

    Periodic quantum-chemistry methods as implemented in the CRYSTAL14 code were considered to analyse the interaction of acid clinoptilolite with water. Initially adsorbed molecules hydrolyse the Al-O bonds, giving rise to defective dealuminated materials. A suitable and representative periodic model of the partially disordered hydrated H-zeolite is the primitive cell (18 T sites) of a decahydrated trialuminated structure of HEU topology. The water distribution inside the material cavities was initially investigated. The model considered for further dealumination was the most stable one from those generated through a combined force field Monte Carlo and ab initio optimization strategy. Optimizations and energy estimations were made at the hybrid DFT level of theory (PBE0 functional) with an atomic basis set of VDZP quality. The energetics of the different pathways involved in the dealumination process was addressed by considering the Gibbs free energy with thermal and zero-point corrections through phonon analysis. It arises that hydrated models exhibit protonated water clusters stabilized by different kinds of H-bonds. The first Al extraction is slightly more energetically favourable from T3 than T2 sites, but at the same time the latter is more probable owing to its larger Al population. However, concerning the second dealumination step, it is more favourable removing the Al atom from both remaining sites after a starting abstraction from T2 rather than T3. These facts determine that the most probable overall pathways go through a first Al removal from T2. The agreement with experimental results is discussed.

  9. Process oriented thinking as a key for integration of ecohydrology, biotechnology and engineering for sustainable water resources management and ecosystems

    Science.gov (United States)

    Zalewski, M.

    2015-04-01

    The recent high rate of environmental degradation due to unsustainable use of water and other natural resources and mismanagement, is, in many cases, the result of a dominant sectoral approach, limited communication between different users and agencies, and lack of knowledge transfer between different disciplines, and especially lack of dialogue between environmental scientists and engineers. There is no doubt that the genuine improvement of human well-being has to be based on understanding the complexity of interactions between abiotic, biotic and socio-economic systems. The major drivers of biogeosphere evolution and function have been the cycles of water and nutrients in a complex array of differing climates and catchment geomorphologies. In the face of global climate change and unequally distributed human populations, the recent sectoral mechanistic approach in natural resources management has to be replaced by an evolutionary systems approach based on well-integrated problem-solving and policy-oriented environmental science. Thus the principles of ecohydrology should be the basis for further integration of ecology, hydrology, engineering, biotechnology and other environmental sciences. Examples from UNESCO IHP VII show how the integration of these will not only increase the efficiency of measures to harmonize ecosystem potentials with societal needs, but also significantly reduce the costs of sustainable environmental management.

  10. Dihydrogen phosphate-water tape and layers vs dihydrogen phosphate layers tuned by hydrophobic isomeric pyridine-diamine functionalized molecules

    Science.gov (United States)

    Huang, Jing; Liu, Tong-Peng; Huo, Li-Hua; Deng, Zhao-Peng; Gao, Shan

    2017-01-01

    Assembly of six isomeric pyridine-diamine-based molecules, N,N‧-bis(pyridin-4-ylmethyl)ethane-1,2-diamine (M1), N,N‧-bis(pyridin-3-ylmethyl)ethane-1,2-diamine (M2), N,N‧-bis(pyridin-2-ylmethyl)ethane-1,2-diamine (M3), N,N‧-bis(pyridin-4-ylmethyl)propane-1,3-diamine (M4), N,N‧-bis(pyridin-3-ylmethyl)propane-1,2-diamine (M5), and N,N‧-bis(pyridin-2-ylmethyl)propane-1,3-diamine (M6), with phosphoric acid (H3PO4) in different ratio (1:2 and 1:4), leads to the formation of nine salts, H2M12+·2H2PO4-·4H2O (1), H2M22+·2H2PO4-·2H2O (2), H2M32+·2H2PO4-·2H2O (3), H4M14+·4H2PO4- (4), H4M24+·4H2PO4- (5), H4M34+·4H2PO4- (6), H2M42+·2H2PO4-·3H2O (7), 2H2M52+·4H2PO4-·2H3PO4 (8), and H2M62+·2H2PO4- (9), which have been characterized by elemental analysis, IR, TG, PL, powder and single-crystal X-ray diffraction. Structural analyses indicate that hydrogen-bonding patterns of H2PO4- anions, conformation of protonated cations can effectively influence the supramolecular architectures through diverse non-covalent interactions. Hydrous salts 1-3 and 7 present 2D and 3D host-guest supramolecular networks, in which the connection of H2PO4- anions and water molecules generates diverse tape and layer motifs. H2PO4- anions in anhydrous salts 4-6 interconnect with each other through hydrogen bonds to form two types of layers, which are joined by discrete H4M4+ cations into 3D inorganic-organic hybrid supramolecular networks. Salts 8-9 also present 2D and 3D host-guest supramolecular networks where the interconnection of H2PO4- anions and its combination with H3PO4 molecules leads to diverse layers. Luminescent analyses indicate that salts 1-9 exhibit violet and blue emission maximum in the range of 390-467 nm at room temperature.

  11. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    Science.gov (United States)

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  12. Surface properties of woody thin boards composed of commercially available lignin and cellulose: Relationship between the orientation of lignin and water repellency

    Energy Technology Data Exchange (ETDEWEB)

    Shimanouchi, Toshinori; Kamba, Tomoya; Yang, Wei [Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530 (Japan); Aoyagi, Satoka [Department of Material and Lie Science, Seikei University, 3-3-1 Musashino, Tokyo 180-8633 (Japan); Kimura, Yukitaka, E-mail: yktkkimu@cc.okayama-u.ac.jp [Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530 (Japan)

    2015-08-30

    Highlights: • Woody thin boards were formed by adequate ratio of lignin/cellulose/moisture. • Component ratio of lignin/cellulose/moisture determined water repellency. • Increase of water repellency resulted from the surface orientation of lignin. - Abstract: Woody thin boards were prepared from lignin, cellulose, and water by compression molding at 180 °C and 25 MPa for 10 min. Boards with higher contact angles gave lower values of relative permittivity on their surface. Attenuated-total reflection Fourier transfer infrared spectroscopy suggested that more lignin existed on the surface of the boards with the high contact angle, which was also supported by scanning electron microscopy and atomic force microscopy. Our findings thus revealed that the orientation of lignin at the surface resulted in increased hydrophobicity of the surface and contributed to the enhancement of water repellency.

  13. 1H NMR detection of immobilized water molecules within a strong distal hydrogen-bonding network of substrate-bound human heme oxygenase-1.

    Science.gov (United States)

    Syvitski, Ray T; Li, Yiming; Auclair, Karine; Ortiz De Montellano, Paul R; La Mar, Gerd N

    2002-12-04

    Solution 1H NMR is used to probe the environments of the donor protons of eight strong hydrogen bonds on the distal side of the heme substrate in the cyanide-inhibited, substrate-bound complex of human heme oxygenase, hHO. It is demonstrated that significant magnetization transfer from the bulk water signal to the eight labile protons does not result from chemical exchange, but from direct nuclear Overhauser effect due to the dipolar interaction of these labile protons with "ordered" water molecules. The enzyme labile proton to water proton distances are estimated at approximately 3 A. It is proposed that the role of the strong hydrogen-bonding network is to immobilize numerous water molecules which both stabilize the activated hydroperoxy species and funnel protons to the active site.

  14. Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules.

    Science.gov (United States)

    Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin

    2009-06-02

    Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems [picture: see text], but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction.Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein-CNT complexes by charging the CNTs.

  15. Toward an improved control of the fixed-node error in quantum Monte Carlo: The case of the water molecule

    CERN Document Server

    Caffarel, Michel; Giner, Emmanuel; Scemama, Anthony

    2016-01-01

    All-electron Fixed-node Diffusion Monte Carlo (FN-DMC) calculations for the nonrelativistic ground-state energy of the water molecule at equilibrium geometry are presented. The determinantal part of the trial wavefunction is obtained from a perturbatively selected Configuration Interaction calculation (CIPSI method) including up to about 1.4 million of determinants. Calculations are made using the cc-pCV$n$Z family of basis sets, with $n$=2 to 5. In contrast with most QMC works no re-optimization of the determinantal part in presence of a Jastrow is performed. For the largest cc-pCV5Z basis set the lowest upper bound for the ground-state energy reported so far of -76.43744(18) is obtained. The fixed-node energy is found to decrease regularly as a function of the cardinal number $n$ and the Complete Basis Set limit (CBS) associated with {\\it exact nodes} is easily extracted. The resulting energy of -76.43894(12) -in perfect agreement with the best experimentally derived value- is the most accurate theoretical ...

  16. Near infrared light-driven water oxidation in a molecule-based artificial photosynthetic device using an upconversion nano-photosensitizer

    NARCIS (Netherlands)

    Liu, X.; Chen, H.C.; Kong, X.; Zhang, Y.; Tu, L.; Chang, Y.; Wu, F.; Wang, T.; Reek, J.N.H.; Brouwer, A.M.; Zhang, H.

    2015-01-01

    We provide the first demonstration of a near infrared light driven water oxidation reaction in a molecule-based artificial photosynthetic device using an upconversion nano-photosensitizer. One very attractive advantage of this system is that using NIR light irradiation does not cause significant pho

  17. Normal vibrations and vibrational amplitudes of the water molecule in crystalline barium nitrite monohydrate, Ba(NO 2) 2 · H 2O

    Science.gov (United States)

    Eriksson, Anders; de Villepin, Jacqueline; Romain, François

    1986-01-01

    Infrared and Raman spectroscopy and normal coordinate analysis used to investigate the detailed forms of the internal vibrations and the librations of the water molecule in Ba(NO 2) 2 · H 2O. The asymmetric bonding situation is shown to result in normal vibrations that tend to give displacements more or less localized to one OH bond of the water molecule. Thus, the mixing of twisting and wagging produces two normal modes which are more like H(1) and H(2) out-of-plane displacement, respectively. The corresponding mixing of bending and rocking also occurs, but to a smaller extent. Vibrational amplitudes for the hydrogen nuclei of the water molecule are derived in two ways; from earlier diffraction studies and from the normal coordinate analysis. The agreement between the two sets of amplitude is found to be very good in the OH bond directions and in the out-of-plane direction, but somewhat poorer in the in-plane direction which is perpendicular to the OH bonds. Some systematic deviations from the equilibrium geometry of the water molecule as obtained by neutron diffraction are discussed in view of the calculated normal vibrations and the vibrational model used in the diffraction experiment.

  18. Seasonal variations of rotifers from a high altitude urban shallow water body, La Cantera Oriente (Mexico City, Mexico)

    Science.gov (United States)

    Gutiérrez, Sergio González; Sarma, S. S. S.; Nandini, S.

    2016-12-01

    La Cantera Oriente is a shallow freshwater volcanic water body located at an altitude of 2 270 m above sea level in the Ecological Reserve of San Angel Pedregal of Mexico City (Mexico). In order to ensure the conservation of its biological heritage including zooplankton, the present work was undertaken to quantify the seasonal changes in the diversity and density of rotifers and the selected physico-chemical variables during 2013-2014. Qualitative analysis of the zooplankton samples yielded 68 rotifer species which represented 24 genera in 15 families. B rachionus calyciflorus Pallas, 1766, B. quadridentatus Hermann, 1783, Polyarthra vulgaris Carlin, 1943, Lecane closterocerca (Schmarda, 1859) and Keratella cochlearis (Gosse, 1851) were the most common species. Preston plots of species frequency-density revealed that as many as 30% of the rotifer taxa were dominant throughout the year. The species with high population densities were Brachionus quadridentatus, Lecane closterocerca, Keratella cochlearis, and Lepadella patella; their peak densities were 2 000, 1 000, 180 and 90 ind./L, all occurring in summer. Canonical correspondence analysis showed that Platyias quadricornis was related to the concentration of phosphates available in the environment and the conductivity, while B. quadridentatus was positively correlated with chlorophyll-a. The trophic status of the lake was eutrophic based on Chl-a content but oligotrophic with relation to the Brachionus:Trichocerca ratio.

  19. Effects of a movement and swimming program on vital capacity and water orientation skills of children with cerebral palsy.

    Science.gov (United States)

    Hutzler, Y; Chacham, A; Bergman, U; Szeinberg, A

    1998-03-01

    Swimming and aquatic exercise are known for their effects on respiration in normal and asthmatic people. The purpose of the present study was to evaluate the effect of a 6-month movement and swimming program on the respiratory function and water orientation skills of children with cerebral palsy (CP). Forty-six kindergarten children aged 5 to 7 years were assigned either to a treatment or control group. The intervention program consisted of swimming sessions twice weekly and sessions of group physical activity in a gym once weekly, each session lasting 30 minutes, for a period of 6 months. Children in the control group were treated (30 minutes, 4 days per week) with Bobath physical therapy. The children in the treatment and control groups had comparable disability types, age, and anthropometric measurements. A 2 x 2 (group x test period) repeated measures ANOVA design confirmed a significant effect of interaction of time with group. The results also confirmed that children with CP have reduced lung function compared with normative data for children in the same age category. The treatment program improved baseline vital capacity results by 65%, while children in the control group improved by only 23%. The movement and swimming exercise program had a better effect than a physical therapy routine implemented in a previous study, consisting of respiratory exercise alone.

  20. Predictive relationships for the effects of triglyceride ester concentration and water uptake on solubility and partitioning of small molecules into lipid vehicles.

    Science.gov (United States)

    Cao, Yichen; Marra, Michelle; Anderson, Bradley D

    2004-11-01

    The ability to predict drug solubility and partitioning in triglyceride solvents from the chemical structures of the solute and the triglyceride would be highly useful in drug formulation development and in screening drug candidates for lipid solubility and possibly drug bioavailability. This study explores the role of triglyceride ester concentration on small molecule partitioning between lipid vehicles and water, including the effect of ester concentration on water uptake. The influence of solvated water is further examined in studies of small molecule solubility in dry and water saturated lipid vehicles varying in triglyceride ester concentration. A series of model solutes with varying hydrogen bond donating/accepting abilities was chosen for this study while triglyceride ester concentrations were varied by using squalane/tricaprylin solvent mixtures. General linear free energy solvation relationships having the form utilized previously by Abraham were obtained at each solvent composition. An examination of the solvent descriptors indicated that those descriptors representing the sensitivity of the solvent to the solute dipolarity/polarizability, s, and to the hydrogen bond acidity of the solute, a, vary systematically with the concentration of ester moieties in the solvent mixture. An empirical equation has been derived that offers the potential for predicting triglyceride/water partition coefficients and in certain cases, solubility in hydrated, fully-saturated triglyceride solvents for any small molecule for which Abraham solute descriptors can be obtained. Water uptake in triglyceride vehicles is shown to be approximately linear with water activity and may also be described by the empirical relationship developed for other solutes providing an adjustment is made in the value of its hydrogen bond acidity parameter. Water uptake enhances the solubility of benzamide and N-methylbenzamide and a modest "water-dragging" effect by N-methylbenzamide in the

  1. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

    Science.gov (United States)

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

    2015-01-01

    In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

  2. 基于水质的水资源模型与水质经济学初探%Water Quality-oriented Water Resources Model and Water Quality Economics Frame

    Institute of Scientific and Technical Information of China (English)

    陈吉宁; 傅涛

    2009-01-01

    在对传统的以水量为核心的水资源模型理论与实践矛盾的分析基础上,阐述了水资源社会及自然循环规律,提出城市-流域系统中水资源利用的水质自然与人工再生过程和自然、人工修复的双要素.提出水质再生和水量循环的水资源模型及其假设和约束条件,确定了模型适用的边际条件和范围,据此进一步辨析了城市污水回用与再生水的异同,将再生水置于流域尺度的城市群上下游用户层面,提出污水回用(包括中水利用)是降低需求,再生水是增加总量的基本结论.在以水质为核心的水资源模型基础上,对现有水资源经济学定义进行了修正和补充,提出了水质经济学的基础概念,并讨论了水质经济学指导下的供水服务和价格模型结构,重新定位了再生水的战略并提出以流域水体的净化成本和人工水质改善成本共同形成的全成本高低来表征流域水资源短缺程度的缺水等级划分新思路.%By analyzing the conflict between the theoretical model and the actual applications of traditional water resource evaluation, this article elaborates the process and essential elements of self-recovery and artificial recovery of water quality within the City-River basin Systems. This article proposes a water resource model of water quality recovery and water exchange and further defines the marginal conditions and applicable scope. In doing so, the comparison between urban wastewater reuse and recycle has been made, where water reuse has been defined at a river-basin level and can be expressed as increasing water volume, while wastewater recycling refers to reducing water demand. This article proposes an innovative model-Water Quality-Oriented Water Resources Model-for evaluating water resources, which takes into account the renewable nature of water quality and water recycling. Based on the Water Quality-Oriented Water Resource Model, this article brings out the idea

  3. The influence of water molecules on NdCl3·3C3H8O in the properties: A DFT study

    Science.gov (United States)

    Li, Na; Sun, Fuquan; Chen, Jiaping; Li, Kelu; Li, Shiyi; Zhao, Liang; Liu, Zhichang; Gao, Jinsen

    2017-09-01

    The catalytic activity of NdCl3-ROH-AlR3 is closely related to the amount of water in NdCl3. Usually NdCl3·6H2O has been dehydrated step by step to NdCl3·2H2O, however, the further dehydration process will be very difficult. In this work, we investigated the effect of added water molecules on structures and properties of NdCl3·3C3H8O, NdCl3·3C3H8O·H2O, and NdCl3·3C3H8O·2H2O, including bond length, angle, mulliken atomic charge, molecular electrostatic potential (MEP), HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital) energy, and natural bond orbital (NBO). All properties were calculated by density functional theory (DFT) using B3PW91 functional and basis set of 6-31G++**/SDDALL. It was found that the bond length of Ndsbnd Cl bond and bond angles of Cl3-Ndsbnd Cl2, O9-Ndsbnd O5, Cl3-Ndsbnd Cl4 could be directly affected due to the addition of water molecule. The MEP analysis revealed that the molecular reaction site should be located around Cl atom. Furthermore, analysis of mulliken atomic charges showed that charge of Nd atom as the active center of the reaction changed from 0.956 to 1.238 and then to 1.301 after addition of one water molecule and two water molecules respectively. HOMO and LUMO orbitals were carried out to investigate the stability of the system, the addition of two water molecules in the system enhanced the electron flow in the system. Also, NBO analysis was further performed to supply an in depth insight into the electronic structure, the distribution of valence electrons and bond orders, which all changed after the addition of water molecule. Therefore, it was necessary to convert NdCl3·2H2O to NdCl3 in order to achieve a higher catalytic activity.

  4. Water Splitting: Strongly Coupled Nafion Molecules and Ordered Porous CdS Networks for Enhanced Visible-Light Photoelectrochemical Hydrogen Evolution (Adv. Mater. 24/2016).

    Science.gov (United States)

    Zheng, Xue-Li; Song, Ji-Peng; Ling, Tao; Hu, Zhen Peng; Yin, Peng-Fei; Davey, Kenneth; Du, Xi-Wen; Qiao, Shi-Zhang

    2016-06-01

    T. Ling, X.-W. Du, S. Z. Qiao, and co-workers report strongly coupled Nafion molecules and ordered-porous CdS networks for visible-light water splitting. The image conceptually shows how the three-dimensional ordered structure effectively harvests incoming light. As described on page 4935, the inorganic CdS skeleton is homogeneously passivated by the organic Nafion molecules to facilitate hydrogen generation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. The accommodation coefficient of water molecules on ice – cirrus cloud studies at the AIDA simulation chamber

    Directory of Open Access Journals (Sweden)

    J. Skrotzki

    2013-04-01

    Full Text Available Cirrus clouds and their impact on the Earth's radiative budget are subjects of current research. The processes governing the growth of cirrus ice particles are central to the radiative properties of cirrus clouds. At temperatures relevant to cirrus clouds, the growth of ice crystals smaller than a few microns in size is strongly influenced by the accommodation coefficient of water molecules on ice, αice, making this parameter relevant for cirrus cloud modeling. However, the experimentally determined magnitude of αice for cirrus temperatures is afflicted with uncertainties of almost three orders of magnitude, and values for αice derived from cirrus cloud data lack significance so far. This has motivated dedicated experiments at the cloud chamber AIDA (Aerosol Interactions and Dynamics in the Atmosphere to determine αice in the cirrus-relevant temperature interval between 190 K and 235 K under realistic cirrus ice particle growth conditions. The experimental data sets have been evaluated independently with two model approaches: the first relying on the newly developed model SIGMA (Simple Ice Growth Model for determining Alpha, the second one on an established model, ACPIM (Aerosol-Cloud-Precipitation Interaction Model. Within both approaches a careful uncertainty analysis of the obtained αice values has been carried out for each AIDA experiment. The results show no significant dependence of αice on temperature between 190 K and 235 K. In addition, we find no evidence for a dependence of αice on ice particle size or on water vapor supersaturation for ice particles smaller than 20 μm and supersaturations of up to 70%. The temperature-averaged and combined result from both models is αice = 0.7−0.5+0.3, which implies that αice may only exert a minor impact on cirrus clouds and their characteristics when compared to the assumption of αice =1. Impact on prior calculations of cirrus cloud properties, e.g., in climate models, with

  6. A hot water extract of Curcuma longa inhibits adhesion molecule protein expression and monocyte adhesion to TNF-α-stimulated human endothelial cells.

    Science.gov (United States)

    Kawasaki, Kengo; Muroyama, Koutarou; Yamamoto, Norio; Murosaki, Shinji

    2015-01-01

    The recruitment of arterial leukocytes to endothelial cells is an important step in the progression of various inflammatory diseases. Therefore, its modulation is thought to be a prospective target for the prevention or treatment of such diseases. Adhesion molecules on endothelial cells are induced by proinflammatory cytokines, including tumor necrosis factor-α (TNF-α), and contribute to the recruitment of leukocytes. In the present study, we investigated the effect of hot water extract of Curcuma longa (WEC) on the protein expression of adhesion molecules, monocyte adhesion induced by TNF-α in human umbilical vascular endothelial cells (HUVECs). Treatment of HUVECs with WEC significantly suppressed both TNF-α-induced protein expression of adhesion molecules and monocyte adhesion. WEC also suppressed phosphorylation and degradation of nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IκBα) induced by TNF-α in HUVECs, suggesting that WEC inhibits the NF-κB signaling pathway.

  7. Suppressing the fragmentation of fragile molecules in helium nanodroplets by co-embedding with water: Possible role of the electric dipole moment

    CERN Document Server

    Ren, Yanfei

    2007-01-01

    When fragile molecules such as glycine, polyglicine, alkanes, and alkanethiols are embedded in liquid helium nanodroplets, electron-impact ionization of the beam leads to fragmentation which is as extensive as that of isolated gas-phase molecules. However, it turns out that if a few molecules of water are co-embedded with the peptide and alkane chains, their fragmentation is drastically reduced or completely eliminated. On the other hand, the fragmentation of alkanethiols remains unaffected. On the basis of these observations, it is proposed that the fragmentation "buffering" effect may correlate with the magnitude of the impurity's electric dipole moment, which steers the migration of the ionizing He^+ hole in the droplet.

  8. Danish orientalism

    National Research Council Canada - National Science Library

    Zerlang, Martin

    2006-01-01

    Orientalism became an important current in nineteenth-century Danish culture, but although it was contemporaneous with the orientalism of the leading European nations - Great Britain, France, Germany...

  9. A theoretical study of water clusters: the relation between hydrogen-bond topology and interaction energy from quantum-chemical computations for clusters with up to 22 molecules.

    Science.gov (United States)

    Lenz, Annika; Ojamäe, Lars

    2005-05-07

    Quantum-chemical calculations of a variety of water clusters with eight, ten and twelve molecules were performed, as well as for selected clusters with up to 22 water molecules. Geometry optimizations were carried out at the B3LYP/cc-pVDZ level and single-point energies were calculated at the B3LYP/aug-cc-pVDZ level for selected clusters. The electronic energies were studied with respect to the geometry of the oxygen arrangement and six different characteristics of the hydrogen-bond arrangement in the cluster. Especially the effect of the placement of the non-hydrogen bonding hydrogens on the interaction energy was studied. Models for the interaction energy with respect to different characteristics of the hydrogen-bond arrangement were derived through least-square fits. The results from the study of the clusters with eight, ten and twelve molecules are used to predict possible low-energy structures for various shapes of clusters with up to 22 molecules.

  10. The Calculation of Lyapunov Exponent of Water Molecules Vibration System%基于水分子振动体系的Lyapunov指数的计算

    Institute of Scientific and Technical Information of China (English)

    刘松红; 庞成群

    2012-01-01

    采用wolf重构法改进了水分子振动体系最大Lyapunov指数的计算,通过对水分子振动体系的最大Lyapunov指数的计算,得到了计算水分子振动体系的最大Lyapunov指数合适的初始长度、延迟时间以及总的演化时间。%By adopting wolf reconstruction method and improving the method, we gained the expression of the maximum Lyapunov exponent of water molecules vibration system o From the results of calculating the maximum Lyapunov exponent of water molecules vibration system, we received the appropriate initial length, duration and the total evolution time.

  11. catena-Poly[[[(oxamide dioxime-κ2N,N')copper(II)]-μ-L-tartrato-κ4O1,O2:O3,O4] tetrahydrate]: a chiral nanochannel framework hosting solvent water molecules.

    Science.gov (United States)

    Bélombé, Michel M; Nenwa, Justin; Kouamo, Jean S T Wankap; Ponou, Siméon; Fischer, Andreas

    2012-05-01

    The crystal structure of the title compound, {[Cu(C(4)H(4)O(6))(C(2)H(6)N(4)O(2))]·4H(2)O}(n), contains the central Cu(II) cation in a distorted octahedral coordination, symmetrically chelated by the two imine N atoms of a neutral oxamide dioxime (H(2)oxado) ligand [Cu-N = 1.9829 (16) Å] and unsymmetrically bis-chelated by two halves of the L-(+)-tartrate(2-) (tart) ligands, each half being linked to the Cu(II) cation via the deprotonated carboxylate group and protonated hydroxy group [Cu-O = 1.9356 (14) and 2.4674 (13) Å, respectively]. The extended asymmetric unit is defined by twofold axes, one passing through the Cu(II) cation and the centre of the oxamide dioxime (H(2)oxado) ligand and the another two (symmetry related) bisecting the central C-C bonds of the tartrate ions. The structure is chiral, consisting of enantiomeric linear-chain polymers oriented along [001], with virtual monomeric {Cu(tart(0.5))(2)(H(2)oxado)} repeat units and with the chains interleaved face-to-face into `twin pillars'. Nanochannels exist, running parallel to the c axis and bisecting a and b, which host `double strings' of solvent water molecules. Extensive hydrogen bonding (O-H···O and N-H···O) between the chains and solvent water molecules, together with extended π-σ interactions, consolidate the bulk crystal structure.

  12. Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: a molecular dynamics study.

    Science.gov (United States)

    Wang, Lingyun; Yan, Feng

    2017-07-20

    Protein phosphatase 5 (PP5), mainly localized in human brain, can dephosphorylate tau protein whose high level of phosphorylation is related to Alzheimer's disease. Similar to other protein phosphatases, PP5 has a conserved motif in the catalytic domain that contains two binding sites for manganese (Mn(2+) ) ions. Structural data indicate that two active site water molecules, one bridging the two Mn(2+) ions and the other terminally coordinated with one of the Mn(2+) ions (Mn1), are involved in catalysis. Recently, a density functional theory study revealed that the two water molecules can be both deprotonated to keep a neutral active site for catalysis. The theoretical study gives us an insight into the catalytic mechanism of PP5, but the knowledge of how the deprotonation states of the two water molecules affect the binding of PP5 with its substrate is still lacking. To approach this problem, molecular dynamics simulations were performed to model the four possible deprotonation states. Through structural, dynamical and energetic analyses, the results demonstrate that the deprotonation states of the two water molecules affect the structure of the active site including the distance between the two Mn(2+) ions and their coordination, impact the interaction energy of residues R275, R400 and H304 which directly interact with the substrate phosphoserine, and mediate the dynamics of helix αJ which is involved in regulation of the enzyme's activity. Furthermore, the deprotonation state that is preferable for PP5 binding of its substrate has been identified. These findings could provide new design strategy for PP5 inhibitor. © 2017 The Protein Society.

  13. Accounting for target flexibility and water molecules by docking to ensembles of target structures: the HCV NS5B palm site I inhibitors case study.

    Science.gov (United States)

    Barreca, Maria Letizia; Iraci, Nunzio; Manfroni, Giuseppe; Gaetani, Rosy; Guercini, Chiara; Sabatini, Stefano; Tabarrini, Oriana; Cecchetti, Violetta

    2014-02-24

    The introduction of new anti-HCV drugs in therapy is an imperative need and is necessary with a view to develop an interferon-free therapy. Thus, the discovery and development of novel small molecule inhibitors of the viral NS5B polymerase represent an exciting area of research for many pharmaceutical companies and academic groups. This study represents a contribution to this field and relies on the identification of the best NS5B model(s) to be used in structure-based computational approaches aimed at identifying novel non-nucleoside inhibitors of one of the protein allosteric sites, namely, palm site I. First, the NS5B inhibitors at palm site I were classified as water-mediated or nonwater-mediated ligands depending on their ability to interact with or displace a specific water molecule. Then, we took advantage of the available X-ray structures of the NS5B/ligand complexes to build different models of protein/water combinations, which were used to investigate the influence on docking studies of solvent sites as well as of the influence of the protein conformations. As the overall trend, we observed improved performance in the docking results of the water-mediated inhibitors by inclusion of explicit water molecules, with an opposite behavior generally happening for the nonwater-mediated inhibitors. The best performing target structures for the two ligand sets were then used for virtual screening simulations of a library containing the known NS5B inhibitors along with related decoys to assess the best performing targets ensembles on the basis of their ability to discriminate active and inactive compounds as well as to generate the correct binding modes. The parallel use of different protein structures/water sets outperformed the use of a single target structure, with the two-protein 3H98/2W-2FVC/7W and 3HKY/NoW-3SKE/NoW models resulting in the best performing ensembles for water-mediated inhibitors and nonwater-mediated inhibitors, respectively. The information

  14. Isolating Site-Specific Spectral Signatures of Individual Water Molecules in H-Bonded Networks with Isotopomer-Selective Ir-Ir Double Resonance Vibrational Predissociation Spectroscopy

    Science.gov (United States)

    Wolke, Conrad T.; Johnson, Mark

    2016-06-01

    We will discuss an experimental method that directly yields the embedded correlations between the two OH stretches and the intramolecular bending modes associated with a single H2O water molecule embedded in an otherwise all-D isotopologue. This is accomplished using isotopomer-selective IR-IR hole-burning on the Cs+(D2O)5(H2O) clusters formed by gas-phase exchange of a single, intact H2O molecule for D2O in the Cs+(D2O)6 ion. The OH stretching pattern of the Cs+(H2O)6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H2O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules. This behavior enables a powerful new way to extract structural information from vibrational spectra of size-selected clusters by explicitly identifying the local environments responsible for specific infrared features. Extension of this method to address the degree to which OH stretches are decoupled in the protonated water clusters will also be discussed.

  15. Energy transfer in complexes of water-soluble quantum dots and chlorin e6 molecules in different environments.

    Science.gov (United States)

    Martynenko, Irina V; Orlova, Anna O; Maslov, Vladimir G; Baranov, Alexander V; Fedorov, Anatoly V; Artemyev, Mikhail

    2013-01-01

    The photoexcitation energy transfer is found and investigated in complexes of CdSe/ZnS cationic quantum dots and chlorin e6 molecules formed by covalent bonding and electrostatic interaction in aqueous solution and in porous track membranes. The quantum dots and chlorin e6 molecules form stable complexes that exhibit Förster resonance energy transfer (FRET) from quantum dots to chlorin e6 regardless of complex formation conditions. Competitive channels of photoexcitation energy dissipation in the complexes, which hamper the FRET process, were found and discussed.

  16. Structures of the Ca2+-regulated photoprotein obelin Y138F mutant before and after bioluminescence support the catalytic function of a water molecule in the reaction.

    Science.gov (United States)

    Natashin, Pavel V; Ding, Wei; Eremeeva, Elena V; Markova, Svetlana V; Lee, John; Vysotski, Eugene S; Liu, Zhi-Jie

    2014-03-01

    Ca(2+)-regulated photoproteins, which are responsible for light emission in a variety of marine coelenterates, are a highly valuable tool for measuring Ca(2+) inside living cells. All of the photoproteins are a single-chain polypeptide to which a 2-hydroperoxycoelenterazine molecule is tightly but noncovalently bound. Bioluminescence results from the oxidative decarboxylation of 2-hydroperoxycoelenterazine, generating protein-bound coelenteramide in an excited state. Here, the crystal structures of the Y138F obelin mutant before and after bioluminescence are reported at 1.72 and 1.30 Å resolution, respectively. The comparison of the spatial structures of the conformational states of Y138F obelin with those of wild-type obelin gives clear evidence that the substitution of Tyr by Phe does not affect the overall structure of both Y138F obelin and its product following Ca(2+) discharge compared with the corresponding conformational states of wild-type obelin. Despite the similarity of the overall structures and internal cavities of Y138F and wild-type obelins, there is a substantial difference: in the cavity of Y138F obelin a water molecule corresponding to W2 in wild-type obelin is not found. However, in Ca(2+)-discharged Y138F obelin this water molecule now appears in the same location. This finding, together with the observed much slower kinetics of Y138F obelin, clearly supports the hypothesis that the function of a water molecule in this location is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion before its decomposition into the excited-state product. Although obelin differs from other hydromedusan Ca(2+)-regulated photoproteins in some of its properties, they are believed to share a common mechanism.

  17. Excitation of water molecules by electron impact with formation of OH-radicals in the A{sup 2}{Sigma}{sup +} state

    Energy Technology Data Exchange (ETDEWEB)

    Khodorkovskii, M A; Murashov, S V [Saint-Petersburg State Polytechnic University, 195251, Saint-Petersburg (Russian Federation); Artamonova, T O; Rakcheeva, L P; Beliaeva, A A; Shakhmin, A L [Russian Scientific Center ' Applied Chemistry' , 197198, Saint-Petersburg (Russian Federation); Michael, D [General Electric Global Research Center, Niskayuna, NY 12309 (United States); Timofeev, N A; Mel' nikov, A S; Shevkunov, I A [Saint-Petersburg State University, 198904, Petrodvorets (Russian Federation); Zissis, G, E-mail: mkhodorkovskii@rscac.spb.r [Universite Touluse 3-Paul Sabatier, LAPLASE Building 3R2, 118rte de Narbonne, F-31062 Touluse Cedex 9 (France)

    2009-11-14

    The excitation cross-sections of the OH-radical band A{sup 2}{Sigma}{sup +} -> X{sup 2} (v' = 0 -> v'' = 0, v' = 1 -> v'' = 1) were measured. OH-radicals were formed during dissociation of water molecules by electron impact in the conditions of crossing of supersonic molecular and electron beams in the energy range 10-120 eV. Measurements were conducted at temperatures of 50, 80 and 200 K. It was shown that the excitation function had a sharp maximum in the region of low energies (at 16 eV) and an extended plateau up to 120 eV. It is proved that there are two channels of molecule dissociation with formation OH (A{sup 2}{Sigma}{sup +}) through excitation of either the triplet b{sup 3}A{sub 1} or the singlet B{sup 1}A{sub 1} states of H{sub 2}O molecules. The form of the excitation function essentially depends on the temperature of water vapours in the beam. With the decrease of the water molecule temperature the height of the plateau in the region 30-120 eV decreases in comparison with that of the peak at 16 eV. The absolute value of the excitation cross-section of the OH band at the temperature 50 K has been measured. It is equal to (1.6 +- 0.5) x 10{sup -18} cm{sup 2} in the maximum at 16 eV. The ratio of cross-sections of bands 1-1 and 0-0 weakly depends on the energy of the exciting electron in the range 12-120 eV and is equal to 0.28 +- 0.05. The appearance threshold is equal to (9.1 +- 0.5) eV.

  18. Librational modes of the water molecules in barium and strontium halide monohydrates, MX 2 · 1H 2O (M = Ba, Sr; X = Cl, Br, I)

    Science.gov (United States)

    Lutz, H. D.; Christian, H.

    1983-09-01

    The IR and Raman spectra of the isotypic alkaline earth halide monohydrates, MX 2 · 1H 2O, with M = Sr, Ba and X = Cl, Br, I, and of deuterated samples are presented for the range 200-700 cm -1 and discussed in terms of normal modes, assignment, coupling, correlation with structure data, and temperature dependence of both the H 2O (D 2O) and the HDO librational modes. The normal modes of the out-of-plane librations of HDO molecules are of the wagging and twisting type rather than H and D out-of-plane vibrations [4], at least for water molecules with C2v or nearly C2v symmetry. Thus the observed H 2O/HDO isotopic shifts can be used as a criterion for assigning the H 2O librations. The librational modes of the halide monohydrates (with tetrahedrally coordinated water oxygen atoms) are found in the order ν Rγ ≫ ν Rt ≫ ν Rr. The intensities of the IR and Raman spectra are in the order Rγ ≫ Rr ≫ Rt (or ˜ Rt in the case of strongly distorted H 2O molecules) and Rt ≫ Rr ≫ Rγ, respectively. Correlations of the H 2O librational modes with structural or bonding data are restricted by frequency shifts due to vibrational coupling and by the fact that the oxygen and the hydrogen atoms of the water molecules are generally affected in a different manner by bond interactions. However, in the case of the twisting vibrations, there are clear correlations with both the size of the metal ions, i.e. increase of ν Rt with decreasing size, and the intermolecular bonding of the hydrogen atoms, as shown by the OH stretching frequencies, i.e. increase of ν Rt with decreasing ν OH.

  19. Bonded hydrogen and hydrogen bonding in reciprocal space. Simulation of diffraction by a water molecule and dimer

    NARCIS (Netherlands)

    Poorthuis, G.H.A.; Feil, D.

    1994-01-01

    There seems to be increasing interest in the electron density distribution in molecules and crystals. In particular, the effect of polarization due to internal fields in condensed matter is studied. X-ray diffraction data can contribute to the knowledge required. As the effects of polarization on di

  20. Effect of water molecules on the fluorescence enhancement of Aflatoxin B1 mediated by Aflatoxin B1:beta-cyclodextrin complexes. A theoretical study.

    Science.gov (United States)

    Ramírez-Galicia, Guillermo; Garduño-Juárez, Ramón; Gabriela Vargas, M

    2007-01-01

    In order to explain the observed fluorescence enhancement of Aflatoxin B1 (AFB1) when forming AFB1:beta-cyclodextrin (AFB1:beta-CD) inclusion complexes, we have performed a theoretical (quantum chemistry calculations) study of AFB1 and AFB1:beta-CD in vacuum and in the presence of aqueous solvent. The AM1 method was used to calculate the absorption and emission wavelengths of these molecules. With the help of density functional theory (DFT) and time-dependent DFT (TDDFT) vibrational frequencies and related excitation energies of AFB1 and AFB1.(H2O)m = 4,5,6,11 were calculated. On the basis of these calculations we propose a plausible mechanism for the fluorescence enhancement of AFB1 in the presence of beta-CD: (1) before photoexcitation of AFB1 to its S1 excited state, there is a vibrational coupling between the vibrational modes involving the AFB1 carbonyl groups and the bending modes of the nearby water molecules (CG + WM); (2) these interactions allow a thermal relaxation of the excited AFB1 molecules that results in fluorescence quenching; (3) when the AFB1 molecules form inclusion complexes with beta-CD the CG + WM interaction decreases; and (4) this gives rise to a fluorescence enhancement.

  1. Molecule nanoweaver

    Science.gov (United States)

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  2. Rats' Orientation at the Start Point Is Important for Spatial Learning in a Water T-Maze

    Science.gov (United States)

    Peckford, Genieve; McRae, Samantha M.; Thorpe, Christina M.; Martin, Gerard M.; Skinner, Darlene M.

    2013-01-01

    When trained to locate a hidden platform in a T-maze moved between two positions, rats appear to adopt a conditional strategy based on start point discrimination. To determine if location cues or orientation cues at the start point underlie this discrimination, separate groups of rats were trained on two place problems, each with unique start…

  3. Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)

    2015-12-14

    In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.

  4. Anisotropic dynamics of water ultra-confined in macroscopically oriented channels of single-crystal beryl: A multi-frequency analysis

    Energy Technology Data Exchange (ETDEWEB)

    Anovitz, Lawrence {Larry} M [ORNL; Mamontov, Eugene [ORNL; Ishai, Paul ben [The Hebrew University of Jerusalem, Israel; Kolesnikov, Alexander I [ORNL

    2013-01-01

    The properties of fluids can be significantly altered by the geometry of their confining environments. While there has been significant work on the properties of such confined fluids, the properties of fluids under ultraconfinement, environments where, at least in one plane, the dimensions of the confining environment are similar to that of the confined molecule, have not been investigated. This paper investigates the dynamic properties of water in beryl (Be3Al2Si6O18), the structure of which contains approximately 5-A-diam channels parallel to the c axis. Three techniques, inelastic neutron scattering, quasielastic neutron scattering, and dielectric spectroscopy, have been used to quantify these properties over a dynamic range covering approximately 16 orders of magnitude. Because beryl can be obtained in large single crystals we were able to quantify directional variations, perpendicular and parallel to the channel directions, in the dynamics of the confined fluid. These are significantly anisotropic and, somewhat counterintuitively, show that vibrations parallel to the c-axis channels are significantly more hindered than those perpendicular to the channels. The effective potential for vibrations in the c direction is harder than the potential in directions perpendicular to it. There is evidence of single-file diffusion of water molecules along the channels at higher temperatures, but below 150 K this diffusion is strongly suppressed. No such suppression, however, has been observed in the channel-perpendicular direction. Inelastic neutron scattering spectra include an intramolecular stretching O-H peak at 465 meV. As this is nearly coincident with that known for free water molecules and approximately 30 meV higher than that in liquid water or ice, this suggests that there is no hydrogen bonding constraining vibrations between the channel water and the beryl structure. However, dielectric spectroscopic measurements at higher temperatures and lower frequencies

  5. Structural Changes of Water Molecules Upon the Reduction of Quinones in The Reaction Center from Rhodobactery Sphaeroides

    Institute of Scientific and Technical Information of China (English)

    T.Iwata; M.L.Paddock; M.Y.Okamura; H.Kandori

    2007-01-01

    1 Results The photosynthetic bacterial reaction center (RC) is a membrane protein complex.The RC is composed of three protein subunits and redox components such as bacteriochlorophylls, bacteriopheophytins,and quinones.The RC performs the photochemical electron transfer from the bacteriochlorophyll dimer through a series of electron donor and acceptor molecules to a secondary quinone,QB.QB accepts electrons from a primary quinone,QA,in two sequential electron transfer reactions.The second electron trans...

  6. Linking the physical and the socio-economic compartments of an integrated water and land use management model on a river basin scale using an object-oriented water supply model

    Science.gov (United States)

    Barthel, Roland; Nickel, Darla; Meleg, Alejandro; Trifkovic, Aleksandar; Braun, Juergen

    Within the framework of the research project ‘GLOWA-Danube’, a model of the water supply sector has been developed. GLOWA-Danube investigates long-term changes in the water cycle of the Upper Danube river basin in light of global change. For this purpose, the decision support system DANUBIA, comprising 15 fully coupled models, has been developed. Within DANUBIA the water supply model (‘WaterSupply’) forms the link between various physical models determining water quality and availability and several socio-economic models determining water consumption and demand. Having a central focus on public drinking water supply, its purpose is to correctly simulate the present day system of water extraction and distribution and the related costs, but also to allow meaningful response to possible future changes of boundary conditions, first and foremost changes in water demand or water availability and quality. Response mechanisms are also envisioned for changes in political and economic boundary conditions, and advances in technology. The model will be used locate critical regions which could experience water stress in the future, but does not aim to find the appropriate solutions or to predict the optimal organisation of water supply in the Danube Basin under such changing conditions. In the object-oriented model structure, both water supply companies (WSC) and communities are represented by main classes. Both classes have a limited view and knowledge of their environment. A community knows where and how much water is consumed and from which WSC it is served. A WSC possesses information regarding extraction sites and water rights, raw water quality and potential collaborating WSC. The WSC can perform actions that are different from ‘business as usual’. These deviations from their usual behaviour can be interpreted by decision makers but should not be regarded as a replacement for the decision-making process itself. The model is conceptualised using object-oriented

  7. An application of the novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: An ionic dissociation of a water molecule in the supercritical water.

    Science.gov (United States)

    Takahashi, Hideaki; Satou, Wataru; Hori, Takumi; Nitta, Tomoshige

    2005-01-22

    A novel quantum chemical approach recently developed has been applied to an ionic dissociation of a water molecule (2H(2)O-->H(3)O(+)+OH(-)) in ambient and supercritical water. The method is based on the quantum mechanical/molecular mechanical (QM/MM) simulations combined with the theory of energy representation (QM/MM-ER), where the energy distribution function of MM solvent molecules around a QM solute serves as a fundamental variable to determine the hydration free energy of the solute according to the rigorous framework of the theory of energy representation. The density dependence of the dissociation free energy in the supercritical water has been investigated for the density range from 0.1 to 0.6 g/cm(3) with the temperature fixed at a constant. It has been found that the product ionic species significantly stabilizes in the high density region as compared with the low density. Consequently, the dissociation free energy decreases monotonically as the density increases. The decomposition of the hydration free energy has revealed that the entropic term (-TDeltaS) strongly depends on the density of the solution and dominates the behavior of the dissociation free energy with respect to the variation of the density. The increase in the entropic term in the low density region can be attributed to the decrease in the translational degrees of freedom brought about by the aggregation of solvent water molecules around the ionic solute.

  8. Water-dispersible nanoparticles via interdigitation of sodium dodecylsulphate molecules in octadecylamine-capped gold nanoparticles at a liquid-liquid interface

    Indian Academy of Sciences (India)

    Anita Swami; Amol Jadhav; Ashavani Kumar; Suguna D Adyanthaya; Murali Sastry

    2003-10-01

    This paper describes the formation of water-dispersible gold nanoparticles capped with a bilayer of sodium dodecylsulphate (SDS) and octadecylamine (ODA) molecules. Vigorous shaking of a biphasic mixture consisting of ODA-capped gold nanoparticles in chloroform and SDS in water results in the rapid phase transfer of ODA-capped gold nanoparticles from the organic to the aqueous phase, the latter acquiring a pink, foam-like appearance in the process. Drying of the coloured aqueous phase results in the formation of a highly stable, reddish powder of gold nanoparticles that may be readily redispersed in water. The water-dispersible gold nanoparticles have been investigated by UV-Vis spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and Fourier transform infrared spectroscopy (FTIR). These studies indicate the presence of interdigitated bilayers consisting of an ODA primary monolayer directly coordinated to the gold nanoparticle surface and a secondary monolayer of SDS, this secondary monolayer providing sufficient hydrophilicity to facilitate gold nanoparticle transfer into water and rendering them water-dispersible.

  9. Vibrational and coherence dynamics of molecules

    CERN Document Server

    Zhang, Zhedong

    2015-01-01

    We {\\it analytically} investigate the population and coherence dynamics and relaxations in the vibrational energy transport in molecules. The corresponding two time scales $t_1$ and $t_2$ are explored. Coherence-population entanglement is found to considerably promote the time scale $t_2$ for dephasing and the amplitude of coherence. This is attributed to the suppression of the environment-induced drift force by coherence. Moreover the population imbalance (magnetization) is shown to be significantly amplified with the coherence-population entanglement. Contrary to the previous studies, we exactly elucidate a coherent process by showing $t_1orientational dynamics of OH-stretching modes in agreement with the recent experiments, when applied to the water molecules dissolved in D$_2$O. Finally we explore the coherence effect on the heat current at the macroscopic level.

  10. Dimethylamine Addition to Formaldehyde Catalyzed by a Single Water Molecule: A Facile Route for Atmospheric Carbinolamine Formation and Potential Promoter of Aerosol Growth.

    Science.gov (United States)

    Louie, Matthew K; Francisco, Joseph S; Verdicchio, Marco; Klippenstein, Stephen J; Sinha, Amitabha

    2016-03-10

    We use ab initio calculations to investigate the energetics and kinetics associated with carbinolamine formation resulting from the addition of dimethylamine to formaldehyde catalyzed by a single water molecule. Further, we compare the energetics for this reaction with that for the analogous reactions involving methylamine and ammonia separately. We find that the reaction barrier for the addition of these nitrogen-containing molecules onto formaldehyde decreases along the series ammonia, methylamine, and dimethylamine. Hence, starting with ammonia, the reaction barrier can be "tuned" by the substitution of an alkyl group in place of a hydrogen atom. The reaction involving dimethylamine has the lowest barrier with the transition state being 5.4 kcal/mol below the (CH3)2NH + H2CO + H2O separated reactants. This activation energy is significantly lower than that for the bare reaction occurring without water, H2CO + (CH3)2NH, which has a barrier of 20.1 kcal/mol. The negative barrier associated with the single-water molecule catalyzed reaction of dimethylamine with H2CO to form the carbinolamine (CH3)2NCH2OH suggests that this reaction should be energetically feasible under atmospheric conditions. This is confirmed by rate calculations which suggest that the reaction will be facile even in the gas phase. As amines and oxidized organics containing carbonyl functional groups are common components of secondary organic aerosols, the present finding has important implications for understanding how larger, less volatile organic compounds can be generated in the atmosphere by combining readily available smaller components as required for promoting aerosol growth.

  11. [Dynamics of Irreversible Evaporation of a Water-Protein Droplet and a Problem of Structural and Dynamical Experiments with Single Molecules].

    Science.gov (United States)

    Shaitan, K V; Armeev, G A; Shaytan, A K

    2016-01-01

    We discuss the effect of isothermal and adiabatic evaporation of water on the state of a water-protein droplet. The discussed problem is of current importance due to development of techniques to perform single molecule experiments using free electron lasers. In such structure-dynamic experiments the delivery of a sample into the X-ray beam is performed using the microdroplet injector. The time between the injection and delivery is in the order of microseconds. In this paper we developed a specialized variant of all-atom molecular dynamics simulations for the study of irreversible isothermal evaporation of the droplet. Using in silico experiments we determined the parameters of isothermal evaporation of the water-protein droplet with the sodium and chloride ions in the concentration range of 0.3 M at different temperatures. The energy of irreversible evaporation determined from in silico experiments at the initial stages of evaporation virtually coincides with the specific heat of evaporation for water. For the kinetics of irreversible adiabatic evaporation an exact analytical solution was obtained in the limit of high thermal conductivity of the droplet (or up to the droplet size of -100 Å). This analytical solution incorporates parameters that are determined using in silico. experiments on isothermal droplet evaporation. We show that the kinetics of adiabatic evaporation and cooling of the droplet scales with the droplet size. Our estimates of the water-protemi droplet. freezing rate in the adiabatic regime in a vacuum chamber show that additional techniques for stabilizing the temperature inside the droplet should be used in order to study the conformational transitions of the protein in single molecules. Isothermal and quasi-isothermal conditions are most suitable for studying the conformational transitions upon object functioning. However, in this case it is necessary to take into account the effects of dehydration and rapid increase of ionic strength in an

  12. An Intramolecular Silylene Borane Capable of Facile Activation of Small Molecules, Including Metal-Free Dehydrogenation of Water.

    Science.gov (United States)

    Mo, Zhenbo; Szilvási, Tibor; Zhou, Yu-Peng; Yao, Shenglai; Driess, Matthias

    2017-02-27

    The first single-component N-heterocyclic silylene borane 1 (LSi-R-BMes2 ; L=PhC(N(t) Bu)2 ; R=1,12-xanthendiyl spacer; Mes=2,4,6-Me3 C6 H2 ), acting as a frustrated Lewis pair (FLP) in small-molecule activation, can be synthesized in 65 % yields. Its HOMO is largely localized at the silicon(II) atom and the LUMO has mainly boron 2p character. In small-molecule activation 1 allows access to the intramolecular silanone-borane 3 featuring a Si=O→B interaction through reaction with O2 , N2 O, or CO2 , and formation of silanethione borane 4 from reaction with S8 . The Si(II) center in 1 undergoes immediate hydrogenation if exposed to H2 at 1 atm pressure in benzene, affording the silane borane 5-H2 , L(H2 )Si-R-BMes2 . Remarkably, no H2 activation occurs if the single silylene LSiPh and Mes3 B intermolecularly separated are exposed to dihydrogen. Unexpectedly, the pre-organized Si-B separation in 1 enables a metal-free dehydrogenation of H2 O to give the silanone-borane 3 as reactive intermediate.

  13. Comparative modeling of combined transport of water and graded-size molecules across the glomerular capillary wall.

    Science.gov (United States)

    Abdel-Mageed, Samir M; Mohamed, Ehab I

    2016-04-07

    Chronic kidney disease is a common and growing problem worldwide that necessitates recognition of individual risk and appropriate laboratory testing before its progression to end-stage renal failure, requiring dialysis or transplantation for survival. Clearance studies using various graded-size probe molecules established that the passage of molecules/proteins across the glomerular capillary barrier of mammalian kidneys is increasingly restricted as their size increase. Few mathematical models were developed to describe the dynamics of the size-selective functions of macromolecules across membranes and gelatins. In the present study, we compare the behavior of three mathematical descriptions for the Fiber Matrix theory, an Extended Fiber Matrix theory, and an Alternative Statistical Physics analysis to describe the size-selective function of the glomerular capillary barrier; using mainly its hemodynamic, morphometric and hydrodynamic variables; in two experimental rat models. The glomerular basement membrane was represented as a homogeneous three-dimensional network of fibers of uniform length (Lf), radius (Rf), total fractional solid volume of fibers (Vf) and characteristic Darcy permeability. The models were appropriate for simulating in vivo fractional clearance data of neutral Dextran and Ficoll macromolecules from two experimental rat models. We believe that the Lf, Rf and Vf best-fit numerical values may signify new insights for the diagnosis of human nephropathies.

  14. Orientation and Alignment Echoes

    CERN Document Server

    Karras, G; Billard, F; Lavorel, B; Hartmann, J -M; Faucher, O; Gershnabel, E; Prior, Y; Averbukh, I Sh

    2015-01-01

    We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses.

  15. Self-assembly of a Co(II) dimer through H-bonding of water molecules to a 3D open-framework structure

    Indian Academy of Sciences (India)

    Sujit K Ghosh; Parimal K Bharadwaj

    2005-01-01

    Reaction of pyridine-2,4,6-tricarboxylic acid (ptcH3) with Co(NO3)2.6H2O in presence of 4,4'-bipyridine (4,4'-bpy) in water at room temperature results in the formation of {[Co2(ptcH)2(4,4'-bpy)(H2O)4].2H2O}, (1). The solid-state structure reveals that the compound is a dimeric Co(II) complex assembled to a 3D architecture via an intricate intra- and inter-molecular hydrogen-bonding interactions involving water molecules and carboxylate oxygens of the ligand ptcH2-. Crystal data: monoclinic, space group 21/, = 11.441(5) Å, = 20.212(2) Å, = 7.020(5) Å, = 103.77(5)°, = 1576.7(1) Å3, = 2, 1 = 0.0363, 2 = 0.0856, = 1.000.

  16. A novel strategy to produce highly stable and transparent aqueous 'nanosolutions' of water-insoluble drug molecules

    Energy Technology Data Exchange (ETDEWEB)

    Wang Jiexin; Zhang Zhibing; Le Yuan; Chen Jianfeng [State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Zhao Hong, E-mail: chenjf@mail.buct.edu.cn [Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029 (China)

    2011-07-29

    A surprisingly large proportion of new drug candidates emerging from drug discovery programmes are water-insoluble and, as a result, have poor oral bioavailability. To overcome insolubility, the drug particles are usually dispersed in a medium during product formation, but large particles that are formed may affect product performance and safety. Many techniques have been used to produce nanodispersions-dispersions with nanometre-scale dimensions-that have properties similar to solutions. However, making nanodispersions requires complex processing, and it is difficult to achieve stability over long periods. In this paper, we report a generic method for preparing drug nanoparticles with a combination of antisolvent precipitation in the presence of water-soluble matrices and spray-drying. The spray-dried powder composites (solid dispersion) are microspherical, highly stable and thus form transparent nanodispersions or so-called 'nanosolutions' of water-insoluble drug when simply added to water. Aqueous nanodispersions of silybin (a kind of water-insoluble drug for liver protection) with an average size of 25 nm produced with this approach display a 10 times faster dissolution rate than that of raw drug. This has great potential to offer a novel solution for innovative drugs of the future.

  17. VUV lamp based on mixtures of inert gases with water molecules pumped by a pulsed-periodic capacitive discharge

    Science.gov (United States)

    Shuaibov, A. K.; Minya, A. I.; Malinin, A. N.; Homoki, Z. T.; Hrytsak, R. V.

    2012-01-01

    The spectral characteristics of the emission in the 140-315 nm range from pulsed-periodic capacitive discharges in mixtures of water vapor and helium and argon are described. In the VUV the most intense bands have maxima at λ = 156.0, 180.3, and 186.0 nm, and in the region of 300-315 nm, at λ = 312.1 and 313.4 nm. The brightness of the emission from the capacitive discharge plasma is optimized with respect to the partial pressures of helium, argon, and water vapor. The electron kinetic coefficients of discharges in argon and water vapor mixtures are calculated for E/N = 1-1000 Td.

  18. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Ignacio Boron

    2015-07-01

    Full Text Available Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O2 and •ŸNO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels interrupted by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify Ÿ•NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, Ÿ•NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

  19. Experimental measurements of water molecule binding energies for the second and third solvation shells of [Ca(H2O)n]2+ complexes

    Science.gov (United States)

    Bruzzi, E.; Stace, A. J.

    2017-01-01

    Further understanding of the biological role of the Ca2+ ion in an aqueous environment requires quantitative measurements of both the short- and long-range interactions experienced by the ion in an aqueous medium. Here, we present experimental measurements of binding energies for water molecules occupying the second and, quite possibly, the third solvation shell surrounding a central Ca2+ ion in [Ca(H2O)n]2+ complexes. Results for these large, previously inaccessible, complexes have come from the application of finite heat bath theory to kinetic energy measurements following unimolecular decay. Even at n = 20, the results show water molecules to be more strongly bound to Ca2+ than would be expected just from the presence of an extended network of hydrogen bonds. For n > 10, there is very good agreement between the experimental binding energies and recently published density functional theory calculations. Comparisons are made with similar data recorded for [Ca(NH3)n]2+ and [Ca(CH3OH)n]2+ complexes.

  20. Just three water molecules can trigger the undesired nonenzymatic reactions of aspartic acid residues: new insight from a quantum-chemical study

    Science.gov (United States)

    Takahashi, O.

    2014-03-01

    Aspartic acid (Asp) residues in peptides and proteins (L-Asp) can undergo spontaneous, nonenzymatic reactions under physiological conditions by which abnormal L-β-Asp, D-Asp, and/or D-β-Asp residues are formed. These altered Asp residues may affect the three-dimensional structures of the peptides and proteins and hence their properties and functions. In fact, the altered Asp residues are relevant to age-related diseases such as cataract and Alzheimer's disease. Most of the above reactions of the L-Asp residue proceed via a cyclic succinimide intermediate. In this paper, I propose a detailed mechanism of cyclization of an Asp residue (forming a precursor of the succinimide) by the B3LYP/6-31+G(d,p) density functional theory calculations carried out for a small Asp-containing model compound complexed with three water molecules which act as general acid-base catalysts in proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form. Then, successive reorientation of a water molecule and conformational change occur followed by the nucleophilic attack of the iminol nitrogen atom on the carboxyl carbon atom of the Asp side chain to form a five-membered ring. A satisfactory agreement was obtained between the calculated and experimental energetics.

  1. Effect of H-bonding interactions of water molecules in the self assembly of supramolecular architecture-joint experimental and computational studies

    Science.gov (United States)

    Jassal, Amanpreet Kaur; Kaur, Rajwinder; Islam, Nasarul; Anu; Mudsainiyan, Rahul Kumar

    2017-08-01

    A new {[Cu(4,4‧-BP)2.(H2O)4].2,6-NDC.3(H2O)} complex has been synthesized by refluxing Cu(NO3)2, 2,6-NDC and 4,4‧-BP (1:1:1 ratio) (2,6-NDC = 2,6-Naphthalene Dicarboxylic acid, 4,4‧-BP = 4,4'-bipyridine) in methanol/ammonia mixture and characterized by various spectroscopic techniques. The geometry around Cu2+ ion is typical octahedral in cationic complex, while the deprotonated 2,6-NDC act as a charge balancing counter anionic part. Water molecules (lattice and coordinated) also play important role in the self-assembly by forming Hsbnd bonded supramolecular architecture involving strong inter/intramolecular secondary interactions. The luminescence property and thermogravimetric analyses were also investigated. Both the intermolecular interactions of molecular and crystal structures of this complex were compared and discussed using Hirshfeld surface analysis and 2D-fingerprint plots. Hirshfeld surface analysis indicates that H⋯H, O⋯H and π···π contacts can account for 40.4, 19.3 and 7.7% respectively of the total Hirshfeld surface area. The DFT calculation at the CAM-B3LYP level of theory revealed the existence of three hydrogens binds in the complex. These hydrogen bonds exist between the oxygen atom of ligand and the hydrogen of coordinated water molecules.

  2. Kerosene-water separation in T-junction with orientation upward branch with a 60° angle: Variation of diameter ratio

    Science.gov (United States)

    Puspitasari, Dewi; Indarto, Purnomo, Khasani

    2016-06-01

    Research on the T-junction is still underway for the flow of liquid-liquid (kerosene-water). Some research on the characteristics of kerosene-water separation was performed using T-junction oriented upward branch with a 60° angle. To observe the effect of diameters ratio on the phase separation that produced T-junction then made a test section with a horizontal pipe diameter 36 mm, while the side arm 36 mm diameter, 26 mm and 19 mm (diameters ratio of 1, 0.7 and 0.5) by using plexiglass pipe type. Based on experimental results and visualization of data flow in the test section, to the value obtained 60% water cut, the maximum separation efficiency of 94%, FK = 0.94 and FW = 0.001 with a diameter ratio of 1. For other diameter ratio of 0.7 and 0.5 respectively separation efficiency of 66%, FK = 1 and Fw = 0.34 for 0.7 and separation efficiency of 84%, FK = 1 and Fw = 0.16 for 0.5, the best value is obtained at a water cut 60% too. All the best conditions to achieve the above-stratified flow pattern.

  3. Molecular dynamics simulation of the behaviour of water in nano-confined ionic liquid-water mixtures

    Science.gov (United States)

    Docampo-Álvarez, B.; Gómez-González, V.; Montes-Campos, H.; Otero-Mato, J. M.; Méndez-Morales, T.; Cabeza, O.; Gallego, L. J.; Lynden-Bell, R. M.; Ivaništšev, V. B.; Fedorov, M. V.; Varela, L. M.

    2016-11-01

    This work describes the behaviour of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid under nanoconfinement, between graphene sheets. By means of molecular dynamics simulations, the adsorption of water molecules at the graphene surface is studied. A depletion of water molecules in the vicinity of the neutral and negatively charged graphene surfaces, and their adsorption at the positively charged surface are observed in line with the preferential hydration of the ionic liquid anions. The findings are appropriately described using a two-level statistical model. The confinement effect on the structure and dynamics of the mixtures is thoroughly analyzed using the density and the potential of mean force profiles, as well as by the vibrational densities of the states of water molecules near the graphene surface. The orientation of water molecules and the water-induced structural transitions in the layer closest to the graphene surface are also discussed.

  4. Orienteering injuries

    OpenAIRE

    Folan, Jean M.

    1982-01-01

    At the Irish National Orienteering Championships in 1981 a survey of the injuries occurring over the two days of competition was carried out. Of 285 individual competitors there was a percentage injury rate of 5.26%. The article discusses the injuries and aspects of safety in orienteering.

  5. Atkins' molecules

    CERN Document Server

    Atkins, Peters

    2003-01-01

    Originally published in 2003, this is the second edition of a title that was called 'the most beautiful chemistry book ever written'. In it, we see the molecules responsible for the experiences of our everyday life - including fabrics, drugs, plastics, explosives, detergents, fragrances, tastes, and sex. With engaging prose Peter Atkins gives a non-technical account of an incredible range of aspects of the world around us, showing unexpected connections, and giving an insight into how this amazing world can be understood in terms of the atoms and molecules from which it is built. The second edition includes dozens of extra molecules, graphical presentation, and an even more accessible and enthralling account of the molecules themselves.

  6. 油纸复合介质中水分子扩散行为的分子动力学模拟%Molecular Dynamics Simulation of the Diffusion Behavior of Water Molecules in Oil and Cellulose Composite Media

    Institute of Scientific and Technical Information of China (English)

    廖瑞金; 朱孟兆; 周欣; 杨丽君; 严家明; 孙才新

    2011-01-01

    The diffusion behaviors of water molecules in oil-cellulose composite media were studied at different temperatures using a molecular dynamics simulation. By analyzing the formation of hydrogen bonds between the water molecules and cellulose we found that the water molecules that were initially present in the oil gradually spread to the cellulose, and hydrogen bonds were formed between them. The water molecules that were present in the cellulose initially also formed hydrogen bonds and were bound to cellulose molecules. By analyzing the diffusion coefficients of the water molecules at different temperatures we found that the diffusion behaviors of the water molecules in the two single-media,namely oil and cellulose, were very different because of their different polarities. The diffusion coefficients of the water molecules in the composite media were influenced greatly by the ratio of water molecules present in the oil and cellulose and a strong correlation was apparent between them. The water molecule-oil interaction energy and the water molecule-cellulose interaction energy were also strongly related to the polarities of the oil and the cellulose. The interaction energies also exhibited a strong correlation to the distribution of water molecules at different temperatures. This was the reason for the weakened influence of temperature on the diffusion coefficient of the water molecules, which was due to the different distributions of water molecules at different temperatures.%对不同温度下水分子在油纸复合介质中的扩散行为进行了分子动力学模拟研究.通过分析水分子与纤维素形成的氢键发现,油中的水分子在模拟过程中会逐渐扩散到纤维素内并与之形成氢键,而纤维素内的水分子则与纤维素形成氢键后被束缚于纤维素中.通过分析水分子的扩散系数发现,由于油和纤维素的极性不同,使得水分子在油和纤维素两种单介质中的扩散行为有较大差别,而在

  7. A comparative study of thermo-sensitive hydrogels with water-insoluble paclitaxel in molecule, nanocrystal and microcrystal dispersions.

    Science.gov (United States)

    Lin, Zhiqiang; Mei, Dong; Chen, Meiwan; Wang, Yitao; Chen, Xianhui; Wang, Zhaoyang; He, Bing; Zhang, Hua; Wang, Xueqing; Dai, Wenbing; Yin, Yuxin; Zhang, Qiang

    2015-09-28

    In situ thermo-sensitive hydrogels have attracted increasing attention for alternative cancer therapies due to their long-term and effective drug levels at local sites. Besides synthesizing new thermo-sensitive polymers, we can also fabricate this delivery system by combining a hydrogel with a thermo-response and drug in a different dispersion state, such as drug nanocrystals. However, the impact of the drug dispersion state or dimension on the quality of such a local injectable system is still unknown. So, here we developed and compared three types of F127 hydrogel systems with either paclitaxel or the near infra-red probe DiR in molecules (MOs), nanocrystals (NCs) and microcrystals (MCs), respectively. With 120 nm rod-shape nanocrystals, the NCs-Gel achieved a high drug loading, moderate drug release rate and gel erosion in vitro and in vivo, medium intratumoral drug residue but the best anti-tumor efficacy in 4T1 tumor bearing BALB/c mice. With the free drug solubilized in 20 nm micelles of the gel, the MOs-Gel system demonstrated the least drug loading and the fastest drug release and gel erosion, leading to the least intratumoral residue as well as the lowest anti-tumor effect. Finally, when dispersed in micron-grade rod-shape drug crystals, the MCs-Gel exhibited a high drug loading but poor stability, precipitating in vitro and in vivo, the highest intratumoral residue but the least drug release, resulting in moderate tumor inhibition. In conclusion, this study clarifies the effect of the drug dispersion state and scale on the behavior of a thermo-sensitive hydrogel, indicating the advantage of the NCs-Gel system, and it provides a basis for the future design of the local delivery of hydrophobic anti-cancer agents.

  8. A comparative study of thermo-sensitive hydrogels with water-insoluble paclitaxel in molecule, nanocrystal and microcrystal dispersions

    Science.gov (United States)

    Lin, Zhiqiang; Mei, Dong; Chen, Meiwan; Wang, Yitao; Chen, Xianhui; Wang, Zhaoyang; He, Bing; Zhang, Hua; Wang, Xueqing; Dai, Wenbing; Yin, Yuxin; Zhang, Qiang

    2015-09-01

    In situ thermo-sensitive hydrogels have attracted increasing attention for alternative cancer therapies due to their long-term and effective drug levels at local sites. Besides synthesizing new thermo-sensitive polymers, we can also fabricate this delivery system by combining a hydrogel with a thermo-response and drug in a different dispersion state, such as drug nanocrystals. However, the impact of the drug dispersion state or dimension on the quality of such a local injectable system is still unknown. So, here we developed and compared three types of F127 hydrogel systems with either paclitaxel or the near infra-red probe DiR in molecules (MOs), nanocrystals (NCs) and microcrystals (MCs), respectively. With 120 nm rod-shape nanocrystals, the NCs-Gel achieved a high drug loading, moderate drug release rate and gel erosion in vitro and in vivo, medium intratumoral drug residue but the best anti-tumor efficacy in 4T1 tumor bearing BALB/c mice. With the free drug solubilized in 20 nm micelles of the gel, the MOs-Gel system demonstrated the least drug loading and the fastest drug release and gel erosion, leading to the least intratumoral residue as well as the lowest anti-tumor effect. Finally, when dispersed in micron-grade rod-shape drug crystals, the MCs-Gel exhibited a high drug loading but poor stability, precipitating in vitro and in vivo, the highest intratumoral residue but the least drug release, resulting in moderate tumor inhibition. In conclusion, this study clarifies the effect of the drug dispersion state and scale on the behavior of a thermo-sensitive hydrogel, indicating the advantage of the NCs-Gel system, and it provides a basis for the future design of the local delivery of hydrophobic anti-cancer agents.

  9. Enumerating molecules.

    Energy Technology Data Exchange (ETDEWEB)

    Visco, Donald Patrick, Jr. (, . Tennessee Technological University, Cookeville, TN); Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  10. Size, shape, and site selectivities in the photochemical reactions of molecules adsorbed on pentasil zeolites. Effects of coadsorbed water

    Energy Technology Data Exchange (ETDEWEB)

    Turro, N.J.; Cheng, C.; Abrams, L.; Corbin, D.R.

    1987-04-15

    The photochemistry of methylbenzyl benzyl ketones (ACOB) in the presence of pentasil zeolites follows strikingly different pathways due to the location of the adsorbed ketone. The product distribution, in terms of the cage effect (efficiency of germinate radical combination), demonstrates the effects of sorption and diffusion on the radical species produced by photolysis. p-ACOB is readily adsorbed within the pentasil framework and produces p-AB as the primary product. In contrast, the photolysis product distributions of o-ACOB can be dramatically varied depending upon the extent of its adsorption into the framework. By addition of a nonreactive titrant, such as water, after the ketone adsorption, the photolysis product distributions can be systematically varied depending upon the aluminum content of the framework. The observed results are completely described by considerations of (a) the size and shape sorption of the pentasil zeolites, (b) the sorption of water by the hydrophilic sites of the pentasil zeolites (which depend upon the framework aluminum content), and (c) the hydrophobic characteristics of the pentasil channels which do not contain framework aluminum.

  11. Formation of the prebiotic molecule NH$_2$CHO on astronomical amorphous solid water surfaces: accurate tunneling rate calculations

    CERN Document Server

    Song, Lei

    2016-01-01

    Investigating how formamide forms in the interstellar medium is a hot topic in astrochemistry, which can contribute to our understanding of the origin of life on Earth. We have constructed a QM/MM model to simulate the hydrogenation of isocyanic acid on amorphous solid water surfaces to form formamide. The binding energy of HNCO on the ASW surface varies significantly between different binding sites, we found values between $\\sim$0 and 100 kJ mol$^{-1}$. The barrier for the hydrogenation reaction is almost independent of the binding energy, though. We calculated tunneling rate constants of H + HNCO $\\rightarrow$ NH$_2$CO at temperatures down to 103 K combining QM/MM with instanton theory. Tunneling dominates the reaction at such low temperatures. The tunneling reaction is hardly accelerated by the amorphous solid water surface compared to the gas phase for this system, even though the activation energy of the surface reaction is lower than the one of the gas-phase reaction. Both the height and width of the ba...

  12. Molecular properties by Quantum Monte Carlo: an investigation on the role of the wave function ansatz and the basis set in the water molecule

    CERN Document Server

    Zen, Andrea; Sorella, Sandro; Guidoni, Leonardo

    2013-01-01

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely: the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Throu...

  13. Attosecond dynamics of electrons in molecules and liquids

    Science.gov (United States)

    Woerner, Hans Jakob

    2016-05-01

    The ultrafast motion of electrons and holes following light-matter interaction is fundamental to a broad range of chemical and biophysical processes. In this lecture, I will discuss two recent experiments carried out in our group that measure the atomic-scale motion of charge with attosecond temporal resolution (1 as = 10-18 s). The first experiment is carried out on isolated, spatially oriented molecules in the gas phase. We advance high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately following ionization of iodoacetylene, while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement of both even and odd harmonic orders, enables us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~ 100 as. We separately reconstruct quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determine the shape of the hole created by ionization. The second experiment is carried out on a free-flowing microjet of liquid water. We use an attosecond pulse train synchronized with a near-infrared laser pulse to temporally resolve the process of photoemission from liquid water using the RABBIT technique. We measure a delay on the order of 50 as between electrons emitted from the HOMO of liquid water compared to that of gas-phase water and a substantially reduced modulation contrast of the corresponding sidebands. Since our measurements on solvated water molecules are referenced to isolated ones, the measured delays reflect (i) the photoionization delays caused by electron transport through the aqueous environment and (ii) the effect of solvation on the parent molecule. The relative modulation contrast, in turn, contains information on (iii) the modification of transition amplitudes and (iv) dephasing processes. These experiments make the liquid phase and its fascinating

  14. User requirements and user acceptance of current and next-generation satellite mission and sensor complement, oriented toward the monitoring of water resources

    Science.gov (United States)

    Castruccio, P. A.; Loats, H. L., Jr.; Fowler, T. R.; Robinson, P.

    1975-01-01

    Principal water resources users were surveyed to determine the applicability of remotely sensed data to their present and future requirements. Analysis of responses was used to assess the levels of adequacy of LANDSAT 1 and 2 in fulfilling hydrological functions, and to derive systems specifications for future water resources-oriented remote sensing satellite systems. The analysis indicates that water resources applications for all but the very large users require: (1) resolutions on the order of 15 meters, (2) a number of radiometric levels of the same order as currently used in LANDSAT 1 (64), (3) a number of spectral bands not in excess of those used in LANDSAT 1, and (4) a repetition frequency on the order of 2 weeks. The users had little feel for the value of new sensors (thermal IR, passive and active microwaves). What is needed in this area is to achieve specific demonstrations of the utility of these sensors and submit the results to the users to evince their judgement.

  15. Estimation of Bridge Height over Water from Polarimetric SAR Image Data Using Mapping and Projection Algorithm and De-Orientation Theory

    Science.gov (United States)

    Wang, Haipeng; Xu, Feng; Jin, Ya-Qiu; Ouchi, Kazuo

    An inversion method of bridge height over water by polarimetric synthetic aperture radar (SAR) is developed. A geometric ray description to illustrate scattering mechanism of a bridge over water surface is identified by polarimetric image analysis. Using the mapping and projecting algorithm, a polarimetric SAR image of a bridge model is first simulated and shows that scattering from a bridge over water can be identified by three strip lines corresponding to single-, double-, and triple-order scattering, respectively. A set of polarimetric parameters based on the de-orientation theory is applied to analysis of three types scattering, and the thinning-clustering algorithm and Hough transform are then employed to locate the image positions of these strip lines. These lines are used to invert the bridge height. Fully polarimetric image data of airborne Pi-SAR at X-band are applied to inversion of the height and width of the Naruto Bridge in Japan. Based on the same principle, this approach is also applicable to spaceborne ALOSPALSAR single-polarization data of the Eastern Ocean Bridge in China. The results show good feasibility to realize the bridge height inversion.

  16. Orientation and the Young Orienteer

    Science.gov (United States)

    Walsh, S. E.; Martland, J. R.

    Orientation within orienteering is dependent on the use of two basic strategies; that is, either a compass or Magnetic-North-based strategy, which relies on the use of one set of information; or the use of a map and landmark-based strategy which relies on the use of at least two sets of information. Walsh and found that, when given the choice, young children use the compass-based strategy when following complex potentially disorientating routes.The efficacy of these two basic orientation strategies was investigated within three different orienteering environments: (1) a familiar known environment; (2) a familiar unknown environment and (3) an unfamiliar unknown environment.Subjects, age range from 9 to 10think aloud particularly the introduction of basic skills to young performers. They support the argument that is essential to introduce the map and compass simultaneously and that relocation and orientation skills should be coached concurrently.

  17. 受限于碳纳米管中水分子微观结构的分子动力学模拟研究%Molecular Dynamics Study on Microscopic Structure of Water Molecules Confined in Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    刘华; 李春艳; 陈建超; 杨晓峰

    2011-01-01

    Molecular dynamics simulation were performed to study microscopic structure of water molecules confined in the different diameters of carbon nanotubes. Changing the temperature, the radial distribution function diagram of the water molecules confined in the carbon nanotubes was made. By doing the mean square displacement versus time graph of water molecules in carbon nanotubes, diffusion coefficient of water molecules in different diameters of carbon nanotubes was calculated with Einstein method, and it was compared with the diffusion coefficient of water molecules calculated by Knudsen diffusion.%利用分子动力学模拟研究受限于不同管径中水分子的微观结构,改变温度,做出受限水分子的径向分布函数图,并对比说明。通过做水分子在碳纳米管内的均方位移与时间关系图,利用Einstein法算出不同管径中水分子的扩散系数,与利用Knudsen扩散公式计算出的水分子的扩散系数进行比较。

  18. The influence of the cutting density on the magnetic properties of non-oriented electrical steels cut through mechanical punching and water jet technologies

    Science.gov (United States)

    Paltanea, V.; Paltanea, G.; Gavrila, H.; Popovici, D.; Jiga, G.

    2017-02-01

    The use of high quality non-oriented electrical steel and of an innovative design for the magnetic cores of the electrical machines are very important, in order to minimize the value of the total energy losses. The energy losses are strongly influenced by the cutting technologies, and the producers of the electrical machines want to minimize the deterioration of the magnetic properties during the manufacturing process. The influence of the cutting density on the magnetic permeability and energy losses was analyzed and one can notice that these magnetic properties are strongly influenced by the cutting technologies. There were tested sheet samples of M400-50A and M700-50A industrial steel grades (thickness of 0.50 mm), cut through mechanical and water jet technologies. All samples have the length equal to 300 mm and the width of 30, 15, 10, 7.5 and 5 mm. The magnetic characterization was performed using a laboratory single strip tester, which can make measurements on samples with an area of 300 × 30 mm2. In order to have the standard width of 30 mm, there were put together side by side 2, 3, 4 and 6 pieces with different widths. The magnetic properties were analyzed at 1000 mT in the frequency range 10 ÷ 400 Hz. It was observed that the processing conditions must be controlled and optimized, in order to maintain a low deterioration of the magnetic properties of the non-oriented steels. In the case of water jet technology an increase of the cutting speed will be useful for the introduction of this method in the large scale manufacturing of the electrical machines.

  19. A DFT study of the interaction between large PAHs and atomic chlorine or hydrogen chloride molecule: Toward a modelling of the influence of chlorinated species on the trapping of water by soot

    Science.gov (United States)

    Garcia-Fernandez, C.; Radola, B.; Martin-Gondre, L.; Picaud, S.; Rayez, M. T.; Rayez, J. C.; Ouf, F. X.; Rubayo-Soneira, J.

    2017-02-01

    First-principle calculations have been performed to characterize the interaction of chlorinated species (HCl and Cl) with large polycyclic aromatic hydrocarbon (PAH) molecules and radicals. Whereas the characterization of the interaction process on the face of the PAH molecules requires taking into account long-range dispersion interactions in the calculations, trapping at the edge of PAH radicals involves stronger interactions that lead to the dissociation of the HCl molecule. Then, the first steps of water adsorption on the corresponding chlorinated species has been characterized, showing that chlorine may act as an efficient nucleation center for water molecules on such aromatic systems mimicking part of the carbonaceous surfaces that are likely present in soot. These results represent a first but necessary step for a better understanding of soot behavior in industrial or domestic fire situations.

  20. Cotransport of clay colloids and viruses through water-saturated vertically oriented columns packed with glass beads: Gravity effects.

    Science.gov (United States)

    Syngouna, Vasiliki I; Chrysikopoulos, Constantinos V

    2016-03-01

    The cotransport of clay colloids and viruses in vertically oriented laboratory columns packed with glass beads was investigated. Bacteriophages MS2 and ΦX174 were used as model viruses, and kaolinite (ΚGa-1b) and montmorillonite (STx-1b) as model clay colloids. A steady flow rate of Q=1.5 mL/min was applied in both vertical up (VU) and vertical down (VD) flow directions. In the presence of KGa-1b, estimated mass recovery values for both viruses were higher for VD than VU flow direction, while in the presence of STx-1b the opposite was observed. However, for all cases examined, the produced mass of viruses attached onto suspended clay particles were higher for VD than VU flow direction, suggesting that the flow direction significantly influences virus attachment onto clays, as well as packed column retention of viruses attached onto suspended clays. KGa-1b hindered the transport of ΦX174 under VD flow, while STx-1b facilitated the transport of ΦX174 under both VU and VD flow directions. Moreover, KGa-1b and STx-1b facilitated the transport of MS2 in most of the cases examined except of the case where KGa-1b was present under VD flow. Also, the experimental data were used for the estimation of virus surface-coverages and virus surface concentrations generated by virus diffusion-limited attachment, as well as virus attachment due to sedimentation. Both sedimentation and diffusion limited virus attachment were higher for VD than VU flow, except the case of MS2 and STx-1b cotransport. The diffusion-limited attachment was higher for MS2 than ΦΧ174 for all cases examined. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Development of a process-oriented vulnerability concept for water travel time in karst aquifers-case study of Tanour and Rasoun springs catchment area.

    Science.gov (United States)

    Hamdan, Ibraheem; Sauter, Martin; Ptak, Thomas; Wiegand, Bettina; Margane, Armin; Toll, Mathias

    2017-04-01

    Key words: Karst aquifer, water travel time, vulnerability assessment, Jordan. The understanding of the groundwater pathways and movement through karst aquifers, and the karst aquifer response to precipitation events especially in the arid to semi-arid areas is fundamental to evaluate pollution risks from point and non-point sources. In spite of the great importance of the karst aquifer for drinking purposes, karst aquifers are highly sensitive to contamination events due to the fast connections between the land-surface and the groundwater (through the karst features) which is makes groundwater quality issues within karst systems very complicated. Within this study, different methods and approaches were developed and applied in order to characterise the karst aquifer system of the Tanour and Rasoun springs (NW-Jordan) and the flow dynamics within the aquifer, and to develop a process-oriented method for vulnerability assessment based on the monitoring of different multi-spatially variable parameters of water travel time in karst aquifer. In general, this study aims to achieve two main objectives: 1. Characterization of the karst aquifer system and flow dynamics. 2. Development of a process-oriented method for vulnerability assessment based on spatially variable parameters of travel time. In order to achieve these aims, different approaches and methods were applied starting from the understanding of the geological and hydrogeological characteristics of the karst aquifer and its vulnerability against pollutants, to using different methods, procedures and monitored parameters in order to determine the water travel time within the aquifer and investigate its response to precipitation event and, finally, with the study of the aquifer response to pollution events. The integrated breakthrough signal obtained from the applied methods and procedures including the using of stable isotopes of oxygen and hydrogen, the monitoring of multi qualitative and quantitative parameters

  2. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip

    2007-01-01

    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  3. Analyzing Orientations

    Science.gov (United States)

    Ruggles, Clive L. N.

    Archaeoastronomical field survey typically involves the measurement of structural orientations (i.e., orientations along and between built structures) in relation to the visible landscape and particularly the surrounding horizon. This chapter focuses on the process of analyzing the astronomical potential of oriented structures, whether in the field or as a desktop appraisal, with the aim of establishing the archaeoastronomical "facts". It does not address questions of data selection (see instead Chap. 25, "Best Practice for Evaluating the Astronomical Significance of Archaeological Sites", 10.1007/978-1-4614-6141-8_25) or interpretation (see Chap. 24, "Nature and Analysis of Material Evidence Relevant to Archaeoastronomy", 10.1007/978-1-4614-6141-8_22). The main necessity is to determine the azimuth, horizon altitude, and declination in the direction "indicated" by any structural orientation. Normally, there are a range of possibilities, reflecting the various errors and uncertainties in estimating the intended (or, at least, the constructed) orientation, and in more formal approaches an attempt is made to assign a probability distribution extending over a spread of declinations. These probability distributions can then be cumulated in order to visualize and analyze the combined data from several orientations, so as to identify any consistent astronomical associations that can then be correlated with the declinations of particular astronomical objects or phenomena at any era in the past. The whole process raises various procedural and methodological issues and does not proceed in isolation from the consideration of corroborative data, which is essential in order to develop viable cultural interpretations.

  4. Photochemistry in the inner layers of clumpy circumstellar envelopes: formation of water in C-rich objects and of C-bearing molecules in O-rich objects

    CERN Document Server

    Agundez, Marcelino; Guelin, Michel

    2010-01-01

    A mechanism based on the penetration of interstellar ultraviolet photons into the inner layers of clumpy circumstellar envelopes around AGB stars is proposed to explain the non-equilibrium chemistry observed in such objects. We show through a simple modelling approach that in circumstellar envelopes with a certain degree of clumpiness or with moderately low mass loss rates (a few 10^(-7) solar masses per year) a photochemistry can take place in the warm and dense inner layers inducing important changes in the chemical composition. In carbon-rich objects water vapor and ammonia would be formed with abundances of 10^(-8) - 10(^-6) relative to H2, while in oxygen-rich envelopes ammonia and carbon-bearing molecules such as HCN and CS would form with abundances of 10^(-9) - 10^(-7) relative to H2. The proposed mechanism would explain the recent observation of warm water vapor in the carbon-rich envelope IRC +10216 with the Herschel Space Observatory, and predict that H2O should be detectable in other carbon-rich o...

  5. Potential-dependent water orientation on Pt(1 1 1) stepped surfaces from laser-pulsed experiments

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Araez, Nuria [Instituto de Electroquimica, Universidad de Alicante, Ap. 99, E-03080 Alicante (Spain); Climent, Victor [Instituto de Electroquimica, Universidad de Alicante, Ap. 99, E-03080 Alicante (Spain)], E-mail: victor.climent@ua.es; Feliu, Juan M. [Instituto de Electroquimica, Universidad de Alicante, Ap. 99, E-03080 Alicante (Spain)

    2009-01-01

    Coulostatic potential transients induced by nanosecond pulsed laser irradiation on Pt(1 1 1) stepped surfaces in perchloric acid solutions are analyzed here. The results provide unique information on the effect of the structure of the metal surface on the potential-dependent water reorientation at the electrified interphase. The most significant information is obtained from the sign and shape of the laser-induced transients. The existence of two potentials where the transient is zero can be related to the local properties of the surface, i.e. the existence of two local potentials of zero free charge, corresponding to the step and terrace sites. The dependency of these quantities with the step density is studied in detail. In addition, it is found that the presence of steps significantly slows down the coulostatic response at potentials in the double-layer region, which has been interpreted as a decrease in the velocity of water reorganization. The corresponding relaxation time is estimated and its dependency with the step density is also analyzed.

  6. Antioxidant, anti-inflammatory and anti-browning activities of hot water extracts of oriental herbal teas.

    Science.gov (United States)

    Wu, Li-Chen; Jou, Amily Fang-Ju; Chen, Si-Han; Tien, Chia-Ying; Cheng, Chih-Fu; Fan, Nien-Chu; Ho, Ja-An Annie

    2010-11-01

    Traditionally, antioxidants are used to scavenge reactive oxygen species (ROS), which are harmful by-products of aerobic metabolism. Inulae Flos, Horsetail, Chinese Leucas, Broomweed and Indian Wikstroemia are five herbal teas commonly consumed by Asians. Our aim was to investigate the hot water extracts of these five herbal teas for their total phenolics/flavonoid contents and antioxidant capacities. Furthermore, with inflammation and hyper-pigmentation considered as two biological processes associated with elevated cellular oxidative stress, Inulae Flos water extract was chosen for further evaluation of its inhibitory effects on the production of LPS-induced inflammatory mediators (such as, TNF-α, IL-6, IL-1β) in RAW 264.7 cells and its anti-tyrosinase activity. Our findings suggest that Inulae Flos might be an alternative source as a potential antioxidant, and a noteworthy inhibitor of production of pro-inflammatory cytokines in a dose-dependent manner. Moreover, it could also serve as a potential natural food additive to prevent browning.

  7. Thermomolecular orientation of nonpolar fluids.

    Science.gov (United States)

    Römer, Frank; Bresme, Fernando; Muscatello, Jordan; Bedeaux, Dick; Rubí, J Miguel

    2012-03-09

    We investigate the response of molecular fluids to temperature gradients. Using nonequilibrium molecular dynamics computer simulations we show that nonpolar diatomic fluids adopt a preferred orientation as a response to a temperature gradient. We find that the magnitude of this thermomolecular orientation effect is proportional to the strength of the temperature gradient and the degree of molecular anisotropy, as defined by the different size or mass of the molecular atomic sites. We show that the preferred orientation of the molecules follows the same trends observed in the Soret effect of binary mixtures. We argue this is a general effect that should be observed in a wide range of length scales.

  8. Happiness Oriented Water Resources Management Strategic Planning in Zhangye Municipality%张掖市面向幸福的水资源管理战略规划

    Institute of Scientific and Technical Information of China (English)

    程国栋; 徐中民; 钟方雷

    2011-01-01

    颠倒了传统规划设定目标找途径的思路,从规划区实际情况出发,探索了一种通过回避发展过程中的陷阱,从而走上可持续发展道路的规划思路.首先以幸福为发展目标,辨晰了面向幸福的发展过程中存在的陷阱.然后,简要阐述了张掖市水资源管理的实践,从金张掖金在水上出发,在注意避免陷入发展陷阱的同时,分总量控制、水资源利用公平体系建设和提高水资源利用效率3个问题,构建起了张掖市面向幸福的水资源管理战略框架.最后,结合研究区的实际情况,针对性地提出了解决问题的对策措施和规划方案.%Setting goals and then finding approach to accomplish that is the traditional planning idea.In this article,the traditional planning idea is reversed.According to the actual situation of the planned municipality,a road to sustainable development by avoiding traps is searched.First,the happiness is taken as the final goal of the development,and some traps which may be encountered during the development are identified.Then the practice of water management in Zhangye Municipality is briefly described.Based on the actual situation of the Golden Zhangye which is very dependent on water resources,for avoiding the traps,a happiness oriented water resources management strategy framework is created,which mainly concerns water use gross control system,equity system and improving the water use efficiency.Finally,combining the framework with the actual situation of the study area,the countermeasures to solve the problems and the planning schemes are put forward.

  9. Vibrational spectroscopy of water interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Du, Quan [Univ. of California, Berkeley, CA (United States)

    1994-12-01

    The second order nonlinear optical processes of second harmonic generation and sum frequency generation are powerful and versatile tools for studying all kinds of surfaces. They possess unusual surface sensitivity due to the symmetry properties of the second order nonlinear susceptibility. The technique of infrared-visible sum frequency generation (SFG) is particularly attractive because it offers a viable way to do vibrational spectroscopy on any surfaces accessible to light with submonolayer sensitivity. In this thesis, the author applies SFG to study a number of important water interfaces. At the air/water interface, hydrophobic solid/water and liquid/water interfaces, it was found that approximately 25% of surface water molecules have one of their hydrogen pointing away from the liquid water. The large number of unsatisfied hydrogen bonds contributes significantly to the large interfacial energy of the hydrophobic surfaces. At the hydrophilic fused quartz/water interface and a fatty acid monolayer covered water surface, the structure and orientation of surface water molecules are controlled by the hydrogen bonding of water molecules with the surface OH groups and the electrostatic interaction with the surface field from the ionization of surface groups. A change of pH value in the bulk water can significantly change the relative importance of the two interactions and cause a drastic change in orientation of the surface water molecules. SFG has also been applied to study the tribological response of some model lubricant films. Monolayers of Langmuir-Blodgett films were found to disorder orientationaly under mildly high pressure and recover promptly upon removal of the applied pressure.

  10. Water infiltration and hydraulic conductivity in a natural Mediterranean oak forest: impacts of hydrology-oriented silviculture on soil hydraulic properties

    Science.gov (United States)

    Di Prima, Simone; Bagarello, Vincenzo; Bautista, Inmaculada; Cerdà, Artemi; Cullotta, Sebastiano; del Campo, Antonio; González-Sanchis, María; Iovino, Massimo; Maetzke, Federico

    2016-04-01

    microcontroller platform, Arduino. The very limited cost of the system could represent a step towards a cheaper and more widespread application of accurate and automated infiltration rate measurement. However, automatic data collection increases measurement speed, permits measurement at short time intervals, improves measurement precision, allows for more efficient data handling and analysis, and reduces the amount of effort involved and the potential for errors that may occur when manual procedures are applied (Di Prima et al., 2016). The main objective of this study was to determine soil hydraulic properties by using the combination of the automated infiltrometer and the BEST algorithm in a natural Mediterranean oak forest. The forest is located in a typical Mediterranean area, within the public forest La Hunde, Valencia (NE Spain). Two contiguous plots established in previous studies conducted by González-Sanchis et al. (2015) were selected, one of them was thinned reducing the forest density from 861 to 414 tree per ha. Control plot was not thinned. These authors studied the water cycle during the period 2012-2013. In particular, they characterized and compared the plots in term of throughfall, stemflow, soil moisture and transpiration, concluding that the AFM results in an increasing water availability, and at the same time in a substantial maintenance of overland and surface flow, precluding therefore enhancement of erosion rate. In this paper, the focus was put on the impacts of thinning on soil hydraulic properties, such as infiltration capacity, hydraulic conductivity and soil water retention, determined by simplified and low-cost methods in connection with a hydrology-oriented silviculture. Acknowledgements This study is a part of research projects: "Indagini sperimentali per la simulazione dei processi di formazione del deflusso superficiale nei suoli boscati, Progetto FIRB 2012 - MIMOSE", and "CGL2011-28776-C02-02, HYDROSIL" References Alagna, V., Bagarello, V., Di

  11. Orienteering club

    CERN Document Server

    Club d'orientation

    2015-01-01

    Course d'orientation La reprise des courses d’orientation était attendue dans la région puisque près de 150 coureurs ont participé à la première épreuve automnale organisée par le club d’orientation du CERN sur le site de La Faucille. Les circuits ont été remportés par Yann Locatelli du club d’Orientation Coeur de Savoie avec 56 secondes d’avance sur Damien Berguerre du club SOS Sallanches pour le parcours technique long, Marie Vuitton du club CO CERN (membre également de l’Equipe de France Jeune) pour le parcours technique moyen avec presque 4 minutes d’avance sur Jeremy Wichoud du club Lausanne-Jorat, Victor Dannecker pour le circuit technique court devant Alina Niggli, Elliot Dannecker pour le facile moyen et Alice Merat sur le facile court, tous membres du club O’Jura. Les résultats comp...

  12. Slow-rise and fast-drop current feature of ultraviolet response spectra for ZnO-nanowire film modulated by water molecules

    Institute of Scientific and Technical Information of China (English)

    Ren Shou-Tian; Wang Qiang; Zhao Feng; Qu Shi-Liang

    2012-01-01

    This study describes the fabrication of ZnO-nanowire films by electro-chemical anodization of Zn foil.The ZnO films are characterized by field emission scanning electron microscopy,X-ray diffraction patterns,and transmission electron microscopy,respectively.The ultraviolet (UV) photo-response properties of the surface-contacted ZnO film are studied through the current evolution processes under different relative humidities.Unlike the usually observed current spectra of the ZnO films,the drop time is shorter than the rise time.The photo-conductivity gain G and the response time γ are both increased with the increase of the applied bias.The photo-conductivity gain G is lowered with the increase of the environmental humidity,while the response time γ is increased.These results can be explained by considering three different surface processes:1) the electron-hole (e-p) pair generation by the UV light illumination,2)the following surface (O-2) species desorption,and 3) the photo-catalytic hydrolysis of water molecules adsorbed on the ZnO surface.The slow-rise and fast-drop current feature is suggested to originate from the sponge-like structure of the ZnO nanowires.

  13. Density functional theory, natural bond orbital and quantum theory of atoms in molecule analyses on the hydrogen bonding interactions in tryptophan-water complexes

    Indian Academy of Sciences (India)

    Xiqian Niu; Zhengguo Huang; Lingling Ma; Tingting Shen; Lingfei Guo

    2013-07-01

    The tryptophan-water (Trp-H2O) complexes formed by hydrogen bonding interactions were investigated at the B97XD/6-311++G(d,p) level. Five Trp-H2O complexes possessing various types of hydrogen bonds (H-bonds) were characterized by geometries, energies, vibrational frequencies. The nature of the H-bonds were characterized by the natural bond orbital (NBO) and the quantum theory of atoms in molecule (QTAIM) analyses as well. The intramolecular H-bond formed between the amino and carboxyl oxygen atom of tryptophan was retained in most of the complexes, and the cooperativity between the intra and intermolecular H-bonds exist in some complexes. The intramolecular H-bond and some intermolecular H-bonds are strong and have partial covalent character. The H-bonds formed between carboxyl and oxygen/nitrogen atoms are stronger than other H-bonds. The H-bonds involving methylene of tryptophan as H-donor are weak H-bonds. For all complexes,ele and ex makes major contributions to the total interaction energy (MP2), while disp is the smallest component of the interaction energy. Both hydrogen bonding interaction and structural deformation play important roles in the relative stabilities of the complexes. Regardless of strong H-bonds, the stabilities of some complexes are weakened by the serious structural deformations.

  14. Molecular Properties by Quantum Monte Carlo: An Investigation on the Role of the Wave Function Ansatz and the Basis Set in the Water Molecule.

    Science.gov (United States)

    Zen, Andrea; Luo, Ye; Sorella, Sandro; Guidoni, Leonardo

    2013-10-08

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely, the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudopotential, and the basis set for QMC calculations. We also introduce a new method for the computation of forces with finite variance on open systems and a new strategy for the definition of the atomic orbitals involved in the Jastrow-Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets.

  15. Sexual Orientation (For Parents)

    Science.gov (United States)

    ... Teaching Kids to Be Smart About Social Media Sexual Orientation KidsHealth > For Parents > Sexual Orientation Print A ... orientation is part of that process. What Is Sexual Orientation? The term sexual orientation refers to the ...

  16. Contributions of tryptophan 24 and glutamate 30 to binding long-lived water molecules in the ternary complex of human dihydrofolate reductase with methotrexate and NADPH studied by site-directed mutagenesis and nuclear magnetic resonance spectroscopy.

    Science.gov (United States)

    Meiering, E M; Li, H; Delcamp, T J; Freisheim, J H; Wagner, G

    1995-03-24

    Previous NMR studies on the ternary complex of human dihydrofolate reductase (hDHFR) with methotrexate (MTX) and NADPH detected six long-lived bound water molecules. Two of the water molecules, WatA and WatB, stabilize the structure of the protein while the other four, WatC, WatD, WatE and WatF, are involved in substrate binding and specificity. WatE may also act as a proton shuttle during catalysis. Here, the contributions of individual residues to the binding of these water molecules are investigated by performing NMR experiments on ternary complexes of mutant enzymes, W24F, E30A and E30Q. W24 and E30 are conserved residues that form hydrogen bonds with WatE in crystal structures of DHFR. Nuclear Overhauser effects (NOEs) are detected between WatE and the protein in all the mutant complexes, hence WatE still has a long lifetime bound to the complex when one of its hydrogen-bonding partners is deleted or altered by mutagenesis. The NOEs for WatE are much weaker, however, in the mutants than in wild-type. The NOEs for the other water molecules in and near the active site, WatA, WatC, WatD and WatF, also tend to be weaker in the mutant complexes. Little or no change is apparent in the NOEs for WatB, which is located outside the active site, farthest from the mutated residues. The decreased NOE intensities for the bound water molecules could be caused by changes in the positions and/or lifetimes of the water molecules. Chemical shift and NOE data indicate that the mutants have structures very similar to that of wild-type hDHFR, with possible conformational changes occurring only near the mutated residues. Based on the lack of structural change in the protein and evidence for increased structural fluctuations in the active sites of the mutant enzymes, it is likely that the NOE changes are caused, at least in part, by decreases in the lifetimes of the bound water molecules.

  17. Hangman Catalysis for Photo–and Photoelectro–Chemical Activation of Water Proton-Coupled Electron Transfer Mechanisms of Small Molecule Activation

    Energy Technology Data Exchange (ETDEWEB)

    Nocera, Daniel G. [Harvard Univ., Cambridge, MA (United States)

    2013-03-15

    The weakest link for the large-scale deployment of solar energy and for that matter, any renewable energy source, is its storage. The energy needs of future society demands are so large that storage must be in the form of fuels owing to their high energy density. Indeed, society has intuitively understood this disparity in energy density as it has developed over the last century as all large-scale energy storage in our society is in the form of fuels. But these fuels are carbon-based. The imperative for the discipline of chemistry, and more generally science, is to develop fuel storage methods that are easily scalable, carbon-neutral and sustainable. These methods demand the creation of catalysts to manage the multi-electron, multi-proton transformations of the conversion of small molecules into fuels. The splitting of water using solar light is a fuel-forming reaction that meets the imperative of large scale energy storage. As light does not directly act on water to engender its splitting into its elemental components, we have designed “hangman” catalysts to effect the energy conversion processes needed for the fuel forming reactions. The hangman construct utilizes a pendant acid/base functionality within the secondary coordination sphere that is “hung” above the redox platform onto which substrate binds. In this way, we can precisely control the delivery of a proton to the substrate, thus ensuring efficient coupling between the proton and electron. An emphasis was on the coupling of electron and proton in the hydrogen evolution reaction (HER) on Ni, Co and Fe porphyrin platforms. Electrokinetic rate laws were developed to define the proton-coupled electron transfer (PCET) mechanism. The HER of Co and Fe porphyrins was metal-centered. Surprisingly, HER this was not the case for Ni porphyrins. In this system, the PCET occurred at the porphyrin platform to give rise to a phlorin. This is one of the first examples of an HER occurring via ligand non

  18. Orienteering Club

    CERN Document Server

    Club d'orientation

    2013-01-01

    Courses d’orientation Une bonne dizaine de clubs étaient représentés samedi dernier à La Faucille pour participer à la  2e manche de la coupe genevoise organisée par le club du CERN. Les 120 coureurs ont pu découvrir des parcours classés "technique". Ceux du Haut-Jura familiarisés à ce type de terrain ont pu sortir leur épingle du jeu et se sont octroyé la victoire sur 4 des 5 circuits. Samedi 21 septembre, la montagne du Haut-Jura était encore plébiscitée puisque les coureurs étaient attendus à Saint Cergue sur la carte des Pralies. Pour les résultats complets de La Faucille et les informations sur la prochaine étape, consultez le site du club http://cern.ch/club-orientation.

  19. Orientation Club

    CERN Multimedia

    Club d'orientation

    2014-01-01

    COURSE ORIENTATION Résultats de samedi 10 mai    C’est sur une carte entièrement réactualisée dans les bois de Versoix, que plus de 100 coureurs sont venus participer à la course d’orientation, type longue distance, préparée par des membres du club du CERN. Le terrain plutôt plat nécessitait une orientation à grande vitesse, ce qui a donné les podiums suivants :  Technique long avec 17 postes : 1er Jurg Niggli, O’Jura en 52:48, 2e Beat Muller, COLJ Lausanne-Jorat en 58:02, 3e Christophe Vuitton, CO CERN en 58:19 Technique moyen avec 13 postes : 1er Jean-Bernard Zosso, CO CERN, en 46:05 ; 2e Yves Rousselot, Balise 25 Besançon, en 55:11 ; 3e Laurent Merat, O'Jura, en 55:13 Technique court avec 13 postes : 1er Julien Vuitton, CO CERN en 40:59, 2e Marc Baumgartner, CO CERN en 43:18, 3e Yaelle Mathieu en 51:42 Su...

  20. Orienteering Club

    CERN Multimedia

    Club d'orientation

    2013-01-01

    Courses d’orientation ce printemps Le Club d’orientation du CERN vous invite à venir découvrir la course d’orientation et vous propose, en partenariat avec d’autres clubs de la région, une dizaine de courses populaires. Celles-ci ont lieu les samedis après-midi, elles sont ouvertes à tous, quel que soit le niveau, du débutant au sportif confirmé, en famille ou en individuel, en promenade ou en course. Si vous êtes débutant vous pouvez profiter d’une petite initiation offerte par l’organisateur avant de vous lancer sur un parcours. Divers types de parcours sont à votre choix lors de chaque épreuve : facile court (2-3 km), facile moyen (3-5 km), technique court (3-4 km), technique moyen (4-5 km) et technique long (5-7 km). Les dates à retenir sont les suivantes : Samedi 23 mars: Pully (Vd) Samedi 13 avril: Pougny...

  1. Molecular rectification in oriented polymers

    Science.gov (United States)

    Sentein, C.; Fiorini, C.; Lorin, A.; Nunzi, J.-M.; Sicot, L.

    1998-06-01

    We underline the intrinsic rectifying nature of an oriented polymeric material. Orientation of the initially symmetric structure is performed through DC-field ordering of the polar molecules contained in the polymer. The internal field induced in the polymeric material is evidenced by the induction of a rectifying current-voltage characteristic. Our preparation technique opens a new route for the improvement of organic-semiconductor devices efficiency. Nous soulignons la nature intrinsèquement rectifiante d'un polymère orienté. L'orientation moléculaire est induite par polarisation sous champ permanent. Le champ interne piégé dans le matériau induit une rectification de la caractéristique courant tension. Notre technique de préparation ouvre une voie nouvelle pour l'amélioration des performances des dispositifs semiconducteurs organiques.

  2. Strong orientational coordinates and orientational order parameters for symmetric objects

    Science.gov (United States)

    Haji-Akbari, Amir; Glotzer, Sharon C.

    2015-12-01

    Recent advancements in the synthesis of anisotropic macromolecules and nanoparticles have spurred an immense interest in theoretical and computational studies of self-assembly. The cornerstone of such studies is the role of shape in self-assembly and in inducing complex order. The problem of identifying different types of order that can emerge in such systems can, however, be challenging. Here, we revisit the problem of quantifying orientational order in systems of building blocks with non-trivial rotational symmetries. We first propose a systematic way of constructing orientational coordinates for such symmetric building blocks. We call the arising tensorial coordinates strong orientational coordinates (SOCs) as they fully and exclusively specify the orientation of a symmetric object. We then use SOCs to describe and quantify local and global orientational order, and spatiotemporal orientational correlations in systems of symmetric building blocks. The SOCs and the orientational order parameters developed in this work are not only useful in performing and analyzing computer simulations of symmetric molecules or particles, but can also be utilized for the efficient storage of rotational information in long trajectories of evolving many-body systems.

  3. The PPII-to-α-helix transition of poly-l-lysine in methanol/water solvent mixtures accompanied by fibrillar self-aggregation: An influence of fluphenazine molecules.

    Science.gov (United States)

    Cieślik-Boczula, Katarzyna

    2017-08-01

    Fourier-transform infrared, vibrational circular dichroism spectroscopy and transmission electron microscopy are used to follow the structural changes of pure and fluphenazine (FPh)-mixed poly-l-lysine (PLL) triggered by variations of the methanol to water ratio in solvent mixtures. FPh molecules are used as an effective psychotic drug but with a strong Parkinson's-related side effect. To answer the question whether FPh molecules can modify the fibril development, the PLL polypeptide was used as a model of α-helix- and PPII-rich fibrils. It was stated that the presence of FPh molecules did not inhibit the creation of both types of PLL fibrils with clustering features. The methanol-poor aqueous solutions promote the formation of extended polyproline II (PPII) helices; however, the methanol-rich aqueous solutions induce the development of α-helices of both pure and FPh-mixed PLL. Unpredicted and interesting features of PLL fibrillogenesis are evidenced by the formation of uncommon fibrillar aggregates, which are developed in methanol/water solvents from PLL molecules rich in either α-helix or PPII structures. Possibility of PLL molecules to form β-sheet-, α-helix- and PPII-rich fibrils demonstrating that fibrillogenesis is a common phenomenon, and fibrillar aggregates can be based on all of the basic protein secondary structures. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Neuroprotective effect of water extract of Panax ginseng on corticosterone-induced apoptosis in PC12 cells and its underlying molecule mechanisms.

    Science.gov (United States)

    Jiang, Yumao; Li, Zongyang; Liu, Yamin; Liu, Xinmin; Chang, Qi; Liao, Yonghong; Pan, Ruile

    2015-01-15

    The root of Panax ginseng C.A. Meyer (Family Araliaceae) is an important medicinal plant which has been employed as a panacea for more than 2,000 years in China. It has the actions of invigorating primordial qi, recovering pulse and desertion, engendering liquid, and calming spirit. The water extract of Panax ginseng (WEG) has been used to treat kinds of central nervous system disorders, such as depression, insomnia, Alzheimer׳s disease and Parkinson׳s disease. Our previous work has demonstrated that WEG possessed antidepressant-like activities in both acute and chronic stress models of depression. Nevertheless, there are no studies on the cytoprotection and potential mechanisms of WEG on corticosterone-induced apoptosis. The present study focuses on cytoprotection against corticosterone-induced neurotoxicity in PC12 cells and its underlying molecule mechanisms of the antidepressant-like effect of WEG. The PC12 cells were treated with 250 μmol/L corticosterone in the absence or presence of WEG for 24h, then 3-(4,5-dimethy thiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay, lactate dehydrogenase (LDH) detection, Hoechst33342 staining and TUNEL staining were investigated to confirm the neuroprotection of WEG. Then, mitochondrial permeability transition pore (mPTP), mitochondrial membrane potential (MMP), intracellular Ca(2+) ([Ca(2+)]i), reactive oxygen species (ROS) concentration, and the expression level of glucocorticoid receptor (GR), heat shock protein 90 (Hsp90), histone deactylase 6 (HDAC6), glucose-regulated protein 78 (GRP78), growth arrest and DNA damage inducible protein 153 (GADD153), X-box DNA-binding protein-1 (XBP-1), caspase-12, cytochrome C, inhibitor of caspase-activated deoxyribonuclease (ICAD), caspase-3 and caspase-9 were assessed by Western Blot analysis to understand the molecule mechanisms of neuroprotection of WEG. WEG partly reversed corticosterone-induced damage in PC12 cells, which increased cell viability, decreased LDH release

  5. Hadron Molecules

    CERN Document Server

    Gutsche, Thomas; Faessler, Amand; Lee, Ian Woo; Lyubovitskij, Valery E

    2010-01-01

    We discuss a possible interpretation of the open charm mesons $D_{s0}^*(2317)$, $D_{s1}(2460)$ and the hidden charm mesons X(3872), Y(3940) and Y(4140) as hadron molecules. Using a phenomenological Lagrangian approach we review the strong and radiative decays of the $D_{s0}^* (2317)$ and $D_{s1}(2460)$ states. The X(3872) is assumed to consist dominantly of molecular hadronic components with an additional small admixture of a charmonium configuration. Determing the radiative ($\\gamma J/\\psi$ and $\\gamma \\psi(2s)$) and strong ($J/\\psi 2\\pi $ and $ J/\\psi 3\\pi$) decay modes we show that present experimental observation is consistent with the molecular structure assumption of the X(3872). Finally we give evidence for molecular interpretations of the Y(3940) and Y(4140) related to the observed strong decay modes $J/\\psi + \\omega$ or $J/\\psi + \\phi$, respectively.

  6. Advising and Optimizing the Deployment of Sustainability-Oriented Technologies in the Integrated Electricity, Light-Duty Transportation, and Water Supply System

    Science.gov (United States)

    Tarroja, Brian

    The convergence of increasing populations, decreasing primary resource availability, and uncertain climates have drawn attention to the challenge of shifting the operations of key resource sectors towards a sustainable paradigm. This is prevalent in California, which has set sustainability-oriented policies such as the Renewable Portfolio Standards and Zero-Emission Vehicle mandates. To meet these goals, many options have been identified to potentially carry out these shifts. The electricity sector is focusing on accommodating renewable power generation, the transportation sector on alternative fuel drivetrains and infrastructure, and the water supply sector on conservation, reuse, and unconventional supplies. Historical performance evaluations of these options, however, have not adequately taken into account the impacts on and constraints of co-dependent infrastructures that must accommodate them and their interactions with other simultaneously deployed options. These aspects are critical for optimally choosing options to meet sustainability goals, since the combined system of all resource sectors must satisfy them. Certain operations should not be made sustainable at the expense of rendering others as unsustainable, and certain resource sectors should not meet their individual goals in a way that hinders the ability of the entire system to do so. Therefore, this work develops and utilizes an integrated platform of the electricity, transportation, and water supply sectors to characterize the performance of emerging technology and management options while taking into account their impacts on co-dependent infrastructures and identify synergistic or detrimental interactions between the deployment of different options. This is carried out by first evaluating the performance of each option in the context of individual resource sectors to determine infrastructure impacts, then again in the context of paired resource sectors (electricity-transportation, electricity-water

  7. Spectroscopic characterizations of non-amphiphilic 2-(4-biphenylyl)-6-phenyl benzoxazole molecules at the air-water interface and in Langmuir-Blodgett films

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, S.A. [Department of Physics, Tripura University, Suryamaninagar, Agartala: 799130 Tripura (India); Deb, S. [Department of Physics, Tripura University, Suryamaninagar, Agartala: 799130 Tripura (India); Bhattacharjee, D. [Department of Physics, Tripura University, Suryamaninagar, Agartala: 799130 Tripura (India)]. E-mail: tuphysic@sancharnet.in

    2005-09-15

    This communication reports about the successful incorporation of a well-known non-amphiphilic derivative of oxazole chromophore 2-(4-biphenylyl)-6-phenyl benzoxazole abbreviated as PBBO, in Langmuir-Blodgett films when mixed with stearic acid (SA) as well as also an inert polymer matrix polymethylmethacrylate (PMMA). The surface pressure versus area per molecule isotherms of the Langmuir films of PBBO mixed with PMMA or SA at different mole fractions reveal that the area per molecule decreases consistently with increasing mole fractions of PBBO. Area per molecule versus mole fraction curve shows that the experimental data points coincide with the ideality curve predicted by the additivity rule, which leads to the conclusion of either ideal mixing or complete demixing of the binary components. The UV-vis absorption and fluorescence spectroscopic studies of mixed LB films of PBBO reveal the nature of complete demixing of the binary components of the sample molecules (PBBO) and PMMA or SA molecules. This complete demixing leads to the formation of clusters and aggregates of PBBO molecules in Langmuir and Langmuir-Blodgett films. J-type aggregates of PBBO molecules in LB films have been confirmed by UV-vis absorption spectroscopic study. Aggregation of PBBO molecules in LB films giving rise to excimeric emission has been demonstrated by fluorescence spectroscopic study. Excitation spectroscopic study clearly confirmed the presence of excimeric sites.

  8. Atomic Hydrogen Surrounded by Water Molecules, H(H2O)m, Modulates Basal and UV-Induced Gene Expressions in Human Skin In Vivo

    Science.gov (United States)

    Shin, Mi Hee; Park, Raeeun; Nojima, Hideo; Kim, Hyung-Chel; Kim, Yeon Kyung; Chung, Jin Ho

    2013-01-01

    Recently, there has been much effort to find effective ingredients which can prevent or retard cutaneous skin aging after topical or systemic use. Here, we investigated the effects of the atomic hydrogen surrounded by water molecules, H(H2O)m, on acute UV-induced responses and as well as skin aging. Interestingly, we observed that H(H2O)m application to human skin prevented UV-induced erythema and DNA damage. And H(H2O)m significantly prevented UV-induced MMP-1, COX-2, IL-6 and IL-1β mRNA expressions in human skin in vivo. We found that H(H2O)m prevented UV-induced ROS generation and inhibited UV-induced MMP-1, COX-2 and IL-6 expressions, and UV-induced JNK and c-Jun phosphorylation in HaCaT cells. Next, we investigated the effects of H(H2O)m on intrinsically aged or photoaged skin of elderly subjects. In intrinsically aged skin, H(H2O)m application significantly reduced constitutive expressions of MMP-1, IL-6, and IL-1β mRNA. Additionally, H(H2O)m significantly increased procollagen mRNA and also decreased MMP-1 and IL-6 mRNA expressions in photoaged facial skin. These results demonstrated that local application of H(H2O)m may prevent UV-induced skin inflammation and can modulate intrinsic skin aging and photoaging processes. Therefore, we suggest that modifying the atmospheric gas environment within a room may be a new way to regulate skin functions or skin aging. PMID:23637886

  9. Egocentric spatial orientation in a water maze by rats subjected to transection of the fimbria-fornix and/or ablation of the prefrontal cortex

    DEFF Research Database (Denmark)

    Mogensen, Jesper; Moustgaard, Anette; Khan, Usman;

    2005-01-01

    prefrontal cortex, hippocampus, fimbria-fornix, egocentrisk spatial orientering, vandlabyrint, adfærdsstrategier, kognitive strategier, funktionel genopretning, rehabilitering, problemløsning, rotter......prefrontal cortex, hippocampus, fimbria-fornix, egocentrisk spatial orientering, vandlabyrint, adfærdsstrategier, kognitive strategier, funktionel genopretning, rehabilitering, problemløsning, rotter...

  10. Reactivity of the Sterically Demanding Siloxanediol Mes2 Si(OH)(μ-O)Si(OH)Mes2 Towards Water and Ether Molecules.

    Science.gov (United States)

    Roesch, Philipp; Warzok, Ulrike; Enke, Martin; Müller, Robert; Schattenberg, Caspar; Schalley, Christoph A; Kaupp, Martin; Braun, Thomas; Wittwer, Philipp

    2017-07-29

    A series of isotopologues of the siloxanediol Mes2 Si(OH)(μ-O)Si(OH)Mes2 (3 a) (Mes=2,4,6-trimethylphenyl) were synthesized by reactions of the corresponding disiloxane precursors Mes2 Si(μ-O)2 SiMes2 (2 a), Mes2 Si(μ-(17) O)2 SiMes2 (2 b) or Mes2 Si(μ-(18) O)2 SiMes2 (2 c) with an excess of H2 O, H2(17) O or H2(18) O. NMR and IR signal assignments for the siloxanediols in benzene are supported by quantum-chemical calculations, which indicate small energy differences between trans and cis conformers, the latter of which exhibits an intramolecular hydrogen bond. (1) H NMR as well as IR data suggest the presence of a mixture of both conformers in C6 D6 . Hydrogen-bonded adducts of Mes2 Si(OH)(μ-O)Si(OH)Mes2 with ethers such as diethylether, dimethoxyethane or dioxane were observed in the solid state, where they form polymeric chain-like structures. The latter appear to be stable only in the crystal. (17) O{(1) H} NMR and IR data in THF solution suggest an interaction of 3 a with at least one THF molecule, whereas diethylether appears not to interact. Water adducts form neither in solution nor in the solid state as indicated by NMR and ATR IR data. (17) O{(1) H} NMR and ESI-MS experiments illustrate the remarkably high stability of the siloxanediols towards water and show no evidence for intra- or intermolecular oxygen-exchange reactions. In marked contrast, a stepwise exchange of all three oxygen atoms-including the one in the Si-O-Si bridge-occurred in the gas phase, when [Mes2 Si((18) OH)(μ-(18) O)Si((18) O)Mes2 ](-) was treated with H2 O in the hexapole of an ESI FT-ICR mass spectrometer. The scrambling between the bridging and the other oxygen atoms likely proceeds through cyclic Si2 O2 intermediates. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Effects of hydrogen-bond environment on single particle and pair dynamics in liquid water

    Indian Academy of Sciences (India)

    Amalendu Chandra; Snehasis Chowdhuri

    2001-10-01

    We have performed molecular dynamics simulations of liquid water at 298 and 258 K to investigate the effects of hydrogen-bond environment on various single-particle and pair dynamical properties of water molecules at ambient and supercooled conditions. The water molecules are modelled by the extended simple point charge (SPC/E) model. We first calculate the distribution of hydrogen-bond environment in liquid water at both temperatures and then investigate how the selfdiffusion and orientational relaxation of a single water molecule and also the relative diffusion and relaxation of the hydrogen-bond of a water pair depend on the nature of the hydrogen-bond environment of the tagged molecules. We find that the various dynamical quantities depend significantly on the hydrogen-bond environment, especially at the supercooled temperature. The present study provides a molecular-level insight into the dynamics of liquid water under ambient and supercooled conditions.

  12. Club Orientation

    CERN Multimedia

    Club d'orientation

    2014-01-01

      COURSE ORIENTATION   Pas moins de 100 concurrents sont venus s’affronter sur les parcours proposés par le club d’orientation du CERN ce samedi 26 avril lors de la 4e étape de la coupe genevoise de printemps. Les podiums ont été attribués à :  Technique long avec 19 postes : 1er Yvan Balliot, ASO Annecy en 1:01:39 ; 2e Dominique Fleurent, ASO Annecy, en 1:05:12 ; 3e Rémi Fournier, SOS Sallanches, en 1:05:40. Technique moyen avec 14 postes : 1er Jean-Bernard Zosso, CO CERN, en 46:42 ; 2e Céline Zosso, CO CERN, en 50:51 ; 3e Clément Poncet, O’Jura Prémanon, en 51:27. Technique court avec 13 postes : 1er Jaakko Murtomaki, YKV Seinaejoki, en 36:04 ; 2e Marc Baumgartner en 41:27 ; 3e Natalia Niggli, O’Jura Prémanon, en 52:43. Sur les parcours facile moyen et facile court, victoire respectivement de Stéphanie...

  13. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2012-01-01

     Course d’orientation C’est sous un magnifique soleil que s’est tenue la 7e épreuve de la coupe genevoise organisée par le club d’orientation du CERN. Les organisateurs avaient concocté des parcours assez techniques sur le site de La Faucille. Sur le parcours technique long, beau podium avec la victoire de Domenico Lepori (double médaillés aux championnats du monde en 2010 en vétéran) du club Care Vevey en 1:00:23, juste devant Jürg Niggli du club O’Jura en 1:00:56 puis Beat Mueller du club Lausanne-Jorat en 1:04:28. Sur le parcours technique moyen, Franck Longchampt s’est octroyé la première place, sur le parcours technique court, le jeune Julien Vuitton, qui n’a pas tout à fait 11 ans, a remporté son circuit. Coté parcours facile moyen, Victor Kuznetsov a une fois de plus gagn&eacut...

  14. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2013-01-01

    Course d’orientation Face aux Championnats de France des Clubs à Poitiers, et à une météo hivernale (vent glaciale et pluie), il ne restait qu’une cinquantaine d’orienteurs pour participer à l’épreuve organisée le samedi 25 mai à Grange-Malval. Les participants ont tout de même bien apprécié les 5 circuits proposés par le Satus Genève. Les résultats sont disponibles sur notre site http://cern.ch/club-orientation. En plus des résultats, vous pourrez noter des informations sur la nouvelle école de CO encadrée par B. Barge, Prof. EPS à Ferney-Voltaire pour les jeunes à partir de 6 ans. La prochaine étape de la coupe genevoise se déroulera samedi 1er juin à Morez (39). Epreuve organisée par le club O’Jura&nb...

  15. Orienteering club

    CERN Multimedia

    Club d'orientation

    2010-01-01

    Course d’orientation : Coupe Genevoise de printemps 2010 Et c’est reparti pour une nouvelle saison! Pour cette coupe de printemps 2010, le Club d’Orientation du CERN, en partenariat avec d’autres clubs de la région, vous propose le calendrier suivant: – samedi 20 mars : Cossonay (Vd) – samedi 10 avril : Echallens (Vd) – samedi 17 avril : Trélex (Vd) – samedi 24 avril : Genolier (Vd) – samedi 1 mai : Vulbens/Valleiry (74) – samedi 8 mai : Bois de la Rippe (Vd) – samedi 29 mai : Sauvabellin (Vd) : relais – samedi 5 juin: St Cergue (Vd) : grande finale Les courses populaires ont lieu en général le samedi après-midi, elles sont ouvertes à tous, quel que soit le niveau, du débutant au sportif confirmé, en famille ou en individuel, en promenade ou en course. Pour cela, divers types de parcours sont &agr...

  16. Orienteering club

    CERN Multimedia

    Club d’Orientation du CERN

    2015-01-01

    Courses d’orientation Nouvelle saison nouveau programme Le Club d’orientation du CERN, en partenariat avec d’autres clubs de la région, vous propose une dizaine de courses populaires comptant pour la coupe Genevoise de printemps: samedi 28 mars: Vernand Dessus samedi 18 avril: Pougny/Challex samedi 25 avril: Chancy/Valleiry samedi 2 mai: Mauvernay samedi 9 mai: Longchaumois samedi 16 mai: Genolier samedi 30 mai: Prevondavaux samedi 6 juin: Biere-Ballens samedi 13 juin: Haut-Jura samedi 20 juin: Bonmont - Finale Ces courses sont ouvertes à tous, quel que soit le niveau, du débutant au sportif confirmé, en famille ou en individuel, en promenade ou en course. Les inscriptions se font sur place le jour de l’épreuve. Si vous êtes débutant, vous pouvez profiter d’une initiation offerte par l’organisateur avant de vous lancer sur un parcours. Le club propose aussi...

  17. Orienteering club

    CERN Multimedia

    Orienteering Club

    2016-01-01

    Course d'orientation Calendrier des courses d’orientation Coupe genevoise d’automne 2016 Samedi 3 septembre : La Faucille (01) Samedi 10 septembre : Prémanon (39) Samedi 17 septembre : Saint-Cergue (VD) Samedi 24 septembre : Jorat / Corcelles (VD) Samedi 1 octobre: Bière - Ballens (VD) -relais Vendredi 14 octobre : Parc Mon Repos (GE) - nocturne Samedi 15 octobre : Terrasse de Genève (74) Samedi 29 octobre : Bonmont (VD) Samedi 5 novembre : Pomier (74) – one-man-relay - Finale   Courses ouvertes à toutes et à tous, sportifs, familles, débutants ou confirmés, du CERN ou d’ailleurs. Cinq circuits disponibles, ceci va du facile court (2 km) adapté aux débutants et aux enfants jusqu’au parcours technique long de 6 km pour les chevronnés en passant par les parcours facile moyen (4&am...

  18. COURSE ORIENTATION

    CERN Multimedia

    Club d'orientation du CERN

    2015-01-01

      Les coureurs d’orientation de la région se sont donné rendez-vous samedi dernier dans les bois de Pougny/Challex lors de l’épreuve organisée par le club d’orientation du CERN. La carte proposée pour les 5 circuits offrait aussi bien un coté très technique avec un relief pentu qu’un coté avec de grandes zones plates à forêt claire. Le parcours technique long comportant 20 postes a été remporté par Beat Muller du COLJ Lausanne en 56:26 devançant Denis Komarov, CO CERN en 57:30 et Yvan Balliot, ASO Annecy en 57:46. Pour les autres circuits les résultats sont les suivants: Technique moyen (13 postes): 1er Joël Mathieu en 52:32 à une seconde du 2e Vladimir Kuznetsov, COLJ Lausanne-Jorat, 3e Jean-Bernard Zosso, CO CERN, en 54:01 Technique court (12 postes): 1er Lennart Jirden, ...

  19. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2017-01-01

    Calendrier des courses de la Coupe Genevoise – printemps 2017 Club d'orientation - Julien,  jeune membre du club. Le Club d’orientation du CERN, en partenariat avec d’autres clubs de la région, vous propose une série de courses populaires, qui se dérouleront des deux côtés de la frontière franco-suisse, à savoir : Samedi 1 avril : Pougny/Challex (01) Samedi 8 avril: Ballens (VD) Samedi 22 avril: Apples (VD) Samedi 29 avril: Mont Mussy (01) Samedi 6 mai: Prémanon (39) Samedi 13 mai: Mont Mourex (01) Samedi 20 mai: Prévondavaux (VD) Samedi 10 juin: Chancy/Valleiry (74) Samedi 17 juin: Trélex - Finale (VD) Ces courses sont ouvertes à tous, quel que soit le niveau, du débutant au sportif confirmé, en famille ou en individuel. Les inscriptions sur un des 5 parcours proposés se font sur place le jour de...

  20. Orienteering Club

    CERN Multimedia

    Club d'orientation

    2010-01-01

    COURSE D’ORIENTATION La finale de la coupe de printemps Après avoir remporté le challenge club, samedi 29 juin lors du relais inter-club à Lausanne, le Club d’orientation du CERN organisait la dernière étape de la coupe genevoise de printemps samedi 5 juin à Saint-Cergue dans les bois de Monteret (Canton de Vaud). Plus de 100 participants se sont déplacés pour venir participer à la finale et découvrir une toute nouvelle carte dans une forêt vallonnée. Les résultats pour chaque circuit de cette étape sont : Technique long : 1. Jurg Niggli du club O’Jura, 2. Clément Poncet, 3. Oystein Midttun. Technique moyen : 1. Zoltan Trocsanyi CO CERN, 2. Christophe Ingold, 3. Christina Falga. Technique court : 1. Pierre-Andre Baum, CARE Vevey, 2. Emese Szunyog, 3. Solène Balay. Facile moyen : 1. Elisa P...

  1. Orienteering Club

    CERN Multimedia

    Le Club d’orientation du CERN

    2017-01-01

    Course orientation Les courses d’orientation comptant pour la coupe genevoise de printemps s’enchainent dans la région franco-suisse. Samedi dernier, une bonne centaine de coureurs se sont retrouvés au Mont Mourex où le club du CERN avait préparé la sixième épreuve. A l’issue de la course, les participants confirmaient l’exigence des circuits, à savoir la condition physique et le côté technique du traçage. Le parcours technique long comportant 20 postes a été remporté par Darrell High du Care Vevey en 1:22:38 devançant Beat Muller du COLJ Lausanne-Jorat en 1:25:25 et Alison High également du Care Vevey en 1:28:51. Le circuit technique moyen a été remporté par Christophe Vuitton du CO CERN et le circuit technique court par Claire-Lise Rouiller, CO CERN. Les trois pr...

  2. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2015-01-01

    Course orientation C’est au pied du Salève, proche du Golf de Bosset, que le club d’orientation du CERN (CO CERN) a organisé samedi 19 septembre une nouvelle épreuve comptant pour la Coupe Genevoise d’automne. La zone « des Terrasses de Genève » avait été cartographiée et mise en service l’année dernière. Les participants ont pu apprécier un terrain ludique avec beaucoup de microreliefs, de points d’eau et de gros rochers, le tout au milieu d’une forêt assez claire et agréable à courir. Sur le parcours technique long, le résultat a été très serré puisque Pierrick Merino du club d’Annecy a gagné avec seulement 9 secondes d’avance sur Gaëtan Vuitton (CO CERN) qui confiait avoir perdu beaucoup du te...

  3. Observation of pendular butterfly Rydberg molecules.

    Science.gov (United States)

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig

    2016-10-05

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  4. Orienteering club

    CERN Document Server

    Club d'orientation

    2011-01-01

    Reprise fin août Le Club d’orientation, en partenariat avec d’autres clubs de la région, vous propose une nouvelle série de courses pour cet automne. Le calendrier à retenir est le suivant : Samedi 27 août : Granges Malval (GE) – type classique Samedi 10 septembre : Lamoura (39) – type classique Samedi 17 septembre : La Dôle (F/VD) – type classique Samedi 24 septembre : Monteret (VD) – relais Samedi 8 octobre : Saint Cergue (VD) – type classique Vendredi 14 octobre : Les Evaux (GE) – nocturne Samedi 15 octobre : Grand Jorat (VD) – type classique Samedi 22 octobre : Pomier (74) – type classique Samedi 5 novembre : Echallens (VD) – type classique Samedi 12 novembre : CERN (GE) - sprint - Finale Généralement cinq circuits sont disponibles : ceci va du facile court (2 km) adapt&eacu...

  5. Orienting hypnosis.

    Science.gov (United States)

    Hope, Anna E; Sugarman, Laurence I

    2015-01-01

    This article presents a new frame for understanding hypnosis and its clinical applications. Despite great potential to transform health and care, hypnosis research and clinical integration is impaired in part by centuries of misrepresentation and ignorance about its demonstrated efficacy. The authors contend that advances in the field are primarily encumbered by the lack of distinct boundaries and definitions. Here, hypnosis, trance, and mind are all redefined and grounded in biological, neurological, and psychological phenomena. Solutions are proposed for boundary and language problems associated with hypnosis. The biological role of novelty stimulating an orienting response that, in turn, potentiates systemic plasticity forms the basis for trance. Hypnosis is merely the skill set that perpetuates and influences trance. This formulation meshes with many aspects of Milton Erickson's legacy and Ernest Rossi's recent theory of mind and health. Implications of this hypothesis for clinical skills, professional training, and research are discussed.

  6. A possibility of a protein-bound water molecule as the ionizable group responsible for pKe at the alkaline side in human matrix metalloproteinase 7 activity.

    Science.gov (United States)

    Morishima, Aiko; Yasukawa, Kiyoshi; Inouye, Kuniyo

    2012-05-01

    Human matrix metalloproteinase 7 (MMP-7) activity exhibits broad bell-shaped pH profile with the acidic and alkaline pK(a) (pK(e1) and pK(e2)) values of about 4 and 10. The ionizable group for pK(e2) was assigned to Lys or Arg by thermodynamic analysis; however, no such residues are present in the active site. Hence, based on the crystal structure, we hypothesized that a water molecule bound to the main-chain nitrogen of Ala162 (W1) or the main-chain carbonyl oxygen of Pro217 (W2) is a candidate for the ionizable group for pK(e2) [Takeharu, H. et al. (2011) Biochim. Biophys. Acta 1814, 1940-1946]. In this study, we inspected this hypothesis. In the hydrolysis of (7-methoxycoumarin-4-yl)acetyl-L-Pro-L-Leu-Gly-L-Leu-[N(3)-(2,4-dinitrophenyl)-L-2,3-diaminopropionyl]-L-Ala-L-Arg-NH(2), all 19 variants, in which one of all Lys and Arg residues was replaced by Ala, retained activity, indicating that neither Lys nor Arg is the ionizable group. pK(e2) values of A162S, A162V and A162G were 9.6 ± 0.1, 9.5 ± 0.1 and 10.4 ± 0.2, respectively, different from that of wild-type MMP-7 (WT) (9.9 ± 0.1) by 0.3-0.5 pH unit, and those of P217S, P217V and P217G were 10.1 ± 0.1, 9.8 ± 0.1 and 9.7 ± 0.1, respectively, different from that of WT by 0.1-0.2 pH unit. These results suggest a possibility of W1 or W2 as the ionizable group for pK(e2).

  7. EDITORIAL: Optical orientation Optical orientation

    Science.gov (United States)

    SAME ADDRESS *, Yuri; Landwehr, Gottfried

    2008-11-01

    priority of the discovery in the literature, which was partly caused by the existence of the Iron Curtain. I had already enjoyed contact with Boris in the 1980s when the two volumes of Landau Level Spectroscopy were being prepared [2]. He was one of the pioneers of magneto-optics in semiconductors. In the 1950s the band structure of germanium and silicon was investigated by magneto-optical methods, mainly in the United States. No excitonic effects were observed and the band structure parameters were determined without taking account of excitons. However, working with cuprous oxide, which is a direct semiconductor with a relative large energy gap, Zakharchenya and his co-worker Seysan showed that in order to obtain correct band structure parameters, it is necessary to take excitons into account [3]. About 1970 Boris started work on optical orientation. Early work by Hanle in Germany in the 1920s on the depolarization of luminescence in mercury vapour by a transverse magnetic field was not appreciated for a long time. Only in the late 1940s did Kastler and co-workers in Paris begin a systematic study of optical pumping, which led to the award of a Nobel prize. The ideas of optical pumping were first applied by Georges Lampel to solid state physics in 1968. He demonstrated optical orientation of free carriers in silicon. The detection method was nuclear magnetic resonance; optically oriented free electrons dynamically polarized the 29Si nuclei of the host lattice. The first optical detection of spin orientation was demonstrated by with the III-V semiconductor GaSb by Parsons. Due to the various interaction mechanisms of spins with their environment, the effects occurring in semiconductors are naturally more complex than those in atoms. Optical detection is now the preferred method to detect spin alignment in semiconductors. The orientation of spins in crystals pumped with circularly polarized light is deduced from the degree of circular polarization of the recombination

  8. Water

    Science.gov (United States)

    ... www.girlshealth.gov/ Home Nutrition Nutrition basics Water Water Did you know that water makes up more ... to drink more water Other drinks How much water do you need? top Water is very important, ...

  9. Geometrical structures, vibrational frequencies, force constants and dissociation energies of isotopic water molecules (H2O, HDO, D2O, HTO, DTO, and T2O) under dipole electric field

    Institute of Scientific and Technical Information of China (English)

    Shi Shun-Ping; Zhang Quan; Zhang Li; Wang Rong; Zhu Zheng-He; Jiang Gang; Fu Yi-Bei

    2011-01-01

    The dissociation limits of isotopic water molecules are derived for the ground state. The equilibrium geometries,the vibrational frequencies, the force constants and the dissociation energies for the ground states of all isotopic water molecules under the dipole electric fields from -0.05 a.u. to 0.05 a.u. are calculated using B3P86/6-311++G(3df,3pf).The results show that when the dipole electric fields change from -0.05 a.u. to 0.05 a.u., the bond length of H-O increases whereas the bond angle of H-O-H decreases because of the charge transfer induced by the applied dipole electric field. The vibrational frequencies and the force constants of isotopic water molecules change under the influence of the strong external torque. The dissociation energies increase when the dipole electric fields change from -0.05 a.u.to 0.05 a.u. and the increased dissociation energies are in the order of H2O, HDO, HTO, D2O, DTO, and T2O under the same external electric fields.

  10. Insights into the mechanism of the reaction between tetrachloro-p-benzoquinone and hydrogen peroxide and their implications in the catalytic role of water molecules in producing the hydroxyl radial.

    Science.gov (United States)

    Li, Ping; Wang, Weihua; Sun, Qiao; Li, Zhen; Du, Aijun; Bi, Siwei; Zhao, Yan

    2013-08-26

    Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro-p-benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H2O2 has been systematically investigated at the B3LYP/6-311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H2O2 onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O-O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate-determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH3 substituents on this reaction have also been studied.

  11. Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy

    NARCIS (Netherlands)

    Nieuwenhuizen, R.P.J.; Nahidiazar, L.; Manders, E.M.M.; Jalink, K.; Stallinga, S.; Rieger, B.

    2015-01-01

    Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer t

  12. Structure and dynamics of ordered water in a thick nanofilm on ionic surfaces

    Institute of Scientific and Technical Information of China (English)

    Ren Xiu-Ping; Zhou Bo; Li Lan-Ting; Wang Chun-Lei

    2013-01-01

    The structure and dynamics of water in a thick film on an ionic surface are studied by molecular dynamic simulations.We find that there is a dense monolayer of water molecules in the vicinity of the surface.Water molecules within this layer not only show an upright hydrogen-down orientation,but also an upright hydrogen-up orientation.Thus,water molecules in this layer can form hydrogen bonds with water molecules in the next layer.Therefore,the two-dimensional hydrogen bond network of the first layer is disrupted,mainly due to the O atoms in this layer,which are affected by the next layer and are unstable.Moreover,these water molecules exhibit delayed dynamic behavior with relatively long residence time compared with those bulk-like molecules in the other layers.Our study should be helpful to further understand the influence of water film thickness on the interfacial water at the solid-liquid interface.

  13. Molecular dynamics study of the water/n-alkane interface

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Molecular dynamics simulations on the interface between liquid water and liquid n-alkane (including octane, nonane, decane, undecane and dodecane) have been performed with the purpose to study the interfacial properties: (Ⅰ) density profile; (Ⅱ) molecular orientation; (Ⅲ) interfacial tension and the temperature effect on the interfacial tension. Simulation results show that at the interface the structures of both water and n-alkane are different from those in the bulk. Water has an orientational preference due to the number of hydrogen bonds per molecule maximized. N-alkane has a more lateral orientation with respect to the interface in order to be in close contact with water. The calculated individual phase bulk density and interfacial tension of water/n-alkane systems are in good agreement with the corresponding experimental ones.

  14. Orienteering Club

    CERN Multimedia

    Club d'orientation

    2011-01-01

    Coupe genevoise, suite Résultats de la course de Saint-Cergue, sur la carte Les Pralies, samedi 17 septembre. Nouvelle victoire du finlandais Ville Keskisaari, du club COLJ sur le parcours technique long avec une belle avance sur le deuxième concurrent Christophe Vuitton du CO CERN. David Cuenin a remporté le parcours technique moyen, Franck Lonchampt du club O’Jura a, lui aussi, remporté à nouveau le parcours technique court, tout comme Julien Vuitton du club CO CERN sur le facile moyen. Pour finir, Stéphane Clément devance Victor Dannecker sur le parcours facile court. Les résultats complets sont disponibles sur le site du club du CERN http://cern.ch/club-orientation. Un abonnement est pris sur le secteur de Saint-Cergue, puisque le club organise les deux prochaines étapes de la coupe genevoise dans le Haut-Jura suisse. Tout d’abord le samedi 24 septembre, un relais inter-club se courr...

  15. Orienteering club

    CERN Multimedia

    Club d'orientation

    2010-01-01

    COURSE D’ORIENTATION  De La Rippe à Sauvabellin, la coupe genevoise continue ! Le rendez-vous était donné samedi 8 mai aux amateurs de course d’orientation dans les bois de La Rippe (Canton de Vaud). Cette 6e épreuve était organisée par le Club Satus Grutli de Genève. Il est dommage que les participants n’aient pas été aussi nombreux que lors des dernières courses, les Championnats de France des clubs à Dijon ayant certainement retenus plus d’un compétiteur. La première place est revenue à : – Technique long : Berni Wehrle – Technique moyen : Jean-Bernard Zosso – Technique court : Berni Wehrle – Facile moyen : Peter Troscanyi – Facile court : Claire Droz. Il ne restera plus que deux épreuves ...

  16. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2012-01-01

    Course d'orientation Ces deux dernières semaines, le club a organisé la troisième puis la quatrième étape de la coupe de printemps, une dans la forêt de Collogny/Moissey près de Vulbens, l’autre vers le parcours vita de Trélex. Les résultats sont: Facile court Vulbens : 1er Léo Lonchampt, O’Jura (16:04), 2e Timothée Bazin (23:07), 3e Francesco Pieri (26:57) Trélex : 1er Noora Maurent (23:11), 2e Sarah Stuber, COLJ (26:51), 3e T. Bazin (28:17) Facile moyen Vulbens : 1er Victor Kuznetsov, CO CERN (25:36), 2e Didier Descourvières (28:03), 3e Konstantinos Haider, CO CERN (36:53) Trélex : 1er V. Kuznetsov, COLJ (38:01), 2e K. Haider, CO CERN (43:15), 3e ex aequo Olivia Nguyen et Sven Vietmeier (58:11) Technique court Vulbens : 1er Benoit Bazin (41:21), 2e Colas Gintzburger (55:12), 3e Nathan Freydoz (55:48) Trélex : 1...

  17. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2011-01-01

    Course d'orientation Avec la CO en nocturne organisée par le club du CERN vendredi 14 octobre au stade des Eveaux (Ge), et la CO à Savigny (Vd) proposée par le club de Lausanne-Jorat le lendemain, les étapes de la coupe genevoise d’automne s’enchainent rapidement. Il ne reste plus que 3 rendez-vous pour boucler la saison. Les premières places devraient certainement se jouer entre des membres du club du CERN, du O’Jura ou de Lausanne-Jorat. La prochaine course du club est programmée pour samedi 22 octobre à Pomier, près de Cruseilles. L’accueil se fera à partir de 12h30 et les départs s’échelonneront de 13h à 15h. * * * * * * * Nouvelle belle victoire samedi 8 octobre à Saint Cergue du jeune finlandais Ville Keskisaari (COLJ) en 50:56 devant Jürg Niggli (O’Jura) en 1:03:32, et Alexandre...

  18. Orienteering club

    CERN Multimedia

    Club d'orientation

    2013-01-01

    Course d'orientation Finale de la coupe genevoise Rapide et méthodique, voilà les qualités dont il fallait faire preuve pour remporter la dernière étape de la coupe organisée par le club du CERN dans les bois de Monteret. Il s’agissait d’une course au score où chaque concurrent disposait d’un temps imparti pour poinçonner le maximum de balises. Le parcours technique a été remporté par Tomas Shellman et le parcours facile par Victor Dannecker. Cette dernière étape était aussi décisive pour la désignation des lauréats de la coupe genevoise de printemps. Les résultats officiels étaient donnés par le président du club, L. Jirden : Circuit Technique Long : Berni Wehrle, Bruno Barge, Edvins Reisons Circuit Technique Moyen : J.-Bernard Zosso, ...

  19. Orienteering Club

    CERN Multimedia

    Club d'orientation

    2013-01-01

    De jour comme de nuit Les amateurs de course d’orientation ont pu s’en donner à cœur joie ce week-end puisqu’ils avaient la possibilité de courir sur deux épreuves en moins de 24 heures. En effet, le club du CERN organisait une course de nuit aux Evaux et la 7e étape de la coupe genevoise se tenait samedi après-midi dans les bois du Grand Jorat à Savigny. Les vainqueurs pour chaque course sont : Technique long CO de nuit: Julien Charlemagne, SOS Sallanches CO samedi: Philipp Khlebnikov, ANCO   Technique moyen CO de nuit: Céline Zosso, CO CERN CO samedi: Pavel Khlebnikov, ANCO Technique court CO de nuit: Colas Ginztburger, SOS Sallanches CO samedi: Victor Kuznetsov, COLJ Lausannne Facile moyen CO de nuit: Gaëtan Rickenbacher, CO CERN CO samedi: Tamas Szoke   Facile court CO de nuit:Oriane Rickenbacher, CO CERN CO samedi: Katya Kuznetsov...

  20. Orienteering club

    CERN Multimedia

    Club d'orientation

    2014-01-01

    Course d'orientation Finale de la coupe d’automne La dernière épreuve de la coupe d’automne organisée par le club s’est déroulée ce samedi 1er novembre avec une course type «one-man-relay» dans la forêt de Trelex (Vd). Les concurrents des circuits techniques devaient parcourir trois boucles et ceux des circuits «faciles» deux boucles, avec changements de carte. Le parcours technique long a été remporté par un membre du club, Berni Wehrle. A l’issue de cette course, le Président du club, L. Jirden annonçait le classement général de la coupe d’automne, basé sur les 6 meilleurs résultats de la saison : Circuit technique long : 1er Juerg Niggli (O’Jura), 2e Berni Wehrle, 3e Beat Mueller. Circuit technique moyen : 1er Laurent Merat (O&r...

  1. Orienteering Club

    CERN Multimedia

    Club d'orientation

    2012-01-01

    Finale de la coupe d’automne   La coupe d’automne organisée par le club d’orientation du CERN s’est terminée ce samedi 10 novembre avec une course sprint à Prévessins. C’était la 12e épreuve de la saison. En stage dans la région, Tanya Ryabkina, championne d’Europe en titre et médaillée de bronze en moyenne distance lors des championnats du monde à La Givrine cet été, a fait l’honneur de sa présence et termine 2e à 8 secondes de Trygve Buanes, norvégien du club de Bergen. A l’issue de cette dernière épreuve, le classement général de la coupe d’automne, basé sur les 8 meilleurs résultats de la saison, est ainsi le suivant : Circuit technique long : 1er Jurg Niggli (O&rsqu...

  2. Orienteering Club

    CERN Multimedia

    Club d'orientation

    2013-01-01

    Finale de la coupe d’automne La dernière épreuve de la coupe d’automne organisée par le club d’orientation du CERN s’est déroulée ce samedi 2 novembre avec une course au score dans le bois Tollot (GE). Les concurrents disposaient d’un temps imparti pour poinçonner le maximum de balises différemment placées selon le circuit choisi. Juerg Niggli (club O’Jura) a remporté le parcours technique long. A l’issue de cette course, le classement général de la coupe d’automne, basé sur les 6 meilleurs résultats de la saison, est le suivant : Circuit technique long : 1er Juerg Niggli (O’Jura), 2e Bruno Barge, 3e Beat Mueller. Circuit technique moyen : 1er Laurent Merat (O’Jura), 2e Jirden Lennart, 3e Daria Niggli. Circuit technique court : 1er Victor Kuznetsov (COLJ), 2e N...

  3. Orienteering club

    CERN Multimedia

    Club d'orientation

    2013-01-01

    Course d'orientation Vers les dernières courses de printemps Une centaine de coureurs se sont déplacés sur le site de la Roche Fendue prés de Morez pour gouter à un des 5 parcours proposés par le club du O’Jura. Le terrain était gras mais que peut-on trouver d’autre avec cette météo! Les vainqueurs de chaque circuit sont : Alina Niggli (O’Jura) facile court, Natalja Niggli (O’Jura) facile moyen, Victor Kuznetsov (COLJ) technique court, Yves Rousselot (Balise 25) technique moyen et pour finir François Gonon (O’Jura) avec une victoire haut la main sur le technique long. Il ne reste plus que deux épreuves pour la coupe genevoise de printemps : à savoir samedi 8 juin, course de type longue distance organisée par le club de Lausanne Jorat (COLJ) dans le bois de Seyte sur Mutrux/Concise, inscription de 12h &...

  4. Orienteering Club

    CERN Multimedia

    Club d'orientation

    2013-01-01

    Course d'orientation Le coup d’envoi de la coupe genevoise a été donné samedi 31 août dans les bois de Combe Froide à Prémanon. Plus de 150 coureurs avaient fait le déplacement. Les parcours facile court, facile moyen et technique court ont été remportés par des coureurs du club O’Jura - Ulysse Dannecker, Léo Lonchampt, Franck Lonchampt, le technique moyen par Pekka Marti du club Ol Biel Seeland et le technique long par Térence Risse du CA Rosé – également membre de l’équipe nationale suisse des moins de 20 ans. Pour le club du CERN, les meilleures résultats ont été obtenus pas Emese Szunyog sur technique court et Marie Vuitton sur technique moyen avec une 4e place. La prochaine course aura lieu samedi 14 septembre à La Faucille. Le club propose aussi...

  5. Orienteering Club

    CERN Multimedia

    CLUB D'ORIENTATION

    2013-01-01

    Calendrier de la coupe d’automne Le Club d’orientation du CERN, en partenariat avec d’autres clubs de la région, vous propose, pour cette nouvelle coupe d’automne genevoise, une série de 10 courses. Le club du O’Jura donnera le coup d’envoi le samedi 31 août. Les courses s’enchaîneront selon le calendrier suivant : Samedi 31 août : Prémanon (39) - longue distance Samedi 14 septembre : La Faucille (01) - longue distance Samedi 21 septembre : Saint Cergue (VD) - longue distance Samedi 28 septembre : Ballens (VD) - relais Samedi 5 octobre : La Pile (VD) - longue distance Vendredi 11 octobre : Les Evaux (GE) - nocturne Samedi 12 octobre : Grand Jorat, Savigny (VD) - longue distance Samedi 19 octobre : Terrasses de Genève (74) - longue distance Samedi 26 octobre : Prémanon (39) - longue distance Samedi 2 novembre : Bois Tollot (GE) - score - Finale Les &a...

  6. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2012-01-01

    Relais inter-club/Challenge Carlo Milan Samedi dernier, lors de l’épreuve de course d’orientation organisée par le club du O’Jura, le moteur de la discipline était l’esprit d’équipe, puisqu’il était question d’un relais inter-club avec le Challenge Carlo Milan. Les clubs avaient aligné leurs coureurs soit sur le relais technique (trois participants) soit sur le relais facile (deux participants). Côté O’Jura, il fallait noter la participation de François Gonon, champion du monde 2011, côté club du CERN, Marie et Gaëtan Vuitton, jeunes espoirs du club, devaient préparer la piste pour lancer le dernier relayeur. Côté Lausanne-Jorat, il fallait compter sur le très jeune Viktor Kuznetsov. Les 31 équipes engagées n’ont pas m&ea...

  7. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2012-01-01

     Finale de la coupe de printemps   La dernière course d’orientation comptant pour la Coupe de printemps a eu lieu samedi dernier dans le village des Rousses et vers le Fort. Il s’agissait d’un sprint organisé par le club O’Jura. Les temps de course ont avoisiné les 20 minutes que ce soit pour le parcours technique moyen ou technique long. Tous les habitués étaient au rendez-vous pour venir consolider ou améliorer leur place au classement. A l’issue de cette course, le classement général de la Coupe de printemps prenant en compte les 6 meilleurs résultats des 9 courses était établi et les lauréats de chaque catégorie sont les suivants: Circuit technique long : 1er Berni Wehrle, 2e Bruno Barge, 3e Edvins Reisons. Circuit technique moyen : 1er Jean-Bernard Zosso, 2e Cédric Wehrl&...

  8. Orienteering Club

    CERN Multimedia

    Club d'Orientation

    2015-01-01

    Course orientation Finale de la coupe genevoise La série des courses de printemps s’est achevée samedi dernier dans les bois de Bonmont (Vaud) avec une épreuve «one-man-relay» organisée par le club. Le vainqueur du parcours technique  long, Yann Locatelli (Club de Chambéry Savoie) a réalisé les deux boucles comportant 24 balises avec presque 6 minutes d’avance sur le second concurrent Domenico Lepori (Club CARE Vevey). Cette dernière étape était aussi décisive pour la désignation des lauréats de la coupe genevoise de printemps, en comptabilisant les 6 meilleurs résultats sur les 10 épreuves. Le podium officiel était donné par le président du club, L. Jirden, qui profitait de l’occasion pour remercier tous les participants et également tous les...

  9. Orienteering club

    CERN Multimedia

    Club d'orientation

    2013-01-01

    Courses d’orientation Samedi 20 avril, les organisateurs du Club de CO du CERN ont accueilli au Mont Mourex 70 participants qui n’ont pas hésité à venir malgré la forte bise. Berni Wehrle du CO CERN s’est octroyé la première place en 1:04:49 sur le parcours technique long devant Pyry Kettunen du Saynso Juankoski en 1:06:52, la 3e place revenant à Bruno Barge, CO CERN, à 7 secondes. Les autres parcours ont été remportés par : Technique moyen : 1er Jacques Moisset, Chamonix (47:44), 2e Yves Rousselot, Balise 25 Besançon (57:16), 3e Jean-Bernard Zosso, CO CERN (59:28). Technique court : 1er Victor Kuznetsov, COLJ (51:53), 2e Pierrick Collet, CO CERN (1:12:52), 3e Dominique Balay, CO CERN (1:16:04). Pour les parcours facile moyen et facile court, Ralf Nardini et Léa Nicolas, tous deux du CO CERN, terminaient respectivement premier. Voi...

  10. Orienteering club

    CERN Multimedia

    Club d'orientation

    2014-01-01

    Course d'orientation C’est sous un beau soleil samedi 4 octobre que s’est déroulée la 6e étape de la Coupe genevoise d’automne organisée par le club. Plus d’une centaine de concurrents provenant de 7 clubs de CO avaient fait le déplacement pour courir sur un des cinq parcours proposés dans les bois de Trélex-Génolier (VD). Le podium est le suivant : Technique long (5,9 km, 19 postes) : 1er Jurg Niggli, O’Jura (1:00:02); 2e Berni Wehrle, CO CERN (1:06:44); 3e Konrad Ehrbar, COLJ (1:07:08) Technique moyen (4,8 km, 18 postes) : 1er Christophe Vuitton, CO CERN (54:25); 2e J.B. Zosso, CO CERN (1:01:19); 3e Jeremy Wichoud, COLJ (1:06:21) Technique court (3,8 km, 14 postes) : 1er Julien Vuitton, CO CERN (36:19); 2e Vladimir Kuznetsov, COLJ (48:47); 3e Natalia Niggli, O’Jura (50:38) Facile moyen (3,2 km, 11 postes) : 1ère Alina Niggli, O&...

  11. Observation of pendular butterfly Rydberg molecules

    CERN Document Server

    Niederprüm, Thomas; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig

    2016-01-01

    Obtaining full control over the internal and external quantum states of molecules is the central goal of ultracold chemistry and allows for the study of coherent molecular dynamics, collisions and tests of fundamental laws of physics. When the molecules additionally have a permanent electric dipole moment, the study of dipolar quantum gases and spin-systems with long-range interactions as well as applications in quantum information processing are possible. Rydberg molecules constitute a class of exotic molecules, which are bound by the interaction between the Rydberg electron and the ground state atom. They exhibit extreme bond lengths of hundreds of Bohr radii and giant permanent dipole moments in the kilo-Debye range. A special type with exceptional properties are the so-called butterfly molecules, whose electron density resembles the shape of a butterfly. Here, we report on the photoassociation of butterfly Rydberg molecules and their orientation in a weak electric field. Starting from a Bose-Einstein cond...

  12. Diversity-Oriented Organic Synthesis

    Institute of Scientific and Technical Information of China (English)

    J. Wu

    2005-01-01

    @@ 1Introduction A goal of chemical genetics is to find small molecules that modulate the individual functions of gene products with high potency and high specificity[1,2]. Natural products and natural product-derived compounds provide many of the most striking examples, particularly in terms of their specificity. It seems unlikely that natural products alone will provide the hypothetical "complete" set of small molecules that would allow the functions of all proteins, as well as their individual domains, to be determined. For chemistry to have its maximal effect on biology, efficient methods based on diversity-oriented organic synthesis for discovering this set of small molecules are in great demand(See Fig. 1).

  13. Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy.

    Directory of Open Access Journals (Sweden)

    Robert P J Nieuwenhuizen

    Full Text Available Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of molecules and orientational alignment of the structures on which they reside as co-orientation. Because the orientation varies with the length scale at which it is evaluated, we consider this scale as a separate informative dimension in the analysis. Additionally we introduce a data driven method for testing the statistical significance of the co-orientation and provide a method for visualizing the local co-orientation strength in images. We demonstrate our methods on simulated localization microscopy data of filamentous structures, as well as experimental images of similar structures acquired with localization microscopy in different color channels. We also show that in cultured primary HUVEC endothelial cells, filaments of the intermediate filament vimentin run close to and parallel with microtubuli. In contrast, no co-orientation was found between keratin and actin filaments. Co-orientation between vimentin and tubulin was also observed in an endothelial cell line, albeit to a lesser extent, but not in 3T3 fibroblasts. These data therefore suggest that microtubuli functionally interact with the vimentin network in a cell-type specific manner.

  14. Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy.

    Science.gov (United States)

    Nieuwenhuizen, Robert P J; Nahidiazar, Leila; Manders, Erik M M; Jalink, Kees; Stallinga, Sjoerd; Rieger, Bernd

    2015-01-01

    Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of molecules and orientational alignment of the structures on which they reside as co-orientation. Because the orientation varies with the length scale at which it is evaluated, we consider this scale as a separate informative dimension in the analysis. Additionally we introduce a data driven method for testing the statistical significance of the co-orientation and provide a method for visualizing the local co-orientation strength in images. We demonstrate our methods on simulated localization microscopy data of filamentous structures, as well as experimental images of similar structures acquired with localization microscopy in different color channels. We also show that in cultured primary HUVEC endothelial cells, filaments of the intermediate filament vimentin run close to and parallel with microtubuli. In contrast, no co-orientation was found between keratin and actin filaments. Co-orientation between vimentin and tubulin was also observed in an endothelial cell line, albeit to a lesser extent, but not in 3T3 fibroblasts. These data therefore suggest that microtubuli functionally interact with the vimentin network in a cell-type specific manner.

  15. Strength of hydrogen bonds of water depends on local environment.

    Science.gov (United States)

    Huš, Matej; Urbic, Tomaz

    2012-04-14

    In-depth knowledge of water-water potential is important for devising and evaluating simple water models if they are to accurately describe water properties and reflect various solvation phenomena. Water-water potential depends upon inter-molecular distance, relative orientation of water molecules, and also local environment. When placed at a favorable distance in a favorable orientation, water molecules exhibit a particularly strong attractive interaction called hydrogen bond. Although hydrogen bond is very important for its effects on the elements of life, industrial applications, and bulk water properties, there is no scientific consensus on its true nature and origin. Using quantum-mechanical methods, hydrogen bond strength was calculated in different local environments. A simple empirical linear relationship was discovered between maximum hydrogen bond strength and the number of water molecules in the local environment. The local environment effect was shown to be considerable even on the second coordination shell. Additionally, a negative linear correlation was found between maximum hydrogen bond strength and the distance, at which it was observed. These results provide novel insights into the nature of hydrogen bonding.

  16. A bio-inspired, small molecule electron-coupled-proton buffer for decoupling the half-reactions of electrolytic water splitting.

    Science.gov (United States)

    Rausch, Benjamin; Symes, Mark D; Cronin, Leroy

    2013-09-18

    Electron-coupled-proton buffers (ECPBs) allow H2 and O2 evolution to be separated from each other in time during the electrolysis of water. Natural photosynthetic systems achieve an analogous feat during water splitting and employ a range of intermediate redox mediators such as quinone derivatives to aid this process. Drawing on this natural example, we show that a low molecular weight quinone derivative is capable of decoupling H2 evolution from O2 evolution at scale during electrochemical water splitting. This work could significantly lower the cost of ECPBs, paving the way for their more widespread adoption in water splitting.

  17. Water's structure around hydrophobic solutes and the iceberg model.

    Science.gov (United States)

    Galamba, N

    2013-02-21

    The structure of water in the hydration shells of small hydrophobic solutes was investigated through molecular dynamics. The results show that a subset of water molecules in the first hydration shell of a nonpolar solute have a significantly enhanced tetrahedrality and a slightly larger number of hydrogen bonds, relative to the molecules in water at room temperature, consistent with the experimentally observed negative excess entropy and increased heat capacity of hydrophobic solutions at room temperature. This ordering results from the rearrangement of a small number of water molecules near the nonpolar solutes that occupy one to two vertices of the enhanced water tetrahedra. Although this structuring is not nearly like that often associated with a literal interpretation of the term "iceberg" in the Frank and Evans iceberg model, it does support a moderate interpretation of this model. Thus, the tetrahedral orientational order of this ensemble of water molecules is comparable to that of liquid water at ~10 °C, although not accompanied by the small contraction of the O-O distance observed in cold water. Further, we show that the structural changes of water in the vicinity of small nonpolar solutes cannot be inferred from the water radial distribution functions, explaining why this increased ordering is not observed through neutron diffraction experiments. The present results restore a molecular view where the slower translational and reorientational dynamics of water near hydrophobic groups has a structural equivalent resembling water at low temperatures.

  18. Gestione delle acque, pace nel Medio Oriente e un ruolo per la Banca Mondiale (Water Management, Middle East Peace and a Role for the World Bank

    Directory of Open Access Journals (Sweden)

    Hossein Askari

    2012-04-01

    Full Text Available The region comprising North Africa and the Middle East is the driest in the world. Thus conflicts over water have been a part of the landscape. These conflicts over water are invariably seen as a zero sum game; such a view does not incorporate the notion that water is an economic good and is therefore scarce. Given the limitation of competitive markets, optimal water allocation could only but help. However, even if one country allocates water efficiently within its own territory, its allocation could be sub-optimal if water interdependencies with other countries are not incorporated in a regional optimization model. The World Bank is in the best position to adopt a regional optimization model and thus ameliorate water conditions in the Middle East and in other regions around the world.       JEL Codes: Q25, Q28, Q15, Q13Keywords: Water

  19. Physical state of poorly water soluble therapeutic molecules loaded into SBA-15 ordered mesoporous silica carriers: a case study with itraconazole and ibuprofen.

    Science.gov (United States)

    Mellaerts, Randy; Jammaer, Jasper A G; Van Speybroeck, Michiel; Chen, Hong; Van Humbeeck, Jan; Augustijns, Patrick; Van den Mooter, Guy; Martens, Johan A

    2008-08-19

    The ordered mesoporous silica material SBA-15 was loaded with the model drugs itraconazole and ibuprofen using three different procedures: (i) adsorption from solution, (ii) incipient wetness impregnation, and (iii) heating of a mixture of drug and SBA-15 powder. The location of the drug molecules in the SBA-15 particles and molecular interactions were investigated using nitrogen adsorption, TGA, DSC, DRS UV-vis, and XPS. The in vitro release of hydrophobic model drugs was evaluated in an aqueous environment simulating gastric fluid. The effectiveness of the loading method was found to be strongly compound dependent. Incipient wetness impregnation using a concentrated itraconazole solution in dichloromethane followed by solvent evaporation was most efficient for dispersing itraconazole in SBA-15. The itraconazole molecules were located on the mesopore walls and inside micropores of the mesopore walls. When SBA-15 was loaded by slurrying it in a diluted itraconazole solution from which the solvent was evaporated, the itraconazole molecules ended up in the mesopores that they plugged locally. At a loading of 30 wt %, itraconazole exhibited intermolecular interactions inside the mesopores revealed by UV spectroscopy and endothermic events traced with DSC. The physical mixing of itraconazole and SBA-15 powder followed by heating above the itraconazole melting temperature resulted in formulations in which glassy itraconazole particles were deposited externally on the SBA-15 particles. Loading with ibuprofen was successful with each of the three loading procedures. Ibuprofen preferably is positioned inside the micropores. In vitro release experiments showed fast release kinetics provided the drug molecules were evenly deposited over the mesoporous surface.

  20. Solar energy driven photocatalytic membrane modules for water reuse in agricultural and food industries. Pre-industrial experience using s-triazines as model molecules

    OpenAIRE

    Ignazio Renato Bellobono; Franca Morazzoni; Riccardo Bianchi; Emilia Simona Mangone; Rodica Stanescu; Cristina Costache; Paola Maria Tozzi

    2005-01-01

    A membrane module, utilizing photocatalytic membranes, has been employed in a pilot plant, in conditions of solar irradiation, to investigate photomineralisation of atrazine, propazine, terbutylazine, symazine, prometryn, and ametryn, as model molecules of s-triazine herbicides, at a standard concentration (1.0 ppm) simulating those of contaminated aquifers, by using ozone as oxygen supplier. Photocatalytic composite membranes immobilised 30±3 wt.% of TiO2 and 6 wt.% of a synergic mixture of ...

  1. Water structures inside and outside single-walled carbon nanotubes under perpendicular electric field

    Institute of Scientific and Technical Information of China (English)

    Zhen XU; Guo-hui HU; Zhi-liang WANG; Zhe-wei ZHOU

    2014-01-01

    The structures of water inside and outside (6,6), (8,8), and (10,10) single-walled carbon nanotubes (SWCNTs) under an electric field perpendicular to the tube axis are investigated by molecular dynamics simulations. The results show that dipole reorientation induced by electric field plays a significant role on the structures of confined water inside and outside SWCNTs. Inside SWCNTs, the average water occupancy and the average number of hydrogen bonds (H-bonds) per water molecule decrease as the electric intensity increases. Because the field intensity is sufficiently strong, the initial water structures inside the SWCNTs are destroyed, and the isolated water clusters are found. Outside SWCNTs, the azimuthal distributions of the density and the average number of H-bonds per water molecule around the solid walls become more and more asymmetric as the electric intensity increases. The percentages of water molecules involved in 0-5 H-bonds for all the three types of SWCNTs under different field intensities are displayed. The results show that those water molecules involved with most H-bonds are the most important to hold the original structures. When the electric field direction is parallel with the original preferred orientation, the density and the H-bond connections in water will be increased; when the electric field direction is perpendicular to the original preferred orientation, the density and the H-bond connections in water will be decreased.

  2. Gestione delle acque, pace nel Medio Oriente e un ruolo per la Banca Mondiale (Water Management, Middle East Peace and a Role for the World Bank

    Directory of Open Access Journals (Sweden)

    Hossein Askari

    2001-06-01

    Full Text Available The region comprising North Africa and the Middle East is the driest in the world. Thus conflicts over water have been a part of the landscape. These conflicts over water are invariably seen as a zero sum game; such a view does not incorporate the notion that water is an economic good and is therefore scarce. Given the limitation of competitive markets, optimal water allocation could only but help. However, even if one country allocates water efficiently within its own territory, its allocation could be sub-optimal if water interdependencies with other countries are not incorporated in a regional optimization model. The World Bank is in the best position to adopt a regional optimization model and thus ameliorate water conditions in the Middle East and in other regions around the world.

  3. Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules.

    Science.gov (United States)

    Higo, J; Sasai, M; Shirai, H; Nakamura, H; Kugimiya, T

    2001-05-22

    We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity "site-dipole field" is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 A in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 A, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

  4. Symmetric Euler orientation representations for orientational averaging.

    Science.gov (United States)

    Mayerhöfer, Thomas G

    2005-09-01

    A new kind of orientation representation called symmetric Euler orientation representation (SEOR) is presented. It is based on a combination of the conventional Euler orientation representations (Euler angles) and Hamilton's quaternions. The properties of the SEORs concerning orientational averaging are explored and compared to those of averaging schemes that are based on conventional Euler orientation representations. To that aim, the reflectance of a hypothetical polycrystalline material with orthorhombic crystal symmetry was calculated. The calculation was carried out according to the average refractive index theory (ARIT [T.G. Mayerhöfer, Appl. Spectrosc. 56 (2002) 1194]). It is shown that the use of averaging schemes based on conventional Euler orientation representations leads to a dependence of the result from the specific Euler orientation representation that was utilized and from the initial position of the crystal. The latter problem can be overcome partly by the introduction of a weighing factor, but only for two-axes-type Euler orientation representations. In case of a numerical evaluation of the average, a residual difference remains also if a two-axes type Euler orientation representation is used despite of the utilization of a weighing factor. In contrast, this problem does not occur if a symmetric Euler orientation representation is used as a matter of principle, while the result of the averaging for both types of orientation representations converges with increasing number of orientations considered in the numerical evaluation. Additionally, the use of a weighing factor and/or non-equally spaced steps in the numerical evaluation of the average is not necessary. The symmetrical Euler orientation representations are therefore ideally suited for the use in orientational averaging procedures.

  5. Optimized localization analysis for single-molecule tracking and super-resolution microscopy

    DEFF Research Database (Denmark)

    Mortensen, Kim; Churchman, L. S.; Spudich, J. A.;

    2010-01-01

    We optimally localized isolated fluorescent beads and molecules imaged as diffraction-limited spots, determined the orientation of molecules and present reliable formulas for the precision of various localization methods. Both theory and experimental data showed that unweighted least-squares fitt......We optimally localized isolated fluorescent beads and molecules imaged as diffraction-limited spots, determined the orientation of molecules and present reliable formulas for the precision of various localization methods. Both theory and experimental data showed that unweighted least...

  6. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

    Science.gov (United States)

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-07

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  7. Thinking in Orienteering.

    Science.gov (United States)

    Johansen, Bjorn Tore

    1997-01-01

    A think-aloud technique, in which 20 orienteers verbalized their exact thoughts during orienteering, was used to examine the phenomenon of cognition during orienteering. Results indicate that orienteering is experienced as a task to be accomplished, a physical movement, and a dynamic process, and that thinking involves attuning perceptions to…

  8. Modeling groundwater-surface water interactions in an operational setting by linking object- oriented river basin management model (RiverWare) with 3-D finite-difference groundwater model (MODFLOW).

    Science.gov (United States)

    Valerio, A.; Rajaram, H.; Zagona, E.

    2007-12-01

    Accurate representation of groundwater-surface water interactions is critical to modeling low river flow periods in riparian environments in the semi-arid southwestern United States. As an example, over-appropriation of human water use in the Middle Rio Grande region adversely impacts the habitat of the endangered Rio Grande silvery minnow. Improved management practices during low flow conditions could prevent channel desiccation and habitat destruction. We present a modeling tool with significant potential for improved decision-making in stream reaches influenced by significant surface-groundwater interactions. While river basin management models typically represent operational complexities such as human elements of water demand and consumption with a high degree of sophistication, they often represent groundwater-surface water interactions semi-empirically or at coarse resolution. In contrast, distributed groundwater models, with an adequately fine grid represent groundwater-surface water interactions accurately, but seldom incorporate complex details of water rights and user demands. To best exploit the strengths of both classes of models, we have developed a link between the object-oriented river management software package RiverWare and the USGS groundwater modeling program MODFLOW. An interactive time stepping approach is used in the linked model. RiverWare and MODFLOW run in parallel exchanging data after each time-step. This linked framework incorporates several features critical to modeling groundwater-surface interactions in riparian zones, including riparian ET, localized variations in seepage rates and rule-based water allocations to users and/or environmental flows, and is expected to be an improved tool for modeling groundwater-surface water interaction in regions where groundwater storage repose to changing river conditions is rapid. The performance of the linked model is illustrated through applications on the Rio Grande in the vicinity of

  9. Synthesis, Structure and Reactivity of Molecules Attached to Electrode Surfaces.

    Science.gov (United States)

    2014-09-26

    Structure and Reactivity of Molecules Attached to Electrode Surfaces", AFOSR #81-0149 III. REPORTING PERIOD: April 15, 1981 through April 14, 1985 IV...Adsorption .... ............... 17 9. Effect of Surface Roughness on Adsorbate Orientation and Reactivity . 20 10. Ordered/ Disordered Packing in Chemisorbed... reactivity only when present in the edge-pendant orientation. Clearly, molecular orientation (i.e., mode of +. .4 o,, -12- attachment to the surface) is a

  10. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab-Initio Molecular Dynamics Simulations

    CERN Document Server

    Kessler, Jan; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-01-01

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

  11. Proton transfer pathways in an aspartate-water cluster sampled by a network of discrete states

    Science.gov (United States)

    Reidelbach, Marco; Betz, Fridtjof; Mäusle, Raquel Maya; Imhof, Petra

    2016-08-01

    Proton transfer reactions are complex transitions due to the size and flexibility of the hydrogen-bonded networks along which the protons may ;hop;. The combination of molecular dynamics based sampling of water positions and orientations with direct sampling of proton positions is an efficient way to capture the interplay of these degrees of freedom in a transition network. The energetically most favourable pathway in the proton transfer network computed for an aspartate-water cluster shows the pre-orientation of water molecules and aspartate side chains to be a pre-requisite for the subsequent concerted proton transfer to the product state.

  12. 面向服务的供水管网模型应用模式及其实证研究%Service-oriented water distribution model application mode

    Institute of Scientific and Technical Information of China (English)

    贾海峰; 赵琦峰

    2011-01-01

    该文提出面向服务的供水管网模型应用模式,通过建立独立的供水管网模型系统,把模型构建与模型应用区分开。在该模式中,集中维护的模型与分布的模型应用通过模拟服务接口连接。进而基于提出的模式,构建供水管网模型系统框架,包括管网模型管理模块和管网模型模拟服务模块,提供了管网模型参数管理、管网模型参数识别、管网模拟服务监控以及系统参数设置等功能,可以解决供水管网管理系统中管网模型管理维护困难的问题。最后以东莞市典型供水管网为案例对象,选择EPANET作为水力与水质模拟的模型软件,采用微软ASP.NETXMLWeb服务%A service-oriented water distribution system model was developed to enable water companies to develop effective water distribution systems by separating model development and management from specific applications.The model can be managed centrally with distributed users with applications using the model by only accessing the interface.A case study for a typical water distribution system in the city of Dongguan shows the use of services-oriented model application mode.

  13. 磷脂分子在水中形成不同聚集体的机制探讨%Discussion on mechanism of the formation of different phospholipid molecules aggregates in water

    Institute of Scientific and Technical Information of China (English)

    薛士兴; 王向涛; 李永吉

    2012-01-01

    Phospholipid molecules are the basic composition of life, which possesses amphiphilic molecular structure and biological homology. The self-assembly aggregates of liposomes is widely used in drug delivery systems. However, the structure of the phospholipid molecule aggregates in water were diverse, including not only spherical liposomes, but also tubular structures (such as microtubules) . By studying related literature, the mechanism of the formation of different phospholipid molecule aggregates was analyzed and summarized, with focus on the effects of the amphiphilic structure and molecular morphology of the phospholipid molecules on the formation of different self-assembly aggregates. This discussion may have important theoretical significance for the preparation of phospholipid molecular aggregates.%磷脂分子作为生命体的基本组成物质,既具有两亲性的分子结构,又具有生物同源性,因此,其自组装聚集体-脂质体在药物载体方面得到广泛应用.但磷脂分子在水中形成的聚集体结构多样,不仅有球状的脂质体,还有管状结构(如微管).本文通过研究国内外相关文献,分析、整理和归纳了磷脂分子在水中形成不同聚集体的机制,主要讲述了磷脂分子的两亲性结构、分子形态对形成不同自组装聚集体的影响,对于磷脂分子聚集体的制备具有重要的理论指导意义.

  14. Temperature dependence of the structure of protein hydration water and the liquid-liquid transition.

    Science.gov (United States)

    Accordino, S R; Malaspina, D C; Rodriguez Fris, J A; Alarcón, L M; Appignanesi, G A

    2012-03-01

    We study the temperature dependence of the structure and orientation of the first hydration layers of the protein lysozyme and compare it with the situation for a model homogeneous hydrophobic surface, a graphene sheet. We show that in both cases these layers are significantly better structured than bulk water. The geometrical constraint of the interface makes the water molecules adjacent to the surface lose one water-water hydrogen bond and expel the fourth neighbors away from the surface, lowering local density. We show that a decrease in temperature improves the ordering of the hydration water molecules, preserving such a geometrical effect. For the case of graphene, this favors an ice Ih-like local structuring, similar to the water-air interface but in the opposite way along the c axis of the basal plane (while the vicinal water molecules of the air interface orient a hydrogen atom toward the surface, the oxygens of the water molecules close to the graphene plane orient a lone pair in such a direction). In turn, the case of the first hydration layers of the lysozyme molecule is shown to be more complicated, but still displaying signs of both kinds of behavior, together with a tendency of the proximal water molecules to hydrogen bond to the protein both as donors and as acceptors. Additionally, we make evident the existence of signatures of a liquid-liquid transition (Widom line crossing) in different structural parameters at the temperature corresponding to the dynamic transition incorrectly referred to as "the protein glass transition."

  15. Ab initio study of the chemical states of water on Cr 2O 3(0 0 0 1): From the isolated molecule to saturation coverage

    Science.gov (United States)

    Costa, Dominique; Sharkas, Kamal; Islam, Mazharul M.; Marcus, Philippe

    2009-08-01

    The reactivity of the (0 0 0 1)-Cr-Cr 2O 3 surface towards water was studied by means of periodic DFT + U. Several water coverages were studied, from 1.2H 2O/nm 2 to 14.1H 2O/nm 2, corresponding to ¼, 1, 2 and 3 water/Cr at the (0 0 0 1)-Cr 2O 3 surface, respectively. With increasing coverage, water gradually completes the coordination sphere of the surface Cr atoms from 3 (dry surface) to 4 (1.2 and 4.7H 2O/nm 2), 5 (9.4H 2O/nm 2) and 6 (14.1H 2O/nm 2). For all studied coverages, water replaces an O atom from the missing above plane. At coverages 1.2 and 4.7H 2O/nm 2, the Cr-O s (surface oxygen) acid-base character and bond directionality govern the water adsorption. The adsorption is molecular at the lowest coverage. At 4.7H 2O/nm 2, molecular and dissociative states are isoenergetic. The activation energy barrier between the two states being as low as 12 kJ/mol, allowing protons exchanges between the OH groups, as evidenced by ab inito molecular dynamics at room temperature. At coverages of 9.4 and 14.1H 2O/nm 2, 1D- (respectively, 2D-) water networks are formed. The resulting surface terminations are -Cr(OH) 2 and -Cr(OH) 3- like, respectively. The increased stability of those terminations as compared to the previous ones are due to the stabilization of the adsorbed phase through a H-bond network and to the increase in the Cr coordination number, stabilizing the Cr ( t2g) orbitals in the valence band. An atomistic thermodynamic approach allows us to specify the temperature and water pressure domains of prevalence for each surface termination. It is found that the -Cr(OH) 3-like, -Cr(OH) 2 and anhydrous surfaces may be stabilized depending on ( T, P) conditions. Calculated energies of adsorption and OH frequencies are in good agreement with published experimental data and support the full hydroxylation model, where the Cr achieves a 6-fold coordination, at saturation.

  16. Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

    Indian Academy of Sciences (India)

    Tapas K Nandi; Hridoy R Bairagya; Bishnu P Mukhopadhyay; K Sekar; Dipankar Sukul; Asim K Bera

    2009-03-01

    The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W1 and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the Ob atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study, it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.

  17. Theoretical vibrational sum-frequency generation spectroscopy of water near lipid and surfactant monolayer interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Roy, S.; Gruenbaum, S. M.; Skinner, J. L. [Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)

    2014-11-14

    Understanding the structure of water near cell membranes is crucial for characterizing water-mediated events such as molecular transport. To obtain structural information of water near a membrane, it is useful to have a surface-selective technique that can probe only interfacial water molecules. One such technique is vibrational sum-frequency generation (VSFG) spectroscopy. As model systems for studying membrane headgroup/water interactions, in this paper we consider lipid and surfactant monolayers on water. We adopt a theoretical approach combining molecular dynamics simulations and phase-sensitive VSFG to investigate water structure near these interfaces. Our simulated spectra are in qualitative agreement with experiments and reveal orientational ordering of interfacial water molecules near cationic, anionic, and zwitterionic interfaces. OH bonds of water molecules point toward an anionic interface leading to a positive VSFG peak, whereas the water hydrogen atoms point away from a cationic interface leading to a negative VSFG peak. Coexistence of these two interfacial water species is observed near interfaces between water and mixtures of cationic and anionic lipids, as indicated by the presence of both negative and positive peaks in their VSFG spectra. In the case of a zwitterionic interface, OH orientation is toward the interface on the average, resulting in a positive VSFG peak.

  18. How trifluoroacetone interacts with water.

    Science.gov (United States)

    Favero, Laura B; Evangelisti, Luca; Maris, Assimo; Vega-Toribio, Alicia; Lesarri, Alberto; Caminati, Walther

    2011-09-01

    The rotational spectra of five isotopologues of the molecular adduct 1,1,1-trifluoroacetone-water have been assigned using pulsed-jet Fourier-transform microwave spectroscopy. All rotational transitions appear as doublets, due to the internal rotation of the methyl group. Analysis of the tunneling splittings allows one to determine accurately the height of the 3-fold barrier to internal rotation of the methyl group and its orientation, leading to V(3) = 3.29 kJ·mol(-1) and ∠(a,i) = 67.5°, respectively. The water molecule is linked to the keton molecule on the side of the methyl group through a O-H···O hydrogen bond and a C-H···O intermolecular contact, lying in the effective plane of symmetry of the complex.

  19. Adsorbed water on iron surface by molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, F.W.; Campos, T.M.B.; Cividanes, L.S., E-mail: flaviano@ita.br; Simonetti, E.A.N.; Thim, G.P.

    2016-01-30

    Graphical abstract: - Highlights: • We developed a new force field to describe the Fe–H{sub 2}O interaction. • We developed a new force field to describe the flexible water model at low temperature. • We analyze the orientation of water along the iron surface. • We calculate the vibrational spectra of water near the iron surface. • We found a complex relationship between water orientation and the atomic vibrational spectra at different sites of adsorption along the iron surface. - Abstract: The adsorption of H{sub 2}O molecules on metal surfaces is important to understand the early process of water corrosion. This process can be described by computational simulation using molecular dynamics and Monte Carlo. However, this simulation demands an efficient description of the surface interactions between the water molecule and the metallic surface. In this study, an effective force field to describe the iron-water surface interactions was developed and it was used in a molecular dynamics simulation. The results showed a very good agreement between the simulated vibrational-DOS spectrum and the experimental vibrational spectrum of the iron–water interface. The water density profile revealed the presence of a water double layer in the metal interface. Furthermore, the horizontal mapping combined with the angular distribution of the molecular plane allowed the analysis of the water structure above the surface, which in turn agrees with the model of the double layer on metal surfaces.

  20. Understanding political market orientation

    DEFF Research Database (Denmark)

    Ormrod, Robert P.; Henneberg, Stephan C.

    This article develops a conceptual framework and measurement model of political market orientation that consists of attitudinal and behavioural constructs. The article reports on perceived relationships among different behavioral aspects of political market orientation and the attitudinal influen......, a more surprising result is the inconclusive effect of a voter orientation on market-oriented behaviours. The article discusses the findings in the context of the existing literature in political marketing and commercial market orientation.......This article develops a conceptual framework and measurement model of political market orientation that consists of attitudinal and behavioural constructs. The article reports on perceived relationships among different behavioral aspects of political market orientation and the attitudinal...... influences of such behavior. The study includes structural equation modeling to investigate several propositions. While the results show that political parties need to focus on several different aspects of market-oriented behavior, especially using an internal and external orientation as cultural antecedents...