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Sample records for d2o solutions structural

  1. Effect of D2O on growth properties and chemical structure of annual ryegrass (Lolium multiflorum)

    SciTech Connect

    Evans, Barbara R; Bali, Garima; Reeves, David T; O'Neill, Hugh Michael; Sun, Qining; Shah, Riddhi S; Ragauskas, Arthur

    2014-01-01

    In present paper, we report the production and detailed structural analysis of deuterium-enriched rye grass (Lolium multiflorum) for neutron scattering experiments. An efficient method to produce deuterated biomass was developed by designing hydroponic perfusion chambers. In preliminary studies, the partial deuterated rye samples were grown in increasing levels of D2O to study the seed germination and the level of deuterium incorporation as a function of D2O concentration. Solution NMR method indicated 36.9 % deuterium incorporation in 50 % D2O grown annual rye samples and further significant increase in the deuterium incorporation level was observed by germinating the rye seedlings in H2O and growing in 50 % D2O inside the perfusion chambers. Moreover, in an effort to compare the substrate characteristics related to enzymatic hydrolysis on deuterated and protiated version of biomass, annual rye grown in 50 % D2O was selected for detailed biomass characterization studies. The compositional analyses, degree of polymerization and cellulose crystallinity were compared with its protiated control. The cellulose molecular weight indicated slight variation with deuteration; however, hemicellulose molecular weights and cellulose crystallinity remain unaffected with the deuteration. Besides the minor differences in biomass components, the development of deuterated biomass for neutron scattering application is essential to understand the complex biomass conversion processes.

  2. High-field NMR T 2 relaxation mechanism in D2O solutions of albumin

    NASA Astrophysics Data System (ADS)

    Yilmaz, A.; Zengin, B.

    2013-07-01

    400 MHz NMR T 2 in D2O solutions of albumin and pure D2O were measured at different temperatures. A relation, based on the chemical exchange between bound HDO and non-exchangeable protein protons, was derived theoretically for the contributions of bound HDO [ P b(1/ T 2b)]. A second relation was also derived theoretically by considering spin-rotation interactions between bound HDO and surrounding protein protons. The P b(1/ T 2b) values in albumin solutions were then determined by replacing experimental data into the first relation. The values of the 1/ T 2 and P b(1/ T 2b) in albumin solutions increase linearly with temperature( T), whereas the 1/ T 2 in D2O decreases with T. In addition, the spin-rotation correlation times were calculated from the second relation. The dipolar correlation time of albumin was then reproduced from the spin-rotation correlation times for confirmative purposes. In conclusion, the 1/ T 2 in albumin solutions with D2O is caused by spin-rotation interactions.

  3. Solution structure of R(2)Sn(IV)-beta-N-acetyl-neuraminate (R = Me, Bu) complexes in D(2)O and DMSO-d(6): experimental NMR and DFT computational study.

    PubMed

    Bertazzi, Nuccio; Casella, Girolamo; Ferrante, Francesco; Pellerito, Lorenzo; Rotondo, Archimede; Rotondo, Enrico

    2007-04-14

    Two diorganotin(IV)-NANA complexes (NANA (1) = beta-N-acetyl-Neuraminic Acid = 5-amino-3,5-dideoxy-D-glycero-beta-D-galactononulosic acid) with formula Me(2)Sn(iv)NANA (2) and Bu(2)Sn(IV)NANA (3) were synthesized and characterized by (1)H, (13)C and (119)Sn NMR spectroscopy, both in D(2)O and DMSO-d(6) solutions. The experimental data in DMSO suggested the monosaccharide bidentate chelation via O1 carboxylate and vicinal O2 alkoxide atoms, which, in D(2)O, can be dynamically extended to a third binding site (O8 atom) of the pendant chain. Coordination at the tin atom is discussed on the basis of experimental NMR data and DFT calculation. PMID:17387406

  4. Influence of isotopic disorder on solid state amorphization and polyamorphism in solid H2O -D2O solutions

    NASA Astrophysics Data System (ADS)

    Gromnitskaya, E. L.; Danilov, I. V.; Lyapin, A. G.; Brazhkin, V. V.

    2015-10-01

    We present a low-temperature and high-pressure ultrasonic study of elastic properties of isotopic H2O-D2O solid solutions, comparing their properties with those of the isotopically pure H2O and D2O ices. Measurements were carried out for solid state amorphization (SSA) from 1h to high-density amorphous (HDA) ice upon compression up to 1.8 GPa at 77 K and for the temperature-induced (77 -190 K ) u-HDA (unrelaxed HDA) → e-HDA (expanded HDA) → low-density amorphous (LDA )→1 c cascade of ice transformations near room pressure. There are many similarities in the elasticity behaviour of H2O ,D2O , and H2O-D2O solid solutions, including the softening of the shear elastic modulus as a precursor of SSA and the HDA →LDA transition. We have found significant isotopic effects during H/D substitution, including elastic softening of H2O -D2O solid solutions with respect to the isotopically pure ices in the case of the bulk moduli of ices 1c and 1h and for both bulk and shear elastic moduli of HDA ice at high pressures (>1 GPa ) . This softening is related to the configurational isotopic disorder in the solid solutions. At low pressures, the isotope concentration dependence of the elastic moduli of u-HDA ice changes remarkably and becomes monotonic with pronounced change of the bulk modulus (≈20 %) .

  5. Isotopomer-selective spectra of a single intact H2O molecule in the Cs(+)(D2O)5H2O isotopologue: Going beyond pattern recognition to harvest the structural information encoded in vibrational spectra.

    PubMed

    Wolke, Conrad T; Fournier, Joseph A; Miliordos, Evangelos; Kathmann, Shawn M; Xantheas, Sotiris S; Johnson, Mark A

    2016-02-21

    We report the vibrational signatures of a single H2O molecule occupying distinct sites of the hydration network in the Cs(+)(H2O)6 cluster. 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. The Cs(+)(H2O)6 structure was unambiguously assigned to the 4.1.1 isomer (a homodromic water tetramer with two additional flanking water molecules) from the fact that its computed IR spectrum matches the observed overall pattern and recovers the embedded correlations in the two OH stretching bands of the water molecule in the Cs(+)(D2O)5(H2O) isotopomers. The 4.1.1 isomer is the lowest in energy among other candidate networks at advanced (e.g., CCSD(T)) levels of theoretical treatment after corrections for (anharmonic) zero-point energy. With the structure in hand, we then explore the mechanical origin of the various band locations using a local electric field formalism. This approach promises to provide a transferrable scheme for the prediction of the OH stretching fundamentals displayed by water networks in close proximity to solute ions. PMID:26896984

  6. Isotopomer-selective spectra of a single intact H2O molecule in the Cs+(D2O)5H2O isotopologue: Going beyond pattern recognition to harvest the structural information encoded in vibrational spectra

    NASA Astrophysics Data System (ADS)

    Wolke, Conrad T.; Fournier, Joseph A.; Miliordos, Evangelos; Kathmann, Shawn M.; Xantheas, Sotiris S.; Johnson, Mark A.

    2016-02-01

    We report the vibrational signatures of a single H2O molecule occupying distinct sites of the hydration network in the Cs+(H2O)6 cluster. 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. The Cs+(H2O)6 structure was unambiguously assigned to the 4.1.1 isomer (a homodromic water tetramer with two additional flanking water molecules) from the fact that its computed IR spectrum matches the observed overall pattern and recovers the embedded correlations in the two OH stretching bands of the water molecule in the Cs+(D2O)5(H2O) isotopomers. The 4.1.1 isomer is the lowest in energy among other candidate networks at advanced (e.g., CCSD(T)) levels of theoretical treatment after corrections for (anharmonic) zero-point energy. With the structure in hand, we then explore the mechanical origin of the various band locations using a local electric field formalism. This approach promises to provide a transferrable scheme for the prediction of the OH stretching fundamentals displayed by water networks in close proximity to solute ions.

  7. Reversible Chromatic Response of Polydiacetylene Derivative Vesicles in D2O Solvent.

    PubMed

    Shin, Min Jae; Kim, Jong-Duk

    2016-01-26

    The thermal chromatic sensitivity of polydiacetylenes (PDAs) with 10,12-pentacosadiynoic acid (PCDA) derivatives, which have a hydroxyl group (HEEPCDA) and an amine group (APPCDA), were investigated using D2O and H2O as solvents. The vesicle solution with polymerized HEEPCDA exhibited a reversible chromatic response during the heating and cooling cycle in D2O, but not in H2O. On the other hand, the vesicle solution with the polymerized APPCDA exhibited a reversible chromatic response in H2O during the heating and cooling cycle, but the color of the solution did not change much in D2O. The critical vesicle concentration of HEEPCDA was lower in D2O than in H2O, and the chromatic sensitivity of the polymerized vesicles to temperature was slower in D2O than in H2O. We think that it is due to D2O being a more highly structured solvent than H2O with the hydrogen bonding in D2O stronger than that in H2O. PMID:26730887

  8. Diffusion Monte Carlo studies of MB-pol (H2O)2-6 and (D2O)2-6 clusters: Structures and binding energies

    NASA Astrophysics Data System (ADS)

    Mallory, Joel D.; Mandelshtam, Vladimir A.

    2016-08-01

    We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H2O)2-6 clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitive to the isotope substitution. Most remarkably, the ground state of the (H2O)6 hexamer is represented by four distinct cage structures, while that of (D2O)6 is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H2O)6 and (D2O)6, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F.

  9. Application of Neutron imaging in pore structure of hydrated wellbore cement: comparison of hydration of H20 with D2O based Portland cements

    NASA Astrophysics Data System (ADS)

    Dussenova, D.; Bilheux, H.; Radonjic, M.

    2012-12-01

    storage of the hydrogen atom. In such case, neutron tomography does not give information of the pore structure as neutrons will strongly scatter of H and the data have low count and low statistics or low neutron transmission. Hence, as the comparison and the possible tuning technique, neutron tomography measurements are performed on a Deuterium Oxide (D2O) or heavy water samples the same dimensions, cement composition, cement/liquid content and hydration time as the H2O samples. The advantage of using heavy water is that the total neutron cross-section for Deuterium is approximately four times smaller than Hydrogen's and, thus, permits better neutron transmission, i.e. better statistics. D2O does not alter cement properties or its chemical composition; therefore, the samples are almost identical. Comparison of the measurements using water and heavy water samples and the preparation of the measurement cement samples are discussed in this

  10. The conformation of the monomethyl ethers of methyl beta-lactoside in D2O and Me2SO-d6 solutions.

    PubMed

    Fernández, P; Jiménez-Barbero, J

    1993-10-01

    The solution conformations of all the possible monomethyl ethers of methyl beta-lactoside have been analysed using molecular mechanics and dynamics calculations and nuclear magnetic resonance data (variable temperature and NOE experiments). The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low-energy region with phi = -100 +/- 40 degrees and psi = -135 +/- 35 degrees, which is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides. PMID:8252531

  11. A comparison of refined X-ray structures of hydrogenated and perdeuterated rat gammaE-crystallin in H2O and D2O.

    PubMed

    Artero, Jean Baptiste; Härtlein, Michael; McSweeney, Sean; Timmins, Peter

    2005-11-01

    Rat gammaE-crystallin was overexpressed, purified under different labelling conditions and crystallized and X-ray data were collected at resolutions between 1.71 and 1.36 A. The structures were determined by molecular replacement. In these structures, the cd loop of the Greek-key motif 3, which is the major structural key motif of the two phase-transition groups of gamma-crystallins, presents a double conformation. The influence of the perdeuteration on the protein structure was determined by comparison of the atomic positions and temperature factors of the different models. The perdeuterated proteins have a similar structure to their hydrogenated counterparts, but partial or full deuteration may have some effect on the atomic B-factor values. PMID:16239733

  12. Freezing D2O clay gels.

    PubMed

    Letellier, M

    1998-01-01

    To obtain the T1 surface value in smectites/D2O diluted suspensions or gels, as was obtained on a monolayer deuterated clay, we freeze them. The broad Pake's doublets similar to ice doublets and with the same T1 show that we can separate frozen from unfrozen D2O. The latter exhibits a narrower line and a single T1 and is attributed to the liquid surface water layer in rapid exchange with the nearby supercooled water, the quantity of which diminishes with the lowering of the temperature depending on the gel porosity. It is possible to measure the supercooled water quantity and to correct the T1 measured values to extract the T1 surface. The value extrapolated at room temperature allows the complete clay surface area measurement. The example of a montmorillonite is given and a comparison with laponite is made. PMID:9803898

  13. Bacterial Ice Nucleation in Monodisperse D2O and H2O-in-Oil Emulsions.

    PubMed

    Weng, Lindong; Tessier, Shannon N; Smith, Kyle; Edd, Jon F; Stott, Shannon L; Toner, Mehmet

    2016-09-13

    Ice nucleation is of fundamental significance in many areas, including atmospheric science, food technology, and cryobiology. In this study, we investigated the ice-nucleation characteristics of picoliter-sized drops consisting of different D2O and H2O mixtures with and without the ice-nucleating bacteria Pseudomonas syringae. We also studied the effects of commonly used cryoprotectants such as ethylene glycol, propylene glycol, and trehalose on the nucleation characteristics of D2O and H2O mixtures. The results show that the median freezing temperature of the suspension containing 1 mg/mL of a lyophilized preparation of P. syringae is as high as -4.6 °C for 100% D2O, compared to -8.9 °C for 100% H2O. As the D2O concentration increases every 25% (v/v), the profile of the ice-nucleation kinetics of D2O + H2O mixtures containing 1 mg/mL Snomax shifts by about 1 °C, suggesting an ideal mixing behavior of D2O and H2O. Furthermore, all of the cryoprotectants investigated in this study are found to depress the freezing phenomenon. Both the homogeneous and heterogeneous freezing temperatures of these aqueous solutions depend on the water activity and are independent of the nature of the solute. These findings enrich our fundamental knowledge of D2O-related ice nucleation and suggest that the combination of D2O and ice-nucleating agents could be a potential self-ice-nucleating formulation. The implications of self-nucleation include a higher, precisely controlled ice seeding temperature for slow freezing that would significantly improve the viability of many ice-assisted cryopreservation protocols. PMID:27495973

  14. Temperature dependence of vibrational frequency fluctuation of N3- in D2O

    NASA Astrophysics Data System (ADS)

    Tayama, Jumpei; Ishihara, Akane; Banno, Motohiro; Ohta, Kaoru; Saito, Shinji; Tominaga, Keisuke

    2010-07-01

    We have studied the temperature dependence of the vibrational frequency fluctuation of the antisymmetric stretching mode of N3- in D2O by three-pulse infrared (IR) photon echo experiments. IR pump-probe measurements were also carried out to investigate the population relaxation and the orientational relaxation of the same band. It was found that the time-correlation function (TCF) of the frequency fluctuation of this mode is well described by a biexponential function with a quasistatic term. The faster decay component has a time constant of about 0.1 ps, and the slower component varies from 1.4 to 1.1 ps in the temperature range from 283 to 353 K. This result indicates that liquid dynamics related to the frequency fluctuation are not highly sensitive to temperature. We discuss the relationship between the temperature dependence of the vibrational frequency fluctuation and that of the molecular motion of the system to investigate the molecular origin of the frequency fluctuation of the solute. We compare the temperature dependence of the frequency fluctuation with that of other dynamics such as dielectric relaxation of water. In contrast to the Debye dielectric relaxation time of D2O, the two time constants of the TCF of the frequency fluctuation do not exhibit strong temperature dependence. We propose a simple theoretical model for the frequency fluctuation in solutions based on perturbation theory and the dipole-dipole interaction between the vibrational mode of the solute and the solvent molecules. This model suggests that the neighboring solvent molecules in the vicinity of the solute play an important role in the frequency fluctuation. We suggest that the picosecond component of the frequency fluctuation results from structural fluctuation of the hydrogen-bonding network in water.

  15. On the neutron scattering length density of proteins in H2O/D2O

    NASA Astrophysics Data System (ADS)

    Efimova, Y. M.; van Well, A. A.; Hanefeld, U.; Wierczinski, B.; Bouwman, W. G.

    2004-07-01

    The structure of the protein layers adsorbed at different interfaces can be determined by using neutron-reflection and small-angle neutron scattering. For highlighting the adsorbed protein layer at the interface, the technique of contrast-variation by changing the H2O/D2O ratio, is often used. For determining the scattering length density, both the protein volume in solution and the total scattering length of the protein is needed. The volume is calculated from the amino-acid sequence. For calculating the scattering length, the H/D exchange of the labile protons of the protein should be taken into account. For monitoring the H/D exchange, Positive Electrospray Ionization Mass Spectroscopy was applied. We compare experimental results for the exchange in lysozyme and β-casein with theoretical calculations. The importance of using the correct protein scattering-length density is elucidated by simultaneous model fitting to neutron reflection data at different water contrasts.

  16. Structure and emissive properties of heterobimetallic Ln-Au coordination polymers: role of Tb and Eu in non-aurophilic [nBu4N]2[Ln(NO3)4Au(CN)2] versus aurophilic Ln[Au(CN)2]3·3H2O/3D2O chains.

    PubMed

    Ahern, John C; Roberts, Ryan J; Follansbee, Philip; McLaughlin, Jeffrey; Leznoff, Daniel B; Patterson, Howard H

    2014-07-21

    This investigation is focused on comparing photophysical properties between two series of lanthanide-dicyanoaurate coordination polymers that contain and lack aurophilic interactions, respectively. Luminescence and crystallographic studies have been carried out on five different coordination polymer chain frameworks: the non-aurophilic [(n)Bu4N]2[LnxGd1-x(NO3)4Au(CN)2] (Ln = Eu, Tb; x = 0.01, 0.02, 0.04, 0.08) and[(n)Bu4N]2[EuxTb1-x(NO3)4Au(CN)2] (x = 0.25, 0.5, 0.75), as well as the analogous solid-solutions of aurophilic LnxGd1-x[Au(CN)2]3·3H2O and EuxTb1-x[Au(CN)2]3·3H2O. The single-crystal structures of M[Au(CN)2]3 ·3H2O (M = Eu, Gd) are also reported for comparison. In the aurophilic frameworks the close proximity of gold(I) centers on neighboring chains allows for Au-Au interactions to take place that facilitate energy transfer between lanthanides. Terbium- and europium-doped aurophilic frameworks show energy transfer between one of the lanthanide ions and dicyanoaurate centers as observed via luminescence measurements. In the non-aurophilic frameworks the [(n)Bu4N] cations separate the Au-Au chains, thereby preventing interaction between them, and preventing energy transfer. By preparing the aurophilic EuxTb1-x[Au(CN)2]3·3D2O frameworks, it was shown that the O-H vibrational energy in the hydrated (aurophilic) samples can partially quench the Ln signal. PMID:24968022

  17. The Elevation of Boiling Points in H_2O and D_2O Electrolytes

    NASA Astrophysics Data System (ADS)

    Miles, M. H.; Arman, H. D.; Carrick, J. D.; Gren, C. K.; Haggerty, K. A.; Kim, H. Y.; Ky, A. G.; Markham, J. E.; Meeks, C. F.; Noga, D. E.

    2002-03-01

    The excess enthalpy effect in cold fusion experiments for Pd/D_2O systems is subject to positive feedback, i.e., increasing the cell temperature increases the excess enthalpy . Therefore, the largest excess enthalpy effects are often observed near or at the boiling point corresponding to that of the electrolyte solution in the cell(M.H. Miles, M. Fleischmann and M.A. Imam, "Calorimetric Analysis of a Heavy Water Electrolysis Experiment Using a Pd-B Alloy Cathode", Naval Research Lab Mem. Rep.,#6320-01-8526, pp. 27-30 (2001).). However, the actual boiling point increases as the D_2O content of the cell decreases. The purpose of this project will be to compare experimental values of the change in temperature ΔT obtained using H_2O and D_2O solutions with theoretical values of ΔT calculated by assuming ideal solutions. The emphasis will be on higher concentrations as well as on saturated solutions where ΔT values may be quite large. Preliminary results for LiOH in H_2O show reasonable agreement with ideal solution ΔT values up to LiOH concentrations of 1.0 molal (m).

  18. Freezing of heavy water (D2O) nanodroplets.

    PubMed

    Bhabhe, Ashutosh; Pathak, Harshad; Wyslouzil, Barbara E

    2013-07-01

    We follow the freezing of heavy water (D2O) nanodroplets formed in a supersonic nozzle apparatus using position resolved pressure trace measurements, Fourier transform infrared spectroscopy, and small-angle X-ray scattering. For these 3-9 nm radii droplets, freezing starts between 223 and 225 K, at volume based ice nucleation rates Jice,V on the order of 10(23) cm(-3) s(-1) or surface based ice nucleation rates Jice,S on the order of 10(16) cm(-2) s(-1). The temperatures corresponding to the onset of D2O ice nucleation are higher than those reported for H2O by Manka et al. [Manka, A.; Pathak, H.; Tanimura, S.; Wölk, J.; Strey, R.; Wyslouzil, B. E. Phys. Chem. Chem. Phys.2012, 14, 4505]. Although the values of Jice,S scale somewhat better with droplet size than values of Jice,V, the data are not accurate enough to state that nucleation is surface initiated. Finally, using current estimates of the thermophysical properties of D2O and the theoretical framework presented by Murray et al. [Murray, B. J.; Broadley, S. L.; Wilson, T. W.; Bull, S. J.; Wills, R. H.; Christenson, H. K.; Murray, E. J. Phys. Chem. Chem. Phys.2010, 12, 10380], we find that the theoretical ice nucleation rates are within 3 orders of magnitude of the measured rates over an ∼15 K temperature range. PMID:23763363

  19. Some Nuclear Calculations of U-235-D2O Gaseous-Core Cavity Reactors

    NASA Technical Reports Server (NTRS)

    Ragsdale, Robert G.; Hyland, Robert E.

    1961-01-01

    The results of a multigroup, diffusion theory study of spherical gaseous-core cavity reactors are presented in this report. The reactor cavity of gaseous U235 is enclosed by a region of hydrogen gas and is separated from an external D2O moderator-reflector by a zirconium structural shell. Some cylindrical reactors are also investigated. A parametric study of spherical reactors indicates that, for the range of variables studied, critical mass increases as: (1) Fuel region is compressed within the reactor cavity, (2) moderator thickness is decreased, (3) structural shell thickness is increased, and (4) moderator temperature is increased. A buckling analogy is used to estimate the critical mass of fully reflected cylindrical reactors from spherical results without fuel compression. For a reactor cavity of a 120-centimeter radius uniformly filled with fuel, no structural shell, a moderator temperature of 70 F, and a moderator thickness of 100 centimeters, the critical mass of a spherical reactor is 3.1 kilograms while that of a cylinder with a length-to-diameter ratio of 1.0 (L/D = 1) is approximately 3.8 kilograms and, with L/D = 2, 5.9 kilograms. For the range of variables considered for U235-D2O gaseous-core cavity reactors, the systems are characterized by 95 to 99 percent thermal absorptions, with the flux reaching a maximum in the moderator about 10 to 15 centimeters from the reactor cavity.

  20. A New Ir-NHC Catalyst for Signal Amplification by Reversible Exchange in D2 O.

    PubMed

    Spannring, Peter; Reile, Indrek; Emondts, Meike; Schleker, Philipp P M; Hermkens, Niels K J; van der Zwaluw, Nick G J; van Weerdenburg, Bram J A; Tinnemans, Paul; Tessari, Marco; Blümich, Bernhard; Rutjes, Floris P J T; Feiters, Martin C

    2016-06-27

    NMR signal amplification by reversible exchange (SABRE) has been observed for pyridine, methyl nicotinate, N-methylnicotinamide, and nicotinamide in D2 O with the new catalyst [Ir(Cl)(IDEG)(COD)] (IDEG=1,3-bis(3,4,5-tris(diethyleneglycol)benzyl)imidazole-2-ylidene). During the activation and hyperpolarization steps, exclusively D2 O was used, resulting in the first fully biocompatible SABRE system. Hyperpolarized (1) H substrate signals were observed at 42.5 MHz upon pressurizing the solution with parahydrogen at close to the Earth's magnetic field, at concentrations yielding barely detectable thermal signals. Moreover, 42-, 26-, 22-, and 9-fold enhancements were observed for nicotinamide, pyridine, methyl nicotinate, and N-methylnicotinamide, respectively, in conventional 300 MHz studies. This research opens up new opportunities in a field in which SABRE has hitherto primarily been conducted in CD3 OD. This system uses simple hardware, leaves the substrate unaltered, and shows that SABRE is potentially suitable for clinical purposes. PMID:27258850

  1. Multi-lamellar vesicle formation in a long-chain nonionic surfactant: C16E4/D2O system.

    PubMed

    Gentile, Luigi; Mortensen, Kell; Rossi, Cesare Oliviero; Olsson, Ulf; Ranieri, Giuseppe A

    2011-10-01

    The temperature dependent rheological and structural behavior of a long-chain C(16)E(4) (tetraethylene glycol monohexadecyl ether) surfactant in D(2)O has been studied within the regime of low shear range. In the absence of shear flow, the system forms a lamellar liquid crystalline phase at relatively high temperatures. The present paper reports on the shear-induced multi-lamellar vesicle (MLV) formation in C(16)E(4)/D(2)O at 40 wt.% of surfactant in the temperature range of 40-55 °C. The transition from planar lamellar structure to multi-lamellar vesicles has been investigated by time-resolved experiments combining rheology and nuclear magnetic resonance (rheo-NMR), rheo small-angle neutron scattering (rheo-SANS) and rheometry. The typical transient viscosity behavior of MLV formation has been discovered at low shear rate value of 0.5s(-1). PMID:21767850

  2. Study of Optimal Cavity Parameter in Optically Pumped D2O Gas Terahertz Laser

    NASA Astrophysics Data System (ADS)

    He, Zhihong; Zhang, Yuping; Zhang, Huiyun; Zhang, Qingmao; Liao, Jianhong; Zhou, Yongheng; Liu, Songhao; Luo, Xizhang

    2010-05-01

    Heavy water gas (D2O gas) which owns special structure property, can generate terahertz radiation by optically pumping technology, and its 385 μm wavelength radiation can be widely used. In this research, on the base of semi-classical density matrix theory, we set up a three-level energy system as its theoretical model, a TEA-CO2 laser 9R (22) output line (λ = 9.26 μm) acted as pumping source, D2O gas molecules were operating medium, the expressions of pumping absorption coefficient G p and Terahertz signal gain coefficient G s were deduced. It was shown that the gain of Terahertz signal was related with the energy-level parameters of operating molecules and some operating parameters of the Terahertz laser cavity, mainly including cavity length. By means of iteration method, the output power density of Terahertz pulse signal was calculated numerically. Changing the parameter of cavity length and keeping others steady, the relationship curve between the output power intensity (Is) of Terahertz pulse laser and the operating cavity length (L) was obtained. The curve showed that the power intensity (Is) increased with cavity length (L) in a certain range, but decreased when the length (L) exceeded some value because of the absorption effect, and there was an optimal cavity length for the highest output power. We used a grating tuned TEA-CO2 laser as pumping power and a sample tube of variable length in 70-160 cm as terahertz laser operating cavity to experiment. The results of theoretical calculation and experiment matched with each other, and it is helpful for miniaturizing terahertz laser volume to make it practical.

  3. Experimental Studies on the Formation of D2O and D2O2 by Implantation of Energetic D+ Ions into Oxygen Ices

    NASA Astrophysics Data System (ADS)

    Bennett, Chris J.; Ennis, Courtney P.; Kaiser, Ralf I.

    2014-02-01

    The formation of water (H2O) in the interstellar medium is intrinsically linked to grain-surface chemistry; thought to involve reactions between atomic (or molecular) hydrogen with atomic oxygen (O), molecular oxygen (O2), and ozone (O3). Laboratory precedent suggests that H2O is produced efficiently when O2 ices are exposed to H atoms (~100 K). This leads to the sequential generation of the hydroxyperoxyl radical (HO2), then hydrogen peroxide (H2O2), and finally H2O and a hydroxyl radical (OH); despite a barrier of ~2300 K for the last step. Recent detection of the four involved species toward ρ Oph A supports this general scenario; however, the precise formation mechanism remains undetermined. Here, solid O2 ice held at 12 K is exposed to a monoenergetic beam of 5 keV D+ ions. Products formed during the irradiation period are monitored through FTIR spectroscopy. O3 is observed through seven archetypal absorptions. Three additional bands found at 2583, 2707, and 1195 cm -1 correspond to matrix isolated DO2 (ν1) and D2O2 (ν1, ν5), and D2O (ν2), respectively. During subsequent warming, the O2 ice sublimates, revealing a broad band at 2472 cm-1 characteristic of amorphous D2O (ν1, ν3). Sublimating D2, D2O, D2O2, and O3 products were confirmed through their subsequent detection via quadrupole mass spectrometry. Reaction schemes based on both thermally accessible and suprathermally induced chemistries were developed to fit the observed temporal profiles are used to elucidate possible reaction pathways for the formation of D2-water. Several alternative schemes to the hydrogenation pathway (O2→HO2→H2O2→H2O) were identified; their astrophysical implications are briefly discussed.

  4. Deuterium oxide (D2O) enhances the photosensitivity of Stentor coeruleus.

    PubMed Central

    Iwatsuki, K; Song, P S

    1985-01-01

    Stentor coeruleus exhibits negative phototaxis and step-up photophobic response (avoiding reaction) to visible light (maximum at 610-620 nm in both responses). In the presence of deuterium oxide (D2O) the step-up photophobic response was markedly enhanced, whereas the phototactic orientation response was inhibited. The induction time for the step-up photophobic response was longer in D2O than in H2O, and the duration of ciliary reversal for the response was also longer in D2O than in H2O, indicating that certain steps of the sensory transduction chain are subject to solvent deuterium isotope effects. The enhancement of the step-up photophobic response in D2O was canceled by LaCl3, while the inhibition of the phototactic orientation response in D2O was partially removed by LaCl3, even though LaCl3 did not affect the phototactic orientation response. These results suggest that the sensory transduction mechanisms for the two photoresponses are different, although the photoreceptors (stentorin) are the same. PMID:3004613

  5. Deuterium oxide (D2O) enhances the photosensitivity of Stentor coeruleus

    SciTech Connect

    Iwatsuki, K.; Song, P.S.

    1985-12-01

    Stentor coeruleus exhibits negative phototaxis and step-up photophobic response (avoiding reaction) to visible light (maximum at 610-620 nm in both responses). In the presence of deuterium oxide (D2O) the step-up photophobic response was markedly enhanced, whereas the phototactic orientation response was inhibited. The induction time for the step-up photophobic response was longer in D2O than in H2O, and the duration of ciliary reversal for the response was also longer in D2O than in H2O, indicating that certain steps of the sensory transduction chain are subject to solvent deuterium isotope effects. The enhancement of the step-up photophobic response in D2O was canceled by LaCl3, while the inhibition of the phototactic orientation response in D2O was partially removed by LaCl3, even though LaCl3 did not affect the phototactic orientation response. These results suggest that the sensory transduction mechanisms for the two photoresponses are different, although the photoreceptors (stentorin) are the same.

  6. Deuterium oxide (D2O) enhances the photosensitivity of Stentor coeruleus.

    PubMed

    Iwatsuki, K; Song, P S

    1985-12-01

    Stentor coeruleus exhibits negative phototaxis and step-up photophobic response (avoiding reaction) to visible light (maximum at 610-620 nm in both responses). In the presence of deuterium oxide (D2O) the step-up photophobic response was markedly enhanced, whereas the phototactic orientation response was inhibited. The induction time for the step-up photophobic response was longer in D2O than in H2O, and the duration of ciliary reversal for the response was also longer in D2O than in H2O, indicating that certain steps of the sensory transduction chain are subject to solvent deuterium isotope effects. The enhancement of the step-up photophobic response in D2O was canceled by LaCl3, while the inhibition of the phototactic orientation response in D2O was partially removed by LaCl3, even though LaCl3 did not affect the phototactic orientation response. These results suggest that the sensory transduction mechanisms for the two photoresponses are different, although the photoreceptors (stentorin) are the same. PMID:3004613

  7. UV photoreaction cross sections of CO and D2O on NiAl(110)

    NASA Astrophysics Data System (ADS)

    Nagai, Kenta; Watanabe, Kazuo

    2016-01-01

    Adsorption states and photoreactions of CO and D2O adsorbed on NiAl(110) at 90 K were studied by temperature-programmed desorption (TPD). Coverage dependence of TPD spectra showed growth behavior of adlayers of these molecules consistent with the literature, but a new path of thermal dissociation of D2O upon adsorption at 90 K was found. The photoreaction cross sections of CO and D2O at 4.7 eV were estimated in the order of 10- 21 cm2 and 10- 20 cm2, respectively. This result suggests that photoexcitation of the NiAl(110) substrate itself, a typical substrate used in supported model catalyst studies, will induce only negligible photoreactions of molecules adsorbed at surfaces of metal nanoparticles supported on ultrathin alumina films formed on NiAl(110).

  8. Neutral current and day night measurements from the pure D 2O phase of SNO

    NASA Astrophysics Data System (ADS)

    Hallin, A. L.; Beier, E. W.; Biller, S. D.; Boulay, M. G.; Bowler, M. G.; Bowles, T. J.; Brice, S. J.; Bullard, T. V.; Cameron, J.; Chan, Y. D.; Chen, X.; Chen, M.; Cleveland, B. T.; Cox, G. A.; Dai, X.; Dalnoki-Veress, F.; Doe, P. J.; Doucas, G.; Dragowsky, M. R.; Duba, C. A.; Duncan, F. A.; Dunford, M.; Dunmore, J. A.; Earle, E. D.; Elliott, S. R.; Evans, H. C.; Ewan, G. T.; Farine, J.; Fergani, H.; Formaggio, J. A.; Fowler, M. M.; Frame, K.; Frati, W.; Gagnon, N.; Graham, K.; Grant, D. R.; Hahn, R. L.; Hallman, E. D.; Hamer, A. S.; Handler, W. B.; Hargrove, C. K.; Harvey, P. J.; Hazama, R.; Heeger, K. M.; Heintzelman, W. J.; Heise, J.; Helmer, R. L.; Hime, A.; Howe, M.; Jagam, P.; Jelley, N. A.; Kazkaz, K.; Keener, P. T.; Klein, J. R.; Kutter, T.; Kyba, C. C. M.; Law, J.; Lawson, I. T.; Lesko, K. T.; Leslie, J. R.; Levine, I.; Luoma, S.; Majerus, S.; Mak, H. B.; Maneira, J.; Manor, J.; Marino, A. D.; McCauley, N.; McDonald, A. B.; McGregor, G.; Miller, G. G.; Nally, C. W.; Noble, A. J.; Norman, E. B.; Okada, C. E.; Orrell, J. L.; Oser, S. M.; Poon, A. W. P.; Robertson, B. C.; Robertson, R. G. H.; Rosendahl, S. S. E.; Rusu, V. L.; Schaffer, K. K.; Schwendener, M. H.; Simpson, J. J.; Sims, C. J.; Sinclair, D.; Skensved, P.; Smith, M. W. E.; Spreitzer, T.; Starinsky, N.; Stokstad, R. G.; Stonehill, L. C.; Tafirout, R.; Tagg, N.; Van Berg, R.; Van de Water, R. G.; Virtue, C. J.; Waltham, C. E.; Wark, D. L.; West, N.; Wilhelmy, J. B.; Wilkerson, J. F.; Wilson, J. R.; Wittich, P.; Wouters, J. M.; Yeh, M.

    2003-04-01

    The Sudbury Neutrino Observatory is a 1000 T D 2O Cerenkov detector that is sensitive to 8B solar neutrinos. The energy, radius, and direction with respect to the sun is measured for each neutrino event; these distributions are used to separately determine the rates of the charged current, neutral current and electron scattering reactions of neutrinos on deuterium. Assuming an undistorted 8B spectrum, the νe component of the 8B solar flux is φe = 1.76 +0.05-0.05(stat.) +0.09-0.09 (syst.) × 10 6 cm -2s -1 based on events with a measured kinetic enegy above 5 MeV. The non- νe component is φμτ = 3.41 +0.45-0.45(stat.) +0.48-0.45 (syst.) × 10 6 cm -2s -1, 5.3 σ greater than zero, providing strong evidence for solar νe flavor transformation. The total flux measured with the NC reaction is φNC = 5.09 +0.044-0.43(stat.) +0.46-0.43 (syst.) × 10 6 cm -2s -1, consistent with solar models. The night minus day rate is 14.0% ± 6.3% +1.5-1.4% of the average rate. If the total flux of active neutrinos is additionally constrained to have no asymmetry, the νe asymmetry is found to be 7.0% ± 4.9% +1.3-1.2%. A global solar neutrino analysis is terms of matter-enhanced oscillations of two active flavors strongly favors the Large Mixing Angle (LMA) solution.

  9. Reactivity of Fe-0 atoms and clusters with D2O over FeO(111)

    SciTech Connect

    Parkinson, Gareth S.; Kim, Yu K.; Dohnalek, Zdenek; Smith, R. Scott; Kay, Bruce D.

    2009-03-26

    The interaction of Fe0 atoms with D2O layers on FeO(111) has been investigated using the “atom dropping” preparation technique and a combination of temperature programmed desorption, x-ray photoelectron spectroscopy, Auger electron spectroscopy, and infrared absorption spectroscopy. The data demonstrate that isolated Fe atoms form DFeOD insertion species upon deposition at 35 K, which then dissociate into FeOD and a surface hydroxyl above 200 K. Interestingly, even at very low Fe0 coverages the D2O is perturbed by the presence of the Fe, but only D2O desorption is observed. At higher (≥ 0.5 ML) coverages, clusters of Fe form which have molecular D2O and OD species adsorbed on the surface. Both molecular and recombinative desorption are observed in TPD. In contrast to the low coverage data, a second reaction pathway emerges at high coverage which leads to desorption of D2 and the formation of stable substoichiometric oxide. The mechanism for this minor channel is concluded to involve a reaction between two (or more) DFeOD complexes.

  10. CO and D2O chemistry on continuous and discontinuous samaria thin films on Pt(111)

    NASA Astrophysics Data System (ADS)

    Jhang, Jin-Hao; Keil, Simona; Schaefer, Andreas; Zielasek, Volkmar; Bäumer, Marcus

    2016-08-01

    The chemistry of CO and D2O, individually adsorbed or co-adsorbed, on epitaxial thin films of samaria on Pt(111) was studied by temperature-programmed desorption spectroscopy (TPD). Continuous thin films as well as discontinuous films composed of samaria islands on bare Pt(111) were prepared. Their comparative study indicates that Sm2O3 islands provide lattice oxygen at their perimeter for CO oxidation on adjacent exposed Pt area where CO adsorption takes place. CO2 production was observed only on as-prepared discontinuous films. While, in particular on thermally reduced samaria islands, TPD after D2O adsorption revealed D2 production which indicates a pathway for D2O dissociation, no evidence for the water gas shift reaction of CO and residual OD species on the surface was found after co-adsorption of CO and D2O. Instead, interaction between CO and OD species at the perimeter of islands on reduced discontinuous SmOx thin films obviously promotes D2 formation without yielding CO2 as desorbing product.

  11. Microdynamics mechanism of D2O absorption of the poly(2-hydroxyethyl methacrylate)-based contact lens hydrogel studied by two-dimensional correlation ATR-FTIR spectroscopy.

    PubMed

    Su, Gehong; Zhou, Tao; Zhang, Yanyan; Liu, Xifei; Zhang, Aiming

    2016-01-28

    A good understanding of the microdynamics of the water absorption of poly(2-hydroxyethyl methacrylate) (PHEMA)-based contact lens is significant for scientific investigation and commercial applications. In this study, time-dependent ATR-FTIR spectroscopy combined with the perturbation correlation moving-window two-dimensional (PCMW2D) technique and 2D correlation analysis was used to study the microdynamics mechanism. PCMW2D revealed that D2O took 3.4 min to penetrate into the contact lens. PCMW2D also found the PHEMA-based contact lens underwent two processes (I and II) during D2O absorption, and the time regions of processes I and II are 3.4-12.4 min and 12.4-57.0 min. According to 2D correlation analysis, it was proved that process I has 5 steps, and process II has 3 steps. For process I, the first step is D2O hydrogen-bonding with "free" C[double bond, length as m-dash]O in the side chains. The second step is the hydrogen bond generation of the O-HO-D structure between D2O and "free" O-H groups in the side chain ends. The third step is the hydrogen bond generation of D2O and the "free" C[double bond, length as m-dash]O groups close to the crosslinking points in the contact lens. The fourth and the fifth steps are the hydration of -CH3 and -CH2- groups by D2O, respectively. For process II, the first step is the same as that of process I. The second step is the hydrogen bonds breaking of bonded O-H groups and the deuterium exchange between D2O and O-H groups in the side chain ends. The third step is also related to the deuterium exchange, which is the hydrogen bonds regeneration between the dissociated C[double bond, length as m-dash]O groups and the new O-D. PMID:26577131

  12. Neutron radiography and modelling of water flow and D2O transport in soil and plants

    NASA Astrophysics Data System (ADS)

    Zare, Mohsen; Carminati, Andrea; Kröner, Eva

    2014-05-01

    Our understanding of soil and plant water relations is currently limited by the lack of experimental methods to measure the water fluxes in soil and plants. Our study aimed to develop a new non-destructive method to measure the local fluxes of water into roots of plants growing in soil. We injected deuterated water (D2O) near the roots of lupines growing in sandy soils, and we used neutron radiography to image the transport of D2O through the root system. The experiments were performed during day, when plants were transpiring, and at night, when transpiration was reduced. The radiographs showed that: 1) the radial transport of D2O from soil and roots depended similarly from diffusion and convection; and 2) the axial transport of D2O along the root xylem was largely dominated by convection. To determine the convective fluxes from the radiographs, we simulated the D2O transport in soils and roots. A dual porosity model was used to describe the apoplastic and symplastic pathways of water across the root tissue. Other features as the endodermis and the xylem were also included in the model. The D2O transport was modelled solving a convection-diffusion numerical model in soil and plants. The diffusion coefficients of the root tissues were inversely estimated by simulating the experiments at night under the assumption that at night the convective fluxes were negligible. Inverse modelling of the experiment at day gave the profile of water fluxes into the roots, as well as the ration between the apoplastic and symplastic flow. For 24 day-old lupine grown in a sandy soil with uniform water content, our modelling results showed that root water uptake was higher at the proximal parts of the roots near soil surface and it decreased toward the distal parts. The results indicated the water crossed the root cortex mainly through the apoplastic pathway. The method allows the quantification of the root properties and the regions of root water uptake along root systems growing in

  13. Appearance of D2O in sweat after oral and oral-intravenous rehydration in men.

    PubMed

    Emmanuel, Holly; Casa, Douglas J; Beasley, Kathleen N; Lee, Elaine C; McDermott, Brendon P; Yamamoto, Linda M; Armstrong, Lawrence E; Maresh, Carl M

    2011-08-01

    Intravenous (IV) rehydration is common in athletics, but its thermoregulatory benefits and ergogenicity have not been elucidated. Availability of orally ingested fluid is dependent on gastric emptying and intestinal absorption rate. Deuterium oxide (D2O) has been used to demonstrate that fluid ingested during exercise appears in sweat within 10 minutes. The purpose of this study was to determine the effect of concurrent IV rehydration on D2O appearance in sweat samples after per ora rehydration with D2O labeled fluid. We hypothesized that the combination method would not be superior to the oral method. Ten fit men (age 23 ± 4, VO2max 59.49 ± 4.09 L·min(-1)) underwent 20 hours of fluid restriction resulting in 1.95 ± 0.25% body weight loss before beginning treadmill exercise and cycling. Exercise was performed in an environmental chamber (35.6 ± 0.2° C, 35.0 ± 1.8% relative humidity) for 2 hours at 55% VO2max, and the participants exhibited a mean body weight deficit of 4.50 ± 0.04%. Thermoregulatory measures were recorded while subjects were rehydrated with oral (OR) or oral combined with intravenous (IVO) fluid traced with D2O. After 30 minutes of rehydration and 30 minutes of seated recovery, the subjects began treadmill exercise at 55-60% VO2max. Forehead sweat samples were collected 0, 5, 10, 20, and 75 minutes from the start of rehydration. The samples were analyzed for D2O via isotope ratio mass spectrometry. D2O did not appear in the sweat within 20 minutes of rehydration; however, it did appear during the subsequent exercise bout. There was no significant difference between rehydration modes. Plasma volume increases and decreased volume of orally ingested fluid did not significantly alter transit time from ingestion to appearance in excreted sweat. The IVO method does not appear to be superior to the traditional OR method of rehydration. PMID:21747289

  14. Intracavity laser absorption spectroscopy of D 2O between 11 400 and 11 900 cm -1

    NASA Astrophysics Data System (ADS)

    Naumenko, O. V.; Mazzotti, F.; Leshchishina, O. M.; Tennyson, J.; Campargue, A.

    2007-03-01

    The weak absorption spectrum of dideuterated water, D 2O, has been recorded by Intracavity Laser Absorption Spectroscopy (ICLAS) between 11 400 and 11 900 cm -1. This spectrum is dominated by the 3 ν1 + ν2 + ν3 and the ν1 + ν2 + 3 ν3 centered at 11 500.25 and 11 816.64 cm -1, respectively. A total of 530 energy levels belonging to eight vibrational states were determined. The rovibrational assignment process of the 840 lines attributed to D 2O was mostly based on the results of new variational calculations consisting in a refinement of the potential energy surface of Shirin et al. [J. Chem. Phys., 120 (2004) 206] on the basis of recent experimental observations, and a dipole moment surface from Schwenke and Partridge [J. Chem. Phys. 113 (2000) 6592]. The overall agreement between these calculations and the observed spectrum is very good both for the line positions and the line intensities.

  15. Neutron powder diffraction study of the layer organic-inorganic hybrid iron(II) methylphosphonate-hydrate, Fe[(CD 3PO 3)(D 2O)

    NASA Astrophysics Data System (ADS)

    Léone, Philippe; Bellitto, Carlo; Bauer, Elvira M.; Righini, Guido; André, Gilles; Bourée, Françoise

    2008-11-01

    The crystal and magnetic structures of the hybrid organic-inorganic layer compound Fe[(CD 3PO 3)(D 2O)] have been studied by neutron powder diffraction as a function of temperature down to 1.5 K. The neutron diffraction pattern recorded at 200 K shows that the fully deuterated compound crystallizes in one of the two known forms of the undeuterated Fe[(CH 3PO 3)(H 2O)]. The crystal structure is orthorhombic, space group Pmn2 1, with the following unit-cell parameters: a=5.7095(1) Å, b=8.8053(3) Å and c=4.7987(1) Å; Z=2. The crystal structure remains unchanged on cooling from 200 to 1.5 K. Moreover, at low temperature, Fe[(CD 3PO 3)(D 2O)] shows a commensurate magnetic structure ( k=(0,0,0)). As revealed by bulk susceptibility measurements on Fe[(CH 3PO 3)(H 2O)], the magnetic structure corresponds to a canted antiferromagnet with a critical temperature TN=25 K. Neutron powder diffraction reveals that below TN=23.5 K the iron magnetic moments in Fe[(CD 3PO 3)(D 2O)] are antiferromagnetically coupled and oriented along the b-axis, perpendicular to the inorganic layers. No ferromagnetic component is observable in the neutron powder diffraction experiment, due to its too small value (<0.1 μB).

  16. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

    PubMed Central

    Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C.; Hanson, Buck T.; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M.; Fowler, Patrick W.; Huang, Wei E.; Wagner, Michael

    2015-01-01

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

  17. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.

    PubMed

    Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C; Hanson, Buck T; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M; Fowler, Patrick W; Huang, Wei E; Wagner, Michael

    2015-01-13

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

  18. Cp2TiCl/D2O/Mn, a formidable reagent for the deuteration of organic compounds

    PubMed Central

    Rodríguez-García, Ignacio

    2016-01-01

    Summary Cp2TiCl/D2O/Mn is an efficient combination, sustainable and cheap reagent that mediates the D-atom transfer from D2O to different functional groups and can contribute to the synthesis of new deuterated organic compounds under friendly experimental conditions and with great economic advantages. PMID:27559410

  19. Electron-Stimulated Reactions in Thin D2O Films on Pt(111) Mediated by Electron Trapping

    SciTech Connect

    Petrik, Nikolay G.; Kimmel, Greg A.

    2004-08-22

    We have measured the electron-stimulated desorption (ESD) of D2, O2 and D2O, the electron-stimulated dissociation of D2O at the D2O/Pt interface, and the total electron-stimulated sputtering in thin D2O films adsorbed on Pt(111) as a function of the D2O coverage (i.e. film thickness). Qualitatively different behavior is observed above and below a threshold coverage of ~2 monolayers (ML). For coverages less than ~2 ML electron irradiation results in D2O ESD and some D2 ESD, but no detectible reactions at the water/Pt interface and no O2 ESD. For larger coverages, electron-stimulated reactions at the water/Pt interface occur, O2 is produced and the total electron-stimulated sputtering of the film increases. An important step in the electron-stimulated reactions is the reaction between water ions (generated by the incident electrons) and electrons trapped in the water films to form dissociative neutral molecules. However, the electron trapping depends sensitively on the water coverage: For coverages less than ~ 2 ML, the electron trapping probability is low and the electrons trap preferentially at the water/vacuum interface. For larger coverages, the electron trapping increases and the electrons are trapped in the bulk of the film. We propose that the coverage dependence of the trapped electrons is responsible for the observed coverage dependence of the electron-stimulated reactions.

  20. Infrared-spectrometric determination of D2O in biological fluids. Reappraisal of the method and application to the measurement of total body water and daily water turnover in the dog.

    PubMed

    Zweens, J; Frankena, H; Reicher, A; Zijlstra, W G

    1980-05-01

    The determination of D2) in biological fluids by means of infrared spectrometry was reinvestigated. When the temperature of a solution, containing D2O in the range from natural abundance to 5 ml . 1-1 increases, its absorbance decreases and the wavenumber of maximum absorption shifts to a higher value. Both changes are linearly related to the change in temperature. Storage for 17 d in either glass or polyethylene tubes does not affect the D2O concentration. Purification of biological fluids by vacuum-sublimation removes all substances which also absorb at the O-D vibration band and the recovery of D2O from plasma and urine is complete. The partition ratio of D2O between plasma water and red cell water equals unity, and the same holds for plasma water and urine water over a wide range of urine flows and osmolalities. The arterial and urinary disappearance curves of D2O, measured over several days, both permit the calculation of the total amount of body water (Vbw), the daily water turn-over (F) and the half-time of water in the body (t1 PMID:7191098

  1. Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O.

    PubMed Central

    Griffith, G D; Cole, J R; Quensen, J F; Tiedje, J M

    1992-01-01

    Desulfomonile tiedjei DCB-1 is a strict anaerobe capable of reductively dechlorinating meta-chlorobenzoates. To probe the mechanism of this aryl dechlorination, we incubated cell suspensions of D. tiedjei in D2O and with 2,5-dichlorobenzoate. The deuterium was incorporated into the dechlorination product exclusively at the position of dehalogenation, as shown by gas chromatography-mass spectrometry and proton magnetic resonance analyses. These results favor a model for dechlorination that should not allow proton exchange at other positions, as would be the case if partial ring reduction occurred. PMID:1539988

  2. Ruthenium Catalyzed Selective α- and α,β-Deuteration of Alcohols Using D2O.

    PubMed

    Chatterjee, Basujit; Gunanathan, Chidambaram

    2015-10-01

    Highly selective ruthenium catalyzed α-deuteration of primary alcohols and α,β-deuteration of secondary alcohols are achieved using deuterium oxide (D2O) as a source of deuterium and reaction solvent. Minimal loading of catalyst (Ru-macho), base (KO(t)Bu), and low temperature heating provided efficient selective deuteration of alcohols making the process practically attractive and environmentally benign. Mechanistic studies indicate the D-O(D/R) bond activations by metal-ligand cooperation and intermediacy of carbonyl compounds resulting from dehydrogenation of alcohols. PMID:26381108

  3. Study (301)-(000) D2O band in 10200 - 10450 cm-1 spectral region

    NASA Astrophysics Data System (ADS)

    Sinitsa, L. N.; Serdyukov, V. I.; Shcherbakov, A. P.; Sergeeva, A. S.; Miheenko, M. O.

    2015-11-01

    Measurements of D2O absorption spectra in the visible spectral region near 0.98 μm are performed using FT-spectrometer IFS-125M and Light-emitting diode (LED) as source of radiation. Water vapor spectrum has been obtained by averaging over 17136 scans recorded at 24 m optical path length, temperature 24 C and pressure of sample 27 mBar. Due to strong emission of LED source it was possible to achieve signal-to-noise ratio about 104 and to record weak lines with intensities of 6 10-27 cm/molecule. Comparisons with results of early works are made.

  4. Electrolysis byproduct D2O provides a third way to mitigate CO2

    SciTech Connect

    Schenewerk, William Ernest

    2009-09-01

    Rapid atomic power deployment may be possible without using fast breeder reactors or making undue demands on uranium resource. Using by-product D2O and thorium-U233 in CANDU and RBMK piles may circumvent need for either fast breeder reactors or seawater uranium. Atmospheric CO2 is presently increasing 2.25%/year in proportion to 2.25%/year exponential fossil fuel consumption increase. Roughly 1/3 anthropologic CO2 is removed by various CO2 sinks. CO2 removal is modelled as being proportional to 45-year-earlier CO2 amount above 280 ppm-C Water electrolysis produces roughly 0.1 kg-D20/kWe-y. Material balance assumes each electrolysis stage increases D2O bottoms concentration times 3. Except for first two electrolysis stages, all water from hydrogen consumption is returned to electrolysis. The unique characteristic of this process is the ability to economically burn all deuterium-enriched H2 in vehicles. Condensate from vehicles returns to appropriate electrolysis stage. Fuel cell condensate originally from reformed natural gas may augment second-sage feed. Atomic power expansion is 5%/year, giving 55000 GWe by 2100. World primary energy increases 2.25%/y, exceeding 4000 EJ/y by 2100. CO2 maximum is roughly 600 ppm-C around year 2085. CO2 declines back below 300 ppm-C by 2145 if the 45-year-delay seawater sink remains effective.

  5. High sensitivity ICLAS of D 2O between 12 450 and 12 850 cm -1

    NASA Astrophysics Data System (ADS)

    Campargue, A.; Mazzotti, F.; Béguier, S.; Polyansky, O. L.; Vasilenko, I. A.; Naumenko, O. V.

    2007-10-01

    The weak absorption spectrum of dideuterated water, D 2O, has been recorded between 12 450 and 12 850 cm -1 by high sensitivity Intracavity Laser Absorption Spectroscopy (ICLAS). This spectral region corresponds to the ( ν1 + ν2/2 + ν3) = 5 polyad, dominated by the 4 ν1 + ν3 band centered at 12 743.035 cm -1. The achieved sensitivity has allowed for the detection of lines with a minimum intensity of 2 × 10 -28 cm/molecule i.e. typically two orders of magnitude lower than previous observations in the region considered. A total of 586 energy levels belonging to 11 vibrational states were determined. The rovibrational assignment process of 1025 lines ascribed to D 2O was based on new results of variational calculations by Shirin et al. [S.V. Shirin, N.F. Zobov, O.L. Polyansky, J. Quant. Spectrosc. Radiat. Transfer, in press, doi:10.1016/j.jqsrt.2007.07.010]. The overall agreement between these calculations and the observed spectrum is good both for the line positions and line intensities. The difficulties encountered while performing the rovibrational labeling and the assignment of the weakest transitions not included in Combination Differences relations, are discussed.

  6. The D2O absorption spectra in SiO2 airgel pores: technical features of treatment

    NASA Astrophysics Data System (ADS)

    Lugovskoi, A.; Duchko, A.

    2015-11-01

    The dynamic of the D2O in silica airgel absorption spectra in 4000…6000 cm-1 were recorded using Fourier Transform spectrometer FS-125M at room temperature and pressure of 23.4 mbar with spectral resolution of 0.03 cm-1. It is shown that the D2O dimers to make a significant contribution into absorption when nanopores filled with gas molecules is small. Is present a detailed description of techniques for processing the primary experimental data.

  7. Myochrysine Solution Structure and Reactivity

    PubMed Central

    Jones, William B.; Zhao, Zheng; Dorsey, John G.; Tepperman, Katherine

    1994-01-01

    We have determined the framework structure of Myochrysine (disodium gold(I)thiomalate) in the solid state and extremely concentrated aqueous solution, previously. It consists of an open chain polymer with linear gold coordination to two thiolates from the thiomalic acid moieties which bridge between pairs of gold atoms providing an Au-S-Au angle of 95°. The question remained: was this structure relevant to the dilute solutions of drugs administered and the still lower concentrations of gold found in the bodies of patients (typically 1 ppm Au in blood and urine or 5 μM in Au). We have provided an answer to that question using extended X-ray absorption spectroscopy (EXAFS) and capillary zone electrophoresis (CZE). EXAFS studies confirm that the polymeric structure with two sulfur atoms per gold atom persists from molar concentrations down to millimolar concentrations. CZE is able to separate and detect Myochrysine at millimolar levels. More importantly, at micromolar levels Myochrysine solutions exhibit identical CZE behavior to that measured at millimolar levels. Thus, aqueous solutions of the drug remain oligomeric at concentrations commensurate with those found in patient blood and urine. The reactivity of Myochrysine with cyanide, a species especially prevalent in smoking patients, was explored using CZE. Cyanide freely replaces thiomalic acid to form [Au(CN)2]- and thiomalic acid via a mixed ligand intermediate. The overall apparent equilibrium constant (Kapp) for the reaction is 6×10-4M-1. Further reaction of [Au(CN)2]- with a large excess of L, where L is cysteine, N-acetylcysteine, or glutathione, shows that these amino acids readily replace cyanide to form [AuL2]-. These species are thus potential metabolites and could possibly be active forms of gold in vivo. That all of these species are readily separated and quantified using CZE demonstrates that capillary electrophoresis is an accessible and powerful tool to add to those used for the study of gold

  8. Preliminary Neutronic Study of D2O-cooled High Conversion PWRs

    SciTech Connect

    Hikaru Hiruta; Gilles Youinou

    2013-10-01

    This paper presents a preliminary neutronics analysis of tight-pitch D2O-cooled high-conversion PWRs loaded with MOX fuel aiming at high Pu conversion and negative void coefficient. SCALE6.1 has been exclusively utilized for this study. The analyses are performed in two separate parts. The first part of this paper investigates the performance of axial and internal blankets and seeks break-even or near-breeder core even without the presence of radial blankets. The second part of this paper performs sensitivity and uncertainty analyses of integral parameters (keff and void coefficient) for selected systems in order to analyze the characters of this high-conversion PWR from different aspects.

  9. Rate of reactions between D 2O and Ca xAl yO z

    NASA Astrophysics Data System (ADS)

    Christensen, A. Nørlund; Lehmann, M. S.

    1984-02-01

    The rate of the reaction between D 2O and the calcium aluminum oxides Ca 3Al 2O 6, Ca 5Al 6O 14, CaAl 2O 4, and CaAl 4O 7 was investigated by on-line neutron diffraction powder methods at temperatures from room temperature to 100°C. The rate of the reaction increases with increasing calcium content of the compounds and with increasing temperature for each of the compounds. The crystallographic stable hydrate Ca 3Al 2(OD) 12 is obtained from CaAl 4O 7 and CaAl 2O 4 at temperatures above 63°C, from Ca 5Al 6O 14 at temperatures above 49°C, and from Ca 3Al 2O 6 at temperatures as low as 7°C.

  10. FTIR studies of H 2O and D 2O decomposition on porous silicon surfaces

    NASA Astrophysics Data System (ADS)

    Gupta, P.; Dillon, A. C.; Bracker, A. S.; George, S. M.

    1991-04-01

    The decomposition of H 2O and D 2O on silicon surfaces was studied using transmission Fourier-transform infrared (FTIR) spectroscopy. These FTIR studies were performed in situ in an ultrahigh vacuum chamber using high surface area porous silicon samples. The FTIR spectra revealed that H 2O (D 2O) initially dissociates upon adsorption at 300 K to form SiH (SiD) and SiOH (SiOD) surface species, i.e., H 2O → SiH + SiOH. The decomposition of these surface species was then monitored using the SiH (SiD) stretch at 2090 cm -1 (1513 cm -1), SiOH (SiOD) stretch at 3680 cm -1 (2707 cm -1) and the SiOSi stretch at 900-1100 cm -1. As the silicon surface was annealed to 650 K, the FTIR spectra revealed that the SiOH surface species progressively decomposed to SiOSi species and additional SiH species, i.e., SiOH → SiH + SiOSi. Above 650 K, the SiH surface species decreased concurrently with the desorption of H -1 from the porous silicon surface. New blue-shifted infrared features in the SiH stretching region were observed at 2119, 2176 and 2268 cm -1 after annealing above 600 K. Additional infrared studies of partially hydrogen-covered porous silicon surfaces exposed to O 2 suggested that these blue-shifted SiH stretching vibrations were associated with silicon surface atoms backbonded to one, two or three oxygen atoms, respectively.

  11. Using a Microwave Resonant Cavity to Study Hydrogen Bonding at Phase Transition in H2O and D2O

    NASA Astrophysics Data System (ADS)

    Roberts, Jim; Dahiya, Jai; Ghosh, S.

    2012-10-01

    The resonant microwave cavity is a very sensitive device for detecting small changes in material properties as they are perturbed by temperature, electric and magnetic fields. In this laboratory all states of mater have studied with the resonant cavity, including the plasma state. In this paper we report on an experiment with water as it changes from liquid (disordered) to water ice (ordered) phase. In that hydrogen bonds are involved in this process, we are able to observe their behavior through the dielectric response of H2O as it is cycled from solid to liquid. The transition through the densest state of water near 4^oC indicates that the structure of the water molecules in the ice phase at 0^o C is less compact than that experienced at the most dense temperature of water. If we associate this density with the interaction of the hydrogen bonds, it can be postulated that the distribution of the structure in snowflakes is a consequence of random processes in sharing the hydrogen bonds as the system cycles from the ``disordered'' state to the more ordered state. In this work phase transition from liquid to solid and solid to liquid was studied for H2O and D2O. It was assumed that the bonding of the two molecules behave the same during the transition from ordered to disordered states and in the reverse transition for disordered to ordered states. The apparatus employed in this investigation is discussed briefly.

  12. Modulation of inhibitory and excitatory fast neurotransmission in the rat CNS by heavy water (D2O).

    PubMed

    Wakita, Masahito; Kotani, Naoki; Shoudai, Kiyomitsu; Yamaga, Toshitaka; Akaike, Norio

    2015-08-01

    The effects of heavy water (deuterium oxide, D2O) on GABAergic and glutamatergic spontaneous and evoked synaptic transmission were investigated in acute brain slice and isolated "synaptic bouton" preparations of rat hippocampal CA3 neurons. The substitution of D2O for H2O reduced the frequency and amplitude of GABAergic spontaneous inhibitory postsynaptic currents (sIPSCs) in a concentration-dependent manner but had no effect on glutamatergic spontaneous excitatory postsynaptic currents (sEPSCs). In contrast, for evoked synaptic responses in isolated neurons, the amplitude of both inhibitory and excitatory postsynaptic currents (eIPSCs and eEPSCs) was decreased in a concentration-dependent manner. This was associated with increases of synaptic failure rate (Rf) and paired-pulse ratio (PPR). The effect was larger for eIPSCs compared with eEPSCs. These results clearly indicate that D2O acts differently on inhibitory and excitatory neurotransmitter release machinery. Furthermore, D2O significantly suppressed GABAA receptor-mediated whole cell current (IGABA) but did not affect glutamate receptor-mediated whole cell current (IGlu). The combined effects of D2O at both the pre- and postsynaptic sites may explain the greater inhibition of eIPSCs compared with eEPSCs. Finally, D2O did not enhance or otherwise affect the actions of the general anesthetics nitrous oxide and propofol on spontaneous or evoked GABAergic and glutamatergic neurotransmissions, or on IGABA and IGlu. Our results suggest that previously reported effects of D2O to mimic and/or modulate anesthesia potency result from mechanisms other than modulation of GABAergic and glutamatergic neurotransmission. PMID:26019316

  13. Experimental Structural Studies of Solutes in Aqueous Solution

    SciTech Connect

    Persson, Ingmar

    2007-11-29

    The principles of experimental methods to study the structure and the hydrogen bonding of hydrated solutes in aqueous solution are presented, and whether theoretical simulations can produce comparable information as the experimental ones is discussed. Two structure methods, extended X-ray absorption fine structure (EXAFS) and large angle X-ray scattering (LAXS), and one method to study the hydrogen bonding in hydrated species in aqueous solution, double difference infrared spectroscopy of HDO, are presented.

  14. Using a Microwave Resonant Cavity to Study Hydrogen Bonding at Phase Transition in H2O and D2O

    NASA Astrophysics Data System (ADS)

    Roberts, James; Dahiya, Jai

    2010-10-01

    The resonant microwave cavity is a very sensitive device for detecting small changes in material properties as they are perturbed by temperature, electric and magnetic fields. In this laboratory all states of mater have studied with the resonant cavity, including the plasma state. In this paper we report on an experiment with water as it changes from liquid (disordered) to water ice (ordered) phase. In that hydrogen bonds are involved n this process, we are able to observe behavior in the dielectric response of H2O as it is cycled from solid to liquid. The transition through the densest state of water near 4^oC indicates that the order of the water molecules in the ice phase is less than that experienced at the most dense temperature of water. If we associate this density with the interaction of the hydrogen bonds, it can be postulated that the distribution of the structure in snowflakes is a consequence of random processes in sharing the hydrogen bonds as the system cycles from the disordered state to the more ordered state. Phase transition from liquid to solid and solid to liquid was studied for H2O and D2O. It is expected that the bonding of the two molecules will behave the same during the transition from ordered to disordered states and in the reverse transition. The apparatus used in this investigation will be discussed.

  15. Preliminary Neutronics Design and Analysis of D2O Cooled High Conversion PWRs

    SciTech Connect

    Hikaru Hiruta; Gilles Youinou

    2012-09-01

    This report presents a neutronics analysis of tight-pitch D2O-cooled PWRs loaded with MOX fuel and focuses essentially on the Pu breeding potential of such reactors as well as on an important safety parameter, the void coefficient, which has to be negative. It is well known that fast reactors have a better neutron economy and are better suited than thermal reactors to breed fissile material from neutron capture in fertile material. Such fast reactors (e.g. sodium-cooled reactors) usually rely on technologies that are very different from those of existing water-cooled reactors and are probably more expensive. This report investigates another possibility to obtain a fast neutron reactor while still relying mostly on a PWR technology by: (1) Tightening the lattice pitch to reduce the water-to-fuel volume ratio compared to that of a standard PWR. Water-to-fuel volume ratios of between 0.45 and 1 have been considered in this study while a value of about 2 is typical of standard PWRs, (2) Using D2O instead of H2O as a coolant. Indeed, because of its different neutron physics properties, the use of D2O hardens the neutron spectrum to an extent impossible with H2O when used in a tight-pitch lattice. The neutron spectra thus obtained are not as fast as those in sodium-cooled reactor but they can still be characterized as fast compared to that of standard PWR neutron spectra. In the phase space investigated in this study we did not find any configurations that would have, at the same time, a positive Pu mass balance (more Pu at the end than at the beginning of the irradiation) and a negative void coefficient. At this stage, the use of radial blankets has only been briefly addressed whereas the impact of axial blankets has been well defined. For example, with a D2O-to-fuel volume ratio of 0.45 and a core driver height of about 60 cm, the fissile Pu mass balance between the fresh fuel and the irradiated fuel (50 GWd/t) would be about -7.5% (i.e. there are 7.5% fewer fissile Pu

  16. Photodesorption of H2O, HDO, and D2O ice and its impact on fractionation

    NASA Astrophysics Data System (ADS)

    Arasa, Carina; Koning, Jesper; Kroes, Geert-Jan; Walsh, Catherine; van Dishoeck, Ewine F.

    2015-03-01

    The HDO/H2O ratio measured in interstellar gas is often used to draw conclusions on the formation and evolution of water in star-forming regions and, by comparison with cometary data, on the origin of water on Earth. In cold cores and in the outer regions of protoplanetary disks, an important source of gas-phase water comes from photodesorption of water ice. This research note presents fitting formulae for implementation in astrochemical models using previously computed photodesorption efficiencies for all water ice isotopologues obtained with classical molecular dynamics simulations. The results are used to investigate to what extent the gas-phase HDO/H2O ratio reflects that present in the ice or whether fractionation can occur during the photodesorption process. Probabilities for the top four monolayers are presented for photodesorption of X (X = H, D) atoms, OX radicals, and X2O and HDO molecules following photodissociation of H2O, D2O, and HDO in H2O amorphous ice at ice temperatures from 10-100 K. Significant isotope effects are found for all possible products: (1) H atom photodesorption probabilities from H2O ice are larger than those for D atom photodesorption from D2O ice by a factor of 1.1; the ratio of H and D photodesorbed upon HDO photodissociation is a factor of 2. This process will enrich the ice in deuterium atoms over time; (2) the OD/OH photodesorption ratio upon D2O and H2O photodissociation is on average a factor of 2, but the OD/OH photodesorption ratio upon HDO photodissociation is almost constant at unity for all ice temperatures; (3) D atoms are more effective in kicking out neighbouring water molecules than H atoms. However, the ratio of the photodesorbed HDO and H2O molecules is equal to the HDO/H2O ratio in the ice, therefore, there is no isotope fractionation when HDO and H2O photodesorb from the ice. Nevertheless, the enrichment of the ice in D atoms due to photodesorption can over time lead to an enhanced HDO/H2O ratio in the ice, and

  17. Reactivity of Fe0 Atoms with mixed CCI4 and D2O films over FeO (111)

    SciTech Connect

    Parkinson, Gareth S.; Dohnalek, Zdenek; Smith, R. Scott; Kay, Bruce D.

    2010-10-14

    The interaction of Fe0 with chlorinated hydrocarbons in an aqueous environment is important for the utilization of Fe0 nanoparticles in groundwater remediation technologies. This article builds upon prior work that utilized an "atom dropping" technique to show that Fe0 atoms react readily with pure CCl4 and D2O upon contact at 30 K to form the ClFeCCl3 and DFeOD insertion complexes, respectively. Here we deposit Fe atoms into films containing both D2O and CCl4 as separate layers. Temperature programmed desorption (TPD) is used to show that the ClFeCCl3 and DFeOD insertion complexes are unreactive with each other and both molecular D2O and CCl4 up to the desorption temperature of each species on an FeO(111) substrate. These results suggest that the Fe insertion complexes are energetically favorable and are thus relatively stable with respect to subsequent reactions.

  18. Structure of supersaturated zincate solutions

    SciTech Connect

    Dmitrenko, V.E.; Balyakina, N.N.; Baulov, V.I.; Kotov, A.V.; Zubov, M.S.

    1985-09-01

    During the discharge of chemical power sources with zinc electrodes, supersaturated zincate solution (SZS) is formed from which zinc oxide or hydroxide precipitates as a function of time. The deposit detracts from the functioning of these power sources. In view of the model suggested for the structure of SZS, it is expected that a stabilizing effect would be exerted on SZS by compounds having proton-donating groups which do not give off the protons in the strongly alkaline medium and are not discharged in this medium. For a check of this, the authors chose to use xylitol and molasses in their experiments. The SZS were produced with a mock-up silver-zinc battery using the procedure previously described.

  19. Helium Diffusion Through H2O and D2O Amorphous Ice: A Lattice Inverse Istope Effect

    SciTech Connect

    Daschbach, John L.; Schenter, Gregory K.; Ayotte, Patrick; Smith, R. Scott; Kay, Bruce D.

    2004-05-14

    The diffusion of helium through both H2O and D2O amorphous solid water (ASW) has been measured between 55K and 110K. We find the diffusion rate is dependent on the isotopic composition of the ASW lattice. This lattice isotope effect is the "inverse" of a normal isotope effect, in that diffusion is faster in the heavier (D2O) isotope. Transition state theory calculations show that the isotope effect is due to a tight transition state results in a large zero point vibrational energy differences at the transition state predominantly due to hindered rotations of water in the lattice.

  20. Search for cold fusion using Pd-D2O cells and Ti-D mixtures

    NASA Astrophysics Data System (ADS)

    Hill, John C.; Stassis, C.; Shinar, J.; Goldman, A. I.; Folkerts, R.; Schwellenbach, D. D.; Peterson, D. T.; Widrig, C.; Porter, M.; Benesh, C. J.; Vary, J. P.

    1990-09-01

    We have searched for cold fusion produced in an electrolytic cell with Pd cathode and Pt anode. The electrolyte was 0.1 molar LiOD in 99.8% D2O. A 2-mm rod of polycrystalline Pd and a 4-mm rod of single crystal Pd were used. No radiation was detected above background by a BF3 neutron and Ge γ-X detector. The D2 loading of the Pd was 0.8 D per Pd atom reaching saturation after 4 hours. We also attempted to duplicate the work of Scaramuzzi and co-workers on the Ti-D2 system. Both powder and pieces of Ti were used. The material was cycled several times between 1100 K and 77 K. No neutron, γ- or x-ray emission above background was observed. The results of a barrier penetration calculation for H-like atoms are presented. The high fusion rates reported for PdD x . are much larger than those expected from theoretical calculations on these systems.

  1. The vibration-rotation-tunneling levels of N2-H2O and N2-D2O

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Gang; Carrington, Tucker

    2015-07-01

    In this paper, we report vibration-rotation-tunneling levels of the van der Waals clusters N2-H2O and N2-D2O computed from an ab initio potential energy surface. The only dynamical approximation is that the monomers are rigid. We use a symmetry adapted Lanczos algorithm and an uncoupled product basis set. The pattern of the cluster's levels is complicated by splittings caused by H-H exchange tunneling (larger splitting) and N-N exchange tunneling (smaller splitting). An interesting result that emerges from our calculation is that whereas in N2-H2O, the symmetric H-H tunnelling state is below the anti-symmetric H-H tunnelling state for both K = 0 and K = 1, the order is reversed in N2-D2O for K = 1. The only experimental splitting measurements are the D-D exchange tunneling splittings reported by Zhu et al. [J. Chem. Phys. 139, 214309 (2013)] for N2-D2O in the v2 = 1 region of D2O. Due to the inverted order of the split levels, they measure the sum of the K = 0 and K = 1 tunneling splittings, which is in excellent agreement with our calculated result. Other splittings we predict, in particular those of N2-H2O, may guide future experiments.

  2. The vibration-rotation-tunneling levels of N2-H2O and N2-D2O.

    PubMed

    Wang, Xiao-Gang; Carrington, Tucker

    2015-07-14

    In this paper, we report vibration-rotation-tunneling levels of the van der Waals clusters N2-H2O and N2-D2O computed from an ab initio potential energy surface. The only dynamical approximation is that the monomers are rigid. We use a symmetry adapted Lanczos algorithm and an uncoupled product basis set. The pattern of the cluster's levels is complicated by splittings caused by H-H exchange tunneling (larger splitting) and N-N exchange tunneling (smaller splitting). An interesting result that emerges from our calculation is that whereas in N2-H2O, the symmetric H-H tunnelling state is below the anti-symmetric H-H tunnelling state for both K = 0 and K = 1, the order is reversed in N2-D2O for K = 1. The only experimental splitting measurements are the D-D exchange tunneling splittings reported by Zhu et al. [J. Chem. Phys. 139, 214309 (2013)] for N2-D2O in the v2 = 1 region of D2O. Due to the inverted order of the split levels, they measure the sum of the K = 0 and K = 1 tunneling splittings, which is in excellent agreement with our calculated result. Other splittings we predict, in particular those of N2-H2O, may guide future experiments. PMID:26178101

  3. Mid-infrared signatures of hydroxyl containing water clusters: Infrared laser Stark spectroscopy of OH-H2O and OH(D2O)n (n = 1-3).

    PubMed

    Hernandez, Federico J; Brice, Joseph T; Leavitt, Christopher M; Liang, Tao; Raston, Paul L; Pino, Gustavo A; Douberly, Gary E

    2015-10-28

    Small water clusters containing a single hydroxyl radical are synthesized in liquid helium droplets. The OH-H2O and OH(D2O)n clusters (n = 1-3) are probed with infrared laser spectroscopy in the vicinity of the hydroxyl radical OH stretch vibration. Experimental band origins are qualitatively consistent with ab initio calculations of the global minimum structures; however, frequency shifts from isolated OH are significantly over-predicted by both B3LYP and MP2 methods. An effective Hamiltonian that accounts for partial quenching of electronic angular momentum is used to analyze Stark spectra of the OH-H2O and OH-D2O binary complexes, revealing a 3.70(5) D permanent electric dipole moment. Computations of the dipole moment are in good agreement with experiment when large-amplitude vibrational averaging is taken into account. Polarization spectroscopy is employed to characterize two vibrational bands assigned to OH(D2O)2, revealing two nearly isoenergetic cyclic isomers that differ in the orientation of the non-hydrogen-bonded deuterium atoms relative to the plane of the three oxygen atoms. The dipole moments for these clusters are determined to be approximately 2.5 and 1.8 D for "up-up" and "up-down" structures, respectively. Hydroxyl stretching bands of larger clusters containing three or more D2O molecules are observed shifted approximately 300 cm(-1) to the red of the isolated OH radical. Pressure dependence studies and ab initio calculations imply the presence of multiple cyclic isomers of OH(D2O)3. PMID:26520510

  4. Solution Accounts for Structural Damping

    NASA Technical Reports Server (NTRS)

    Roussos, L. A.; Hyer, M. W.; Thornton, E. A.

    1982-01-01

    New analytical technique determines dynamic response of damped structures dominated by internal structural damping mechanisms. Though structural damping is often negligible compared with damping due to air friction and friction in joints, structural damping can be of major importance in structures having heavy damping treatments or in outer-space structures. Finite-element model includes nonlinear, nonviscous internal damping.

  5. Quantitative imaging of water transport in soil and roots using neutron radiography, D2O and a new numerical model

    NASA Astrophysics Data System (ADS)

    Zarebanadkouki, M.; Kroener, E.; Ahmed, M. A.; Carminati, A.

    2014-12-01

    Our understanding of soil and plant water relations is currently limited by the lack of experimental methods to measure the water fluxes in soil and plants. Our study aimed to develop a new non-destructive method to measure the local fluxes of water into roots of plants growing in soils. We injected deuterated water (D2O) near the roots of lupines growing in sandy soils, and we used neutron radiography to image the transport of D2O through the root system. The experiments were performed during day, when plants were transpiring, and at night, when transpiration was reduced. The radiographs showed that: 1) the radial transport of D2O from soil and roots depended similarly to diffusion and convection; and 2) the axial transport of D2O along the root xylem was largely dominated by convection. To determine the convective fluxes from the radiographs, we simulated the D2O transport in soils and roots. A dual porosity model was used to describe the apoplastic and symplastic pathways of water across the root tissue. Other features such as the endodermis and the xylem were also included in the model. The D2O transport was modelled solving a convection-diffusion numerical model in soil and plants. The diffusion coefficients of the root tissues were inversely estimated by simulating the experiments at night under the assumption that at night the convective fluxes were negligible. Inverse modelling of the experiment at day gave the profile of water fluxes into the roots. For 24 day-old lupine grown in a sandy soil with uniform water content, our modelling results showed that root water uptake was higher at the proximal parts of the roots near soil surface and it decreased toward the distal parts. The method allows the quantification of the root properties and the regions of root water uptake along root systems growing in soils. Future applications of this method include the characterization of varying root systems, the radial and axial hydraulic conductivity of different root

  6. Proteomics and lipids of lipoproteins isolated at low salt concentrations in D2O/sucrose or in KBr.

    PubMed

    Ståhlman, Marcus; Davidsson, Pia; Kanmert, Ida; Rosengren, Birgitta; Borén, Jan; Fagerberg, Björn; Camejo, Germán

    2008-02-01

    There is much interest in the significance of apolipoproteins and proteins that are noncovalently associated with lipoproteins. It is possible that the high ionic strength used for isolation of lipoproteins with KBr and NaI could alter the pattern of associated exchangeable proteins. Here we describe lipoprotein classes fractionation from up to 0.5 ml of serum or plasma with buffers of physiological ionic strength and pH prepared with deuterium oxide (D(2)O) and sucrose. An advantage of the D(2)O/sucrose procedure was that the lipoproteins could be directly analyzed by the techniques described without need for desalting. We compared the isolated lipoproteins with those obtained using ultracentrifugation in KBr from the same plasma pool. Electrophoretic homogeneity of the lipoproteins was very similar using the two methods, as well as their lipid composition evaluated by HPLC. Two-dimensional electrophoresis and surface-enhanced laser adsorption/ionization time-of-flight mass spectrometry indicated that the patterns of exchangeable proteins of VLDL isolated using with the two procedures were very similar. However, significant differences were found in the profiles of LDL and HDL, indicating that the D(2)O/sucrose method allowed a more complete characterization of its exchangeable apolipoproteins and proteins. PMID:18025001

  7. Anomalous scattering of keV neutrons from H2O and D2O : I. Single scattering events

    NASA Astrophysics Data System (ADS)

    Chatzidimitriou-Dreismann, C. A.; Krzystyniak, M.

    2006-05-01

    Scattering of neutrons in the 24-150 keV incident energy range from H2O relative to that of D2O and H2O-D2O mixtures was reported recently by Moreh et al. This work is related to neutron Compton scattering experiments regarding the 'anomalous' scattering from protons, observed earlier at ISIS by Chatzidimitriou-Dreismann et al in the 5-100 eV range. Here we provide the complete data reduction scheme of time-of-flight integrated intensities measured at keV energy transfers, within the impulse approximation of standard theory and for single scattering events. Current investigations of multiple scattering events and the associated preliminary results are mentioned. Direct application of the theoretical results to the new keV scattering data reveals an anomalous ratio of scattering intensity of H2O relative to that of D2O of about 20%, thus being in good agreement with the earlier results of the original experiment at ISIS.

  8. Gelation Behavior of 5-Chloro-8-hydroxyquinoline, an Antituberculosis Agent in Aqueous Alcohol Solutions

    PubMed Central

    Kolehmainen, Erkki; Salo, Hannu; Korpela, Jukka

    2012-01-01

    It was shown that 5-chloro-8-hydroxyquinoline, an antituberculosis agent, gels aqueous alcohol solutions efficiently. Thermal stability and gel-to-sol transition temperature of 1% gel in CD3OD/D2O (2:1) was studied by 1H-NMR. Fibrous structures of four xerogels have been characterized by scanning electron microscope. PMID:27029417

  9. NMR solution structure of butantoxin.

    PubMed

    Holaday, S K; Martin, B M; Fletcher, P L; Krishna, N R

    2000-07-01

    The NMR structure of a new toxin, butantoxin (BuTX), which is present in the venoms of the three Brazilian scorpions Tityus serrulatus, Tityus bahiensis, and Tityus stigmurus, has been investigated. This toxin was shown to reversibly block the Shaker B potassium channels (K(d) approximately 660 nM) and inhibit the proliferation of T-cells and the interleukin-2 production of antigen-stimulated T-helper cells. BuTX is a 40 amino acid basic protein stabilized by the four disulfide bridges: Cys2-Cys5, Cys10-Cys31, Cys16-Cys36, and Cys20-Cys38. The latter three are conserved among all members of the short-chain scorpion toxin family, while the first is unique to BuTX. The three-dimensional structure of BuTX was determined using (1)H-NMR spectroscopy. NOESY, phase sensitive COSY (PH-COSY), and amide hydrogen exchange data were used to generate constraints for molecular modeling calculations. Distance geometry and simulated annealing calculations were performed to generate a family of 49 structures free of constraint violations. The secondary structure of BuTX consists of a short 2(1/2) turn alpha-helix (Glu15-Phe23) and a beta-sheet. The beta-sheet is composed of two well-defined antiparallel strands (Gly29-Met32 and Lys35-Cys38) connected by a type-I' beta-turn (Asn33-Asn34). Residues Cys5-Ala9 form a quasi-third strand of the beta-sheet. The N-terminal C2-C5 disulfide bridge unique to this toxin does not appear to confer stability to the protein. PMID:10864437

  10. Superconductivity in epitaxial thin films of NaxCoO2•yD2O

    NASA Astrophysics Data System (ADS)

    Krockenberger, Y.; Fritsch, I.; Christiani, G.; Habermeier, H.-U.; Yu, Li; Bernhard, C.; Keimer, B.; Alff, L.

    2006-04-01

    The observation of superconductivity in the layered transition metal oxide NaxCoO2•yH2O [K. Takada et al., Nature (London) 422, 53 (2003)] has caused a tremendous upsurge of scientific interest due to its similarities and its differences to the copper based high-temperature superconductors. Two years after the discovery, we report the fabrication of single-phase superconducting epitaxial thin films of Na0.3CoO2•1.3D2O grown by pulsed laser deposition technique. This opens additional roads for experimental research exploring the superconducting state and the phase diagram of this unconventional material.

  11. Double and zero quantum filtered 2H NMR analysis of D2O in intervertebral disc tissue

    NASA Astrophysics Data System (ADS)

    Ooms, Kristopher J.; Vega, Alexander J.; Polenova, Tatyana; Cannella, Marco; Marcolongo, Michele

    2015-09-01

    The analysis of double and zero quantum filtered 2H NMR spectra obtained from D2O perfused in the nucleus pulposus of human intervertebral disc tissue samples is reported. Fitting the spectra with a three-site model allows for residual quadrupolar couplings and T2 relaxation times to be measured. The analysis reveals changes in both the couplings and relaxation times as the tissue begins to show signs of degradation. The full analysis demonstrates that information about tissue hydration, water collagen interactions, and sample heterogeneity can be obtained and used to better understand the biochemical differences between healthy and degraded tissue.

  12. Ionization yield and absorption spectra reveal superexcited Rydberg state relaxation processes in H2O and D2O

    NASA Astrophysics Data System (ADS)

    Fillion, J.-H.; Dulieu, F.; Baouche, S.; Lemaire, J.-L.; Jochims, H. W.; Leach, S.

    2003-07-01

    The absorption cross section and the ionization quantum yield of H2O have been measured using a synchrotron radiation source between 9 and 22 eV. Comparison between the two curves highlights competition between relaxation processes for Rydberg states converging to the first tilde A 2A 1 and to the second tilde B 2B 2 excited states of H2O+. Comparison with D2O absorption and ionization yields, derived from Katayama et al (1973 J. Chem. Phys. 59 4309), reveals specific energy-dependent deuteration effects on competitive predissociation and autoionization relaxation channels. Direct ionization was found to be only slightly affected by deuteration.

  13. Complex structures – smart solutions

    PubMed Central

    2011-01-01

    The siliceous skeletal elements of the sponges, the spicules, represent one of the very few examples from where the molecule toolkit required for the formation of an extracellular mineral-based skeleton, has been elucidated. The distinguished feature of the inorganic matrix, the bio-silica, is its enzymatic synthesis mediated by silicatein. Ortho-silicate undergoes in the presence of silicatein a polycondensation reaction and forms bio-silica under release of reaction water. The protein silicatein aggregates non-covalently to larger filaments, a process that is stabilized by the silicatein-associated protein, silintaphin-1. These structured clusters form the axial filament that is located in the center of the spicules, the axial canal. Surprisingly it has now been found that the initial axial orientation, in which the spicules grow, is guided by cell processes through evagination. The approximately two µm wide cell extensions release silicatein that forms the first organic axial filament, which then synthesizes the inner core of the siliceous spicule rods. In parallel, the radial growth of the spicules is controlled by a telescopic arrangement of organic layers, into which bio-silica and ortho-silicate are deposited. Hence, the formation of a mature siliceous spicule is completed by a centrifugal accretion of bio-silica mediated by the silicatein in the axial filament, and a centripetal bio-silica deposition catalyzed by the extra-spicular silicatein. Finally this contribution highlights that for the ultimate determination of the spicule shapes, their species-specific morphologies, bio-silica hardens during a process which removes reaction water. The data presented can also provide new blueprints for the fabrication of novel biomaterials for biomedical applications.  PMID:22446527

  14. Water structure in concentrated lithium chloride solutions

    NASA Astrophysics Data System (ADS)

    Tromp, R. H.; Neilson, G. W.; Soper, A. K.

    1992-06-01

    The radial pair distribution functions gHH(r) and gOH(r) (to a good approximation) of 1 and 10 m solutions of lithium chloride in water have been obtained from neutron diffraction. It turns out that the intermolecular water structure in a solution of 10 m is affected considerably by the presence of ions—the number of hydrogen bonds is about 70% lower than in pure water. The intermolecular water structure in 1 m lithium chloride as well as the intramolecular water structure in both 1 and 10 m lithium chloride is not distinguishable from that of pure water in any measurable extent.

  15. Investigation of the Performance of D2O-Cooled High-Conversion Reactors for Fuel Cycle Calculations

    SciTech Connect

    Hikaru Hiruta; Gilles Youinou

    2013-09-01

    This report presents FY13 activities for the analysis of D2O cooled tight-pitch High-Conversion PWRs (HCPWRs) with U-Pu and Th-U fueled cores aiming at break-even or near breeder conditions while retaining the negative void reactivity. The analyses are carried out from several aspects which could not be covered in FY12 activities. SCALE 6.1 code system is utilized, and a series of simple 3D fuel pin-cell models are developed in order to perform Monte Carlo based criticality and burnup calculations. The performance of U-Pu fueled cores with axial and internal blankets is analyzed in terms of their impact on the relative fissile Pu mass balance, initial Pu enrichment, and void coefficient. In FY12, Pu conversion performances of D2O-cooled HCPWRs fueled with MOX were evaluated with small sized axial/internal DU blankets (approximately 4cm of axial length) in order to ensure the negative void reactivity, which evidently limits the conversion performance of HCPWRs. In this fiscal year report, the axial sizes of DU blankets are extended up to 30 cm in order to evaluate the amount of DU necessary to reach break-even and/or breeding conditions. Several attempts are made in order to attain the milestone of the HCPWR designs (i.e., break-even condition and negative void reactivity) by modeling of HCPWRs under different conditions such as boiling of D2O coolant, MOX with different 235U enrichment, and different target burnups. A similar set of analyses are performed for Th-U fueled cores. Several promising characteristics of 233U over other fissile like 239Pu and 235U, most notably its higher fission neutrons per absorption in thermal and epithermal ranges combined with lower ___ in the fast range than 239Pu allows Th-U cores to be taller than MOX ones. Such an advantage results in 4% higher relative fissile mass balance than that of U-Pu fueled cores while retaining the negative void reactivity until the target burnup of 51 GWd/t. Several other distinctions between U-Pu and

  16. Solution structure of copper ion-induced molecular aggregates of tyrosine melanin.

    PubMed

    Gallas, J M; Littrell, K C; Seifert, S; Zajac, G W; Thiyagarajan, P

    1999-08-01

    Melanin, the ubiquitous biological pigment, provides photoprotection by efficient filtration of light and also by its antioxidant behavior. In solutions of synthetic melanin, both optical and antioxidant behavior are affected by the aggregation states of melanin. We have utilized small-angle x-ray and neutron scattering to determine the molecular dimensions of synthetic tyrosine melanin in its unaggregated state in D(2)O and H(2)O to study the structure of melanin aggregates formed in the presence of copper ions at various copper-to-melanin molar ratios. In the absence of copper ions, or at low copper ion concentrations, tyrosine melanin is present in solution as a sheet-like particle with a mean thickness of 12.5 A and a lateral extent of approximately 54 A. At a copper-to-melanin molar ratio of 0.6, melanin aggregates to form long, rod-like structures with a radius of 32 A. At a higher copper ion concentration, with a copper-to-melanin ratio of 1.0, these rod-like structures further aggregate, forming sheet-like structures with a mean thickness of 51 A. A change in the charge of the ionizable groups induced by the addition of copper ions is proposed to account for part of the aggregation. The data also support a model for the copper-induced aggregation of melanin driven by pi stacking assisted by peripheral Cu(2+) complexation. The relationship between our results and a previous hypothesis for reduced cellular damage from bound-to-melanin redox metal ions is also discussed. PMID:10423458

  17. NMR Solution Structure and Condition-Dependent Oligomerization of the Antimicrobial Peptide Human Defensin 5

    PubMed Central

    Wommack, Andrew J.; Robson, Scott A.; Wanniarachchi, Yoshitha A.; Wan, Andrea; Turner, Christopher J.; Wagner, Gerhard; Nolan, Elizabeth M.

    2012-01-01

    Human defensin 5 (HD5) is a 32-residue host-defense peptide expressed in the gastrointestinal, reproductive, and urinary tracts that has antimicrobial activity. It exhibits six cysteine residues that are regiospecifically oxidized to form three disulfide bonds (Cys3—Cys31, Cys5—Cys20, and Cys10—Cys30) in the oxidized form (HD5ox). To probe the solution structure and oligomerization properties of HD5ox, and select mutant peptides lacking one or more disulfide bonds, NMR solution studies and analytical ultracentrifugation experiments are reported in addition to in vitro peptide stability assays. The NMR solution structure of HD5ox, solved at pH 4 in 90:10 H2O/D2O, is presented (PDB: 2LXZ). Relaxation T1/T2 measurements and the rotational correlation time (Tc) estimated from a [15N,1H]-TRACT experiment demonstrate that HD5ox is dimeric under these experimental conditions. Exchange broadening of the Hα signals in the NMR spectra suggests that residues 19-21 (Val19-Cys20-Glu21) contribute to the dimer interface in solution. Exchange broadening is also observed for residues 7-14 comprising the loop. Sedimentation velocity and equilibrium studies conducted in buffered aqueous solution reveal that the oligomerization state of HD5ox is pH-dependent. Sedimentation coefficients of ca. 1.8 S and a molecular weight of 14,363 Da were determined for HD5ox at pH 7, supporting a tetrameric form ([HD5ox] ≥ 30 μM). At pH 2, a sedimentation coefficient of ca. 1.0 S and a molecular weight of 7,079 Da, corresponding to a HD5ox dimer, were obtained. Millimolar concentrations of NaCl, CaCl2, and MgCl2 have negligible effect on the HD5ox sedimentation coefficients in buffered aqueous solution at neutral pH. Removal of a single disulfide bond results in a loss of peptide fold and quaternary structure. These biophysical investigations highlight the dynamic and environment-sensitive behavior of HD5ox in solution, and provide important insights into HD5ox structure

  18. REdiii: a pipeline for automated structure solution

    PubMed Central

    Bohn, Markus-Frederik; Schiffer, Celia A.

    2015-01-01

    High-throughput crystallographic approaches require integrated software solutions to minimize the need for manual effort. REdiii is a system that allows fully automated crystallographic structure solution by integrating existing crystallographic software into an adaptive and partly autonomous workflow engine. The program can be initiated after collecting the first frame of diffraction data and is able to perform processing, molecular-replacement phasing, chain tracing, ligand fitting and refinement without further user intervention. Preset values for each software component allow efficient progress with high-quality data and known parameters. The adaptive workflow engine can determine whether some parameters require modifications and choose alternative software strategies in case the preconfigured solution is inadequate. This integrated pipeline is targeted at providing a comprehensive and efficient approach to screening for ligand-bound co-crystal structures while minimizing repetitiveness and allowing a high-throughput scientific discovery process. PMID:25945571

  19. REdiii: a pipeline for automated structure solution.

    PubMed

    Bohn, Markus Frederik; Schiffer, Celia A

    2015-05-01

    High-throughput crystallographic approaches require integrated software solutions to minimize the need for manual effort. REdiii is a system that allows fully automated crystallographic structure solution by integrating existing crystallographic software into an adaptive and partly autonomous workflow engine. The program can be initiated after collecting the first frame of diffraction data and is able to perform processing, molecular-replacement phasing, chain tracing, ligand fitting and refinement without further user intervention. Preset values for each software component allow efficient progress with high-quality data and known parameters. The adaptive workflow engine can determine whether some parameters require modifications and choose alternative software strategies in case the preconfigured solution is inadequate. This integrated pipeline is targeted at providing a comprehensive and efficient approach to screening for ligand-bound co-crystal structures while minimizing repetitiveness and allowing a high-throughput scientific discovery process. PMID:25945571

  20. VizieR Online Data Catalog: Photodesorption of H2O, HDO and D2O ice (Arasa+, 2015)

    NASA Astrophysics Data System (ADS)

    Arasa, C.; Koning, J.; Kroes, G.-Jan; Walsh, C.; van Dishoeck, E. F.

    2015-03-01

    The data listed in this electronic table are the results of molecular dynamics simulations of water ice photodissociation and subsequent desorption mechanisms. Upon photoexcitation and dissociation of a water molecule within an ice mantle frozen onto an interstellar or circumstellar dust grain, there are several potential chemical outcomes, the probabilities for which are dependent upon ice temperature and ice monolayer. Here, we list the probabilities per monolayer as a function of temperature for each outcome following the dissociation of a H2O, HDO, or D2O molecule in water (H2O) ice. DOH refers to the dissociation of HDO into D+OH and HOD to the dissocation of HDO into H+OD; hence, the data contain probabilies for 4 dissociation events. These data have been compiled from the raw simulation data which considers around 6000 trajectories or initial conditions. (4 data files).

  1. Photoionization of rotationally cooled H2O and D2O in the region 650-990 A

    NASA Astrophysics Data System (ADS)

    Dehmer, P. M.; Holland, D. M. P.

    1991-03-01

    Room temperature and rotationally cooled relative photoionization cross sections for H2O and D2O were determined in the wavelength region 650-990 A with a wavelength resolution of 0.06-0.11 A. The spectra were normalized to the absolute photoionization cross sections determined by Katayama et al. (1973) with lower resolution. A rotational analysis of the Pi subbands in the (0,6,0) and (0,8,0) bands of a Rydberg transition determined the symmetry of the upper state; in addition, the series was extended to higher principal quantum numbers. The analysis of these and other bands was made difficult both by the large natural linewidths of the rotational transitions and by the absence of transitions to rotational levels with N-prime above 3.

  2. Synchrotron based infrared imaging and spectroscopy via focal plane array on live fibroblasts in D2O enriched medium

    SciTech Connect

    Quaroni, Luca; Zlateva, Theodora; Sarafimov, Blagoj; Kreuzer, Helen W.; Wehbe, Katia; Hegg, Eric L.; Cinque, Gianfelice

    2014-03-26

    We tested the viability of using synchrotron based infrared imaging to study biochemical processes inside living cells. As a model system, we studied fibroblast cells exposed to a medium highly enriched with D2O. We could show that the experimental technique allows us to reproduce at the cellular level measurements that are normally performed on purified biological molecules. We can obtain information about lipid conformation and distribution, kinetics of hydrogen/deuterium exchange, and the formation of concentration gradients of H and O isotopes in water that are associated with cell metabolism. The implementation of the full field technique in a sequential imaging format gives a description of cellular biochemistry and biophysics that contains both spatial and temporal information.

  3. Rovibrational energy levels of the F(-)(H2O) and F(-)(D2O) complexes.

    PubMed

    Sarka, János; Lauvergnat, David; Brites, Vincent; Császár, Attila G; Léonard, Celine

    2016-06-29

    The variational nuclear-motion codes ElVibRot and GENIUSH have been used to compute rotational-vibrational states of the F(-)(H2O) anion and its deuterated isotopologue, F(-)(D2O), employing a full-dimensional, semiglobal potential energy surface (PES) called SLBCL, developed as part of this study for the ground electronic state of the complex. The PES is determined from all-electron, explicitly correlated coupled-cluster singles, doubles, and connected triples [CCSD(T)-F12a] computations with an atom-centered, fixed-exponent Gaussian basis set of cc-pCVTZ-F12 quality. The SLBCL PES accurately reproduces the two equivalent minima of the complex, the corresponding transition barrier of C2v point-group symmetry, as well as the proton transfer and the dissociation asymptotes towards the products HF + OH(-) and F(-) + H2O, respectively. The code ElVibRot has been updated so that it can use curvilinear internal coordinates corresponding to a reaction path. The variationally computed vibrational energy levels are compared to relevant experimental and previously determined first-principles results. The vibrational states reveal the presence of pronounced anharmonic effects and considerable intermode couplings resulting in strong resonances, involving in particular the HOH bend and the ionic OH stretch motions. Tunneling results in particularly significant splittings for F(-)(H2O); as expected, the splittings are orders of magnitude smaller for the F(-)(D2O) molecule. The rovibrational energy levels reveal that, despite the large-amplitude vibrational motions, the rotations of F(-)(H2O) basically follow rigid-rotor characteristics. PMID:27306786

  4. Solution structure of RNase P RNA

    PubMed Central

    Kazantsev, Alexei V.; Rambo, Robert P.; Karimpour, Sina; SantaLucia, John; Tainer, John A.; Pace, Norman R.

    2011-01-01

    The ribonucleoprotein enzyme ribonuclease P (RNase P) processes tRNAs by cleavage of precursor-tRNAs. RNase P is a ribozyme: The RNA component catalyzes tRNA maturation in vitro without proteins. Remarkable features of RNase P include multiple turnovers in vivo and ability to process diverse substrates. Structures of the bacterial RNase P, including full-length RNAs and a ternary complex with substrate, have been determined by X-ray crystallography. However, crystal structures of free RNA are significantly different from the ternary complex, and the solution structure of the RNA is unknown. Here, we report solution structures of three phylogenetically distinct bacterial RNase P RNAs from Escherichia coli, Agrobacterium tumefaciens, and Bacillus stearothermophilus, determined using small angle X-ray scattering (SAXS) and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. A combination of homology modeling, normal mode analysis, and molecular dynamics was used to refine the structural models against the empirical data of these RNAs in solution under the high ionic strength required for catalytic activity. PMID:21531920

  5. Impact of D2O/H2O Solvent Exchange on the Emission of HgTe and CdTe Quantum Dots: Polaron and Energy Transfer Effects.

    PubMed

    Wen, Qiannan; Kershaw, Stephen V; Kalytchuk, Sergii; Zhovtiuk, Olga; Reckmeier, Claas; Vasilevskiy, Mikhail I; Rogach, Andrey L

    2016-04-26

    We have studied light emission kinetics and analyzed carrier recombination channels in HgTe quantum dots that were initially grown in H2O. When the solvent is replaced by D2O, the nonradiative recombination rate changes highlight the role of the vibrational degrees of freedom in the medium surrounding the dots, including both solvent and ligands. The contributing energy loss mechanisms have been evaluated by developing quantitative models for the nonradiative recombination via (i) polaron states formed by strong coupling of ligand vibration modes to a surface trap state (nonresonant channel) and (ii) resonant energy transfer to vibration modes in the solvent. We conclude that channel (i) is more important than (ii) for HgTe dots in either solution. When some of these modes are removed from the relevant spectral range by the H2O to D2O replacement, the polaron effect becomes weaker and the nonradiative lifetime increases. Comparisons with CdTe quantum dots (QDs) served as a reference where the resonant energy loss (ii) a priori was not a factor, also confirmed by our experiments. The solvent exchange (H2O to D2O), however, is found to slightly increase the overall quantum yield of CdTe samples, probably by increasing the fraction of bright dots in the ensemble. The fundamental study reported here can serve as the foundation for the design and optimization principles of narrow bandgap quantum dots aimed at applications in long wavelength colloidal materials for infrared light emitting diodes and photodetectors. PMID:26958866

  6. Neutron diffraction studies of H2O/D2O at supercritical temperatures. A direct determination of gHH(r), gOH(r), and gOO(r)

    NASA Astrophysics Data System (ADS)

    Tromp, R. H.; Postorino, P.; Neilson, G. W.; Ricci, M. A.; Soper, A. K.

    1994-10-01

    Neutron diffraction studies are reported on H2O at temperatures of 300 and 400 °C. The method of isotopic substitution is applied to three mixtures of H2O and D2O, and the diffraction data are used to determine the three radial distribution functions gHH(r), gOH(r), and gOO(r). These results can be used to discuss changes in nearest neighbor structure between water molecules, and to assess the degree of usefulness of representative (usually pairwise) model potentials.

  7. Intra-molecular Structural Change of PAMAM Dendrimers in Aqueous Solutions Revealed by Small Angle Neutron Scattering

    SciTech Connect

    Porcar, L.; Hong, Kunlun; Butler, Paul D; Herwig, Kenneth W; Smith, Gregory Scott; Liu, Yun; Chen, Wei-Ren

    2010-01-01

    Small-angle neutron scattering (SANS) experiments were carried out to investigate the structure of aqueous (D2O) G4 PAMAM dendrimer solutions as a function of molecular protonation and dendrimer concentration. Our results indicate unambiguously that, although the radius of gyration RG remains nearly invariant, the dendrimer radial density profile (r) decreases in the dendrimer core with a continuous increase in protonation. This discovery also suggests that RG, which is commonly adopted by numerous simulation and experimental works in describing the global dendrimer size, is not suitable as the index parameter to characterize the dendrimer conformation change. We also found that RG and (r), for dendrimers dissolved in both neutral and acidified solutions, remain nearly constant over the studied concentration range. We further demonstrate that the outcome of the widely used Guinier method is questionable for extracting RG in the concentration range studied. Our results reveal the polymer colloid structural duality as benchmarks for future experimental and theoretical studies and provide a critical step toward understanding drug encapsulation by ionic bonds.

  8. Reconstructing the history of water ice formation from HDO/H2O and D2O/HDO ratios in protostellar cores

    NASA Astrophysics Data System (ADS)

    Furuya, K.; van Dishoeck, E. F.; Aikawa, Y.

    2016-02-01

    Recent interferometer observations have found that the D2O/HDO abundance ratio is higher than that of HDO/H2O by about one order of magnitude in the vicinity of low-mass protostar NGC 1333-IRAS 2A, where water ice has sublimated. Previous laboratory and theoretical studies show that the D2O/HDO ice ratio should be lower than the HDO/H2O ice ratio, if HDO and D2O ices are formed simultaneously with H2O ice. In this work, we propose that the observed feature, D2O/HDO > HDO/H2O, is a natural consequence of chemical evolution in the early cold stages of low-mass star formation as follows: 1) majority of oxygen is locked up in water ice and other molecules in molecular clouds, where water deuteration is not efficient; and 2) water ice formation continues with much reduced efficiency in cold prestellar/protostellar cores, where deuteration processes are highly enhanced as a result of the drop of the ortho-para ratio of H2, the weaker UV radiation field, etc. Using a simple analytical model and gas-ice astrochemical simulations, which traces the evolution from the formation of molecular clouds to protostellar cores, we show that the proposed scenario can quantitatively explain the observed HDO/H2O and D2O/HDO ratios. We also find that the majority of HDO and D2O ices are likely formed in cold prestellar/protostellar cores rather than in molecular clouds, where the majority of H2O ice is formed. This work demonstrates the power of the combination of the HDO/H2O and D2O/HDO ratios as a tool to reveal the past history of water ice formation in the early cold stages of star formation, and when the enrichment of deuterium in the bulk of water occurred. Further observations are needed to explore if the relation, D2O/HDO > HDO/H2O, is common in low-mass protostellar sources.

  9. Single Crystal Neutron Diffraction Study of Organic Multiferroic (ND4)2[FeCl5(D2O)

    NASA Astrophysics Data System (ADS)

    Tian, Wei; Cao, Huibo; Yan, Jiaqiang; Chakoumakos, Bryan; Sales, Brian; Fernandez-Baca, Jaime

    2015-03-01

    (NH4)2 [FeCl5(H2O)] is a new organic multiferroic that exhibits intriguing magnetic/multiferroic behavior as a function of temperature and applied magnetic field. Unlike its counterpart compounds where NH4 group is replaced by K, Cs, and Rb, (NH4)2 [FeCl5(H2O)] is the only system that undergoes two successive magnetic transitions accompanied by pronounced spontaneous electric polarization. Large deuterated (ND4)2 [FeCl5(D2O)] single crystals were grown and characterized by specific heat and magnetization measurements showing no significant effects due to deuteration. Here we report single crystal neutron diffraction results that reveal an incommensurate antiferromagnetic order below TN ~ 7.3 K with a propagation vector of (0 0 ~ 0.77). Higher harmonic Bragg peaks were observed indicate ``squaring up'' behavior upon further cooling. At 1.5 K, a field induced incommensurate-to-commensurate transition was also observed by applying magnetic field along the a-axis. Research conducted at ORNL's High Flux Isotope Reactor was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U. S. Department of Energy.

  10. Automated structure solution with the PHENIX suite

    SciTech Connect

    Terwilliger, Thomas C; Zwart, Peter H; Afonine, Pavel V; Grosse - Kunstleve, Ralf W

    2008-01-01

    Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

  11. Automated Structure Solution with the PHENIX Suite

    SciTech Connect

    Zwart, Peter H.; Zwart, Peter H.; Afonine, Pavel; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei; Ioerger, Tom R.; McCoy, A.J.; McKee, Eric; Moriarty, Nigel; Read, Randy J.; Sacchettini, James C.; Sauter, Nicholas K.; Storoni, L.C.; Terwilliger, Tomas C.; Adams, Paul D.

    2008-06-09

    Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

  12. Structuring of polymer solutions upon solvent evaporation

    NASA Astrophysics Data System (ADS)

    Schaefer, C.; van der Schoot, P.; Michels, J. J.

    2015-02-01

    The morphology of solution-cast, phase-separated polymers becomes finer with increasing solvent evaporation rate. We address this observation theoretically for a model polymer where demixing is induced by steady solvent evaporation. In contrast to what is the case for a classical, thermal quench involving immiscible blends, the spinodal instability initially develops slowly and the associated length scale is not time invariant but decreases with time as t-1 /2. After a time lag, phase separation accelerates. Time lag and characteristic length exhibit power-law behavior as a function of the evaporation rate with exponents of -2 /3 and -1 /6 . Interestingly, at later stages the spinodal structure disappears completely while a second length scale develops. The associated structure coarsens but does not follow the usual Lifshitz-Slyozov-Wagner kinetics.

  13. Structure and aggregation in model tetramethylurea solutions

    SciTech Connect

    Gupta, Rini; Patey, G. N.

    2014-08-14

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32 000, 64 000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, X{sub t}, ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at X{sub t} = 0.005, aggregation is a well established feature of the solution at X{sub t} = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (X{sub t} ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At X{sub t} = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations.

  14. Infrared diode laser spectroscopy of the Ne-D2O van der Waals complex: Strong Coriolis and angular-radial coupling

    NASA Astrophysics Data System (ADS)

    Li, Song; Zheng, Rui; Zhu, Yu; Duan, Chuanxi

    2011-10-01

    Four internal-rotation/vibration bands of the Ne-D2O complex have been measured in the v2 bend region of D2O using a tunable infrared diode laser spectrometer to probe a slit supersonic expansion. Three ortho bands are excited from the ground state Σ(000) to the Σ and Π(111, υ2 = 1) internal rotor states and the n = 1, Σ(000, υ2 = 1) stretching-internal rotor combination state. Strong perturbations between the excited vibrational states are evident. The observed spectra are analyzed separately with a three-state J-dependent Coriolis plus J-independent angular-radial coupling model [M. J. Weida and D. J. Nesbitt, J. Chem. Phys. 106, 3078 (1997), 10.1063/1.473051] and a three-state Coriolis coupling model [R. C. Cohen and R. J. Saykally, J. Chem. Phys. 95, 7891 (1991), 10.1063/1.461318]. The former model works more successfully than the latter. Molecular constants for the ground and excited vibrational states of ortho 20Ne-D2O isotopomer as well as the Coriolis and angular-radial coupling constants are determined accurately. The van der Waals stretching frequency is estimated to be νs = 24.85 cm-1 in the ground state and decreases to about 20.8 cm-1 upon vibrational excitation of the D2O bend.

  15. Solution structure of human sorting nexin 22.

    PubMed

    Song, Jikui; Zhao, Kate Qin; Newman, Carrie L Loushin; Vinarov, Dmitriy A; Markley, John L

    2007-05-01

    The sorting nexins (SNXs) constitute a large group of PX domain-containing proteins that play critical roles in protein trafficking. We report here the solution structure of human sorting nexin 22 (SNX22). Although SNX22 has <30% sequence identity with any PX domain protein of known structure, it was found to contain the alpha/beta fold and compact structural core characteristic of PX domains. Analysis of the backbone dynamics of SNX22 by NMR relaxation measurements revealed that the two walls of the ligand binding cleft undergo internal motions: on the picosecond timescale for the beta1/beta2 loop and on the micro- to millisecond timescale for the loop between the polyproline motif and helix alpha2. Regions of the SNX22 structure that differ from those of other PX domains include the loop connecting strands beta1 and beta2 and the loop connecting helices alpha1 and alpha2, which appear to be more mobile than corresponding loops in other known structures. The interaction of dibutanoyl-phosphatidylinositol-3-phosphate (dibutanoyl-PtdIns(3)P) with SNX22 was investigated by an NMR titration experiment, which identified the binding site in a basic cleft and indicated that ligand binding leads only to a local structural rearrangement as has been found with other PX domains. Because motions in the loops are damped out when dibutanoyl-PtdIns(3)P binds, entropic effects could contribute to the lower affinity of SNX22 for this ligand compared to other PX domains. PMID:17400918

  16. Internal comparison between deuterium oxide (D2O) and L-[ring-13C6] phenylalanine for acute measurement of muscle protein synthesis in humans

    PubMed Central

    Wilkinson, Daniel J; Cegielski, Jessica; Phillips, Bethan E; Boereboom, Catherine; Lund, Jonathan N; Atherton, Philip J; Smith, Kenneth

    2015-01-01

    Stable isotope tracer methodologies are becoming increasingly widespread in metabolic research; yet a number of factors restrict their implementation, such as, i.v infusions, multiple cannulae, tissue samples, and significant cost. We recently validated the sensitivity of the orally administered stable isotope tracer deuterium oxide (D2O) for quantifying day-to-day changes in muscle protein synthesis (MPS). This method is less invasive, restrictive, and more cost-effective than traditional amino acid (AA) tracer techniques. In the present study, we hypothesized the sensitivity of our analytical techniques (GC-Pyrolysis-IRMS) would permit D2O-derived measurements of MPS over much shorter periods (i.e., hours) usually only possible using AA-tracer techniques. We recruited nine males (24 ± 3 year, BMI: 25 ± 3 kg·m−²) into an internally controlled comparison of D2O versus 13C AA-tracers. The day before the acute study subjects consumed 400 mL D2O, and on the study day, received a primed (0.3 mg·kg−1) continuous (0.6 mg·kg·h−1) i.v infusion of L-[ring-13C6]-phenylalanine to quantify MPS under both: (1) basal [postabsorptive] and; (2) stimulated [postprandial] that is, consumption of 20 g EAA, conditions. Measures of MPS yielded indistinguishable technique differences with respect to EAA, 13C: 0.065 ± 0.004 to 0.089 ± 0.006%·h−1 (P < 0.05) and D2O: 0.050 ± 0.007 to 0.088 ± 0.008%·h−1 (P < 0.05) with qualitatively similar increases. Our findings reveal that acute measurement of MPS, usually only possible using AA-tracers, are feasible over shorter periods with orally administered D2O when used in tandem with GC-Pyrolysis-IRMS. We conclude that this D2O approach provides a less invasive, cost-effective, and flexible means by which to quantify MPS acutely over several hours. PMID:26149278

  17. Neutron reflectometry study on an interface of octane and D 2O at low surfactant (C 10E 4) concentration

    NASA Astrophysics Data System (ADS)

    Jeng, U.; Esibov, L.; Crow, M. L.; Steyerl, A.

    1996-02-01

    We study the surface and interface roughness of a two-liquid film system using neutron reflectometry. The middle phase and bottom phase are extracted from a three-phase microemulsion containing 2 wt% non-ionic surfactant C 10E 4, 81 wt% D 2O and 17 wt% octane (C 8H 18). The system is formed by spreading a few drops of the middle phase of the microemulsion on the bottom phase of the microemulsion. The middle phase does not wet the bottom phase, but demixes to form a top octane-water mixture layer with a thickness of ∼ 580 Å. The mean surface roughness of the system is found to be 7 Å but the data are insensitive to interface roughness. An extended capillary wave model for a two-liquid-film system is derived to account for the coupling between the surface and interface. The dispersion relation yields two fundamental modes. In a calculation of mean-square roughness (< ζ2> 1/2) a high- k-cutoff is needed to account for non-linear terms in the Navier-Stokes equation. A low- k cutoff is also needed to avoid a “slip phenomenon” at the interface, which characterizes one of the modes. It turns out that for the parameters of our experiment the narrowing of k region is so significant that the mode causing the slip is strongly suppressed. As a consequence, the calculated interface roughness is much smaller than that derived from ordinary capillary wave theory.

  18. Magnetically-induced ferroelectricity in the (ND4)2[FeCl5(D2O)] molecular compound

    PubMed Central

    Alberto Rodríguez-Velamazán, José; Fabelo, Óscar; Millán, Ángel; Campo, Javier; Johnson, Roger D.; Chapon, Laurent

    2015-01-01

    The number of magnetoelectric multiferroic materials reported to date is scarce, as magnetic structures that break inversion symmetry and induce an improper ferroelectric polarization typically arise through subtle competition between different magnetic interactions. The (NH4)2[FeCl5(H2O)] compound is a rare case where such improper ferroelectricity has been observed in a molecular material. We have used single crystal and powder neutron diffraction to obtain detailed solutions for the crystal and magnetic structures of (NH4)2[FeCl5(H2O)], from which we determined the mechanism of multiferroicity. From the crystal structure analysis, we observed an order-disorder phase transition related to the ordering of the ammonium counterion. We have determined the magnetic structure below TN, at 2 K and zero magnetic field, which corresponds to a cycloidal spin arrangement with magnetic moments contained in the ac-plane, propagating parallel to the c-axis. The observed ferroelectricity can be explained, from the obtained magnetic structure, via the inverse Dzyaloshinskii-Moriya mechanism. PMID:26417890

  19. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  20. Organoactinide chemistry: synthesis, structure, and solution dynamics

    SciTech Connect

    Brennan, J.G.

    1985-12-01

    This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp/sub 2/MX/sub 2/. Ligand redistribution processes are present throughout the synthetic work, as has often been observed in uranium cyclopentadienyl chemistry. The effects of covalent M-L bonding on the solution and solid state properties of U(III) coordination complexes are considered. In particular, the nature of the more subtle interaction between the metal and the neutral ligand are examined. Using relative basicity data obtained in solution, and solid state structural data (and supplemented by gas phase photoelectron measurements), it is demonstrated that the more electron rich U(III) centers engage in significant U ..-->.. L ..pi..-donation. Trivalent uranium is shown to be capable of acting either as a one- or two-electron reducing agent toward a wide variety of unsaturated organic and inorganic molecules, generating molecular classes unobtainable via traditional synthetic approaches, as well as offering an alternative synthetic approach to molecules accessible via metathesis reactions. Ligand redistribution processes are again observed, but given the information concerning ligand lability, this reactivity pattern is applied to the synthesis of pure materials inaccessible from redox chemistry. 214 refs., 33 figs., 10 tabs.

  1. Characterization of Swollen States of Polyelectrolyte Brushes in Salt Solution by Neutron Reflectivity

    NASA Astrophysics Data System (ADS)

    Kobayashi, Motoyasu; Mitamura, Koji; Terada, Masami; Yamada, Norifumi L.; Takahara, Atsushi

    2011-01-01

    Cationic and zwitterionic polyelectrolyte brushes on quartz substrate were synthesized by surface-initiated atom transfer radical polymerization of 2-(methacryloyloxy)-ethyltrimethylammonium chloride (MTAC) and 2-(methacryloyloxy)ethyl phosphorylcholine (MPC). The effects of ionic strength on brush structure are investigated by neutron reflectivity (NR) in NaCl deuterium oxide (D2O) solutions. We observed that poly(MTAC) chains were drastically shrunk at concentrations above 0.1 M NaCl/D2O, which may be the change in charge-screening effect against ions on poly(MTAC). On the other hand, effect of salt concentration on a swollen state of poly(MPC) brush was negligible, even at the high concentration (5.0 M) close to saturation. The behaviour of poly(MPC) in salt aqueous solution is completely different from that of poly(MTAC), which may arise from the unique interaction properties, neutral nature, and hydrated water structure of phosphorylcholine units.

  2. Small-angle neutron scattering study of pH dependence of the liquid structure factor of concentrated solutions of eye lens gamma-B crystallin

    NASA Astrophysics Data System (ADS)

    Desmond, Kenneth; Thurston, George; Stradner, Anna; Schurtenberger, Peter

    2006-03-01

    We are evaluating the pH dependence of the liquid structure of aqueous solutions of the eye lens protein, gammaB crystallin, near its critical point for liquid-liquid phase separation, to help evaluate the influence of protein charge on the phase separation. We have obtained small-angle neutron scattering data from gammaB crystallin solutions at pH 6.4, 7.1 and 7.4 in a 0.1 M sodium phosphate buffer, and at pH 4.5 in a 0.020M sodium acetate buffer, all in D2O. Protein concentrations ranged from 6 to 260 mg protein/ml solution and the scattering vector magnitude (q) ranged from 0.004 to 0.45 inverse Angstroms. At pH 6.4 to 7.4 liquid structure factors vs. concentration and temperature near the cloud point for liquid-liquid phase separation are well represented, in general, by the Baxter sticky sphere model. In contrast, at pH 4.5, concentrated gammaB shows a very different liquid structure indicating highly repulsive interprotein interactions, consistent with both high net protein charge and reduced screening.

  3. Synthesis, Solution and Solid State Structure of Titanium-Maltol Complex

    PubMed Central

    Lamboy, José L.; Pasquale, Antonio; Rheingold, Arnold. L.; Meléndez, Enrique

    2007-01-01

    The reaction of Cp2TiCl2 with two equivalents of maltol (3-hydroxy-2-methyl-4-pyrone) in water, at room temperature and pH of 5.4, leads to a complete replacement of Cp and chloride ligands affording, Ti(maltolato)2(OH)2. The complex has been characterized by IR, NMR and ESI-MS spectroscopic and cyclic voltammetry methods. In DMSO-d6 solution, the complex shows two isomers in a ratio of 4:1, in which one OH signal can be identified per isomer. This suggests that in solution the complex is monomeric, most likely a chiral cis-Ti(maltolato)2(OH)2 and trans-Ti(maltolato)2(OH)2. The monomeric nature of the complex (in water/methanol 1:1) was verified by ESI-MS spectroscopy, showing a parent peak at 329 m/z. Electrochemical behavior of Ti(maltolato)2(OH)2 using cyclic voltammetry experiments showed the complex undergoes irreversible reduction in aprotic solvents. In D2O solution, at pH of 8.4, the 1H NMR spectrum of the complex shows a mixture of monomer and tetramer Ti(IV)-maltol complexes in a ratio of 1:1. The crystallization of Ti(maltolato)2(OH)2 at pH of 8.4 leads to the formation of [Ti4(maltolato)8(μ-O4)]•18H2O. A single crystal of [Ti4(maltolato)8(μ-O4)]•18H2O was analyzed by X-ray diffraction methods. The complex crystallizes in a monoclinic space group P2(1)/c with a = 12.617(4) Å, b = 24.058(8) Å, c = 22.686(7) Å, β= 97.678(4)° and V = 6824(4) Å3 for Z = 4. Solid state structure determination of the Ti-maltol complex showed to be tetrameric, containing two bridging oxides (in cis position) and two bidentate maltol ligands per titanium in a pseudo-octahedral coordination geometry. PMID:18425211

  4. An autonomous structural health monitoring solution

    NASA Astrophysics Data System (ADS)

    Featherston, Carol A.; Holford, Karen M.; Pullin, Rhys; Lees, Jonathan; Eaton, Mark; Pearson, Matthew

    2013-05-01

    Combining advanced sensor technologies, with optimised data acquisition and diagnostic and prognostic capability, structural health monitoring (SHM) systems provide real-time assessment of the integrity of bridges, buildings, aircraft, wind turbines, oil pipelines and ships, leading to improved safety and reliability and reduced inspection and maintenance costs. The implementation of power harvesting, using energy scavenged from ambient sources such as thermal gradients and sources of vibration in conjunction with wireless transmission enables truly autonomous systems, reducing the need for batteries and associated maintenance in often inaccessible locations, alongside bulky and expensive wiring looms. The design and implementation of such a system however presents numerous challenges. A suitable energy source or multiple sources capable of meeting the power requirements of the system, over the entire monitoring period, in a location close to the sensor must be identified. Efficient power management techniques must be used to condition the power and deliver it, as required, to enable appropriate measurements to be taken. Energy storage may be necessary, to match a continuously changing supply and demand for a range of different monitoring states including sleep, record and transmit. An appropriate monitoring technique, capable of detecting, locating and characterising damage and delivering reliable information, whilst minimising power consumption, must be selected. Finally a wireless protocol capable of transmitting the levels of information generated at the rate needed in the required operating environment must be chosen. This paper considers solutions to some of these challenges, and in particular examines SHM in the context of the aircraft environment.

  5. Structure of void space in polymer solutions.

    PubMed

    Sung, Bong June; Yethiraj, Arun

    2010-03-01

    The structure of void space in two- and three-dimensional (3D) polymer solutions is studied using Voronoi tessellation and percolation theory. The polymer molecules are modeled as freely jointed chains of N tangent hard disks (two dimensions) or spheres (three dimensions). Polymer chains are equilibrated via Monte Carlo simulations and the pore space in configurations of equilibrated chains is mapped using Voronoi tessellation. In d dimensions a Voronoi vertex is the center of the sphere tangent to the d+1 nearest monomers. An edge of the Voronoi diagram is the shortest route between two neighboring vertices. The edge is considered connected if a monomer can pass through and disconnected otherwise. The Voronoi construction is used to calculate the percolation threshold of the void space. The most interesting result is that the polymer area fraction at the percolation threshold is a nonmonotonic function of N in two dimensions but monotonically reaches a constant value in three dimensions. The crossover behavior of the percolation threshold is also observed in pseudo-3D. The pore size distribution decreases monotonically with increasing pore size. This is markedly different from that in configurations of hard disks (monomeric fluid) where the pore size distribution is peaked at finite size. PMID:20365759

  6. High resolution spectroscopy of the Ar-D2O and Ar-HDO molecular complexes in the near-infrared range.

    PubMed

    Didriche, K; Földes, T

    2013-03-14

    Three rovibrational bands of Ar-D2O and two rovibrational bands of Ar-HDO were observed in the 1.5 μm range by continuous wave cavity ringdown spectroscopy. Their analyses led to the determination of rotational constants for the upper states and vibrational shifts indicating that the potential energy surface is only slightly affected by the vibrational excitation. Some Coriolis couplings were identified. The observed lines were fitted to retrieve a 3.5 ns lifetime of the upper state, showing that even with a triple or double excitation quanta in the water subunit, the Ar-D2O and Ar-HDO complexes are long-lived species. PMID:23514489

  7. The bond-forming reaction between CF22+ and H2O/D2O: A computational and experimental study

    NASA Astrophysics Data System (ADS)

    Lambert, Natalie; Kaltsoyannis, Nikolas; Price, Stephen D.

    2003-07-01

    Ground-state stationary points on the potential energy surface of the reaction CF22++H2O→OCF++HF+H+ were calculated using the density-functional theory hybrid method B3LYP and the ab initio coupled cluster singles and doubles with perturbative triples [CCSD(T)] algorithm. The calculations reveal a reaction mechanism involving two transition states. The first transition state involves the migration of one hydrogen within the primary collision complex and the second corresponds to the loss of a proton. The neutral HF molecular product is formed in its stable ground 1Σ state. Comparison of activation energies for the reactions of CF22+ with H2O and with D2O, calculated from Becke three parameter Lee-Yang-Parr (B3LYP) zero-point energies, slightly favor the H2O pathway by 0.04 and 0.07 eV for the first and second activations, respectively. Rate constant calculations using Rice-Ramsperger-Kassel-Marcus/quasiequilibrium theory also kinetically favor the H2O pathway in comparison with the D2O pathway. However, the magnitudes of the calculated rate constants are so large (1012-1014 s-1) that the differences between the rates of reaction of CF22+ with H2O and with D2O should not be distinguished by a crossed-beam time-of-flight mass spectrometer experiment. Indeed, the ion yields reported in this paper from new collision experiments between CF22+ and D2O showed no isotope effect when compared with previous data from collisions of CF22+ with H2O.

  8. Theory for Surface Structure of Electrolyte Solutions.

    NASA Astrophysics Data System (ADS)

    Nichols, Albert Loyd, III

    A theory is developed for the salt concentration profile and ion-ion correlations near surfaces of electrolyte solutions. We use the random phase approximation to study the primitive surface model employed by Onsager and Samaras, and others. In this model the chief technical complication is the correct treatment of image forces. We invent an exact rearrangement of the mathematical formulation of the problem which makes especially transparent the special case solutions (infinite dielectric constant mismatch) previously found. This reformulation guides an analytical solution for arbitrary dielectric constant mismatch between the two phases, subject to other assumptions adopted by previous workers. Similarly general results are derived for mixtures of ionic and dipolar solutes. These general results form the basis for extending our theoretical studies in several new directions. First, higher concentration corrections are investigated. It is shown that over an experimentally significant range of low concentrations for aqueous solutions the initial concentration correction to the Onsager-Samaras absorption has a negative definite sign. The theory, including concentration corrections, is compared to available computer simulation data, and close agreement is found for aqueous solutions below a few tenths molar. Second, the theory is developed to treat asymmetric electrolytes, and applied to ionic surfactants spread on water-hydrocarbon interfaces. Again, the theory accurately describes available experimental data. Third, the theory is broadened to acknowledge the solubility of the salt in both phases. It is found that this generalization changes the qualitative nature of the low concentration limiting law for the excess surface tension: the limiting behavior is changed from the (rho)ln(rho) dependence predicted by Onsager and Samaras to a more generally correct (rho)(' 1/2) dependence. Experimental data which might test this (rho)(' 1/2) behavior are not presently

  9. WAXS studies of the structural diversity of hemoglobin in solution.

    SciTech Connect

    Makowski, L.; Bardhan, J.; Gore, D.; Lal, J.; Mandava, S.; Park, S.; Rodi, D. J.; Ho, N. T.; Ho, C.; Fischetti, R. F.

    2011-01-01

    Specific ligation states of hemoglobin are, when crystallized, capable of taking on multiple quaternary structures. The relationship between these structures, captured in crystal lattices, and hemoglobin structure in solution remains uncertain. Wide-angle X-ray solution scattering (WAXS) is a sensitive probe of protein structure in solution that can distinguish among similar structures and has the potential to contribute to these issues. We used WAXS to assess the relationships among the structures of human and bovine hemoglobins in different liganded forms in solution. WAXS data readily distinguished among the various forms of hemoglobins. WAXS patterns confirm some of the relationships among hemoglobin structures that have been defined through crystallography and NMR and extend others. For instance, methemoglobin A in solution is, as expected, nearly indistinguishable from HbCO A. Interestingly, for bovine hemoglobin, the differences between deoxy-Hb, methemoglobin and HbCO are smaller than the corresponding differences in human hemoglobin. WAXS data were also used to assess the spatial extent of structural fluctuations of various hemoglobins in solution. Dynamics has been implicated in allosteric control of hemoglobin, and increased dynamics has been associated with lowered oxygen affinity. Consistent with that notion, WAXS patterns indicate that deoxy-Hb A exhibits substantially larger structural fluctuations than HbCO A. Comparisons between the observed WAXS patterns and those predicted on the basis of atomic coordinate sets suggest that the structures of Hb in different liganded forms exhibit clear differences from known crystal structure.

  10. A spectroscopic study on the coordination and solution structures of the interaction systems between biperoxidovanadate complexes and the pyrazolylpyridine-like ligands.

    PubMed

    Yu, Xian-Yong; Deng, Lin; Zheng, Baishu; Zeng, Bi-Rong; Yi, Pinggui; Xu, Xin

    2014-01-28

    In order to understand the substitution effects of pyrazolylpyridine (pzpy) on the coordination reaction equilibria, the interactions between a series of pzpy-like ligands and biperoxidovanadate ([OV(O2)2(D2O)](-)/[OV(O2)2(HOD)](-), abbrv. bpV) have been explored using a combination of multinuclear ((1)H, (13)C, and (51)V) magnetic resonance, heteronuclear single quantum coherence (HSQC), and variable temperature NMR in a 0.15 mol L(-1) NaCl D2O solution that mimics the physiological conditions. Both the direct NMR data and the equilibrium constants are reported for the first time. A series of new hepta-coordinated peroxidovanadate species [OV(O2)2L](-) (L = pzpy-like chelating ligands) are formed due to several competitive coordination interactions. According to the equilibrium constants for products between bpV and the pzpy-like ligands, the relative affinity of the ligands is found to be pzpy > 2-Ester-pzpy ≈ 2-Me-pzpy ≈ 2-Amide-pzpy > 2-Et-pzpy. In the interaction system between bpV and pzpy, a pair of isomers (Isomers A and B) are observed in aqueous solution, which are attributed to different types of coordination modes between the metal center and the ligands, while the crystal structure of NH4[OV(O2)2(pzpy)]·6H2O (CCDC 898554) has the same coordination structure as Isomer A (the main product for pzpy). For the N-substituted ligands, however, Isomer A or B type complexes can also be observed in solution but the molar ratios of the isomer are reversed (i.e., Isomer B type is the main product). These results demonstrate that when the N atom in the pyrazole ring has a substitution group, hydrogen bonding (from the H atom in the pyrazole ring), the steric effect (from alkyl) and the solvation effect (from the ester or amide group) can jointly affect the coordination reaction equilibrium. PMID:24213652

  11. pH and concentration dependence of the optical properties of thiol-capped CdTe nanocrystals in water and D2O.

    PubMed

    Schneider, R; Weigert, F; Lesnyak, V; Leubner, S; Lorenz, T; Behnke, T; Dubavik, A; Joswig, J-O; Resch-Genger, U; Gaponik, N; Eychmüller, A

    2016-07-28

    The optical properties of semiconductor nanocrystals (SC NCs) are largely controlled by their size and surface chemistry, i.e., the chemical composition and thickness of inorganic passivation shells and the chemical nature and number of surface ligands as well as the strength of their bonds to surface atoms. The latter is particularly important for CdTe NCs, which - together with alloyed CdxHg1-xTe - are the only SC NCs that can be prepared in water in high quality without the need for an additional inorganic passivation shell. Aiming at a better understanding of the role of stabilizing ligands for the control of the application-relevant fluorescence features of SC NCs, we assessed the influence of two of the most commonly used monodentate thiol ligands, thioglycolic acid (TGA) and mercaptopropionic acid (MPA), on the colloidal stability, photoluminescence (PL) quantum yield (QY), and PL decay behavior of a set of CdTe NC colloids. As an indirect measure for the strength of the coordinative bond of the ligands to SC NC surface atoms, the influence of the pH (pD) and the concentration on the PL properties of these colloids was examined in water and D2O and compared to the results from previous dilution studies with a set of thiol-capped Cd1-xHgxTe SC NCs in D2O. As a prerequisite for these studies, the number of surface ligands was determined photometrically at different steps of purification after SC NC synthesis with Ellman's test. Our results demonstrate ligand control of the pH-dependent PL of these SC NCs, with MPA-stabilized CdTe NCs being less prone to luminescence quenching than TGA-capped ones. For both types of CdTe colloids, ligand desorption is more pronounced in H2O compared to D2O, underlining also the role of hydrogen bonding and solvent molecules. PMID:27357335

  12. Solution structure of oxidized Saccharomyces cerevisiae iso-1-cytochrome c.

    PubMed

    Banci, L; Bertini, I; Bren, K L; Gray, H B; Sompornpisut, P; Turano, P

    1997-07-22

    The solution structure of oxidized Saccharomycescerevisiae Cys102Ser iso-1-cytochromechas been determined using 1361 meaningful NOEs (of 1676 total) after extending the published proton assignment [Gao, Y., et al. (1990) Biochemistry 29, 6994-7003] to 77% of all proton resonances. The NOE patterns indicate that secondary structure elements are maintained upon oxidation in solution with respect to the solid state and solution structures of the reduced species. Constraints derived from the pseudocontact shifts [diamagnetic reference shift values are those of the reduced protein [Baistrocchi, P., et al. (1996) Biochemistry 35, 13788-13796

  13. Differences in the Vibrational Dynamics of H2O and D2O: Observation of Symmetric and Antisymmetric Stretching Vibrations in Heavy Water.

    PubMed

    De Marco, Luigi; Carpenter, William; Liu, Hanchao; Biswas, Rajib; Bowman, Joel M; Tokmakoff, Andrei

    2016-05-19

    Water's ability to donate and accept hydrogen bonds leads to unique and complex collective dynamical phenomena associated with its hydrogen-bond network. It is appreciated that the vibrations governing liquid water's molecular dynamics are delocalized, with nuclear motion evolving coherently over the span of several molecules. Using two-dimensional infrared spectroscopy, we have found that the nuclear motions of heavy water, D2O, are qualitatively different than those of H2O. The nonlinear spectrum of liquid D2O reveals distinct O-D stretching resonances, in contrast to H2O. Furthermore, our data indicates that condensed-phase O-D vibrations have a different character than those in the gas phase, which we understand in terms of weakly delocalized symmetric and antisymmetric stretching vibrations. This difference in molecular dynamics reflects the shift in the balance between intra- and intermolecular couplings upon deuteration, an effect which can be understood in terms of the anharmonicity of the nuclear potential energy surface. PMID:27115316

  14. Solution Structure and Backbone Dynamics of Streptopain

    PubMed Central

    Wang, Chih-Chieh; Houng, Hsiang-Chee; Chen, Chun-Liang; Wang, Pei-Ju; Kuo, Chih-Feng; Lin, Yee-Shin; Wu, Jiunn-Jong; Lin, Ming T.; Liu, Ching-Chuan; Huang, Wenya; Chuang, Woei-Jer

    2009-01-01

    Streptococcal pyrogenic exotoxin B (SPE B) is a cysteine protease expressed by Streptococcus pyogenes. The D9N, G163S, G163S/A172S, and G239D mutant proteins were expressed to study the effect of the allelic variants on their protease activity. In contrast to other mutants, the G239D mutant was ∼12-fold less active. The Gly-239 residue is located within the C-terminal S230-G239 region, which cannot be observed in the x-ray structure. The three-dimensional structure and backbone dynamics of the 28-kDa mature SPE B (mSPE B) were determined. Unlike the x-ray structure of the 40-kDa zymogen SPE B (proSPE B), we observed the interactions between the C-terminal loop and the active site residues in mSPE B. The structural differences between mSPE B and proSPE B were the conformation of the C-terminal loop and the orientation of the catalytic His-195 residue, suggesting that activation and inactivation of SPE B is involved in the His-195 side-chain rotation. Dynamics analysis of mSPE B and the mSPE B/inhibitor complexes showed that the catalytic and C-terminal loops were the most flexible regions with low order parameter values of 0.5 to 0.8 and exhibited the motion on the ps/ns timescale. These findings suggest that the flexible C-terminal loop of SPE B may play an important role in controlling the substrate binding, resulting in its broad substrate specificity. PMID:19237546

  15. Conformation of Oligo(Ethylene Glycol) grafted Poly(Norbornene) in solutions: A Small Angle Neutron Scattering Study

    SciTech Connect

    Cheng, Gang; Melnichenko, Yuri B; Hua, Fengjun; Hong, Kunlun; Wignall, George D; Hammouda, B.; Mays, Jimmy

    2008-01-01

    The structure of thermo sensitive poly(methoxyoligo(ethylene glycol) norbornenyl esters) homopolymers in dilute solution was investigated by Small Angle Neutron Scattering (SANS). The homopolymers consist of a polynorbornene (PNB) backbone with a degree of polymerization (DP) of 50, and each backbone monomer has a grafted Ethylene Glycol (EG) side chain with an average DP of 6.6. The hydrophobic backbone and hydrophilic side chains interact differently with solvents depending on their polarity, which makes the conformation very sensitive to the solvent quality. The polymer conformation was studied in two solvents, d-toluene and D2O, with the aim of understanding the influence of solvent/polymer interactions on the resulting structures. It was found that in a 0.5 wt. % solution in d-toluene the polymers assume wormlike chains and gradually contract with increasing polymer concentration. In a 0.5 wt. % solution in D2O, the polymers are partially contracted at room temperature and their conformation can be described by the form factor of a rigid cylinder. The volume of the cylinder shows no concentration dependence. Furthermore, the polymers in D2O collapse at higher temperatures due to decreasing solubility of the side chains in water.

  16. Discovery of Water Structural Transitions near Interfaces of Polarizable Solutes

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Matyushov, Dmitry

    2015-03-01

    The standard harmonic approximation describing polarization around the solute is expected to break down with increasing solute polarizability. The focus of this study is to investigate the structure of water around dipolar-polarizable solutes by Monte Carlo (MC) simulations in the non-harmonic regime. We observe a structural transition in the water hydration shell and its condensation, which are driven by increasing the solute polarizability. There is also a crossover in the orientational structure near the point of breakdown of the harmonic approximation. At lower polarizabilities, waters in the hydration shell point their hydrogens toward the solute. The dipoles flip their orientations at the transition to the non-harmonic regime. Both the hydration shell compressibility and the electric field susceptibility display maxima in the transition region. Using the water electric field at the center of the polarizable solute as the order parameter, a Landau-type model is formulated. Its predictions are in reasonable agreement with MC simulations performed for hard sphere and Lennard Jones polarizable solutes in a TIP3P water model. The observed structural transition suggests a general crossover phenomenon driven by the stabilization energy required to polarize the solute. This research was supported by the National Science Foundation (CHE-1213288). CPU time was provided by the National Science Foundation through XSEDE resources (TG-MCB080116N).

  17. Complexation of Actinides in Solution: Thermodynamic Measurementsand Structural Characterization

    SciTech Connect

    Rao, L.

    2007-02-01

    This paper presents a brief introduction of the studies of actinide complexation in solution at Lawrence Berkeley National Laboratory. An integrated approach of thermodynamic measurements and structural characterization is taken to obtain fundamental understanding of actinide complexation in solution that is of importance in predicting the behavior of actinides in separation processes and environmental transport.

  18. Energy Structure of Emission Centers in Solutions with Silver Impurity

    NASA Astrophysics Data System (ADS)

    Zashivailo, T. V.; Kushnirenko, V. I.

    The spectral properties of solutions of oxygen-containing salts and acids with admixture of Аg+ ions were studied. The spectra of absorption, photoluminescence, and photoluminescence excitation for such systems are measured in the temperature range of 4.2-290 K. The energy structure of absorption and emission centers in the solution was determined. It is shown that the spectra under study are caused by the electron transitions between the energy levels, whose structure is deformed as a result of the interaction of ions Ag+ with the environment. The experimental results are interpreted on the basis of an ionic model for complexes for investigated solutions.

  19. Neutron Diffraction of Aqueous Tetramethylammonium Chloride (TMA) Solutions and TMA Intercalated Swelling Clays Under Burial Conditions

    NASA Astrophysics Data System (ADS)

    Patel, R.; Howard, C. A.; Greenwell, C.; Youngs, T.; Soper, A. K.; Skipper, N. T.

    2014-12-01

    There is a need for the improvement and optimisation of clay swelling inhibitors for the enhancement of oil and gas exploration. The hydration region of both ions and the possibility of ion pairing in 1 molar aqueous solution of clay swelling inhibitor, tetramethylammonium chloride (TMACl), in D2O, under elevated hydrostatic-pressures and temperatures has been determined with unprecedented detail using a combination of neutron diffraction and small-angle scattering in conjunction with hydrogen/deuterium isotopic labeling. The O-H correlation function (H-bonds) for the water in the 1.0M solution is measured and compared with that for pure D2O. Also investigated is the effect of burial conditions on the d-spacing of TMA-intercalated vermiculite. Contrary to expectations, no aggregation of TMA ions due to hydrophobic interactions is observed, nor are any ionic pairs of TMA+ and Cl- at these burial conditions. The data revealed a more ordered water-water structure with the addition of TMACl from bulk D2O. There is no change in the hydration structure measured at the applied elevated conditions. This is in remarkable contrast to pure water at the same conditions which is well known to be compressible. The dry d-spacing of the TMA-exchanged Eucatex vermiculite is measured at 13.66 Å which increases to 14.03 Å with the addition of D2O. Beyond this, there is no change in d-spacing with increasing pressure and temperature indicating the strength of the TMA ions binding to the clay interlayers and therefore its performance as a clay-swelling inhibitor.

  20. A validation of the application of D(2)O stable isotope tracer techniques for monitoring day-to-day changes in muscle protein subfraction synthesis in humans.

    PubMed

    Wilkinson, Daniel J; Franchi, Martino V; Brook, Matthew S; Narici, Marco V; Williams, John P; Mitchell, William K; Szewczyk, Nathaniel J; Greenhaff, Paul L; Atherton, Philip J; Smith, Kenneth

    2014-03-01

    Quantification of muscle protein synthesis (MPS) remains a cornerstone for understanding the control of muscle mass. Traditional [(13)C]amino acid tracer methodologies necessitate sustained bed rest and intravenous cannulation(s), restricting studies to ~12 h, and thus cannot holistically inform on diurnal MPS. This limits insight into the regulation of habitual muscle metabolism in health, aging, and disease while querying the utility of tracer techniques to predict the long-term efficacy of anabolic/anticatabolic interventions. We tested the efficacy of the D2O tracer for quantifying MPS over a period not feasible with (13)C tracers and too short to quantify changes in mass. Eight men (22 ± 3.5 yr) undertook one-legged resistance exercise over an 8-day period (4 × 8-10 repetitions, 80% 1RM every 2nd day, to yield "nonexercised" vs. "exercise" leg comparisons), with vastus lateralis biopsies taken bilaterally at 0, 2, 4, and 8 days. After day 0 biopsies, participants consumed a D2O bolus (150 ml, 70 atom%); saliva was collected daily. Fractional synthetic rates (FSRs) of myofibrillar (MyoPS), sarcoplasmic (SPS), and collagen (CPS) protein fractions were measured by GC-pyrolysis-IRMS and TC/EA-IRMS. Body water initially enriched at 0.16-0.24 APE decayed at ~0.009%/day. In the nonexercised leg, MyoPS was 1.45 ± 0.10, 1.47 ± 0.06, and 1.35 ± 0.07%/day at 0-2, 0-4, and 0-8 days, respectively (~0.05-0.06%/h). MyoPS was greater in the exercised leg (0-2 days: 1.97 ± 0.13%/day; 0-4 days: 1.96 ± 0.15%/day, P < 0.01; 0-8 days: 1.79 ± 0.12%/day, P < 0.05). CPS was slower than MyoPS but followed a similar pattern, with the exercised leg tending to yield greater FSRs (0-2 days: 1.14 ± 0.13 vs. 1.45 ± 0.15%/day; 0-4 days: 1.13 ± 0.07%/day vs. 1.47 ± 0.18%/day; 0-8 days: 1.03 ± 0.09%/day vs. 1.40 ± 0.11%/day). SPS remained unchanged. Therefore, D2O has unrivaled utility to quantify day-to-day MPS in humans and inform on short-term changes in anabolism and

  1. High-energy diode-pumped D2O-cooled multislab Yb:YAG and Yb:QX-glass lasers.

    PubMed

    Siebold, Mathias; Loeser, Markus; Harzendorf, Gunter; Nehring, Harald; Tsybin, Igor; Roeser, Fabian; Albach, Daniel; Schramm, Ulrich

    2014-06-15

    We investigated the lasing performance of a multislab Yb:QX and Yb:YAG laser amplifiers using a facet-cooled design. Di-deuterium oxide (D2O) was used as the coolant flowing between the active slabs with the pump and laser light passing through the very low absorbing heavy-water films. A square pump profile at a maximum intensity of 40  kW/cm2 drove the amplifier with a peak fluence of 5.5  J/cm2 and a pulse duration of 6 ns. We demonstrated a maximum pulse energy of 1 J for each gain medium as well as a repetition rate of 10 Hz for Yb:YAG and 1 Hz for Yb:QX glass, thus showing the feasibility and scalability of directly water-cooled, diode-pumped, high-energy short-pulse lasers. PMID:24978549

  2. Quantum Local Monomer IR Spectrum of Liquid D2O at 300 K from 0 to 4000 cm(-1) Is in Near-Quantitative Agreement with Experiment.

    PubMed

    Liu, Hanchao; Wang, Yimin; Bowman, Joel M

    2016-03-17

    The local monomer model is applied, with ab initio potential energy and dipole moment surfaces, to a calculation of the IR spectrum of liquid D2O at 300 K, over the spectral range 0 to 4000 cm(-1). The spectrum is an incoherent superposition of spectra of many monomers over snapshots of a molecular dynamics trajectory, where both intramolecular and intermolecular coupling in each monomer is treated. The comparison to experiment shows an unprecedented level of agreement for the stretch, bend, and libration bands and also the bend+libration and stretch+bend combination bands. This indicates that the incoherent approach captures much of the dynamics underlying the spectrum, provided monomer couplings are considered. The calculated spectrum is compared to the recently calculated IR spectrum of H2O, using the same method and potential energy and dipole moment surfaces, and shifts relative to that spectrum are presented and discussed. PMID:26906967

  3. In situ ATR-FTIR study of H2O and D2O adsorption on TiO2 under UV irradiation.

    PubMed

    Belhadj, Hamza; Hakki, Amer; Robertson, Peter K J; Bahnemann, Detlef W

    2015-09-21

    The adsorption of water and deuterium oxide on TiO2 surfaces was investigated in the dark as well as under UV(A) irradiation using in situ ATR-FTIR spectroscopy under oxygen and oxygen free conditions. Adsorption of H2O-D2O mixtures revealed an isotopic exchange reaction occurring onto the surface of TiO2 in the dark. Under UV(A) irradiation, the amount of both OH and OD groups was found to be increased by the presence of molecular oxygen. Furthermore, the photocatalytic formation of hydroperoxide under oxygenated condition has been recorded utilizing Attenuated Total Reflection Fourier Transformed Infrared (ATR-FTIR) spectroscopy which appeared as new band at 3483 cm(-1). Different possible mechanisms are discussed in terms of the source of hydroxyl groups formed and/or hydration water on the TiO2 surface for the photocatalytic reaction and photoinduced hydrophilicity. PMID:26266701

  4. Chain dimensions in free and immobilized brush states of polysulfobetaine in aqueous solution at various salt concentrations

    NASA Astrophysics Data System (ADS)

    Terayama, Y.; Arita, H.; Ishikawa, T.; Kikuchi, M.; Mitamura, K.; Kobayashi, M.; Yamada, N. L.; Takahara, A.

    2011-01-01

    The chain dimensions of free and immobilized polysulfobetaine in aqueous solution at various salt concentrations were investigated by size-exclusion chromatography with multiangle light scattering and neutron reflectivity measurement, respectively. The dependence of the z-average mean square radius of gyration (z1/2) on the weight-average molecular weight (Mw) of free poly(3-(N-2-methacryloyloxyethyl-N,N-dimethyl)ammonatopropanesulfo-nate) (MAPS) in aqueous solution at salt concentrations of 74, 100, 200, and 500 mM was described by the perturbed wormlike chain model using the chain stiffness parameter λ-1 the molar mass per unit contour length ML, and the excluded volume effect B. B increased from 0 to 1.8 nm with increasing salt concentration to 500 mM due to the screening of attractive electrostatic interaction between ammonium cations and sulfonyl anions by salt ions. The swollen structure of the poly(MAPS) brush in D2O changed from a shrunken state to a relatively extended state with increasing salt concentration from 0 to 500 mM NaCl/D2O solution. The thickness of the swollen poly(MAPS) brush in 500 mM NaCl/D2O was 9.0 times greater than 2z1/2 of free poly(MAPS) due to high osmotic pressure generated by the excluded volume effect of densely grafted polymer chains.

  5. Hydrogen-deuterium exchange reactions of cis- and trans-cyclopropane derivatives with D(2)O and CD(3)OD in the gas phase

    PubMed

    Li; Liu

    2000-01-01

    Gas-phase hydrogen-deuterium (H/D) exchange reactions involving four isomeric cyclopropane derivatives were investigated under chemical ionization (CI) conditions, using D(2)O and CD(3)OD as reagent gases. There are abundant ions at [M + 1](+), [M + 2](+) and [M + 3](+) in the D(2)O and CD(3)OD positive-ion CI mass spectra of the two isomer pairs 1, 2 and 3, 4. Their CI mass spectra are identical with each pair, and so are the collision-induced dissociation (CID) spectra of ions [M + 1](+), [M + 2](+) and [M + 3](+) of each of the two isomer pairs. The CID spectra of [M + 1](+) ions indicate that they have common D/H exchange reactions within each pair, which take place between molecular ions and deuterium-labeling reagents to form the [M - H + D](+) ions. Those of their [M + 2](+) ions show that they have common D/H exchange reactions within each pair, which form the [M(d1) + H](+) ions. Those of their [M + 3](+) ions show that they have common D/H exchange reactions within each pair, which take place between the [M(d1)] and deuterium-labeling reagents to produce [M(d2) + H](+) for the isomer pair 1, 2 and [M(d1) + D](+) for the isomer pair 3, 4. The number and position, and active order of the active hydrogen atoms of the isomer pairs 1, 2 and 3, 4 were determined. Copyright 2000 John Wiley & Sons, Ltd. PMID:10637425

  6. Molecular Ornstein-Zernike approach to the solvent effects on solute electronic structures in solution

    NASA Astrophysics Data System (ADS)

    Yoshida, Norio; Kato, Shigeki

    2000-09-01

    A new approach to ab initio electronic structure calculations of solute molecules in solution is presented. Combined with the molecular Ornstein-Zernike (MOZ) integral equation theory for polyatomic liquids, solute electronic wave function and solvent distribution around a solute are determined in a self-consistent manner. The hypernetted chain approximation is employed for solving the MOZ equation. In order to describe the short-range solute-solvent interactions, the effective potential operating solute electron is placed on a solute molecule, which is determined by a least-squares fitting to ab initio exchange repulsion/charge transfer energies. The present method, referred to as the MOZ self-consistent-field (SCF) method, is applied to a solute H2O molecule in water solvent. The solvent shift for the vertical excitation to the nπ* state of H2CO in aqueous solution is also examined. The results obtained by the MOZ-SCF calculations are compared with those by the reference interaction site model-SCF theory and the polarizable continuum model.

  7. [Structure and Activity of Fungal Lipases in Bile Salt Solutions].

    PubMed

    Bogdanova, L R; Bakirova, D R; Valiullina, Yu A; Idiyatullin, B Z; Faizullin, D A; Zueva, O S; Zuev, Yu F

    2016-01-01

    The changes in structure and catalytic properties of fungal lipases (Candida rugosa, Rhizomucor miehei, Mucor javanicus) were investigated in micellar solutions of bile salts that differ in hydrophilic-lypophilic balance and reaction medium properties. The methods of circular dichroism and tryptophan fluorescence were applied to estimate the changes in peptide structure within complexes with bile salt micelles. Bile salts do not exert a significant influence on the structure of the enzymes under study: in Rh. miehei and M. javanicus lipases the alpha helix content slightly decreased, the influence of bile salts on the C. rugosa structure was not revealed. Despite negligible structural modifications in the enzymes, in bile salt solutions a considerable change in their catalytic properties was observed: an abrupt decrease in catalytic effectiveness. Substrate-bile salts micelles complex formation was demonstrated by the NMR self-diffusion method. The model of a regulation of fungal lipase activity was proposed. PMID:27192825

  8. Water's structure around hydrophobic solutes and the iceberg model.

    PubMed

    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. PMID:23360515

  9. Solution structure of ligands involved in purine salvage pathway.

    PubMed

    Karnawat, Vishakha; Puranik, Mrinalini

    2015-12-01

    Analogues of intermediates involved in the purine salvage pathway can be exploited as potential drug molecules against enzymes of protozoan parasites. To develop such analogues we need knowledge of the solution structures, predominant tautomer at physiological pH and protonation-state of the corresponding natural ligand. In this regard, we have employed ultraviolet resonance Raman spectroscopy (UVRR) in combination with density functional theory (DFT) to study the solution structures of two relatively unexplored intermediates, 6-phosphoryl IMP (6-pIMP) and succinyl adenosine-5'-monophosphate (sAMP), of purine salvage pathway. These molecules are intermediates in a two step enzymatic process that converts inosine-5'-monpophosphate (IMP) to adenosine-5'-monophosphate (AMP). Experimental data on the molecular structure of these ligands is lacking. We report UVRR spectra of these two ligands, obtained at an excitation wavelength of 260 nm. Using isotope induced shifts and DFT calculations we assigned observed spectra to computed normal modes. We find that sAMP exists as neutral species at physiological pH and the predominant tautomer in solution bears proton at N10 position of purine ring. Though transient in solution, 6-pIMP is captured in the enzyme-bound form. This work provides the structural information of these ligands in solution state at physiological pH. We further compare these structures with the structures of AMP and IMP. Despite the presence of similar purine rings in AMP and sAMP, their UVRR spectra are found to be very different. Similarly, though the purine ring in 6-pIMP resembles that of IMP, UVRR spectra of the two molecules are distinct. These differences in the vibrational spectra provide direct information on the effects of exocyclic groups on the skeletal structures of these molecules. Our results identify key bands in the vibrational spectra of these ligands which may serve as markers of hydrogen bonding interactions upon binding to the active

  10. General analytical shakedown solution for structures with kinematic hardening materials

    NASA Astrophysics Data System (ADS)

    Guo, Baofeng; Zou, Zongyuan; Jin, Miao

    2016-04-01

    The effect of kinematic hardening behavior on the shakedown behaviors of structure has been investigated by performing shakedown analysis for some specific problems. The results obtained only show that the shakedown limit loads of structures with kinematic hardening model are larger than or equal to those with perfectly plastic model of the same initial yield stress. To further investigate the rules governing the different shakedown behaviors of kinematic hardening structures, the extended shakedown theorem for limited kinematic hardening is applied, the shakedown condition is then proposed, and a general analytical solution for the structural shakedown limit load is thus derived. The analytical shakedown limit loads for fully reversed cyclic loading and non-fully reversed cyclic loading are then given based on the general solution. The resulting analytical solution is applied to some specific problems: a hollow specimen subjected to tension and torsion, a flanged pipe subjected to pressure and axial force and a square plate with small central hole subjected to biaxial tension. The results obtained are compared with those in literatures, they are consistent with each other. Based on the resulting general analytical solution, rules governing the general effects of kinematic hardening behavior on the shakedown behavior of structure are clearly.

  11. Processes of ordered structure formation in polypeptide thin film solutions.

    SciTech Connect

    Botiz, I.; Schlaad, H.; Reiter, G.

    2010-06-17

    An experimental study is presented on the hierarchical assembly of {alpha}-helical block copolymers polystyrene-poly({gamma}-benzyl-L-glutamate) into anisotropic ordered structures. We transformed thin solid films into solutions through exposure to solvent vapor and studied the nucleation and growth of ordered three-dimensional structures in such solutions, with emphasis on the dependence of these processes on supersaturation with respect to the solubility limit. Interestingly, polymer solubility could be significantly influenced via variation of humidity in the surrounding gas phase. It is concluded that the interfacial tension between the ordered structures and the solution increased with humidity. The same effect was observed for other protic non-solvents in the surrounding gas phase and is attributed to a complexation of poly({gamma}-benzyl-L-glutamate) by protic non-solvent molecules (via hydrogen-bonding interactions). This change of polymer solubility was demonstrated to be reversible by addition or removal of small amounts of protic non-solvent in the surrounding gas phase. At a constant polymer concentration, ordered ellipsoidal structures could be dissolved by removing water or methanol present in the solution. Such structures formed once again when water or methanol was reintroduced via the vapor phase.

  12. Solution Structures of Two Homologous Venom Peptides from Sicarius dolichocephalus

    PubMed Central

    Loening, Nikolaus M.; Wilson, Zachary N.; Zobel-Thropp, Pamela A.; Binford, Greta J.

    2013-01-01

    We present solution-state NMR structures for two putative venom peptides from Sicarius dolichocephalus. These peptides were identified from cDNA libraries created from venom gland mRNA and then recombinantly expressed. They are the first structures from any species of Sicarius spiders, and the first peptide structures for any haplogyne spiders. These peptides are homologous to one another, and while they have at most only 20% sequence identity with known venom peptides their structures follow the inhibitor cystine knot motif that has been found in a broad range of venom peptides. PMID:23342149

  13. Mixed Consolidation Solution for a Reinforced Concrete Structure

    NASA Astrophysics Data System (ADS)

    Lute, M.

    2016-06-01

    During the last years, reinforced concrete structures become subject for rehabilitation due to two factors: their long life span and large change in norms that leaded to a large increase of seismic loads in Eastern Europe. These lead to a necessity for rehabilitation of existing building stock in order to use them during their entire life span at the maximum potential. The present paper proposes a solution for rehabilitation for three reinforced concrete building of a hospital, that consumed a half of their life span and do not correspond anymore to present norms. The chosen solution is a combination between CFRP rehabilitation and increase of structural elements cross section in order to achieve the stiffness balance in the structure nodes that is required by present norms. As a further matter, correction in stiffness of local elements diminished the lateral drifts of the structure and improved the global seismic response of the building.

  14. Dealing with Multiple Solutions in Structural Vector Autoregressive Models.

    PubMed

    Beltz, Adriene M; Molenaar, Peter C M

    2016-01-01

    Structural vector autoregressive models (VARs) hold great potential for psychological science, particularly for time series data analysis. They capture the magnitude, direction of influence, and temporal (lagged and contemporaneous) nature of relations among variables. Unified structural equation modeling (uSEM) is an optimal structural VAR instantiation, according to large-scale simulation studies, and it is implemented within an SEM framework. However, little is known about the uniqueness of uSEM results. Thus, the goal of this study was to investigate whether multiple solutions result from uSEM analysis and, if so, to demonstrate ways to select an optimal solution. This was accomplished with two simulated data sets, an empirical data set concerning children's dyadic play, and modifications to the group iterative multiple model estimation (GIMME) program, which implements uSEMs with group- and individual-level relations in a data-driven manner. Results revealed multiple solutions when there were large contemporaneous relations among variables. Results also verified several ways to select the correct solution when the complete solution set was generated, such as the use of cross-validation, maximum standardized residuals, and information criteria. This work has immediate and direct implications for the analysis of time series data and for the inferences drawn from those data concerning human behavior. PMID:27093380

  15. Emerging applications of small angle solution scattering in structural biology

    PubMed Central

    Chaudhuri, Barnali N

    2015-01-01

    Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu. PMID:25516491

  16. Solution structure by site directed tryptophan fluorescence in tear lipocalin.

    PubMed

    Gasymov, O K; Abduragimov, A R; Yusifov, T N; Glasgow, B J

    1997-10-01

    The solution structure of the G strand of human tear lipocalin was deduced by site directed tryptophan fluorescence (SDTF). The fluorescent amino acid, tryptophan, was sequentially substituted for each native amino acid in the sequence of the G strand. The fluorescent properties resolved alternating periodicity as predicted for beta sheet structure, twists in the beta sheet, strand orientation in the lipocalin cavity, and the relative depth of residues in the cavity. A distribution of microstates with various orientations of dipoles in the side chain environments of the G strand revealed mobility on the nanosecond time scale. SDTF is broadly applicable to most proteins and will complement x-ray crystallography, site directed spin labeling by electron paramagnetic resonance (EPR), and nuclear magnetic resonance (NMR) in the determination of solution structure. PMID:9345294

  17. Structure and rheology of associative triblocks in microemulsion solutions

    NASA Astrophysics Data System (ADS)

    Bhatia, Surita Rani

    This thesis describes our theoretical and experimental work on the rheology, static structure, and phase behavior of associative solutions. Our theoretical efforts have centered on solving the diffusion equation model of Dolan and Edwards for ideal associative triblocks between surfaces to yield the segment density profile and free energy. We have shown that polymers between two spheres cause an O(kT) attraction, similar to that calculated by Milner and Witten for associative polymer brushes between flat plates. The attraction we calculate is weaker than that given by the Derjaguin approximation, and excluded volume moderates the attraction and softens the repulsion between spheres. The free energy was used to estimate an interparticle potential, which in turn was used to compute structure factors for solutions of associative polymers via Monte Carlo simulations. As a model system for our experiments, we have chosen PEO-PI-PEO triblocks in an AOT/water/decane microemulsion. Upon dilution with decane, the solutions phase separate into a dense, high viscosity phase and a dilute, low viscosity phase. We have performed both small-angle neutron scattering (SANS) and rheology on these solutions. Structure factors derived from our SANS data agree fairly well with those predicted by our theory and indicate that the droplets reside in an attractive minimum. The rheology of these solutions shows several interesting features that are not predicted by classical reversible network theory. Data from oscillatory experiments indicate a single relaxation time at low polymer concentrations but show evidence of a slower relaxation for higher concentrations. In addition, some solutions exhibit a maximum in the high shear viscosity. Some of our observations are predicted by the flowerlike micelle theory developed by Semenov and co-workers; however, our data is not completely consistent with the theoretical predictions. The high frequency modulus scales roughly quadratically with

  18. Structure of graphene oxide membranes in solvents and solutions

    NASA Astrophysics Data System (ADS)

    Klechikov, Alexey; Yu, Junchun; Thomas, Diana; Sharifi, Tiva; Talyzin, Alexandr V.

    2015-09-01

    The change of distance between individual graphene oxide sheets due to swelling is the key parameter to explain and predict permeation of multilayered graphene oxide (GO) membranes by various solvents and solutions. In situ synchrotron X-ray diffraction study shows that swelling properties of GO membranes are distinctly different compared to precursor graphite oxide powder samples. Intercalation of liquid dioxolane, acetonitrile, acetone, and chloroform into the GO membrane structure occurs with maximum one monolayer insertion (Type I), in contrast with insertion of 2-3 layers of these solvents into the graphite oxide structure. However, the structure of GO membranes expands in liquid DMSO and DMF solvents similarly to precursor graphite oxide (Type II). It can be expected that Type II solvents will permeate GO membranes significantly faster compared to Type I solvents. The membranes are found to be stable in aqueous solutions of acidic and neutral salts, but dissolve slowly in some basic solutions of certain concentrations, e.g. in NaOH, NaHCO3 and LiF. Some larger organic molecules, alkylamines and alkylammonium cations are found to intercalate and expand the lattice of GO membranes significantly, e.g. up to ~35 Å in octadecylamine/methanol solution. Intercalation of solutes into the GO structure is one of the limiting factors for nano-filtration of certain molecules but it also allows modification of the inter-layer distance of GO membranes and tuning of their permeation properties. For example, GO membranes functionalized with alkylammonium cations are hydrophobized and they swell in non-polar solvents.The change of distance between individual graphene oxide sheets due to swelling is the key parameter to explain and predict permeation of multilayered graphene oxide (GO) membranes by various solvents and solutions. In situ synchrotron X-ray diffraction study shows that swelling properties of GO membranes are distinctly different compared to precursor graphite

  19. Neutron Scattering Study of the S=1/2 Heisenberg AFM Chain Cu(C_6D_5COO)2 \\cdot 3D_2O

    NASA Astrophysics Data System (ADS)

    Dender, D. C.; Reich, D. H.; Broholm, C.; Lefmann, K.; Aeppli, G.

    1996-03-01

    Quasi-one-dimensional magnetic materials provide the opportunity to test rigorously models of simple, interacting many-body systems. We present triple-axis neutron scattering measurements of the temperature and magnetic field dependence of spin correlations in the quasi-1D S=1/2 Heisenberg antiferromagnet Cu(C_6D_5COO)2 \\cdot3D_2O. We have measured the temperature evolution of the spin-spin correlation length κ over the temperature range 0.1J < k_BT < 0.8J, where J is the nearest-neighbor coupling strength. Measurements of S^zz(q = π , ω , T) are found to be described by a finite temperature field theory.(H. J. Schulz, Phys. Rev. B 34), 6372 (1986). At high magnetic fields, new features are observed close to q=π consistent with predictions of non-classical behavior.(N. Ishimura and H. Shiba, Prog. Theor. Phys. Jpn. 57), 1862 (1977).^,(G. Müller, H. Thomas, H. Beck, and J. C. Bonner, Phys. Rev. B 24), 1429 (1981). ^*supported by NSF Grants DMR93-02065 and DMR94-53362, and by the David and Lucile Packard Foundation.

  20. Equation of state and phase transition of deuterated ammonia monohydrate (ND3.D2O) measured by high-resolution neutron powder diffraction up to 500 MPa

    NASA Astrophysics Data System (ADS)

    Fortes, A. Dominic; Suard, Emmanuelle; Lemée-Cailleau, Marie-Hélène; Pickard, Christopher J.; Needs, Richard J.

    2009-10-01

    We describe the results of a neutron powder diffraction study of perdeuterated ammonia monohydrate (AMH, ND3ṡD2O) carried out in the range 102

  1. Temporal Behavior of the Pump Pulses, Residual Pump Pulses, and THz Pulses for D2O Gas Pumped by a TEA CO2 Laser

    NASA Astrophysics Data System (ADS)

    Geng, Lijie; Zhang, Zhifeng; Zhai, Yusheng; Su, Yuling; Zhou, Fanghua; Qu, Yanchen; Zhao, Weijiang

    2016-08-01

    Temporal behavior of the pump pulses, residual pump pulses, and THz pulses for optically pumped D2O gas molecules was investigated by using a tunable TEA CO2 laser as the pumping source. The pulse profiles of pump laser pulses, residual pump pulses, and the THz output pulses were measured, simultaneously, at several different gas pressures. For THz pulse, the pulse delay between the THz pulse and the pump pulse was observed and the delay time was observed to increase from 40 to 70 ns with an increase in gas pressure from 500 to 1700 Pa. Both THz pulse broadening and compression were observed, and the pulse broadening effect transformed to the compression effect with increasing the gas pressure. For the residual pump pulse, the full width at half maximum (FWHM) of the main pulse decreased with increasing gas pressure, and the main pulse disappeared at high gas pressures. The secondary pulses were observed at high gas pressure, and the time intervals of about 518 and 435 ns were observed between the THz output pulse and the secondary residual pump pulse at the pressure of 1400 Pa and 1700 Pa, from which the vibrational relaxation time constants of about 5.45 and 5.55 μs Torr were obtained.

  2. Study of temperature effect on far-infrared spectra of liquid H2O and D2O by analytical theory and molecular dynamic simulations.

    PubMed

    Zasetsky, Alexander Y; Gaiduk, Vladimir I

    2007-06-28

    The results of a combined study of dielectric loss (epsilon"(nu)) and power-absorption coefficient (alpha(nu)) are reported. The epsilon"(nu) and alpha(nu) values are obtained for liquid water (H2O) and heavy water (D2O) using analytical modeling and the molecular dynamics (MD) simulations method. The calculated spectra span the microwave and far-infrared (FIR) region. The temperature range probed is 220-355 K. Appropriate parametrization of the analytical model for liquid water enables the quantitative description of the dielectric spectra over the frequency range of 0-1000 cm-1. An excellent agreement between the calculated spectra and the experimental data demonstrates the accuracy of the applied analytical approximations. The spectra obtained using the MD simulations agree rather qualitatively with the experimental epsilon"(nu) and alpha(nu) dependences. The observed spectra are interpreted in terms of four molecular mechanisms that have been recently described [J. Phys. Chem. A 2006, 110, 9361]. PMID:17552503

  3. Implantation of Energetic D+ Ions into Carbon Dioxide Ices and Implications for our Solar System: Formation of D2O and D2CO3

    NASA Astrophysics Data System (ADS)

    Bennett, Chris J.; Ennis, Courtney P.; Kaiser, Ralf I.

    2014-10-01

    Carbon dioxide (CO2) ices were irradiated with energetic D+ ions to simulate the exposure of oxygen-bearing solar system ices to energetic protons from the solar wind and magnetospheric sources. The formation of species was observed online and in situ by exploiting FTIR spectroscopy. Molecular products include ozone (O3), carbon oxides (CO3(C 2v , D 3h ), CO4, CO5, CO6), D2-water (D2O), and D2-carbonic acid (D2CO3). Species released into the gas phase were sampled via a quadrupole mass spectrometer, and possible minor contributions from D2-formaldehyde (D2CO), D4-methanol (CD3OD), and D2-formic acid (DCOOD) were additionally identified. The feasibility of several reaction networks was investigated by determining their ability to fit the observed temporal column densities of 10 key species that were quantified during the irradiation period. Directly relevant to the CO2-bearing ices of comets, icy satellites in the outer solar system, and the ice caps on Mars, this work illustrates for the first time that D2-water is formed as a product of the exposure of CO2 ices to D+ ions. These findings provide strong support for water formation from oxygen-bearing materials via non-thermal hydrogen atoms, and predict reaction pathways that are likely to be unfolding on the surfaces of asteroids and the Moon.

  4. Photodissociation of water. II. Wave packet calculations for the photofragmentation of H2O and D2O in the B˜ band

    NASA Astrophysics Data System (ADS)

    van Harrevelt, Rob; van Hemert, Marc C.

    2000-04-01

    A complete three-dimensional quantum mechanical description of the photodissociation of water in the B˜ band, starting from its rotational ground state, is presented. In order to include B˜-X˜ vibronic coupling and the B˜-Ã Renner-Teller coupling, diabatic electronic states have been constructed from adiabatic electronic states and matrix elements of the electronic angular momentum operators, following the procedure developed by A. J. Dobbyn and P. J. Knowles [Mol. Phys. 91, 1107 (1997)], using the ab initio results discussed in the preceding paper. The dynamics is studied using wave packet methods, and the evolution of the time-dependent wave function is discussed in detail. Results for the H2O and D2O absorption spectra, OH(A)/OH(X) and OD(A)/OD(X) branching ratios, and rovibrational distributions of the OH and OD fragments are presented and compared with available experimental data. The present theoretical results agree at least qualitatively with the experiments. The calculations show that the absorption spectrum and the product state distributions are strongly influenced by long-lived resonances on the adiabatic B˜ state. It is also shown that molecular rotation plays an important role in the photofragmentation process, due to both the Renner-Teller B˜-X˜ mixing, and the strong effect of out-of-plane molecular rotations (K>0) on the dynamics at near linear HOH and HHO geometries.

  5. Electronic structures of Ascaris trypsin inhibitor in solution

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    2003-11-01

    The electronic structures of Ascaris trypsin inhibitor in solution are obtained by the first-principles, all-electron, ab initio calculation using the self-consistent cluster-embedding (SCCE) method. The inhibitor, made up of 62 amino acid residues with 912 atoms, has two three-dimensional solution structures: 1ata and 1atb. The calculated ground-state energy of structure 1atb is lower than that of structure 1ata by 6.12 eV. The active sites are determined and explained: only structure 1atb has a N terminal at residue ARG+31. This shows that the structure 1atb is the stable and active form of the inhibitor, which is in agreement with the experimental results. The calculation reveals that some parts of the inhibitor can be easily changed while the inhibitor’s biological activity may be kept. This kind of information may be helpful in fighting viruses such as AIDS, SARS, and flu, since these viruses have higher variability. The calculation offers an independent theoretical estimate of the precision of structure determination.

  6. Development of solution techniques for nonlinear structural analysis

    NASA Technical Reports Server (NTRS)

    Vos, R. G.; Andrews, J. S.

    1974-01-01

    Nonlinear structural solution methods in the current research literature are classified according to order of the solution scheme, and it is shown that the analytical tools for these methods are uniformly derivable by perturbation techniques. A new perturbation formulation is developed for treating an arbitrary nonlinear material, in terms of a finite-difference generated stress-strain expansion. Nonlinear geometric effects are included in an explicit manner by appropriate definition of an applicable strain tensor. A new finite-element pilot computer program PANES (Program for Analysis of Nonlinear Equilibrium and Stability) is presented for treatment of problems involving material and geometric nonlinearities, as well as certain forms on nonconservative loading.

  7. Association and Structure of Thermo Sensitive Comblike Block Copolymers in Aqueous Solutions

    SciTech Connect

    Cheng, Gang; Hua, Fengjun; Melnichenko, Yuri B; Hong, Kunlun; Wignall, George D; Mays, Jimmy; Hammouda, B.

    2008-01-01

    The structures and association properties of thermo sensitive poly(methoxyoligo(ethylene glycol) norbornenyl esters) block copolymers in D2O were investigated by Small Angle Neutron Scattering (SANS). Each block is a comb-like polymer with a polynorbornene (PNB) backbone and oligo ethylene glycol (OEG) side chains (one side chain per NB monomer). The chemical formula of the block copolymer is (OEG3NB)79-(OEG6.6NB)67, where subscripts represent the degree of polymerization (DP) of OEG and NB in each block The polymer concentration was fixed at 2.0 wt % and the structural changes were investigated over a temperature range between 25 C and 68 C. It was found that at room temperature polymers associate to form micelles with a spherical core formed by the block (OEG3NB)79 and corona formed by the block (OEG6.6NB)67 and that the shape of the polymer in the corona could be described by the form factor of rigid cylinders. At elevated temperatures, the aggregation number increases and the micelles become more compact. At temperatures round the cloud point temperature (CPT) T = 60 C a correlation peak started to appear and became pronounced at 68 C due to the formation of a partially ordered structure with a correlation length ~ 349 .

  8. Steady state solutions to dynamically loaded periodic structures

    NASA Technical Reports Server (NTRS)

    Kalinowski, A. J.

    1980-01-01

    The general problem of solving for the steady state (time domain) dynamic response (i.e., NASTRAN rigid format-8) of a general elastic periodic structure subject to a phase difference loading of the type encountered in traveling wave propagation problems was studied. Two types of structural configurations were considered; in the first type, the structure has a repeating pattern over a span that is long enough to be considered, for all practical purposes, as infinite; in the second type, the structure has structural rotational symmetry in the circumferential direction. The theory and a corresponding set of DMAP instructions which permits the NASTRAN user to automatically alter the rigid format-8 sequence to solve the intended class of problems are presented. Final results are recovered as with any ordinary rigid format-8 solution, except that the results are only printed for the typical periodic segment of the structure. A simple demonstration problem having a known exact solution is used to illustrate the implementation of the procedure.

  9. On the solution of creep induced buckling in general structure

    NASA Technical Reports Server (NTRS)

    Padovan, J.; Tovichakchaikul, S.

    1982-01-01

    This paper considers the pre and post buckling behavior of general structures exposed to high temperature fields for long durations wherein creep effects become significant. The solution to this problem is made possible through the use of closed upper bounding constraint surfaces which enable the development of a new time stepping algorithm. This permits the stable and efficient solution of structural problems which exhibit indefinite tangent properties. Due to the manner of constraining/bounding successive iterates, the algorithm developed herein is largely self adaptive, inherently stable, sufficiently flexible to handle geometric material and boundary induced nonlinearity, and can be incorporated into either finite element or difference simulations. To illustrate the capability of the procedure, as well as, the physics of creep induced pre and post buckling behavior, the results of several numerical experiments are included.

  10. Supersaturated lysozyme solution structure studied by chemical cross-linking.

    PubMed

    Hall, Clayton L; Clemens, John R; Brown, Amanda M; Wilson, Lori J

    2005-06-01

    Glutaraldehyde cross-linking followed by separation has been used to detect aggregates of chicken egg-white lysozyme (CEWL) in supersaturated solutions. In solutions of varying NaCl content, the number of aggregates was found to be related to the ionic strength of the solution. Separation by SDS-PAGE showed that percentage of dimer in solution ranged from 25.3% for no NaCl to 27.1% at 15% NaCl, and the aggregates larger than dimer increased from 1.9% for no NaCl to 36.8% at 15% NaCl. Conversely, the percentage of monomers decreased from 72.8% without NaCl to 36.1% at 15% NaCl. Molecular weights by capillary electrophoresis (SDS-CE) were found to be multiples of the monomer molecular weights, with the exception of trimer, which indicates a very compact structure. Native separation was accomplished using size-exclusion chromatography (SEC) and gave a lower monomer concentration and higher aggregate concentration than SDS-CE, which is a denaturing separation method. Most noticeably, trimers were absent in the SEC separation. The number of aggregates did not change with increased time between addition of NaCl and addition of cross-linking agent when separated by gel electrophoresis (SDS-PAGE). The results suggest that high ionic strength CEWL solutions are highly aggregated and that denaturing separation methods disrupt cross-linked products. PMID:15930646

  11. Effect of Ternary Solutes on the Evolution of Structure and Gel Formation in Amphiphilic Copolymer Solutions

    NASA Astrophysics Data System (ADS)

    Meznarich, Norman Anthony Kang

    Aqueous solutions of polyoxyethylene-polyoxypropylene-polyoxyethylene (PEO-PPO-PEO) amphiphilic triblock copolymers (commercially known as Pluronic surfactants) undergo reversible and temperature-dependent micellization and arrangement into cubic ordered lattices known as "micelle gels". The macroscopic behavior of the ordering is a transition from a liquid to a gel. While the phase behavior and gel structure of pure Pluronic surfactant solutions have been well studied, less is known about the effects of added ternary solutes. In this dissertation, a comprehensive investigation into the effects of the added pharmaceutical methylparaben on solutions of F127 ranging from 10 to 30 wt% was conducted in order to better understand the behavior of F127 in multicomponent pharmaceutical formulations. The viscoelastic properties of F127 gel formation were studied using rheometry, where heating rates of 0.1, 1, and 10 degrees C/min were also used to probe the kinetics of the gel transition. In solutions containing methylparaben, F127 gelation occurred at up to 15 degrees C lower temperatures and was accelerated by a factor of three to four. Small angle x-ray scattering (SAXS) was used to characterize the structure of the ordered domains, and how they were affected by the presence of dissolved pharmaceuticals. It was found that ordered domain formation changed from heterogeneous nucleation and growth to possible homogeneous nucleation and growth. A roughly 2% reduction in the cubic lattice parameter was also observed for solutions containing methylparaben. Differential scanning calorimetry (DSC) experiments were performed on a series of different Pluronic surfactants in order to characterize the micellization behavior as a function of PPO center block length and PEO/PPO ratio. Added methylparaben suppressed the micellization endotherm, the degree of suppression depending linearly on the amount of added methylparaben, as well as the length of the PPO center block and PEO

  12. Light scattering measurements supporting helical structures for chromatin in solution.

    PubMed

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model. PMID:662693

  13. The Solution Structure of the Regulatory Domain of Tyrosine Hydroxylase

    PubMed Central

    Zhang, Shengnan; Huang, Tao; Ilangovan, Udayar; Hinck, Andrew P.; Fitzpatrick, Paul F.

    2014-01-01

    Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine in the biosynthesis of the catecholamine neurotransmitters. The activity of the enzyme is regulated by phosphorylation of serine residues in a regulatory domain and by binding of catecholamines to the active site. Available structures of TyrH lack the regulatory domain, limiting the understanding of the effect of regulation on structure. We report the use of NMR spectroscopy to analyze the solution structure of the isolated regulatory domain of rat TyrH. The protein is composed of a largely unstructured N-terminal region (residues 1-71) and a well-folded C-terminal portion (residues 72-159). The structure of a truncated version of the regulatory domain containing residues 65-159 has been determined and establishes that it is an ACT domain. The isolated domain is a homodimer in solution, with the structure of each monomer very similar to that of the core of the regulatory domain of phenylalanine hydroxylase. Two TyrH regulatory domain monomers form an ACT domain dimer composed of a sheet of eight strands with four α-helices on one side of the sheet. Backbone dynamic analyses were carried out to characterize the conformational flexibility of TyrH65-159. The results provide molecular details critical for understanding the regulatory mechanism of TyrH. PMID:24361276

  14. Solution structure of leptospiral LigA4 Big domain.

    PubMed

    Mei, Song; Zhang, Jiahai; Zhang, Xuecheng; Tu, Xiaoming

    2015-11-13

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca(2+) binding property of LigA4 Big domain. PMID:26449456

  15. On the atomic structure of cocaine in solution.

    PubMed

    Johnston, Andrew J; Busch, Sebastian; Pardo, Luis Carlos; Callear, Samantha K; Biggin, Philip C; McLain, Sylvia E

    2016-01-14

    Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ∼5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function. PMID:26660073

  16. Solution to certain problems in the failure of composite structures

    NASA Astrophysics Data System (ADS)

    Goodsell, Johnathan

    The present work contains the solution of two problems in composite structures. In the first, an approximate elasticity solution for prediction of the displacement, stress and strain fields within the m-layer, symmetric and balanced angle-ply composite laminate of finite-width subjected anticlastic bending deformation is developed. The solution is shown to recover classical laminated plate theory predictions at interior regions of the laminate and thereby illustrates the boundary layer character of this interlaminar phenomenon. The results exhibit the anticipated response in congruence with the solutions for uniform axial extension and uniform temperature change, where divergence of the interlaminar shearing stress is seen to occur at the intersection of the free-edge and planes between lamina of +theta and -theta orientation. The analytical results show excellent agreement with the finite-element predictions for the same boundary-value problem and thereby provide an efficient and compact solution available for parametric studies of the influence of geometry and material properties. The solution is combined with previously developed solutions for uniform axial extension and uniform temperature change of the identical laminate and the combined solution is exercised to compare the relative magnitudes of free-edge phenomenon arising from the different loading conditions, to study very thick laminates and laminates where the laminate width is less than the laminate thickness. Significantly, it was demonstrated that the solution is valid for arbitrary stacking sequence and the solution was exercised to examine antisymmetric and non-symmetric laminates. Finally, the solution was exercised to determine the dimensions of the boundary layer for very large numbers of layers. It was found that the dimension of the boundary layer width in bending is approximately twice that in uniform axial extension and uniform temperature change. In the second, the intrinsic flaw concept is

  17. Solution structure of the human signaling protein RACK1

    PubMed Central

    2010-01-01

    Background The adaptor protein RACK1 (receptor of activated kinase 1) was originally identified as an anchoring protein for protein kinase C. RACK1 is a 36 kDa protein, and is composed of seven WD repeats which mediate its protein-protein interactions. RACK1 is ubiquitously expressed and has been implicated in diverse cellular processes involving: protein translation regulation, neuropathological processes, cellular stress, and tissue development. Results In this study we performed a biophysical analysis of human RACK1 with the aim of obtaining low resolution structural information. Small angle X-ray scattering (SAXS) experiments demonstrated that human RACK1 is globular and monomeric in solution and its low resolution structure is strikingly similar to that of an homology model previously calculated by us and to the crystallographic structure of RACK1 isoform A from Arabidopsis thaliana. Both sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation techniques showed that RACK1 is predominantly a monomer of around 37 kDa in solution, but also presents small amounts of oligomeric species. Moreover, hydrodynamic data suggested that RACK1 has a slightly asymmetric shape. The interaction of RACK1 and Ki-1/57 was tested by sedimentation equilibrium. The results suggested that the association between RACK1 and Ki-1/57(122-413) follows a stoichiometry of 1:1. The binding constant (KB) observed for RACK1-Ki-1/57(122-413) interaction was of around (1.5 ± 0.2) × 106 M-1 and resulted in a dissociation constant (KD) of (0.7 ± 0.1) × 10-6 M. Moreover, the fluorescence data also suggests that the interaction may occur in a cooperative fashion. Conclusion Our SAXS and analytical ultracentrifugation experiments indicated that RACK1 is predominantly a monomer in solution. RACK1 and Ki-1/57(122-413) interact strongly under the tested conditions. PMID:20529362

  18. The three-dimensional solution structure of RANTES.

    PubMed

    Chung, C W; Cooke, R M; Proudfoot, A E; Wells, T N

    1995-07-25

    The solution structure of the chemokine RANTES (regulated on activation, normal T-cell expressed and secreted) has been determined using NMR spectroscopy. Backbone and side-chain 1H and 15N assignments have been obtained using a combination of two-dimensional homonuclear and three-dimensional heteronuclear spectra. Regular elements of secondary structure have been identified on the basis of a qualitative interpretation of NOE data, J(NH-H alpha) coupling constants, and amide exchange rates. Three-dimensional structures were calculated from a total of 2146 experimental restraints using a combination of distance geometry and simulated annealing protocols. For the 13 best structures the average backbone (N, C alpha, C) atomic rmsd from the mean coordinates for residues 5-65 is 0.64 A (+/- 0.14 A) for the dimer and 0.50 A (+/- 0.08 A) for the individual monomers. Each monomer consists of a three-stranded antiparallel beta-sheet (residues 26-30, 38-43, 48-51) in a Greek key motif with a C-terminal helix (56-65) packed across the sheet, an arrangement similar to the monomeric structure of other members of this chemokine family (IL-8, PF4, MGSA/Gro alpha, and MIP-1 beta). Overall, the RANTES dimer resembles that previously reported for MIP-1 beta. PMID:7542919

  19. Interfacial structures of acidic and basic aqueous solutions

    SciTech Connect

    Tian, C.; Ji, N.; Waychunas, G.; Shen, Y.R.

    2008-10-20

    Phase-sensitive sum-frequency vibrational spectroscopy was used to study water/vapor interfaces of HCl, HI, and NaOH solutions. The measured imaginary part of the surface spectral responses provided direct characterization of OH stretch vibrations and information about net polar orientations of water species contributing to different regions of the spectrum. We found clear evidence that hydronium ions prefer to emerge at interfaces. Their OH stretches contribute to the 'ice-like' band in the spectrum. Their charges create a positive surface field that tends to reorient water molecules more loosely bonded to the topmost water layer with oxygen toward the interface, and thus enhances significantly the 'liquid-like' band in the spectrum. Iodine ions in solution also like to appear at the interface and alter the positive surface field by forming a narrow double-charge layer with hydronium ions. In NaOH solution, the observed weak change of the 'liquid-like' band and disappearance of the 'ice-like' band in the spectrum indicates that OH{sup -} ions must also have excess at the interface. How they are incorporated in the interfacial water structure is however not clear.

  20. Structure and dynamics of of solution polymerized polyureas

    NASA Astrophysics Data System (ADS)

    Choi, Taeyi; Jeong, Youmi; Runt, James

    2011-03-01

    Polyureas consisting of alternating soft and hard (urea containing) segments exhibit physical properties that are closely related to their microphase separated structure, which consist of rigid (high Tg and sometimes crystalline) hard domains embedded in a matrix dominated by flexible polyether segments. Polyurea properties can be controlled over a rather broad range by varying the chemical structures, molecular weight of the components, and reaction stoichiometry. In the present study, we focus primarily on linear polyureas synthesized using methylene diphenyl diisocyanate and polytetramethylene oxide-di-p-aminobenzoate using a solution polymerization method. Soft segment (diamine) molecular weights were varied from 460 to 860 to 1200 g/mol and characterize their morphology, hydrogen bonding, mechanical behavior and dielectric properties upon varying molecular weight of diamines. This presentation will focus on our latest findings, particularly details of the microphase separated morphology and molecular dynamics as measured using dielectric relaxation spectroscopy This work is supported by Office of Naval Research.

  1. Structure of a passivated Ge surface prepared from aqueous solution.

    SciTech Connect

    Lyman, P. F.; Sakata, O.; Marasco, D, L.; Lee, T.-L.; Breneman, K. D.; Keane, D. T.; Bedzyk, M. J.; Materials Science Division; Northwestern Univ.; Univ. of Wisconsin at Milwaukee

    2000-08-10

    The structure of a passivating sulfide layer on Ge(001) was studied using X-ray standing waves and X-ray fluorescence. The sulfide layer was formed by reacting clean Ge substrates in (NH{sub 4}){sub 2}S solutions of various concentrations at 80{sup o}C. For each treatment, a sulfide layer containing approximately two to three monolayers (ML) of S was formed on the surface, and an ordered structure was found at the interface that contained approximately 0.4 ML of S. Our results suggest the rapid formation of a glassy GeS{sub x} layer containing 1.5-2.5 ML S residing atop a partially ordered interfacial layer of bridge-bonded S. The passivating reaction appears to be self-limited to 2-3 ML at this reaction temperature.

  2. Structural investigations of block copolymer melts and solutions

    NASA Astrophysics Data System (ADS)

    Kossuth, Mary Beth

    1999-11-01

    Block copolymers have been observed to spontaneously self-assemble into a variety of ordered liquid crystalline phases, much like surfactant and lipid solutions. Among these structures are two cubic morphologies: spheres packed on a body-centered cubic lattice and a bicontinuous structure known as the gyroid. The viscoelastic behavior of these two microstructures was examined in detail for nine chemically distinct systems using oscillatory shear. Remarkable similarities were seen in the rheological responses of the two phases, and a universal picture of the viscoelastic behavior of cubic phases was proposed. Two features were observed in every system: a low frequency crossover of the storage and loss moduli, oxx, and a frequency independent plateau in the storage modulus, Gcubic°. The plateau modulus is related experimentally to the characteristic domain spacing d* of the microstructures by Gcubic °˜d*-3, while theory predicts a d*-2 dependence. There are similarities between the phase behavior of melt-state block copolymers and surfactant solutions both in the phases that appear and the order in which they occur. The phase behavior for a series of low molecular weight block copolymers of poly(ethylene oxide)-poly(ethyl ethylene) (PEO-PEE) was examined in the presence of water and both water and dodecane (oil) using small-angle x-ray scattering. In the binary aqueous solutions, phase behavior similar to that of nonionic surfactants was observed, with evidence of lamellae, hexagonally packed cylinders, and body-centered cubic spheres; however, no gyroid phase was seen. The phases were remarkably robust; ordered structures persisted even to high temperatures. Above a critical concentration only lyotropic phase behavior was seen; below this composition thermotropic behavior was evident. Addition of dodecane to a symmetric block copolymer produced a very different phase diagram than its aqueous counterpart. Face-centered cubic spheres and a small window of the

  3. Aqueous Solutions on Silica Surfaces: Structure and Dynamics from Simulations

    NASA Astrophysics Data System (ADS)

    Striolo, Alberto; Argyris, Dimitrios; Tummala, Naga Rajesh

    2009-03-01

    Our group is interested in understanding the properties of aqueous electrolyte solutions at interfaces. The fundamental questions we seek to answer include: (A) how does a solid structure perturb interfacial water? (B) How far from the solid does this perturbation persist? (C) What is the rate of water reorientation and exchange in the perturbed layer? (D) What happens in the presence of simple electrolytes? To address such topics we implemented atomistic molecular dynamics simulations. Recent results for water and simple electrolytes near silicon dioxide surfaces of various degrees of hydroxylation will be presented. The data suggest the formation of a layered aqueous structure near the interface. The density profile of interfacial water seems to dictate the density profiles of aqueous solutions containing NaCl, CaCl2, CsCl, and SrCl2 near the solid surfaces. These results suggest that ion-ion and ion-water correlations are extremely important factors that should be considered when it is desired to predict the distribution of electrolytes near a charged surface. Our results will benefit a number of practical applications including water desalination, exploitation of the oil shale in the Green River Basin, nuclear waste sites remediation, and design of nanofluidic devices.

  4. Solution Structures of Rat Amylin Peptide: Simulation, Theory, and Experiment

    PubMed Central

    Reddy, Allam S.; Wang, Lu; Lin, Yu-Shan; Ling, Yun; Chopra, Manan; Zanni, Martin T.; Skinner, James L.; De Pablo, Juan J.

    2010-01-01

    Abstract Amyloid deposits of amylin in the pancreas are an important characteristic feature found in patients with Type-2 diabetes. The aggregate has been considered important in the disease pathology and has been studied extensively. However, the secondary structures of the individual peptide have not been clearly identified. In this work, we present detailed solution structures of rat amylin using a combination of Monte Carlo and molecular dynamics simulations. A new Monte Carlo method is presented to determine the free energy of distinct biomolecular conformations. Both folded and random-coil conformations of rat amylin are observed in water and their relative stability is examined in detail. The former contains an α-helical segment comprised of residues 7–17. We find that at room temperature the folded structure is more stable, whereas at higher temperatures the random-coil structure predominates. From the configurations and weights we calculate the α-carbon NMR chemical shifts, with results that are in reasonable agreement with experiments of others. We also calculate the infrared spectrum in the amide I stretch regime, and the results are in fair agreement with the experimental line shape presented herein. PMID:20141758

  5. Solution structure of an A-tract DNA bend.

    PubMed

    MacDonald, D; Herbert, K; Zhang, X; Pologruto, T; Lu, P; Polgruto, T

    2001-03-01

    The solution structure of a DNA dodecamer d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) containing an A-tract has been determined by NMR spectroscopy with residual dipolar couplings. The structure shows an overall helix axis bend of 19 degrees in a geometry consistent with solution and gel electrophoresis experiments. Fourteen degrees of the bending occurs in the GC regions flanking the A-tract. The remaining 5 degrees is spread evenly over its six AT base-pairs. The A-tract is characterized by decreasing minor groove width from the 5' to the 3' direction along the A strand. This is a result of propeller twist in the AT pairs and the increasing negative inclination of the adenine bases at the 3' side of the run of adenine bases. The four central thymine bases all have negative inclination throughout the A-tract with an average value of -6.1 degrees. Although this negative inclination makes the geometry of the A-tract different from all X-ray structures, the proton on N6 of adenine and the O4 of thymine one step down the helix are within distance to form bifurcated hydrogen bonds. The 5' bend of 4 degrees occurs at the junction between the GC flank and the A-tract through a combination of tilt and roll. The larger 3' bend, 10 degrees, occurs in two base steps: the first composed of tilt, -4.1 degrees, and the second a combination of tilt, -4.2 degrees, and roll, 6.0 degrees. This second step is a direct consequence of the change in inclination between an adjacent cytosine base, which has an inclination of -12 degrees, and the next base, a guanine, which has 3 degrees inclination. This bend is a combination of tilt and roll. The large change in inclination allows the formation of a hydrogen bond between the protons of N4 of the 3' cytosine and the O6 of the next 3' base, a guanine, stabilizing the roll component in the bend. These structural features differ from existing models for A-tract bends.For comparison, we also determined the structure of the control sequence, d

  6. Solution structure, aggregation behavior, and flexibility of human relaxin-2.

    PubMed

    Haugaard-Kedström, Linda M; Hossain, Mohammed Akhter; Daly, Norelle L; Bathgate, Ross A D; Rinderknecht, Ernst; Wade, John D; Craik, David J; Rosengren, K Johan

    2015-03-20

    Relaxin is a member of the relaxin/insulin peptide hormone superfamily and is characterized by a two-chain structure constrained by three disulfide bonds. Relaxin is a pleiotropic hormone and involved in a number of physiological and pathogenic processes, including collagen and cardiovascular regulation and tissue remodelling during pregnancy and cancer. Crystallographic and ultracentrifugation experiments have revealed that the human form of relaxin, H2 relaxin, self-associates into dimers, but the significance of this is poorly understood. Here, we present the NMR structure of a monomeric, amidated form of H2 relaxin and compare its features and behavior in solution to those of native H2 relaxin. The overall structure of H2 relaxin is retained in the monomeric form. H2 relaxin amide is fully active at the relaxin receptor RXFP1 and thus dimerization is not required for biological activity. Analysis of NMR chemical shifts and relaxation parameters identified internal motion in H2 relaxin at the pico-nanosecond and milli-microsecond time scales, which is commonly seen in other relaxin and insulin peptides and might be related to function. PMID:25547165

  7. Structure and dynamics of aqueous solution of uranyl ions

    SciTech Connect

    Chopra, Manish; Choudhury, Niharendu

    2014-04-24

    The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied.

  8. Hydration structure of salt solutions from ab initio molecular dynamics.

    PubMed

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L

    2013-01-01

    The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed. PMID:23298049

  9. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  10. Hydration structure of salt solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  11. Structure and phase behavior of aqueous methylcellulose solutions

    NASA Astrophysics Data System (ADS)

    McAllister, John; Schmidt, Peter; Lodge, Timothy; Bates, Frank

    2015-03-01

    Cellulose ethers (CE) constitute a multi-billion dollar industry, and have found end uses in a broad array of applications from construction materials, food products, personal care products, and pharmaceuticals for more than 80 years. Methylcellulose (MC, with the trade name METHOCEL™) is a CE in which there is a partial substitution of -OH groups with -OCH3 groups. This results in a polymer that is water-soluble at low temperatures, and aqueous solutions of MC display gelation and phase separation at higher temperatures. The nature of MC gelation has been debated for many years, and this project has made significant advances in the understanding of the solution properties of CEs. We have characterized a fibrillar structure of MC gels by cryogenic transmission electron microscopy (cryo-TEM) and small angle neutron scattering (SANS). Using light scattering, turbidity measurements, and dynamic mechanical spectroscopy (DMS) we report that MC microphase separates by nucleation and growth of fibril aggregates, and is a different process from LCST phase separation.

  12. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  13. Highly efficient D2 generation by dehydrogenation of formic acid in D2O through H+/D+ exchange on an iridium catalyst: application to the synthesis of deuterated compounds by transfer deuterogenation.

    PubMed

    Wang, Wan-Hui; Hull, Jonathan F; Muckerman, James T; Fujita, Etsuko; Hirose, Takuji; Himeda, Yuichiro

    2012-07-23

    Deuterated compounds have received increasing attention in both academia and industrial fields. However, preparations of these compounds are limited for both economic and practical reasons. Herein, convenient generation of deuterium gas (D(2)) and the preparation of deuterated compounds on a laboratory scale are demonstrated by using a half-sandwich iridium complex with 4,4'-dihydroxy-2,2'-bipyridine. The "umpolung" (i.e., reversal of polarity) of a hydrogen atom of water was achieved in consecutive reactions, that is, a cationic H(+)/D(+) exchange reaction and anionic hydride or deuteride transfer, under mild conditions. Selective D(2) evolution (purity up to 89 %) was achieved by using HCO(2)H as an electron source and D(2)O as a deuterium source; a rhodium analogue provided HD gas (98 %) under similar conditions. Furthermore, pressurized D(2) (98 %) without CO gas was generated by using DCO(2)D in D(2)O in a glass autoclave. Transfer deuterogenation of ketones gave α-deuterated alcohols with almost quantitative yields and high deuterium content by using HCO(2)H in D(2)O. Mechanistic studies show that the H(+)/D(+) exchange reaction in the iridium hydride complex was much faster than β-elimination and hydride (deuteride) transfer. PMID:22718518

  14. Solution NMR Structure of Membrane-Integral Diacylglycerol Kinase

    PubMed Central

    Van Horn, Wade D.; Kim, Hak-Jun; Ellis, Charles D.; Hadziselimovic, Arina; Sulistijo, Endah S.; Karra, Murthy D.; Tian, Changlin; Sönnichsen, Frank D.; Sanders, Charles R.

    2009-01-01

    Escherichia coli diacylglycerol kinase (DAGK) represents a family of integral membrane enzymes that is unrelated to all other phosphotransferases. We have determined the three-dimensional structure of the DAGK homotrimer using solution NMR. The third transmembrane helix from each subunit is domain-swapped with the first and second transmembrane segments from an adjacent subunit. Each of DAGK’s three active sites resembles a portico. The cornice of the portico appears to be the determinant of DAGK’s lipid substrate specificity and overhangs the site of phosphoryl transfer near the water-membrane interface. Mutations to cysteine that caused severe misfolding were located in or near the active site, indicating a high degree of overlap between sites responsible for folding and for catalysis. PMID:19556511

  15. Identifying duplicate crystal structures: XTALCOMP, an open-source solution

    NASA Astrophysics Data System (ADS)

    Lonie, David C.; Zurek, Eva

    2012-03-01

    applications may consider enantiomorphic structures to be identical. Solution method: The XtalComp algorithm overcomes these issues to detect duplicate structures regardless of differences in representation. It begins by performing a Niggli reduction on the inputs, standardizing the translation vectors and orientations. A transform search is performed to identify candidate sets of rotations, reflections, and translations that potentially map the description of one crystal onto the other, solving the problems of enantiomorphs and rotationally degenerate lattices. The atomic positions resulting from each candidate transform are then compared, using a cell-expansion technique to remove periodic boundary issues. Computational noise is treated by comparing non-integer quantities using a specified tolerance. Running time: The test run provided takes less than a second to complete.

  16. The NMR solution structure of recombinant RGD-hirudin

    SciTech Connect

    Song, Xia; Mo, Wei; Liu, Xingang; Zhu, Lina; Yan, Xiaomin; Song, Houyan . E-mail: hysong@shmu.edu.cn; Dai, Linsen . E-mail: lsdai@fudan.edu.cn

    2007-08-17

    The solution structure of a new recombinant RGD-hirudin, which has the activities of anti-thrombin and anti-platelet aggregation, was determined by {sup 1}H nuclear magnetic resonance spectroscopy and compared with the conformations of recombinant wild-type hirudin and hirudin (variant 2, Lys47) of the hirudin thrombin complex. On the basis of total 1284 distance and dihedral angle constraints derived from a series of NMR spectra, 20 conformers were computed with ARIA/CNS programs. The structure of residues 3-30 and 37-48 form a molecular core with two antiparallel {beta}-sheets as the other two hirudins. However, significant differences were found in the surface electrostatic charge distributions among the three hirudins, especially in the RGD segment of recombinant RGD-hirudin. This difference may be greatly beneficial to its additional function of anti-platelet aggregation. The difference in extended C-terminal makes its both ionic and hydrophobic interactions with the fibrinogen recognition exosite of thrombin more effective.

  17. Hierarchical structure formation in unentangled polymer solutions under extension

    NASA Astrophysics Data System (ADS)

    Semenov, Alexander N.; Subbotin, Andrey V.

    2016-05-01

    The phase separation processes in unentangled polymer solutions induced by the coil-stretch transition due to high-rate extension flow are considered theoretically. The results are in qualitative agreement with recent rheological experiments on PAN solutions.

  18. Structure of Solutions of Multidimensional Conservation Laws with Discontinuous Flux and Applications to Uniqueness

    NASA Astrophysics Data System (ADS)

    Crasta, Graziano; De Cicco, Virginia; De Philippis, Guido; Ghiraldin, Francesco

    2016-08-01

    We investigate the structure of solutions of conservation laws with discontinuous flux under quite general assumption on the flux. We show that any entropy solution admits traces on the discontinuity set of the coefficients and we use this to prove the validity of a generalized Kato inequality for any pair of solutions. Applications to uniqueness of solutions are then given.

  19. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

    Nuclear magnetic resonance (NMR) is a marvelous spectroscopic technique that chemists, physicists, and biochemists routinely employ for their research around the world. This year half of the Nobel Prize for chemistry went to Kurt Wüthrich, who was recognized for the development of NMR-based techniques that lead to the structure determination of biomolecules in solution. In addition to implementing novel pulse sequences and software packages, Wüthrich also applied his methods to several biological systems of key importance to human health. These include the prion protein, which is heavily involved in the spongiform encephalopathy (best known as 'mad cow disease'), which recently caused numerous human deaths, particularly in the UK, due to ingestion of contaminated meat. Transverse relaxation optimized spectroscopy (TROSY) is the most intriguing new NMR method recently developed by Wüthrich and coworkers. This and other closely related pulse sequences promise to play a pivotal role in the extension of NMR to the conformational analysis of very large (up to the megadalton range) macromolecules and macromolecular complexes. More exciting new developments are expected in the near future.

  20. a Procedural Solution to Model Roman Masonry Structures

    NASA Astrophysics Data System (ADS)

    Cappellini, V.; Saleri, R.; Stefani, C.; Nony, N.; De Luca, L.

    2013-07-01

    The paper will describe a new approach based on the development of a procedural modelling methodology for archaeological data representation. This is a custom-designed solution based on the recognition of the rules belonging to the construction methods used in roman times. We have conceived a tool for 3D reconstruction of masonry structures starting from photogrammetric surveying. Our protocol considers different steps. Firstly we have focused on the classification of opus based on the basic interconnections that can lead to a descriptive system used for their unequivocal identification and design. Secondly, we have chosen an automatic, accurate, flexible and open-source photogrammetric pipeline named Pastis Apero Micmac - PAM, developed by IGN (Paris). We have employed it to generate ortho-images from non-oriented images, using a user-friendly interface implemented by CNRS Marseille (France). Thirdly, the masonry elements are created in parametric and interactive way, and finally they are adapted to the photogrammetric data. The presented application, currently under construction, is developed with an open source programming language called Processing, useful for visual, animated or static, 2D or 3D, interactive creations. Using this computer language, a Java environment has been developed. Therefore, even if the procedural modelling reveals an accuracy level inferior to the one obtained by manual modelling (brick by brick), this method can be useful when taking into account the static evaluation on buildings (requiring quantitative aspects) and metric measures for restoration purposes.

  1. Structure and solution properties of enzymatically synthesized glycogen.

    PubMed

    Kajiura, Hideki; Takata, Hiroki; Kuriki, Takashi; Kitamura, Shinichi

    2010-04-19

    Recently, a new enzymatic process for glycogen production was developed. In this process, short-chain amylose is used as a substrate for branching enzymes (BE, EC 2.4.1.18). The molecular weight of the enzymatically synthesized glycogen (ESG) depends on the size and concentration of the substrate. Structural and physicochemical properties of ESG were compared to those of natural source glycogen (NSG). The average chain length, interior chain length, and exterior chain length of ESG were 8.2-11.6, 2.0-3.3, and 4.2-7.6, respectively. These values were within the range of variation of NSG. The appearances of both ESG and NSG in solution were opalescent (milky white and slightly bluish). Furthermore, transmission electron microscopy and atomic force microscopy showed that ESG molecules formed spherical particles, and that there were no differences between ESG and NSG. Viscometric analyses also showed the spherical nature of both glycogens. When ESG and NSG were treated with pullulanase, a glucan-hydrolyzing enzyme known to degrade glycogen only on its surface portion, both glycogens were similarly degraded. These analyses revealed that ESG shares similar molecular shapes and surface properties with NSG. PMID:20153852

  2. Solution structures of stromelysin complexed to thiadiazole inhibitors.

    PubMed Central

    Stockman, B. J.; Waldon, D. J.; Gates, J. A.; Scahill, T. A.; Kloosterman, D. A.; Mizsak, S. A.; Jacobsen, E. J.; Belonga, K. L.; Mitchell, M. A.; Mao, B.; Petke, J. D.; Goodman, L.; Powers, E. A.; Ledbetter, S. R.; Kaytes, P. S.; Vogeli, G.; Marshall, V. P.; Petzold, G. L.; Poorman, R. A.

    1998-01-01

    Unregulated or overexpressed matrix metalloproteinases (MMPs), including stromelysin, collagenase, and gelatinase. have been implicated in several pathological conditions including arthritis and cancer. Small-molecule MMP inhibitors may have therapeutic value in the treatment of these diseases. In this regard, the solution structures of two stromelysin/ inhibitor complexes have been investigated using 1H, 13C, and 15N NMR spectroscopy. Both-inhibitors are members of a novel class of matrix metalloproteinase inhibitor that contain a thiadiazole group and that interact with stromelysin in a manner distinct from other classes of inhibitors. The inhibitors coordinate the catalytic zinc atom through their exocyclic sulfur atom, with the remainder of the ligand extending into the S1-S3 side of the active site. The binding of inhibitor containing a protonated or fluorinated aromatic ring was investigated using 1H and 19F NMR spectroscopy. The fluorinated ring was found to have a reduced ring-flip rate compared to the protonated version. A strong, coplanar interaction between the fluorinated ring of the inhibitor and the aromatic ring of Tyr155 is proposed to account for the reduced ring-flip rate and for the increase in binding affinity observed for the fluorinated inhibitor compared to the protonated inhibitor. Binding interactions observed for the thiadiazole class of ligands have implications for the design of matrix metalloproteinase inhibitors. PMID:9827994

  3. Can ultrashort-TE (UTE) MRI sequences on a 3-T clinical scanner detect signal directly from collagen protons: freeze-dry and D2 O exchange studies of cortical bone and Achilles tendon specimens.

    PubMed

    Ma, Ya-Jun; Chang, Eric Y; Bydder, Graeme M; Du, Jiang

    2016-07-01

    Ultrashort-TE (UTE) sequences can obtain signal directly from short-T2 , collagen-rich tissues. It is generally accepted that bound and free water can be detected with UTE techniques, but the ability to detect protons directly on the collagen molecule remains controversial. In this study, we investigated the potential of UTE sequences on a 3-T clinical scanner to detect collagen protons via freeze-drying and D2 O-H2 O exchange studies. Experiments were performed on bovine cortical bone and human Achilles tendon specimens, which were either subject to freeze-drying for over 66 h or D2 O-H2 O exchange for 6 days. Specimens were imaged using two- and three-dimensional UTE with Cones trajectory techniques with a minimum TE of 8 μs at 3 T. UTE images before treatment showed high signal from all specimens with bi-component T2 * behavior. Bovine cortical bone showed a shorter T2 * component of 0.36 ms and a longer T2 * component of 2.30 ms with fractions of 78.2% and 21.8% by volume, respectively. Achilles tendon showed a shorter T2 * component of 1.22 ms and a longer T2 * component of 15.1 ms with fractions of 81.1% and 18.9% by volume, respectively. Imaging after freeze-drying or D2 O-H2 O exchange resulted in either the absence or near-absence of signal. These results indicate that bound and free water are the sole sources of UTE signal in bovine cortical bone and human Achilles tendon samples on a clinical 3-T scanner. Protons on the native collagen molecule are not directly visible when imaged using UTE sequences. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27148693

  4. An examination of the initial oxidation of a uranium-base alloy (U-14.1 at.% Nb) by O 2 and D 2O using surface-sensitive techniques

    NASA Astrophysics Data System (ADS)

    Manner, William L.; Lloyd, Jane A.; Hanrahan, Robert J.; Paffett, Mark T.

    1999-08-01

    The corrosion resistance of uranium is greatly enhanced by alloying with niobium. In this study the initial stages of corrosion of a specific uranium-base alloy (U-14.1 at.% Nb) by O 2 or D 2O have been examined using the surface specific techniques of X-ray photoelectron spectroscopy (XPS), thermal programmed desorption (TPD), static secondary-ion mass spectroscopy (SSIMS), and sputtered neutrals mass spectroscopy (SNMS). XPS studies of the U-14.1 at.% Nb surface following oxidation using O 2 at 300 K indicate production of a thin oxide overlayer of stoichiometric UO 2.0 intermixed with Nb 2O 5. The same stoichiometry is exhibited for uranium when the oxide is prepared at 500 K with O 2; although, niobium is much less oxidized exhibiting a mixture of NbO and Nb. Contrary to previous XPS literature, SNMS depth profiling studies reveal that oxidation by O 2 is much greater (as judged by oxide layer thickness) than that exhibited by D 2O. An oxide layer thickness of less than 20 Å was created using D 2O as an oxidant at 300 K with exposures >3500 L (oxide layers created from O 2 are significantly greater at much smaller exposures). Formation of a critical density of Nb 2O 5 is suggested to be responsible for the enhanced corrosion resistance by preventing diffusion of O - (O 2-) or OD -/OH - into the oxide/metal interface region. The domains of stability of hydroxyl formation have also been followed using TPD, SSIMS and XPS. Maximal surface hydroxyl concentrations ( Θrel=0.30) are obtained at a surface temperature of 175 K for these experimental conditions.

  5. Solution structure of the chromomycin-DNA complex

    SciTech Connect

    Gao, X.; Patel, D.J. )

    1989-01-24

    The structure of the chromomycin-DNA complex at the deoxyoctanucleotide duplex level has been determined from one- and two-dimensional proton NMR studies in Mg-containing aqueous solution. The NMR results demonstrate that the antitumor agent binds as a symmetrical dimer to the self-complementary d(T-T-G-G-C-C-A-A) duplex with retention of the 2-fold symmetry in the complex. A set of intermolecular nuclear Overhauser enhancements (NOEs) established that two chromomycin molecules in the dimer share the minor groove at the G-G-C-C{center dot}G-G-C-C segment in such a way that each hydrophilic edge of the chromophore is located next to the G-G{center dot}C-C half-site and each C-D-E trisaccharide chain extends toward the 3{prime}-direction of the octanucleotide duplex. In addition, the A-B disaccharide segment and the hydrophilic side chain of the antitumor agent are directed toward the phosphate backbone. The observed changes in nucleic acid NOEs and coupling patterns on complex formation establish a transition to a wider and shallower minor groove at the central G-G-C-C{center dot}G-G-C-C segment required for accommodating the chromomycin dimer. The present demonstration that chromomycin binds as a dimer and switches the conformation of the DNA at its G{center dot}C-rich minor groove binding site provides new insights into antitumor agent design and the sequence specificity of antitumor agent-DNA recognition.

  6. Structural changes of CF 1-ATPase in solution

    NASA Astrophysics Data System (ADS)

    Calmettes, P.; Pezennec, S.; Berger, G.; Girault, G.

    1992-06-01

    Small changes in neutron scattering spectra were observed when spinach CF 1-ATPase is activated by dithiothreitol or allowed to bind to a nucleotide. It is shown that activation induces a significant conformation change whereas substrate binding does not. In solution, MgATP or MgAMP mainly modifies the interactions between the solute molecules.

  7. Formation mechanisms, structure, solution behavior, and reactivity of aminodiborane.

    PubMed

    Li, Huizhen; Ma, Nana; Meng, Wenjuan; Gallucci, Judith; Qiu, Yongqing; Li, Shujun; Zhao, Qianyi; Zhang, Jie; Zhao, Ji-Cheng; Chen, Xuenian

    2015-09-30

    A facile synthesis of cyclic aminodiborane (NH2B2H5, ADB) from ammonia borane (NH3·BH3, AB) and THF·BH3 has made it possible to determine its important characteristics. Ammonia diborane (NH3BH2(μ-H)BH3, AaDB) and aminoborane (NH2BH2, AoB) were identified as key intermediates in the formation of ADB. Elimination of molecular hydrogen occurred from an ion pair, [H2B(NH3) (THF)](+)[BH4](-). Protic-hydridic hydrogen scrambling was proved on the basis of analysis of the molecular hydrogen products, ADB and other reagents through (2)H NMR and MS, and it was proposed that the scrambling occurred as the ion pair reversibly formed a BH5-like intermediate, [(THF)BH2NH2](η(2)-H2)BH3. Loss of molecular hydrogen from the ion pair led to the formation of AoB, most of which was trapped by BH3 to form ADB with a small amount oligomerizing to (NH2BH2)n. Theoretical calculations showed the thermodynamic feasibility of the proposed intermediates and the activation processes. The structure of the ADB·THF complex was found from X-ray single crystal analysis to be a three-dimensional array of zigzag chains of ADB and THF, maintained by hydrogen and dihydrogen bonding. Room temperature exchange of terminal and bridge hydrogens in ADB was observed in THF solution, while such exchange was not observed in diethyl ether or toluene. Both experimental and theoretical results confirm that the B-H-B bridge in ADB is stronger than that in diborane (B2H6, DB). The B-H-B bridge is opened when ADB and NaH react to form sodium aminodiboronate, Na[NH2(BH3)2]. The structure of the sodium salt as its 18-crown-6 ether adduct was determined by X-ray single crystal analysis. PMID:26335760

  8. Comparison of the crystal and solution structures of two RNA oligonucleotides.

    PubMed Central

    Rife, J P; Stallings, S C; Correll, C C; Dallas, A; Steitz, T A; Moore, P B

    1999-01-01

    Until recently, there were no examples of RNAs whose structures had been determined by both NMR and x-ray crystallography, and thus there was no experimental basis for assessing the accuracy of RNA solution structures. A comparison of the solution and the crystal structures of two RNAs is presented, which demonstrates that NMR can produce solution structures that resemble crystal structures and thus validates the application to RNA of a methodology developed initially for the determination of protein conformations. Models for RNA solution structures are appreciably affected by the parameters used for their refinement that describe intramolecular interactions. For the RNAs of interest here, the more realistic those parameters, the greater the similarity between solution structures and crystal structures. PMID:9876123

  9. Valence Electronic Structure of Aqueous Solutions: Insights from Photoelectron Spectroscopy

    NASA Astrophysics Data System (ADS)

    Seidel, Robert; Winter, Bernd; Bradforth, Stephen E.

    2016-05-01

    The valence orbital electron binding energies of water and of embedded solutes are crucial quantities for understanding chemical reactions taking place in aqueous solution, including oxidation/reduction, transition-metal coordination, and radiation chemistry. Their experimental determination based on liquid-photoelectron spectroscopy using soft X-rays is described, and we provide an overview of valence photoelectron spectroscopy studies reported to date. We discuss principal experimental aspects and several theoretical approaches to compute the measured binding energies of the least tightly bound molecular orbitals. Solutes studied are presented chronologically, from simple electrolytes, via transition-metal ion solutions and several organic and inorganic molecules, to biologically relevant molecules, including aqueous nucleotides and their components. In addition to the lowest vertical ionization energies, the measured valence photoelectron spectra also provide information on adiabatic ionization energies and reorganization energies for the oxidation (ionization) half-reaction. For solutes with low solubility, resonantly enhanced ionization provides a promising alternative pathway.

  10. Valence Electronic Structure of Aqueous Solutions: Insights from Photoelectron Spectroscopy.

    PubMed

    Seidel, Robert; Winter, Bernd; Bradforth, Stephen E

    2016-05-27

    The valence orbital electron binding energies of water and of embedded solutes are crucial quantities for understanding chemical reactions taking place in aqueous solution, including oxidation/reduction, transition-metal coordination, and radiation chemistry. Their experimental determination based on liquid-photoelectron spectroscopy using soft X-rays is described, and we provide an overview of valence photoelectron spectroscopy studies reported to date. We discuss principal experimental aspects and several theoretical approaches to compute the measured binding energies of the least tightly bound molecular orbitals. Solutes studied are presented chronologically, from simple electrolytes, via transition-metal ion solutions and several organic and inorganic molecules, to biologically relevant molecules, including aqueous nucleotides and their components. In addition to the lowest vertical ionization energies, the measured valence photoelectron spectra also provide information on adiabatic ionization energies and reorganization energies for the oxidation (ionization) half-reaction. For solutes with low solubility, resonantly enhanced ionization provides a promising alternative pathway. PMID:27023757

  11. Novel two-step laser ablation and ionization mass spectrometry (2S-LAIMS) of actor-spectator ice layers: Probing chemical composition of D2O ice beneath a H2O ice layer

    NASA Astrophysics Data System (ADS)

    Yang, Rui; Gudipati, Murthy S.

    2014-03-01

    In this work, we report for the first time successful analysis of organic aromatic analytes imbedded in D2O ices by novel infrared (IR) laser ablation of a layered non-absorbing D2O ice (spectator) containing the analytes and an ablation-active IR-absorbing H2O ice layer (actor) without the analyte. With these studies we have opened up a new method for the in situ analysis of solids containing analytes when covered with an IR laser-absorbing layer that can be resonantly ablated. This soft ejection method takes advantage of the tenability of two-step infrared laser ablation and ultraviolet laser ionization mass spectrometry, previously demonstrated in this lab to study chemical reactions of polycyclic aromatic hydrocarbons (PAHs) in cryogenic ices. The IR laser pulse tuned to resonantly excite only the upper H2O ice layer (actor) generates a shockwave upon impact. This shockwave penetrates the lower analyte-containing D2O ice layer (spectator, a non-absorbing ice that cannot be ablated directly with the wavelength of the IR laser employed) and is reflected back, ejecting the contents of the D2O layer into the vacuum where they are intersected by a UV laser for ionization and detection by a time-of-flight mass spectrometer. Thus, energy is transmitted from the laser-absorbing actor layer into the non-absorbing spectator layer resulting its ablation. We found that isotope cross-contamination between layers was negligible. We also did not see any evidence for thermal or collisional chemistry of PAH molecules with H2O molecules in the shockwave. We call this "shockwave mediated surface resonance enhanced subsurface ablation" technique as "two-step laser ablation and ionization mass spectrometry of actor-spectator ice layers." This method has its roots in the well-established MALDI (matrix assisted laser desorption and ionization) method. Our method offers more flexibility to optimize both the processes—ablation and ionization. This new technique can thus be

  12. Novel two-step laser ablation and ionization mass spectrometry (2S-LAIMS) of actor-spectator ice layers: probing chemical composition of D2O ice beneath a H2O ice layer.

    PubMed

    Yang, Rui; Gudipati, Murthy S

    2014-03-14

    In this work, we report for the first time successful analysis of organic aromatic analytes imbedded in D2O ices by novel infrared (IR) laser ablation of a layered non-absorbing D2O ice (spectator) containing the analytes and an ablation-active IR-absorbing H2O ice layer (actor) without the analyte. With these studies we have opened up a new method for the in situ analysis of solids containing analytes when covered with an IR laser-absorbing layer that can be resonantly ablated. This soft ejection method takes advantage of the tenability of two-step infrared laser ablation and ultraviolet laser ionization mass spectrometry, previously demonstrated in this lab to study chemical reactions of polycyclic aromatic hydrocarbons (PAHs) in cryogenic ices. The IR laser pulse tuned to resonantly excite only the upper H2O ice layer (actor) generates a shockwave upon impact. This shockwave penetrates the lower analyte-containing D2O ice layer (spectator, a non-absorbing ice that cannot be ablated directly with the wavelength of the IR laser employed) and is reflected back, ejecting the contents of the D2O layer into the vacuum where they are intersected by a UV laser for ionization and detection by a time-of-flight mass spectrometer. Thus, energy is transmitted from the laser-absorbing actor layer into the non-absorbing spectator layer resulting its ablation. We found that isotope cross-contamination between layers was negligible. We also did not see any evidence for thermal or collisional chemistry of PAH molecules with H2O molecules in the shockwave. We call this "shockwave mediated surface resonance enhanced subsurface ablation" technique as "two-step laser ablation and ionization mass spectrometry of actor-spectator ice layers." This method has its roots in the well-established MALDI (matrix assisted laser desorption and ionization) method. Our method offers more flexibility to optimize both the processes--ablation and ionization. This new technique can thus be potentially

  13. The Lunar Internal Structure Model: Problems and Solutions

    NASA Astrophysics Data System (ADS)

    Nefedyev, Yuri; Gusev, Alexander; Petrova, Natalia; Varaksina, Natalia

    decomposition of gravitational field of the Moon of members up to 165th order with a high degree of accuracy. Judging from the given data, the distinctive feature of the Moon’s gravitational field is that harmonics of the third and even the fourth order are comparable with harmonics of the second order, except for member J2. General conclusion: according to recent data, the true figure of the Moon is much more complex than a three-axis ellipsoid. Gravitational field and dynamic figure of the multilayered Moon: One of the main goals of selenodesy is the study of a dynamic figure of the Moon which determines distribution of the mass within the Moon’s body. A dynamic figure is shaped by the inertia ellipsoid set by values of resultant moments of inertia of the Moon A, B, C and their orientation in space. Selenoid satellites (SS) open new and most perspective opportunities in the study of gravitational field and the Moon’s figure. SSs “Moon 10”, “Apollo”, “Clementine”, “Lunar Prospector” trajectory tracking data processing has allowed for identification of coefficients in decomposition of gravitational field of the Moon of members up to 165th order with a high degree of accuracy. Judging from the given data, the distinctive feature of the Moon’s gravitational field is that harmonics of the third and even the fourth order are comparable with harmonics of the second order. Difference from zero of c-coefficients proves asymmetry of gravitational fields on the visible and invisible sides of the Moon. As a first attempt at solving the problem, the report presents the survey of internal structure of the Moon, tabulated values of geophysical parameters and geophysical profile of the Moon, including liquid lunar core, analytical solution of Clairaut’s equation for the two-layer model of the Moon; mathematical and bifurcational analysis of solution based on physically justified task options; original debugged software in VBA programming language for computer

  14. The structure of ionic aqueous solutions at interfaces: An intrinsic structure analysis

    NASA Astrophysics Data System (ADS)

    Bresme, Fernando; Chacón, Enrique; Tarazona, Pedro; Wynveen, Aaron

    2012-09-01

    We investigate the interfacial structure of ionic solutions consisting of alkali halide ions in water at concentrations in the range 0.2-1.0 molal and at 300 K. Combining molecular dynamics simulations of point charge ion models and a recently introduced computational approach that removes the averaging effect of interfacial capillary waves, we compute the intrinsic structure of the aqueous interface. The interfacial structure is more complex than previously inferred from the analysis of mean profiles. We find a strong alternating double layer structure near the interface, which depends on the cation and anion size. Relatively small changes in the ion diameter disrupt the double layer structure, promoting the adsorption of anions or inducing the density enhancement of small cations with diameters used in simulation studies of lithium solutions. The density enhancement of the small cations is mediated by their strong water solvation shell, with one or more water molecules "anchoring" the ion to the outermost water layer. We find that the intrinsic interfacial electrostatic potential features very strong oscillations with a minimum at the liquid surface that is ˜4 times stronger than the electrostatic potential in the bulk. For the water model employed in this work, SPC/E, the electrostatic potential at the water surface is ˜-2 V, equivalent to ˜80 kBT (for T = 300 K), much stronger than previously considered. Furthermore, we show that the utilization of the intrinsic surface technique provides a route to extract ionic potentials of mean force that are not affected by the thermal fluctuations, which limits the accuracy of most past approaches including the popular umbrella sampling technique.

  15. Solution structure and dynamics, stability, and NIR emission properties of lanthanide complexes with a carboxylated bispyrazolylpyridyl ligand.

    PubMed

    Mato-Iglesias, Marta; Rodríguez-Blas, Teresa; Platas-Iglesias, Carlos; Starck, Matthieu; Kadjane, Pascal; Ziessel, Raymond; Charbonnière, Loïc

    2009-02-16

    The complexation behavior of the ligand 2,6-bis{3-[N,N-bis(carboxymethyl)aminomethyl]pyrazol-1-yl}-pyridine, L, toward lanthanide cations was investigated throughout the series. Potentiometric titration experiments on L (0.1 M KCl) revealed the presence of four protonation steps in the 2-12 pH domain, associated with the protonation of the two tertiary amine nitrogen atoms and with two of the four carboxylate functions. The stability constants for the formation of the [LnL](-) complexes (Ln = La, Nd, Eu, Ho, and Lu) were determined in water and evidenced a hill-shaped complexation trend along the series, with log K increasing from 14.56(9) (La) to 16.68(2) (Ho) and decreasing to 15.42(2) (Lu). Geometry optimizations showed the [LnL](-) complexes (Ln = La, Nd, Eu, Ho, Yb, and Lu) adopting a C(2) symmetry with the symmetry axis going through the metal atom and the nitrogen atom of the central pyridine ring, leading to the presence of Delta and Lambda helical enantiomers. Analysis of the calculated Ln-O and Ln-N bond lengths showed a marked deviation from the expected values at the end of the series, which accounts for the observed decreased complexation affinity. (1)H and (13)C NMR experiments in D(2)O (room temperature) showed the shortening of the bond distances in [LnL](-) complexes from La to Lu to be accompanied by a rigidification of the structure, leading to a decreased C(2) symmetry for the Lu complex compared to C(2v) for La. This decreased symmetry was attributed to a slow Delta <--> Lambda interconversion that was followed by variable-temperature (13)C NMR experiments on the Lu complex. The activation parameters determined by line broadening analysis for this interconversion process point to an associatively assisted interconversion process. The (1)H NMR spectrum of the paramagnetic [YbL](-) complex was investigated in D(2)O, and a lanthanide induced shift analysis showed good agreement between the observed paramagnetic chemical shifts and those calculated

  16. Electronic structures of intermolecular hydrogen bond contacts with solute in aqueous solution: glycine as a working prototype.

    PubMed

    Meng, Lingbiao; Wu, Weidong; Lin, Zijing

    2016-06-21

    The intermolecular hydrogen bond (H-bond) interactions play vital roles in many biological systems. Despite continued interest, the nature of their electronic structures has remained elusive. Based on the unique features of aqueous solution, a simple model depicting the H-bond electronic states by orbital hybridizations is developed. The model is demonstrated by reproducing the experimental IR data and yielding favorable solute-solvent interactions for the prototype glycine. The H-bond state for solute H, O and N atoms is found to be characterized by sp(1), sp(2), and sp(3) hybridizations, respectively. The model provides a new way for probing the intricate solute-solvent contacts. PMID:27243041

  17. Structural qualia: a solution to the hard problem of consciousness

    PubMed Central

    Loorits, Kristjan

    2014-01-01

    The hard problem of consciousness has been often claimed to be unsolvable by the methods of traditional empirical sciences. It has been argued that all the objects of empirical sciences can be fully analyzed in structural terms but that consciousness is (or has) something over and above its structure. However, modern neuroscience has introduced a theoretical framework in which also the apparently non-structural aspects of consciousness, namely the so called qualia or qualitative properties, can be analyzed in structural terms. That framework allows us to see qualia as something compositional with internal structures that fully determine their qualitative nature. Moreover, those internal structures can be identified which certain neural patterns. Thus consciousness as a whole can be seen as a complex neural pattern that misperceives some of its own highly complex structural properties as monadic and qualitative. Such neural pattern is analyzable in fully structural terms and thereby the hard problem is solved. PMID:24672510

  18. Solution structure of p53 core domain: Structural basis for its instability

    PubMed Central

    Cañadillas, José Manuel Pérez; Tidow, Henning; Freund, Stefan M. V.; Rutherford, Trevor J.; Ang, Hwee Ching; Fersht, Alan R.

    2006-01-01

    The 25-kDa core domain of the tumor suppressor p53 is inherently unstable and melts at just above body temperature, which makes it susceptible to oncogenic mutations that inactivate it by lowering its stability. We determined its structure in solution using state-of-the-art isotopic labeling techniques and NMR spectroscopy to complement its crystal structure. The structure was very similar to that in the crystal but far more mobile than expected. Importantly, we were able to analyze by NMR the structural environment of several buried polar groups, which indicated structural reasons for the instability. NMR spectroscopy, with its ability to detect protons, located buried hydroxyl and sulfhydryl groups that form suboptimal hydrogen-bond networks. We mutated one such buried pair, Tyr-236 and Thr-253 to Phe-236 and Ile-253 (as found in the paralogs p63 and p73), and stabilized p53 by 1.6 kcal/mol. We also detected differences in the conformation of a mobile loop that might reflect the existence of physiologically relevant alternative conformations. The effects of temperature on the dynamics of aromatic residues indicated that the protein also experiences several dynamic processes that might be related to the presence of alternative hydrogen-bond patterns in the protein interior. p53 appears to have evolved to be dynamic and unstable. PMID:16461916

  19. A New Solution to the Problem of Finding All Numerical Solutions to Ordered Metric Structures.

    ERIC Educational Resources Information Center

    Lehner, Paul E.; Norma, Elliot

    1980-01-01

    A new algorithm is used to test and describe the set of all possible solutions for any linear model of an empirical ordering derived from techniques such as additive conjoint measurement, unfolding theory, general Fechnerian scaling, and ordinal multiple regression. The algorithm is computationally faster and numerically superior to previous…

  20. The structure of water in solutions containing di- and trivalent cations by empirical potential structure refinement

    NASA Astrophysics Data System (ADS)

    Bowron, Daniel T.; Díaz Moreno, Sofia

    2013-11-01

    Empirical potential structure refinement (EPSR) has been used to build experimentally consistent models of a range of electrolyte solutions containing di- and trivalent cations: Cu(ClO4)2 at concentrations of 0.5 and 2.0 m, and Cr(NO3)3, YCl3 and LaCl3 at a concentration of 1.0 m. The resulting models are used to investigate the perturbation of these electrolytes on the pair distribution and triplet angle correlations between solvent water molecules, compared with those found in the pure solvent. The results elucidate the differences that derive from the reflected range of highly structured local cation environments and provide a complementary viewpoint on the hydration shell geometries.

  1. Structure and interaction among protein and nanoparticle mixture in solution: Effect of temperature

    NASA Astrophysics Data System (ADS)

    Kundu, Sarathi; Das, Kaushik; Mehan, S.; Aswal, V. K.; Kohlbrecher, Joachim

    2015-11-01

    Structure and interaction among globular protein bovine serum albumin (BSA) and silica nanoparticle mixtures in solutions have been studied using small angle neutron scattering technique by varying the solution temperature. Our study shows that in absence of nanoparticles and up to 70 °C, an intermediate range repulsive and one long range attractive interaction potential between the proteins exist. Above that temperature, fractal structure forms. In presence of nanoparticles, fractal structures form even at room temperature by both the protein and nanoparticles. Fractal dimension increases with the increase of BSA concentration and solution temperature, and this temperature induced structural transition is irreversible.

  2. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  3. Growing market acceptance for fiber optic solutions in civil structures

    NASA Astrophysics Data System (ADS)

    Graver, Thomas; Inaudi, Daniele; Doornink, Justin

    2004-12-01

    Owners must manage and ensure the safety of their civil structures even as use of many structures extends well beyond their design lifetime. Traditionally, most structures rely on strict maintenance procedures, visual inspections, and very few sensors. But maintenance is very expensive, visual inspections can miss critical problems, and conventional sensors can fail in harsh environments. Can fiber-optic sensing (FOS) address these issues? This is not a new question, but there are some new answers. This paper highlights several structures where FOS is used, and describes the associated successes and challenges for each application. Many successes are coupled to improved FOS tools: better sensor packages, simpler and less expensive instrumentation, improved installation techniques, and more efficient data analysis tools. Examples of each are provided. Particular attention is given to the economics of instrumenting civil structures - when and how it pays. Conclusions include recommendations for future developments that will further accelerate FOS acceptance and use.

  4. NMR solution structure of the neurotrypsin Kringle domain.

    PubMed

    Ozhogina, Olga A; Grishaev, Alexander; Bominaar, Emile L; Patthy, László; Trexler, Maria; Llinás, Miguel

    2008-11-25

    Neurotrypsin is a multidomain protein that serves as a brain-specific serine protease. Here we report the NMR structure of its kringle domain, NT/K. The data analysis was performed with the BACUS (Bayesian analysis of coupled unassigned spins) algorithm. This study presents the first application of BACUS to the structure determination of a 13C unenriched protein for which no prior experimental 3D structure was available. NT/K adopts the kringle fold, consisting of an antiparallel beta-sheet bridged by an overlapping pair of disulfides. The structure reveals the presence of a surface-exposed left-handed polyproline II helix that is closely packed to the core beta-structure. This feature distinguishes NT/K from other members of the kringle fold and points toward a novel functional role for a kringle domain. Functional divergence among kringle domains is discussed on the basis of their surface and electrostatic characteristics. PMID:18956887

  5. Controlling molecular ordering in solution-state conjugated polymers

    NASA Astrophysics Data System (ADS)

    Zhu, J.; Han, Y.; Kumar, R.; He, Y.; Hong, K.; Bonnesen, P. V.; Sumpter, B. G.; Smith, S. C.; Smith, G. S.; Ivanov, I. N.; Do, C.

    2015-09-01

    of the conjugated polymer can be tuned in hexagonal, micellar and lamellar phases of the surfactant solution. The controlled molecular ordering in conjugated polymer assembly is demonstrated as a key factor determining the electronic interaction and optical function. Electronic supplementary information (ESI) available: Theoretical simulations for polymer/surfactant interaction and coiled-to-rod-like chain conformational transition; transmission electron microscopy (TEM) imaging and analysis; small angle X-ray and neutron scattering procedure and fitting methods; UV-Vis absorption of P3EOT/C12E5/D2O solution; 1H-NMR analysis of P3EOT/D2O solution. See DOI: 10.1039/c5nr02037a

  6. Integrated Force Method Solution to Indeterminate Structural Mechanics Problems

    NASA Technical Reports Server (NTRS)

    Patnaik, Surya N.; Hopkins, Dale A.; Halford, Gary R.

    2004-01-01

    Strength of materials problems have been classified into determinate and indeterminate problems. Determinate analysis primarily based on the equilibrium concept is well understood. Solutions of indeterminate problems required additional compatibility conditions, and its comprehension was not exclusive. A solution to indeterminate problem is generated by manipulating the equilibrium concept, either by rewriting in the displacement variables or through the cutting and closing gap technique of the redundant force method. Compatibility improvisation has made analysis cumbersome. The authors have researched and understood the compatibility theory. Solutions can be generated with equal emphasis on the equilibrium and compatibility concepts. This technique is called the Integrated Force Method (IFM). Forces are the primary unknowns of IFM. Displacements are back-calculated from forces. IFM equations are manipulated to obtain the Dual Integrated Force Method (IFMD). Displacement is the primary variable of IFMD and force is back-calculated. The subject is introduced through response variables: force, deformation, displacement; and underlying concepts: equilibrium equation, force deformation relation, deformation displacement relation, and compatibility condition. Mechanical load, temperature variation, and support settling are equally emphasized. The basic theory is discussed. A set of examples illustrate the new concepts. IFM and IFMD based finite element methods are introduced for simple problems.

  7. Solution theorems for the standard eigenvalue problem of structures with uncertain-but-bounded parameters

    NASA Astrophysics Data System (ADS)

    Qiu, Zhiping; Wang, Xiaojun

    2005-04-01

    Generalized eigenvalue problems from the modal analysis are often converted to the standard eigenvalue problems. In this paper, it evaluates the upper and lower bounds on the eigenvalues of the standard eigenvalue problem of structures subject to severely deficient information about the structural parameters. Here, we focus on non-probabilistic interval analysis models of uncertainty, which are adapted to the case of severe lack of information on uncertainty. Non-probabilistic, interval analysis method in which uncertainties are defined by interval numbers appears as an alternative to the classical probabilistic models. For the standard eigenvalue problem of structures with uncertain-but-bounded parameters, the vertex solution theorem, the positive semi-definite solution theorem and the parameter decomposition solution theorem for the standard eigenvalue problem are presented, and compared with Deif's solution theorem in numerical examples. It is shown that, for the upper and lower bounds on the eigenvalues of the standard eigenvalue problem with uncertain-but-bounded parameters, the presented vertex solution theorem is unconditional, and the positive semi-definite solution theorem and the parameter decomposition solution theorem have less limitary conditions compared with Deif's solution theorem. The effectiveness of the vertex solution theorem, the positive semi-definite solution theorem and the parameter decomposition solution theorem are illustrated by numerical examples

  8. The Surface Structure of Concentrated Aqueous salt Solutions

    SciTech Connect

    Sloutskin,E.; Baumert, J.; Ocko, B.; Kuzmenko, I.; Checco, A.; Tamam, L.; Ofer, E.; Gog, T.; Deutsch, M.

    2007-01-01

    The surface-normal electron density profile {rho}{sub s}(z) of concentrated aqueous salt solutions of RbBr, CsCl, LiBr, RbCl, and SrCl{sub 2} was determined by x-ray reflectivity (XR). For all but RbBr and SrCl{sub 2} {rho}{sub s}(z) increases monotonically with depth z from {rho}{sub s}(z)=0 in the vapor (z<0) to {rho}{sub s}(z) = {rho}{sub b} of the bulk (z>0) over a width of a few angstroms. The width is commensurate with the expected interface broadening by thermally excited capillary waves. Anomalous (resonant) XR of RbBr reveals a depletion at the surface of Br{sup -} ions to a depth of {approx}10 A. For SrCl{sub 2}, the observed {rho}{sub s}(z)>{rho}{sub b} may imply a similar surface depletion of Cl{sup -} ions to a depth of a few angstroms. However, as the deviations of the XRs of RbBr and SrCl{sub 2} from those of the other solutions are small, the evidence for a different ion composition in the surface and the bulk is not strongly conclusive. Overall, these results contrast earlier theoretical and simulational results and nonstructural measurements, where significant surface layering of alternate, oppositely charged, ions is concluded.

  9. Structure and morphology of charged graphene platelets in solution by small-angle neutron scattering.

    PubMed

    Milner, Emily M; Skipper, Neal T; Howard, Christopher A; Shaffer, Milo S P; Buckley, David J; Rahnejat, K Adam; Cullen, Patrick L; Heenan, Richard K; Lindner, Peter; Schweins, Ralf

    2012-05-23

    Solutions of negatively charged graphene (graphenide) platelets were produced by intercalation of nanographite with liquid potassium-ammonia followed by dissolution in tetrahydrofuran. The structure and morphology of these solutions were then investigated by small-angle neutron scattering. We found that >95 vol % of the solute is present as single-layer graphene sheets. These charged sheets are flat over a length scale of >150 Å in solution and are strongly solvated by a shell of solvent molecules. Atomic force microscopy on drop-coated thin films corroborated the presence of monolayer graphene sheets. Our dissolution method thus offers a significant increase in the monodispersity achievable in graphene solutions. PMID:22574888

  10. Finite element solution of transient fluid-structure interaction problems

    NASA Technical Reports Server (NTRS)

    Everstine, Gordon C.; Cheng, Raymond S.; Hambric, Stephen A.

    1991-01-01

    A finite element approach using NASTRAN is developed for solving time-dependent fluid-structure interaction problems, with emphasis on the transient scattering of acoustic waves from submerged elastic structures. Finite elements are used for modeling both structure and fluid domains to facilitate the graphical display of the wave motion through both media. For the liquid, the use of velocity potential as the fundamental unknown results in a symmetric matrix equation. The approach is illustrated for the problem of transient scattering from a submerged elastic spherical shell subjected to an incident tone burst. The use of an analogy between the equations of elasticity and the wave equation of acoustics, a necessary ingredient to the procedure, is summarized.

  11. Disproportionation and thermochemical sulfate reduction reactions in S-H20-Ch4 and S-D2O-CH4 systems from 200 to 340 °C at elevated pressures

    USGS Publications Warehouse

    Yuan, Shunda; Chou, I-Ming; Burruss, Robert A.

    2013-01-01

    Elemental sulfur, as a transient intermediate compound, by-product, or catalyst, plays significant roles in thermochemical sulfate reduction (TSR) reactions. However, the mechanisms of the reactions in S-H2O-hydrocarbons systems are not clear. To improve our understanding of reaction mechanisms, we conducted a series of experiments between 200 and 340 °C for S-H2O-CH4, S-D2O-CH4, and S-CH4-1m ZnBr2 systems in fused silica capillary capsules (FSCC). After a heating period ranging from 24 to 2160 hours (hrs), the quenched samples were analyzed by Raman spectroscopy. Combined with the in situ Raman spectra collected at high temperatures and pressures in the S-H2O and S-H2O-CH4 systems, our results showed that (1) the disproportionation of sulfur in the S-H2O-CH4 system occurred at temperatures above 200 °C and produced H2S, SO42-, and possibly trace amount of HSO4-; (2) sulfate (and bisulfate), in the presence of sulfur, can be reduced by methane between 250 and 340 °C to produce CO2 and H2S, and these TSR temperatures are much closer to those of the natural system (2O-CH4 system may take place simultaneously, with TSR being favored at higher temperatures; and (4) in the system S-D2O-CH4, both TSR and the competitive disproportionation reactions occurred simultaneously at temperatures above 300 °C, but these reactions were very slow at lower temperatures. Our observation of methane reaction at 250 °C in a laboratory time scale suggests that, in a geologic time scale, methane may be destroyed by TSR reactions at temperatures > 200 °C that can be reached by deep drilling for hydrocarbon resources.

  12. Comprehensive Structural Studies of 2′,3′-Difluorinated Nucleosides: Comparison of Theory, Solution, and Solid State

    PubMed Central

    Barchi, Joseph J.; Karki, Rajeshri G.; Nicklaus, Marc C.; Siddiqui, Maqbool A.; George, Clifford; Mikhailopulo, Igor A.; Marquez, Victor E.

    2009-01-01

    The conformations of three 2′,3′-difluoro uridine nucleosides were studied by X-ray crystallography, NMR spectroscopy, and ab initio calculations in an attempt to define the roles that the two vicinal fluorine atoms play in the puckering preferences of the furanose ring. Two of the compounds examined contained fluorine atoms in either the arabino or xylo dispositions at C2′ and C3′ of a 2′,3′-dideoxyuridine system. The third compound also incorporated fluorine atoms in the xylo configuration on the furanose ring but was substituted with a 6-azauracil base in place of uracil. A battery of NMR experiments in D2O solution was used to identify conformational preferences primarily from coupling constant and NOE data. Both 1H and 19F NMR data were used to ascertain the preferred sugar pucker of the furanose ring through the use of the program PSEUROT. Compound-dependent parameters used in the PSEUROT calculations were newly derived from complete sets of conformations calculated from high-level ab initio methods. The solution and theoretical data were compared to the conformations of each molecule in the solid state. It was shown that both gauche and antiperiplanar effects may be operative to maintain a pseudodiaxial arrangement of the C2′and C3′ vicinal fluorine atoms. These data, along with previously reported data by us and others concerning monofluorinated nucleoside conformations, were used to propose a model of how fluorine influences different aspects of nucleoside conformations. PMID:18558684

  13. Structure and photophysics in C 60-micellar solutions

    NASA Astrophysics Data System (ADS)

    Eastoe, Julian; Crooks, Esther R.; Beeby, Andrew; Heenan, Richard K.

    1995-11-01

    Routes to the preparation of monomeric and colloidal C 60 in micellar solutions of non-ionic surfactants are described. UV-visible spectra and small-angle neutron scattering provide clear evidence for these two different forms. The micelles serve to stabilise the excited triplet state 3C 60 and the lifetime τT is increased by a factor of 3 as compared to 3C 60 in toluene. Furthermore, with monomeric dispersions in the presence of the electron donor DABCO, the radical anion C 60- is formed, with an unusually long lifetime τA = 16 ms. This lifetime is approximately 270 times longer than for γ-cyclodextrin. stabilised systems.

  14. Comparison of the crystal and solution structures of calmodulin and troponin C

    SciTech Connect

    Heidorn, D.B.; Trewhella, J.

    1988-02-09

    X-ray solution scattering data from skeletal muscle troponin C and from calmodulin have been measured. Modeling studies based on the crystal structure coordinates for these proteins show discrepancies between the solution data and the crystal structure that indicate that if the size and shape of the globular domains are the same in solution as in the crystal, the distances between them must be smaller by several angstroms. Bringing the globular domains closer together requires structural changes in the interconnecting helix that joins them.

  15. Solution structure of a dsDNA:LNA triplex

    PubMed Central

    Sørensen, Jesper J.; Nielsen, Jakob T.; Petersen, Michael

    2004-01-01

    We have determined the NMR structure of an intramolecular dsDNA:LNA triplex, where the LNA strand is composed of alternating LNA and DNA nucleotides. The LNA oligonucleotide binds to the dsDNA duplex in the major groove by formation of Hoogsteen hydrogen bonds to the purine strand of the duplex. The structure of the dsDNA duplex is changed to accommodate the LNA strand, and it adopts a geometry intermediate between A- and B-type. There is a substantial propeller twist between base-paired nucleobases. This propeller twist and a concomitant large propeller twist between the purine and LNA strands allows the pyrimidines of the LNA strand to interact with the 5′-flanking duplex pyrimidines. Altogether, the triplex has a regular global geometry as shown by a straight helix axis. This shows that even though the third strand is composed of alternating DNA and LNA monomers with different sugar puckers, it forms a seamless triplex. The thermostability of the triplex is increased by 19°C relative to the unmodified DNA triplex at acidic pH. Using NMR spectroscopy, we show that the dsDNA:LNA triplex is stable at pH 8, and that the triplex structure is identical to the structure determined at pH 5.1. PMID:15550567

  16. Element-by-element Solution Procedures for Nonlinear Structural Analysis

    NASA Technical Reports Server (NTRS)

    Hughes, T. J. R.; Winget, J. M.; Levit, I.

    1984-01-01

    Element-by-element approximate factorization procedures are proposed for solving the large finite element equation systems which arise in nonlinear structural mechanics. Architectural and data base advantages of the present algorithms over traditional direct elimination schemes are noted. Results of calculations suggest considerable potential for the methods described.

  17. Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines

    PubMed Central

    de Sanctis, Daniele; Oscarsson, Marcus; Popov, Alexander; Svensson, Olof; Leonard, Gordon

    2016-01-01

    The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated. PMID:26960128

  18. The young hard active Sun: soft X-ray irradiation of tryptophan in water solutions

    NASA Astrophysics Data System (ADS)

    Ciaravella, A.; Bongiorno, D.; Cecchi-Pestellini, C.; Testa, M. L.; Indelicato, S.; Barbera, M.; Collura, A.; La Barbera, A.; Mingoia, F.

    2011-01-01

    The X-ray emission of the young Sun was much harder and intense than today and might have played a significant role in the evolution of complex organics in protoplanetary environments. We investigate the effects of soft X-rays on tryptophan molecules in aqueous solutions at room temperature. As results of the irradiation experiments we detect several light species indicative of fragmentation, together with large molecular structures such as tryptophan dipeptide and tripeptide. Complexification is more evident in H2O solution than in D2O, probably due to isotopic effects. The abundances of peptides depend on the irradiation dose and decrease with increasing energy deposition. Radicals such as D, OD, H and OH, induced by the X-ray interaction with solvents, play a major role in determining the final products.

  19. Molecular solutes in ionic liquids: a structural perspective.

    PubMed

    Pádua, Agílio A H; Costa Gomes, Margarida F; Canongia Lopes, José N A

    2007-11-01

    Understanding physicochemical properties of ionic liquids is important for their rational use in extractions, reactions, and other applications. Ionic liquids are not simple fluids: their ions are generally asymetric, flexible, with delocalized electrostatic charges, and available in a wide variety. It is difficult to capture their subtle properties with models that are too simplistic. Molecular simulation using atomistic force fields, which describe structures and interactions in detail, is an excellent tool to gain insights into their liquid-state organization, how they solvate different compounds, and what molecular factors determine their properties. The identification of certain ionic liquids as self-organized phases, with aggregated nonpolar and charged domains, provides a new way to interpret the solvation and structure of their mixtures. Many advances are the result of a successful interplay between experiment and modeling, possible in this field where none of the two methodologies had a previous advance. PMID:17661440

  20. Assembly and solution structure of the core retromer protein complex.

    PubMed

    Norwood, Suzanne J; Shaw, Daniel J; Cowieson, Nathan P; Owen, David J; Teasdale, Rohan D; Collins, Brett M

    2011-01-01

    Retromer is a peripheral membrane protein complex that has pleiotropic roles in endosomal membrane trafficking. The core of retromer possesses three subunits, VPS35, VPS29 and VPS26, that play different roles in binding to cargo, regulatory proteins and complex stabilization. We have performed an investigation of the thermodynamics of core retromer assembly using isothermal titration calorimetry (ITC) demonstrating that VPS35 acts as the central subunit to which VPS29 and VPS26 bind independently. Furthermore, we confirm that the conserved PRLYL motif of the large VPS35 subunit is critical for direct VPS26 interaction. Heat capacity measurements of VPS29 and VPS26 binding to VPS35 indicate extensive binding interfaces and suggest conformational alterations in VPS29 or VPS35 upon complex formation. Solution studies of the retromer core using small-angle X-ray scattering allow us to propose a model whereby VPS35 forms an extended platform with VPS29 and VPS26 bound at distal ends, with the potential for forming dimeric assemblies. PMID:20875039

  1. Structure and solution properties of tamarind-seed polysaccharide.

    PubMed

    Gidley, M J; Lillford, P J; Rowlands, D W; Lang, P; Dentini, M; Crescenzi, V; Edwards, M; Fanutti, C; Reid, J S

    1991-07-30

    The major polysaccharide in tamarind seed is a galactoxyloglucan for which the ratios galactose:xylose:glucose are 1:2:25:2.8. A minor polysaccharide (2-3%) contains branched (1----5)-alpha-L-arabinofuranan and unbranched (1----4)-beta-D-galactopyranan features. Small-angle X-ray scattering experiments gave values for the cross-sectional radius of the polymer in aqueous solution that were typical of single-stranded molecules. Marked stiffness of the chain (C infinity 110) was deduced from static light-scattering studies and is ascribed partially to the restriction of the motion of the (1----4)-beta-D-glucan backbone by its extensive (approximately 80%) glycosylation. The rigidity of the polymer caused significant draining effects which heavily influenced the hydrodynamic behaviour. The dependence of "zero-shear" viscosity on concentration was used to characterise "dilute" and "semi-dilute" concentration regimes. The marked dependence on concentration in the "semi-dilute" region was similar to that for other stiff neutral polysaccharide systems, ascribed to "hyper-entanglements", and it is suggested that these may have arisen through a tenuous alignment of stiffened chains. PMID:1769022

  2. ANOVA-HDMR structure of the higher order nodal diffusion solution

    SciTech Connect

    Bokov, P. M.; Prinsloo, R. H.; Tomasevic, D. I.

    2013-07-01

    Nodal diffusion methods still represent a standard in global reactor calculations, but employ some ad-hoc approximations (such as the quadratic leakage approximation) which limit their accuracy in cases where reference quality solutions are sought. In this work we solve the nodal diffusion equations utilizing the so-called higher-order nodal methods to generate reference quality solutions and to decompose the obtained solutions via a technique known as High Dimensional Model Representation (HDMR). This representation and associated decomposition of the solution provides a new formulation of the transverse leakage term. The HDMR structure is investigated via the technique of Analysis of Variance (ANOVA), which indicates why the existing class of transversely-integrated nodal methods prove to be so successful. Furthermore, the analysis leads to a potential solution method for generating reference quality solutions at a much reduced calculational cost, by applying the ANOVA technique to the full higher order solution. (authors)

  3. Nuclear magnetic resonance studies of 2'- and 3'-ribonucleotide structures in solution.

    PubMed

    Davies, D B; Danyluk, S S

    1975-02-11

    A systematic 220-MHz proton nuclear magnetic resonance (nmr) study has been made of all common purine and pyrimidine 2'(3')-ribonucleotides in D2O solutions at 20 plus or minus 2 degrees. Spectra for the entire series were measured under similar conditions of concentration, temperature, and ionic strength, thereby facilitating intercomparisons of spectral properties. Spectral assignments were accomplished with the aid of selected 31P-1H decoupling experiments and accurate values of nmr parameters were derived by simulation-iteration procedures. A detailed analysis of the coupling constants and chemical shifts permitted a determination of conformational properties for ribose rings, exocyclic carbinol and phosphate groups, and the orientation of base-ribose rings. Following procedures described elsewhere, an evaluation was made of ribose ring pseudorotational parameters for each 2'(3')-nucleotide. The results show that both the degree of pucker and pseudorotational angle vary only slightly throughout the entire series of molecules, and lie within the ranges found in the crystalline state. Furthermore, the ribose rings are in rapid equilibrium between N type (C(3')-ENDO, C(2')-exo) and S type (C(2')-endo, C(3')-exo) conformers, N forms and is formed by S, with an S type conformer favored in purine 2'(3')-ribonucleotides (-60:40) while pyrimidines exhibit approximately equal compositions. Thus, the phosphate location on the ring has less of an effect on ring properties than the nature of the base ring. An analysis is also reported of rotamer equilibria about C(4')-C(5'), C(2')-O(2'), and C(3')-O(3') bonds. For the former the nmr coupling constant data are consistent with a predominant gg rotamer (-70%) with gt and tg rotamers populated to the extent of -20 and -10%, respectively. No correlation of the type seen for 5'-nucleotides appears to exist between C(4')-C(5') gg population and ribose ring equilibrium composition. For 2'-nucleotides the 31P-H(2') coupling data

  4. Phase Behavior of a Single Structured Ionomer Chain in Solution

    DOE PAGESBeta

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; Grest, Gary S.

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. Inmore » hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.« less

  5. Phase Behavior of a Single Structured Ionomer Chain in Solution

    SciTech Connect

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; Grest, Gary S.

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. In hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.

  6. Structural characterization of human general transcription factor TFIIF in solution

    PubMed Central

    Akashi, Satoko; Nagakura, Shinjiro; Yamamoto, Seiji; Okuda, Masahiko; Ohkuma, Yoshiaki; Nishimura, Yoshifumi

    2008-01-01

    Human general transcription factor IIF (TFIIF), a component of the transcription pre-initiation complex (PIC) associated with RNA polymerase II (Pol II), was characterized by size-exclusion chromatography (SEC), electrospray ionization mass spectrometry (ESI-MS), and chemical cross-linking. Recombinant TFIIF, composed of an equimolar ratio of α and β subunits, was bacterially expressed, purified to homogeneity, and found to have a transcription activity similar to a natural one in the human in vitro transcription system. SEC of purified TFIIF, as previously reported, suggested that this protein has a size >200 kDa. In contrast, ESI-MS of the purified sample gave a molecular size of 87 kDa, indicating that TFIIF is an αβ heterodimer, which was confirmed by matrix-assisted laser desorption/ionization (MALDI) MS of the cross-linked TFIIF components. Recent electron microscopy (EM) and photo-cross-linking studies showed that the yeast TFIIF homolog containing Tfg1 and Tfg2, corresponding to the human α and β subunits, exists as a heterodimer in the PIC, so the human TFIIF is also likely to exist as a heterodimer even in the PIC. In the yeast PIC, EM and photo-cross-linking studies showed different results for the mutual location of TFIIE and TFIIF along DNA. We have examined the direct interaction between human TFIIF and TFIIE by ESI-MS, SEC, and chemical cross-linking; however, no direct interaction was observed, at least in solution. This is consistent with the previous photo-cross-linking observation that TFIIF and TFIIE flank DNA separately on both sides of the Pol II central cleft in the yeast PIC. PMID:18218714

  7. Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Eckert, S.; Miedema, P. S.; Quevedo, W.; O'Cinneide, B.; Fondell, M.; Beye, M.; Pietzsch, A.; Ross, M.; Khalil, M.; Föhlisch, A.

    2016-03-01

    The speciation of 2-Mercaptopyridine in aqueous solution has been investigated with nitrogen 1s Near Edge X-ray Absorption Fine Structure spectroscopy and time dependent Density Functional Theory. The prevalence of distinct species as a function of the solvent basicity is established. No indications of dimerization towards high concentrations are found. The determination of different molecular structures of 2-Mercaptopyridine in aqueous solution is put into the context of proton-transfer in keto-enol and thione-thiol tautomerisms.

  8. Thermodynamic and structural aspects of sulfonamide crystals and solutions.

    PubMed

    Perlovich, German L; Tkachev, Valery V; Strakhova, Nadezda N; Kazachenko, Vladimir P; Volkova, Tatyana V; Surov, Oleg V; Schaper, Klaus-Jürgen; Raevsky, Oleg A

    2009-12-01

    The crystal structures of three sulfonamides with the general structure 4-NH(2)-C(6)H(4)-SO(2)NH-C(6)H(4/3)-R (R = 4-Et; 4-OMe; 5-Cl-2-Me) have been determined by X-ray diffraction. On the basis of our previous data and the results obtained a comparative analysis of crystal properties was performed: molecular conformational states, packing architecture, and hydrogen bond networks using graph set notations. The thermodynamic aspects of the sulfonamide sublimation process have been studied by investigating the temperature dependence of vapor pressure using the transpiration method. A regression equation was derived describing the correlation between sublimation entropy terms and crystal density data calculated from X-ray diffraction results. Also correlations between sublimation Gibbs energies and melting points, on the one hand, and between sublimation enthalpies and fusion enthalpies at 298 K, on the other hand, were found. These dependencies give the opportunity to predict sublimation thermodynamic parameters by simple thermo-physical experiments (fusion characteristics). Solubility processes of the compounds in water, n-hexane, and n-octanol (as phases modeling various drug delivery pathways and different types of membranes) were investigated and corresponding thermodynamic functions were calculated as well. Thermodynamic characteristics of sulfonamide solvation were evaluated. For compounds with similar structures processes of transfer from one solvent to another one were studied by a diagram method combined with analysis of enthalpic and entropic terms. Distinguishing between enthalpy and entropy, as is possible through the present approach, leads to the insight that the contribution of these terms is different for different molecules (entropy- or enthalpy-determined). Thus, in contrast to interpretation of only the Gibbs energy of transfer, being extensively used for pharmaceuticals in the form of the partition coefficient (log P), the analysis of

  9. Minimizing distortion in truss structures - A Hopfield network solution

    NASA Technical Reports Server (NTRS)

    Fu, B.; Hajela, P.

    1992-01-01

    Distortions in truss structures can result from random errors in element lengths that are typical of a manufacturing process. These distortions may be minimized by an optimal selection of elements from those available for placement between the prescribed nodes - a combinatorial optimization problem requiring significant investment of computational resource for all but the smallest problems. The present paper describes a formulation in which near-optimal element assignments are obtained as minimum-energy stable states, of an analogous Hopfield neural network. This requires mapping of the optimization problem into an energy function of the appropriate Liapunov form. The computational architecture is ideally suited to a parallel processor implementation and offers significant savings in computational effort. A numerical implementation of the approach is discussed with reference to planar truss problems.

  10. Minimizing distortion in truss structures -- a Hopfield network solution

    NASA Technical Reports Server (NTRS)

    Fu, B.; Hajela, P.

    1993-01-01

    Distortions in truss structures can result from random errors in elemental lengths that are typical of a manufacturing process. These distortions may be minimized by an optimal selection of elements from those available for placement between the prescribed nodes -- a combinatorial optimization problem requiring significant investment of computational resource for all but the smallest problems. The present paper describes a formulation in which near-optimal element assignments are obtained as minimum energy, stable states, of an analogous Hopfield neural network. This requires mapping of the optimization problem into an energy function of the appropriate Lyapunov form. The computational architecture is ideally suited to a parallel processor implementation and offers significant savings in computational effort. A numerical implementation of the approach is discussed with reference to planar truss problems.

  11. Solution structure of a designed cyclic peptide ligand for nickel and copper ions

    PubMed Central

    Eshelman, Matthew R.; Aldous, Amanda R.; Neupane, Kosh P.; Kritzer, Joshua A.

    2014-01-01

    Nuclear magnetic resonance (NMR) spectroscopy was used to study a cyclic peptide derived from the amino-terminal copper-and-nickel-binding (ATCUN) motif. The three-dimensional structure of the unliganded peptide in aqueous solution was solved by simulated annealing using distance constraints derived from Nuclear Overhauser Effects. A structural model for the Ni(II)-bound complex was also produced based on NMR evidence and prior spectroscopic data, which are consistent with crystal structures of linear ATCUN complexes. Structural interpolation, or “morphing,” was used to understand the transition of this highly structured cyclic peptide from its unliganded structure to its metal-ion-bound structure. PMID:25414527

  12. Exploiting special problem structure when reliably investigating the solution of systems of IVPs and DDEs

    NASA Astrophysics Data System (ADS)

    Enright, W. H.

    2016-06-01

    In recent years we have developed a class of reliable order p methods for the approximate solution of general systems of initial value problems (IVPs) and delay differential equations (DDEs). In the theoretical analysis of these methods we have identified several trade-offs that do arise and have to be addressed when applying these methods to problems that exhibit special structure. Similar trade-offs also arise when one is concerned with investigating other important properties of the solutions. We will give examples of such trade-offs that arise when investigating the sensitivities of the solutions, and when very accurate approximate solutions are required.

  13. Modifications in structure and interaction of nanoparticle-protein-surfactant complexes in electrolyte solution

    NASA Astrophysics Data System (ADS)

    Mehan, Sumit; Kumar, S.; Aswal, V. K.; Schweins, R.

    2016-05-01

    SANS experiments of three-component system of anionic silica nanoparticles, anionic BSA protein and anionic SDS surfactants have been carried out without and with electrolyte in aqueous solution. In both the cases, the interaction of surfactant with protein results in formation of bead-necklace structure of protein-surfactant complexes in solution. These protein-surfactant complexes interact very differently with nanoparticles in absence and presence of electrolyte. In absence of electrolyte, nanoparticles remain in dispersed phase in solution, whereas with the addition of electrolyte the nanoparticles fractal aggregates are formed. SANS describes the phase behavior to be governed by competition of electrostatic and depletion interactions among the components solution.

  14. Global structure of black hole and brane solutions in a multidimensional model with anisotropic fluid

    NASA Astrophysics Data System (ADS)

    Bolokhov, S. V.; Ivashchuk, V. D.

    We analyse the global causal structure of a family of multidimensional spherically-symmetric solutions with a horizon which appear in the model with 1-component anisotropic fluid. This family can be considered as a generalized analogs of the well-known black hole solutions (including the Reissner--Nordström one) and some black brane solutions. The structure of regular horizons and singular boundaries is studied, and the corresponding Carter--Penrose diagrams are constructed for various values of the parameters of the model.

  15. Regular branched Macromolecules: Structure of Bottlebrush Polymers in Solution

    NASA Astrophysics Data System (ADS)

    Pakula, T.; Rathgeber, S.; Matyjaszewski, K.

    2001-03-01

    The shape and internal structure of bottlebrush (comb) macromolecules under good solvent conditions have been studied using small angle neutron scattering and computer simulations. The form factor S(Q) was measured at low concentrations in toluene for comb polymers consisting of a p(BPEM) backbone with p(nBA) side chains. The following intramolecular parameters were varied: (1) backbone length, (2) grafting density and (3) length of the side chains. Using models which have been successfully applied to other regular branched polymers we derive the range of the hydrodynamic interaction within the polymer and the particle dimension from which we can conclude on the overall shape of the macromolecular brush. In addition we determined the radius of the gyration of the backbone R_g^bb and of the side chains R_g^sc. These parameters give information about the stiffness of the polymer. Experimental findings are compared with computer simulation results performed for a single bottlebrush macromolecule using the cooperative motion algorithm. The simulation gives direct access to R_g^bb and R_g^sc and allows an independent determination of S(Q). Good agreement between experiment and simulation has been found.

  16. Solution structure of the cAMP-dependent protein kinase

    SciTech Connect

    Trewhella, J.; Olah, G.A.; Walsh, D.A.; Mitchell, R.D.

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project as Los Alamos National Laboratory (LANL). Protein phosphorylation is well established as one of the most important mechanisms of signal transduction and cellular regulation. Two of the key enzymes that catalyze these phosphorylation reactions are the cAMP- (PKA) and cGMP- (PKG) dependent protein kinases. PKA has served as the prototypic model of this class of enzymes that now comprises in excess of 300 phylogenetically related proteins. A large number of these protein kinases are critical for the regulation of cell function and a full analysis of their similarities and differences is essential to understand their diverse physiological roles. The cAMP-dependent protein kinase has the subunit structure R2C2, in which C and R refer to the catalytic and regulatory subunits, respectively. The cGMP-dependent protein kinase (PKG) is highly homologous to PKA but is distinguished from it by having the regulatory and catalytic domains on a contiguous polypeptide. The studies described here use small-angle scattering and Fourier Transform InfraRed (FTIR) spectroscopy to study domain movements and conformational changes in these enzymes in different functional states in order to elucidate the molecular bases for the regulation of their activities.

  17. A structured multi-block solution-adaptive mesh algorithm with mesh quality assessment

    NASA Technical Reports Server (NTRS)

    Ingram, Clint L.; Laflin, Kelly R.; Mcrae, D. Scott

    1995-01-01

    The dynamic solution adaptive grid algorithm, DSAGA3D, is extended to automatically adapt 2-D structured multi-block grids, including adaption of the block boundaries. The extension is general, requiring only input data concerning block structure, connectivity, and boundary conditions. Imbedded grid singular points are permitted, but must be prevented from moving in space. Solutions for workshop cases 1 and 2 are obtained on multi-block grids and illustrate both increased resolution of and alignment with the solution. A mesh quality assessment criteria is proposed to determine how well a given mesh resolves and aligns with the solution obtained upon it. The criteria is used to evaluate the grid quality for solutions of workshop case 6 obtained on both static and dynamically adapted grids. The results indicate that this criteria shows promise as a means of evaluating resolution.

  18. Investigations on the structure of DMSO and acetone in aqueous solution

    SciTech Connect

    McLain, Sylvia E; Soper, Alan K

    2007-01-01

    Aqueous solutions of dimethyl sulfoxide (DMSO) and acetone have been investigated using neutron diffraction augmented with isotopic substitution and empirical potential structure refinement computer simulations. Each solute has been measured at two concentrations-1:20 and 1:2 solute:water mole ratios. At both concentrations for each solute, the tetrahedral hydrogen bonding network of water is largely unperturbed, though the total water molecule coordination number is reduced in the higher 1:2 concentrations. With higher concentrations of acetone, water tends to segregate into clusters, while in higher concentrations of DMSO the present study reconfirms that the structure of the liquid is dominated by DMSO-water interactions. This result may have implications for the highly nonideal behavior observed in the thermodynamic functions for 1:2 DMSO-water solutions.

  19. Structure and Interactions in Concentrated Diblock Copolymer Solutions

    NASA Astrophysics Data System (ADS)

    McConnell, Glen A.

    We report on investigations of polystyrene/polyisoprene (PS/PI) diblock copolymers suspended in decane using small angle scattering techniques. The primary objective of this research is the understanding of the bulk properties and structure in concentrated diblock copolymers in a solvent selective for one block. In this case, decane is a good solvent for polyisoprene. Suspending PS/PI diblocks in decane at low concentrations produces monodisperse, spherical micelles comprising a dense core of polystyrene and a diffuse corona of polyisoprene. These micelles are well idealized as spherical cores with a fixed number of polyisoprene chains tethered to the surface. Since the local curvature plays an important role in determining the coronal density profile, the core radius and aggregation number are experimentally calculated. This experimental characterization lends each polymeric micelle to a description of the micellar architecture and pair-interaction potential through use of self-consistent mean field equations for tethered-chain systems. We use these pair-potentials to describe the liquid-like interference and disorder-order transition observed experimentally. Gillan's method, subject to a Rogers-Young closure, provides a description of the liquid-state. Density functional theory, specifically the modified weighted density approximation of Denton and Ashcroft, is used to estimate the solid-state. We supplement these calculations with a semi-quantitative phase diagram demonstrating the diversity in phase behavior resulting from tuning the range of the repulsions by varying block asymmetry; the phase diagram includes regions of face-centered cubic (FCC) and body-centered cubic (BCC) crystals depending on the range of the coronal layer thickness relative to the core dimension. In addition to these studies, we conclude with a discussion of the phase behavior of diblock copolymers at concentrations intermediate to those witnessing cubic micellar crystals and the ordered

  20. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

    SciTech Connect

    Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E.; Jenney Jr, Francis E.; Classen, Scott; Frankel, Kenneth A.; Hopkins, Robert C.; Yang, Sungjae; Scott, Joseph W.; Dillard, Bret D.; Adams, Michael W. W.; Tainer, John A.

    2009-07-20

    We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

  1. High-accuracy deterministic solution of the Boltzmann equation for the shock wave structure

    NASA Astrophysics Data System (ADS)

    Malkov, E. A.; Bondar, Ye. A.; Kokhanchik, A. A.; Poleshkin, S. O.; Ivanov, M. S.

    2015-07-01

    A new deterministic method of solving the Boltzmann equation has been proposed. The method has been employed in numerical studies of the plane shock wave structure in a hard sphere gas. Results for Mach numbers and have been compared with predictions of the direct simulation Monte Carlo (DSMC) method, which has been used to obtain the reference solution. Particular attention in estimating the solution accuracy has been paid to a fine structural effect: the presence of a total temperature peak exceeding the temperature value further downstream. The results of solving the Boltzmann equation for the shock wave structure are in excellent agreement with the DSMC predictions.

  2. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

    Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

    2015-07-01

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

  3. An Analytical Solution for Transient Thermal Response of an Insulated Structure

    NASA Technical Reports Server (NTRS)

    Blosser, Max L.

    2012-01-01

    An analytical solution was derived for the transient response of an insulated aerospace vehicle structure subjected to a simplified heat pulse. This simplified problem approximates the thermal response of a thermal protection system of an atmospheric entry vehicle. The exact analytical solution is solely a function of two non-dimensional parameters. A simpler function of these two parameters was developed to approximate the maximum structural temperature over a wide range of parameter values. Techniques were developed to choose constant, effective properties to represent the relevant temperature and pressure-dependent properties for the insulator and structure. A technique was also developed to map a time-varying surface temperature history to an equivalent square heat pulse. Using these techniques, the maximum structural temperature rise was calculated using the analytical solutions and shown to typically agree with finite element simulations within 10 to 20 percent over the relevant range of parameters studied.

  4. Exact solution to the problem of N bodies forming a multi-layer rotating structure.

    PubMed

    Smulsky, Joseph J

    2015-01-01

    Exact solutions to the problem of the Newtonian gravitational interaction of N material points moving around N 2 concentric circular orbits are considered. Each circular orbit contains N 3 axisymmetrically located bodies having identical masses. The structure as a whole rotates around its symmetry axis. Such structures are identical to the homographic-dynamics configurations, or planar central configurations, known from literature. Conceptually, those structures can be considered as structures formed by mutually embedded polygons with point bodies placed at polygon vortices. For structures involving less than 20 bodies, solutions were obtained using Hamiltonian-mechanics methods. In the study, the forces acting on each body in the rotating structure from the side of all other bodies were found. The differential motion equations of the bodies were reduced to a system of linear algebraic equations for the body masses. Solutions in various forms were obtained. For specifying the initial parameters and for calculating all other characteristics of the structures, a computer program RtCrcSt2.for has been developed. Structures comprising up to one million bodies have been calculated. Graphical images of obtained structures are presented, and their properties are described. Stability problems for examined structures are considered, and possible application of obtained results to celestial- and space-mechanics problems is discussed. PMID:26203407

  5. The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution

    SciTech Connect

    Weber, C.; Wilder, G.; von Freyberg, B.; Braun, W.; Wuethrich, K. ); Traber, R.; Widmer, H. )

    1991-07-02

    Cyclosporin A bound to the presumed receptor protein cyclophilin was studied in aqueous solution at pH 6.0 by nuclear magnetic resonance spectroscopy using uniform {sup 15}N- or {sup 13}C-labeling of cyclosporin A and heteronuclear spectral editing techniques. With an input of 108 intramolecular NOEs and four vicinal {sup 3}J{sub HN{alpha}} coupling constants, the three-dimensional structure of cyclosporin A bound to cyclophilin was calculated with the distance geometry program DISMAN, and the structures resulting from 181 converged calculations were energy refined with the program FANTOM. A group of 120 conformers was selected on the basis of the residual constraint violations and energy criteria to represent the solution structure. The average of the pairwise root-mean-square distances calculated for the backbone atoms of the 120 structures was 0.58 {angstrom}. The structure represents a novel conformation of cyclosporin A, for which the backbone conformation is significantly different from the previously reported structures in single crystals and in chloroform solution. The structure has all peptide bonds in the trans form, contains no elements of regular secondary structure and no intramolecular hydrogen bonds, and exposes nearly all polar groups to its environment. The root-mean-square distance between the backbone atoms of the crystal structure of cyclosporin A and the mean of the 120 conformers representing the NMR structure of cyclosporin A bound to cyclophilin is 2.5 {angstrom}.

  6. The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophus.

    PubMed Central

    Thompson, G. S.; Leung, Y. C.; Ferguson, S. J.; Radford, S. E.; Redfield, C.

    2000-01-01

    The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35+/-0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two alpha-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. PMID:10850794

  7. Discussions on equivalent solutions and localized structures via the mapping method based on Riccati equation

    NASA Astrophysics Data System (ADS)

    Xu, Ling; Cheng, Xuan; Dai, Chao-Qing

    2015-12-01

    Although the mapping method based on Riccati equation was proposed to obtain variable separation solutions many years ago, two important problems have not been studied: i) the equivalence of variable separation solutions by means of the mapping method based on Riccati equation with the radical sign combined ansatz; and ii) lack of physical meanings for some localized structures constructed by variable separation solutions. In this paper, we re-study the (2+1)-dimensional Boiti-Leon-Pempinelli equation via the mapping method based on Riccati equation and prove that nine types of variable separation solutions are actually equivalent to each other. Moreover, we also re-study localized structures constructed by variable separation solutions. Results indicate that some localized structures reported in the literature are lacking real values due to the appearance of the divergent and un-physical phenomenon for the initial field. Therefore, we must be careful with the initial field to avoid the appearance of some un-physical or even divergent structures in it when we construct localized structures for the potential field.

  8. Local structure of the halite-sylvine solid solution according to the computer simulation data

    SciTech Connect

    Urusov, V. S. Leonenko, E. V.

    2008-09-15

    The structural, elastic, and thermodynamic properties of halite NaCl and sylvine KCl and the miscibility properties of the NaCl-KCl solid solution found by computer simulation are in good agreement with the experimental data. Analysis of the relaxation of the solid solution structure suggests that both anion and cation sublattices are distorted; however, the anion sublattice is distorted much more strongly. Calculations of the local bond valence at all types of ions in the solid solution show opposite deviations from the balance at cations, whereas the general balance is retained. The values of the electrostatic potential in the ion positions reflect weakening of bonding in the solid solution with respect to its pure components. In addition, with an increase in the average interatomic distance in the first coordination sphere around cations, the modulus of the electrostatic potential at cations decreases.

  9. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

    SciTech Connect

    Pröpper, Kevin; Meindl, Kathrin; Sammito, Massimo; Dittrich, Birger; Sheldrick, George M.; Pohl, Ehmke; Usón, Isabel

    2014-06-01

    The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

  10. Stability of the grain structure in 2219-O aluminum alloy friction stir welds during solution treatment

    SciTech Connect

    Chen, Y.C. . E-mail: armstrong@hit.edu.cn; Feng, J.C.; Liu, H.J.

    2007-02-15

    The stability of the grain structure in 2219-O aluminum alloy friction stir welds during solution treatment has been investigated. Experimental results show that the solution treatment causes drastic grain growth, Grain growth initiates at the surface and the bottom of the weld and then extends to the weld centre within several minutes. The solution treatment temperature and the welding heat input have a significant effect on grain growth. The higher the solution temperature, or the higher the welding heat input, the greater the grain growth. The instability of the grains is attributed to an imbalance between thermodynamic driving forces for grain growth and the pinning forces impeding grain boundary migration during solution treatment.

  11. An efficient closed-form solution for acoustic emission source location in three-dimensional structures

    SciTech Connect

    Li, Xibing; Dong, Longjun

    2014-02-15

    This paper presents an efficient closed-form solution (ECS) for acoustic emission(AE) source location in three-dimensional structures using time difference of arrival (TDOA) measurements from N receivers, N ≥ 6. The nonlinear location equations of TDOA are simplified to linear equations. The unique analytical solution of AE sources for unknown velocity system is obtained by solving the linear equations. The proposed ECS method successfully solved the problems of location errors resulting from measured deviations of velocity as well as the existence and multiplicity of solutions induced by calculations of square roots in existed close-form methods.

  12. Ice crystallization in ultrafine water-salt aerosols: nucleation, ice-solution equilibrium, and internal structure.

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-01

    Atmospheric aerosols have a strong influence on Earth's climate. Elucidating the physical state and internal structure of atmospheric aqueous aerosols is essential to predict their gas and water uptake, and the locus and rate of atmospherically important heterogeneous reactions. Ultrafine aerosols with sizes between 3 and 15 nm have been detected in large numbers in the troposphere and tropopause. Nanoscopic aerosols arising from bubble bursting of natural and artificial seawater have been identified in laboratory and field experiments. The internal structure and phase state of these aerosols, however, cannot yet be determined in experiments. Here we use molecular simulations to investigate the phase behavior and internal structure of liquid, vitrified, and crystallized water-salt ultrafine aerosols with radii from 2.5 to 9.5 nm and with up to 10% moles of ions. We find that both ice crystallization and vitrification of the nanodroplets lead to demixing of pure water from the solutions. Vitrification of aqueous nanodroplets yields nanodomains of pure low-density amorphous ice in coexistence with vitrified solute rich aqueous glass. The melting temperature of ice in the aerosols decreases monotonically with an increase of solute fraction and decrease of radius. The simulations reveal that nucleation of ice occurs homogeneously at the subsurface of the water-salt nanoparticles. Subsequent ice growth yields phase-segregated, internally mixed, aerosols with two phases in equilibrium: a concentrated water-salt amorphous mixture and a spherical cap-like ice nanophase. The surface of the crystallized aerosols is heterogeneous, with ice and solution exposed to the vapor. Free energy calculations indicate that as the concentration of salt in the particles, the advance of the crystallization, or the size of the particles increase, the stability of the spherical cap structure increases with respect to the alternative structure in which a core of ice is fully surrounded by

  13. Solution- and Adsorbed-State Structural Ensembles Predicted for the Statherin-Hydroxyapatite System

    PubMed Central

    Masica, David L.; Gray, Jeffrey J.

    2009-01-01

    Abstract We have developed a multiscale structure prediction technique to study solution- and adsorbed-state ensembles of biomineralization proteins. The algorithm employs a Metropolis Monte Carlo-plus-minimization strategy that varies all torsional and rigid-body protein degrees of freedom. We applied the technique to fold statherin, starting from a fully extended peptide chain in solution, in the presence of hydroxyapatite (HAp) (001), (010), and (100) monoclinic crystals. Blind (unbiased) predictions capture experimentally observed macroscopic and high-resolution structural features and show minimal statherin structural change upon adsorption. The dominant structural difference between solution and adsorbed states is an experimentally observed folding event in statherin's helical binding domain. Whereas predicted statherin conformers vary slightly at three different HAp crystal faces, geometric and chemical similarities of the surfaces allow structurally promiscuous binding. Finally, we compare blind predictions with those obtained from simulation biased to satisfy all previously published solid-state NMR (ssNMR) distance and angle measurements (acquired from HAp-adsorbed statherin). Atomic clashes in these structures suggest a plausible, alternative interpretation of some ssNMR measurements as intermolecular rather than intramolecular. This work demonstrates that a combination of ssNMR and structure prediction could effectively determine high-resolution protein structures at biomineral interfaces. PMID:19383454

  14. Effects of solvent on the solution properties, structural characteristics and properties of silk sericin.

    PubMed

    Jo, Yoon Nam; Um, In Chul

    2015-07-01

    Sericin films have attracted much attention from researchers in biomedical and cosmetic fields because of its unique properties, including good cytocompatibility and its promotion of wound healing. However, poor mechanical properties of sericin films have restricted its application in these fields. In this study, a new solvent, formic acid, was used to fabricate sericin solutions and films. The effects of formic acid on the structural characteristics and mechanical properties of the sericin solutions and films were examined and compared with water. The sericin/formic acid solution showed fewer aggregated sericin molecules, resulting in a lower turbidity than that of the sericin/water solution. In addition, the gelation of the sericin solution was retarded in formic acid compared to that of water. Sericin films cast from the formic acid solution exhibited a much higher crystallinity index than that produced from water. The tensile strength and elongation of the sericin films cast from the formic acid solution were more than double that of the sericin films cast from water. It is expected that the more stable sericin solution and high-crystallinity sericin films, which have significantly improved mechanical properties, produced by using formic acid as the solvent could be utilized in biomedical and cosmetic applications. PMID:25869308

  15. A Solution Adaptive Structured/Unstructured Overset Grid Flow Solver with Applications to Helicopter Rotor Flows

    NASA Technical Reports Server (NTRS)

    Duque, Earl P. N.; Biswas, Rupak; Strawn, Roger C.

    1995-01-01

    This paper summarizes a method that solves both the three dimensional thin-layer Navier-Stokes equations and the Euler equations using overset structured and solution adaptive unstructured grids with applications to helicopter rotor flowfields. The overset structured grids use an implicit finite-difference method to solve the thin-layer Navier-Stokes/Euler equations while the unstructured grid uses an explicit finite-volume method to solve the Euler equations. Solutions on a helicopter rotor in hover show the ability to accurately convect the rotor wake. However, isotropic subdivision of the tetrahedral mesh rapidly increases the overall problem size.

  16. Frequency modelling and solution of fluid-structure interaction in complex pipelines

    NASA Astrophysics Data System (ADS)

    Xu, Yuanzhi; Johnston, D. Nigel; Jiao, Zongxia; Plummer, Andrew R.

    2014-05-01

    Complex pipelines may have various structural supports and boundary conditions, as well as branches. To analyse the vibrational characteristics of piping systems, frequency modelling and solution methods considering complex constraints are developed here. A fourteen-equation model and Transfer Matrix Method (TMM) are employed to describe Fluid-Structure Interaction (FSI) in liquid-filled pipes. A general solution for the multi-branch pipe is proposed in this paper, offering a methodology to predict frequency responses of the complex piping system. Some branched pipe systems are built for the purpose of validation, indicating good agreement with calculated results.

  17. Backbone Solution Structures of Proteins Using Residual Dipolar Couplings: Application to a Novel Structural Genomics Target

    PubMed Central

    Valafar, H.; Mayer, K. L.; Bougault, C. M.; LeBlond, P. D.; Jenney, F. E.; Brereton, P. S.; Adams, M.W.W.; Prestegard, J.H.

    2006-01-01

    Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on determination of backbone structures of proteins as opposed to full structures with all side chains in place. This focus is appropriate given the presumption that many protein structures in the future will be built using computational methods that start from representative fold family structures and replace as many as 70% of the side chains in the course of structure determination. The methodology we present is based primarily on residual dipolar couplings (RDCs), readily accessible NMR observables that constrain the orientation of backbone fragments irrespective of separation in space. A new software tool is described for the assembly of backbone fragments under RDC constraints and an application to a structural genomics target is presented. The target is an 8.7 kDa protein from Pyrococcus furiosus, PF1061, that was previously not well annotated, and had a nearest structurally characterized neighbor with only 33% sequence identity. The structure produced shows structural similarity to this sequence homologue, but also shows similarity to other proteins that suggests a functional role in sulfur transfer. Given the backbone structure and a possible functional link this should be an ideal target for development of modeling methods. PMID:15704012

  18. Nuclear magnetic resonance solution structure of dendrotoxin K from the venom of Dendroaspis polylepis polylepis.

    PubMed

    Berndt, K D; Güntert, P; Wüthrich, K

    1993-12-01

    The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectroscopy. On the basis of virtually complete sequence-specific 1H NMR assignments, including individual assignments for 38 pairs of diastereotopic substituents and side-chain amide protons, a total of 818 nuclear Overhauser effect distance constraints and 123 dihedral angle constraints were identified. Using this input, the solution structure of Toxin K was calculated with the program DIANA, and refined by restrained energy-minimization with a modified version of the program AMBER. The average root-mean-square deviation (r.m.s.d.) relative to the mean atomic co-ordinates of the 20 conformers selected to represent the solution structure is 0.31 A for all backbone atoms N, C alpha and C', and 0.90 A for all heavy-atoms of residues 2 to 56. The solution structure of Toxin K is very similar to the solution structure of the basic pancreatic trypsin inhibitor (BPTI) and the X-ray crystal structure of the alpha-dendrotoxin from Dendroaspis angusticeps (alpha-DTX), with r.m.s.d. values of 1.31 A and 0.92 A, respectively, for the backbone atoms of residues 2 to 56. Some local structural differences between Toxin K and BPTI are directly related to the fact that intermolecular interactions with two of the four internal molecules of hydration water in BPTI are replaced by intramolecular hydrogen bonds in Toxin K. PMID:8254670

  19. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

    PubMed Central

    Pröpper, Kevin; Meindl, Kathrin; Sammito, Massimo; Dittrich, Birger; Sheldrick, George M.; Pohl, Ehmke; Usón, Isabel

    2014-01-01

    Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures. PMID:24914984

  20. Comparison of shock structure solutions using independent continuum and kinetic theory approaches

    NASA Technical Reports Server (NTRS)

    Fiscko, Kurt A.; Chapman, Dean R.

    1988-01-01

    A vehicle traversing the atmosphere will experience flight regimes at high altitudes in which the thickness of a hypersonic shock wave is not small compared to the shock standoff distance from the hard body. When this occurs, it is essential to compute accurate flow field solutions within the shock structure. In this paper, one-dimensional shock structure is investigated for various monatomic gases from Mach 1.4 to Mach 35. Kinetic theory solutions are computed using the Direct Simulation Monte Carlo method. Steady-state solutions of the Navier-Stokes equations and of a slightly truncated form of the Burnett equations are determined by relaxation to a steady state of the time-dependent continuum equations. Monte Carlo results are in excellent agreement with published experimental data and are used as bases of comparison for continuum solutions. For a Maxwellian gas, the truncated Burnett equations are shown to produce far more accurate solutions of shock structure than the Navier-Stokes equations.

  1. Structural characterization of NaOH aqueous solution in the glass and liquid states

    NASA Astrophysics Data System (ADS)

    Bruni, F.; Ricci, M. A.; Soper, A. K.

    2001-05-01

    Using the technique of hydrogen and deuterium substitution, the structure of water in concentrated NaOH solution (10 M) is explored. It is found that major changes in water structure occur both in the liquid phase at T=300 K and in the glassy phase at T=173 K. In particular the 4.4 Å peak in the OO pair correlation function of pure water, which is normally viewed as indicating tetrahedral short-range coordination in water, is totally absent in the NaOH solution at room temperature, and shows up only as a small feature in the NaOH solution in the glassy state. Corresponding changes occur in the OH and HH correlation functions: The hydrogen bond peak position is shifted from 1.85 Å in pure water to 1.65 Å for both the liquid and glassy NaOH, with a reduced number of hydrogen bonds in the glassy phase. The intramolecular HH distance, 1.5 Å, of the water molecule is unaffected by the presence of the solute, but the positions of the peaks in the HH function at 2.4 and 3.8 Å, due to the orientational correlation between neighboring pure water molecules, are respectively, shifted to 2.15 and 3.5 Å. The above findings indicate that ions in aqueous solutions induce a change in water structure equivalent to the application of high pressures.

  2. Local structure in the disordered solid solution of cis- and trans-perinones.

    PubMed

    Teteruk, Jaroslav L; Glinnemann, Jürgen; Heyse, Winfried; Johansson, Kristoffer E; van de Streek, Jacco; Schmidt, Martin U

    2016-06-01

    The cis- and trans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures of cis-perinone (Pigment Red 194) and trans-perinone (Pigment Orange 34) and exhibits a combined positional and orientational disorder: In the crystal, each molecular position is occupied by either a cis- or trans-perinone molecule, both of which have two possible molecular orientations. The structure of cis-perinone exhibits a twofold orientational disorder, whereas the structure of trans-perinone is ordered. The crystal structure of the solid solution was determined by single-crystal X-ray analysis. Extensive lattice-energy minimizations with force-field and DFT-D methods were carried out on combinatorially complete sets of ordered models. For the disordered systems, local structures were calculated, including preferred local arrangements, ordering lengths, and probabilities for the arrangement of neighbouring molecules. The superposition of the atomic positions of all energetically favourable calculated models corresponds well with the experimentally determined crystal structures, explaining not only the atomic positions, but also the site occupancies and anisotropic displacement parameters. PMID:27240774

  3. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    SciTech Connect

    Barends, Thomas R. M.; Brosi, Richard W. W.; Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten; Seidel, Ralf; Shoeman, Robert L.; Zimmermann, Sabine; Bittl, Robert; Schlichting, Ilme; Reinstein, Jochen

    2013-08-01

    The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

  4. Structure and rheology studies of poly(oxyethylene-oxypropylene-oxyethylene) aqueous solution

    SciTech Connect

    Prud`homme, R.K.; Wu, G.; Schneider, D.K.

    1996-10-02

    Small-angle neutron scattering (SANS) and rheometry were used to investigate the supramolecular structure formed by a ploy(oxyethylene-oxypropylene-oxyethylene)(PEO{sub 100}PPO{sub 65 }PEO{sub 100}, Pluronic F127) copolymer in aqueous solution over a temperature range of 10-75 {degree}C and a concentration range of 10-20 wt%. At copolymer concentrations of less than 12.5% the solutions are Newtonian fluids. Gels with an ordered structure (cubic packing of spherical micelles) are observed over a well-defined temperature window when the copolymer concentrations are greater than 17 wt%. The SANS results show that the aggregation number of the micelles is independent of temperature and concentrations. Low-yield stresses, very high zero shear viscosities (nearly 10{sup 6} P), and shear thinning are the major rheological characteristics of the gels. Near, but outside, the gel phase boundary the solutions are non-Newtonian (shear thinning). However, SANS shows these solutions contain domains having the same structure as that in the gel phase. The temperature window for ordered structures and non-Newtonian behavior becomes wider with increasing copolymer concentration. The degree of overlap of the micellar shells increases with increasing copolymer concentration at a given temperature and reaches a maximum at nearly 40 {degree}C at a fixed polymer concentration. The yield stress is due to repulsive interactions of PEO chains in the overlapped micellar shell. 36 refs., 16 figs., 2 tabs.

  5. Comparing Multiple Solutions in the Structured Problem Solving: Deconstructing Japanese Lessons from Learner's Perspective

    ERIC Educational Resources Information Center

    Hino, Keiko

    2015-01-01

    The purpose of this study is to enhance our understanding of how students listen and attend to multiple solutions proposed by their classmates during the activity of comparison. This study examines ten consecutive lessons in each of the two eighth-grade classrooms in Tokyo that are organized in the style of "structured problem solving".…

  6. Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

    NASA Technical Reports Server (NTRS)

    Weaver, D. L.

    1982-01-01

    Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

  7. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX autosol wizard

    SciTech Connect

    Terwilliger, Thomas C; Adams, Paul D; Read, Randy J; Mccoy, Airlie J

    2008-01-01

    Ten measures of experimental electron-density-map quality are examined and the skewness of electron density is found to be the best indicator of actual map quality. A Bayesian approach to estimating map quality is developed and used in the PHENIX AutoSol wizard to make decisions during automated structure solution.

  8. Structure and Dynamics of NaCl Ion Pairing in Solutions of Water and Methanol.

    PubMed

    Kelley, Morgan; Donley, Amber; Clark, Sue; Clark, Aurora

    2015-12-24

    Ion pairing can have profound effects upon the ionic strength of electrolyte solutions but is poorly understood in solutions containing more than one solvent. Herein a combined density functional theory and molecular dynamics approach is used to examine the effect of both methanol concentration and interionic distance upon the structure and dynamics within successive solvation shells of Na(+) and Cl(-) in water/methanol binary solutions. The structure and dynamics of the first and second solvation shells were studied along a reaction coordinate associated with ion pair formation using potential of mean force simulations. The lifetimes of the solvent-solvent hydrogen bonds become perturbed when the second solvation shells of the ions begin to interact. In contrast, the structural properties within the first and second solvation shells of the ions were found to be largely independent of both methanol concentration and interionic distance until a contact ion pair is formed. Thus, as the ions are brought together, the effect of the opposing ion manifests itself in the solvation dynamics before any structural changes are observed. As anticipated based upon the decreased dielectric constant of the binary solution, ion pair formation becomes energetically more favorable as the concentration of methanol increases. PMID:26641882

  9. Reformulation of Maxwell's equations to incorporate near-solute solvent structure.

    PubMed

    Yang, Pei-Kun; Lim, Carmay

    2008-09-01

    Maxwell's equations, which treat electromagnetic interactions between macroscopic charged objects in materials, have explained many phenomena and contributed to many applications in our lives. Derived in 1861 when no methods were available to determine the atomic structure of macromolecules, Maxwell's equations assume the solvent to be a structureless continuum. However, near-solute solvent molecules are highly structured, unlike far-solute bulk solvent molecules. Current methods cannot treat both the near-solute solvent structure and time-dependent electromagnetic interactions in a macroscopic system. Here, we derive "microscopic" electrodynamics equations that can treat macroscopic time-dependent electromagnetic field problems like Maxwell's equations and reproduce the solvent molecular and dipole density distributions observed in molecular dynamics simulations. These equations greatly reduce computational expense by not having to include explicit solvent molecules, yet they treat the solvent electrostatic and van der Waals effects more accurately than continuum models. They provide a foundation to study electromagnetic interactions between molecules in a macroscopic system that are ubiquitous in biology, bioelectromagnetism, and nanotechnology. The general strategy presented herein to incorporate the near-solute solvent structure would enable studies on how complex cellular protein-ligand interactions are affected by electromagnetic radiation, which could help to prevent harmful electromagnetic spectra or find potential therapeutic applications. PMID:18698705

  10. Structural Analysis of Protein-RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements.

    PubMed

    Hennig, Janosch; Warner, Lisa R; Simon, Bernd; Geerlof, Arie; Mackereth, Cameron D; Sattler, Michael

    2015-01-01

    Biological activity in the cell is predominantly mediated by large multiprotein and protein-nucleic acid complexes that act together to ensure functional fidelity. Nuclear magnetic resonance (NMR) spectroscopy is the only method that can provide information for high-resolution three-dimensional structures and the conformational dynamics of these complexes in solution. Mapping of binding interfaces and molecular interactions along with the characterization of conformational dynamics is possible for very large protein complexes. In contrast, de novo structure determination by NMR becomes very time consuming and difficult for protein complexes larger than 30 kDa as data are noisy and sparse. Fortunately, high-resolution structures are often available for individual domains or subunits of a protein complex and thus sparse data can be used to define their arrangement and dynamics within the assembled complex. In these cases, NMR can therefore be efficiently combined with complementary solution techniques, such as small-angle X-ray or neutron scattering, to provide a comprehensive description of the structure and dynamics of protein complexes in solution. Particularly useful are NMR-derived paramagnetic relaxation enhancements (PREs), which provide long-range distance restraints (ca. 20Å) for structural analysis of large complexes and also report on conformational dynamics in solution. Here, we describe the use of PREs from sample production to structure calculation, focusing on protein-RNA complexes. On the basis of recent examples from our own research, we demonstrate the utility, present protocols, and discuss potential pitfalls when using PREs for studying the structure and dynamic features of protein-RNA complexes. PMID:26068746

  11. ZnO Nanoporous Structure Growth, Optical and Structural Characterization by Aqueous Solution Route

    NASA Astrophysics Data System (ADS)

    Kashif, M.; Ali, Syed M. Usman; Foo, K. L.; Hashim, U.; Willander, Magnus

    2011-05-01

    In this study, we have demonstrated the structural and optical characterization of ZnO nanoporous structure grown on gold coated plastic substrate using low temperature aqueous chemical growth (ACG) technique and the annealing temperature was kept at 150° C. ZnO nanoporous structures were fabricated using hydrolysis process by reacting zinc acetate dehydrate with anhydrous ethanol. The crystalline morphology of ZnO nanoporous structures were investigated by using X-ray diffraction (XRD), surface morphology was observed by field emission scanning electron microscope (FESEM). The optical characteristics of ZnO nanoporous structures were investigated at room temperature, PL was observed using UV-Vis Spectrophotometer and the chemical composition is analyzed using Fourier Transform Infra-Red spectrometer (FTIR).

  12. Refined solution structure of the oligomerization domain of the tumour suppressor p53.

    PubMed

    Clore, G M; Ernst, J; Clubb, R; Omichinski, J G; Kennedy, W M; Sakaguchi, K; Appella, E; Gronenborn, A M

    1995-04-01

    The NMR solution structure of the oligomerization domain of the tumour suppressor p53 (residues 319-360) has been refined. The structure comprises a dimer of dimers, oriented in an approximately orthogonal manner. The present structure determination is based on 4,472 experimental NMR restraints which represents a three and half fold increase over our previous work in the number of NOE restraints at the tetramerization interface. A comparison with the recently solved 1.7 A resolution X-ray structure shows that the structures are very similar and that the average angular root-mean-square difference in the interhelical angles is about 1 degree. The results of recent extensive mutagenesis data and the possible effects of mutations which have been identified in human cancers are discussed in the light of the present structure. PMID:7796267

  13. Structure and dynamics of a polysaccharide matrix: aqueous solutions of bacterial levan.

    PubMed

    Benigar, Elizabeta; Dogsa, Iztok; Stopar, David; Jamnik, Andrej; Kralj Cigić, Irena; Tomšič, Matija

    2014-04-15

    The polysaccharide levan is a homopolymer of fructose and appears in nature as an important structural component of some bacterial biofilms. This paper reports the structural and dynamic properties of aqueous solutions of levan of various origin obtained from dynamic rheological, small-angle X-ray scattering, static and dynamic light scattering, as well as density and sound velocity measurements, determination of polymer branching after per-O-methylation, and microscopy. Besides samples of commercially available levan from Zymomonas mobilis and Erwinia herbicola, we also isolated, purified, and studied a levan sample from the biofilm of Bacillus subtilis. The results of dynamic rheological and light scattering measurements revealed very interesting viscoelastic properties of levan solutions even at very low polymer concentrations. The findings were complemented by small-angle X-ray scattering data that revealed some important differences in the structure of the aqueous levan solutions at the molecular level. Besides presenting detailed dynamic and structural results on the polysaccharide systems of various levans, one of the essential goals of this work was to point out the level of structural information that may be obtained for such polymer systems by combining basic physicochemical, rheological, and various light scattering techniques. PMID:24654746

  14. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

    SciTech Connect

    Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek; Lee, Weontae

    2014-01-10

    Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA, which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.

  15. Grain boundary structure and solute segregation in titanium-doped sapphire bicrystals

    SciTech Connect

    Taylor, Seth T.

    2002-05-17

    Solute segregation to ceramic grain boundaries governs material processing and microstructure evolution, and can strongly influence material properties critical to engineering performance. Understanding the evolution and implications of grain boundary chemistry is a vital component in the greater effort to engineer ceramics with controlled microstructures. This study examines solute segregation to engineered grain boundaries in titanium-doped sapphire (Al2O3) bicrystals, and explores relationships between grain boundary structure and chemistry at the nanometer scale using spectroscopic and imaging techniques in the transmission electron microscope (TEM). Results demonstrate dramatic changes in solute segregation stemming from small fluctuations in grain boundary plane and structure. Titanium and silicon solute species exhibit strong tendencies to segregate to non-basal and basal grain boundary planes, respectively. Evidence suggests that grain boundary faceting occurs in low-angle twis t boundaries to accommodate nonequilibrium solute segregation related to slow specimen cooling rates, while faceting of tilt grain boundaries often occurs to expose special planes of the coincidence site lattice (CSL). Moreover, quantitative analysis of grain boundary chemistry indicates preferential segregation of charged defects to grain boundary dislocations. These results offer direct proof that static dislocations in ionic materials can assume a net charge, and emphasize the importance of interactions between charged point, line, and planar defects in ionic materials. Efforts to understand grain boundary chemistry in terms of space charge theory, elastic misfit and nonequilibrium segregation are discussed for the Al2O3 system.

  16. Structural and Electronic Properties of a Wide-Gap Quaternary Solid Solution: \\(Zn, Mg\\) \\(S, Se\\)

    NASA Astrophysics Data System (ADS)

    Saitta, A. M.; de Gironcoli, S.; Baroni, S.

    1998-06-01

    The structural properties of the (Zn, Mg) (S, Se) solid solutions are determined by a combination of the computational alchemy and the cluster expansion methods with Monte Carlo simulations. We determine the phase diagram of the alloy and show that the homogeneous phase is characterized by a large amount of short-range order occurring among first-nearest neighbors. Electronic-structure calculations performed using the special quasirandom structure approach indicate that the energy gap of the alloy is rather sensitive to this short-range order.

  17. Automating crystallographic structure solution and refinement of protein–ligand complexes

    PubMed Central

    Echols, Nathaniel; Moriarty, Nigel W.; Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; Headd, Jeffrey J.; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-01-01

    High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation. PMID:24419387

  18. Solution structure of sialyl Lewis X mimics studied by two-dimensional NMR

    NASA Astrophysics Data System (ADS)

    Demura, Makoto; Noda, Masatoshi; Kajimoto, Tetsuya; Uchiyama, Taketo; Umemoto, Kimiko; Wong, Chi-Huey; Asakura, Tetsuo

    2002-01-01

    A structure of the peptidic mimic of sialyl Lewis X (Sle X) (α- N-acetyl-neuraminyl-(2,3)-β- D-galactopyranosyl-(1,4)-[α- L-fucopyranosyl-(1,3)-β- D- N-acetyl-glucosamine]) in an aqueous solution was studied using two-dimensional 1H NMR spectroscopy. Complete assignments of 1H NMR chemical shift of the SLe X mimic have been performed. The presence of three conformers of the SLe X mimic in a solution was proposed by using distance geometry calculation based on NOE constraints, which were obtained from NOESY experiments. In addition, intermolecular interaction between the mimic and the crystal structure of E-selectin was refined using molecular dynamics. This suggested the conformational rearrangement of the functional groups of the conformers to the active sites of E-selectin. The relationship between the binding activities toward E-selectin and the three-dimensional structures of other mimics was also discussed.

  19. Structural Properties and Phase Behavior of Crosslinked Networks in Polymer Solutions

    PubMed Central

    Benmouna, Farida; Zemmour, Samira; Benmouna, Mustapha

    2016-01-01

    ABSTRACT Structural properties and phase behavior of crosslinked networks embedded in polymer solutions are theoretically investigated. The partial structure factor of the network is calculated using a matrix formulation of the random phase approximation and the forward scattering limit is correlated with the phase behavior. Swelling and deswelling processes are analyzed in terms of the polymer concentration, the mismatch of solvent quality with respect to polymer and network, the polymers incompatibility and their characteristic sizes. Most studies reported so far in the literature have focussed on the swelling of crosslinked networks and gels in pure solvents but the correlation of the structural properties with the phase behavior in the presence of high molecular weight polymers in solution has not been given sufficient attention. The present work is intended to fill this gap in view of the current efforts to develop novel drug encapsulating and targeted delivery devices. PMID:27134310

  20. Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination.

    PubMed

    Bieri, Michael; Kwan, Ann H; Mobli, Mehdi; King, Glenn F; Mackay, Joel P; Gooley, Paul R

    2011-03-01

    A strength of NMR spectroscopy is its ability to monitor, on an atomic level, molecular changes and interactions. In this review, which is intended for non-spectroscopist, we describe major uses of NMR in protein science beyond solution structure determination. After first touching on how NMR can be used to quickly determine whether a mutation induces structural perturbations in a protein, we describe the unparalleled ability of NMR to monitor binding interactions over a wide range of affinities, molecular masses and solution conditions. We discuss the use of NMR to measure the dynamics of proteins at the atomic level and over a wide range of timescales. Finally, we outline new and expanding areas such as macromolecular structure determination in multicomponent systems, as well as in the solid state and in vivo. PMID:21214861

  1. Structural properties and adsorption capacity of holocellulose aerogels synthesized from an alkali hydroxide-urea solution

    NASA Astrophysics Data System (ADS)

    Kwon, Gu-Joong; Kim, Dae-Young; Hwang, Jae-Hyun; Kang, Joo-Hyon

    2014-05-01

    A tulip tree was used to synthesize a holocellulose aerogel from an aqueous alkali hydroxide-urea solution with the substitution of an organic solvent followed by freeze-drying. For comparison, the synthesized holocellulose aerogels were divided into two groups according to the source of the hydrogel, an upper suspended layer and a bottom concentrated layer of the centrifuged solution of cellulose and NaOH/urea solvents. We investigated the effects of the temperature of the pre-cooled NaOH/urea solution ( i.e., dissolution temperature) on the pore structure and the adsorption capacity of the holocellulose aerogel. A nano-fibrillar network structure of the holocellulose aerogel was observed, with little morphological difference in pore structure for different dissolution temperatures. Both micropores and mesopores were observed in the holocellulose aerogel. The specific surface area of the holocellulose aerogel was generally greater at lower dissolution temperatures. In a series of adsorption tests using methylene blue, the holocellulose aerogel showed the greatest adsorption capacity at the lowest dissolution temperature tested (-2°C). However, the dissolution temperature generally had little effect on the adsorption capacity. The holocellulose aerogel produced from the upper suspended layer of the centrifuged hydrogel solution showed a greater porosity and adsorption capacity than the one produced from the bottom concentrated layer. Overall, the aerogel made by utilizing a delignified tulip tree display a high surface area and a high adsorption property, indicating its possible application in eco-friendly adsorption materials.

  2. In vitro studies on the structure and properties of silk fibroin aqueous solutions in silkworm.

    PubMed

    Jin, Yuan; Hang, Yichun; Luo, Jie; Zhang, Yaopeng; Shao, Huili; Hu, Xuechao

    2013-11-01

    The spinning process of silkworm in vivo attracts great attentions. In this work, the structures and properties of the silk fibroin (SF) aqueous solutions from different divisions of silk glands of silkworms were investigated by using polarized microscope, rotational rheometer, Raman spectrometer and dynamic laser light scattering instrument. It was found that only the anterior (A) division and the anterior part of middle division (MA) of silk gland showed birefringence. With flowing from the posterior part (MP) to the MA part in the middle division of silk gland, the SF aqueous solutions was gradually transformed from random coil/α-helix to β-sheet conformation. Meantime, the elastic and viscous nature of the SF aqueous solution changed, and the mean diameter of SF aggregates increased from 118 nm to 331 nm. It could be concluded that the structures and properties of the SF aqueous solutions were gradually changed along the silk gland and the liquid crystal structure was initially formed in the MA part of silk gland. PMID:23994738

  3. Structure from solute-solvent interactions in supercritical polyatomic molecular mixtures

    SciTech Connect

    Lee, L.L.; Cochran, H.D.

    1994-12-31

    Solute-solvent and solute-solute microstructures at the sueprcritical state are important in elucidating chemical reaction and spectroscopic data. We can classify the range of pair correlations into two regions: a short range (r {le} r{sub min}) and a long range (r from r{sub min} to 20 {approximately} 50 molecular diameters). The often cited local density enhacement referes to the short range corelations and is shown not to be related to the critical behavior of the mixture. The long-range behavior of the pair correlations is responsible for the buildup of osmotic susceptibility and is related to the closeness to solvent`s critical point. In the class of attractive supercritical mixtures, the solute-solvent short-range pair correlation exhibits complicated bheavior: enhanced solvation (within the first neighborhood) at low to medium densities and peak attenuation followed by peak growth at higher densities. Earlier theor. studies (integral equations) dealt with idealized model of solute molecules as spheres (molecular size effects accounted for, but not molecular shape effects). This study examines behavioral change due to molecular shapes and orientations as the solutes take the shape of polyatomic molecules. For example the case of di-tert-butylnitroxide radicals in supercritical ethylene can be modeled as linear dimeric molecules. Reference interaction site model integral equation is used to produce site-site correlation functions. We map out the density ranges where structural changes take place and elucidate their practical implications.

  4. Structure and dimerization of translation initiation factor aIF5B in solution

    SciTech Connect

    Rasmussen, Louise Caroe Vohlander; Oliveira, Cristiano Luis Pinto; Byron, Olwyn; Jensen, Janni Mosgaard; Pedersen, Jan Skov; Sperling-Petersen, Hans Uffe; Mortensen, Kim Kusk

    2011-12-09

    Highlights: Black-Right-Pointing-Pointer aIF5B forms maximum 5.0-6.8% irreversible dimers in solution. Black-Right-Pointing-Pointer Sedimentation coefficients for monomer and dimer are 3.64 and 5.51 {+-} 0.29 S. Black-Right-Pointing-Pointer Adding only 2% glycerol prevents dimerization. Black-Right-Pointing-Pointer SAXS on aIF5B monomer gave an R{sub g} of 37.5 {+-} 0.2 A and a D{sub max} of {approx}130 A. Black-Right-Pointing-Pointer There are universal structural differences between aIF5B and Escherichia coli IF2. -- Abstract: Translation initiation factor 5B (IF5B) is required for initiation of protein synthesis. The solution structure of archaeal IF5B (aIF5B) was analysed by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) and was indicated to be in both monomeric and dimeric form. Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) of aIF5B indicated that aIF5B forms irreversible dimers in solution but only to a maximum of 5.0-6.8% dimer. Sedimentation velocity (SV) AUC at higher speed also indicated the presence of two species, and the sedimentation coefficients s{sub 20,w}{sup 0} were determined to be 3.64 and 5.51 {+-} 0.29 S for monomer and dimer, respectively. The atomic resolution (crystallographic) structure of aIF5B (Roll-Mecak et al. ) was used to model monomer and dimer, and theoretical sedimentation coefficients for these models were computed (3.89 and 5.63 S, respectively) in good agreement with the sedimentation coefficients obtained from SV analysis. Thus, the structure of aIF5B in solution must be very similar to the atomic resolution structure of aIF5B. SAXS data were acquired in the same buffer with the addition of 2% glycerol to inhibit dimerization, and the resultant monomeric aIF5B in solution did indeed adopt a structure very similar to the one reported earlier for the protein in crystalline form. The p(r) function indicated an elongated conformation supported by a radius of gyration of 37.5 {+-} 0.2 A

  5. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

    DOE PAGESBeta

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.; Schmidt, Martin U.

    2016-01-01

    In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

  6. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

    PubMed

    Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data. PMID:26697868

  7. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

    SciTech Connect

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.; Schmidt, Martin U.

    2016-01-01

    In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

  8. A hybrid computational-experimental approach for automated crystal structure solution

    NASA Astrophysics Data System (ADS)

    Meredig, Bryce; Wolverton, C.

    2013-02-01

    Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li-air batteries; and high-pressure silane, SiH4.

  9. Electrostatic Effect on the Solution Structure and Dynamics of PEDOT:PSS

    NASA Astrophysics Data System (ADS)

    Leaf, Michael; Muthukumar, Murugappan

    Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonic acid) (PEDOT:PSS) is a popular material used in organic electronic devices as a conductor. It consists of PEDOT polycations complexed with PSS polyanions which are initially suspended in aqueous solution and eventually cast into a film. Various annealing and doping methods dramatically enhance PEDOT:PSS film conductivity. To understand the physical interactions at play, we explore structural and dynamic aspects of PEDOT:PSS solutions through scattering and rheology techniques. We highlight several aspects of the phase behavior of PEDOT:PSS, and the significance of electrostatic interactions.

  10. Solution structure of peptide AG4 used to form silver nanoparticles

    SciTech Connect

    Lee, Eunjung; Kim, Dae-Hee; Woo, Yoonkyung; Hur, Ho-Gil; Lim, Yoongho

    2008-11-21

    The preparation of silver nanoparticles (AgNPs) is of great interest due to their various biological activities, such as observed in their antimicrobial and wound healing actions. Moreover, the formation of AgNPs using silver-binding peptide has certain advantages because they can be made in aqueous solution at ambient temperature. The solution structure of the silver-binding peptide AG4 was determined using nuclear magnetic resonance spectroscopy, and the site of the AG4 interaction with AgNPs was elucidated.

  11. Families of solutions to the generalized Ginzburg-Landau equation and structural transitions between them

    SciTech Connect

    Ovchinnikov, Yu. N.

    2013-09-15

    Solutions to the generalized Ginzburg-Landau equations for superconductors are obtained for a Ginzburg-Landau parameter {kappa} close to unity. The families of solutions with arbitrary number n of flux quanta in a unit cell are analyzed. It is shown that under certain conditions, a cascade of phase transitions between different structures in a magnetic field appears near T{sub c}. Algebraic equations are derived for determining the boundaries of coexistence of different phases on the (T, H{sub 0}) plane.

  12. Measure-valued solutions for a hierarchically size-structured population

    NASA Astrophysics Data System (ADS)

    Ackleh, Azmy S.; Ito, Kazufumi

    We present a hierarchically size-structured population model with growth, mortality and reproduction rates which depend on a function of the population density ( environment). We present an example to show that if the growth rate is not always a decreasing function of the environment (e.g., a growth which exhibits the Allee effect) the emergence of a singular solution which contains a Dirac delta mass component is possible, even if the vital rates of the individual and the initial data are smooth functions. Therefore, we study the existence of measure-valued solutions. Our approach is based on the vanishing viscosity method.

  13. Characterization of Physical Structure from Measurements of Sound Velocity in Aqueous Solutions of Various Saccharides and Alditols.

    NASA Astrophysics Data System (ADS)

    Smith, David Eugene

    Little basic research has been reported on the physical structure of aqueous solutions of saccharides. Sound velocimeters can be used to study physical structure of solutions, non-destructively. The La Place relationship was used to calculate adiabatic compressibility values for solutions from experimentally determined values for sound velocity and density. Using a sound velocimeter, aqueous solutions of twelve alditols and saccharides were studied at various concentrations and temperatures. Data indicated that over most of the temperature range employed (20 to 70 C) adiabatic compressibility of the solutions was the dominant factor in defining sound velocity through and structural rigidity of solution. As concentration of solute increased, more rigid structures were formed in solution, which caused sound velocity values to increase with increasing concentrations of solute; maximum sound velocity values were obtained at progressively lower temperatures. Analysis of data for sound velocity, density and adiabatic compressibility of various solutions provided partial insight into effects of each solute molecule on structure of solutions. A furanose form in a monosaccharide contributed to a more rigid structure than did a pyranose ring when below 30C. At higher temperatures the pyranose ring provided more rigidity than did the furanose ring. Hydroxyl groups in the equatorial position generally contributed more to rigidity of structure than did OH groups in axial positions. Disaccharides contributed differences from the inherent monosaccharides. A (beta) glycosidic linkage provided more structural rigidity of solution than did a linkage. Among the alditols, mannitol and sorbitol contributed very similar characteristics to solutions. Xylitol, in solution provided less rigidity, density and sound velocity than did mannitol-sorbitol in proportion to the lower molecular weight or xylitol. From the data for velocity of sound through single sugar solutions values for

  14. Structure of 2 molar NaOH in aqueous solution from neutron diffraction and empirical potential structure refinement

    SciTech Connect

    McLain, Sylvia E.; Imberti, Silvia; Soper, Alan K.; Botti, Alberto; Bruni, Fabio; Ricci, Maria Antonietta

    2006-09-01

    Neutron diffraction with isotopic substitution has been used to investigate aqueous solutions of 2M NaOH in the liquid state. The data were modeled using empirical potential structure refinement which allows for the extraction of the ion-water and water-water correlations. The data show that the ion-water radial distribution functions are in accordance with those found by previous studies on NaOH solutions and follow a trend which is dependent on the concentration of the solute. In particular, the shape of the hydroxide hydration shell is found to be concentration independent, but the number of water molecules occupying this shell increases with dilution. Additionally, the water-water correlations show that there is still a measurable effect on water structure with the addition of ions at this concentration, as the second shell in the water oxygen radial distribution function is compressed relative to the first shell. The data are also used to discuss the recent claims that the published radial distribution functions of water are unreliable, showing that data taken at different neutron sources, with different diffraction geometry and systematic errors lead to the same structural information when analyzed via a realistic modeling regime.

  15. Elongation factor TFIIS contains three structural domains: solution structure of domain II.

    PubMed Central

    Morin, P E; Awrey, D E; Edwards, A M; Arrowsmith, C H

    1996-01-01

    Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. Limited proteolytic digestion showed that yeast TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III) are required for transcription activity. The structure of domain III has been solved previously by using NMR spectroscopy. Here, we report the NMR-derived structure of domain II: a three-helix bundle built around a hydrophobic core composed largely of three tyrosines protruding from one face of the C-terminal helix. The arrangement of known inactivating mutations of TFIIS suggests that two surfaces of domain II are critical for transcription activity. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855225

  16. Solution structure of RicC3, a 2S albumin storage protein from Ricinus communis.

    PubMed

    Pantoja-Uceda, David; Bruix, Marta; Giménez-Gallego, Guillermo; Rico, Manuel; Santoro, Jorge

    2003-12-01

    The three-dimensional structure in aqueous solution of recombinant (15)N labeled RicC3, a 2S albumin protein from the seeds of castor bean (Ricinus communis), has been determined by NMR methods. The computed structures were based on 1564 upper limit distance constraints derived from NOE cross-correlation intensities measured in the 2D-NOESY and 3D-HSQC-NOESY experiments, 70 phi torsion angle constraints obtained from (3)J(HNH)(alpha) couplings measured in the HNHA experiment, and 30 psi torsion angle constraints derived from (3)J(H)(alpha)(Ni+1) couplings measured in the HNHB experiment. The computed structures showed a RMSD radius of 0.64 A for the structural core. The resulting structure consists of five amphipatic helices arranged in a right-handed super helix, a folding motif first observed in nonspecific lipid transfer proteins. Different than the latter, RicC3 does have not an internal cavity, a fact that can be related to the exchange in the pairing of disulfide bridges in the segment.CXC. Previous attempts to determine high resolution structures of a 2S albumin protein by either X-ray crystallography or NMR methods failed because of the heterogeneity of the protein prepared from natural sources. Both 2S albumins and nonspecific lipid transfer proteins belong to the prolamine superfamily, some of whose members are food allergens. The solution structure for recombinant RicC3 determined here is a suitable representative structure for the broad family of seed 2S albumin proteins, which may help to establish meaningful relationships between structure and allergenicity. RicC3 is also the peptidic component of the immunomodulator Inmunoferon, a widely used pharmaceutical product, and its structure is expected to help understand its pharmaceutical activity. PMID:14636051

  17. Invisibility and cloaking structures as weak or strong solutions of Devaney-Wolf theorem.

    PubMed

    Labate, Giuseppe; Matekovits, Ladislau

    2016-08-22

    Inspired by a general theorem on non-radiating sources demonstrated by Devaney and Wolf, a unified theory for invisible and cloaking structures is here proposed. By solving Devaney-Wolf theorem in the quasi-static limit, a weak solution is obtained, demonstrating the existence of Anapole modes, Mantle Cloaking and Plasmonic Cloaking. Beyond the quasi-static regime, a strong solution of Devaney-Wolf theorem can be formulated, predicting general non-scattering devices based on directional invisibility, Transformation Optics, neutral inclusions and refractive index continuity. Both weak and strong solutions are analytically demonstrated to depend on the concept of contrast, mathematically defined as a normalized difference between constitutive parameters (or wave-impedance property) of a material and its surrounding background. PMID:27557204

  18. Crystal versus solution structures of enzymes: NMR spectroscopy of a crystalline serine protease.

    PubMed

    Smith, S O; Farr-Jones, S; Griffin, R G; Bachovchin, W W

    1989-05-26

    The hydrogen-bonding status of His57 in the catalytic triad (Asp-His-Ser) of serine protease has important mechanistic implications for this class of enzymes. Recent nitrogen-15 nuclear magnetic resonance (NMR) studies of alpha-lytic protease find His57 and Ser195 to be strongly hydrogen-bonded, a result that conflicts with the corresponding crystallographic studies, thereby suggesting that the crystal and solution structures may differ. This discrepancy is addressed and resolved in a nitrogen-15 NMR study of the enzyme in the crystalline state. The results show that the His-Ser and Asp-His interactions are identical in crystals and solutions, but that in crystals His57 titrates with a pKa of 7.9, nearly one pKa unit higher than in solution. This elevated pKa accounts for the absence of the His-Ser hydrogen bond in previous x-ray studies. PMID:2499045

  19. A dielectric spectroscopic study of the disperse structure of asphaltene solutions at high pressures

    SciTech Connect

    Syunyaev, R.Z.; Sh. Abid, R.

    1994-03-01

    The disperse structure of oil asphaltenes in benzene and toluene solutions at different temperatures and concentrations were studied at pressures up to 1.0 GPa. The polarity of the asphaltene molecules allows the dielectric spectroscopic method to be used. A sharp increase in the relaxation time and the sizes of the asphaltene aggregates, calculated according to the Debye model near the phase transition point, were found in the benzene solution. The pressure value corresponding to crystallization is much higher in the toluene solution, and only the border region can be investigated. An explanation of the pressure dependences of the relaxation times are presented. The activation energies and the coefficients of isothermal compressibility are calculated.

  20. Calculating excess volumes of binary solutions with allowance for structural differences between mixed components

    NASA Astrophysics Data System (ADS)

    Balankina, E. S.

    2016-06-01

    Analytical dependences of a volume's properties on the differences between the geometric structures of initial monosystems are obtained for binary systems simulated by a grain medium. The effect of microstructural parameter k (the ratio of volumes of molecules of mixed components) on the concentration behavior of the relative excess molar volume of different types of real binary solutions is analyzed. It is established that the contribution due to differences between the volumes of molecules and coefficients of the packing density of mixed components is ~80-100% for mutual solutions of n-alkanes and ~55-80% of the experimental value of the relative excess molar volume for water solutions of n-alcohols.

  1. A structural study of the intermolecular interactions of tyramine in the solid state and in solution

    NASA Astrophysics Data System (ADS)

    Quevedo, Rodolfo; Nuñez-Dallos, Nelson; Wurst, Klaus; Duarte-Ruiz, Álvaro

    2012-12-01

    The nature of the interactions between tyramine units was investigated in the solid state and in solution. Crystals of tyramine in its free base form were analyzed by Fourier transform infrared (FT-IR) spectroscopy and single-crystal X-ray diffraction (XRD). The crystal structure shows a linear molecular organization held together by "head-to-tail" intermolecular hydrogen bonds between the amino groups and the phenolic hydroxyl groups. These chains are arranged in double layers that can geometrically favor the formation of templates in solution, which may facilitate macrocyclization reactions to form azacyclophane-type compounds. Computational calculations using the PM6-DH+ method and electrospray ionization mass spectrometry (ESI-HRMS) reveal that the formation of a hydrogen-bonded tyramine dimer is favored in solution.

  2. The Method of Decomposition in Invariant Structures: Exact Solutions for N Internal Waves in Three Dimensions

    NASA Astrophysics Data System (ADS)

    Miroshnikov, Victor

    2015-11-01

    The Navier-Stokes system of PDEs is reduced to a system of the vorticity, continuity, Helmholtz, and Lamb-Helmholtz PDEs. The periodic Dirichlet problems are formulated for conservative internal waves vanishing at infinity in upper and lower domains. Stationary kinematic Fourier (SKF) structures, stationary kinematic Euler-Fourier (SKEF) structures, stationary dynamic Euler-Fourier (SDEF) structures, and SKEF-SDEF structures of three spatial variables and time are constructed to consider kinematic and dynamic problems of the three-dimensional theory of the Newtonian flows with harmonic velocity. Exact solutions for propagation and interaction of N internal waves in the upper and lower domains are developed by the method of decomposition in invariant structures and implemented through experimental and theoretical programming in Maple. Main results are summarized in a global existence theorem for the strong solutions. The SKEF, SDEF, and SKEF-SDEF structures of the cumulative flows are visualized by two-parametric surface plots for six fluid-dynamic variables.

  3. Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate†

    PubMed Central

    Zornetzer, Gregory A.; Fox, Brian G.; Markley, John L.

    2008-01-01

    Acyl carrier protein (ACP) is a cofactor in a variety of biosynthetic pathways, including fatty acid metabolism. Thus it is of interest to determine structures of physiologically relevant ACP-fatty acid complexes. We report here the NMR solution structures of spinach ACP with decanoate (10:0-ACP) and stearate (18:0-ACP) attached to the 4′ phosphopantetheine prosthetic group. The protein in the fatty acid complexes adopts a single conformer, unlike apo- and holo-ACP, which interconvert in solution between two major conformers. The protein component of both 10:0- and 18:0-ACP adopts the four-helix bundle topology characteristic of ACP, and a fatty acid binding cavity was identified in both structures. Portions of the protein close in space to the fatty acid and the 4′ phosphopantetheine were identified using filtered/edited NOESY experiments. A docking protocol was used to generate protein structures containing bound fatty acid for 10:0- and 18:0-ACP. In both cases, the predominant structure contained fatty acid bound down the center of the helical bundle, in agreement with the location of the fatty acid binding pockets. These structures demonstrate the conformational flexibility of spinach-ACP and suggest how the protein changes to accommodate its myriad binding partners. PMID:16618110

  4. Cryogenic Ion Mobility-Mass Spectrometry: Tracking Ion Structure from Solution to the Gas Phase.

    PubMed

    Servage, Kelly A; Silveira, Joshua A; Fort, Kyle L; Russell, David H

    2016-07-19

    Electrospray ionization (ESI) combined with ion mobility-mass spectrometry (IM-MS) is adding new dimensions, that is, structure and dynamics, to the field of biological mass spectrometry. There is increasing evidence that gas-phase ions produced by ESI can closely resemble their solution-phase structures, but correlating these structures can be complicated owing to the number of competing effects contributing to structural preferences, including both inter- and intramolecular interactions. Ions encounter unique hydration environments during the transition from solution to the gas phase that will likely affect their structure(s), but many of these structural changes will go undetected because ESI-IM-MS analysis is typically performed on solvent-free ions. Cryogenic ion mobility-mass spectrometry (cryo-IM-MS) takes advantage of the freeze-drying capabilities of ESI and a cryogenically cooled IM drift cell (80 K) to preserve extensively solvated ions of the type [M + xH](x+)(H2O)n, where n can vary from zero to several hundred. This affords an experimental approach for tracking the structural evolution of hydrated biomolecules en route to forming solvent-free gas-phase ions. The studies highlighted in this Account illustrate the varying extent to which dehydration can alter ion structure and the overall impact of cryo-IM-MS on structural studies of hydrated biomolecules. Studies of small ions, including protonated water clusters and alkyl diammonium cations, reveal structural transitions associated with the development of the H-bond network of water molecules surrounding the charge carrier(s). For peptide ions, results show that water networks are highly dependent on the charge-carrying species within the cluster. Specifically, hydrated peptide ions containing lysine display specific hydration behavior around the ammonium ion, that is, magic number clusters with enhanced stability, whereas peptides containing arginine do not display specific hydration around the

  5. Pseudopeptides and beta folding: x-ray structures compared with structures in solution.

    PubMed

    Aubry, A; Marraud, M

    1989-01-01

    In order to restrain the flexibility of the peptide molecules and reduce their biodegradation, modifications of the main chain are now introduced in pseudopeptide analogues. Surprisingly, there is very little data on the conformational properties of these derivatives. We have examined pseudopeptide analogues of RCO-X-Y-NHR' model dipeptides in the depsi, N-methylated, reduced, retro, alpha, beta-dehydro, beta-amino acid, and hydrazino series, in the solid state by x-ray diffraction, and in solution by ir and 1H-nmr spectroscopy. This study provides us with accurate dimensions of the peptide surrogates, and gives some information on the conformational tendencies induced by these substitutions, with reference to those of the related dipeptide sequences. PMID:2720098

  6. Structure and growth of bis(2-ethylhexyl) sulfosuccinate micelles in aqueous solutions

    SciTech Connect

    Sheu, E.Y.; Chen, S.; Huang, J.S.

    1987-06-04

    The structure and growth of micelles formed by anionic surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT) in aqueous solutions have been studied by small angle neutron scattering (SANS). They used the contrast variation technique to determine the aggregation number, the effective charge, and two molecular parameters of the micelles in solutions of 0.8 g/dL surfactant concentration. They then used these two molecular parameters to analyze micellar solutions at other concentrations. Two micellar parameters, the mean aggregation number n and the effective charge z0, have been extracted from experimental data for solutions with surfactant concentrations ranging from 0.2 to 1.0 g/dL. The minimum micellar aggregation number is predicted to be 15 at the critical micellar concentration (cmc) and the structure is a compact spherical aggregate having well-defined hydrophobic and hydrophilic regions. The micelles grow moderately as the surfactant concentration increases, transforming from a spherical to an oblate spheroidal shape in a manner describable by the ladder model.

  7. Indentation-induced formation of low-dimensional Si structures in KOH solution

    NASA Astrophysics Data System (ADS)

    Yang, Fuqian; Li, Ding

    2010-03-01

    Low-dimensional Si structures, including Si nanobelts and Si micropyramids, were formed on the surface of n-type silicon by microindentation and anisotropic etching in 30 wt% KOH solution at a temperature of 50 °C. The indentation was performed to create local plastic deformation and residual stresses. The residual stresses caused the formation of the Si nanobelts around the sites of indents on the surface of Si (1 1 1) and the Si micropyramids at the sites of indents on the surface of Si (1 0 0). The formation of the Si micropyramids was due to the local 'mask' created by the indentation and the residual stress around the indents. The residual hydrostatic stress at the tensile state increased the local etching rate, which resulted in a surface depression around the indents. The combination of indentation and wet etching process provides a maskless process to potentially produce low-dimensional Si structures in KOH solution at low temperatures.

  8. Mechanical degradation of porous titanium with entangled structure filled with biodegradable magnesium in Hanks' solution.

    PubMed

    Li, Qiuyan; Jiang, Guofeng; Wang, Cunlong; Dong, Jie; He, Guo

    2015-12-01

    The degradation behavior of the porous titanium with entangled structure filled with biodegradable magnesium (p-Ti/Mg) in Hanks' solution was investigated. It was found that the p-Ti/Mg composite had higher strength than pure magnesium and porous titanium with entangled structure (p-Ti). Although the magnesium in p-Ti/Mg was completely dissolved in Hanks' solution after immersion for 104 h, the rest of the sample still maintained strength of about 86 MPa. Moreover, the produced porousness (due to magnesium-degradation) could provide channels for the ingrowth and transportation of bone cells. However, the high corrosion rate of p-Ti/Mg is still a problem when used as a candidate biomedical material, which needs further improvement. PMID:26354275

  9. Numerical solution of quadratic matrix equations for free vibration analysis of structures

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1975-01-01

    This paper is concerned with the efficient and accurate solution of the eigenvalue problem represented by quadratic matrix equations. Such matrix forms are obtained in connection with the free vibration analysis of structures, discretized by finite 'dynamic' elements, resulting in frequency-dependent stiffness and inertia matrices. The paper presents a new numerical solution procedure of the quadratic matrix equations, based on a combined Sturm sequence and inverse iteration technique enabling economical and accurate determination of a few required eigenvalues and associated vectors. An alternative procedure based on a simultaneous iteration procedure is also described when only the first few modes are the usual requirement. The employment of finite dynamic elements in conjunction with the presently developed eigenvalue routines results in a most significant economy in the dynamic analysis of structures.

  10. Structuring and sedimentation stability of titanium phosphate nanoparticles in polymer solutions.

    PubMed

    Uryupina, O Ya; Serebryakova, N V; Roldughin, V I

    2003-07-01

    The influence of dispersed phase nature on the sedimentation stability as well as coagulation structure of titanium phosphate (TP) nanoparticles in polymer suspensions has been investigated. Two systems are considered: (i). TP suspension in toluene/ethyl cellosolve mixed solution of ephoxy resin E-40 and (ii). multicomponent system, ferric oxide, talc and TP suspension in toluene/ethyl cellosolve solution of E-40, as a model of the practical varnish-paint systems. For the case of a polar solvent, a unique phenomenon, extremal dependence of the strength of model systems on the concentration TP, is detected and increase of sedimentation stability of TP organic suspensions with time of contact of TP with a solvent is observed. Data of FTIR-spectroscopy show that phenomena detected result from the formation adsorption shell possessing high structural viscosity on TP nanopaticles. PMID:12818497

  11. Solution spectroelectrochemical cell for in situ X-ray absorption fine structure

    SciTech Connect

    Antonio, M.R.; Soderholm, L.; Song, I.

    1995-06-12

    A purpose-built spectroelectrochemical cell for in situ fluorescence XAFS (X-ray Absorption Fine Structure) measurements of bulk solution species during constant-potential electrolysis is described. The cell performance was demonstrated by the collection of europium L{sub 3}-edge XANES (X-ray Absorption Near Edge Structure) throughout the course of electrolysis of an aqueous solution of EuCl{sub 3}{center_dot}6H{sub 2}O in 1 M H{sub 2}SO{sub 4}. The europium L{sub 3}-edge resonances reported here for the Eu{sup III} and Eu{sup II} ions demonstrate that their 2p{sub 3/2} {yields} 5d electronic transition probabilities are not the same.

  12. Parameter degeneracy in neutrino oscillation — Solution network and structural overview

    NASA Astrophysics Data System (ADS)

    Minakata, Hisakazu; Uchinami, Shoichi

    2010-04-01

    It is known that there is a phenomenon called “parameter degeneracy” in neutrino oscillation measurement of lepton mixing parameters; A set of the oscillation probabilities, e.g., P( ν μ → ν e ) and its CP-conjugate Pleft( {{{bar ν }_μ } to {{bar ν }_e}} right) at a particular neutrino energy does not determine uniquely the values of θ 13 and δ. With use of the approximate form of the oscillation probability á la Cervera et al., a complete analysis of the eightfold parameter degeneracy is presented. We propose a unified view of the various types of the degeneracy as invariance of the oscillation probabilities under discrete mappings of the mixing parameters. Explicit form of the mapping is obtained either by symmetry argument, or by deriving exact analytic expressions of all the degeneracy solutions for a given true solution. Due to the one-to-one mapping structure the degeneracy solutions are shown to form a network. We extend our analysis into the parameter degeneracy in T- and CPT-conjugate measurement as well as to the setup with the golden and the silver channels, P( ν e → ν μ ) and P( ν e → ν τ ). Some characteristic features of the degeneracy solutions in CP-conjugate measurement, in particular their energy dependences, are illuminated by utilizing the explicit analytic solutions.

  13. Solution Structure and Properties of AlgH from Pseudomonas aeruginosa

    PubMed Central

    Urbauer, Jeffrey L.; Cowley, Aaron B.; Broussard, Hayley P.; Niedermaier, Henry T.; Bieber Urbauer, Ramona J.

    2015-01-01

    In Pseudomonas aeruginosa, the algH gene regulates the cellular concentrations of a number of enzymes and the production of several virulence factors, and is suggested to serve a global regulatory function. The precise mechanism by which the algH gene product, the AlgH protein, functions is unknown. The same is true for AlgH family members from other bacteria. In order to lay the groundwork for understanding the physical underpinnings of AlgH function, we examined the structure and physical properties of AlgH in solution. Under reducing conditions, results of NMR, electrophoretic mobility, and sedimentation equilibrium experiments indicate AlgH is predominantly monomeric and monodisperse in solution. Under non-reducing conditions intra- and intermolecular disulfide bonds form, the latter promoting AlgH oligomerization. The high-resolution solution structure of AlgH reveals alpha/beta-sandwich architecture fashioned from ten beta strands and seven alpha helices. Comparison with available structures of orthologues indicates conservation of overall structural topology. The region of the protein most strongly conserved structurally also shows the highest amino acid sequence conservation and, as revealed by hydrogen-deuterium exchange studies, is also the most stable. In this region, evolutionary trace analysis identifies two clusters of amino acid residues with the highest evolutionary importance relative to all other AlgH residues. These frame a partially solvent exposed shallow hydrophobic cleft, perhaps identifying a site for intermolecular interactions. The results establish a physical foundation for understanding the structure and function of AlgH and AlgH family proteins and should be of general importance for further investigations of these and related proteins. PMID:25857636

  14. Approximate analytic solutions for the ionization structure of a pressure equilibrium Strömgren sphere

    NASA Astrophysics Data System (ADS)

    Tinoco Arenas, A.; González Bolívar, M.; Medina Covarrubias, R.; Raga, A. C.

    2015-10-01

    We present analytic models for a photoionized region in pressure equilibrium with the surrounding, neutral material. The models are based on the assumption of a linear relation between the H ionization fraction and the square of the sound speed of the gas. We show that under these assumptions the "grey" radiative transfer equation has analytic solutions that provide the ionization structure and the density of the nebula as a function of radius.

  15. Total assignment and structure in solution of tetrandrine by NMR spectroscopy and molecular modelling

    NASA Astrophysics Data System (ADS)

    Thevand, André; Stanculescu, Ioana; Mandravel, Cristina; Woisel, Patrice; Surpateanu, Gheorghe

    2004-07-01

    High-resolution 1- and 2D NMR spectra of tetrandrine and molecular modelling were employed to characterise its structure in solution. Complete and unambiguous assignment of all proton and carbon resonance signals is reported. Scalar couplings were determined from dihedral angles with the Karplus equation. Inter-proton distances were evaluated from NOE correlation peaks. Comparison of simulated and X-ray conformations of tetrandrine reveals only small differences.

  16. Structural and photoluminescence studies of TiO{sub 2} nanoparticles synthesized by solution combustion method

    SciTech Connect

    Balamurugan, M. Silambarasan, M.; Saravanan, S.; Soga, Tetsuo

    2015-06-24

    In this study titanium dioxide nanoparticle is prepared by simple solution combustion method. The powder X-ray diffraction pattern indicates the prepared titanium dioxide nanoparticles crystalline nature with tetragonal structure. Also it shows the nanoparticle is anatase and rutile mixed phase. The Field Emission Scanning Electron Microscopy image shows the nanostructure of particles in the size range about 50 nm. Room temperature photoluminescence shows intrinsic defects of oxygen vacancies.

  17. Exact combined traveling wave solutions and multi-symplectic structure of the variant Boussinesq-Whitham-Broer-Kaup type equations

    NASA Astrophysics Data System (ADS)

    Yang, Xiao-Feng; Deng, Zi-Chen; Li, Qing-Jun; Wei, Yi

    2016-07-01

    The homogeneous balance of undetermined coefficients method (HBUCM) is firstly proposed to construct not only the exact traveling wave solutions, three-wave solutions, homoclinic solutions, N-soliton solutions, but also multi-symplectic structures of some nonlinear partial differential equations (NLPDEs). By applying the proposed method to the variant Boussinesq equations (VBEs), the exact combined traveling wave solutions and a multi-symplectic structure of the VBEs are obtained directly. Then, the definition and a multi-symplectic structure of the variant Boussinesq-Whitham-Broer-Kaup type equations (VBWBKTEs) which can degenerate to the VBEs, the Whitham-Broer-Kaup equations (WBKEs) and the Broer-Kaup equations (BKEs) are given in the multi-symplectic sense. The HBUCM is also a standard and computable method, which can be generalized to obtain the exact solutions and multi-symplectic structures for some types of NLPDEs.

  18. Structure and dimerization of translation initiation factor aIF5B in solution

    SciTech Connect

    Carø VohlanderRasmussen, Louise; Oliveira, Cristiano Luis Pinto; Byron, Olwyn; Jensen, Janni Mosgaard; Pedersen, Jan Skov; Sperling-Petersen, Hans Uffe; Mortensen, Kim Kusk

    2012-02-07

    Translation initiation factor 5B (IF5B) is required for initiation of protein synthesis. The solution structure of archaeal IF5B (aIF5B) was analysed by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) and was indicated to be in both monomeric and dimeric form. Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) of aIF5B indicated that aIF5B forms irreversible dimers in solution but only to a maximum of 5.0-6.8% dimer. Sedimentation velocity (SV) AUC at higher speed also indicated the presence of two species, and the sedimentation coefficients s{sub 20,w}{sup 0} were determined to be 3.64 and 5.51 {+-} 0.29 S for monomer and dimer, respectively. The atomic resolution (crystallographic) structure of aIF5B (Roll-Mecak et al. [6]) was used to model monomer and dimer, and theoretical sedimentation coefficients for these models were computed (3.89 and 5.63 S, respectively) in good agreement with the sedimentation coefficients obtained from SV analysis. Thus, the structure of aIF5B in solution must be very similar to the atomic resolution structure of aIF5B. SAXS data were acquired in the same buffer with the addition of 2% glycerol to inhibit dimerization, and the resultant monomeric aIF5B in solution did indeed adopt a structure very similar to the one reported earlier for the protein in crystalline form. The p(r) function indicated an elongated conformation supported by a radius of gyration of 37.5 {+-} 0.2 {angstrom} and a maximum dimension of {approx}130 {angstrom}. The effects of glycerol on the formation of dimers are discussed. This new model of aIF5B in solution shows that there are universal structural differences between aIF5B and the homologous protein IF2 from Escherichia coli.

  19. Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease

    SciTech Connect

    Yun, Ji-Hye; Kim, Heeyoun; Park, Jung Eun; Lee, Jung Sup; Lee, Weontae

    2013-01-11

    Highlights: Black-Right-Pointing-Pointer We have determined solution structures of vEP C-terminal regulatory domain. Black-Right-Pointing-Pointer vEP C-ter100 has a compact {beta}-barrel structure with eight anti-parallel {beta}-strands. Black-Right-Pointing-Pointer Solution structure of vEP C-ter100 shares its molecular topology with that of the collagen-binding domain of collagenase. Black-Right-Pointing-Pointer Residues in the {beta}3 region of vEP C-ter100 might be important in putative ligand/receptor binding. Black-Right-Pointing-Pointer vEP C-ter100 interacts strongly with iron ion. -- Abstract: An extracellular metalloprotease (vEP) secreted by Vibrio vulnificus ATCC29307 is a 45-kDa proteolytic enzyme that has prothrombin activation and fibrinolytic activities during bacterial infection. The action of vEP could result in clotting that could serve to protect the bacteria from the host defense machinery. Very recently, we showed that the C-terminal propeptide (C-ter100), which is unique to vEP, is involved in regulation of vEP activity. To understand the structural basis of this function of vEP C-ter100, we have determined the solution structure and backbone dynamics using multidimensional nuclear magnetic resonance spectroscopy. The solution structure shows that vEP C-ter100 is composed of eight anti-parallel {beta}-strands with a unique fold that has a compact {beta}-barrel formation which stabilized by hydrophobic and hydrogen bonding networks. Protein dynamics shows that the overall structure, including loops, is very rigid and stabilized. By structural database analysis, we found that vEP C-ter100 shares its topology with that of the collagen-binding domain of collagenase, despite low sequence homology between the two domains. Fluorescence assay reveals that vEP C-ter100 interacts strongly with iron (Fe{sup 3+}). These findings suggest that vEP protease might recruit substrate molecules, such as collagen, by binding at C-ter100 and that vEP participates

  20. Effective protein-protein interaction from structure factor data of a lysozyme solution

    SciTech Connect

    Abramo, M. C.; Caccamo, C.; Costa, D.; Ruberto, R.; Wanderlingh, U.; Cavero, M.; Pellicane, G.

    2013-08-07

    We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated.

  1. Mechanical and structural properties of solution-cast high-amylose maize starch films.

    PubMed

    Koch, Kristine; Gillgren, Thomas; Stading, Mats; Andersson, Roger

    2010-01-01

    Environmental issues have forced the introduction of sustainable solutions such as annually renewable resources being used as a raw material for packaging and disposables. This paper examined the effects of time and temperature during manufacturing and plasticiser content on the molecular structure of high-amylose maize starch films. It also analysed how manufacturing conditions, plasticiser content and molecular structure of the films affected their material properties. It was found that increased time or temperature increased the degradation of amylose and of amylopectin, which in turn negatively affected film cohesiveness. However, neither time nor temperature had any effect on tensile properties. PMID:19828118

  2. Numerical solution of the vertical structure equation in the normal mode method. [in meteorology

    NASA Technical Reports Server (NTRS)

    Sasaki, Y. K.; Chang, L. P.

    1985-01-01

    In the present model of multilayered stability stratification, aimed at obtaining the analytic eigensolutions of the vertical structure equation, each layer is characterized by its own static stability value. By requiring continuity of pressure and vertical velocity across each interface level, and by imposing suitable upper and lower boundary conditions, matching eigensolutions are obtained in terms of the Bessel functions. Attention is given to an explicit example of a double-layered stratified atmosphere which demonstrates the mathematical manipulations involved; the resultant vertical structure functions are used to check the accuracy of the numerical solutions by the finite difference and finite element methods.

  3. The confluence of structure and dynamics in lanthanide(III) chelates: how dynamics help define structure in solution

    PubMed Central

    Webber, Benjamin C.; Woods, Mark

    2013-01-01

    Coordination exchange processes tend to dominate the solution state behaviour of lanthanide chelates and generally prohibit the study of small conformational changes. In this article we take advantage of coordinatively rigid Eu3+ chelates to examine the small conformational changes that occur in these chelates as water dissociatively exchanges in and out of the inner coordination sphere. The results show that the time-averaged conformation of the chelate alters as the water exchange rate increases. This conformational change reflects a change in the hydration state (q/rLnH6) of the chelate. The hydration state has recently come to be expressed as two separate parameters q and rLnH. However, these two parameters simultaneously describe the same structural considerations which in solution, are indistinguishable and intrinsically related to, and dependent upon, the dissociative water exchange rate. This realization leads to the broader understanding that a solution state structure can only be appreciated with reference to the dynamics of the system. PMID:24100299

  4. A comparison of the structure of solute clusters formed during thermal ageing and irradiation.

    PubMed

    Hyde, J M; Sha, G; Marquis, E A; Morley, A; Wilford, K B; Williams, T J

    2011-05-01

    Nanometre scale clusters form in Cu-containing reactor pressure vessel (RPV) steels during neutron irradiation. These clusters have a deleterious effect on mechanical properties, which can result in embrittlement and limit the reactor operating life. Thermal ageing of RPV steels can also induce the formation of solute clusters but it is not clear how similar these are to those formed during irradiation. In this work atom probe tomography, combined with detailed structural assessments of the structure of solute clusters, is used to address this issue. A series of thermal ageing heat treatments has been performed on several high- and low-Ni RPV welds to produce 1-4 nm diameter solute clusters. The same materials have also been neutron irradiated. The results show that CuMnNiSi enriched clusters formed during thermal ageing have, on average, higher Cu contents and lower Mn, Ni and Si contents than those found in irradiation-induced clusters. The effect of increasing bulk Ni is to encourage the formation of clusters with significantly higher Ni content, slightly higher Mn and Si contents and significantly lower Cu contents. At very high doses and dose rates MnNiSi enriched clusters can form even in high-Cu welds. Despite differences in the compositions of individual clusters formed during irradiation and during thermal ageing, clusters in both exhibit similar structure. In particular, well developed clusters in both materials have Cu-enriched cores whose peripheries are enriched in Ni, Mn and, in most cases, Si. PMID:21227587

  5. Analysis of the structure of aqueous solutions of isopropanol based on optical, volumetric, and elastic data

    NASA Astrophysics Data System (ADS)

    Abramovich, A. I.; Lanshina, L. V.

    2015-07-01

    The curve of the concentration dependence of the total molecular light scattering coefficient of xC3H7OH-(1 - x)H2O solutions showed two sharp maxima (at x = 0.04 and 0.09) and a minimum at x = 0.06 mole fractions, suggesting a considerable rearrangement of the structure of the solutions near these concentrations. The concentration dependences of excess molar volume, adiabatic compressibility, and molar refraction showed negative deviations from the ideal with a minimum in the range x = 0.18-0.3. The structure of water was assumed to undergo a rearrangement at x = 0.04 accompanied by structural fluctuations, which dispersed at 0.04 < x < 0.06. At x = 0.06, associates of isopropanol molecules started to form, whose number and size increased linearly up to x = 0.13. In the 0.13 < x < 0.35 concentration range, some kind of an aqueous alcohol emulsion containing pure alcohol "nanodrops" formed and the solutions became microheterogeneous.

  6. Structure and properties of novel regenerated cellulose fibers prepared in NaOH complex solution.

    PubMed

    Wang, Wencong; Zhang, Peng; Zhang, Shuai; Li, Faxue; Yu, Jianyong; Lin, Jinyou

    2013-10-15

    Novel spinning solution, prepared by dissolving hydroxyethyl cellulose (HEC) owning a low molar substitution (MS) into NaOH/urea/thiouea aqueous solution with a specific weight ratio of 8:8:6.5, was employed to fabricate a new type of regenerated fibers by wet-spun method. The structure and properties of the resultant HEC fibers were characterized by (13)C NMR, FTIR, synchrotron WAXS, SEM, and tensile tester. The results showed that HEC fibers exhibited structure identical with HEC because of the physical dissolution and coagulation processes, but quite different from native cellulose due to partial breakage of hydrogen bonds and crystal transformation from cellulose I to cellulose II during cellulose modification. The resultant HEC fibers with relatively dense and homogenous structure displayed good moisture related properties and stayed stable in alkali solution with low concentration. Moreover, the novel fibers owned good dry mechanical properties in spit of their slightly poor wet mechanical properties comparable to viscose rayon, showing great potential in substituting the traditional viscose fibers. PMID:23987444

  7. New structural insights into Golgi Reassembly and Stacking Protein (GRASP) in solution

    PubMed Central

    Mendes, Luís F. S.; Garcia, Assuero F.; Kumagai, Patricia S.; de Morais, Fabio R.; Melo, Fernando A.; Kmetzsch, Livia; Vainstein, Marilene H.; Rodrigues, Marcio L.; Costa-Filho, Antonio J.

    2016-01-01

    Among all proteins localized in the Golgi apparatus, a two-PDZ (PSD95/DlgA/Zo-1) domain protein plays an important role in the assembly of the cisternae. This Golgi Reassembly and Stacking Protein (GRASP) has puzzled researchers due to its large array of functions and relevance in Golgi functionality. We report here a biochemical and biophysical study of the GRASP55/65 homologue in Cryptococcus neoformans (CnGRASP). Bioinformatic analysis, static fluorescence and circular dichroism spectroscopies, calorimetry, small angle X-ray scattering, solution nuclear magnetic resonance, size exclusion chromatography and proteolysis assays were used to unravel structural features of the full-length CnGRASP. We detected the coexistence of regular secondary structures and large amounts of disordered regions. The overall structure is less compact than a regular globular protein and the high structural flexibility makes its hydrophobic core more accessible to solvent. Our results indicate an unusual behavior of CnGRASP in solution, closely resembling a class of intrinsically disordered proteins called molten globule proteins. To the best of our knowledge, this is the first structural characterization of a full-length GRASP and observation of a molten globule-like behavior in the GRASP family. The possible implications of this and how it could explain the multiple facets of this intriguing class of proteins are discussed. PMID:27436376

  8. New structural insights into Golgi Reassembly and Stacking Protein (GRASP) in solution.

    PubMed

    Mendes, Luís F S; Garcia, Assuero F; Kumagai, Patricia S; de Morais, Fabio R; Melo, Fernando A; Kmetzsch, Livia; Vainstein, Marilene H; Rodrigues, Marcio L; Costa-Filho, Antonio J

    2016-01-01

    Among all proteins localized in the Golgi apparatus, a two-PDZ (PSD95/DlgA/Zo-1) domain protein plays an important role in the assembly of the cisternae. This Golgi Reassembly and Stacking Protein (GRASP) has puzzled researchers due to its large array of functions and relevance in Golgi functionality. We report here a biochemical and biophysical study of the GRASP55/65 homologue in Cryptococcus neoformans (CnGRASP). Bioinformatic analysis, static fluorescence and circular dichroism spectroscopies, calorimetry, small angle X-ray scattering, solution nuclear magnetic resonance, size exclusion chromatography and proteolysis assays were used to unravel structural features of the full-length CnGRASP. We detected the coexistence of regular secondary structures and large amounts of disordered regions. The overall structure is less compact than a regular globular protein and the high structural flexibility makes its hydrophobic core more accessible to solvent. Our results indicate an unusual behavior of CnGRASP in solution, closely resembling a class of intrinsically disordered proteins called molten globule proteins. To the best of our knowledge, this is the first structural characterization of a full-length GRASP and observation of a molten globule-like behavior in the GRASP family. The possible implications of this and how it could explain the multiple facets of this intriguing class of proteins are discussed. PMID:27436376

  9. Solution structure of the Drosha double-stranded RNA-binding domain

    PubMed Central

    2010-01-01

    Background Drosha is a nuclear RNase III enzyme that initiates processing of regulatory microRNA. Together with partner protein DiGeorge syndrome critical region 8 (DGCR8), it forms the Microprocessor complex, which cleaves precursor transcripts called primary microRNA to produce hairpin precursor microRNA. In addition to two RNase III catalytic domains, Drosha contains a C-terminal double-stranded RNA-binding domain (dsRBD). To gain insight into the function of this domain, we determined the nuclear magnetic resonance (NMR) solution structure. Results We report here the solution structure of the dsRBD from Drosha (Drosha-dsRBD). The αβββα fold is similar to other dsRBD structures. A unique extended loop distinguishes this domain from other dsRBDs of known structure. Conclusions Despite uncertainties about RNA-binding properties of the Drosha-dsRBD, its structure suggests it retains RNA-binding features. We propose that this domain may contribute to substrate recognition in the Drosha-DGCR8 Microprocessor complex. PMID:20226070

  10. Perspectives of solution NMR spectroscopy for structural and functional studies of integral membrane proteins

    NASA Astrophysics Data System (ADS)

    Reckel, Sina; Hiller, Sebastian

    2013-04-01

    This article discusses future perspectives of solution NMR spectroscopy to study structures and functions of integral membrane proteins at atomic resolution, based on a review of recent progress in this area. Several selected examples of structure determinations, as well as functional studies of integral membrane proteins are highlighted. We expect NMR spectroscopy to make future key scientific contributions to understanding membrane protein function, in particular for large membrane protein systems with known three-dimensional structure. Such situations can benefit from the fact that functional NMR studies have substantially less limitations by molecular size than a full de novo structure determination. Therefore, the general potential for NMR spectroscopy to solve biologic key questions associated with integral membrane proteins is very promising.

  11. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy

    SciTech Connect

    Gronenborn, A.M.; Clore, G.M.

    1994-12-01

    Complete understanding of a protein`s function and mechanism of action can only be achieved with a knowledge of its three-dimensional structure at atomic resolution. At present, there are two methods available for determining such structures. The first method, which has been established for many years, is x-ray diffraction of protein single crystals. The second method has blossomed only in the last 5 years and is based on the application of nuclear magnetic resonance (NMR) spectroscopy to proteins in solution. This review paper describes three- and four-dimensional NMR methods applied to protein structure determination and was adapted from Clore and Gronenborn. The review focuses on the underlying principals and practice of multidimensional NMR and the structural information obtained.

  12. Atomically resolved three-dimensional structures of electrolyte aqueous solutions near a solid surface

    NASA Astrophysics Data System (ADS)

    Martin-Jimenez, Daniel; Chacon, Enrique; Tarazona, Pedro; Garcia, Ricardo

    2016-07-01

    Interfacial liquid layers play a central role in a variety of phenomena ranging from friction to molecular recognition. Liquids near a solid surface form an interfacial layer where the molecular structure is different from that of the bulk. Here we report atomic resolution three-dimensional images of electrolyte solutions near a mica surface that demonstrate the existence of three types of interfacial structures. At low concentrations (0.01-1 M), cations are adsorbed onto the mica. The cation layer is topped by a few hydration layers. At higher concentrations, the interfacial layer extends several nanometres into the liquid. It involves the alternation of cation and anion planes. Fluid Density Functional calculations show that water molecules are a critical factor for stabilizing the structure of the interfacial layer. The interfacial layer stabilizes a crystal-like structure compatible with liquid-like ion and solvent mobilities. At saturation, some ions precipitate and small crystals are formed on the mica.

  13. Thorium nanochemistry: the solution structure of the Th(IV)-hydroxo pentamer

    SciTech Connect

    Walther, Clemens; Rothe, Jörg; Schimmelpfennig, Bernd; Fuss, Markus

    2012-10-10

    Tetravalent thorium exhibits a strong tendency towards hydrolysis and subsequent polymerization. Polymeric species play a crucial role in understanding thorium solution chemistry, since their presence causes apparent solubility several orders of magnitude higher than predicted by thermodynamic data bases. Although electrospray mass spectrometry (ESI MS) identifies Th(IV) dimers and pentamers unequivocally as dominant species close to the solubility limit, the molecular structure of Th5(OH)y polymers was hitherto unknown. In the present study, X-ray absorption fine structure (XAFS) spectroscopy, high energy X-ray scattering (HEXS) measurements, and quantum chemical calculations are combined to solve the pentamer structure. The most favourable structure is represented by two Th(IV) dimers linked by a central Th(IV) cation through hydroxide bridges.

  14. Nanoscopic imaging of thick heterogeneous soft-matter structures in aqueous solution.

    PubMed

    Bartsch, Tobias F; Kochanczyk, Martin D; Lissek, Emanuel N; Lange, Janina R; Florin, Ernst-Ludwig

    2016-01-01

    Precise nanometre-scale imaging of soft structures at room temperature poses a major challenge to any type of microscopy because fast thermal fluctuations lead to significant motion blur if the position of the structure is measured with insufficient bandwidth. Moreover, precise localization is also affected by optical heterogeneities, which lead to deformations in the imaged local geometry, the severity depending on the sample and its thickness. Here we introduce quantitative thermal noise imaging, a three-dimensional scanning probe technique, as a method for imaging soft, optically heterogeneous and porous matter with submicroscopic spatial resolution in aqueous solution. By imaging both individual microtubules and collagen fibrils in a network, we demonstrate that structures can be localized with a precision of ∼10 nm and that their local dynamics can be quantified with 50 kHz bandwidth and subnanometre amplitudes. Furthermore, we show how image distortions caused by optically dense structures can be corrected for. PMID:27596919

  15. Identification of silver cubic structures during ultrasonication of chitosan AgNO3 solution.

    PubMed

    Raghavendra, Gownolla Malegowd; Jung, Jeyoung; Kim, Dowan; Varaprasad, Kokkarachedu; Seo, Jongchul

    2016-11-01

    During ultrasonication of chitosan AgNO3 solution (10mM), silver cubic structures were identified along with other dispersed silver nanoparticles. Temperature influenced the formation of the cubic structures. Formation of the silver cubic structures occurred via initial formation of 'four petal flower-like' structures that underwent transformation to the "cubic morphology" in the latter stages. Aging of the reaction mixture led to formation of complete dendrites. These dendrites comprised a large quantity of silver nanoparticles. Upon repetition of the experiment with starch instead of chitosan, the identified silver cubic structures were completely absent, indicating that formation of the 'silver cubic structures' is dependent on the polysaccharide used. It is believed that the structural features of chitosan facilitate the formation of 'silver cubic structures' under ultrasonic conditions. The phenomena occurring during the experiments were evaluated via scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), ultraviolet-visible (UV-vis) spectra, transmission electron microscopy (TEM), and selected area electron diffraction (SAED) analysis. PMID:27516304

  16. Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state.

    PubMed

    Cornilescu, Gabriel; Ulijasz, Andrew T; Cornilescu, Claudia C; Markley, John L; Vierstra, Richard D

    2008-11-01

    The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B' cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80 degrees relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B' GAF domain can, by itself, complete the Pr --> Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework. PMID:18762196

  17. Structural Stability of Riemann Solutions for a Multiphase Kinematic Conservation Law Model that Changes Type.

    NASA Astrophysics Data System (ADS)

    Vinod, Vaidyanath

    We consider a model for 2-way traffic flow introduced by Bick and Newell in 1960 (2). The model problem is: p_{t} + (pu)_{x } = 0; quad q_{t} + (qv)_ {x} = 0.eqno(0.1)Here p and q are the densities of cars in the two directions of flow and u and v are the respective velocities in the p and q directions; a choice suggested in (2) is u = 1 - p - beta q, v = -1 + q + beta p.. In this model, beta is a measure of the interaction between the two directions of flow. For the problem to be physically feasible, we require 0<=beta<1.. Equation (0.1) is a conservation law that changes type. The domain of the solution is p>=0, q<=0, 1 - p - beta q>=0, and -1 + q + beta p>=0.. When beta = 0, there is no interaction between the two directions of flow and then the system (0.1) reduces to a system of scalar equation for which the Riemann problem (Cauchy problem) to (0.1) with initial data of the form: U(x,0) = cases{{U_0,quad x < 0} crcr{U_1,quad x > 0} cr}has a unique solution in the class of Lax entropy or admissible wave solutions. In this case, there is an open set of initial states (U_0, U_1) for which the solution exhibits the phenomenon of 'overlapping rarefaction waves'. These waves occupy the same position in the physical plane and they are stable. When beta>0, for the same initial values U_0 and U_1, these overlapping rarefaction solutions disappear due to the presence of an elliptic region. For these states, we introduce a new shock solution which we term a critical shock (this is qualitatively similar to a Buckley-Leverett shock). The strength of the shock goes to zero as beta tends to zero; and this solution approaches the overlapping wave solution. The main result of this thesis is that these constructed solutions are structurally stable as beta approaches zero (that is, the elliptic region shrinks to a line); and that they converge strongly in L^1. The construction might prove useful in solving other problems that change type, for example models for three-phase flow

  18. Structural stability of Riemann solutions for a multiphase kinematic conservation law model that changes type

    SciTech Connect

    Vinod, V.

    1992-01-01

    The authors consider a model for 2-way traffic flow introduced by Bick and Newell in 1960. The model problem is: pt + (pu)x = 0; qt + (qv)x = 0. Here p and q are the densities of cars in the two directions of flow and u and v are the respective velocities in the p and q directions; a choice suggested is u = 1 - p - [beta]q, v = [minus]1 + q + [beta]p. In this model, [beta] is a measure of the interaction between the two directions of flow. For the problem to be physically feasible, one requires 0 [le] [beta] [le] 1. Equation (0.1) is a conservation law that changes type. The domain of the solution is p [ge] 0,q [le] 0, 1 - p - [beta]q [ge] 0, and [minus]1 + q + [beta]p [ge] 0. When [beta] = 0, there is no interaction between the two directions of flow and then the system (0.1) reduces to a system of scalar equation for which the Riemann problem (Cauchy problem) to (0.1) with initial data of the form: U(x,0) = U[sub 0], x<0 U[sub 1], x>0 has a unique solution in the class of Lax entropy or admissible wave solutions. In this case, there is an open set of initial states (U[sub 0], U[sub 1]) for which the solution exhibits the phenomenon of [open quotes]overlapping rarefaction waves.[close quotes] These waves occupy the same position in the physical plane and they are stable. When [beta] > 0, for the same initial values U[sub o] and U[sub 1], these overlapping rarefaction solutions disappear due to the presence of an elliptic region. For these states, the authors introduce a new shock solution which they term a critical shock (this is qualitatively similar to a Buckley-Leverett shock). The strength of the shock goes to zero as [beta] tends to zero; and this solution approaches the overlapping wave solution. The main result of this thesis is that these constructed solutions are structurally stable as [beta] approaches zero (that is, the elliptic region shrinks to a line); and that they converge strongly in L[sup 1].

  19. Supercooling of aqueous dimethylsulfoxide solution at normal and high pressures: Evidence for the coexistence of phase-separated aqueous dimethylsulfoxide solutions of different water structures

    NASA Astrophysics Data System (ADS)

    Kanno, H.; Kajiwara, K.; Miyata, K.

    2010-05-01

    Supercooling behavior of aqueous dimethylsulfoxide (DMSO) solution was investigated as a function of DMSO concentration and at high pressures. A linear relationship was observed for TH (homogeneous ice nucleation temperature) and Tm (melting temperature) for the supercooling of aqueous DMSO solution at normal pressure. Analysis of the DTA (differential thermal analysis) traces for homogeneous ice crystallization in the bottom region of the TH curve for a DMSO solution of R =20 (R: moles of water/moles of DMSO) at high pressures supported the contention that the second critical point (SCP) of liquid water should exist at Pc2=˜200 MPa and at Tc2<-100 °C (Pc2: pressure of SCP, Tc2: temperature of SCP). The presence of two TH peaks for DMSO solutions (R =15, 12, and 10) suggests that phase separation occurs in aqueous DMSO solution (R ≤15) at high pressures and low temperatures (<-90 °C). The pressure dependence of the two TH curves for DMSO solutions of R =10 and 12 indicates that the two phase-separated components in the DMSO solution of R =10 have different liquid water structures [LDL-like and HDL-like structures (LDL: low-density liquid water, HDL: high-density liquid water)] in the pressure range of 120-230 MPa.

  20. Supercooling of aqueous dimethylsulfoxide solution at normal and high pressures: Evidence for the coexistence of phase-separated aqueous dimethylsulfoxide solutions of different water structures.

    PubMed

    Kanno, H; Kajiwara, K; Miyata, K

    2010-05-21

    Supercooling behavior of aqueous dimethylsulfoxide (DMSO) solution was investigated as a function of DMSO concentration and at high pressures. A linear relationship was observed for T(H) (homogeneous ice nucleation temperature) and T(m) (melting temperature) for the supercooling of aqueous DMSO solution at normal pressure. Analysis of the DTA (differential thermal analysis) traces for homogeneous ice crystallization in the bottom region of the T(H) curve for a DMSO solution of R=20 (R: moles of water/moles of DMSO) at high pressures supported the contention that the second critical point (SCP) of liquid water should exist at P(c2)= approximately 200 MPa and at T(c2)<-100 degrees C (P(c2): pressure of SCP, T(c2): temperature of SCP). The presence of two T(H) peaks for DMSO solutions (R=15, 12, and 10) suggests that phase separation occurs in aqueous DMSO solution (Rsolutions of R=10 and 12 indicates that the two phase-separated components in the DMSO solution of R=10 have different liquid water structures [LDL-like and HDL-like structures (LDL: low-density liquid water, HDL: high-density liquid water)] in the pressure range of 120-230 MPa. PMID:20499975

  1. Lanthanide-binding helix-turn-helix peptides: Solution structure of a designed metallonuclease

    PubMed Central

    Welch, Joel T.; Kearney, William R.; Franklin, Sonya J.

    2003-01-01

    A designed lanthanide-binding chimeric peptide based on the strikingly similar geometries of the EF-hand and helix-turn-helix (HTH) motifs was investigated by NMR and CD spectroscopy and found to retain the same overall solution structure of the parental motifs. CD spectroscopy showed that the 33-mer peptide P3W folds on binding lanthanides, with an increase in α-helicity from 20% in the absence of metal to 38% and 35% in the presence of excess Eu(III) and La(III) ions, respectively. The conditional binding affinities of P3W for La(III) (5.9 ± 0.3 μM) and for Eu(III) (6.2 ± 0.3 μM) (pH 7.8, 5 mM Tris) were determined by tryptophan fluorescence titration. The La(III) complex of peptide P3, which differs from P3W by only one Trp-to-His substitution, has much less signal dispersion in the proton NMR spectra than LaP3W, indicating that the Trp residue is a critical hydrophobic anchor for maintaining a well-folded helix-turn-helix structure. A chemical-shift index analysis indicates the metallopeptide has a helix-loop-helix secondary structure. A structure calculated by using nuclear Overhauser effect and other NMR constraints reveals that P3W not only has a tightly folded metal-binding loop but also retains the α−α corner supersecondary structure of the parental motifs. Although the solution structure is undefined at both the N and C termini, the NMR structure confirms the successful incorporation of a metal-binding loop into a HTH sequence. PMID:12644701

  2. Structural-energy states of water and aqueous solutions under external influences

    NASA Astrophysics Data System (ADS)

    Gorlenko, Nikolay; Laptev, Boris; Sidorenko, Galina; Sarkisov, Yuri; Minakova, Tamara; Kylchenko, Anton; Zubkova, Olga

    2016-01-01

    Methods are proposed for evaluating changes in the structure of water or aqueous electrolyte solutions under the influence of temperature, magnetic field and surface material by means of determining the electrical capacity of the liquid and the quality factor of the anti-resonant circuit in the frequency range from 1 kHz to 3000 kHz. The condenser plates in different types of electrochemical cells are placed one in front of the other, each at a distance of more than 5 cm, or relative to each other in parallel planes, or in one plane in which case the liquid is located on the condenser plates. The current density on the plates in various cells ranged from 10 to 100 nA/cm2. When measuring the electrical capacity, the voltage applied to the plates was reduced in proportion to the increase in the frequency of oscillator. The apparatus allows us to increase the dynamic range of the signal change from an electrochemical cell, reduce the impact of measurements on the structure of liquids, and also evaluate the direction and extent of changes in the structure of water and aqueous solutions under various external influences. Criteria are proposed for evaluating the structure of fluids.

  3. Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy.

    PubMed

    Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing; Di Cera, Enrico

    2016-08-26

    The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr(93) in kringle-1 onto Trp(547) in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. The open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase. PMID:27435675

  4. Structural changes of nucleic acid base in aqueous solution as observed in X-ray absorption near edge structure (XANES)

    NASA Astrophysics Data System (ADS)

    Shimada, Hiroyuki; Fukao, Taishi; Minami, Hirotake; Ukai, Masatoshi; Fujii, Kentaro; Yokoya, Akinari; Fukuda, Yoshihiro; Saitoh, Yuji

    2014-01-01

    X-ray absorption near edge structure (XANES) spectra for adenine-containing nucleotides, adenosine 5‧-monophosphate (AMP) and adenosine 5‧-triphosphate (ATP) in aqueous solutions at the nitrogen K-edge region were measured. The two intense peaks in XANES spectra are assigned to transitions of 1s electrons to the π∗ orbitals of different types of N atoms with particular bonding characteristics. The difference between their spectra is ascribed to protonation of a particular N atom. Similarity observed in XANES spectra of guanosine 5‧-monophosphate (GMP) and ATP is also interpreted as similar bonding characters of the N atoms in the nucleobase moiety.

  5. Effect of ionic liquid treatment on the structures of lignins in solutions

    SciTech Connect

    Cheng, Gang; Kent, Michael S; He, Lilin; Varanasi, Patanjali; Dibble, Dean; Melnichenko, Yuri B; Simmons, Blake; Singh, Seema

    2012-01-01

    The solution structures of three types of isolated lignin - organosolv (OS), Kraft (K), and low sulfonate (LS) - before and after treatment with 1-ethyl-3-methylimidazolium acetate were studied using small-angle neutron scattering (SANS) and dynamic light scattering (DLS) over a concentration range of 0.3-2.4 wt %. The results indicate that each of these lignins is comprised of aggregates of well-defined basal subunits, the shapes and sizes of which, in D{sub 2}O and DMSO-d{sub 6}, are revealed using these techniques. LS lignin contains a substantial amount of nanometer-scale individual subunits. In aqueous solution these subunits have a well-defined elongated shape described well by ellipsoidal and cylindrical models. At low concentration the subunits are highly expanded in alkaline solution, and the effect is screened with increasing concentration. OS lignin dissolved in DMSO was found to consist of a narrow distribution of aggregates with average radius 200 {+-} 30 nm. K lignin in DMSO consists of aggregates with a very broad size distribution. After ionic liquid (IL) treatment, LS lignin subunits in alkaline solution maintained the elongated shape but were reduced in size. IL treatment of OS and K lignins led to the release of nanometer-scale subunits with well-defined size and shape.

  6. Structure of charged cyclohexyldiamines in aqueous solution: a theoretical and experimental study.

    PubMed

    Lopes Jesus, A J; Teixeira, M Helena S F; Redinha, J S

    2012-04-26

    The structure of mono- and diprotonated cyclohexyldiamine isomers in aqueous solution is investigated theoretically by the application of the CPCM continuum solvation model combined with the MP2/aug-cc-pVDZ model chemistry. The calculated Gibbs energy of hydration (ΔGhyd) is expressed in different terms with physical meaning: cavity formation, solute conformational variation, and solute-solvent interaction. Significant differences of the ΔGhyd values are found among isomers, which are interpreted based on the analysis of the factors accounting for the stability of the conformers/isomers in the gas and solution phases. Particular attention is given to the role played by the formation of an intramolecular hydrogen bond in the monoprotonated forms and by the Coulombic repulsion between the NH3(+) groups in the diprotonated ones. From the Gibbs energies of the acid/base pairs in the gas phase and respective hydration Gibbs energies, the acidity constants (pKa) are calculated and interpreted. For some isomers, the constants are also determined experimentally by potentiometric titration. A good agreement was found between the calculated and experimental values. PMID:22462689

  7. The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes

    PubMed Central

    Huang, Lin; Lilley, David M. J.

    2015-01-01

    With the growing number of crystal structures of RNA and RNA/protein complexes, a critical next step is understanding the dynamic behavior of these entities in solution in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the widespread RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA/protein complexes in solution and uncovers the behavior of an important RNA/protein motif. This type of information will be necessary to understand, predict, and engineer the behavior and function of RNAs and their protein complexes. PMID:26727239

  8. Structure of the electrical double layer at aqueous gold and silver interfaces for saline solutions.

    PubMed

    Hughes, Zak E; Walsh, Tiffany R

    2014-12-15

    We report the structure of the electrical double layer, determined from molecular dynamics simulations, for a range of saline solutions (NaCl, KCl, MgCl2 and CaCl2) at both 0.16 and 0.60 mol kg(-1) on different facets of the gold and silver aqueous interfaces. We consider the Au/Ag(111), native Au/Ag(100) and reconstructed Au(100)(5×1) facets. For a given combination of metallic surface and facet, some variations in density profile are apparent across the different cations in solution, with the corresponding chloride counterion profiles remaining broadly invariant. All density profiles at the higher concentration are predicted to be very similar to their low-concentration counterparts. We find that each electrolyte responds differently to the different metallic surface and facets, particularly those of the divalent metal ions. Our findings reveal marked differences in density profiles between facets for a given metallic interface for both Mg(2+) and Ca(2+), with Na(+) and K(+) showing much less distinction. Mg(2+) was the only ion for which we find evidence of materials-dependent differences in interfacial solution structuring between the Ag and Au. PMID:25265591

  9. Ascorbic Acid and BSA Protein in Solution and Films: Interaction and Surface Morphological Structure

    PubMed Central

    Maciel, Rafael R. G.; de Almeida, Adriele A.; Godinho, Odin G. C.; Gorza, Filipe D. S.; Pedro, Graciela C.; Trescher, Tarquin F.; Silva, Josmary R.; de Souza, Nara C.

    2013-01-01

    This paper reports on the study of the interactions between ascorbic acid (AA) and bovine serum albumin (BSA) in aqueous solution as well as in films (BSA/AA films) prepared by the layer-by-layer technique. Regarding to solution studies, a hyperchromism (in the range of ultraviolet) was found as a function of AA concentration, which suggested the formation of aggregates from AA and BSA. Binding constant, K, determined for aggregates from BSA and AA was found to be about 102 M−1, which indicated low affinity of AA with BSA. For the BSA/AA films, it was also noted that the AA adsorption process and surface morphological structures depended on AA concentration. By changing the contact time between the AA and BSA, a hypochromism was revealed, which was associated to decrease of accessibility of solvent to tryptophan due to formation of aggregates. Furthermore, different morphological structures of aggregates were observed, which were attributed to the diffusion-limited aggregation. Since most of studies of interactions of drugs and proteins are performed in solution, the analysis of these processes by using films can be very valuable because this kind of system is able to employ several techniques of investigation in solid state. PMID:23984366

  10. Ascorbic acid and BSA protein in solution and films: interaction and surface morphological structure.

    PubMed

    Maciel, Rafael R G; de Almeida, Adriele A; Godinho, Odin G C; Gorza, Filipe D S; Pedro, Graciela C; Trescher, Tarquin F; Silva, Josmary R; de Souza, Nara C

    2013-01-01

    This paper reports on the study of the interactions between ascorbic acid (AA) and bovine serum albumin (BSA) in aqueous solution as well as in films (BSA/AA films) prepared by the layer-by-layer technique. Regarding to solution studies, a hyperchromism (in the range of ultraviolet) was found as a function of AA concentration, which suggested the formation of aggregates from AA and BSA. Binding constant, K, determined for aggregates from BSA and AA was found to be about 10(2) M(-1), which indicated low affinity of AA with BSA. For the BSA/AA films, it was also noted that the AA adsorption process and surface morphological structures depended on AA concentration. By changing the contact time between the AA and BSA, a hypochromism was revealed, which was associated to decrease of accessibility of solvent to tryptophan due to formation of aggregates. Furthermore, different morphological structures of aggregates were observed, which were attributed to the diffusion-limited aggregation. Since most of studies of interactions of drugs and proteins are performed in solution, the analysis of these processes by using films can be very valuable because this kind of system is able to employ several techniques of investigation in solid state. PMID:23984366

  11. Deuterium labeling for neutron structure-function-dynamics analysis.

    PubMed

    Meilleur, Flora; Weiss, Kevin L; Myles, Dean A A

    2009-01-01

    Neutron scattering and diffraction provide detailed information on the structure and dynamics of biological materials across time and length scales that range from picoseconds to nanoseconds and from 1 to 10,000 A, respectively. The particular sensitivity of neutrons to the isotopes of hydrogen makes selective deuterium labeling of biological systems an essential tool for maximizing the return from neutron scattering experiments. In neutron protein crystallography, the use of fully deuterated protein crystals improves the signal-to-noise ratio of the data by an order of magnitude and enhances the visibi-lity of the molecular structure (Proc Natl Acad Sci U S A 97:3872-3877, 2000; Acta Crystallogr D Biol Crystallogr 61:1413-1417, 2005; Acta Crystallogr D Biol Crystallogr 61:539-544, 2005). In solution and surface scattering experiments, the incorporation of deuterium-labeled subunits or components into complex assemblies or structures makes it possible to deconvolute the scattering of the labeled and unlabeled subunits and to determine their relative dispositions within the complex (J Mol Biol 93:255-265, 1975). With multiple labeling patterns, it is also possible to reconstruct the locations of multiple subunits in ternary and higher-order complexes (Science 238:1403-1406, 1987; J Mol Biol 271:588-601, 1997; J Biol Chem 275:14432-14439, 2000; Biochemistry 42:7790-7800, 2003). In inelastic neutron scattering experiments, which probe hydrogen dynamics in biological materials, the application of site, residue, or region-specific hydrogen-deuterium-labeling patterns can be used to distinguish and highlight the specific dynamics within a system (Proc Natl Acad Sci U S A 95:4970-4975, 1998).Partial, selective, or fully deuterated proteins can be readily produced by endogenous expression of recombinant proteins in bacterial systems that are adapted to growth in D(2)O solution and using selectively deuterated carbon sources. Adaptation can be achieved either by gradual

  12. Structure and flow properties of micelle-nanoparticle solutions from Molecular Dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sureshkumar, Radhakrishna; Dhakal, Subas; Sambasivam, Abhinanden

    2014-03-01

    In aqueous media, cationic surfactant molecules spontaneously self-assemble into diverse morphologies depending upon temperature, surfactant concentration and solution ionic strength. Spherical, cylindrical and long (~ microns) flexible wormlike structures with or without branches with distinct rheological properties are observed. Inclusion of nanoparticles (NPs) provides additional means to manipulate structure and create active ``nano-fluids'' that respond to optical, magnetic or electrical stimuli. We study self-assembly, dynamics and rheology of such fluids using coarse-grained Molecular Dynamics simulations in presence of explicit solvent and salt. Specifically, we will discuss the mechanisms underlying fascinating phenomenology observed experimentally such as the pronounced non-monotonic dependence of the zero shear viscosity on salt/NP concentration, shear-induced structure formation, and isotropic to nematic transitions. NSF grants 1049489, 1049454 for the financial support, and Pittsburg Super Computer Centre for providing HPC resources.

  13. Solution structure of an "open" E. coli Pol III clamp loader sliding clamp complex.

    PubMed

    Tondnevis, Farzaneh; Weiss, Thomas M; Matsui, Tsutomu; Bloom, Linda B; McKenna, Robert

    2016-06-01

    Sliding clamps are opened and loaded onto primer template junctions by clamp loaders, and once loaded on DNA, confer processivity to replicative polymerases. Previously determined crystal structures of eukaryotic and T4 clamp loader-clamp complexes have captured the sliding clamps in either closed or only partially open interface conformations. In these solution structure studies, we have captured for the first time the clamp loader-sliding clamp complex from Escherichia coli using size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS). The data suggests the sliding clamp is in an open conformation which is wide enough to permit duplex DNA binding. The data also provides information about spatial arrangement of the sliding clamp with respect to the clamp loader subunits and is compared to complex crystal structures determined from other organisms. PMID:26968362

  14. Investigation on species distribution and EXAFS structure of aqueous rubidium pentaborate solutions

    NASA Astrophysics Data System (ADS)

    Miao, J. T.; Fang, C. H.; Fang, Y.; Zhu, F. Y.; Liu, H. Y.; Zhou, Y. Q.; Ge, H. W.; Sun, P. C.; Zhao, X. C.

    2016-04-01

    Based on the measured pH data and reported equilibrium constants, the main polyborate species formation existing in solution was investigated using the Newton iteration method at 298 and 333 K, and checked by the method of 11B nuclear magnetic resonance (NMR) spectroscopy. The neighboring structure of rubidium ion was studied at room temperature, which the structural parameters, including the coordination number, interatomic distance of Rb-O and Debye-Waller factor, were determined by the synchrotron radiation extended X-ray absorption fine structure (EXAFS). The results show that the average interatomic distance of Rb-O is 2.93 ± 0.004 Å and coordination number is 7.7 ± 0.9 in the first hydration shell around rubidium ion.

  15. Probing the solution structure of Factor H using hydroxyl radical protein footprinting and cross-linking.

    PubMed

    Baud, Anna; Gonnet, Florence; Salard, Isabelle; Le Mignon, Maxime; Giuliani, Alexandre; Mercère, Pascal; Sclavi, Bianca; Daniel, Régis

    2016-06-15

    The control protein Factor H (FH) is a crucial regulator of the innate immune complement system, where it is active on host cell membranes and in the fluid phase. Mutations impairing the binding capacity of FH lead to severe autoimmune diseases. Here, we studied the solution structure of full-length FH, in its free state and bound to the C3b complement protein. To do so, we used two powerful techniques, hydroxyl radical protein footprinting (HRPF) and chemical cross-linking coupled with mass spectrometry (MS), to probe the structural rearrangements and to identify protein interfaces. The footprint of C3b on the FH surface matches existing crystal structures of C3b complexed with the N- and C-terminal fragments of FH. In addition, we revealed the position of the central portion of FH in the protein complex. Moreover, cross-linking studies confirmed the involvement of the C-terminus in the dimerization of FH. PMID:27099340

  16. Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops

    PubMed Central

    Marušič, Maja; Šket, Primož; Bauer, Lubos; Viglasky, Viktor; Plavec, Janez

    2012-01-01

    We herein report on the formation and high-resolution NMR solution-state structure determination of a G-quadruplex adopted by d[G3ATG3ACACAG4ACG3] comprised of four G-tracts with the third one consisting of four guanines that are intervened with non-G streches of different lengths. A single intramolecular antiparallel (3+1) G-quadruplex exhibits three stacked G-quartets connected with propeller, diagonal and edgewise loops of different lengths. The propeller and edgewise loops are well structured, whereas the longer diagonal loop is more flexible. To the best of our knowledge, this is the first high-resolution G-quadruplex structure where all of the three main loop types are present. PMID:22532609

  17. Mechanism driven structural elucidation of forced degradation products from hydrocortisone in solution.

    PubMed

    Zhang, Fa; Zhou, Jay; Shi, Yiqun; Tavlarakis, Panagiotis; Karaisz, Kenneth

    2016-09-01

    Hydrocortisone degradation products 1, 2, 3, and 4 along with hemiacetal derivatives 5, 6, 7, and 8 were observed through stressed hydrocortisone in solution. Their structures were identified based on HPLC-UV, HPLC-MS, and HPLC-HRMS (high resolution/high accuracy mass spectrometry) analyses as well as reaction mechanistic investigation and synthesis for structural confirmation. 1 and 2 are a pair of E/Z isomers and they were generated through acid catalyzed tautomerization/dehydration of hydrocortisone. Incorporation of water to 1 and 2 resulted in the formation of 3. We also discovered new degradation product 4 which was converted from 3 by oxidation. The degradation products were synthesized by stressing hydrocortisone under the optimized conditions and their structures were characterized by NMR ((1)H/(13)C, COSY, HMBC, HSQC, NOESY) and HRMS analyses. The degradation pathway of hydrocortisone is postulated. PMID:27328360

  18. Hydrogen bonded structure of water and aqueous solutions of sodium halides: a Raman spectroscopic study

    NASA Astrophysics Data System (ADS)

    Li, Ruihua; Jiang, Zhanpeng; Chen, Fengen; Yang, Hongwei; Guan, Yuntao

    2004-11-01

    The OH stretching (2500-4000 cm -1) Raman spectra from pure water and sodium halides solutions are obtained. The Raman contours are deconvoluted with five Gaussian components that their center frequencies are 3051, 3233, 3393, 3511 and 3628 cm -1, respectively. From the Raman spectra and their deconvolutions similarities and differences of the effects of temperature and sodium halides on hydrogen bond structure of water are shown clearly. Like temperature, all of sodium halides break tetrahedral structure of water, and the Gaussian component of 3233 cm -1 decreases and the components of 3393 and 3511 cm -1 increase basically. The differences lie in their effects on the component 3051 and 3628 cm -1. All of halogenic ions break tetrahedral structure of water and their breaking actions are in the order of F -1

  19. Solution structure of a chemosensory protein from the moth Mamestra brassicae.

    PubMed Central

    Mosbah, Amor; Campanacci, Valérie; Lartigue, Audrey; Tegoni, Mariella; Cambillau, Christian; Darbon, Hervé

    2003-01-01

    Chemosensory proteins (CSPs) are believed to be involved in chemical communication and perception. A number of such proteins, of molecular mass approximately 13 kDa, have been isolated from different sensory organs of a wide range of insect species. Several CSPs have been identified in the antennae and proboscis of the moth Mamestra brassicae. CSPMbraA6, a 112-amino-acid antennal protein, has been expressed in a soluble form in large quantities in the Escherichi coli periplasm. NMR structure determination of CSPMbraA6 has been performed with 1H- and 15N-labelled samples. The calculated structures present an average root mean square deviation about the mean structure of 0.63 A for backbone atoms and 1.27 A for all non-hydrogen atoms except the 12 N-terminal residues. The protein is well folded from residue 12 to residue 110, and consists of a non-bundle alpha-helical structure with six helices connected by alpha alpha loops. It has a globular shape, with overall dimensions of 32 A x 28 A x 24 A. A channel is visible in the hydrophobic core, with dimensions of 3 A x 9 A x 21 A. In some of the 20 solution structures calculated, this channel is closed either by Trp-94 at one end or by Tyr-26 at the other end; in some other solutions, this channel is closed at both ends. Binding experiments with 12-bromododecanol indicate that the CSPMbraA6 structure is modified upon ligand binding. PMID:12217077

  20. Solution structure of the DNA binding domain of HIV-1 integrase.

    PubMed

    Lodi, P J; Ernst, J A; Kuszewski, J; Hickman, A B; Engelman, A; Craigie, R; Clore, G M; Gronenborn, A M

    1995-08-01

    The solution structure of the DNA binding domain of HIV-1 integrase (residues 220-270) has been determined by multidimensional NMR spectroscopy. The protein is a dimer in solution, and each subunit is composed of a five-stranded beta-barrel with a topology very similar to that of the SH3 domain. The dimer is formed by a stacked beta-interface comprising strands 2, 3, and 4, with the two triple-stranded antiparallel beta-sheets, one from each subunit, oriented antiparallel to each other. One surface of the dimer, bounded by the loop between strands beta 1 and beta 2, forms a saddle-shaped groove with dimensions of approximately 24 x 23 x 12 A in cross section. Lys264, which has been shown from mutational data to be involved in DNA binding, protrudes from this surface, implicating the saddle-shaped groove as the potential DNA binding site. PMID:7632683

  1. REVIEWS OF TOPICAL PROBLEMS: Supermolecular liquid-crystalline structures in solutions of amphiphilic molecules

    NASA Astrophysics Data System (ADS)

    Vedenov, A. A.; Levchenko, E. B.

    1983-09-01

    This paper reviews the physical properties of liquid-crystalline phases arising in solutions containing molecules of amphiphilic substances. The basic characteristics of micelle formation in dilute solutions, models of sphere-disk or sphere-cylinder structural transformations, as well as phase transitions related to the appearance of lyotropic mesophases in the system, including nematic, lamellar, hexagonal, and others, are examined. The results of experimental and theoretical investigation of "solvation" forces acting between micelles in the solvent, as well as recently studied models of swelling of lamellar phases are presented. The phenomena occurring near the inversion point of microemulsions in amphiphile-oil-water systems are examined briefly. The role of liquid-crystalline ordering in some biological systems is discussed.

  2. Surface structure and electrical properties of solution processed lanthanum nickelate films

    NASA Astrophysics Data System (ADS)

    Pandya, Nirav C.; Joshi, U. S.

    2014-04-01

    Conducting oxides with perovskite crystal structure have many advantages over the simple Pt or Au, Pt based metal bottom electrodes (BE), particularly in fabrication of ferroelectric as well as resistive random access memory devices, if they possess smooth surface morphology. LaNiO3 (LNO) thin films were prepared by modified chemical solution deposition method. Precursor solutions were spin coated onto SiO2-substrates. Deposited layers were thermally treated in a pre-heated furnace at 550 °C and oxygenated up to 800 °C. Results of AFM and FESEM showed that films are very smooth (Ra = 1.69 nm), dense, crack-free and with monodispersed nanocrystallites. Growth conditions such as spinning rate, annealing rates and temperatures etc. have been optimized for mono dispersed crystallinity with very smooth surface morphology. Sheet resistivity, carrier concentration and RMS roughness were correlated with growth temperatures.

  3. Water structure at the air-aqueous interface of divalent cation and nitrate solutions.

    PubMed

    Xu, Man; Spinney, Rick; Allen, Heather C

    2009-04-01

    The water surface structure of aqueous magnesium, calcium, and strontium nitrate solutions with six to seven water molecules on average solvating each ion was investigated using vibrational sum frequency generation (VSFG) spectroscopy. Raman (polarized) and infrared spectroscopies were used for understanding solvation effects. Infrared reflection spectra were analyzed to further understand the VSFG data. The VSFG spectral changes indicate that the divalent countercation species play a key role in the surface perturbation of the water. In addition, the data show that the solvated ions, and possibly their ion pairs, approach the aqueous surface. The identity of the divalent cation may cause a difference in the concentration gradient near the surface, thereby increasing the VSFG-active region, which then indicates an increase in the interfacial depth. The interface becomes thickened with Mg(2+) < Ca(2+) < Sr(2+). The free OH orientation measured from the surface normal from the salt solutions changes from 33 (from neat water) to approximately 60 degrees . PMID:19239253

  4. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    PubMed Central

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

    The hydroxide anion OH−(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH−(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH−(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions. PMID:27550616

  5. Influence of Building Material Solution of Structures to Effectiveness of Real Estate Development

    NASA Astrophysics Data System (ADS)

    Somorová, Viera

    2015-11-01

    Real estate development is in its essence the development process characterized by a considerable dynamics. The purpose of the development process is the creation of buildings which can be either rented by future unknown users or sold in the real estate market. A first part of the paper is dedicated to the analysis of the parameters of buildings solutions considering the future operating costs in a phase of designing. Material solution of external structures is a main factor not only in determining the future operating costs but also in achieving the subsequent economic effectiveness of the real estate development. To determine the relationship between economic efficiency criteria and determine the optimal material variant of building constructions for the specific example is the aim of the second part of paper.

  6. Surface structure and electrical properties of solution processed lanthanum nickelate films

    SciTech Connect

    Pandya, Nirav C. Joshi, U. S.

    2014-04-24

    Conducting oxides with perovskite crystal structure have many advantages over the simple Pt or Au, Pt based metal bottom electrodes (BE), particularly in fabrication of ferroelectric as well as resistive random access memory devices, if they possess smooth surface morphology. LaNiO{sub 3} (LNO) thin films were prepared by modified chemical solution deposition method. Precursor solutions were spin coated onto SiO{sub 2}-substrates. Deposited layers were thermally treated in a pre-heated furnace at 550 °C and oxygenated up to 800 °C. Results of AFM and FESEM showed that films are very smooth (Ra = 1.69 nm), dense, crack-free and with monodispersed nanocrystallites. Growth conditions such as spinning rate, annealing rates and temperatures etc. have been optimized for mono dispersed crystallinity with very smooth surface morphology. Sheet resistivity, carrier concentration and RMS roughness were correlated with growth temperatures.

  7. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores.

    PubMed

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

    The hydroxide anion OH(-)(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH(-)(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH(-)(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions. PMID:27550616

  8. Periodic solutions of a nonautonomous predator-prey system with stage structure and time delays

    NASA Astrophysics Data System (ADS)

    Xu, Rui; Wang, Zhiqiang

    2006-11-01

    A nonautonomous Lotka-Volterra type predator-prey model with stage structure and time delays is investigated. It is assumed in the model that the individuals in each species may belong to one of two classes: the immatures and the matures, the age to maturity is presented by a time delay, and that the immature predators do not feed on prey and do not have the ability to reproduce. By some comparison arguments we first discuss the permanence of the model. By using the continuation theorem of coincidence degree theory, sufficient conditions are derived for the existence of positive periodic solutions to the model. By means of a suitable Lyapunov functional, sufficient conditions are obtained for the uniqueness and global stability of the positive periodic solutions to the model.

  9. Structure of reduced DsbA from Escherichia coli in solution.

    PubMed

    Schirra, H J; Renner, C; Czisch, M; Huber-Wunderlich, M; Holak, T A; Glockshuber, R

    1998-05-01

    The three-dimensional structure of reduced DsbA from Escherichia coli in aqueous solution has been determined by nuclear magnetic resonance (NMR) spectroscopy and is compared with the crystal structure of oxidized DsbA [Guddat, L. W., Bardwell, J. C. A., Zander, T., and Martin, J. L. (1997) Protein Sci. 6, 1148-1156]. DsbA is a monomeric 21 kDa protein which consists of 189 residues and is required for disulfide bond formation in the periplasm of E. coli. On the basis of sequence-specific 1H NMR assignments, 1664 nuclear Overhauser enhancement distance constraints, 118 hydrogen bond distance constraints, and 293 dihedral angle constraints were obtained as the input for the structure calculations by simulated annealing with the program X-PLOR. The enzyme is made up of two domains. The catalytic domain has a thioredoxin-like fold with a five-stranded beta-sheet and three alpha-helices, and the second domain consists of four alpha-helices and is inserted into the thioredoxin motif. The active site between Cys30 and Cys33 is located at the N terminus of the first alpha-helix in the thioredoxin-like domain. The solution structure of reduced DsbA is rather similar to the crystal structure of the oxidized enzyme but exhibits a different relative orientation of both domains. In addition, the conformations of the active site and a loop between strand beta5 and helix alpha7 are slightly different. These structural differences may reflect important functional requirements in the reaction cycle of DsbA as they appear to facilitate the release of oxidized polypeptides from reduced DsbA. The extremely low pKa value of the nucleophilic active site thiol of Cys30 in reduced DsbA is most likely caused by its interactions with the dipole of the active site helix and the side chain of His32, as no other charged residues are located next to the sulfur atom of Cys30 in the solution structure. PMID:9572841

  10. A vibrational spectroscopy study on anserine and its aqueous solutions.

    PubMed

    Akkaya, Y; Balci, K; Goren, Y; Akyuz, S; Stricker, M C; Stover, D D; Ritzhaupt, G; Collier, W B

    2015-10-01

    In this study based on vibrational spectroscopic measurements and Density Functional Theory (DFT), we aimed for a reliable interpretation of the IR and Raman spectra recorded for anserine in the solid phase and water (H2O) and heavy water (D2O) solutions. Initial DFT calculations at the B3LYP/6-31G(d) searched possible conformers of the anserine zwitterion using a systematic conformational search. The corresponding equilibrium geometrical parameters and vibrational spectral data were determined for each of the stable conformers (in water) by the geometry optimization and hessian calculations performed at the same level of theory using the polarized continuum model (PCM). The same calculations were repeated to determine the most energetically preferred dimer structure for the molecule and the associated geometry, force field and vibrational spectral data. The harmonic force constants obtained from these calculations were scaled by the Scaled Quantum Mechanical Force Field (SQM) method and then used in the calculation of the refined wavenumbers, potential energy distributions, IR and Raman intensities. These refined theoretical data, which confirm the zwitterion structure for anserine in the solid phase or aqueous solvents, revealed the remarkable effects of intermolecular hydrogen bonding on the structural properties and observed IR and Raman spectra of this molecule. PMID:25997178

  11. Validation of a new restraint docking method for solution structure determinations of protein-ligand complexes.

    PubMed

    Polshakov, V I; Morgan, W D; Birdsall, B; Feeney, J

    1999-06-01

    A new method is proposed for docking ligands into proteins in cases where an NMR-determined solution structure of a related complex is available. The method uses a set of experimentally determined values for protein-ligand, ligand-ligand, and protein-protein restraints for residues in or near to the binding site, combined with a set of protein-protein restraints involving all the other residues which is taken from the list of restraints previously used to generate the reference structure of a related complex. This approach differs from ordinary docking methods where the calculation uses fixed atomic coordinates from the reference structure rather than the restraints used to determine the reference structure. The binding site residues influenced by replacing the reference ligand by the new ligand were determined by monitoring differences in 1H chemical shifts. The method has been validated by showing the excellent agreement between structures of L. casei dihydrofolate reductase trimetrexate calculated by conventional methods using a full experimentally determined set of restraints and those using this new restraint docking method based on an L. casei dihydrofolate reductase methotrexate reference structure. PMID:10610140

  12. Solution structure of an EGF module pair from the Plasmodium falciparum merozoite surface protein 1.

    PubMed

    Morgan, W D; Birdsall, B; Frenkiel, T A; Gradwell, M G; Burghaus, P A; Syed, S E; Uthaipibull, C; Holder, A A; Feeney, J

    1999-05-28

    The solution structure of the 96-residue C-terminal fragment of the merozoite surface protein 1 (MSP-1) from Plasmodium falciparum has been determined using nuclear magnetic resonance (NMR) spectroscopic measurements on uniformly13C/15N-labelled protein, efficiently expressed in the methylotrophic yeast Komagataella (Pichia) pastoris. The structure has two domains with epidermal growth factor (EGF)-like folds with a novel domain interface for the EGF domain pair interactions, formed from a cluster of hydrophobic residues. This gives the protein a U-shaped overall structure with the N-terminal proteolytic processing site close to the C-terminal glycosyl phosphatidyl inositol (GPI) membrane anchor site, which is consistent with the involvement of a membrane-bound proteinase in the processing of MSP-1 during erythrocyte invasion. This structure, which is the first protozoan EGF example to be determined, contrasts with the elongated structures seen for EGF-module pairs having shared Ca2+-ligation sites at their interface, as found, for example, in fibrillin-1. Recognition surfaces for antibodies that inhibit processing and invasion, and antibodies that block the binding of these inhibitory antibodies, have been mapped on the three-dimensional structure by considering specific MSP-1 mutants. PMID:10339410

  13. Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus

    PubMed Central

    Leyrat, Cedric; Renner, Max; Harlos, Karl; Grimes, Jonathan M.

    2013-01-01

    Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (Pced) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of Pced using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of Pced. Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (Pcore), that is surrounded by flexible regions with α-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales Pced structures suggests that Pced evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes. PMID:24224051

  14. Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.

    PubMed

    Shu, Qin; Krezel, Andrzej M; Cusumano, Zachary T; Pinkner, Jerome S; Klein, Roger; Hultgren, Scott J; Frieden, Carl

    2016-06-28

    Curli, consisting primarily of major structural subunit CsgA, are functional amyloids produced on the surface of Escherichia coli, as well as many other enteric bacteria, and are involved in cell colonization and biofilm formation. CsgE is a periplasmic accessory protein that plays a crucial role in curli biogenesis. CsgE binds to both CsgA and the nonameric pore protein CsgG. The CsgG-CsgE complex is the curli secretion channel and is essential for the formation of the curli fibril in vivo. To better understand the role of CsgE in curli formation, we have determined the solution NMR structure of a double mutant of CsgE (W48A/F79A) that appears to be similar to the wild-type (WT) protein in overall structure and function but does not form mixed oligomers at NMR concentrations similar to the WT. The well-converged structure of this mutant has a core scaffold composed of a layer of two α-helices and a layer of three-stranded antiparallel β-sheet with flexible N and C termini. The structure of CsgE fits well into the cryoelectron microscopy density map of the CsgG-CsgE complex. We highlight a striking feature of the electrostatic potential surface in CsgE structure and present an assembly model of the CsgG-CsgE complex. We suggest a structural mechanism of the interaction between CsgE and CsgA. Understanding curli formation can provide the information necessary to develop treatments and therapeutic agents for biofilm-related infections and may benefit the prevention and treatment of amyloid diseases. CsgE could establish a paradigm for the regulation of amyloidogenesis because of its unique role in curli formation. PMID:27298344

  15. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria.

    PubMed Central

    Tam, R; Saier, M H

    1993-01-01

    sequence conservation in their N-terminal domains than in their C-terminal domains. Signature sequences for these eight protein families are presented. The results reveal that binding proteins specific for the same solute from different bacteria are generally more closely related to each other than are binding proteins specific for different solutes from the same organism, although exceptions exist. They also suggest that a requirement for high-affinity solute binding imposes severe structural constraints on a protein. The occurrence of two distinct classes of bacterial cytoplasmic repressor proteins which are homologous to two different clusters of periplasmic binding proteins suggests that the gene-splicing events which allowed functional conversion of these proteins with retention of domain structure have occurred repeatedly during evolutionary history.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:8336670

  16. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    PubMed Central

    Barends, Thomas R. M.; Brosi, Richard W. W.; Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten; Seidel, Ralf; Shoeman, Robert L.; Zimmermann, Sabine; Bittl, Robert; Schlichting, Ilme; Reinstein, Jochen

    2013-01-01

    Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ. PMID:23897477

  17. Controlled Bulk Properties of Composite Polymeric Solutions for Extensive Structural Order of Honeycomb Polysulfone Membranes

    PubMed Central

    Gugliuzza, Annarosa; Perrotta, Maria Luisa; Drioli, Enrico

    2016-01-01

    This work provides additional insights into the identification of operating conditions necessary to overcome a current limitation to the scale-up of the breath figure method, which is regarded as an outstanding manufacturing approach for structurally ordered porous films. The major restriction concerns, indeed, uncontrolled touching droplets at the boundary. Herein, the bulk of polymeric solutions are properly managed to generate honeycomb membranes with a long-range structurally ordered texture. Water uptake and dynamics are explored as chemical environments are changed with the intent to modify the hydrophilic/hydrophobic balance and local water floatation. In this context, a model surfactant such as the polyoxyethylene sorbitan monolaurate is used in combination with alcohols at different chain length extents and a traditional polymer such as the polyethersufone. Changes in the interfacial tension and kinematic viscosity taking place in the bulk of composite solutions are explored and examined in relation to competitive droplet nucleation and growth rate. As a result, extensive structurally ordered honeycomb textures are obtained with the rising content of the surfactant while a broad range of well-sized pores is targeted as a function of the hydrophilic-hydrophobic balance and viscosity of the composite polymeric mixture. The experimental findings confirm the consistency of the approach and are expected to give propulsion to the commercially production of breath figures films shortly. PMID:27196938

  18. Controlled Bulk Properties of Composite Polymeric Solutions for Extensive Structural Order of Honeycomb Polysulfone Membranes.

    PubMed

    Gugliuzza, Annarosa; Perrotta, Maria Luisa; Drioli, Enrico

    2016-01-01

    This work provides additional insights into the identification of operating conditions necessary to overcome a current limitation to the scale-up of the breath figure method, which is regarded as an outstanding manufacturing approach for structurally ordered porous films. The major restriction concerns, indeed, uncontrolled touching droplets at the boundary. Herein, the bulk of polymeric solutions are properly managed to generate honeycomb membranes with a long-range structurally ordered texture. Water uptake and dynamics are explored as chemical environments are changed with the intent to modify the hydrophilic/hydrophobic balance and local water floatation. In this context, a model surfactant such as the polyoxyethylene sorbitan monolaurate is used in combination with alcohols at different chain length extents and a traditional polymer such as the polyethersufone. Changes in the interfacial tension and kinematic viscosity taking place in the bulk of composite solutions are explored and examined in relation to competitive droplet nucleation and growth rate. As a result, extensive structurally ordered honeycomb textures are obtained with the rising content of the surfactant while a broad range of well-sized pores is targeted as a function of the hydrophilic-hydrophobic balance and viscosity of the composite polymeric mixture. The experimental findings confirm the consistency of the approach and are expected to give propulsion to the commercially production of breath figures films shortly. PMID:27196938

  19. Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii

    PubMed Central

    Singarapu, Kiran K.; Otte, Michele M.; Tonelli, Marco; Westler, William M.; Escalante-Semerena, Jorge C.; Markley, John L.

    2015-01-01

    GTP:adenosylcobinamide-phosphate (AdoCbi-P) guanylyl transferase (CobY) is an enzyme that transfers the GMP moiety of GTP to AdoCbi yielding AdoCbi-GDP in the late steps of the assembly of Ado-cobamides in archaea. The failure of repeated attempts to crystallize ligand-free (apo) CobY prompted us to explore its 3D structure by solution NMR spectroscopy. As reported here, the solution structure has a mixed α/β fold consisting of seven β-strands and five α-helices, which is very similar to a Rossmann fold. Titration of apo-CobY with GTP resulted in large changes in amide proton chemical shifts that indicated major structural perturbations upon complex formation. However, the CobY:GTP complex as followed by 1H-15N HSQC spectra was found to be unstable over time: GTP hydrolyzed and the protein converted slowly to a species with an NMR spectrum similar to that of apo-CobY. The variant CobYG153D, whose GTP complex was studied by X-ray crystallography, yielded NMR spectra similar to those of wild-type CobY in both its apo- state and in complex with GTP. The CobYG153D:GTP complex was also found to be unstable over time. PMID:26513744

  20. The pore wall structure of porous semi-crystalline anatase TiO2.

    SciTech Connect

    Kim, Dr Man-Ho; Han, Seong Chul; Chae, Keun Hwa; Yu, Byung-Yong; Hong, Kyung Tea; Jackson, Andrew; Anovitz, Lawrence {Larry} M

    2011-01-01

    The structure of porous TiO2 prepared by electrochemical anodization in a fluoride-containing ethylene glycol electrolyte solution was quantitatively studied using small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS). The cylindrical pores along the coaxial direction were somewhat irregular in shape, were widely distributed in diameter, and seemed to have a broadly pseudo-hexagonal arrangement. The scattering from the pore wall showed a negative deviation from Porod scattering, indicating that the interface between TiO2 and the pore was not sharp. A density gradient of around 40 60 A at the pore wall (i.e. the interface between the pore and the TiO2 matrix) was estimated using both constant and semi-sigmoidal interface models. This gradient may be due to the presence of fluorine and carbon partially absorbed by the pore wall from the fluoride-containing electrolyte or to sorbed water molecules on the wall. The neutron contrast-matching point between the TiO2 matrix and the pores filled with liquid H2O/D2O mixtures was 51/49%(v/v) H2O/D2O, yielding an estimated mass density of 3.32 g cm3. The specific surface area of the sample derived from the (U)SANS data was around 939 1003 m2 cm3 (283 302 m2 g1).

  1. [Structural analysis of vinorelbine in solution determined by nuclear magnetic resonance spectrometry].

    PubMed

    Ribet, J P; Zalavari, P; Commenges, G; Fahy, J; Duflos, A; Schambel, P

    1997-01-01

    An active partnership between the National Centre for Scientific Research (CNRS) and the laboratories Pierre Fabre is underpinning the development of a new molecule, vinorelbine, whose tartrate received marketing authorization in France in 1989, under the name of Navelbine. This medicine was first recommended for the treatment of bronchial cancer "not small cell", then, in 1991, for the treatment of metastatic breast cancer. In 1994, its registration in United States was granted for the treatment of bronchial cancer "not small cell". Vinorelbine is obtained by hemisynthesis using two antecedent monomeric alkaloids, catharanthine and vindoline, followed by a modification of the catharanthine nucleus, so as to produce the first 5' nor vinca-alkaloid. The chemical structure of vinorelbine has been examined in our laboratory using nuclear magnetic resonance spectrometry. Bearing in mind their complexity, the total attribution of the proton spectrum and the carbon-13 spectrum has required experiments for homonuclear (1H-1H) and heteronuclear (1H-13C and 1H-15N) correlation. These experiments have been carried out using a BRUKER spectrometer operating at the nominal proton frequency of 200 MHz in direct detection mode, then with a 400 MHz spectrometer equipped with the reverse detection mode. The chemical structure has thus been analyzed with no ambiguity. The results of this structural study will be presented in due course. We have also undertaken a comparative conformational study between base vinorelbine in chloroform solution and ditartrate vinorelbine (Navelbine) in methanolic solution. The conformation of the vinorelbine molecule in solution in these different solvents have been studied with NOESY (Nuclear Overhauser Effect Spectroscopy) experiments. The results of these experiments have been confirmed by data stemming from molecular modelization. PMID:9138318

  2. Structure of the Glycyl-L-histidyl-L-lysine--copper(II) complex in solution.

    PubMed

    Freedman, J H; Pickart, L; Weinstein, B; Mims, W B; Peisach, J

    1982-09-14

    Optical, electron paramagnetic resonance, and electron spin-echo envelope spectroscopies were used to examine the structure of the Cu(II) complex of glycyl-L-histidyl-L-lysine (GHL) in solution. At neutral pH, GHL forms a mononuclear 1:1 Cu(II) compound having an EPR spectrum resembling that of Cu(II) equatorially coordinated by two or three nitrogen atoms. Electron spin-echo studies demonstrate that one of these is located in the histidyl imidazole ring. A pH titration of Cu(II)-GHL shows three optical transitions with apparent pKs of 3.6, 9.2 and 11.4 and molecularities, with respect to protons, of 2, 2, and 1, respectively. At the lowest pK, GHL binds Cu(II), forming the species present at physiological pH. At elevated pH, spectroscopic experiments suggest that an alteration of the Cu(II) structure occurs, yet the bound imidazole is retained. These solution studies are consistent with nitrogen coordination of Cu(II) in Cu(II)-GHL, but the solid-state polymeric structure, with oxygen-bridged Cu(II) pairs as previously determined by X-ray crystallographic analysis [Pickart, L., Freedman, J. H., Loker, W. J., Peisach, J., Perkins, C. M., Steinkamp, R. E., & Weinstein, B. (1980) Nature (London) 288, 715-717; C. M. Perkins, N. J. Rose, R. E. Steinkamp, L. H. Jensen, B. Weinstein, and L. Pickart, unpublished results], does not exist in solution. PMID:6291585

  3. Solution Structure and Dynamics of LptE from Pseudomonas aeruginosa.

    PubMed

    Moehle, Kerstin; Kocherla, Harsha; Bacsa, Bernadett; Jurt, Simon; Zerbe, Katja; Robinson, John A; Zerbe, Oliver

    2016-05-31

    LptE is an outer membrane (OM) lipoprotein found in Gram-negative bacteria, where it forms a complex with the β-barrel lipopolysaccharide (LPS) transporter LptD. The LptD/E complex plays a key role in OM biogenesis, by translocating newly synthesized LPS molecules from the periplasm into the external leaflet of the asymmetric OM during cell growth. The LptD/E complex in Pseudomonas aeruginosa (Pa) is a target for macrocyclic β-hairpin-shaped peptidomimetic antibiotics, which inhibit the transport of LPS to the cell surface. So far, the three-dimensional structure of the Pa LptD/E complex and the mode of interaction with these antibiotics are unknown. Here, we report the solution structure of a Pa LptE derivative lacking the N-terminal lipid membrane anchor, determined by multidimensional solution nuclear magnetic resonance (NMR) spectroscopy. The structure reveals a central five-stranded β-sheet against which pack a long C-terminal and a short N-terminal α-helix, as found in homologues of LptE from other Gram-negative bacteria. One unique feature is an extended C-terminal helix in Pa LptE, which in a model of the Pa LptD/E complex appears to be long enough to contact the periplasmic domain of LptD. Chemical shift mapping experiments suggest only weak interactions occur between LptE and the oligosaccharide chains of LPS. The NMR structure of Pa LptE will be valuable for more detailed structural studies of the LptD/E complex from P. aeruginosa. PMID:27166502

  4. Primary structure and solution conditions determine conformational ensemble properties of intrinsically disordered proteins

    NASA Astrophysics Data System (ADS)

    Mao, Hsuan-Han Alberto

    Intrinsically disordered proteins (IDPs) are a class of proteins that do not exhibit well-defined three-dimensional structures. The absence of structure is intrinsic to their amino acid sequences, which are characterized by low hydrophobicity and high net charge per residue compared to folded proteins. Contradicting the classic structure-function paradigm, IDPs are capable of interacting with high specificity and affinity, often acquiring order in complex with protein and nucleic acid binding partners. This phenomenon is evident during cellular activities involving IDPs, which include transcriptional and translational regulation, cell cycle control, signal transduction, molecular assembly, and molecular recognition. Although approximately 30% of eukaryotic proteomes are intrinsically disordered, the nature of IDP conformational ensembles remains unclear. In this dissertation, we describe relationships connecting characteristics of IDP conformational ensembles to their primary structures and solution conditions. Using molecular simulations and fluorescence experiments on a set of base-rich IDPs, we find that net charge per residue segregates conformational ensembles along a globule-to-coil transition. Speculatively generalizing this result, we propose a phase diagram that predicts an IDP's average size and shape based on sequence composition and use it to generate hypotheses for a broad set of intrinsically disordered regions (IDRs). Simulations reveal that acid-rich IDRs, unlike their oppositely charged base-rich counterparts, exhibit disordered globular ensembles despite intra-chain repulsive electrostatic interactions. This apparent asymmetry is sensitive to simulation parameters for representing alkali and halide salt ions, suggesting that solution conditions modulate IDP conformational ensembles. We refine the ion parameters using a calibration procedure that relies exclusively on crystal lattice properties. Simulations with these parameters recover swollen

  5. Structure and Dynamics of Full Length HIV-1 Capsid Protein in Solution

    PubMed Central

    Deshmukh, Lalit; Schwieters, Charles D.; Grishaev, Alexander; Ghirlando, Rodolfo; Baber, James L.; Clore, G. Marius

    2013-01-01

    The HIV-1 capsid protein plays a crucial role in viral infectivity, assembling into a cone that encloses the viral RNA. In the mature virion, the N-terminal domain of the capsid protein forms hexameric and pentameric rings, while C-terminal domain homodimers connect adjacent N-terminal domain rings to one another. Structures of disulfide-linked hexamer and pentamer assemblies, as well as structures of the isolated domains have been solved previously. The dimer configuration in C-terminal domain constructs differs in solution (residues 144–231) and crystal (residues 146–231) structures by ~30°, and it has been postulated that the former connects the hexamers while the latter links pentamers to hexamers. Here we study the structure and dynamics of full-length capsid protein in solution, comprising a mixture of monomeric and dimeric forms in dynamic equilibrium, using ensemble simulated annealing driven by experimental NMR residual dipolar couplings and X-ray scattering data. The complexity of the system necessitated the development of a novel computational framework that should be generally applicable to many other challenging systems that currently escape structural characterization by standard application of mainstream techniques of structural biology. We show that the orientation of the C-terminal domains in dimeric full-length capsid and isolated C-terminal domain constructs is the same in solution, and obtain a quantitative description of the conformational space sampled by the N-terminal domain relative to the C-terminal domain on the nano- to millisecond time-scale. The positional distribution of the N-terminal domain relative to the C-terminal domain is large and modulated by the oligomerization state of the C-terminal domain. We also show that a model of the hexamer/pentamer assembly can be readily generated with a single configuration of the C-terminal domain dimer, and that capsid assembly likely proceeds via conformational selection of sparsely

  6. Analytical solution to a fracture problem in a tough layered structure

    NASA Astrophysics Data System (ADS)

    Hamamoto, Yukari; Okumura, Ko

    2008-08-01

    Nacre causes the shining beauty of pearl due to its remarkable layered structure, which is also strong. We reconsider a simplified layered model of nacre proposed previously [Okumura and de Gennes, Eur. Phys. J. E 4, 121 (2001)] and obtain an analytical solution to a fundamental crack problem. The result asserts that the fracture toughness is enhanced due to a large displacement around the crack tip (even if the crack-tip stress is not reduced). The derivation offers ideas for solving a number of boundary problems for partial differential equations important in many fields.

  7. Colloidal structure and stabilization mechanism of aqueous solutions of unmodified fullerene C{sub 60}

    SciTech Connect

    Khokhryakov, A. A. Kyzyma, O. A.; Bulavin, L. A.; Len, A.; Avdeev, M. V.; Aksenov, V. L.

    2007-05-15

    Despite the inability of fullerenes to be directly dissolved in water, there are methods for preparing stable dispersions of fullerenes in water without any particular modifications of the fullerene or addition of stabilizers. The colloidal properties of such systems prepared by replacing the solvent and structural changes in them during coagulation have been studied. The coagulation dynamics has been investigated by spectroscopy and small-angle neutron scattering. The results obtained confirm the colloidal nature of such systems. During coagulation, particles retain a large volume of water around them, an indication of interaction between fullerene and water during solution stabilization.

  8. Data describing the solution structure of the WW3* domain from human Nedd4-1.

    PubMed

    Panwalkar, Vineet; Schulte, Marianne; Lecher, Justin; Stoldt, Matthias; Willbold, Dieter; Dingley, Andrew J

    2016-09-01

    The third WW domain (WW3*) of human Nedd4-1 (Neuronal precursor cell expressed developmentally down-regulated gene 4-1) interacts with the poly-proline (PY) motifs of the human epithelial Na+ channel (hENaC) subunits at micromolar affinity. This data supplements the article (Panwalkar et al., 2015) [1]. We describe the NMR experiments used to solve the solution structure of the WW3* domain. We also present NOE network data for defining the rotameric state of side chains of peptide binding residues, and complement this data with χ 1 dihedral angles derived from (3) J couplings and molecular dynamics simulations data. PMID:27419198

  9. Correlations between structure, spectra, and thermodynamics in solutions of cobalt chloride in sodium tetrachloroaluminates

    SciTech Connect

    Newman, D.S.; Tumidajski, P.J.; Blander, M.

    1990-01-01

    An EMF technique using the cell Co/CoCl{sub 2} {minus} Na AlCl{sub 4}//(AgCl)x {minus} NaAlCl{sub 4} (x fixed)/Ag was used to measure the solubility of CoCl{sub 2} in NaCl{center dot}AlCl{sub 3} melts. The changes in EMF as a function of changes in melt composition were correlated with changes in the UV-Vis spectra of the dissolved cobalt species. From these data the microscopic structural contributions to the macroscopic thermodynamic properties of the solutions were estimated. 14 refs., 5 figs., 1 tab.

  10. Solution structure of detergent micelles at conditions relevant to membrane protein crystallization.

    SciTech Connect

    Littrell, K.; Thiyagarajan, P.; Tiede, D.; Urban, V.

    1999-07-02

    In this study small angle neutron scattering was used to characterize the formation of micelles in aqueous solutions of the detergents DMG and SPC as a function of detergent concentration and ionic strength of the solvent. The effects on the micelle structure of the additives glycerol and PEG, alone as well as in combination typical for actual membrane protein crystallization, were also explored. This research suggests that the micelles are cigar-like in form at the concentrations studied. The size of the micelles was observed to increase with increasing ionic strength but decrease with the addition of glycerol or PEG.

  11. [Wide-angle x-ray scattering comparison of the structure of crystalline cytochrome c and cytochrome c in solution].

    PubMed

    Timchenko, A A; Denesiuk, A I; Fedorov, B A

    1981-01-01

    Large-angle X-ray diffuse scattering has been used for studying the conformational changes in cytochrome c during its transition from crystal into solution and during a change of the electron state of the heme. It has been found that the structure of cytochrome c in solution differs from its structure in crystal by a shift of the chain fragment in the region of 60-77 amino acid residues. The studies of the oxidized, reduced and cyanoforms of protein in solution have not revealed noticeable changes in the protein structure. PMID:6261840

  12. Nuclear Magnetic Resonance Solution Structure of DNA Featuring Clustered 2'-Deoxyribonolactone and 8-Oxoguanine Lesions.

    PubMed

    Zálešák, Jan; Constant, Jean-François; Jourdan, Muriel

    2016-07-19

    Ionizing radiation, free radicals, and reactive oxygen species produce hundreds of different DNA lesions. Clustered lesions are typical for ionizing radiation. They compromise the efficiency of the base excision repair (BER) pathway, and as a consequence, they are much more toxic and mutagenic than isolated lesions. Despite their biological relevance, e.g., in cancer radiotherapy and accidental exposure, they are not very well studied from a structural point of view, and while insights provided by structural studies contribute to the understanding of the repair process, only three nuclear magnetic resonance (NMR) studies of DNA containing clusters of lesions were reported. Herein, we report the first NMR solution structure of two DNAs containing a bistranded cluster with the 2'-deoxyribonolactone and 8-oxoguanine lesions. Both DNA duplexes feature a 2'-deoxyribonolactone site in the middle of the sequence of one strand and differ by the relative position of the 8-oxoguanine, staggered 3' or 5' side on the complementary strand at a three-nucleotide distance. Depending on its relative position, the repair of the 8-oxoguanine lesion by the base excision repair protein Fpg is either almost complete or inhibited. We found that the structures of the two DNAs containing a bistranded cluster of two lesions are similar and do not deviate very much from the standard B-form. As no obvious structural deformations were observed between the two duplexes, we concluded that the differences in Fpg activity are not due to differences in their global conformation. PMID:27322640

  13. Structure of the nidogen binding LE module of the laminin gamma1 chain in solution.

    PubMed

    Baumgartner, R; Czisch, M; Mayer, U; Pöschl, E; Huber, R; Timpl, R; Holak, T A

    1996-04-01

    The structure of the single LE module between residues 791 and 848 of the laminin gamma1 chain, which contains the high affinity binding site for nidogen, has been probed using NMR methods. The module folds into an autonomous domain which has a stable and unique three-dimensional (3D) structure in solution. The 3D structure was determined on the basis of 362 interproton distance constraints derived from nuclear Overhauser enhancement measurements and 39 phi angles, supplemented by 5 psi and 22 chi1 angles. The main features of the NMR structures are two-stranded antiparallel beta-sheets which are separated by loops and cross-connected by four disulfide bridges. The N-terminal segment which contains the first three disulfide bridges is similar to epidermal growth factor. The C-terminal segment has an S-like backbone profile with a crossover at the last disulfide bridge and comprises two three-residue long beta-strands that form an antiparallel beta-sheet. The LE module possesses an exposed nidogen binding loop that projects away from the main body of the protein. The side-chains of three amino acids which are crucial for binding (Asp, Asn, Val) are all exposed at the domain surface. An inactivating Asn-Ser mutation in this region showed the same 3D structure indicating that these three residues, and possibly an additional Tyr in an adjacent loop, provide direct contacts in the interaction with nidogen. PMID:8648631

  14. Unexpected structural softening of interstitial boron solid solution WB{sub 3+x}

    SciTech Connect

    Wu, Hao; Sun, Hong E-mail: chen@physics.unlv.edu; Chen, Changfeng E-mail: chen@physics.unlv.edu

    2014-11-24

    Using first-principles calculations, we reveal an unexpected structural softening in a recently proposed WB{sub 3+x} structural model that tries to explain the X-ray diffraction, high resolution TEM, pressure dependence of the normalized lattice c/a ratio, and hardness experimental results of the synthesized tungsten boride compounds with a nominal composition WB{sub 4}. We show that the interstitial boron in WB{sub 3+x}, which was proposed to strengthen the covalent bonding network, unexpectedly weakens the atomic bonding, resulting in a large reduction of its indentation strength to well below that of WB{sub 3}. This is in direct contradiction to the experimental results showing that synthesized WB{sub 4} is harder than WB{sub 3}. The unusual structural softening is attributed to the unique three-center covalent bonding formed by the interstitial boron atoms that can easily deform under indentation. Our results show that the proposed interstitial boron solid solution WB{sub 3+x} structure is incompatible with experimental results, which calls for further investigations to determine the crystal structure of the synthesized WB{sub 4}.

  15. [Application of nuclear magnetic resonance for the determination of the structure of proteins in solution].

    PubMed

    Charretier, E; Guéron, M

    1991-01-01

    Knowledge of three-dimensional structure is a key factor in protein engineering. It is useful, for example, in predicting and understanding the functional consequences of specific substitution of one or more amino acids of the polypeptide chain. It is also necessary for the design of new effectors or analogs of the substrates of enzymes and receptors. X-ray diffraction by crystals of the biomolecule was for a long time the only method of determining three-dimensional structures. In the last 5 years, it has been joined by a new technique, two-dimensional nuclear magnetic resonance (2D NMR), which can resolve the structure of middle-sized proteins (less than 10 kilodaltons). The technique is applied on solutions whose pH, ionic strength, and temperature can be chosen and changed. The two basic measurements, COSY and NOESY, detect respectively the systems of hydrogen nuclei, or protons, coupled through covalent bonds, and those in which the interproton distances are less than 0.5 nm. A systematic strategy leads from resonance assignments of the two-dimensional spectrum to molecular modeling with constraints and finally to the determination of the molecular structure in the solution. Much sophistication is needed even today for the first task, the assignment of the resonances. Each of the COSY and NOESY spectra is a two-dimensional map, where the diagonal line is the one-dimensional spectrum, and the off-diagonal peaks indicate connectives between protons. Peak assignment to a specific type of amino acid is based on the pattern of scalar couplings observed in the COSY spectrum. Next, the amino acids are positioned in the primary sequence, using the spatial proximities of polypeptide chain protons, as observed in the NOESY spectrum. The principal secondary structures (alpha helix, beta sheets, etc.) are then identified by their specific connectivities. The tertiary structure is detected by NOESY connectivities between protons of different amino acids which are far apart

  16. Inverse solution technique of steady-state responses for local nonlinear structures

    NASA Astrophysics Data System (ADS)

    Wang, Xing; Guan, Xin; Zheng, Gangtie

    2016-03-01

    An inverse solution technique with the ability of obtaining complete steady-state primary harmonic responses of local nonlinear structures in the frequency domain is proposed in the present paper. In this method, the nonlinear dynamic equations of motion is first condensed from many to only one algebraic amplitude-frequency equation of relative motion. Then this equation is transformed into a polynomial form, and with its frequency as the unknown variable, the polynomial equation is solved by tracing all the solutions of frequency with the increase of amplitude. With this solution technique, some complicated dynamic behaviors such as sharp tuning, anomalous jumps, breaks in responses and detached resonance curves could be obtained. The proposed method is demonstrated and validated through a finite element beam under force excitations and a lumped parameter model with a local nonlinear element under base excitations. The phenomenon of detached resonance curves in the frequency response and its coupling effects with multiple linear modes in the latter example are observed.

  17. Hydrogen bonding and solution state structure of salicylaldehyde-4-phenylthiosemicarbazone: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Novak, Predrag; Pičuljan, Katarina; Hrenar, Tomica; Biljan, Tomislav; Meić, Zlatko

    2009-02-01

    Hydrogen bonding in salicylaldehyde-4-phenylthiosemicarbazone ( 1) has been studied by using experimental (NMR, Raman and UV spectroscopies) and quantum chemical (DFT) methods. It has been demonstrated that 1 adopted the hydroxy-thione tautomeric form in solution as found also in the solid state and previously indicated by secondary deuterium isotope effects. Apart from the intra-molecular hydrogen bonds new interactions between 1 and solvent molecules were formed as well. Changes in NMR chemical shifts and calculations have pointed towards a formation of inter-molecular three-centered hydrogen bonds in each of the studied complexes involving OH and NH groups of 1 and associated solvent molecules. Stabilization energies of intra-molecular hydrogen bonds were found to decrease with the increase of the solvent polarity. Two-dimensional NOESY spectra indicated conformational changes in solution with respect to the structure observed in the solid state. These were accounted for by a relatively low barrier of the rotation of the N sbnd N single bond thus enabling a molecule to posses a higher conformational flexibility in solution with portions of skewed conformations. The results presented here can help in a better understanding of the role hydrogen bonds can play in bioactivity of related thiosemicarbazone derivatives and their metal complexes.

  18. Numerical solutions of Navier-Stokes equations for the structure of a trailing vortex

    NASA Technical Reports Server (NTRS)

    Jain, A. C.

    1977-01-01

    The structure and decay of a trailing vortex were analyzed during the numerical solutions of the full Navier-Stokes equations. Unsteady forms of the governing equations were recast in terms of circulation, vorticity, and stream function as dependent variables, and a second upwind finite difference scheme was used to integrate them with prescribed initial and boundary conditions. The boundary conditions at the outer edge and at the outflow section of the trailing vortex were considered. Different models of the flow were postulated, and solutions were obtained describing the development of the flow as integration proceeds in time. A parametric study was undertaken with a view to understanding the various phenomena that may possibly occur in the trailing vortex. Using the Hoffman and Joubert law of circulation at the inflow section, the results of this investigation were compared with experimental data for a Convair 990 wind model and a rectangular wing. With an exponentially decaying law of circulation at the inflow section and an adverse pressure gradient at the outer edge of the trailing vortex, solutions depict vortex bursting through the sudden expansion of the core and/or through the stagnation and consequent reversal of the flow on the axis. It was found that this bursting takes place at lower values of the swirl ratio as the Reynolds number increases.

  19. Structural Evidence for Inter-Residue Hydrogen Bonding Observed for Cellobiose in Aqueous Solution

    PubMed Central

    O'Dell, William B.; Baker, David C.; McLain, Sylvia E.

    2012-01-01

    The structure of the disaccharide cellulose subunit cellobiose (4-O-β-D-glucopyranosyl-D-glucose) in solution has been determined via neutron diffraction with isotopic substitution (NDIS), computer modeling and nuclear magnetic resonance (NMR) spectroscopic studies. This study shows direct evidence for an intramolecular hydrogen bond between the reducing ring HO3 hydroxyl group and the non-reducing ring oxygen (O5′) that has been previously predicted by computation and NMR analysis. Moreover, this work shows that hydrogen bonding to the non-reducing ring O5′ oxygen is shared between water and the HO3 hydroxyl group with an average of 50% occupancy by each hydrogen-bond donor. The glycosidic torsion angles φH and ψH from the neutron diffraction-based model show a fairly tight distribution of angles around approximately 22° and −40°, respectively, in solution, consistent with the NMR measurements. Similarly, the hydroxymethyl torsional angles for both reducing and non-reducing rings are broadly consistent with the NMR measurements in this study, as well as with those from previous measurements for cellobiose in solution. PMID:23056199

  20. Solution structure and antiparasitic activity of scorpine-like peptides from Hoffmannihadrurus gertschi.

    PubMed

    Flores-Solis, David; Toledano, Yanis; Rodríguez-Lima, Oscar; Cano-Sánchez, Patricia; Ramírez-Cordero, Belen Ernestina; Landa, Abraham; Rodríguez de la Vega, Ricardo C; Del Rio-Portilla, Federico

    2016-07-01

    Scorpine-like peptides are two domain peptides found in different scorpion venoms displaying various antimicrobial, cytolytic, and potassium channel-blocking activities. The relative contribution of each domain to their different activities remains to be elucidated. Here, we report the recombinant production, solution structure, and antiparasitic activity of Hge36, first identified as a naturally occurring truncated form of a Scorpine-like peptide from the venom of Hoffmannihadrurus gertschi. We also show that removing the first four residues from Hge36 renders a molecule with enhanced potassium channel-blocking and antiparasitic activities. Our results are important to rationalize the structure-function relationships of a pharmacologically versatile molecular scaffold. PMID:27314815

  1. Elliptical vortex solutions, integrable Ermakov structure, and Lax pair formulation of the compressible Euler equations.

    PubMed

    An, Hongli; Fan, Engui; Zhu, Haixing

    2015-01-01

    The 2+1-dimensional compressible Euler equations are investigated here. A power-type elliptic vortex ansatz is introduced and thereby reduction obtains to an eight-dimensional nonlinear dynamical system. The latter is shown to have an underlying integral Ermakov-Ray-Reid structure of Hamiltonian type. It is of interest to notice that such an integrable Ermakov structure exists not only in the density representations but also in the velocity components. A class of typical elliptical vortex solutions termed pulsrodons corresponding to warm-core eddy theory is isolated and its behavior is simulated. In addition, a Lax pair formulation is constructed and the connection with stationary nonlinear cubic Schrödinger equations is established. PMID:25679730

  2. Structure of leech derived tryptase inhibitor (LDTI-C) in solution.

    PubMed

    Mühlhahn, P; Czisch, M; Morenweiser, R; Habermann, B; Engh, R A; Sommerhoff, C P; Auerswald, E A; Holak, T A

    1994-12-01

    The three-dimensional solution structure of the leech derived tryptase inhibitor form C (LDTI-C), an inhibitor of 46 amino acids which contains 3 disulfide bridges, has been determined using 2D NMR spectroscopy. The 3D structure was determined on the basis of 262 interresidue interproton distance constraints derived from nuclear Overhauser enhancement measurements and 25 phi angles, supplemented by 3 psi and 15 chi 1 angles. The core of LDTI-C is very well defined and consists of a short 3(10)-helix-loop and a short two-stranded antiparallel beta-sheet between residues 13-14 and 20-21. The N-terminus is fixed to the core by two disulfide bridges, while the C-terminus is connected to the beta-sheet via the third disulfide bridge. The binding loop in LDTI exhibits lowest energy conformations belonging to the canonical conformation of serine proteinase inhibitors. PMID:7988692

  3. Ab Initio Approach for Prediction of Oxide Surface Structure, Stoichiometry, and Electrocatalytic Activity in Aqueous Solution.

    PubMed

    Rong, Xi; Kolpak, Alexie M

    2015-05-01

    The design of efficient, stable, and inexpensive catalysts for oxygen evolution and reduction is crucial for the development of electrochemical energy conversion devices such as fuel cells and metal-air batteries. Currently, such design is limited by challenges in atomic-scale experimental characterization and computational modeling of solid-liquid interfaces. Here, we begin to address these issues by developing a general-, first-principles-, and electrochemical-principles-based framework for prediction of catalyst surface structure, stoichiometry, and stability as a function of pH, electrode potential, and aqueous cation concentration. We demonstrate the approach by determining the surface phase diagram of LaMnO3, which has been studied for oxygen evolution and reduction and computing the reaction overpotentials on the relevant surface phases. Our results illustrate the critical role of solvated cation species in governing the catalyst surface structure and stoichiometry, and thereby catalytic activity, in aqueous solution. PMID:26263350

  4. Phenix - a comprehensive python-based system for macromolecular structure solution

    SciTech Connect

    Terwilliger, Thomas C; Hung, Li - Wei; Adams, Paul D; Afonine, Pavel V; Bunkoczi, Gabor; Chen, Vincent B; Davis, Ian; Echols, Nathaniel; Headd, Jeffrey J; Grosse Kunstleve, Ralf W; Mccoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert; Read, Randy J; Richardson, David C; Richardson, Jane S; Zwarta, Peter H

    2009-01-01

    Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

  5. Effect of polymer matrix on structure of Se particles formed in aqueous solutions during redox process

    NASA Astrophysics Data System (ADS)

    Suvorova, E. I.; Klechkovskaya, V. V.

    2010-12-01

    Transmission electron microscopy and X-ray energy dispersive microanalysis study of the structure of particles formed during the reduction of Se(IV) to Se(0) in aqueous solutions in the presence of amphiphilic polymers showed the formation of Se/polymer composite particles. The content of carbon inside the particles can be as large as 80 at %. Polymers deeply influence the structure of particles. Depending on polymers, the composite particles may be unstable with time and they spontaneously evolve from Se/polymer composite particles to crystalline particles of monoclinic Se. For the stable ones, addition of bacterial cellulose Acetobacter xylinum gel-film can induce crystallization in the particles which expel the polymeric material. The Se/polymer composite particles and Se crystalline particles exhibit different sensitivity to electron irradiation and stiffness.

  6. Effect of polymer matrix on structure of Se particles formed in aqueous solutions during redox process

    SciTech Connect

    Suvorova, E. I. Klechkovskaya, V. V.

    2010-12-15

    Transmission electron microscopy and X-ray energy dispersive microanalysis study of the structure of particles formed during the reduction of Se(IV) to Se(0) in aqueous solutions in the presence of amphiphilic polymers showed the formation of Se/polymer composite particles. The content of carbon inside the particles can be as large as 80 at %. Polymers deeply influence the structure of particles. Depending on polymers, the composite particles may be unstable with time and they spontaneously evolve from Se/polymer composite particles to crystalline particles of monoclinic Se. For the stable ones, addition of bacterial cellulose Acetobacter xylinum gel-film can induce crystallization in the particles which expel the polymeric material. The Se/polymer composite particles and Se crystalline particles exhibit different sensitivity to electron irradiation and stiffness.

  7. Solid-State and Solution Structures of Glycinimine-Derived Lithium Enolates.

    PubMed

    Jin, Kyoung Joo; Collum, David B

    2015-11-18

    A combination of crystallographic, spectroscopic, and computational studies was applied to study the structures of lithium enolates derived from glycinimines of benzophenone and (+)-camphor. The solvents examined included toluene and toluene containing various concentrations of tetrahydrofuran, N,N,N',N'-tetramethylethylenediamine (TMEDA), (R,R)-N,N,N',N'-tetramethylcyclohexanediamine [(R,R)-TMCDA], and (S,S)-N,N,N',N'-tetramethylcyclohexanediamine [(S,S)-TMCDA]. Crystal structures show chelated monomers, symmetric disolvated dimers, S4-symmetric tetramers, and both S6- and D3d-symmetric hexamers. (6)Li NMR spectroscopic studies in conjunction with the method of continuous variations show how these species distribute in solution. Density functional theory computations offer insights into experimentally elusive details. PMID:26554898

  8. Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine.

    PubMed

    Karnawat, Vishakha; Puranik, Mrinalini

    2016-03-01

    Deaza analogues of nucleobases are potential drugs against infectious diseases caused by parasites. A caveat is that apart from binding their target parasite enzymes, they also bind and inhibit enzymes of the host. In order to design derivatives of deaza analogues which specifically bind target enzymes, knowledge of their molecular structure, protonation state, and predominant tautomers at physiological conditions is essential. We have employed resonance Raman spectroscopy at an excitation wavelength of 260 nm, to decipher solution structure of 9-deazaguanine (9DAG) and 9-deazahypoxanthine (9DAH). These are analogues of guanine and hypoxanthine, respectively, and have been exploited to study static complexes of nucleobase binding enzymes. Such enzymes are known to perturb pKa of their ligands, and thus, we also determined solution structures of these analogues at two, acidic and alkaline, pH. Structure of each possible protonation state and tautomer was computed using density functional theoretical calculations. Species at various pHs were identified based on isotopic shifts in experimental wavenumbers and by comparing these shifts with corresponding computed isotopic shifts. Our results show that at physiological pH, N1 of pyrimidine ring in 9DAG and 9DAH bears a proton. At lower pH, N3 is place of protonation, and at higher pH, deprotonation occurs at N1 position. The proton at N7 of purine ring remains intact even at pH 12.5. We have further compared these results with naturally occurring nucleotides. Our results identify key vibrational modes which can report on hydrogen bonding interactions, protonation and deprotonation in purine rings upon binding to the active site of enzymes. PMID:25894214

  9. The solution structure of a superpotent B-chain-shortened single-replacement insulin analogue.

    PubMed Central

    Kurapkat, G.; Siedentop, M.; Gattner, H. G.; Hagelstein, M.; Brandenburg, D.; Grötzinger, J.; Wollmer, A.

    1999-01-01

    This paper reports on an insulin analogue with 12.5-fold receptor affinity, the highest increase observed for a single replacement, and on its solution structure, determined by NMR spectroscopy. The analogue is [D-AlaB26]des-(B27-B30)-tetrapeptide-insulin-B26-amide. C-terminal truncation of the B-chain by four (or five) residues is known not to affect the functional properties of insulin, provided the new carboxylate charge is neutralized. As opposed to the dramatic increase in receptor affinity caused by the substitution of D-Ala for the wild-type residue TyrB26 in the truncated molecule, this very substitution reduces it to only 18% of that of the wild-type hormone when the B-chain is present in full length. The insulin molecule in solution is visualized as an ensemble of conformers interrelated by a dynamic equilibrium. The question is whether the "active" conformation of the hormone, sought after in innumerable structure/function studies, is or is not included in the accessible conformational space, so that it could be adopted also in the absence of the receptor. If there were any chance for the active conformation, or at least a predisposed state to be populated to a detectable extent, this chance should be best in the case of a superpotent analogue. This was the motivation for the determination of the three-dimensional structure of [D-AlaB26]des-(B27-B30)-tetrapeptide-insulin-B26-amide. However, neither the NMR data nor CD spectroscopic comparison of a number of related analogues provided a clue concerning structural features predisposing insulin to high receptor affinity. After the present study it seems more likely than before that insulin will adopt its active conformation only when exposed to the force field of the receptor surface. PMID:10091652

  10. Aqueous phase synthesized CdSe magic-sized clusters: solution composition dependence of adsorption layer structure.

    PubMed

    Park, Yeon-Su; Okamoto, Yukihiro; Kaji, Noritada; Tokeshi, Manabu; Baba, Yoshinobu

    2012-01-01

    We report dispersion solution composition dependence of the adsorption layer structure and the physical and optical properties of aqueous phase-synthesized semiconductor nanoparticles (NPs). We synthesized cysteine (Cys)-capped CdSe NPs with well-defined core structures, dispersed them in a series of aqueous solutions with different compositions, and then investigated their adsorption layer structure and physical and optical properties. Each CdSe NP consisted of a (CdSe)33 or (CdSe)34 magic-sized cluster (d - 1.45 nm) core, a ligand-Cys shell, and an adsorption layer. The dispersion solution composition strongly affected the adsorption layer structure of the CdSe NPs. The solution with a composition close to that of the as-prepared solution stabilized the physical and optical properties of the NPs. The solution with a composition different from that of the as-prepared solution, however, resulted in large changes in their adsorption layer structure and thus their physical and optical properties. The solution composed of neutral or weakly charged Cys and Cd-Cys complexes led to the adsorption layer with low charge density and that destabilized the NPs. The solution containing only neutral or weakly charged forms of Cys, without Cd-Cys complexes, was favorable to the formation of a thick adsorption layer with low charge density and that destabilized the NPs. The amount of adsorbed Cys in the adsorption layer depended on the dispersion solution composition. However, the amount of adsorbed Cd-Cys complexes in the adsorption layer was almost constant regardless of the dispersion solution composition. PMID:22524016

  11. Solution structure of eggcase silk protein and its implications for silk fiber formation

    PubMed Central

    Lin, Zhi; Huang, Weidong; Zhang, Jingfeng; Fan, Jing-Song; Yang, Daiwen

    2009-01-01

    Spider silks are renowned for their excellent mechanical properties and biomimetic and industrial potentials. They are formed from the natural refolding of water-soluble fibroins with α-helical and random coil structures in silk glands into insoluble fibers with mainly β-structures. The structures of the fibroins at atomic resolution and silk formation mechanism remain largely unknown. Here, we report the 3D structures of individual domains of a ≈366-kDa eggcase silk protein that consists of 20 identical type 1 repetitive domains, one type 2 repetitive domain, and conserved nonrepetitive N- and C-terminal domains. The structures of the individual domains in solution were determined by using NMR techniques. The domain interactions were investigated by NMR and dynamic light-scattering techniques. The formation of micelles and macroscopic fibers from the domains was examined by electron microscopy. We find that either of the terminal domains covalently linked with at least one repetitive domain spontaneously forms micelle-like structures and can be further transformed into fibers at ≥37 °C and a protein concentration of >0.1 wt%. Our biophysical and biochemical experiments indicate that the less hydrophilic terminal domains initiate the assembly of the proteins and form the outer layer of the micelles whereas the more hydrophilic repetitive domains are embedded inside to ensure the formation of the micelle-like structures that are the essential intermediates in silk formation. Our results establish the roles of individual silk protein domains in fiber formation and provide the basis for designing miniature fibroins for producing artificial silks. PMID:19458259

  12. The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.

    PubMed

    Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; Heinecke, A; Bungartz, H-J; Lederer, H

    2014-05-28

    Obtaining the eigenvalues and eigenvectors of large matrices is a key problem in electronic structure theory and many other areas of computational science. The computational effort formally scales as O(N(3)) with the size of the investigated problem, N (e.g. the electron count in electronic structure theory), and thus often defines the system size limit that practical calculations cannot overcome. In many cases, more than just a small fraction of the possible eigenvalue/eigenvector pairs is needed, so that iterative solution strategies that focus only on a few eigenvalues become ineffective. Likewise, it is not always desirable or practical to circumvent the eigenvalue solution entirely. We here review some current developments regarding dense eigenvalue solvers and then focus on the Eigenvalue soLvers for Petascale Applications (ELPA) library, which facilitates the efficient algebraic solution of symmetric and Hermitian eigenvalue problems for dense matrices that have real-valued and complex-valued matrix entries, respectively, on parallel computer platforms. ELPA addresses standard as well as generalized eigenvalue problems, relying on the well documented matrix layout of the Scalable Linear Algebra PACKage (ScaLAPACK) library but replacing all actual parallel solution steps with subroutines of its own. For these steps, ELPA significantly outperforms the corresponding ScaLAPACK routines and proprietary libraries that implement the ScaLAPACK interface (e.g. Intel's MKL). The most time-critical step is the reduction of the matrix to tridiagonal form and the corresponding backtransformation of the eigenvectors. ELPA offers both a one-step tridiagonalization (successive Householder transformations) and a two-step transformation that is more efficient especially towards larger matrices and larger numbers of CPU cores. ELPA is based on the MPI standard, with an early hybrid MPI-OpenMPI implementation available as well. Scalability beyond 10,000 CPU cores for problem

  13. The solution structures of two soybean calmodulin isoforms provide a structural basis for their selective target activation properties.

    PubMed

    Ishida, Hiroaki; Huang, Hao; Yamniuk, Aaron P; Takaya, Yoshiaki; Vogel, Hans J

    2008-05-23

    The intracellular calcium ion is one of the most important secondary messengers in eukaryotic cells. Ca(2+) signals are translated into physiological responses by EF-hand calcium-binding proteins such as calmodulin (CaM). Multiple CaM isoforms occur in plant cells, whereas only a single CaM protein is found in animals. Soybean CaM isoform 1 (sCaM1) shares 90% amino acid sequence identity with animal CaM (aCaM), whereas sCaM4 is only 78% identical. These two sCaM isoforms have distinct target-enzyme activation properties and physiological functions. sCaM4 is highly expressed during the self-defense reaction of the plant and activates the enzyme nitric-oxide synthase (NOS), whereas sCaM1 is incapable of activating NOS. The mechanism of selective target activation by plant CaM isoforms is poorly understood. We have determined high resolution NMR solution structures of Ca(2+)-sCaM1 and -sCaM4. These were compared with previously determined Ca(2+)-aCaM structures. For the N-lobe of the protein, the solution structures of Ca(2+)-sCaM1, -sCaM4, and -aCaM all closely resemble each other. However, despite the high sequence identity with aCaM, the C-lobe of Ca(2+)-sCaM1 has a more open conformation and consequently a larger hydrophobic target-protein binding pocket than Ca(2+)-aCaM or -sCaM4, the presence of which was further confirmed through biophysical measurements. The single Val-144 --> Met substitution in the C-lobe of Ca(2+)-sCaM1, which restores its ability to activate NOS, alters the structure of the C-lobe to a more closed conformation resembling Ca(2+)-aCaM and -sCaM4. The relationships between the structural differences in the two Ca(2+)-sCaM isoforms and their selective target activation properties are discussed. PMID:18347016

  14. Solution structure of Syrian hamster prion protein rPrP(90-231).

    PubMed

    Liu, H; Farr-Jones, S; Ulyanov, N B; Llinas, M; Marqusee, S; Groth, D; Cohen, F E; Prusiner, S B; James, T L

    1999-04-27

    NMR has been used to refine the structure of Syrian hamster (SHa) prion protein rPrP(90-231), which is commensurate with the infectious protease-resistant core of the scrapie prion protein PrPSc. The structure of rPrP(90-231), refolded to resemble the normal cellular isoform PrPC spectroscopically and immunologically, has been studied using multidimensional NMR; initial results were published [James et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 10086-10091]. We now report refinement with better definition revealing important structural and dynamic features which can be related to biological observations pertinent to prion diseases. Structure refinement was based on 2778 unambiguously assigned nuclear Overhauser effect (NOE) connectivities, 297 ambiguous NOE restraints, and 63 scalar coupling constants (3JHNHa). The structure is represented by an ensemble of 25 best-scoring structures from 100 structures calculated using ARIA/X-PLOR and further refined with restrained molecular dynamics using the AMBER 4.1 force field with an explicit shell of water molecules. The rPrP(90-231) structure features a core domain (residues 125-228), with a backbone atomic root-mean-square deviation (RMSD) of 0.67 A, consisting of three alpha-helices (residues 144-154, 172-193, and 200-227) and two short antiparallel beta-strands (residues 129-131 and 161-163). The N-terminus (residues 90-119) is largely unstructured despite some sparse and weak medium-range NOEs implying the existence of bends or turns. The transition region between the core domain and flexible N-terminus, i.e., residues 113-128, consists of hydrophobic residues or glycines and does not adopt any regular secondary structure in aqueous solution. There are about 30 medium- and long-range NOEs within this hydrophobic cluster, so it clearly manifests structure. Multiple discrete conformations are evident, implying the possible existence of one or more metastable states, which may feature in conversion of PrPC to PrPSc. To

  15. Slip and interfacial structure of polymer melts and solutions in contact with end-tethered polymers

    NASA Astrophysics Data System (ADS)

    Gutfreund, Philipp; Korolkovas, Airidas; Liesche, Georg; Dennison, Andrew; Theis-Bröhl, Katharina; Wolff, Max; Akgun, Bulent; Barrat, Jean-Louis

    2014-03-01

    We present a neutron reflectometry (NR) study on polystyrene (PS) sheared in contact with functionalized solid surfaces. These methods provide a non-invasive tool to elucidate the structure of the buried interface with sub-nm resolution. We combine the scattering experiments with in situ surface sensitive rheology to gather information about the microscopic origin of interfacial slip. We have performed in situ shear-NR on PS melts and solutions in contact with chemically grafted PS chains. Entangled polymers can exhibit macroscopic slippage and its origin is supposed to arise from stretching of surface adsorbed chains and subsequent disentanglement from the free flowing chains. The combination of surface sensitive rheometry in a plate-plate torsional shear set-up and NR is potentially a unique technique to address this question by using labeled polymer chains chemically attached to the surface or in the free liquid. We present first results on in situ shear NR on PS melts in contact with high density PS brushes as well as entangled PS solutions flowing over grafted PS chains of the same length of lower density. In both cases we observe a structural change of the grafted PS at a certain shear rate that may be linked tostretching and/or disentanglement of the interfacial chains.

  16. Structural and transport properties of Nafion in hydrobromic-acid solutions

    SciTech Connect

    Kusoglu, A; Cho, KT; Prato, RA; Weber, AZ

    2013-12-01

    Proton-exchange membranes are key solid-state ion carriers in many relevant energy technologies including flow batteries, fuel cells, and solar-fuel generators. In many of these systems, the membranes are in contact with electrolyte solutions. In this paper, we focus on the impact of different HBr, a flow-battery and exemplary acid electrolyte, external concentrations on the conductivity of Nafion, a perfluorosulfonic acid membrane that is commonly used in many energy-related applications. The peak and then decrease in conductivity is correlated with measured changes in the water and HBr content within the membrane. In addition, small-angle x-ray scattering is used to probe the nanostructure to correlate how the interactions of the bromide ion with the fixed sulfonic-acid sites impact conductivity and hydrophilic domain distance. It is also shown that membrane pretreatment has a large impact on the underlying structure/function relationship. The obtained data and results are useful for delineation of optimal operating regimes for flow batteries and similar technologies as well as in understanding underlying structure/function relationships of ionomers in electrolyte solutions. (C) 2013 Elsevier B.V. All rights reserved.

  17. Structure of P3HT crystals, thin films, and solutions by UV/Vis spectral analysis.

    PubMed

    Böckmann, Marcus; Schemme, Thomas; de Jong, Djurre H; Denz, Cornelia; Heuer, Andreas; Doltsinis, Nikos L

    2015-11-21

    Optical absorption spectra of poly(3-hexylthiophene) (P3HT) are calculated in solution, spin-coated thin films, and the bulk crystal using a multiscale simulation approach. The structure of the amorphous thin film is obtained from coarse grained molecular dynamics (MD) simulations and subsequent back-mapping onto an atomistic force field representation. The absorption spectra are computed using TDDFT by statistically averaging over an ensemble of molecules taken from the MD simulations. Experimental UV/Vis spectra of spin-coated thin films and solutions are recorded with varying ratios of 'good' versus 'poor' solvent. The theoretical approach is able to faithfully predict the spectral position in the various phases and offers fundamental insight into the cause of any spectral shifts. The position of the main absorption peak is found to be chiefly determined by the level of torsion between the thiophene rings inside each molecule, while intermolecular effects are less important. Hence, optical absorption spectra hold valuable clues about the microscopic structure of disordered P3HT phases. PMID:26443229

  18. Solution thermodynamics and structures of biscatecholamide complexes of Fe(III) and U(VI)

    SciTech Connect

    Gohdes, J.W.; Reilly, S.D.; Pecha, A.W.; Neu, M.P.

    1996-12-31

    We have studied the solution and solid-state complexes of a bis-catecholamide ligand, 2-LICAMS, with Fe(III) and U(VI). The first protonation constant was found to be pK{sub al} = 14.2(3) using {sup 1}H NMR titrations. Subsequent protonation constants were determined by potentiometric titration in 0.1 M TMAOTf at 25{degrees}C to be pK{sub a2} = 11.2(1), pK{sub 13} =6.5(1), pK{sub a4}= 5.9(1). Ligand-metal formation constants, {Beta}{sub mlh}, were found to be log {beta}{sub 110} = 31.4(2), log {beta}{sub 111} = 31.7(2), log {beta}{sub 112} = 34.9(2), and log {beta}11.1 = 18.0(1) for uranium(VI). To discriminate between monomeric or dimeric species models which both fit the potentiometric titration data, we isolated the hydroxide species and determined its single-crystal X-ray structure and EXAFS. The structure consists of a dimeric, bis-hydroxide bridged iron core which is spanned by two ligands. This study of solution equilibria indicates a higher stability for iron complexes of 2-LICAMS relative to uranyl complexes.

  19. The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

    PubMed

    Shi, Xuesong; Huang, Lin; Lilley, David M J; Harbury, Pehr B; Herschlag, Daniel

    2016-03-01

    With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes. PMID:26727239

  20. The effect of compatible solute ectoines on the structural organization of lipid monolayer and bilayer membranes.

    PubMed

    Harishchandra, Rakesh Kumar; Wulff, Stephanie; Lentzen, Georg; Neuhaus, Thorsten; Galla, Hans-Joachim

    2010-08-01

    Compatible solutes are small organic osmolytes responsible for osmotic balance and at the same time compatible with the cellular metabolism. Here, we have investigated the effect of the compatible solutes, ectoine and hydroxyectoine, on the fluid-rigid domain structure of lipid monolayer and bilayer membranes. Mainly saturated dipalmitoyl-phosphatidylcholine membranes exhibiting a clear le/lc phase transition were used. Fluorescence microscopy showed that ectoines added to the aqueous subphase expand and fluidize the lipid monolayers especially at surface pressures below 30mN/m. The domain structure at the le/lc phase transition is sensitively modified leading to smaller but more numerous domains in the presence of ectoines. Hydroxyectoine was more efficient than ectoine. These results are explained by the replacement theory assuming that the ectoines are likely to be expelled from the membrane surface thus favoring the hydration of the lipid membrane. This effect reduces the line tension, which is the interfacial energy at the domain edges leading to reduced domain sizes and increased number of rigid domains. Isotherms of negatively charged phosphatidylglycerol membranes show a similar expansion, while unsaturated lipids are less affected. Mixed phosphatidylcholine/phosphatidylglycerol membranes exhibit the same effect on the line tension increasing the tendency for a phase separation. This could be shown also in bilayer vesicles, where the compatible solutes have only a minor effect on the lipid main phase transition in pure DPPC membranes but reduce the extent of the pretransition. In mixed DPPC/DPPG bilayer membranes ectoines cause a phase separation leading to the enrichment of expanded DPPC domains. In conclusion, our study gives for the first time evidence that ectoines have an effect on lipid membranes increasing the hydration of the surface and thus increasing the mobility of the lipid head groups and fluidizing the lipid layer accordingly. This increased

  1. Analytical solutions for the seismic response of underground structures under SH wave propagation

    SciTech Connect

    Smerzini, C.; Aviles, J.; Sanchez-Sesma, F. J.

    2008-07-08

    A theoretical approach is presented to study the antiplane seismic response of underground structures subjected to the incidence of plane waves. The structure is assumed to be a circular inclusion embedded in a homogenous, isotropic and linear visco-elastic halfspace and its mathematical formulation is approached through the theory of multiple scattering and diffraction. The inclusion may consist either of a cavity, with or without a ring-shaped boundary, or it may be filled in with a linear-elastic material, without loss of generality. The seismic response of the inclusion and its influence on surface ground motions are analyzed in both frequency and time domains. The dependence of the transfer function amplitudes on several parameters, such as the angle of incident SH waves, the frequency content of the excitation, the impedance contrast between the inclusion and the surrounding medium and the position along the ground surface, is underlined. Considering the lack of analytical solutions for quantifying the modification of ground motions induced by subterranean inhomogeneities, the results of this study can be used, on one side, as benchmark for both geophysical investigations and numerical dynamic soil-structure interaction studies, and, on the other side, to support the formulation of simplified approaches and/or formulas for the seismic design and assessment of underground structures.

  2. Yeast Frataxin Solution Structure, Iron Binding, and Ferrochelatase Interaction†‡

    PubMed Central

    He, Yanan; Alam, Steven L.; Proteasa, Simona V.; Zhang, Yan; Lesuisse, Emmanuel; Dancis, Andrew; Stemmler, Timothy L.

    2010-01-01

    The mitochondrial protein frataxin is essential for cellular regulation of iron homeostasis. Although the exact function of frataxin is not yet clear, recent reports indicate the protein binds iron and can act as a mitochondrial iron chaperone to transport Fe(II) to ferrochelatase and ISU proteins within the heme and iron–sulfur cluster biosynthetic pathways, respectively. We have determined the solution structure of apo yeast frataxin to provide a structural basis of how frataxin binds and donates iron to the ferrochelatase. While the protein's α–β-sandwich structural motif is similar to that observed for human and bacterial frataxins, the yeast structure presented in this report includes the full N-terminus observed for the mature processed protein found within the mitochondrion. In addition, NMR spectroscopy was used to identify frataxin amino acids that are perturbed by the presence of iron. Conserved acidic residues in the helix 1–strand 1 protein region undergo amide chemical shift changes in the presence of Fe(II), indicating a possible iron-binding site on frataxin. NMR spectroscopy was further used to identify the intermolecular binding interface between ferrochelatase and frataxin. Ferrochelatase appears to bind to frataxin's helical plane in a manner that includes its iron-binding interface. PMID:15610019

  3. Solution structures of 1:1 complexes of oxyphenonium bromide with beta- and gamma-cyclodextrins.

    PubMed

    Funasaki, Noriaki; Sumiyoshi, Tomoko; Ishikawa, Seiji; Neya, Saburo

    2004-01-01

    The solution structures of complexes of oxyphenonium bromide (OB) with beta- and gamma-cyclodextrins (beta- and gamma-CDs, respectively) in deuterium oxide have been investigated by 500 MHz proton NMR spectroscopy and molecular mechanics calculations. The chemical shifts induced by complex formation provide the 1:1 binding constants and the chemical shift variations, DeltadeltaOB-CD, with complexation for the protons of OB and the CDs. The observed binding constants are very close to those obtained by other methods and are in the following order: beta-CD > gamma-CD > alpha-CD. Initial structures of the complexes are constructed on the basis of the ROESY spectra and the DeltadeltaOB-CD values and are optimized by molecular mechanics calculations. The intermolecular distances between the protons of OB and CD calculated for these structures are well-correlated with the observed ROESY intensities. The cyclohexyl group of OB penetrates deeply into a beta-CD cavity, and the phenyl group is close to the wide rim of the cavity. The phenyl and cyclohexyl groups of OB are both incorporated into a gamma-CD cavity. Furthermore, these structures of the complexes are consistent with the suppression of bitter taste and basic hydrolysis of OB by CDs and the polarity of binding sites of OB. PMID:15832513

  4. Atomically resolved three-dimensional structures of electrolyte aqueous solutions near a solid surface

    PubMed Central

    Martin-Jimenez, Daniel; Chacon, Enrique; Tarazona, Pedro; Garcia, Ricardo

    2016-01-01

    Interfacial liquid layers play a central role in a variety of phenomena ranging from friction to molecular recognition. Liquids near a solid surface form an interfacial layer where the molecular structure is different from that of the bulk. Here we report atomic resolution three-dimensional images of electrolyte solutions near a mica surface that demonstrate the existence of three types of interfacial structures. At low concentrations (0.01–1 M), cations are adsorbed onto the mica. The cation layer is topped by a few hydration layers. At higher concentrations, the interfacial layer extends several nanometres into the liquid. It involves the alternation of cation and anion planes. Fluid Density Functional calculations show that water molecules are a critical factor for stabilizing the structure of the interfacial layer. The interfacial layer stabilizes a crystal-like structure compatible with liquid-like ion and solvent mobilities. At saturation, some ions precipitate and small crystals are formed on the mica. PMID:27416784

  5. Solution structure of a two-repeat fragment of major vault protein.

    PubMed

    Kozlov, Guennadi; Vavelyuk, Olga; Minailiuc, Ovidiu; Banville, Denis; Gehring, Kalle; Ekiel, Irena

    2006-02-17

    Major vault protein (MVP) is the main constituent of vaults, large ribonucleoprotein particles implicated in resistance to cancer therapy and correlated with poor survival prognosis. Here, we report the structure of the main repeat element in human MVP. The approximately 55 amino acid residue MVP domain has a unique, novel fold that consists of a three-stranded antiparallel beta-sheet. The solution NMR structure of a two-domain fragment reveals the interdomain contacts and relative orientations of the two MVP domains. We use these results to model the assembly of 672 MVP domains from 96 MVP molecules into the ribs of the 13MDa vault structure. The unique features include a thin, skin-like structure with polar residues on both the cytoplasmic and internal surface, and a pole-to-pole arrangement of MVP molecules. These studies provide a starting point for understanding the self-assembly of MVP into vaults and their interactions with other proteins. Chemical shift perturbation studies identified the binding site of vault poly(ADP-ribose) polymerase, another component of vault particles, indicating that MVP domains form a new class of interaction-mediating modules. PMID:16373071

  6. Atomically resolved three-dimensional structures of electrolyte aqueous solutions near a solid surface.

    PubMed

    Martin-Jimenez, Daniel; Chacon, Enrique; Tarazona, Pedro; Garcia, Ricardo

    2016-01-01

    Interfacial liquid layers play a central role in a variety of phenomena ranging from friction to molecular recognition. Liquids near a solid surface form an interfacial layer where the molecular structure is different from that of the bulk. Here we report atomic resolution three-dimensional images of electrolyte solutions near a mica surface that demonstrate the existence of three types of interfacial structures. At low concentrations (0.01-1 M), cations are adsorbed onto the mica. The cation layer is topped by a few hydration layers. At higher concentrations, the interfacial layer extends several nanometres into the liquid. It involves the alternation of cation and anion planes. Fluid Density Functional calculations show that water molecules are a critical factor for stabilizing the structure of the interfacial layer. The interfacial layer stabilizes a crystal-like structure compatible with liquid-like ion and solvent mobilities. At saturation, some ions precipitate and small crystals are formed on the mica. PMID:27416784

  7. Solution structure of the PWWP domain of the hepatoma-derived growth factor family

    PubMed Central

    Nameki, Nobukazu; Tochio, Naoya; Koshiba, Seizo; Inoue, Makoto; Yabuki, Takashi; Aoki, Masaaki; Seki, Eiko; Matsuda, Takayoshi; Fujikura, Yukiko; Saito, Miyuki; Ikari, Masaomi; Watanabe, Megumi; Terada, Takaho; Shirouzu, Mikako; Yoshida, Mayumi; Hirota, Hiroshi; Tanaka, Akiko; Hayashizaki, Yoshihide; Güntert, Peter; Kigawa, Takanori; Yokoyama, Shigeyuki

    2005-01-01

    Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins. In this study, we determined the solution structure of the PWWP domain of HDGF-related protein-3 (HRP-3) by NMR spectroscopy. The structure consists of a five-stranded β-barrel with a PWWP-specific long loop connecting β2 and β3 (PR-loop), followed by a helical region including two α-helices. Its structure was found to have a characteristic solvent-exposed hydrophobic cavity, which is composed of an abundance of aromatic residues in the β1/β2 loop (β-β arch) and the β3/β4 loop. A similar ligand binding cavity occurs at the corresponding position in the Tudor, chromo, and MBT domains, which have structural and probable evolutionary relationships with PWWP domains. These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity. PMID:15689505

  8. Cryogenic Electron Microscopy Studies: Structure and Formation of Self-assembled Nanostructures in Solution

    NASA Astrophysics Data System (ADS)

    Lee, Han Seung

    Cryogenic electron microscopy (Cryo-EM) techniques are among the most powerful to characterize self-assembling soft materials (colloids, polymers, and microemulsions, etc.) at the nanometer scale, without any need for implicit models or assumptions about the structure. We can even visualize structure under dynamic conditions, capturing each stage of development. In this thesis, cryo-EM has been used to investigate the formation and structure of a variety of self-assembling soft materials. Visualization is complemented by small angle X-ray scattering (SAXS), dynamic light scattering, and conductivity measurements. In each case, cryo-EM provides new insights, not otherwise available, into the nanostructure development. Self-assembly phenomena at the molecular level are critical to the performance of tremendous number of applied systems ranging from personal care products to industrial products. To evaluate these self-assembled materials, multiple characterization techniques are required. We investigated aggregation behavior of cesium dodecyl sulfate (CsDS) ionic surfactant in aqueous solution. Coupled with the real space data from cryogenic transmission electron microscopy (Cryo-TEM) and the inverse space data from SAXS, the experimental result of CsDS in aqueous solution gave a new insight in CsDS micellar structures and their development as a function of concentration. Cryo-TEM showed the presence of the liquid-like hydrocarbon core in the CsDS micelles and relatively thick shell structures at a low CsDS concentration. The core-shell sphere structure micelle shifted to core-shell cylindrical micelle structure at high concentration. The morphology and structure of paclitaxel silicate (PTX) prodrug, encapsulated with amphiphilic poly(ethylene glycol)-b-poly(lactic-co-glycolic acid) diblock copolymers were studied. The six different silicate PTX prodrug candidates were characterized with cryo-TEM. Direct imaging with cryo-TEM illustrated structure of prodrug

  9. Nano-Structure of PVME in a Good Solvent

    NASA Astrophysics Data System (ADS)

    Sukumaran, Sathish; Beaucage, Gregory

    1998-03-01

    Poly(vinylmethylether) (PVME) has been widely studied in blends with polystyrene (PS) as a standard example of an LCST blend. Despite the wide study of this system using theoretical approaches based on assumptions of Gaussian scaling and constant persistence length, a detailed analysis of scattering data from this system at high-q indicates that unusual structural and non-Gaussian scaling features dominate at least the PVME part of this system. In order to understand these structural features, aqueous (D2O) solutions of PVME at variable concentration and temperature were studied using small-angle neutron scattering at Argonne National Laboratories SAND facility. PVME displays LCST behavior in water (parallel to its phase behavior in blends with PS) with a critical temperature close to room temperature. In these simple solution studies unusual structural features were observed for PVME. The 'persistence length' was strongly dependent on concentration as well as temperature. In approach to the critical point the increase in zero-angle scattering can be structurally modeled with chain growth due to secondary associations. The structural features observed can be explained in terms of self-associations between PVME units. Extrapolation of the phenomena seen in solution can be made to understand the structural features seen in polymer blends.

  10. Solution structure of the isolated histone H2A-H2B heterodimer

    PubMed Central

    Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi

    2016-01-01

    During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1–β1–α2–β2–α3–αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {1H}-15N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27–34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506

  11. Solution structure of the isolated histone H2A-H2B heterodimer.

    PubMed

    Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-Ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi

    2016-01-01

    During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1-β1-α2-β2-α3-αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {(1)H}-(15)N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27-34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506

  12. Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

    SciTech Connect

    Lee, A L

    1996-05-01

    Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the {delta}-Al-{var_epsilon} activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a {beta}{alpha}{beta}-{beta}{alpha}{beta} pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel {beta}-sheet. In addition {sup 15}N T{sub 1}, T{sub 2}, and {sup 15}N/{sup 1}H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone {sup 1}H, {sup 13}C, and {sup 15}N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and {sup 15}N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

  13. Solution structure of telomere binding domain of AtTRB2 derived from Arabidopsis thaliana

    SciTech Connect

    Yun, Ji-Hye; Lee, Won Kyung; Kim, Heeyoun; Kim, Eunhee; Cheong, Chaejoon; Cho, Myeon Haeng; Lee, Weontae

    2014-09-26

    Highlights: • We have determined solution structure of Myb domain of AtTRB2. • The Myb domain of AtTRB2 is located in the N-terminal region. • The Myb domain of AtTRB2 binds to plant telomeric DNA without fourth helix. • Helix 2 and 3 of the Myb domain of AtTRB2 are involved in DNA recognition. • AtTRB2 is a novel protein distinguished from other known plant TBP. - Abstract: Telomere homeostasis is regulated by telomere-associated proteins, and the Myb domain is well conserved for telomere binding. AtTRB2 is a member of the SMH (Single-Myb-Histone)-like family in Arabidopsis thaliana, having an N-terminal Myb domain, which is responsible for DNA binding. The Myb domain of AtTRB2 contains three α-helices and loops for DNA binding, which is unusual given that other plant telomere-binding proteins have an additional fourth helix that is essential for DNA binding. To understand the structural role for telomeric DNA binding of AtTRB2, we determined the solution structure of the Myb domain of AtTRB2 (AtTRB2{sub 1–64}) using nuclear magnetic resonance (NMR) spectroscopy. In addition, the inter-molecular interaction between AtTRB2{sub 1–64} and telomeric DNA has been characterized by the electrophoretic mobility shift assay (EMSA) and NMR titration analyses for both plant (TTTAGGG)n and human (TTAGGG)n telomere sequences. Data revealed that Trp28, Arg29, and Val47 residues located in Helix 2 and Helix 3 are crucial for DNA binding, which are well conserved among other plant telomere binding proteins. We concluded that although AtTRB2 is devoid of the additional fourth helix in the Myb-extension domain, it is able to bind to plant telomeric repeat sequences as well as human telomeric repeat sequences.

  14. Multiple solution of linear algebraic systems by an iterative method with recomputed preconditioner in the analysis of microstrip structures

    NASA Astrophysics Data System (ADS)

    Ahunov, Roman R.; Kuksenko, Sergey P.; Gazizov, Talgat R.

    2016-06-01

    A multiple solution of linear algebraic systems with dense matrix by iterative methods is considered. To accelerate the process, the recomputing of the preconditioning matrix is used. A priory condition of the recomputing based on change of the arithmetic mean of the current solution time during the multiple solution is proposed. To confirm the effectiveness of the proposed approach, the numerical experiments using iterative methods BiCGStab and CGS for four different sets of matrices on two examples of microstrip structures are carried out. For solution of 100 linear systems the acceleration up to 1.6 times, compared to the approach without recomputing, is obtained.

  15. Evaluation of solution procedures for material and/or geometrically nonlinear structural analysis by the direct stiffness method.

    NASA Technical Reports Server (NTRS)

    Stricklin, J. A.; Haisler, W. E.; Von Riesemann, W. A.

    1972-01-01

    This paper presents an assessment of the solution procedures available for the analysis of inelastic and/or large deflection structural behavior. A literature survey is given which summarized the contribution of other researchers in the analysis of structural problems exhibiting material nonlinearities and combined geometric-material nonlinearities. Attention is focused at evaluating the available computation and solution techniques. Each of the solution techniques is developed from a common equation of equilibrium in terms of pseudo forces. The solution procedures are applied to circular plates and shells of revolution in an attempt to compare and evaluate each with respect to computational accuracy, economy, and efficiency. Based on the numerical studies, observations and comments are made with regard to the accuracy and economy of each solution technique.

  16. Solution Structure of the Pseudomonas putida protein PpPutA45 and its DNA Complex

    PubMed Central

    Halouska, Steven; Zhou, Yuzhen; Becker, Donald F.; Powers, Robert

    2008-01-01

    Proline utilization A (PutA) is a membrane associated multifunctional enzyme that catalyzes the oxidation of proline to glutamate in a two step process. In certain Gram-negative bacteria such as Pseudomonas putida, PutA also acts as an auto repressor in the cytoplasm when an insufficient concentration of proline is available. Here the N-terminal residues 1–45 of PutA from P. putida (PpPutA45), are shown to be responsible for DNA binding and dimerization. The solution structure of PpPutA45 was determined using NMR methods, where the protein is shown to be a symmetrical homodimer (12 kDa) consisting of two ribbon-helix-helix (RHH) structures. DNA sequence recognition by PpPutA45 was determined using DNA gel mobility shift assays and NMR chemical shift perturbations. PpPutA45 was shown to bind a 14 base-pair DNA oligomer (5′-GCGGTTGCACCTTT-3′). A model of the PpPutA45-DNA oligomer complex was generated using Haddock 2.1. The antiparallel β-sheet that results from PpPutA45 dimerization serves as the DNA recognition binding site by inserting into the DNA major groove. The dimeric core of four α-helices provides a structural scaffold for the β-sheet from which residues Thr5, Gly7, and Lys9 make sequence specific contacts with the DNA. The structural model implies flexibility of Lys9 which can either make hydrogen bond contacts with guanine or thymine. The high sequence and structure conservation of the PutA RHH domain suggest interdomain interactions play an important role in the evolution of the protein. PMID:18767154

  17. Solution Structure of Inhibitor-Free Human Metalloelastase (MMP-12) Indicates an Internal Conformational Adjustment

    PubMed Central

    Bhaskaran, Rajagopalan; Palmier, Mark O.; Bagegni, Nusayba A.; Liang, Xiangyang; Van Doren, Steven R.

    2007-01-01

    Macrophage metalloelastase or MMP-12 appears to exacerbate atherosclerosis, emphysema, aortic aneurysm, rheumatoid arthritis, and inflammatory bowel disease. An inactivating E219A mutation, validated by crystallography and NMR spectra, prevents autolysis of MMP-12 and allowed us to determine its NMR structure without an inhibitor. The structural ensemble of the catalytic domain without inhibitor is based on 2813 NOEs and has an average RMSD to the mean of 0.25 Å for the backbone and 0.61 Å for all heavy atoms for residues Trp109 - Gly263. Compared to crystal structures of MMP-12, helix B (hB) at the active site is unexpectedly more deeply recessed under the beta-sheet. This opens a pocket between hB and β-strand sIV in the active site cleft. Both hB and an internal cavity are shifted toward β-strands sI and sIII and hA on the back side of the protease. About 25 internal NOE contacts distinguish the inhibitor-free solution structure and indicate hB’s greater depth and proximity to the sheet and hA. Line broadening and multiplicity of amide proton NMR peaks from hB are consistent with hB undergoing slow conformational exchange among subtly different environments. Inhibitor binding-induced perturbations of NMR spectra of MMP-1 and -3 map to similar locations across MMP-12 and encompassing its internal conformational adjustments. Evolutionary trace analysis suggests a functionally important network of residues that encompasses most of the locations that adjust in conformation, including 18 residues with NOE contacts unique to inhibitor-free MMP-12. The conformational change, sequence analysis, and inhibitor perturbations of NMR spectra agree in the network they identify between structural scaffold and active site of MMPs. PMID:17997411

  18. Insight into the Structure of Light Harvesting Complex II and its Stabilization in Detergent Solution

    SciTech Connect

    Cardoso, Mateus B; Smolensky, Dmitriy; Heller, William T; O'Neill, Hugh Michael

    2009-01-01

    The structure of spinach light-harvesting complex II (LHC II), stabilized in a solution of the detergent n-octyl-{beta}-d-glucoside (BOG), was investigated by small-angle neutron scattering (SANS). Physicochemical characterization of the isolated complex indicated that it was pure (>95%) and also in its native trimeric state. SANS with contrast variation was used to investigate the properties of the protein-detergent complex at three different H{sub 2}O/D{sub 2}O contrast match points, enabling the scattering properties of the protein and detergent to be investigated independently. The topological shape of LHC II, determined using ab initio shape restoration methods from the SANS data at the contrast match point of BOG, was consistent with the X-ray crystallographic structure of LHC II (Liu et al. Nature 2004 428, 287-292). The interactions of the protein and detergent were investigated at the contrast match point for the protein and also in 100% D{sub 2}O. The data suggested that BOG micelle structure was altered by its interaction with LHC II, but large aggregate structures were not formed. Indirect Fourier transform analysis of the LHC II/BOG scattering curves showed that the increase in the maximum dimension of the protein-detergent complex was consistent with the presence of a monolayer of detergent surrounding the protein. A model of the LHC II/BOG complex was generated to interpret the measurements made in 100% D{sub 2}O. This model adequately reproduced the overall size of the LHC II/BOG complex, but demonstrated that the detergent does not have a highly regular shape that surrounds the hydrophobic periphery of LHC II. In addition to demonstrating that natively structured LHC II can be produced for functional characterization and for use in artificial solar energy applications, the analysis and modeling approaches described here can be used for characterizing detergent-associated {alpha}-helical transmembrane proteins.

  19. Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

    PubMed Central

    Anfinrud, Philip

    2010-01-01

    We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02–2.5 Å-1, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 Å), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 Å3 volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume ∼2 Å3 larger than MbCO within ∼10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them. PMID:20406909

  20. NMR solution structure of the theta subunit of DNA polymerase III from Escherichia coli.

    PubMed Central

    Keniry, M. A.; Berthon, H. A.; Yang, J. Y.; Miles, C. S.; Dixon, N. E.

    2000-01-01

    The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits (alpha, epsilon, and theta). The theta subunit is the smallest, but the least understood of the three. As a first step in a program aimed at understanding its function, the structure of the theta subunit has been determined by triple-resonance multidimensional NMR spectroscopy. Although only a small protein, theta was difficult to assign fully because approximately one-third of the protein is unstructured, and some sections of the remaining structured parts undergo intermediate intramolecular exchange. The secondary structure was deduced from the characteristic nuclear Overhauser effect patterns, the 3J(HN alpha) coupling constants and the consensus chemical shift index. The C-terminal third of the protein, which has many charged and hydrophilic amino acid residues, has no well-defined secondary structure and exists in a highly dynamic state. The N-terminal two-thirds has three helical segments (Gln10-Asp19, Glu38-Glu43, and His47-Glu54), one short extended segment (Pro34-Ala37), and a long loop (Ala20-Glu29), of which part may undergo intermediate conformational exchange. Solution of the three-dimensional structure by NMR techniques revealed that the helices fold in such a way that the surface of theta is bipolar, with one face of the protein containing most of the acidic residues and the other face containing most of the long chain basic residues. Preliminary chemical shift mapping experiments with a domain of the epsilon subunit have identified a loop region (Ala20-Glu29) in theta as the site of association with epsilon. PMID:10794414

  1. The Solution Structure of Heparan Sulfate Differs from That of Heparin

    PubMed Central

    Khan, Sanaullah; Fung, Ka Wai; Rodriguez, Elizabeth; Patel, Rima; Gor, Jayesh; Mulloy, Barbara; Perkins, Stephen J.

    2013-01-01

    The highly sulfated polysaccharides heparin and heparan sulfate (HS) play key roles in the regulation of physiological and pathophysiological processes. Despite its importance, no molecular structures of free HS have been reported up to now. By combining analytical ultracentrifugation, small angle x-ray scattering, and constrained scattering modeling recently used for heparin, we have analyzed the solution structures for eight purified HS fragments dp6–dp24 corresponding to the predominantly unsulfated GlcA-GlcNAc domains of heparan sulfate. Unlike heparin, the sedimentation coefficient s20,w of HS dp6–dp24 showed a small rotor speed dependence, where similar s20,w values of 0.82–1.26 S (absorbance optics) and 1.05–1.34 S (interference optics) were determined. The corresponding x-ray scattering measurements of HS dp6–dp24 gave radii of gyration RG values from 1.03 to 2.82 nm, cross-sectional radii of gyration RXS values from 0.31 to 0.65 nm, and maximum lengths L from 3.0 to 10.0 nm. These data showed that HS has a longer and more bent structure than heparin. Constrained scattering modeling starting from 5,000 to 12,000 conformationally randomized HS structures gave best fit dp6–dp24 molecular structures that were longer and more bent than their equivalents in heparin. Alternative fits were obtained for HS dp18 and dp24, indicating their higher bending and flexibility. We conclude that HS displays bent conformations that are significantly distinct from that for heparin. The difference is attributed to the different predominant monosaccharide sequence and reduced sulfation of HS, indicating that HS may interact differently with proteins compared with heparin. PMID:23921391

  2. Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

    SciTech Connect

    Cho, Hyun Sun; Dashdorj, Naranbaatar; Schotte, Friedrich; Graber, Timothy; Henning, Robert; Anfinruda, Philip

    2010-04-21

    We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02-2.5 {angstrom}{sup -1}, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 {angstrom}), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 {angstrom}{sup 3} volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume {approx}2 {angstrom}{sup 3} larger than MbCO within {approx}10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them.

  3. Elastic properties and electronic structures of Y atom solid solute supercell γ-Fe

    NASA Astrophysics Data System (ADS)

    Yang, Jian; Hou, Xiaoru; Xing, Xiaolei; Yun, Xiao; Yang, Yulin; Ren, Xuejun; Yang, Qingxiang

    2014-11-01

    Elastic properties and electronic structures of a Y atom solid solute supercell γ-Fe structure, which includes either a Y atom octahedral interstitial solid solute (Y-OISS), a Y atom tetrahedral interstitial solid solute (Y-TISS), a Y atom vertex substitutional solid solute (Y-VSSS) and a Y atom face-centered substitutional solid solute (Y-FSSS) have been calculated using a first-principles density functional theory plane-wave ultrasoft pseudopotential method, i.e. the Generalized Gradient Approximation (GGA) Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. The results indicate that, the Y-VSSS and Y-FSSS supercell γ-Fe are stable, while the Y-OISS and Y-TISS supercell γ-Fe are both unstable, especially Y-TISS. The bulk moduli of the Y-OISS, Y-TISS, Y-VSSS and Y-FSSS supercell γ-Fe are 234.72, 200.32, 262.45 and 262.56 GPa, and the shear moduli are 74.23, 52.02, 156.78 and 156.76 GPa, which shows that the directional bonding in Y-SSS supercell γ-Fe is stronger than that in Y-ISS and that the Y-ISS supercell γ-Fe is much stiff than the Y-SSS. The ratios between the shear modulus and bulk modulus of Y-OISS, Y-TISS, Y-VSSS and Y-FSSS supercell γ-Fe are 0.32, 0.26, 0.60 and 0.60, respectively, which implies that the Y-SSS supercell γ-Fe is essentially brittle and that the Y-ISS is slightly ductile. Poisson's ratio of them are 0.47, 0.38, 0.25 and 0.35, which shows that compared with Y-ISS supercell γ-Fe, the Y-SSS supercell γ-Fe has good plasticity in the investigated binary alloys. The universal elastic anisotropy indexes of the Y-OISS, Y-TISS, Y-VSSS and Y-FSSS supercell γ-Fe are 1.765, 1.205, 0.965 and 0.95, the result indicates that the anisotropy decreases in the following sequence: Y-OISS supercell γ-Fe > Y-TISS > Y-FSSS > Y-VSSS. The amounts of transferred charges (per supercell) from Fe atom to Y atom is in the order of Y-VSSS supercell γ-Fe = Y-FSSS > Y-TISS > Y-OISS, respectively, which indicates that their ionicity is Y

  4. Solution structure of the ubiquitin-binding domain in Swa2p from Saccharomyces cerevisiae.

    PubMed

    Chim, Nicholas; Gall, Walter E; Xiao, Jing; Harris, Mark P; Graham, Todd R; Krezel, Andrzej M

    2004-03-01

    The SWA2/AUX1 gene has been proposed to encode the Saccharomyces cerevisiae ortholog of mammalian auxilin. Swa2p is required for clathrin assembly/dissassembly in vivo, thereby implicating it in intracellular protein and lipid trafficking. While investigating the 287-residue N-terminal region of Swa2p, we found a single stably folded domain between residues 140 and 180. Using binding assays and structural analysis, we established this to be a ubiquitin-associated (UBA) domain, unidentified by bioinformatics of the yeast genome. We determined the solution structure of this Swa2p domain and found a characteristic three-helix UBA fold. Comparisons of structures of known UBA folds reveal that the position of the third helix is quite variable. This helix in Swa2p UBA contains a bulkier tyrosine in place of smaller residues found in other UBAs and cannot pack as close to the second helix. The molecular surface of Swa2p UBA has a mostly negative potential, with a single hydrophobic surface patch found also in the UBA domains of human protein, HHR23A. The presence of a UBA domain implicates Swa2p in novel roles involving ubiquitin and ubiquitinated substrates. We propose that Swa2p is a multifunctional protein capable of recognizing several proteins through its protein-protein recognition domains. PMID:14997574

  5. The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA

    PubMed Central

    Gully, Benjamin S.; Cowieson, Nathan; Stanley, Will A.; Shearston, Kate; Small, Ian D.; Barkan, Alice; Bond, Charles S.

    2015-01-01

    The pentatricopeptide repeat (PPR) protein family is a large family of RNA-binding proteins that is characterized by tandem arrays of a degenerate 35-amino-acid motif which form an α-solenoid structure. PPR proteins influence the editing, splicing, translation and stability of specific RNAs in mitochondria and chloroplasts. Zea mays PPR10 is amongst the best studied PPR proteins, where sequence-specific binding to two RNA transcripts, atpH and psaJ, has been demonstrated to follow a recognition code where the identity of two amino acids per repeat determines the base-specificity. A recently solved ZmPPR10:psaJ complex crystal structure suggested a homodimeric complex with considerably fewer sequence-specific protein–RNA contacts than inferred previously. Here we describe the solution structure of the ZmPPR10:atpH complex using size-exclusion chromatography-coupled synchrotron small-angle X-ray scattering (SEC-SY-SAXS). Our results support prior evidence that PPR10 binds RNA as a monomer, and that it does so in a manner that is commensurate with a canonical and predictable RNA-binding mode across much of the RNA–protein interface. PMID:25609698

  6. Studies of implicit and explicit solution techniques in transient thermal analysis of structures

    NASA Technical Reports Server (NTRS)

    Adelman, H. M.; Haftka, R. T.; Robinson, J. C.

    1982-01-01

    Studies aimed at an increase in the efficiency of calculating transient temperature fields in complex aerospace vehicle structures are reported. The advantages and disadvantages of explicit and implicit algorithms are discussed and a promising set of implicit algorithms with variable time steps, known as GEARIB, is described. Test problems, used for evaluating and comparing various algorithms, are discussed and finite element models of the configurations are described. These problems include a coarse model of the Space Shuttle wing, an insulated frame tst article, a metallic panel for a thermal protection system, and detailed models of sections of the Space Shuttle wing. Results generally indicate a preference for implicit over explicit algorithms for transient structural heat transfer problems when the governing equations are stiff (typical of many practical problems such as insulated metal structures). The effects on algorithm performance of different models of an insulated cylinder are demonstrated. The stiffness of the problem is highly sensitive to modeling details and careful modeling can reduce the stiffness of the equations to the extent that explicit methods may become the best choice. Preliminary applications of a mixed implicit-explicit algorithm and operator splitting techniques for speeding up the solution of the algebraic equations are also described.

  7. Solution structure of the potassium channel inhibitor agitoxin 2: caliper for probing channel geometry.

    PubMed Central

    Krezel, A. M.; Kasibhatla, C.; Hidalgo, P.; MacKinnon, R.; Wagner, G.

    1995-01-01

    The structure of the potassium channel blocker agitoxin 2 was solved by solution NMR methods. The structure consists of a triple-stranded antiparallel beta-sheet and a single helix covering one face of the beta-sheet. The cysteine side chains connecting the beta-sheet and the helix form the core of the molecule. One edge of the beta-sheet and the adjacent face of the helix form the interface with the Shaker K+ channel. The fold of agitoxin is homologous to the previously determined folds of scorpion venom toxins. However, agitoxin 2 differs significantly from the other channel blockers in the specificity of its interactions. This study was thus focused on a precise characterization of the surface residues at the face of the protein interacting with the Shaker K+ channel. The rigid toxin molecule can be used to estimate dimensions of the potassium channel. Surface-exposed residues, Arg24, Lys27, and Arg31 of the beta-sheet, have been identified from mutagenesis studies as functionally important for blocking the Shaker K+ channel. The sequential and spatial locations of Arg24 and Arg31 are not conserved among the homologous toxins. Knowledge on the details of the channel-binding sites of agitoxin 2 formed a basis for site-directed mutagenesis studies of the toxin and the K+ channel sequences. Observed interactions between mutated toxin and channel are being used to elucidate the channel structure and mechanisms of channel-toxin interactions. PMID:8520473

  8. Mathematical Models, Analytical Solutions and Numerical Simulations of Self-Assembled Magnetic Colloidal Structures

    NASA Astrophysics Data System (ADS)

    Piet, David L.

    Ferromagnetic microparticles suspended at the interface between immiscible liquids and energized by an external alternating magnetic field show a rich variety of self-assembled structures, from linear snakes to radial asters, elongated wires to spinning chains to less dense clouds of particles called snails. In order to obtain insight into the fundamental physical mechanisms and the overall balance of forces governing self-assembly, we develop a modeling approach based on analytical solutions of the time-averaged Navier-Stokes equations. These analytical expressions for the self-consistent hydrodynamic flows are then employed to modify effective interactions between the particles, which in turn are formulated in terms of the time-averaged quantities. Our method allows effective computational verification of the mechanisms of self-assembly and leads to a testable predictions on the transitions between various self-assembled patterns. In one set of experiments, it was observed that viscosity is the primary driving force that determines whether asters or snakes appear at steady state. In the second set of experiments where hydrodynamics are less critical, the amplitude and frequency of the applied magnetic field determine whether wires, spinners or snails will appear. The ability to better understand what drives self-assembly and how to control which dynamic structures appear is necessary for further development of such structures and their applications.

  9. Solution structure of villin 14T, a domain conserved among actin-severing proteins.

    PubMed Central

    Markus, M. A.; Nakayama, T.; Matsudaira, P.; Wagner, G.

    1994-01-01

    The solution structure of the N-terminal domain of the actin-severing protein villin has been determined by multidimensional heteronuclear resonance spectroscopy. Villin is a member of a family of actin-severing proteins that regulate the organization of actin in the eukaryotic cytoskeleton. Members of this family are built from 3 or 6 homologous repeats of a structural domain of approximately 130 amino acids that is unrelated to any previously known structure. The N-terminal domain of villin (14T) contains a central beta-sheet with 4 antiparallel strands and a fifth parallel strand at one edge. This sheet is sandwiched between 2 helices on one side and a 2-stranded parallel beta-sheet with another helix on the other side. The strongly conserved sequence characteristic of the protein family corresponds to internal hydrophobic residues. Calcium titration experiments suggest that there are 2 binding sites for Ca2+, a stronger site near the N-terminal end of the longest helix, with a Kd of 1.8 +/- 0.4 mM, and a weaker site near the C-terminal end of the same helix, with a Kd of 11 +/- 2 mM. Mutational and biochemical studies of this domain in several members of the family suggest that the actin monomer binding site is near the parallel strand at the edge of the central beta-sheet. PMID:8142900

  10. Interlayer structure in YBCO-coated conductors prepared by chemical solution deposition

    NASA Astrophysics Data System (ADS)

    Molina-Luna, Leopoldo; Egoavil, Ricardo; Turner, Stuart; Thersleff, Thomas; Verbeeck, Jo; Holzapfel, Bernhard; Eibl, Oliver; Van Tendeloo, Gustaaf

    2013-07-01

    The functionality of YBa2Cu3O7-δ (YBCO)-coated conductor technology depends on the reliability and microstructural properties of a given tape or wire architecture. Particularly, the interface to the metal tape is of interest since it determines the adhesion, mechanical stability of the film and thermal contact of the film to the substrate. A trifluoroacetate (TFA)—metal organic deposition (MOD) prepared YBCO film deposited on a chemical solution-derived buffer layer architecture based on CeO2/La2Zr2O7 and grown on a flexible Ni5 at.%W substrate with a {100}<001> biaxial texture was investigated. The YBCO film had a thickness was 440 nm and a jc of 1.02 MA cm-2 was determined at 77 K and zero external field. We present a sub-nanoscale analysis of a fully processed solution-derived YBCO-coated conductor by aberration-corrected scanning transmission electron microscopy (STEM) combined with electron energy-loss spectroscopy (EELS). For the first time, structural and chemical analysis of the valence has been carried out on the sub-nm scale. Intermixing of Ni, La, Ce, O and Ba takes place at these interfaces and gives rise to nanometer-sized interlayers which are a by-product of the sequential annealing process. Two distinct interfacial regions were analyzed in detail: (i) the YBCO/CeO2/La2Zr2O7 region (10 nm interlayer) and (ii) the La2Zr2O7/Ni-5 at.%W substrate interface region (20 nm NiO). This is of particular significance for the functionality of these YBCO-coated conductor architectures grown by chemical solution deposition.

  11. Structural effects of anions and cations on the aggregation behavior of ionic liquids in aqueous solutions.

    PubMed

    Wang, Huiyong; Wang, Jianji; Zhang, Shibiao; Xuan, Xiaopeng

    2008-12-25

    The formation of ionic liquids aggregates in aqueous solution is of great importance to the future applications of ionic liquids. In this work, aggregation behavior of 1-alkyl-3-methylimidazolium salts [C8mim]X (X = Cl, Br, [NO3], [CH3COO], [CF3COO], [CF3SO3], and [ClO4]), 1-octyl-4-methylpyridinium bromide (4m-[C8pyr]Br), and 1-methyl-1-octylpyrrolidinium ([C8mpyrr]Br) has been investigated in aqueous solutions by conductivity, volume, fluorescence, dynamic light scattering, and transmission electron microscopy. The critical aggregation concentration (CAC), ionization degree of the aggregates alpha, the standard Gibbs energy of aggregation deltaG(m)degrees, the average aggregation number N, the apparent molar volumes at critical aggregation concentration V(phi,CAC), the apparent molar volumes in aggregation phase V(phi)mic, and the change of the apparent molar volumes upon aggregation deltaV(phi,m), have been derived from the experimental data for these ionic liquids. It is found that both nature of the anions and ring type of the cations significantly affect the aggregation in aqueous solution. The anionic effect basically follows the Hofmeister series, and the ability of anionic hydration is predominant for the aggregation behavior of the ionic liquids. Hydrophobicity and steric hindrance of the cations as well as binding strength of the cations with the anions are suggested to play important roles in the aggregation of [C8mim]Br, 4m-[C8pyr]Br, and [C8mpyrr]Br. The investigated ILs were found to form spherical aggregates. Structures of anions and cations have very weak effects on the morphology, but they do affect the aggregate sizes. PMID:19367863

  12. Structure and dynamics of hyaluronic acid semidilute solutions: A dielectric spectroscopy study

    NASA Astrophysics Data System (ADS)

    Vuletić, T.; Dolanski Babić, S.; Ivek, T.; Grgičin, D.; Tomić, S.; Podgornik, R.

    2010-07-01

    Dielectric spectroscopy is used to investigate fundamental length scales describing the structure of hyaluronic acid sodium salt (Na-HA) semidilute aqueous solutions. In salt-free regime, the length scale of the relaxation mode detected in MHz range scales with HA concentration as cHA-0.5 and corresponds to the de Gennes-Pfeuty-Dobrynin correlation length of polyelectrolytes in semidilute solution. The same scaling was observed for the case of long, genomic DNA. Conversely, the length scale of the mode detected in kilohertz range also varies with HA concentration as cHA-0.5 which differs from the case of DNA (cDNA-0.25) . The observed behavior suggests that the relaxation in the kilohertz range reveals the de Gennes-Dobrynin renormalized Debye screening length, and not the average size of the chain, as the pertinent length scale. Similarly, with increasing added salt the electrostatic contribution to the HA persistence length is observed to scale as the Debye length, contrary to scaling pertinent to the Odijk-Skolnick-Fixman electrostatic persistence length observed in the case of DNA. We argue that the observed features of the kilohertz range relaxation are due to much weaker electrostatic interactions that lead to the absence of Manning condensation as well as a rather high flexibility of HA as compared to DNA.

  13. Structure and properties of alizarin complex formed with alkali metal hydroxides in methanol solution.

    PubMed

    Jeliński, Tomasz; Cysewski, Piotr

    2016-06-01

    Quantum chemical computations were used for prediction of the structure and color of alizarin complex with alkali metal hydroxides in methanolic solutions. The color prediction relying on the single Gaussian-like band once again proved the usefulness of the PBE0 density functional due to the observed smallest color difference between computed and experimentally derived values. It was found that the alkali metal hydroxide molecules can bind to the two oxygen atoms of both hydroxyl groups of alizarin or to one of these atoms and the oxygen atom from the keto group in a complex with three methanol molecules. This means that two electronic transitions need to be taken into account when considering the spectra of the studied complexes. The resulting bond lengths and angles are correlated with the properties of the alkali metal atoms. The molar mass, the atomic radius, and the Pauling electronegativity of studied metals are quite accurate predictors of the geometric properties of hydroxide complexes with alizarin in methanol solution. Graphical abstract The spectra of the neutral and monoanionic form of alizarin together with color changes resulting from addition of different metal hydroxides and represented in CIE color space. PMID:27178415

  14. Exact solutions of magnetohydrodynamics for describing different structural disturbances in solar wind

    NASA Astrophysics Data System (ADS)

    Grib, S. A.; Leora, S. N.

    2016-03-01

    We use analytical methods of magnetohydrodynamics to describe the behavior of cosmic plasma. This approach makes it possible to describe different structural fields of disturbances in solar wind: shock waves, direction discontinuities, magnetic clouds and magnetic holes, and their interaction with each other and with the Earth's magnetosphere. We note that the wave problems of solar-terrestrial physics can be efficiently solved by the methods designed for solving classical problems of mathematical physics. We find that the generalized Riemann solution particularly simplifies the consideration of secondary waves in the magnetosheath and makes it possible to describe in detail the classical solutions of boundary value problems. We consider the appearance of a fast compression wave in the Earth's magnetosheath, which is reflected from the magnetosphere and can nonlinearly overturn to generate a back shock wave. We propose a new mechanism for the formation of a plateau with protons of increased density and a magnetic field trough in the magnetosheath due to slow secondary shock waves. Most of our findings are confirmed by direct observations conducted on spacecrafts (WIND, ACE, Geotail, Voyager-2, SDO and others).

  15. Metal–5-Fluorouracil–Histamine Complexes: Solution, Structural, and Antitumour Studies

    PubMed Central

    Tyagi, Sadhna; Singh, Sukh Mahendra; Gencaslan, Sujan; Sheldrick, W. S.

    2002-01-01

    Solution studies were performed pH-metrically to study the interaction of Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) metal ions with 5-fluorouracil (5FU) and histamine (Hm) separately (binary) and in the presence of each other (ternary) at 25±0.1 °C temperature and a constant ionic strength of 0.1 M NaNO3 in aqueous solution. The ternary complexes have been found to be more stable than the corresponding binary complexes as shown by the positive value of ΔlogK. The species distribution curves have been obtained using the computer programme BEST. On the basis of species distribution results, efforts were also made to prepare some mixed complexes of Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) ions by performing the reaction of their metal nitrates, 5FU and Hm in aqueous ethanol medium at suitable pH. The isolated solid complexes were characterized by different physico-chemical method in order to suggest the possible binding site of the ligands and the structure of the resultant complexes. All these complexes were checked for their antitumour activity by injecting in Dalton's lymphoma (DL) and Sarcoma-180 (S-180) bearing C3H/He mice. The results indicate that some complexes have good antitumour activity both in vivo and in vitro. PMID:18476016

  16. The mechanics of delamination in fiber-reinforced composite materials. I - Stress singularities and solution structure

    NASA Technical Reports Server (NTRS)

    Wang, S. S.; Choi, I.

    1983-01-01

    The fundamental mechanics of delamination in fiber composite laminates is studied. Mathematical formulation of the problem is based on laminate anisotropic elasticity theory and interlaminar fracture mechanics concepts. Stress singularities and complete solution structures associated with general composite delaminations are determined. For a fully open delamination with traction-free surfaces, oscillatory stress singularities always appear, leading to physically inadmissible field solutions. A refined model is introduced by considering a partially closed delamination with crack surfaces in finite-length contact. Stress singularities associated with a partially closed delamination having frictional crack-surface contact are determined, and are found to be different from the inverse square-root one of the frictionless-contact case. In the case of a delamination with very small area of crack closure, a simplified model having a square-root stress singularity is employed by taking the limit of the partially closed delamination. The possible presence of logarithmic-type stress singularity is examined; no logarithmic singularity of any kind is found in the composite delamination problem. Numerical examples of dominant stress singularities are shown for delaminations having crack-tip closure with different frictional coefficients between general (1) and (2) graphite-epoxy composites. Previously announced in STAR as N84-13221

  17. Structural Dynamics of Star-Shaped Weak Polyelectrolytes in Dilute Aqueous Solution

    NASA Astrophysics Data System (ADS)

    Qu, Chen; Zhu, Y. Elaine

    Weak polyelectrolyte (PE) bearing tunable charges along their backbones show great potential as ``smart'' polymer materials for diverse applications from drug delivery to energy storage. With the introduction of branched topology, the local counterion distribution in the vicinity to the polyelectrolyte segments becomes highly inhomogeneous. To experimentally investigate the interplay between structural dynamics and local electric environment of a branched polyelectrolyte, in this work we custom synthesized star-shaped poly(2-vinylpyridine) (P2VP) using reversible addition fragmentation chain transfer (RAFT) polymerization and labeled P2VP stars with pH-sensitive fluorophore precisely either in the center or periphery. By employing fluorescence correlation spectroscopy (FCS) with photon counts histogram (PCH) analysis, we observed gradual stretched-to-collapses conformational transition with increasing solution pH for both P2VP stars of different fluorophore labeling locations. However, the measured local pH, or local proton concentration, shows strong dependence of the fluorophore labeling locations. Higher electric potential yet lower ionization degree was observed in the core of P2VP star than that in the periphery. Ongoing work is carried out to examine the scaling behaviors of P2VP star sizes with varied number of arms, arm lengths and counterion concentrations in dilute aqueous solutions.

  18. Controlling the Electronic Structures of Perovskite Oxynitrides and their Solid Solutions for Photocatalysis.

    PubMed

    Umezawa, Naoto; Janotti, Anderson

    2016-05-10

    Band-gap engineering of oxide materials is of great interest for optoelectronics, photovoltaics, and photocatalysis applications. In this study, electronic structures of perovskite oxynitrides, LaTiO2 N and SrNbO2 N, and solid solutions, (SrTiO3 )1-x (LaTiO2 N)x and (SrTiO3 )1-x (SrNbO2 N)x , are investigated using hybrid density functional calculations. Band gaps of LaTiO2 N and SrNbO2 N are much smaller than that of SrTiO3 owing to the formation of a N 2p band, which is higher in energy than the O 2p band. The valence- and conduction-band offsets of SrTiO3 /LaTiO2 N and SrTiO3 /SrNbO2 N are computed, and the adequacy for H2 evolution is analyzed by comparing the positions of the band edges with respect to the standard hydrogen electrode (SHE). The band gap of (SrTiO3 )1-x (LaTiO2 N)x and (SrTiO3 )1-x (SrNbO2 N)x solid solutions are also discussed. PMID:27072042

  19. Crystal structures and conformational behavior in solution of two isomeric dicyanobiphenyls

    NASA Astrophysics Data System (ADS)

    Savicheva, Elisaveta A.; Fonari, Marina S.; Boyarskaya, Irina А.; Boyarskiy, Vadim P.

    2011-07-01

    Two dicyanobiphenyls, 3-phenylphtalodinitrile ( 1) and 4-phenylphtalodinitrile ( 2) were synthesized by Pd(II)-catalyzed cyanation of relevant dichlorobiphenyls (РСВ5 and PCB12), and their structures were determined by single crystal X-ray diffraction. The dihedral angle between the phenyl rings is equal to 51.50° in o-substituted molecule 1 and 30.76° in 2. To rationalize the conformational differences between two molecules the optimized geometries and potential energy curves (relative energy vs. torsion angle) were calculated at the B3LYP/6-31+G(d) level of theory using the PCM solvation model. The electronic properties of substituents were found to affect slightly on the conformational characteristics of the substituted biphenyls in solution.

  20. Solution State Structure Determination of Silicate Oligomers by 29Si NMR Spectroscopy and Molecular Modeling

    SciTech Connect

    Cho, Herman M.; Felmy, Andrew R.; Craciun, Raluca; Keenum, Johnathan P.; Shah, Neil K.; Dixon, David A.

    2006-02-22

    Evidence for nine new solution state silicate oligomers has been discovered by 29Si NMR homonuclear correlation experiments of 29Si-enriched samples. In addition to enhancing signal sensitivity, the isotopic enrichment increases the probability of the 29Si–29Si two-bond scalar couplings that are necessary for the observation of internuclear correlations in 2-D experiments. The proposed assignments are validated by comparisons of experimental and simulated crosspeaks obtained with high digital resolution. The internuclear connectivity indicated by the NMR data suggests that several of these oligomers can have multiple stereoisomers, including conformers and/or diastereomers. The stability of these oligomers and their possible stereoisomers have been investigated by electronic structure calculations.

  1. Solution state structure determination of silicate oligomers by 29SI NMR spectroscopy and molecular modeling.

    PubMed

    Cho, Herman; Felmy, Andrew R; Craciun, Raluca; Keenum, J Patrick; Shah, Neil; Dixon, David A

    2006-02-22

    Evidence for nine new solution state silicate oligomers has been discovered by (29)Si NMR homonuclear correlation experiments of (29)Si-enriched samples. In addition to enhancing signal sensitivity, the isotopic enrichment increases the probability of the (29)Si-(29)Si two-bond scalar couplings that are necessary for the observation of internuclear correlations in 2-D experiments. The proposed assignments are validated by comparisons of experimental and simulated cross-peaks obtained with high digital resolution. The internuclear connectivity indicated by the NMR data suggests that several of these oligomers can have multiple stereoisomers, including conformers and/or diastereomers. The stabilities of these oligomers and their possible stereoisomers have been investigated by electronic structure calculations. PMID:16478188

  2. Influence of Lithium Solutes on Double-Layer Structure of Ionic Liquids.

    PubMed

    Smith, Alexander M; Perkin, Susan

    2015-12-01

    The ionic liquid-electrode interface has attracted much recent interest owing to its importance for development of energy storage devices; however, the important step of adding electro-active ions is not yet well understood at the molecular level. Using direct force measurements across confined electrolyte films, we study the effect of added lithium-ion solute on the double-layer structure of an ionic liquid electrolyte with molecular resolution. We find anionic clusters involving lithium can persist adjacent to the surfaces, and in many cases, this inhibits direct adsorption of lithium ions to the negative surface. Two apparently similar ionic liquid solvents show diverging properties, with one facilitating and the other preventing direct Li-ion adsorption onto the negative surface. The results have implications for the selection of ionic liquids as electrolytes in lithium-ion batteries. PMID:26580815

  3. A salt-bridge structure in solution revealed by 2D-IR spectroscopy.

    PubMed

    Huerta-Viga, Adriana; Domingos, Sérgio R; Amirjalayer, Saeed; Woutersen, Sander

    2014-08-14

    Salt bridges are important interactions for the stability of protein conformations, but up to now it has been difficult to determine salt-bridge geometries in solution. Here we characterize the spatial structure of a salt bridge between guanidinium (Gdm(+)) and acetate (Ac(-)) using two-dimensional vibrational (2D-IR) spectroscopy. We find that as a result of salt bridge formation there is a significant change in the infrared response of Gdm(+) and Ac(-), and cross peaks between them appear in the 2D-IR spectrum. From the 2D-IR spectrum we determine the relative orientation of the transition-dipole moments of the vibrational modes of Gdm(+) and Ac(-), as well as the coupling between them. PMID:24676430

  4. Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase.

    PubMed

    Van Horn, Wade D; Kim, Hak-Jun; Ellis, Charles D; Hadziselimovic, Arina; Sulistijo, Endah S; Karra, Murthy D; Tian, Changlin; Sönnichsen, Frank D; Sanders, Charles R

    2009-06-26

    Escherichia coli diacylglycerol kinase (DAGK) represents a family of integral membrane enzymes that is unrelated to all other phosphotransferases. We have determined the three-dimensional structure of the DAGK homotrimer with the use of solution nuclear magnetic resonance. The third transmembrane helix from each subunit is domain-swapped with the first and second transmembrane segments from an adjacent subunit. Each of DAGK's three active sites resembles a portico. The cornice of the portico appears to be the determinant of DAGK's lipid substrate specificity and overhangs the site of phosphoryl transfer near the water-membrane interface. Mutations to cysteine that caused severe misfolding were located in or near the active site, indicating a high degree of overlap between sites responsible for folding and for catalysis. PMID:19556511

  5. Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects.

    PubMed

    Hack, John; Grills, David C; Miller, John R; Mani, Tomoyasu

    2016-02-18

    Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent. PMID:26807492

  6. Identification of ion-pair structures in solution by vibrational stark effects

    DOE PAGESBeta

    Hack, John; Mani, Tomoyasu; Grills, David C.; Miller, John R.

    2016-01-25

    Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

  7. Monitoring Solution Structures of Peroxisome Proliferator-Activated Receptor β/δ upon Ligand Binding.

    PubMed

    Schwarz, Rico; Tänzler, Dirk; Ihling, Christian H; Sinz, Andrea

    2016-01-01

    Peroxisome proliferator-activated receptors (PPARs) have been intensively studied as drug targets to treat type 2 diabetes, lipid disorders, and metabolic syndrome. This study is part of our ongoing efforts to map conformational changes in PPARs in solution by a combination of chemical cross-linking and mass spectrometry (MS). To our best knowledge, we performed the first studies addressing solution structures of full-length PPAR-β/δ. We monitored the conformations of the ligand-binding domain (LBD) as well as full-length PPAR-β/δ upon binding of two agonists. (Photo-) cross-linking relied on (i) a variety of externally introduced amine- and carboxyl-reactive linkers and (ii) the incorporation of the photo-reactive amino acid p-benzoylphenylalanine (Bpa) into PPAR-β/δ by genetic engineering. The distances derived from cross-linking experiments allowed us to monitor conformational changes in PPAR-β/δ upon ligand binding. The cross-linking/MS approach proved highly advantageous to study nuclear receptors, such as PPARs, and revealed the interplay between DBD (DNA-binding domain) and LDB in PPAR-β/δ. Our results indicate the stabilization of a specific conformation through ligand binding in PPAR-β/δ LBD as well as full-length PPAR-β/δ. Moreover, our results suggest a close distance between the N- and C-terminal regions of full-length PPAR-β/δ in the presence of GW1516. Chemical cross-linking/MS allowed us gaining detailed insights into conformational changes that are induced in PPARs when activating ligands are present. Thus, cross-linking/MS should be added to the arsenal of structural methods available for studying nuclear receptors. PMID:26992147

  8. NMR Solution Structure and DNA Binding Model of the DNA Binding Domain of Competence Protein A

    PubMed Central

    Hobbs, Carey A.; Bobay, Benjamin G.; Thompson, Richele J.; Perego, Marta; Cavanagh, John

    2010-01-01

    Competence protein A (ComA) is a response regulator protein involved in the development of genetic competence in the Gram-positive spore forming bacterium Bacillus subtilis, as well as the regulation of the production of degradative enzymes and antibiotic synthesis. ComA belongs to the NarL family of proteins which are characterized by a C-terminal transcriptional activator domain that consists of a bundle of four helices, where the second and third helices (α8 and α9) form a helix-turn-helix DNA binding domain. Using NMR spectroscopy, the high resolution three-dimensional solution structure of the C-terminal DNA-binding domain of ComA (ComAC) has been determined. In addition, surface plasmon resonance and NMR protein-DNA titration experiments allowed for the analysis of the interaction of ComAC with its target DNA sequences. Combining the solution structure and biochemical data, a model of ComAC bound to the ComA recognition sequences on the srfA promoter has been developed. The model shows that for DNA binding, ComA uses the conserved helix-turn-helix motif present in other NarL family members. However, the model also reveals that ComA may use a slightly different part of the helix-turn-helix motif and there appears to be some associated domain re-orientation. These observations suggest a basis for DNA binding specificity within the NarL family. PMID:20302877

  9. Monitoring Solution Structures of Peroxisome Proliferator-Activated Receptor β/δ upon Ligand Binding

    PubMed Central

    Schwarz, Rico; Tänzler, Dirk; Ihling, Christian H.; Sinz, Andrea

    2016-01-01

    Peroxisome proliferator-activated receptors (PPARs) have been intensively studied as drug targets to treat type 2 diabetes, lipid disorders, and metabolic syndrome. This study is part of our ongoing efforts to map conformational changes in PPARs in solution by a combination of chemical cross-linking and mass spectrometry (MS). To our best knowledge, we performed the first studies addressing solution structures of full-length PPAR-β/δ. We monitored the conformations of the ligand-binding domain (LBD) as well as full-length PPAR-β/δ upon binding of two agonists. (Photo-) cross-linking relied on (i) a variety of externally introduced amine- and carboxyl-reactive linkers and (ii) the incorporation of the photo-reactive amino acid p-benzoylphenylalanine (Bpa) into PPAR-β/δ by genetic engineering. The distances derived from cross-linking experiments allowed us to monitor conformational changes in PPAR-β/δ upon ligand binding. The cross-linking/MS approach proved highly advantageous to study nuclear receptors, such as PPARs, and revealed the interplay between DBD (DNA-binding domain) and LDB in PPAR-β/δ. Our results indicate the stabilization of a specific conformation through ligand binding in PPAR-β/δ LBD as well as full-length PPAR-β/δ. Moreover, our results suggest a close distance between the N- and C-terminal regions of full-length PPAR-β/δ in the presence of GW1516. Chemical cross-linking/MS allowed us gaining detailed insights into conformational changes that are induced in PPARs when activating ligands are present. Thus, cross-linking/MS should be added to the arsenal of structural methods available for studying nuclear receptors. PMID:26992147

  10. Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.

    PubMed Central

    Gao, Y.; Kaluarachchi, K.; Giedroc, D. P.

    1998-01-01

    Retroviral nucleocapsid proteins (NCPs) are CCHC-type zinc finger proteins that mediate virion RNA binding activities associated with retrovirus assembly and genomic RNA encapsidation. Mason-Pfizer monkey virus (MPMV), a type D retrovirus, encodes a 96-amino acid nucleocapsid protein, which contains two Cys-X2-Cys-X4-His-X4-Cys (CCHC) zinc fingers connected by an unusually long 15-amino acid linker. Homonuclear, two-dimensional sensitivity-enhanced 15N-1H, three-dimensional 15N-1H, and triple resonance NMR spectroscopy have been used to determine the solution structure and residue-specific backbone dynamics of the structured core domain of MPMV NCP containing residues 21-80. Structure calculations and spectral density mapping of N-H bond vector mobility reveal that MPMV NCP 21-80 is best described as two independently folded, rotationally uncorrelated globular domains connected by a seven-residue flexible linker consisting of residues 42-48. The N-terminal CCHC zinc finger domain (residues 24-37) appears to adopt a fold like that described previously for HIV-1 NCP; however, residues within this domain and the immediately adjacent linker region (residues 38-41) are characterized by extensive conformational averaging on the micros-ms time scale at 25 degrees C. In contrast to other NCPs, residues 49-77, which includes the C-terminal CCHC zinc-finger (residues 53-66), comprise a well-folded globular domain with the Val49-Pro-Gly-Leu52 sequence and C-terminal tail residues 67-77 characterized by amide proton exchange properties and 15N R1, R2, and (1H-15N) NOE values indistinguishable to residues in the core C-terminal finger. Twelve refined structural models of MPMV NCP residues 49-80 (pairwise backbone RMSD of 0.77 A) reveal that the side chains of the conserved Pro50 and Trp62 are in van der Waals contact with one another. Residues 70-73 in the C-terminal tail adopt a reverse turn-like structure. Ile77 is involved in extensive van der Waals contact with the core

  11. Secrets of solid state and aqueous solution structures of [Ni(tmdta)](2-).

    PubMed

    Meier, Roland; Platas-Iglesias, Carlos; Heinemann, Frank W; Linti, Gerald; Schulte, Jürgen; Srivastava, Sunil K

    2014-07-01

    The molecular structures of Li2[Ni(tmdta)]·5H2O (1a, tmdta = trimethylenediaminetetraacetate), {C(NH2)3}2[Ni(tmdta)]·6H2O (1b), and {Ni(H2O)6}[Ni(tmdta)]·2H2O (2a) have been determined. The central trimethylenediamine chelate ring shows half-chair (hc) geometries in 1a and 1b, while a twist-boat (tb) conformation is encountered in 2a. The coexistence of tb and hc forms in the solid state prompted us to elucidate the existence of a tb ⇌ hc equilibrium in aqueous solution. Evaluation of the data from solid state vibrational spectra (Raman and IR) for the hc and tb forms showed excellent agreement with simulated spectra obtained with DFT computations (TPSSh/TZVP). This outstanding matching between theory and experiment enabled us to build composite spectra with varying hc:tb ratios. Comparison of these results with Raman and IR spectra recorded for [Ni(tmdta)](2-) in aqueous solution revealed that simulated Raman and IR spectra with a hc:tb ratio = 2:3 match the solution spectra in an accurate way. This equilibrium ratio enabled us to compute (13)C NMR sifts for the paramagnetic solution spectrum of [Ni(tmdta)](2-) based on the relative contributions by hc and tb fractions. This leads to computed shifts that agree closely with the experimental ones. Also, the kinetics of the skeleton dynamics could be estimated quantitatively by temperature-dependent (13)C NMR spectroscopic measurements. An interesting effect encountered for the very first time here concerns a drastic intensity difference of the 10Dq band ((3)A2g → (3)T2g(F) transition) in solid state electronic spectra of tb vs hc isomers, where the intensity of this band in the case of the hc form is much lower than that of the tb conformer and thus more similar to the case of the usual Ni(II) chromophore in octahedral environment. The equilibrium constants for complex formation and protonation of Ni(II)-tmdta at low pH have been estimated by pH-dependent UV-vis titration experiments. Correlation of these

  12. Solution structure of the E3 ligase HOIL-1 Ubl domain.

    PubMed

    Beasley, Steven A; Safadi, Susan S; Barber, Kathryn R; Shaw, Gary S

    2012-07-01

    The E3 ligases HOIL-1 and parkin are each comprised of an N-terminal ubiquitin-like (Ubl) domain followed by a zinc-binding region and C-terminal RING-In-between-RING-RING domains. These two proteins, involved in the ubiquitin-mediated degradation pathway, are the only two known E3 ligases to share this type of multidomain architecture. Further, the Ubl domain of both HOIL-1 and parkin has been shown to interact with the S5a subunit of the 26S proteasome. The solution structure of the HOIL-1 Ubl domain was solved using NMR spectroscopy to compare it with that of parkin to determine the structural elements responsible for S5a intermolecular interactions. The final ensemble of 20 structures had a β-grasp Ubl-fold with an overall backbone RMSD of 0.59 ± 0.10 Å in the structured regions between I55 and L131. HOIL-1 had a unique extension of both β1 and β2 sheets compared to parkin and other Ubl domains, a result of a four-residue insertion in this region. A similar 15-residue hydrophobic core in the HOIL-1 Ubl domain resulted in a comparable stability to the parkin Ubl, but significantly lower than that observed for ubiquitin. A comparison with parkin and other Ubl domains indicates that HOIL-1 likely uses a conserved hydrophobic patch (W58, V102, Y127, Y129) found on the β1 face, the β3-β4 loop and β5, as well as a C-terminal basic residue (R134) to recruit the S5a subunit as part of the ubiquitin-mediated proteolysis pathway. PMID:22517668

  13. Solution structure of Gfi-1 zinc domain bound to consensus DNA.

    PubMed

    Lee, Soojin; Doddapaneni, Kiran; Hogue, Amber; McGhee, Laura; Meyers, Shari; Wu, Zhengrong

    2010-04-01

    Gfi-1 is a crucial transcriptional repressor for the precise regulation of cell proliferation and differentiation in hematopoiesis. Recently, this protein has also been demonstrated to be capable of restricting the proliferation of hematopoietic stem cells, a process that appears to be vital for the long-term competency of hematopoietic stem cells. These two seemingly opposite outcomes of regulation are likely to arise from its interactions with a variety of cellular partners. Such interactions can directly affect the genes that Gfi-1 recognizes through its DNA binding zinc-finger domain. In this work, we report the determination of the solution structure of Gfi-1 zinc fingers 3-5 in complex with a 16-mer consensus DNA using multidimensional NMR method. Unlike a proposed minor-groove binding model based on methylation interference experiments, our structure clearly shows that Gfi-1 zinc fingers 3-5 bind into the major groove of the target DNA reminiscent of canonical C(2)H(2) zinc-finger domains. The fourth and fifth zinc fingers recognize the AATC core sequence by forming base-specific hydrogen bonds between the side chains of Asn382, Gln379, and Asp354 and the bases of the invariant adenines and cytosine. Overall, the current work provides valuable insight into the structural determinants for DNA binding specificity, in particular for the TCA triplet that has not been observed in any other structures of zinc finger-DNA complexes, as well as molecular rationales for a naturally occurring mutation that causes acute myeloid leukemia. PMID:20153336

  14. Coordination Structure Conversion of Hydrazone-Palladium(II) Complexes in the Solid State and in Solution.

    PubMed

    Kitamura, Fumi; Sawaguchi, Kana; Mori, Asami; Takagi, Shoji; Suzuki, Takayoshi; Kobayashi, Atsushi; Kato, Masako; Nakajima, Kiyohiko

    2015-09-01

    We prepared hydrazone-palladium(II) complexes of [PdCl2(HL(n))] and [PdCl(L(n))] (n = 1-3) by the reaction of [PdCl2(cod)] or [PdCl2(PhCN)2] and the hydrazone ligands of HL(n) {N'-(pyridin-2-ylmethylene)picolinohydrazide (HL(1)), N'-[1-(pyridin-2-yl)ethylidene]picolinohydrazide (HL(2)), and N'-[(6-methylpyridin-2-yl)methylene]picolinohydrazide (HL(3))}. The structures of the complexes were determined by X-ray analysis. The hydrazone ligands had κN(py1),κN(imine) and κN(amidate),κN(py2) bidentate coordination modes in [PdCl2(HL(n))] (1, n = 1; 2, n = 2) and in [PdCl2(HL(3))] (3), respectively. In contrast, tridentate coordination modes of κN(py1),κN(imine),κN(py2) and κN(py1),κN(amidate),κN(py2) were observed in [PdCl(L(n))] (4, n = 1; 5, n = 2) and in [PdCl(L(n))] (6, n = 1; 7, n = 2; 8, n = 3). Thermal conversion of complexes 1-3 to complexes 6-8 proceeded in acetonitrile. Complexes 4 and 5 were obtained from complexes 1 and 2, respectively, in a basic acetonitrile solution under dark conditions. Complex 4 reverted immediately to complex 1 in an acidic acetonitrile solution that included hydrochloric acid. However, under room light, in the basic acetonitrile solution that included trimethylamine, complex 4 converted photochemically to complex 6. The thermochromic or vapochromic structure conversion of these complexes also occurred in the solid state. On heating at 180 °C, the color of the crystals of complexes 1, 2, and 3 changed from yellow to orange in the solid state. (1)H NMR and/or UV-vis absorption spectroscopy confirmed that the orange complexes 6-8 were produced. The reddish-orange crystals of complexes 4 and 5 were exposed to hydrogen chloride vapor to yield the yellow products of complexes 1 and 2, respectively. PMID:26305775

  15. 1H NMR characterization of the intermediate formed upon UV-A excitation of biopterin, neopterin and 6-hydroxymethylpterin in O 2-free aqueous solutions

    NASA Astrophysics Data System (ADS)

    Vignoni, Mariana; Salum, M. Laura; Erra-Balsells, Rosa; Thomas, Andres H.; Cabrerizo, Franco M.

    2010-01-01

    Pterins belong to a family of heterocyclic compounds present in a wide range of living systems and participate in relevant biological functions. Under anaerobic conditions, the unstable red intermediate generated by UV-A irradiation of biopterin, neopterin and 6-hydroxymethylpterin was identified by 1H NMR analysis, in alkaline D 2O solutions, as 5,8-dihydro-6-formylpterin.

  16. The solution structure of liquid-crystal polymers with small liquid-crystal thermoset maleimides and nadimides

    SciTech Connect

    Hjelm, R.P.; Douglas, E.P.; Benicewicz, B.C.

    1995-03-01

    The solution structure of the deuterated liquid-crystal polyamide polymer (LCP) poly(p-phenylene-2-nitroterephthalamide), alone and mixed with small, rodlike, amide, liquid-crystal molecules (LCT) in N-methyl-2-pyrrolidinone (NMP), is studied using small-angle neutron scattering. Measurements were made as a function of LCP concentration using different LCTs mixed at 20 and 40 wt% relative to LCP. Our motivation for studying this system comes from a need to connect solution structure with film morphology in processing these materials for high-performance molecular composites. Our analysis shows that LCP in NMP forms large domain-like structures. The presence of LCT breaks up the LCP domains into smaller structures, some of which are filamentous LCP-LCT aggregates. This result suggests that the simple entropic description of the solution behavior of mixtures of long and short rods is not adequate in describing systems of this type.

  17. Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state

    SciTech Connect

    Jacques, David A.; Streamer, Margaret; Rowland, Susan L.; King, Glenn F.; Guss, J. Mitchell; Trewhella, J.; Langley, David B.

    2009-09-02

    The crystal structure of the DNA-damage checkpoint inhibitor of sporulation, Sda, from Bacillus subtilis, has been solved by the MAD technique using selenomethionine-substituted protein. The structure closely resembles that previously solved by NMR, as well as the structure of a homologue from Geobacillus stearothermophilus solved in complex with the histidine kinase KinB. The structure contains three molecules in the asymmetric unit. The unusual trimeric arrangement, which lacks simple internal symmetry, appears to be preserved in solution based on an essentially ideal fit to previously acquired scattering data for Sda in solution. This interpretation contradicts previous findings that Sda was monomeric or dimeric in solution. This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations.

  18. Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state

    PubMed Central

    Jacques, David A.; Streamer, Margaret; Rowland, Susan L.; King, Glenn F.; Guss, J. Mitchell; Trewhella, Jill; Langley, David B.

    2009-01-01

    The crystal structure of the DNA-damage checkpoint inhibitor of sporulation, Sda, from Bacillus subtilis, has been solved by the MAD technique using selenomethionine-substituted protein. The structure closely resembles that previously solved by NMR, as well as the structure of a homologue from Geobacillus stearothermophilus solved in complex with the histidine kinase KinB. The structure contains three molecules in the asymmetric unit. The unusual trimeric arrangement, which lacks simple internal symmetry, appears to be preserved in solution based on an essentially ideal fit to previously acquired scattering data for Sda in solution. This interpretation contradicts previous findings that Sda was monomeric or dimeric in solution. This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations. PMID:19465772

  19. [Comparison of the structures of different forms of sperm whale myoglobin in solution using wide angle x-ray scattering].

    PubMed

    Dolgikh, D A; Denesiuk, A I; Fedorov, B A; Postnikova, G B

    1980-01-01

    Experimental X-ray diffuse scattering curves in a wide range of angles for oxy-, deoxy-, met- and cyan-forms of sperm whale myoglobin in solution have been obtained. It has been found that scattering indicatrices of these ligand forms of myoglobin are well compatible with each other and differ from the theoretical scattering curve of met-myoglobin, calculated from the structure of this protein in crystal. The conclusions have been drawn: (1) on the similarity of myoglobin structures in solution for all the protein forms studied; (2) on the difference in the structure of the above ligand forms of myoglobin in solution from the structure of the protein in crystal by a slight shift (about 2 A) of the "hairpin" GH. PMID:7189418

  20. Global structure stability of Riemann solutions of quasilinear hyperbolic systems of conservation laws: shocks and contact discontinuities

    NASA Astrophysics Data System (ADS)

    Kong, De-Xing

    In this paper, the author proves the global structure stability of the Lax's Riemann solution u=U( {x}/{t}) , containing only shocks and contact discontinuities, of general n× n quasilinear hyperbolic system of conservation laws. More precisely, the author proves the global existence and uniqueness of the piecewise C1 solution u= u( t, x) of a class of generalized Riemann problem, which can be regarded as a perturbation of the corresponding Riemann problem, for the quasilinear hyperbolic system of conservation laws; moreover, this solution has a global structure similar to that of the solution u=U( {x}/{t}) . Combining the results in Kong (Global structure instability of Riemann solutions of quasilinear hyperbolic systems of conservation laws: rarefaction waves, to appear), the author proves that the Lax's Riemann solution of general n× n quasilinear hyperbolic system of conservation laws is globally structurally stable if and only if it contains only non-degenerate shocks and contact discontinuities, but no rarefaction waves and other weak discontinuities.

  1. Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB

    PubMed Central

    Tanabe, Mikio; Nimigean, Crina M.; Iverson, T. M.

    2010-01-01

    PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been determined to 2.3 Å resolution. Structural analysis and cocrystallization studies identify three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one transports cations nonselectively, and one facilitates the specific uptake of sugars. During infection, PorB likely binds host mitochondrial ATP, and cocrystallization with the ATP analog AMP–PNP suggests that binding of nucleotides regulates these translocation pathways both by partial occlusion of the pore and by restricting the motion of a putative voltage gating loop. PorB is located on the surface of N. meningitidis and can be recognized by receptors of the host innate immune system. Features of PorB suggest that Toll-like receptor mediated recognition outer membrane proteins may be initiated with a nonspecific electrostatic attraction. PMID:20351243

  2. Structure and pH-induced alterations of recombinant and natural spider silk proteins in solution.

    PubMed

    Leclerc, Jérémie; Lefèvre, Thierry; Pottier, Fabien; Morency, Louis-Philippe; Lapointe-Verreault, Camille; Gagné, Stéphane M; Auger, Michèle

    2012-06-01

    The spinning process of spiders can modulate the mechanical properties of their silk fibers. It is therefore of primary importance to understand what are the key elements of the spider spinning process to develop efficient industrial spinning processes. We have exhaustively investigated the native conformation of major ampullate silk (MaS) proteins by comparing the content of the major ampullate gland of Nephila clavipes, solubilized MaS (SolMaS) fibers and the recombinant proteins rMaSpI and rMaSpII using (1) H solution NMR spectroscopy. The results indicate that the protein secondary structure is basically identical for the recombinant protein rMaSpI, SolMaS proteins, and the proteins in the dope, and corresponds to a disordered protein rich in 3(1) -helices. The data also show that glycine proton chemical shifts of rMaSpI and SolMaS are affected by pH, but that this change is not due to a modification of the secondary structure. Using a combination of NMR and dynamic light scattering, we have found that the spectral alteration of glycine is concomitant to a modification of the hydrodynamical diameter of recombinant and solubilized MaS. This led us to suggest new potential roles for the pH acidification in the spinning process of MaS proteins. PMID:21898365

  3. Aggregation properties and structural studies of anticancer drug Irinotecan in DMSO solution based on NMR measurements

    NASA Astrophysics Data System (ADS)

    D'Amelio, N.; Aroulmoji, V.; Toraldo, A.; Sundaraganesan, N.; Anbarasan, P. M.

    2012-04-01

    Irinotecan is an antitumor drug mostly used in the treatment of colorectal cancer. Its efficacy is influenced by the chemical state of the molecule undergoing chemical equilibria, metabolic changes and photodegradation. In this work, we describe the chemical equilibria of the drug in dimethyl sulfoxide (DMSO). The energetic barrier for hindered rotation around the bond connecting the piperidino—piperidino moiety with the camptothecin-like fragment was evaluated. Furthermore, we showed how the molecule aggregates in DMSO solution forming dimeric species able to prevent its degradation. The equilibrium constant for self-aggregation was determined by NMR based on the assumption of the isodesmic model. The formation of a dimer was highlighted by NMR diffusion ordered spectroscopy (NMR-DOSY) experiments at the concentrations used. Structural features of the complex were inferred by NOE and 13C chemical shift data. Molecular modelling of the complex driven by experimental data, lead to a structure implying the formation of two hydrogen bonds involving the lactone ring whose opening is one of the main causes of drug degradation. This species is probably responsible for the improved stability of the drug at concentrations higher than 1 mM.

  4. Analysis of structure and orientation of adsorbed polymers in solution subject to a dynamic shear stress

    SciTech Connect

    Smith, G.; Baker, S.; Toprakcioglu, C.

    1996-09-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Polymer-based separation techniques rely on the ability of a binding portion of the polymer to interact with a specific molecule in a solution flowing past the polymer. The location of the binding site within or out of the entangled polymer chains is thus crucial to the effectiveness of these methods. For this reason, the details of flow induced deformation of the polymer chains is important in such applications as exclusion chromatography, waste water treatment, ultrafiltration, enhanced oil recovery and microbial adhesion. Few techniques exist to examine the structure and orientation of polymeric materials, and even fewer to examine systems in a dynamic fluid flow. The goal of this project was to understand the molecular structure and orientation of adsorbed polymers with and without active binding ligands as a function of solvent shear rate, solvent power, polymer molecular weight, surface polymer coverage and heterogeneity of the surface polymer chains by neutron reflectometry in a newly designed shear cell. Geometrical effects on binding of molecules in the flow was also studied subject to the same parameters.

  5. Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB

    SciTech Connect

    Tanabe, Mikio; Nimigean, Crina M.; Iverson, T.M.

    2010-06-25

    PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been determined to 2.3 {angstrom} resolution. Structural analysis and cocrystallization studies identify three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one transports cations nonselectively, and one facilitates the specific uptake of sugars. During infection, PorB likely binds host mitochondrial ATP, and cocrystallization with the ATP analog AMP-PNP suggests that binding of nucleotides regulates these translocation pathways both by partial occlusion of the pore and by restricting the motion of a putative voltage gating loop. PorB is located on the surface of N. meningitidis and can be recognized by receptors of the host innate immune system. Features of PorB suggest that Toll-like receptor mediated recognition outer membrane proteins may be initiated with a nonspecific electrostatic attraction.

  6. Ruthenium nanoparticles in ionic liquids: structural and stability effects of polar solutes.

    PubMed

    Salas, Gorka; Podgoršek, Ajda; Campbell, Paul S; Santini, Catherine C; Pádua, Agílio A H; Costa Gomes, Margarida F; Philippot, Karine; Chaudret, Bruno; Turmine, Mireille

    2011-08-14

    Ionic liquids are a stabilizing medium for the in situ synthesis of ruthenium nanoparticles. Herein we show that the addition of molecular polar solutes to the ionic liquid, even in low concentrations, eliminates the role of the ionic liquid 3D structure in controlling the size of ruthenium nanoparticles, and can induce their aggregation. We have performed the synthesis of ruthenium nanoparticles by decomposition of [Ru(COD)(COT)] in 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C(1)C(4)Im][NTf(2)], under H(2) in the presence of varying amounts of water or 1-octylamine. For water added during the synthesis of metallic nanoparticles, a decrease of the solubility in the ionic liquid was observed, showed by nanoparticles located at the interface between aqueous and ionic phases. When 1-octylamine is present during the synthesis, stable nanoparticles of a constant size are obtained. When 1-octylamine is added after the synthesis, aggregation of the ruthenium nanoparticles is observed. In order to explain these phenomena, we have explored the molecular interactions between the different species using (13)C-NMR and DOSY (Diffusional Order Spectroscopy) experiments, mixing calorimetry, surface tension measurements and molecular simulations. We conclude that the behaviour of the ruthenium nanoparticles in [C(1)C(4)Im][NTf(2)] in the presence of 1-octylamine depends on the interaction between the ligand and the nanoparticles in terms of the energetics but also of the structural arrangement of the amine at the nanoparticle's surface. PMID:21603700

  7. Solution structure of DinI provides insight into its mode of RecA inactivation.

    PubMed Central

    Ramirez, B. E.; Voloshin, O. N.; Camerini-Otero, R. D.; Bax, A.

    2000-01-01

    The Escherichia coli RecA protein triggers both DNA repair and mutagenesis in a process known as the SOS response. The 81-residue E. coli protein DinI inhibits activity of RecA in vivo. The solution structure of DinI has been determined by multidimensional triple resonance NMR spectroscopy, using restraints derived from two sets of residual dipolar couplings, obtained in bicelle and phage media, supplemented with J couplings and a moderate number of NOE restraints. DinI has an alpha/beta fold comprised of a three-stranded beta-sheet and two alpha-helices. The beta-sheet topology is unusual: the central strand is flanked by a parallel and an antiparallel strand and the sheet is remarkably flat. The structure of DinI shows that six negatively charged Glu and Asp residues on DinI's kinked C-terminal alpha-helix form an extended, negatively charged ridge. We propose that this ridge mimics the electrostatic character of the DNA phospodiester backbone, thereby enabling DinI to compete with single-stranded DNA for RecA binding. Biochemical data confirm that DinI is able to displace ssDNA from RecA. PMID:11152126

  8. The structure and properties of PEDOT synthesized by template-free solution method

    PubMed Central

    2014-01-01

    In this study, a simple one-step template-free solution method was developed for the preparation of poly(3,4-ethylenedioxythiophene) (PEDOTs) with different morphologies by adjusting various ratios of oxidant (FeCl3·6H2O) to monomer (3,4-ethylenedioxythiophene (EDOT)). The results from structural analysis showed that the structure of PEDOT was strongly affected by the oxidant/monomer ratio, and the polymerization degree, conjugation length, doping level, and crystallinity of PEDOT decreased with increasing of the oxidant/monomer ratio. The morphological analysis showed that PEDOT prepared from an oxidant/monomer ratio of 3:1 displayed a special coral-like morphology, and the branches of ‘coral’ would adjoin or grow together with increasing content of oxidant in the reaction medium; consequently, the morphology of PEDOT changed from coral to sheets (at an oxidant/monomer ratio of 9:1). The electrochemical analysis proved that the PEDOT prepared from an oxidant/monomer ratio of 3:1 had the lowest resistance and the highest specific capacitances (174 F/g) at a current density of 1 A/g with a capacity retention rate of 74% over 1,500 cycles, which indicated that the PEDOT with a coral-like morphology could be applied as a promising electrode material for supercapacitors. PMID:25317104

  9. Simulation of intrathrombus fluid and solute transport using in vivo clot structures with single platelet resolution.

    PubMed

    Voronov, Roman S; Stalker, Timothy J; Brass, Lawrence F; Diamond, Scott L

    2013-06-01

    The mouse laser injury thrombosis model provides up to 0.22 μm-resolved voxel information about the pore architecture of the dense inner core and loose outer shell regions of an in vivo arterial thrombus. Computational studies were conducted on this 3D structure to quantify transport within and around the clot: Lattice Boltzmann method defined vessel hemodynamics, while passive Lagrangian Scalar Tracking with Brownian motion contribution simulated diffusive-convective transport of various inert solutes (released from lumen or the injured wall). For an input average lumen blood velocity of 0.478 cm/s (measured by Doppler velocimetry), a 0.2 mm/s mean flow rate was obtained within the thrombus structure, most of which occurred in the 100-fold more permeable outer shell region (calculated permeability of the inner core was 10(-11) cm(2)). Average wall shear stresses were 80-100 dyne/cm(2) (peak values >200 dyne/cm(2)) on the outer rough surface of the thrombus. Within the thrombus, small molecule tracers (0.1 kDa) experienced ~70,000 collisions/s and penetrated/exited it in about 1 s, whereas proteins (~50 kDa) had ~9000 collisions/s and required about 10 s (tortuosity ~2-2.5). These simulations help define physical processes during thrombosis and constraints for drug delivery to the thrombus. PMID:23423707

  10. Structure of steady state accretion shocks with several cooling functions: Closed integral-form solution

    NASA Technical Reports Server (NTRS)

    Wu, Kinwah; Chanmugam, G.; Shaviv, G.

    1994-01-01

    We present, for the first time, a closed integral-form solution to the accretion shock structures for the case where the cooling is due to optically thin bremsstrahlung emission and a series of power-law cooling functions of density and temperature. Our results can provide useful checks on numerical calculations and simple accurate estimates for valuable parameters such as the shock height. For the case where the cooling rate j = (2/3)Arho(exp 2)(P/rho)(exp 1/2)(1 + epsilon (sub s)(P/P(sub s)(exp alpha)(rho(sub s)/rho)(exp beta)), we find that a substantial amount of the accretion energy is released at the base of the accretion shock in the form of bremsstrahlung radiation. This implies that for a cyclotron-dominated shock (qualitatively given by alpha = 2.0, beta = 3.85, and epsilon(sub s) is much greater than 1), bremsstrahlung cooling still plays a crucial role in determining the shock structure. Our results are shown to be consistent with detailed numerical calculations.

  11. Asymptotic structure and similarity solutions for three-dimensional turbulent boundary layers

    NASA Technical Reports Server (NTRS)

    Degani, A. T.; Walker, J. D. A.

    1989-01-01

    The asymptotic structure of the three-dimensional turbulent boundary layer is investigated in the limit of large Reynolds numbers. A self-consistent, but relatively complex, two-layer structure exists and the simplest situation, corresponding to a plane of symmetry, is considered in this paper as a first step. The adjustment of the streamwise velocity to relative rest, through an outer defect layer and then an inner wall layer, is similar to that in two-dimensional flow. The adjustment of the cross-streamwise velocity is more complicated and it is shown that two terms in the expansion are required to obtain useful results, and in particular to obtain the velocity skew angle at the wall near the symmetry plane. The conditions under which self-similarity is achieved near a plane of symmetry are investigated. A set of ordinary differential equations is developed which describe the streamwise and cross-streamwise velocities near a plane of symmetry in a self-similar flow through two orders of magnitude. Calculated numerical solutions of these equations yield trends which are consistent with experimental observations.

  12. Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?

    PubMed

    Urzhumtsev, Alexandre; Urzhumtseva, Ludmila; Baumann, Ulrich

    2016-01-01

    Crystallographic molecular replacement method is the key tool to define an atomic structure of nucleic acids. Frequently nucleic acids are packed forming continuous helices in the crystal. This arrangement of individual molecules in "infinite" pseudo helical structures in crystal may be the reason why the molecular replacement fails to find a unique position of the search atomic model as the method requires. The Patterson function, calculated as a Fourier series with diffraction intensities, has auxiliary peaks for such a molecular packing. Those near the origin peak indicate the orientation of the helices. The coordinates of other peaks are related to the molecular position and the rotation angle between two such "infinite" helices. Thus, the peak analysis allows getting molecular position even without a search model. An intelligent selecting and averaging of the phase sets corresponding to multiple probable positions of the search model again result in a unique solution but in the form of a Fourier synthesis and not a model. This synthesis can be used then to build an atomic model as it is the case for usual phasing methods. PMID:26227048

  13. Preparation, stability, and structural characterization of plutonium(VII) in alkaline aqueous solution.

    PubMed

    Antonio, Mark R; Williams, C W; Sullivan, James A; Skanthakumar, S; Hu, Yung-Jin; Soderholm, L

    2012-05-01

    A freshly prepared solution of Pu(VI) in 2 M NaOH was oxidized to Pu(VII), via ozonolysis, while simultaneously collecting X-ray absorption spectra. Analyses of the XANES (X-ray absorption near edge structure) and EXAFS (extended X-ray absorption fine structure) data, acquired throughout the in situ experiments, show a dioxo coordination environment for Pu(VI), PuO(2)(2+), typical for it and the hexavalent actinyl species of U and Np, and its evolution into a tetraoxo-coordination environment for Pu(VII), PuO(4)(-), like that known for Np(VII). The EXAFS data provide average Pu-O distances of 1.79(1) and 1.88(1) Å, respectively. The second coordination shells, also fit as O atoms, provide Pu-O distances of 2.29-2.32 Å that are independent of the Pu oxidation state. The coordination numbers for the distant O atoms in sums with those for the nearest O atoms are consistent with 6-O environments for both Pu(VI) and Pu(VII) ions in accordance with their previously proposed speciation as [Pu(VI)O(2)(OH)(4)](2-) and [Pu(VII)O(4)(OH)(2)](3-), respectively. This solution speciation accounts precisely for the Pu(VI) and Pu(VII) coordination environments reported in various solid state structures. The Pu(VII) tetraoxo-dihydroxo anion was found to have a half-life of 3.7 h. Its instability is attributed to spontaneous reduction to Pu(VI) and not to a measurable extent of disproportionation. We found no direct evidence for Pu(VIII) in the X-ray data and, furthermore, the stoichiometry of the oxidation of Cr(III) by Pu is consistent with that expected for a valence-pure Pu(VII) preparation by ozonation and, in turn, stoichiometrically equivalent to the established Np(VII)/Cr(III) redox reaction. PMID:22524489

  14. Structurally colored biopolymer thin films for detection of dissolved metal ions in aqueous solution

    NASA Astrophysics Data System (ADS)

    Cathell, Matthew David

    Natural polymers, such as the polysaccharides alginate and chitosan, are noted sorbents of heavy metals. Their polymer backbone structures are rich in ligands that can interact with metal ions through chelation, electrostatics, ion exchange and nonspecific mechanisms. These water-soluble biopolymer materials can be processed into hydrogel thin films, creating high surface area interfaces ideal for binding and sequestering metal ions from solution. By virtue of their uniform nanoscale dimensions (with thicknesses smaller than wavelengths of visible light) polymer thin films exhibit structure-based coloration. This phenomenon, frequently observed in nature, causes the transparent and essentially colorless films to reflect light in a wide array of colors. The lamellar film structures act as one-dimensional photonic crystals, allowing selective reflection of certain wavelengths of light while minimizing other wavelengths by out-of-phase interference. The combination of metal-binding and reflective properties make alginate and chitosan thin films attractive candidates for analyte sensing. Interactions with metal ions can induce changes in film thicknesses and refractive indices, thus altering the path of light reflected through the film. Small changes in dimensional or optical properties can lead to shifts in film color that are perceivable by the unaided eye. These thin films offer the potential for optical sensing of toxic dissolved materials without the need for instrumentation, external power or scientific expertise. With the use of a spectroscopic ellipsometer and a fiber optic reflectance spectrometer, the physical and optical characteristics of biopolymer thin films have been characterized in response to 50 ppm metal ion solutions. It has been determined that metal interactions can lead to measurable changes in both film thicknesses and effective refractive indices. The intrinsic response behaviors of alginate and chitosan, as well as the responses of modified

  15. Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP

    PubMed Central

    Butterwick, Joel A.; MacKinnon, Roderick

    2010-01-01

    Voltage-sensor domains (VSDs) are specialized transmembrane segments that confer voltage sensitivity to many proteins such as ion channels and enzymes. The activities of these domains are highly dependent on both the chemica