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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. Nuclear Magnetic Resonance Evidence using D2O for Structured Water in Muscle and Brain

    PubMed Central

    Cope, Freeman W.

    1969-01-01

    The electric quadrupole moment of the deuterium nucleus provides a nuclear magnetic resonance (NMR) probe of electric field gradients, and thereby of organization of tissue water. 8-17% of H2O in rat muscle and brain was replaced by D2O from 50% deuterated drinking water. The peak height of the steady-state NMR spectrum of D in muscle water was 74% lower than that of an equal concentration of D2O in liquid water. Longitudinal NMR relaxation times (T1) of D in water of muscle and brain averaged 0.092 and 0.131 sec, respectively, compared with 0.47 sec in D2O in liquid water. Transverse NMR relaxation times (T2) averaged 0.009 and 0.022 sec in D2O of muscle and brain, respectively, compared with 0.45 sec in D2O in liquid water. These differences cannot be explained by paramagnetic ions or by magnetic inhomogeneities, which leaves increased organization of tissue water as the only tenable hypothesis. Evidence was also obtained that 27% of muscle water and 13% of brain water exist as a separate fraction with T2 of D2O less than 2 × 10-3 sec, which implies an even higher degree of structure. Each of the two fractions may consist of multiple subfractions of differing structure. PMID:5780710

  3. Mode structure in an optically pumped D2O far-infrared ring laser

    NASA Astrophysics Data System (ADS)

    Yuan, D. C.; Soumagne, G.; Siegrist, M. R.

    1990-02-01

    The mode structures in an optically pumped D2O far-infrared ring laser and a corresponding linear resonator have been compared. While single-mode operation can be obtained over the whole useful pressure range in the ring structure, this is only possible at pressures greater than 8 torr in the linear resonator case. A numerical model predicts quite well the pulse shape, pressure dependence, and influence of the resonator quality in the ring cavity.

  4. Pressure and temperature effects on 2H spin-lattice relaxation times and 1H chemical shifts in tert-butyl alcohol- and urea-D2O solutions

    NASA Astrophysics Data System (ADS)

    Yoshida, Koji; Ibuki, Kazuyasu; Ueno, Masakatsu

    1998-01-01

    The pressure and temperature effects of hydrophobic hydration were studied by NMR spectroscopy. The 1H chemical shifts (δ) were measured at 7.7, 29.9, and 48.4 °C under high pressure up to 294 MPa for HDO contained as impurity in neat D2O, 1 mol kg-1 tert-butyl alcohol (TBA)-D2O, and 1 mol kg-1 urea-D2O solutions, for the methyl group of TBA in the TBA-D2O solution, and for the amino group of urea in the urea-D2O solution. The 2H spin-lattice relaxation times (T1) were measured under the same conditions as the chemical shift measurements for D2O in neat D2O, TBA-D2O and urea-D2O solutions with organic contents up to 8 mol%. The following features are observed for the pressure effect on δ (HDO) and 2H-T1 in TBA-D2O solutions: (1) The δ (HDO) exhibits a downfield shift relative to that in neat D2O, and the difference of δ (HDO) between TBA solution and neat D2O becomes larger with increasing pressure at lower temperature. (2) The decrement of the rotational correlation time of water in the hydration shell of TBA (τcs) relative to the value at atmospheric pressure is smaller than that in the bulk (τc0). (3) The pressure coefficients of T1 are positive in dilute solutions but are negative in more than 4 to 5 mol% solutions. These results suggest that the hydrophobic hydration shell of TBA is different than the open structure of water present in bulk, and resists pressure more strongly than the open structure of water in the bulk. In solutions of 4 to 5 mol%, the hydration shell collapses. On the other hand, the τcs in the hydration shell of urea is slightly larger than that in bulk water at lower pressure, but is obviously larger at higher pressure. In view of the rotational motion of water molecules, urea seems to strengthen the water structure slightly rather than weaken it, although δ (HDO) approaches that in the bulk with pressure. It is difficult to classify urea into a structure maker or a breaker.

  5. Differential stability of the triple helix of (Pro-Pro-Gly)10 in H2O and D2O: thermodynamic and structural explanations.

    PubMed

    Gough, C A; Bhatnagar, R S

    1999-12-01

    (Pro-Pro-Gly)10 [(PPG10)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5 degrees C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D2O to an H2O solution of (PPG)10, with the melting temperature reaching 40 degrees C in pure D2O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalpy of unfolding in D2O vs. H2O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)10 that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H2O or D2O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D2O resulted in a significant lowering of the potential energy of hydrated (PPG)10. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG10) energy, plus the water-(PPG10) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D2O vs. H2O. This result indicates that the geometry of the carbonyl-D2O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of

  6. Water (H2O and D2O) molar absorptivity in the 1000-4000 cm-1 range and quantitative infrared spectroscopy of aqueous solutions.

    PubMed

    Venyaminov SYu; Prendergast, F G

    1997-06-01

    Water (H2O and D2O) molar absorptivity was measured by Fourier transform infrared transmission spectroscopy in the 1000-4000 cm-1 range at 25 degrees C. A series of assembled cells with path lengths from 1.2 to 120.5 microns was used for these measurements. The optimal path length (the path length of aqueous solution at which the IR spectrum of solute, corrected for water absorbance, has the highest signal-to-noise ratio) was calculated for all water absorbance bands. The results presented here show that the optimal path length does not depend on solute properties and is inversely proportional to the solvent (water) molar absorptivity. The maximal signal-to-noise ratio for measurements of IR spectra of aqueous solution in the 1650 cm-1 spectral region, of primary interest in biological applications, can be obtained at an optimal cell path lengths of 3-4 microns (H2O) and 40-60 microns (D2O). As an example, the signal-to-noise ratio was calculated as a function of the cell path length for the amide I (H2O) and amide I' (D2O) bands of an aqueous lysozyme solution. The molar absorptivities of water bands are several orders of magnitude weaker than those of the strongest bands of biological macromolecules in the same spectral regions. High net water absorbance in aqueous solutions is due simply to the very high molar concentration of water. A method is proposed for the quantitative measuring of the path length of the cell which exploits the molar absorptivity of the strongest water bands (stretching vibrations) or of bands which do not overlap with solute absorbance. A path length in the range from approximately 0.01 micron to approximately 1.0 mm can be determined with high precision using this technique for a samples of known concentration. Problems involved in the proper correction of strong water absorbance in IR spectra of aqueous solutions of biomolecules are discussed, including multiple reflections within the cell, the effects of pH, temperature, and

  7. 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

    SciTech Connect

    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 water 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 (ZPE). 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.

  8. 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.

  9. 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.

  10. Hybrid quantum/classical simulations of the vibrational relaxation of the amide I mode of N-methylacetamide in D2O solution.

    PubMed

    Bastida, Adolfo; Soler, Miguel A; Zúñiga, José; Requena, Alberto; Kalstein, Adrián; Fernández-Alberti, Sebastián

    2012-03-08

    Hybrid quantum/classical molecular dynamics (MD) is applied to simulate the vibrational relaxation (VR) of the amide I mode of deuterated N-methylacetamide (NMAD) in aqueous (D(2)O) solution. A novel version of the vibrational molecular dynamics with quantum transitions (MDQT) treatment is developed in which the amide I mode is treated quantum mechanically while the remaining degrees of freedom are treated classically. The instantaneous normal modes of the initially excited NMAD molecule (INM(0)) are used as internal coordinates since they provide a proper initial partition of the system in quantum and classical subsystems. The evolution in time of the energy stored in each individual normal mode is subsequently quantified using the hybrid quantum-classical instantaneous normal modes (INM(t)). The identities of both the INM(0)s and the INM(t)s are tracked using the equilibrium normal modes (ENMs) as templates. The results extracted from the hybrid MDQT simulations show that the quantum treatment of the amide I mode accelerates the whole VR process versus pure classical simulations and gives better agreement with experiments. The relaxation of the amide I mode is found to be essentially an intramolecular vibrational redistribution (IVR) process with little contribution from the solvent, in agreement with previous theoretical and experimental studies. Two well-defined relaxation mechanisms are identified. The faster one accounts for ≈40% of the total vibrational energy that flows through the NMAD molecule and involves the participation of the lowest frequency vibrations as short-life intermediate modes. The second and slower mechanism accounts for the remaining ≈60% of the energy released and is associated to the energy flow through specific mid-range and high-frequency modes.

  11. Structure of Calcium Aluminate Decahydrate (CaAl2O4.10D2O) from Neutron and X-ray Powder Diffraction Data

    SciTech Connect

    Christensen,A.; Lebech, B.; Sheptyakov, D.; Hanson, J.

    2007-01-01

    Calcium aluminate decahydrate is hexagonal with the space group P63/m and Z = 6. The compound has been named CaAl2O4{center_dot}10H2O (CAH10) for decades and is known as the product obtained by hydration of CaAl2O4 (CA) in the temperature region 273-288 K - one of the main components in high-alumina cements. The lattice constants depend on the water content. Several sample preparations were used in this investigation: one CAH10, three CAD10 and one CA(D/H)10, where the latter is a zero-matrix sample showing no coherent scattering contribution from the D/H atoms in a neutron diffraction powder pattern. The crystal structure including the positions of the H/D atoms was determined from analyses of four neutron diffraction powder patterns by means of the ab initio crystal structure determination program FOX and the FULLPROF crystal structure refinement program. Additionally, eight X-ray powder diffraction patterns (Cu K[alpha]1 and synchrotron X-rays) were used to establish phase purity. The analyses of these combined neutron and X-ray diffraction data clearly show that the previously published positions of the O atoms in the water molecules are in error. Thermogravimetric analysis of the CAD10 sample preparation used for the neutron diffraction studies gave the composition CaAl2(OD)8(D2O)2{center_dot}2.42D2O. Neutron and X-ray powder diffraction data gave the structural formula CaAl2(OX)8(X2O)2{center_dot}[gamma]X2O (X = D, H and D/H), where the [gamma] values are sample dependent and lie between 2.3 and 3.3.

  12. Thermal effects of added propanol on the helix-coil transition of (Pro-Pro-Gly) 10 in D 2O solution: An NMR study

    NASA Astrophysics Data System (ADS)

    Kai, Tsutomu; Uchiyama, Susumu; Nishi, Yoshinori; Kobayashi, Yuji; Tomiyama, Tetsuo

    2010-05-01

    The conformational transition of collagen model peptide, (Pro-Pro-Gly) 10, from the triple helical structure to the statistical coil was observed in various aqueous alcohol solutions by NMR measurements. In methanol or ethanol solution, the thermal transition temperature, Tm, of the peptide increased regularly with the concentration of alcohols. In 1- or 2-propanol, however, Tm first decreased and then increased steeply, in apparent contrast to the general trend that the addition of alcohol on aqueous solution increases the stability of ordered structure of polypeptides. This exceptional behavior of the collagen model peptide in propanols might provide a clue to investigate the mechanism of stabilization of protein conformation.

  13. 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

  14. Threshold ionization spectroscopy of H2O, HDO and D2O and low-lying vibrational levels of HDO+ and D2O+

    NASA Astrophysics Data System (ADS)

    Lauzin, Clément; Jacovella, Ugo; Merkt, Frédéric

    2015-12-01

    Rotationally resolved photoelectron spectra of jet-cooled H2O, HDO and D2O have been recorded near the origin of the ? photoionising transition following single-photon ionization using the complementary techniques of mass-analysed threshold-ionization (MATI) and pulsed-field-ionization zero-kinetic-energy (PFI-ZEKE) photoelectron spectroscopy. A gas mixture of H2O, HDO and D2O with Ar was obtained by mixing H2O (ℓ) and D2O (ℓ) in a reservoir and bubbling Ar gas through the mixture. To unambiguously assign the photoelectron bands to H2O, HDO or D2O, the PFI-ZEKE photoelectron spectra of the mixture were compared to MATI spectra and to spectra of H2O. Analysis of the rotational structure of the origin bands (v+1 = 0, v2+ = 0, v+3 = 0) ← (v1 = 0, v2 = 0, v3 = 0) of H2O, HDO and D2O and of the transitions to the (010), (020) and (100) levels of D2O+ and the first excited level of the O-D stretching mode of HDO+ provided new information on the photoionization dynamics of water and the energy level structure of HDO+ and D2O+.

  15. 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.

  16. Interactions of D2O with methane and fluoromethane surfaces.

    PubMed

    Souda, R; Kawanowa, H; Kondo, M; Gotoh, Y

    2004-03-22

    TOF-SIMS is used to investigate the interactions between D2O and hydrophobic molecules, such as CH4, CH3F, CH2F2, CHF3, and CF4, at cryogenic temperatures (15 K). By irradiation with a 1.5-keV He+ beam, the D(+)(D2O)n ions are ejected efficiently from the D2O nanoclusters physisorbed on the CF4 layer due to Coulomb explosion: the ion yields are by about two orders of magnitude higher than those from a thick D2O layer via the kinetic sputtering. The D(+)(D2O)n yields decrease on the CHnF(4-n) layer with increasing the number of the C-H group. This is because the Coulombic fission is quenched due to the delocalization of valence holes through the C-H...H-C and C-H...D2O contacts. A pure D2O film is hardly grown on the CH4 layer as a consequence of intermixing whereas the D2O molecules basically adsorb on the surfaces of fluoromethanes, suggesting the attractive (water-repellent) interactions in the C-H...D2O (C-F...D2O) contacts. The C-H...O bond behaves like a conventional O-H...O hydrogen bond as far as the collision-induced proton transfer reaction is concerned.

  17. 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.

  18. Characterization of swollen structure of high-density polyelectrolyte brushes in salt solution by neutron reflectivity

    NASA Astrophysics Data System (ADS)

    Kobayashi, Motoyasu; Terayama, Yuki; Hino, Masahiro; Ishihara, Kazuhiko; Takahara, Atsushi

    2009-08-01

    Zwitterionic and cationic polyelectrolyte brushes on quartz substrate were prepared by surface-initiated atom transfer radical polymerization of 2-(methacryloyloxy)ethyl phosphorylcholine (MPC) and 2-(methacryloyloxy)ethyltrimethylammonium chloride (METAC), respectively. The effects of ionic strength on brush structure and surface properties of densely grafted polyelectrolyte brushes were analysed by neutron reflectivity (NR) measurements. NR at poly(METAC)/D2O and poly(MPC)/D2O interface revealed that the grafted polymer chains were fairly extended from the substrate surface, while the thickness reduction of poly(METAC) brush was observed in 5.6 M NaCl/D2O solution due to the screening of the repulsive interaction between polycations by hydrated salt ions. Interestingly, no structural change was observed in poly(MPC) brush even in a salt solution probably due to the unique interaction properties of phosphorylcholine units.

  19. Molecular dynamics simulations of D2O ice photodesorption

    NASA Astrophysics Data System (ADS)

    Arasa, C.; Andersson, S.; Cuppen, H.; van Dishoeck, E. F.; Kroes, G. J.

    2011-05-01

    We present results of MD calculations performed to study the photodissociation of D2O in an amorphous ice at different ice temperatures in order to investigate isotope effects on the photodesorption processes. In dense interstellar clouds, small dust particles of micrometer silicates are covered by ice mantles, mainly consisting of H2O and also of CO, CO2. Previous MD calculations of H2O ice at Tice=10-90 K show that the photodesorption of H while OH remains trapped is the main outcome in the first three monolayers (MLs). On the other hand, the H and OH photofragments released recombine or are trapped at separate positions in the deeper MLs and can react with other species in the ice. Desorption and trapping probabilities have been calculated following photoexcitation of D2O amorphous ice at 10, 20, 60 and 90 K, and the main conclusions agree with previous calculations of H2O ice. But, the average D photodesorption probability is smaller than that of the H atom, whereas the average OD radical photodesorption probability is larger than that of OH, and the average D2O photodesorption probability is larger than that for H2O due to the D2O kick-out mechanism. The total (OD + D2O) yield has been compared with experiments and the total (OH + H2O) yield from previous simulations. We find better agreement when we compare experimental yields with calculated yields for D2O ice than when we compare with calculated yields for H2O ice.

  20. Terahertz absorption spectrum of D 2O vapor

    NASA Astrophysics Data System (ADS)

    Yu, B. L.; Yang, Y.; Zeng, F.; Xin, X.; Alfano, R. R.

    2006-02-01

    The absorption spectrum of D2O vapor from 0.2 to 2.0 THz (6.7-67 cm-1) which is associated with rotational modes was measured at one atmosphere using terahertz time-domain spectroscopy (THz-TDS). The linewidth and collisional dephasing times were measured for 26 pure rotational transitions in the ground vibrational state (0 0 0). The temperature dependence of the linewidth (Δν) behaves as Δν ∼ T-3/4 and the linewidth decrease with increasing temperature is attributed to the 1/r6 force of interaction between colliding D2O molecules.

  1. FT-IR Spectra of Antifreeze Glycoproteins in Heavy Water and D2O Ice.

    NASA Astrophysics Data System (ADS)

    Tsvetkova, N. M.; Crowe, J. H.; Feeney, R. H.; Fink, W. H.; Yeh, Yin

    2000-03-01

    This work presents FT-IR studies on the antifreeze glycoprotein (AFGP)/heavy water (D2O) mixtures during freezing and melting. AFGP in the blood serum of polar fish are known to prevent ice crystal growth by a non-colligative mechanism. There are 8 known fractions of AFGP (1 8) that range in molecular mass from 33.7 to 2.6 kD respectively, each composed of alanine-alanine-threonine repeats, with a disaccharide attached to the threonine residue. The smallest peptide (AFGP-8) is structurally different from fractions 1-5 in that it contains proline substituting for alanine in certain positions. Substantial linewidth change of the D20 bending mode (ca. 1210 cm-1) was measured with solutions containing fractions 2-5 during both freezing and thawing cycles, suggesting significant coupling between protein and water molecules. At the same time, the Amide I band between 1620 and 1675 cm-1 shows that 310 helix and random coils are the main conformations of fractions 2-5 and fraction 8 in the presence of ice. In liquid state, b-sheet dominates the secondary structure of AFGP 8, whereas b-sheet and random coil are the main conformations of AFGP 2-5. These results are discussed in terms of the ability of AFGP 2-5 to affect the surface states of ice.

  2. Anomalous H+ and D+ conductance in H2O-D2O mixtures

    NASA Astrophysics Data System (ADS)

    Weingärtner, H.; Chatzidimttriou-Dreismann, C. A.

    1990-08-01

    A KNOWLEDGE of proton-transfer dynamics and hydrogen-bonding in water and aqueous solutions is necessary for the understanding of many important chemical and biological processes. For example, quantum effects related to proton transfer (or tunnelling) in H+(H2O)n clusters of liquid water (where n = 1,2,· · ·) are known to have a dominant role in the proton conductance mechanism1,2 and are responsible for the high conductances of H+ and OH- in water. A new quantum theoretical approach to this process has been presented3, which is based on the hypothesis that there are quantum correlations4-8 between each H+ and the protons of the surrounding water molecules, leading to the formation of coherent dissipative structures3,8. From further investigations, one of us predicted that an anomalous decrease of H+ conductance in H2O-D2O mixtures would take place9. Having thought of an experiment to test these predictions9 we now report the experimental results and conclude that an anomalous decrease in proton conductance does indeed occur.

  3. Dynamical properties of LiI.D2O. II. Vibrational modes and disordering effects

    NASA Astrophysics Data System (ADS)

    Migliardo, P.; Romano, G. F.; Aliotta, F.; Bartolotta, A.; di Marco, G.

    1987-12-01

    The vibrational dynamics of α-phase lithium iodide monodeuterate (LID) is investigated by Raman scattering as a function of temperature. A simple model is presented in order to explain the linkage between the D2O reorientation and the Li+ hopping motion in the superionic α form. The internal O-D stretching and D2O bending regions are analyzed, within this model, by a suitable deconvolution of the symmetric lines. Spectral contributions that might originate from two possible polarization states of the D2O molecule are discovered. Raman spectra of the melt, both in the polarized (VV) and depolarized (VH) geometries, are also presented. The experimental data reveal that the melt, in spite of stronger anharmonicity effects, exhibits the same local order which is found in the α phase. Furthermore, a measurement performed at a fixed temperature (T=-70 °C) as a function of time shows a dependence of the spectral features on time, which confirms the existence of a structural phase transition towards an orthorhombic β form, as also suggested by neutron diffraction data. The low-frequency translational region shows the characteristic broad features of a density of vibrational states both in the α phase and in the melt, thus confirming the highly cooperative nature of the dynamics of the system.

  4. Submillimeter D2O-18 molecular laser with optical pumping

    NASA Astrophysics Data System (ADS)

    Svich, V. A.; Pokormiakho, N. G.; Topkov, A. N.

    1980-11-01

    In the considered investigation, nine new emission lines of the D2O-18 molecule were observed over the wavelength range from 96 to 140 micrometers. In the experiments, a CO2 TEA laser was used for optical pumping. The TEA laser was operated at atmospheric pressure with an output energy up to 2 J and a pulse length of 100 ns. A gaseous mixture with a composition of CO2:N2:He = 1:1:4 was excited by means of a pulsed transverse discharge. A resonator with a length of 1 m was formed by a spherical mirror with a radius of curvature of 10 m, and a gold-plated echelette grating with 100 lines/mm. The submillimeter cell consisted of a glass tube with an inside diameter of 80 mm and a length of 1270 mm, and the spherical mirrors of the submillimeter resonator.

  5. 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.

  6. 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.

  7. Heparin's solution structure determined by small-angle neutron scattering.

    PubMed

    Rubinson, Kenneth A; Chen, Yin; Cress, Brady F; Zhang, Fuming; Linhardt, Robert J

    2016-12-01

    Heparin is a linear, anionic polysaccharide that is widely used as a clinical anticoagulant. Despite its discovery 100 years ago in 1916, the solution structure of heparin remains unknown. The solution shape of heparin has not previously been examined in water under a range of concentrations, and here is done so in D2 O solution using small-angle neutron scattering (SANS). Solutions of 10 kDa heparin-in the millimolar concentration range-were probed with SANS. Our results show that when sodium concentrations are equivalent to the polyelectrolyte's charge or up to a few hundred millimoles higher, the molecular structure of heparin is compact and the shape could be well modeled by a cylinder with a length three to four times its diameter. In the presence of molar concentrations of sodium, the molecule becomes extended to nearly its full length estimated from reported X-ray measurements on stretched fibers. This stretched form is not found in the presence of molar concentrations of potassium ions. In this high-potassium environment, the heparin molecules have the same shape as when its charges were mostly protonated at pD ≈ 0.5, that is, they are compact and approximately half the length of the extended molecules.

  8. 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.

  9. 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.

  10. Infrared Spectroscopy of the H2/HD/D2-O2 Van Der Waals Complexes

    NASA Astrophysics Data System (ADS)

    Raston, Paul; Bunn, Hayley

    2016-06-01

    Hydrogen is the most abundant element in the universe and oxygen is the third, so understanding the interaction between the two in their different forms is important to understanding astrochemical processes. The interaction between H2 and O2 has been explored in low energy scattering experiments and by far infrared synchrotron spectroscopy of the van der Waals complex. The far infrared spectra suggest a parallel stacked average structure with seven bound rotationally excited states. Here, we present the far infrared spectrum of HD/D2-O2 and the mid infrared spectrum of H2-O2 at 80 K, recorded at the infrared beamline facility of the Australian Synchrotron. We observed 'sharp' peaks in the mid infrared region, corresponding to the end over end rotation of H2-O2, that are comparatively noisier than analogous peaks in the far infrared where the synchrotron light is brightest. The larger reduced mass of HD and D2 compared to H2 is expected to result in more rotational bound states and narrower bands. The latest results in our ongoing efforts to explore this system will be presented. Y. Kalugina, et al., Phys. Chem. Chem. Phys. 14, 16458 (2012) S. Chefdeville et al. Science 341, 1094 (2013) H. Bunn et al. ApJ 799, 65 (2015)

  11. 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.

  12. 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.

  13. 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.

  14. Spin-lattice coupling mediated multiferroicity in (ND4)2FeCl5.D2O

    NASA Astrophysics Data System (ADS)

    Tian, W.; Cao, Huibo; Wang, Jincheng; Ye, Feng; Matsuda, M.; Yan, J.-Q.; Liu, Yaohua; Garlea, V. O.; Agrawal, Harish K.; Chakoumakos, B. C.; Sales, B. C.; Fishman, Randy S.; Fernandez-Baca, J. A.

    2016-12-01

    We report a neutron diffraction study of the multiferroic mechanism in (ND4)2FeCl5.D2O , a molecular compound that exhibits magnetically induced ferroelectricity. This material exhibits two successive magnetic transitions on cooling: a long-range order transition to an incommensurate (IC) collinear sinusoidal spin state at TN=7.3 K, followed by a second transition to an IC cycloidal spin state at TF E=6.8 K, the latter of which is accompanied by spontaneous ferroelectric polarization. The cycloid structure is strongly distorted by spin-lattice coupling, as evidenced by the observations of both odd and even higher-order harmonics associated with the cycloid wave vector, and a weak commensurate phase that coexists with the IC phase. The second-order harmonic appears at TF E, thereby providing unambiguous evidence that the onset of the electric polarization is accompanied by a lattice modulation due to spin-lattice interaction. The neutron results, in conjunction with the negative thermal expansion and large magnetostriction observed in Ref. [19], indicate that spin-lattice coupling plays a critical role in the ferroelectric mechanism of (ND4)2FeCl5.D2O .

  15. Spin-lattice coupling mediated multiferroicity in (ND4)2FeCl5·D2O

    DOE PAGES

    Tian, Wei; Cao, Huibo; Wang, Jincheng; ...

    2016-12-07

    In this paper, we report a neutron diffraction study of the multiferroic mechanism in (ND4)2FeCl5 • D2O, a molecular compound that exhibits magnetically induced ferroelectricity. This material exhibits two successive magnetic transitions on cooling: a long-range order transition to an incommensurate (IC) collinear sinusoidal spin state at TN = 7.3 K, followed by a second transition to an IC cycloidal spin state at TFE = 6.8 K, the latter of which is accompanied by spontaneous ferroelectric polarization. The cycloid structure is strongly distorted by spin-lattice coupling, as evidenced by the observations of both odd and even higher-order harmonics associated withmore » the cycloid wave vector, and a weak commensurate phase that coexists with the IC phase. The second-order harmonic appears at TFE, thereby providing unambiguous evidence that the onset of the electric polarization is accompanied by a lattice modulation due to spin-lattice interaction. The neutron results, in conjunction with the negative thermal expansion and large magnetostriction observed, indicate that spin-lattice coupling plays a critical role in the ferroelectric mechanism of (ND4)2FeCl5 • D2O.« less

  16. Spin-lattice coupling mediated multiferroicity in (ND4)2FeCl5 • D2O

    DOE PAGES

    Tian, Wei; Cao, Huibo; Wang, Jincheng; ...

    2016-12-07

    In this paper, we report a neutron diffraction study of the multiferroic mechanism in (ND4)2FeCl5 • D2O, a molecular compound that exhibits magnetically induced ferroelectricity. This material exhibits two successive magnetic transitions on cooling: a long-range order transition to an incommensurate (IC) collinear sinusoidal spin state at TN = 7.3 K, followed by a second transition to an IC cycloidal spin state at TFE = 6.8 K, the latter of which is accompanied by spontaneous ferroelectric polarization. The cycloid structure is strongly distorted by spin-lattice coupling, as evidenced by the observations of both odd and even higher-order harmonics associated withmore » the cycloid wave vector, and a weak commensurate phase that coexists with the IC phase. The second-order harmonic appears at TFE, thereby providing unambiguous evidence that the onset of the electric polarization is accompanied by a lattice modulation due to spin-lattice interaction. The neutron results, in conjunction with the negative thermal expansion and large magnetostriction observed, indicate that spin-lattice coupling plays a critical role in the ferroelectric mechanism of (ND4)2FeCl5 • D2O.« less

  17. Absolute cross sections for dissociative electron attachment to H2O and D2O

    NASA Astrophysics Data System (ADS)

    Rawat, Prashant; Prabhudesai, Vaibhav S.; Aravind, G.; Rahman, M. A.; Krishnakumar, E.

    2007-12-01

    The dissociative electron attachment (DEA) process to water (H2O) and heavy water (D2O) has been studied in the gas phase in a cross beam experiment for electron energies up to 20 eV. The apparatus used eliminates discrimination due to the kinetic energy and angular distribution of the ions. The cross sections are normalized to absolute values using the cross section for production of O- from O2 (Rapp and Briglia 1965 J. Chem. Phys. 43 1480). These are the first exhaustive measurements of absolute cross sections for both the H- and O- from H2O and D- and O- from D2O at all the three resonances. The results are compared with the scarce data available in the literature. Isotope effect is observed at the 12 eV resonance in the H- channel and at all the three resonances in the O- channel.

  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. Experimental and theoretical studies of charge transfer and deuterium ion transfer between D2O+ and C2H4

    NASA Astrophysics Data System (ADS)

    Liu, Li; Cai, Xiaohui; Li, Yue; Richards O'Grady, Elizabeth; Farrar, James M.

    2004-08-01

    The charge transfer and deuterium ion transfer reactions between D2O+ and C2H4 have been studied using the crossed beam technique at relative collision energies below one electron volt and by density functional theory (DFT) calculations. Both direct and rearrangement charge transfer processes are observed, forming C2H4+ and C2H3D+, respectively. Independent of collision energy, deuterium ion transfer accounts for approximately 20% of the reactive collisions. Between 22 and 36 % of charge transfer collisions occur with rearrangement. In both charge transfer processes, comparison of the internal energy distributions of products with the photoelectron spectrum of C2H4 shows that Franck-Condon factors determine energy disposal in these channels. DFT calculations provide evidence for transient intermediates that undergo H/D migration with rearrangement, but with minimal modification of the product energy distributions determined by long range electron transfer. The cross section for charge transfer with rearrangement is approximately 103 larger than predicted from the Rice-Ramsperger-Kassel-Marcus isomerization rate in transient complexes, suggesting a nonstatistical mechanism for H/D exchange. DFT calculations suggest that reactive trajectories for deuterium ion transfer follow a pathway in which a deuterium atom from D2O+ approaches the π-cloud of ethylene along the perpendicular bisector of the C-C bond. The product kinetic energy distributions exhibit structure consistent with vibrational motion of the D-atom in the bridged C2H4D+ product perpendicular to the C-C bond. The reaction quantitatively transforms the reaction exothermicity into internal excitation of the products, consistent with mixed energy release in which the deuterium ion is transferred in a configuration in which both the breaking and the forming bonds are extended.

  20. The effect of rock particles and D2O replacement on the flow behaviour of ice.

    PubMed

    Middleton, Ceri A; Grindrod, Peter M; Sammonds, Peter R

    2017-02-13

    Ice-rock mixtures are found in a range of natural terrestrial and planetary environments. To understand how flow processes occur in these environments, laboratory-derived properties can be extrapolated to natural conditions through flow laws. Here, deformation experiments have been carried out on polycrystalline samples of pure ice, ice-rock and D2O-ice-rock mixtures at temperatures of 263, 253 and 233 K, confining pressure of 0 and 48 MPa, rock fraction of 0-50 vol.% and strain-rates of 5 × 10(-7) to 5 × 10(-5) s(-1) Both the presence of rock particles and replacement of H2O by D2O increase bulk strength. Calculated flow law parameters for ice and H2O-ice-rock are similar to literature values at equivalent conditions, except for the value of the rock fraction exponent, here found to be 1. D2O samples are 1.8 times stronger than H2O samples, probably due to the higher mass of deuterons when compared with protons. A gradual transition between dislocation creep and grain-size-sensitive deformation at the lowest strain-rates in ice and ice-rock samples is suggested. These results demonstrate that flow laws can be found to describe ice-rock behaviour, and should be used in modelling of natural processes, but that further work is required to constrain parameters and mechanisms for the observed strength enhancement.This article is part of the themed issue 'Microdynamics of ice'.

  1. The effect of rock particles and D2O replacement on the flow behaviour of ice

    NASA Astrophysics Data System (ADS)

    Middleton, Ceri A.; Grindrod, Peter M.; Sammonds, Peter R.

    2017-02-01

    Ice-rock mixtures are found in a range of natural terrestrial and planetary environments. To understand how flow processes occur in these environments, laboratory-derived properties can be extrapolated to natural conditions through flow laws. Here, deformation experiments have been carried out on polycrystalline samples of pure ice, ice-rock and D2O-ice-rock mixtures at temperatures of 263, 253 and 233 K, confining pressure of 0 and 48 MPa, rock fraction of 0-50 vol.% and strain-rates of 5 × 10-7 to 5 × 10-5 s-1. Both the presence of rock particles and replacement of H2O by D2O increase bulk strength. Calculated flow law parameters for ice and H2O-ice-rock are similar to literature values at equivalent conditions, except for the value of the rock fraction exponent, here found to be 1. D2O samples are 1.8 times stronger than H2O samples, probably due to the higher mass of deuterons when compared with protons. A gradual transition between dislocation creep and grain-size-sensitive deformation at the lowest strain-rates in ice and ice-rock samples is suggested. These results demonstrate that flow laws can be found to describe ice-rock behaviour, and should be used in modelling of natural processes, but that further work is required to constrain parameters and mechanisms for the observed strength enhancement. This article is part of the themed issue 'Microdynamics of ice'.

  2. Activation process and absorption/desorption of D2O for Zr-V-Fe getter

    NASA Astrophysics Data System (ADS)

    Ichimura, K.; Inoue, N.; Ashida, K.; Watanabe, K.; Takeuchi, T.

    1984-12-01

    Nonevaporable getters have wide applicability for tritium handling systems. From this view point, the activation process of the Zr-V-Fe getter (St-707) and absorption/desorption of D2O on the getter surface were investigated, by means of XPS-SIMS and mass analyzed thermal desorption spectroscopy. XPS-SIMS measurements revealed that the getter surface exposed to air was covered with adsorbed H2O, CO and small amounts of hydrocarbons and that the getter components are oxidized. Upon heating of the getter above 500 °C, the adsorbed species disappeared from the surface, partly due to desorption and partly due to migration into the bulk. Consequently, metallic Zr and V appeared on the surface, whereas Fe disappeared. The surface composition was evaluated to be 87 at% Zr-13 at% V. After the activation, water (D2O ) was readily absorbed into the getter at 300 °C in the form of deuterium atoms. The absorption rate was proportional to the partial pressure of water, indicating that the rate determining step for the absorption is the dissociation of water molecules on the surface. The absorption rate constant was 0.009 and 0.24 cc/s/cm2 (net surface area) [or 1.5 and 39 cc/s/cm2 (projected area)] at 25 and 300°C, respectively. Only D2 was desorbed from the getter exposed to D2O at 25 and 300 °C. The rate determining step for the desorption is association of deuterium atoms on the surface diffused from the bulk.

  3. 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.

  4. The vibrational Stokes shift of water (HOD in D2O)

    NASA Astrophysics Data System (ADS)

    Wang, Zhaohui; Pang, Yoonsoo; Dlott, Dana D.

    2004-05-01

    The vibrational Stokes shift of the OH stretching transition νOH of water is the shift between the ground-state absorption and the excited-state (v=1) emission. A recent measurement on HOD in D2O solvent [S. Woutersen and H. J. Bakker, Phys. Rev. Lett. 83, 2077 (1999)] of a 70 cm-1 redshift, and a subsequent calculation of a 57 cm-1 redshift using equilibrium molecular dynamics simulations [C. P. Lawrence and J. L. Skinner, J. Chem. Phys. 117, 8847 (2002)] were in good agreement. We now report extensive measurements of the vibrational Stokes shift in HOD/D2O using an ultrafast IR pump, Raman probe method. The vibrational Stokes shift is seen to depend on the pump pulse frequency and on time delay; by varying these parameters it can be made to range from 112 to -32 cm-1 (negative values indicate a blueshift in the excited state). The equilibrium vibrational Stokes shift is actually a negative rather than a positive quantity. Possible reasons for the disagreement between experiment and theory are briefly discussed.

  5. 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.

  6. Transition state structures in solution

    SciTech Connect

    Bertran, J.; Lluch, J. M.; Gonzalez-Lafont, A.; Dillet, V.; Perez, V.

    1995-04-05

    In the present paper the location of transition state structures for reactions in solution has been studied. Continuum model calculations have been carried out on the Friedel-Crafts alkylation reaction and a proton transfer through a water molecule between two oxygen atoms in formic acid. In this model the separation between the chemical system and the solvent has been introduced. On the other hand, the discrete Monte Carlo methodology has also been used to simulate the solvent effect on dissociative electron transfer processes. In this model, the hypothesis of separability is not assumed. Finally, the validity of both approaches is discussed.

  7. Transition state structures in solution

    NASA Astrophysics Data System (ADS)

    Bertrán, J.; Lluch, J. M.; Gonzàlez-Lafont, A.; Dillet, V.; Pérez, V.

    1995-04-01

    In the present paper the location of transition state structures for reactions in solution has been studied. Continuum model calculations have been carried out on the Friedel-Crafts alkylation reaction and a proton transfer through a water molecule between two oxygen atoms in formic acid. In this model the separation between the chemical system and the solvent has been introduced. On the other hand, the discrete Monte Carlo methodology has also been used to simulate the solvent effect on dissociative electron transfer processes. In this model, the hypothesis of separability is not assumed. Finally, the validity of both approaches is discussed.

  8. 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.

  9. 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

  10. Estimation of water flow velocity in small plants using cold neutron imaging with D 2O tracer

    NASA Astrophysics Data System (ADS)

    Matsushima, U.; Herppich, W. B.; Kardjilov, N.; Graf, W.; Hilger, A.; Manke, I.

    2009-06-01

    Water flow imaging may help to better understand various problems related to water stress of plants. It may help to fully understand the water relations of plants. The objective of this research was to estimate the velocity of water flow in plant samples. Cut roses ( Rosa hybrida, var. 'Milva') were used as samples. Cold neutron radiography (CNR) was conducted at CONRAD, Helmholtz Center Berlin for Materials and Energy, Berlin, Germany. D 2O and H 2O were interchangeably injected into the water feeding system of the sample. After the uptake of D 2O, the neutron transmission increased due to the smaller attenuation coefficient of D 2O compared to H 2O. Replacement of D 2O in the rose peduncle was clearly observed. Three different optical flow algorithms, Block Matching, Horn-Schunck and Lucas-Kanade, were used to calculate the vector of D 2O tracer flow. The quality of sequential images providing sufficient spatial and temporal resolution allowed to estimate flow vector.

  11. 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.

  12. The H2O/D2O isotope effect in crystalline lanthanide sulfates at photo-, radio-, and triboluminescence

    NASA Astrophysics Data System (ADS)

    Sharipov, G. L.; Tukhbatullin, A. A.; Mescheryakova, E. S.

    2016-02-01

    We comparatively studied the H2O/D2O isotope effect of lanthanide sulfate crystallohydrates on photo-, radio-, and triboluminescence and lifetimes of the excited Ln3+ ions. Replacing H2O by D2O leads to an increase in the luminescence intensity whereas this process does not affect the maxima positions in photo-, radio-, and triboluminescence spectra. This isotope effect agrees with the known concepts of changes in luminescence quantum yields of the Ln3+ ions being the main emitters. The bands of OH and OD radicals arise in triboluminescence spectra of lanthanide sulfate crystallohydrates (with H2O or D2O) registered in argon atmosphere in UV region. This supports the proposition that water destruction occurs at the degradation of the crystallohydrates.

  13. Exact vibrational energies of non-rotating H 2O and D 2O using an accurate ab initio potential

    NASA Astrophysics Data System (ADS)

    Bowman, Joel M.; Wierzbicki, Andrzej; Zúñiga, Jose

    1988-09-01

    Variationally exact vibrational energies are reported for non-rotating H 2O and D 2O using the recent CCSDT-1 ab initio potential of Bartlett, Cole, Purvis, Ermler, Hsieh and Shavitt as fit to an SPF quartic force field by Ermler. Twenty vibrational states are calculated for H 2O and D 2O and compared with experimental data. The agreement with experiment is fairly good; however, when the second-order bending force constant is reduced slightly, the agreement with experiment improves significantly. For eighteen states of H 2O the largest error is 15 cm -1 and the average absolute error is 6 cm -1. For eight states of D 2O the largest error is 7 cm -1 and the average absolute error is 4 cm -1.

  14. 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.

  15. 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.

  16. On the Effect of an Error in a Standard D2O-Moderated 252Cf Energy Spectrum

    SciTech Connect

    Frederick Cummings

    2009-12-01

    There appears to be an error in the neutron fluence for neutrons with energies between 9 and 10 MeV for the tabulated D2O-moderated 252Cf source in ISO 8529-1. The error contributes a total error to neutron dose values from this source of approximately 3%.

  17. On the effect of an error in a standard D2O-moderated 252Cf energy spectrum.

    PubMed

    Cummings, F M

    2009-12-01

    There appears to be an error in the neutron fluence for neutrons with energies between 9 and 10 MeV for the tabulated D2O-moderated Cf source in ISO 8529-1. If the referenced spectrum is used as tabulated, the error contributes a total error to neutron dose values from this source of approximately 3%.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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.

  19. Fully Deuterated Aliphatic Hydrocarbons Obtained From Iron Carbide Treated with DCl and D2O

    NASA Technical Reports Server (NTRS)

    Marquez, C.; Lazcano, A.; Miller, S. L.; Oro, J.

    1966-01-01

    According to Oparin, Mendeleev thought that the origin of petroleum was the result of the hydrolysis of iron carbides by superheated steam under pressure from the deep interior of the Earth through geological formations where the metal carbides exist. As early as 1877, Mendeleev described the reaction leading to the synthesis of hydrocarbons according to the general equation 3Fe(sub m)C(sub n) + mH2O yields mFe3O4 + C(sub 3n)H(sub 8m). Other experimental studies on the production of hydrocarbons from cast iron have been reported. Because of the possibility that hydrocarbons may have been trapped within the carbon matrix of the cast iron, which usually has a high content of carbon, we have studied the reaction of pure iron carbide with deuterium chloride and deuterated water. This was done in order to distinguish any newly formed deuterated hydrocarbons from any possible impurities of trapped hydrocarbons. The experiments were carried out by simply allowing iron carbide to react with concentrated deuterium chloride in D2O. The volatile hydrocarbon fraction examined by gas chromatography-mass spectrometry (GC/MS), using a Finnigan 1020/OWA instrument. contained low molecular weight hydrocarbons in a range C3 to C7. Lower molecular weight hydrocarbons were not detected by GC/MS because the MS scanning mode was preset above mass 40 to exclude components of air. The identified hydrocarbons are similar to those obtained under prebiotic conditions using high frequency discharge. The hydrocarbons found in common were propane, butane, pentane, 3-methylpentane, hexane, and heptane. The percent yields decline with increasing carbon number (propane 11%, n-heptane 1%). Similar results have been obtained by the direct treatment of metal carbides by pulse laser vaporization mass spectrometry. These results show that the hydrolysis of iron carbides may have been a significant source of hydrocarbons on the primitive Earth. There appears to be a predominance of straight chain

  20. A four-dimensional potential energy surface and predicted infrared spectra for the Ne-D2O van der Waals complex in the ν2 bending region of D2O molecule

    NASA Astrophysics Data System (ADS)

    He, Shanshan; Chen, Dong; Li, Ya; Feng, Eryin; Huang, Wuying

    2016-11-01

    In this paper, a four-dimensional potential energy surface (PES) for the Ne-D2O complex is constructed theoretically. The calculations are carried out at CCSD(T) level with large basis sets augmented with mid-bond functions. The PES includes explicit dependence on the ν2 symmetric bending coordinate Q2 of the D2O molecule. Two vibrationally averaged potentials in the ground and first excited bending states are obtained respectively. Using these two potentials we calculate the bound states of the complexes. The theoretical rovibrational transition frequencies for three bands: П(111,ν2 = 1)←Σ000, Σ(111,ν2 = 1)←Σ000 and n = 1, Σ(000,ν2 = 1)←Σ000 are predicted and generally in good agreement with the experimental observed values.

  1. 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

  2. Evaluation of the characteristics of the neutron reference field using D2O-moderated 252Cf source.

    PubMed

    Kowatari, M; Fujii, K; Takahashi, M; Yoshizawa, M; Shimizu, S; Kawasaki, K; Yamaguchi, Y

    2007-01-01

    The ambient/personal dose equivalent per fluence for D(2)O moderated (252)Cf neutron source was determined by measurement. An appropriate subtraction of the scattered neutrons is required for the accurate measurement of direct neutrons. A cubic shadow object was used for the subtraction of the scattered neutrons from the surroundings. The scattered neutrons to be subtracted vary with the position of the shadow object due to the large volume of the source. Using the Monte Carlo code MCNP-4C, the optimum positions of the shadow object were surveyed for subtracting the scattered neutrons. The energy spectra of direct neutrons were measured in the optimum position. The dosimetric parameters for the D(2)O moderated (252)Cf neutron source were reasonable, taking into account the uncertainties of the parameters.

  3. Monitoring allostery in D2O: a necessary control in studies using hydrogen/deuterium exchange to characterize allosteric regulation.

    PubMed

    Prasannan, Charulata B; Artigues, Antonio; Fenton, Aron W

    2011-08-01

    There is currently a renewed focus aimed at understanding allosteric mechanisms at atomic resolution. This current interest seeks to understand how both changes in protein conformations and changes in protein dynamics contribute to relaying an allosteric signal between two ligand binding sites on a protein (e.g., active and allosteric sites). Both nuclear magnetic resonance (NMR), by monitoring protein dynamics directly, and hydrogen/deuterium exchange, by monitoring solvent accessibility of backbone amides, offer insights into protein dynamics. Unfortunately, many allosteric proteins exceed the size limitations of standard NMR techniques. Although hydrogen/deuterium exchange as detected by mass spectrometry (H/DX-MS) offers an alternative evaluation method, any application of hydrogen/deuterium exchange requires that the property being measured functions in both H(2)O and D(2)O. Due to the promising future H/DX-MS has in the evaluation of allosteric mechanisms in large proteins, we demonstrate an evaluation of allosteric regulation in D(2)O. Exemplified using phenylalanine inhibition of rabbit muscle pyruvate kinase, we find that binding of the inhibitor is greatly reduced in D(2)O, but the effector continues to elicit an allosteric response.

  4. Quantitative photoabsorption and fluorescence study of H2O and D2O at 50-190 nm

    NASA Technical Reports Server (NTRS)

    Lee, L. C.; Suto, Masako

    1986-01-01

    The photoabsorption cross sections and the fluorescence quantum yields of H2O and D2O were measured in the 50-190 nm region using synchrotron radiation as a light source. The oscillator strengths for the Rydberg states of H2O and D2O were determined from the absorption cross sections measured. The processes for the production of fluorescence from the excited species H(asterisk) (n greater than 2), D(asterisk) (n greater than 2), OH(asterisk) (A) and OD(asterisk) (A) are discussed. The upper limit for the dissociation energy of D(D-OD) was determined, from the threshold of the OD(A-X) fluorescence, to be 5.14 + or - 0.01 eV. The upper limit for the cross section of visible fluorescence from the excited H2O(+) ions was determined to be 2 x 10 to the -19th sq cm. A comparison between the photoexcitation spectra of H2O and D2O is made.

  5. 13C NMR studies of the molecular dynamics of chlorpromazine in solution

    NASA Astrophysics Data System (ADS)

    Sakamoto, Yohko; Ishii, Tomoko; Kurokawa, Noriko; Aoki, Toshikazu; Ohshima, Shigeru

    1996-02-01

    The optimum structure, which is expected to lead to biological activity, of chlorpromazine hydrochloride salt (compound ( I)) in solution was determined on the basis of NMR data and molecular orbital calculations; compound ( I) favours a bent structure in which the side-chain tilts toward the chlorinated benzene ring. The molecular mobility of compound ( I) in CDCl 3 and D 2O was also examined on the basis of 13C NMR spin-lattice relaxation time ( T1). T1 depends on the magnetic field strength and the solvent. The dependence indicates that the molecular mobility of compound ( I) is larger in D 2O than in CDCl 3

  6. Deuterium isotope effects on the ionization constant of acetic acid in H2O and D2O by AC conductance from 368 to 548 K at 20 MPa.

    PubMed

    Erickson, K M; Arcis, H; Raffa, D; Zimmerman, G H; Tremaine, P R

    2011-03-31

    Values of the ionization constant of acetic acid in H(2)O and D(2)O (K(HAc) and K(DAc)) and the deuterium isotope effect, ΔpK = pK(DAc) - pK(HAc), have been determined from T = 368 K to T = 548 K at p = 20 MPa, using a flow-through ac conductance cell built at the University of Delaware. Measurements were made on dilute (ionic strength ∼ 10(-4) mol·kg(-1)) solutions of acetic acid, sodium acetate, hydrochloric acid, and sodium chloride in H(2)O and D(2)O, injected in sequence at each temperature and pressure, so that systematic errors in the measured conductance of each solution would cancel. Experimental values for the molar conductivity, Λ, of the strong electrolytes were used to calculate the molar conductivity at infinite dilution, Λ°, using the Fuoss-Hsia-Fernández-Prini (FHFP) equation. These were used to calculate the molar conductivity at infinite dilution for acetic acid which was in turn used to calculate the degree of dissociation and finally the ionization constants of acetic acid. This same procedure was done for the pertinent deuterated solutes in D(2)O. Measured values of log K(HAc), log K(DAc), and ΔpK were obtained to a precision of ±0.008. The present results are in agreement with the only other accurate study at high temperatures and pressures (Mesmer, R. E.; Herting, D. L. J. Solution Chem.1978, 7, 901-913). The deuterium isotope effects, ΔpK, become independent of temperature above ∼420 K, at a value approximately 0.1 unit lower than that at 298 K. These values are ΔpK = 0.43 ± 0.01 and ΔpK = 0.51 ± 0.01, respectively. The temperature dependence of the Walden product ratio, (λ°η)(D(2)O)/(λ°η)(H(2)O), indicates a change in the relative hydration behavior of ions, whereby the effective Stokes radii of the sodium, chloride, and acetate ions in D(2)O relative to H(2)O reverse above ∼423 K. The results also suggest that the greater efficiency of the well-established proton-hopping transport mechanisms for OH(-) and H(3)O

  7. Urban infrastructure choices structure climate solutions

    NASA Astrophysics Data System (ADS)

    Creutzig, Felix; Agoston, Peter; Minx, Jan C.; Canadell, Josep G.; Andrew, Robbie M.; Quéré, Corinne Le; Peters, Glen P.; Sharifi, Ayyoob; Yamagata, Yoshiki; Dhakal, Shobhakar

    2016-12-01

    Cities are becoming increasingly important in combatting climate change, but their overall role in global solution pathways remains unclear. Here we suggest structuring urban climate solutions along the use of existing and newly built infrastructures, providing estimates of the mitigation potential.

  8. 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.

  9. Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-β-d-maltoside using small-angle neutron scattering and molecular dynamics simulation

    SciTech Connect

    Le, Rosemary K.; Harris, Bradley J.; Iwuchukwu, Ifeyinwa J.; Bruce, Barry D.; Cheng, Xiaolin; Qian, Shuo; Heller, William T.; O’Neill, Hugh; Frymier, Paul D.

    2014-05-01

    Small-angle neutron scattering (SANS) and molecular dynamics (MD) simulation were used to investigate the structure of trimeric photosystem I (PSI) from Thermosynechococcus elongatus (T. elongatus) stabilized in n-dodecyl-β-d-maltoside (DDM) detergent solution. Scattering curves of detergent and protein–detergent complexes were measured at 18% D2O, the contrast match point for the detergent, and 100% D2O, allowing observation of the structures of protein/detergent complexes. It was determined that the maximum dimension of the PSI–DDM complex was consistent with the presence of a monolayer belt of detergent around the periphery of PSI. A dummy-atom reconstruction of the shape of the complex from the SANS data indicates that the detergent envelope has an irregular shape around the hydrophobic periphery of the PSI trimer rather than a uniform, toroidal belt around the complex. A 50 ns MD simulation model (a DDM ring surrounding the PSI complex with extra interstitial DDM) of the PSI–DDM complex was developed for comparison with the SANS data. The results suggest that DDM undergoes additional structuring around the membrane-spanning surface of the complex instead of a simple, relatively uniform belt, as is generally assumed for studies that use detergents to solubilize membrane proteins.

  10. Metabolic-Activity-Based Assessment of Antimicrobial Effects by D2O-Labeled Single-Cell Raman Microspectroscopy.

    PubMed

    Tao, Yifan; Wang, Yun; Huang, Shi; Zhu, Pengfei; Huang, Wei E; Ling, Junqi; Xu, Jian

    2017-04-04

    To combat the spread of antibiotic resistance, methods that quantitatively assess the metabolism-inhibiting effects of drugs in a rapid and culture-independent manner are urgently needed. Here using four oral bacteria as models, we show that heavy water (D2O)-based single-cell Raman microspectroscopy (D2O-Raman) can probe bacterial response to different drugs using the Raman shift at the C-D (carbon-deuterium vibration) band in 2040 to 2300 cm(-1) as a universal biomarker for metabolic activity at single-bacterial-cell resolution. The "minimum inhibitory concentration based on metabolic activity" (MIC-MA), defined as the minimal dose under which the median ΔC-D-ratio at 8 h of drug exposure is ≤0 and the standard deviation (SD) of the ΔC-D ratio among individual cells is ≤0.005, was proposed to evaluate the metabolism-inhibiting efficacy of drugs. In addition, heterogeneity index of MIC-MA (MIC-MA-HI), defined as SD of C-D ratio among individual cells, quantitatively assesses the among-cell heterogeneity of metabolic activity after drug regimens. When exposed to 1× MIC of sodium fluoride (NaF), 1× MIC of chlorhexidine (CHX), or 60× MIC of ampicillin, the cariogenic oral pathogen Streptococcus mutans UA159 ceased propagation yet remained metabolically highly active. This underscores the advantage of MIC-MA over the growth-based MIC in being able to detect the "nongrowing but metabolically active" (NGMA) cells that underlie many latent or recurring infections. Moreover, antibiotic susceptible and resistant S. mutans strains can be readily discriminated at as early as 0.5 h. Thus, D2O-Raman can serve as a universal method for rapid and quantitative assessment of antimicrobial effects based on general metabolic activity at single-cell resolution.

  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. High Efficient, Intense and Compact Pulsed D2O Terahertz Laser Pumped With a TEA CO2 Laser

    NASA Astrophysics Data System (ADS)

    Geng, Lijie; Qu, Yanchen; Zhao, Weijiang; Du, Jun

    2013-12-01

    A high efficient, intense and compact pulsed D2O terahertz laser is presented, which is pumped by a multi-transverse mode TEA CO2 laser. For D2O gas as the active medium, with the cavity length of 120 cm, pulse energy of the THz laser has been investigated as the variation of pump energy and gas pressure. When the pump energy was 1.41 J, the maximum single pulse energy of 6.2 mJ was achieved at the wavelength of 385 μm. Photon conversion efficiency as high as 36.5% was obtained when laser operated at the maximum output energy. As the pump energy was raised from 0.57 to 1.41 J, the optimum pressure was slightly changed from 400 to 700 Pa. The THz pulse consisted of a spike pulse with pulse width of 120 ns and a tail pulse with pulse width of about 170 ns. The peak power of the spike pulse is about 44.3 kW. Comparing with the occurring time and pulse width of pump pulse, 70 ns delay and 10ns broadening were observed in the THz spike pulse.

  13. 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

  14. 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.

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

    PubMed Central

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

    1999-01-01

    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

  16. Fourier transform infrared spectra studies of protein in reverse micelles: effect of AOT/isooctane on the secondary structure of alpha-chymotrypsin.

    PubMed

    Chang, Q; Liu, H; Chen, J

    1994-06-12

    The amide I region Fourier transform infrared (FTIR) spectra of alpha-chymotrypsin have been studied in deuterium oxide (D2O) solution and also in reverse micellar solution of AOT/isooctane. The Fourier second derivative was applied to all spectra, revealing that the amide I band of alpha-chymotrypsin in D2O and in reverse micellar solution consists of nine components. The band frequencies are assigned to alpha-helix, beta-sheet, random and turn structure. The second derivative spectra of alpha-chymotrypsin have been shifted in the reverse micellar solution of AOT/isooctane in comparison with its spectra in D2O. This shift has also changed the intensity of each band. Through accurate measurement of the band intensities, the relative amount of different structure of alpha-chymotrypsin can be estimated. The comparison of the calculated results obtained in D2O with those obtained in reverse micellar solution provides the possibility to analyze the effect of reverse micellar solution of AOT/isooctane on the secondary structure of alpha-chymotrypsin. The results indicate that the reverse micellar solution has decreased the amount of alpha-helix and beta-sheet structure and increased the amount of random and turn structure in alpha-chymotrypsin. The increase of the amount of random structure might loosen the structure of alpha-chymotrypsin and change the activity of the enzyme.

  17. 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.

  18. Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map.

    PubMed

    Hayashi, Tomoyuki; la Cour Jansen, Thomas; Zhuang, Wei; Mukamel, Shaul

    2005-01-13

    An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D(2)O solvent obtained from molecular dynamics simulations, we calculate the infrared absorption of the O-H stretch. The resulting solvent shift and infrared line shape for three force fields (TIP4P, SPC/E, and SW) are in good agreement with the experiment. A collective coordinate response for the solvent effect is constructed by identifying the main electrostatic field and gradient components contributing to the line shape. This allows a realistic stochastic Liouville equation simulation of the line shapes which is not restricted to Gaussian frequency fluctuations.

  19. Crystallization Kinetics and Excess Free Energy of H2O and D2O Nanoscale Films of Amorphous Solid Water

    SciTech Connect

    Smith, R. Scott; Matthiesen, Jesper; Knox, Jake R.; Kay, Bruce D.

    2011-06-16

    Temperature-programmed desorption (TPD) and reflection absorption infrared spectroscopy (RAIRS) are used to investigate the crystallization kinetics and measure the excess free energy of metastable amorphous solid water films (ASW) of H2O and D2O grown using molecular beams. The desorption rates from the amorphous and crystalline phases of ASW are distinct, and as such, crystallization manifests can be observed in the TPD spectrum. The crystallization kinetics were studied by varying the TPD heating rate from 0.001 to 3 K/s. A coupled desorptioncrystallization kinetic model accurately simulates the desorption spectra and accurately predicts the observed temperature shifts in the crystallization. Isothermal crystallization studies using RAIRS are in agreement with the TPD results. Furthermore, highly sensitive measurements of the desorption rates were used to determine the excess free energy of ASW near 150 K. The excess entropy obtained from these data are consistent with there being a thermodynamic continuity between ASW and supercooled liquid water.

  20. Universal BPS structure of stationary supergravity solutions

    NASA Astrophysics Data System (ADS)

    Bossard, Guillaume; Nicolai, Hermann; Stelle, K. S.

    2009-07-01

    We study asymptotically flat stationary solutions of four-dimensional supergravity theories via the associated fraktur G/fraktur H* pseudo-Riemannian non-linear sigma models in three spatial dimensions. The Noether charge Script C associated to fraktur G is shown to satisfy a characteristic equation that determines it as a function of the four-dimensional conserved charges. The matrix Script C is nilpotent for non-rotating extremal solutions. The nilpotency degree of Script C is directly related to the BPS degree of the corresponding solution when they are BPS. Equivalently, the charges can be described in terms of a Weyl spinor |Script Crangle of Spin*(2Script N), and then the characteristic equation becomes equivalent to a generalisation of the Cartan pure spinor constraint on |Script Crangle. The invariance of a given solution with respect to supersymmetry is determined by an algebraic `Dirac equation' on the Weyl spinor |Script Crangle. We explicitly solve this equation for all pure supergravity theories and we characterise the stratified structure of the moduli space of asymptotically Taub-NUT black holes with respect to their BPS degree. The analysis is valid for any asymptotically flat stationary solutions for which the singularities are protected by horizons. The fraktur H*-orbits of extremal solutions are identified as Lagrangian submanifolds of nilpotent orbits of fraktur G, and so the moduli space of extremal spherically symmetric black holes is identified as a Lagrangian subvariety of the variety of nilpotent elements of fraktur g. We also generalise the notion of active duality transformations to an `almost action' of the three-dimensional duality group fraktur G on asymptotically flat stationary solutions.

  1. Structure and dynamics of calmodulin in solution.

    PubMed Central

    Wriggers, W; Mehler, E; Pitici, F; Weinstein, H; Schulten, K

    1998-01-01

    To characterize the dynamic behavior of calmodulin in solution, we have carried out molecular dynamics (MD) simulations of the Ca2+-loaded structure. The crystal structure of calmodulin was placed in a solvent sphere of radius 44 A, and 6 Cl- and 22 Na+ ions were included to neutralize the system and to model a 150 mM salt concentration. The total number of atoms was 32,867. During the 3-ns simulation, the structure exhibits large conformational changes on the nanosecond time scale. The central alpha-helix, which has been shown to unwind locally upon binding of calmodulin to target proteins, bends and unwinds near residue Arg74. We interpret this result as a preparative step in the more extensive structural transition observed in the "flexible linker" region 74-82 of the central helix upon complex formation. The major structural change is a reorientation of the two Ca2+-binding domains with respect to each other and a rearrangement of alpha-helices in the N-terminus domain that makes the hydrophobic target peptide binding site more accessible. This structural rearrangement brings the domains to a more favorable position for target binding, poised to achieve the orientation observed in the complex of calmodulin with myosin light-chain kinase. Analysis of solvent structure reveals an inhomogeneity in the mobility of water in the vicinity of the protein, which is attributable to the hydrophobic effect exerted by calmodulin's binding sites for target peptides. PMID:9545028

  2. Dissociative recombination of H+(H2O)3 and D+(D2O)3 water cluster ions with electrons: Cross sections and branching ratios

    NASA Astrophysics Data System (ADS)

    Öjekull, J.; Andersson, P. U.; Nâgârd, M. B.; Pettersson, J. B. C.; Marković, N.; Derkatch, A. M.; Neau, A.; Al Khalili, A.; Rosén, S.; Larsson, M.; Semaniak, J.; Danared, H.; Källberg, A.; Österdahl, F.; af Ugglas, M.

    2007-11-01

    Dissociative recombination (DR) of the water cluster ions H+(H2O)3 and D+(D2O)3 with electrons has been studied at the heavy-ion storage ring CRYRING (Manne Siegbahn Laboratory, Stockholm University). For the first time, absolute DR cross sections have been measured for H+(H2O)3 in the energy range of 0.001-0.8eV, and relative cross sections have been measured for D+(D2O)3 in the energy range of 0.001-1.0eV. The DR cross sections for H+(H2O)3 are larger than previously observed for H+(H2O)n (n=1,2), which is in agreement with the previously observed trend indicating that the DR rate coefficient increases with size of the water cluster ion. Branching ratios have been determined for the dominating product channels. Dissociative recombination of H+(H2O)3 mainly results in the formation of 3H2O+H (probability of 0.95±0.05) and with a possible minor channel resulting in 2H2O+OH+H2 (0.05±0.05). The dominating channels for DR of D+(D2O)3 are 3D2O+D (0.88±0.03) and 2D2O+OD+D2 (0.09±0.02). The branching ratios are comparable to earlier DR results for H+(H2O)2 and D+(D2O)2, which gave 2X2O+X (X=H,D) with a probability of over 0.9.

  3. Static Structure of Polydisperse Micellar Solutions.

    PubMed

    Mileva

    2000-12-15

    A model study of polydisperse micellar solutions formed by ionic amphiphiles in the presence of added salt is proposed. The structural peculiarities of the system are determined by effective potentials including the screened electrostatic and the hardcore interactions. A perturbation procedure is applied to expand the characteristic parameters of the system around a reference system. The basic result is a model size distribution curve that accounts not only for the inherent polydispersity of the system but also includes the interaggregate interactions and the space correlation of the aggregates. Copyright 2000 Academic Press.

  4. 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.

  5. 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.

  6. 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.

  7. Structure and aggregation in model tetramethylurea solutions.

    PubMed

    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(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(t) = 0.005, aggregation is a well established feature of the solution at X(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(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(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.

  8. STRUCTURE AND PROPERTIES OF SOLID SOLUTIONS.

    DTIC Science & Technology

    Contents: solid solution strengthening and strain aging in Ag-base Al alloys; solid solution strengthening and aging in Cu-base Al alloys; solid ... solution strengthening in NaCl-base NaBr solutions; short-range order; solid solution strength in the gold-silver system.

  9. 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

  10. Communication: Quasiclassical trajectory calculations of correlated product-state distributions for the dissociation of (H2O)2 and (D2O)2

    NASA Astrophysics Data System (ADS)

    Czakó, Gábor; Wang, Yimin; Bowman, Joel M.

    2011-10-01

    Stimulated by recent experiments [B. E. Rocher-Casterline, L. C. Ch'ng, A. K. Mollner, and H. Reisler, J. Chem. Phys. 134, 211101 (2011)], we report quasiclassical trajectory calculations of the dissociation dynamics of the water dimer, (H2O)2 (and also (D2O)2) using a full-dimensional ab initio potential energy surface. The dissociation is initiated by exciting the H-bonded OH(OD)-stretch, as done experimentally for (H2O)2. Normal mode analysis of the fragment pairs is done and the correlated vibrational populations are obtained by (a) standard histogram binning (HB), (b) harmonic normal-mode energy-based Gaussian binning (GB), and (c) a modified version of (b) using accurate vibrational energies obtained in the Cartesian space. We show that HB allows opening quantum mechanically closed states, whereas GB, especially via (c), gives physically correct results. Dissociation of both (H2O)2 and (D2O)2 mainly produces either fragment in the bending excited (010) state. The H2O(J) and D2O(J) rotational distributions are similar, peaking at J = 3-5. The computations do not show significant difference between the ro-vibrational distributions of the donor and acceptor fragments. Diffusion Monte Carlo computations are performed for (D2O)2 providing an accurate zero-point energy of 7247 cm-1, and thus, a benchmark D0 of 1244 ± 5 cm-1.

  11. High repetition-rate neutron generation by several-mJ, 35 fs pulses interacting with free-flowing D2O

    NASA Astrophysics Data System (ADS)

    Hah, J.; Petrov, G. M.; Nees, J. A.; He, Z.-H.; Hammig, M. D.; Krushelnick, K.; Thomas, A. G. R.

    2016-10-01

    Using several-mJ energy pulses from a high-repetition rate (1/2 kHz), ultrashort (35 fs) pulsed laser interacting with a ˜ 10 μm diameter stream of free-flowing heavy water (D2O), we demonstrate a 2.45 MeV neutron flux of 105/s. Operating at high intensity (of order 1019 W/cm2), laser pulse energy is efficiently absorbed in the pre-plasma, generating energetic deuterons. These collide with deuterium nuclei in both the bulk target and the large volume of low density D2O vapor surrounding the target to generate neutrons through d ( d , n ) 3 He reactions. The neutron flux, as measured by a calibrated neutron bubble detector, increases as the laser pulse energy is increased from 6 mJ to 12 mJ. A quantitative comparison between the measured flux and the results derived from 2D-particle-in-cell simulations shows comparable neutron fluxes for laser characteristics similar to the experiment. The simulations reveal that there are two groups of deuterons. Forward moving deuterons generate deuterium-deuterium fusion reactions in the D2O stream and act as a point source of neutrons, while backward moving deuterons propagate through the low-density D2O vapor filled chamber and yield a volumetric source of neutrons.

  12. 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.

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

    PubMed

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

    2011-10-07

    Four internal-rotation/vibration bands of the Ne-D(2)O complex have been measured in the v(2) bend region of D(2)O using a tunable infrared diode laser spectrometer to probe a slit supersonic expansion. Three ortho bands are excited from the ground state Σ(0(00)) to the Σ and Π(1(11), υ(2) = 1) internal rotor states and the n = 1, Σ(0(00), υ(2) = 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)] and a three-state Coriolis coupling model [R. C. Cohen and R. J. Saykally, J. Chem. Phys. 95, 7891 (1991)]. The former model works more successfully than the latter. Molecular constants for the ground and excited vibrational states of ortho (20)Ne-D(2)O isotopomer as well as the Coriolis and angular-radial coupling constants are determined accurately. The van der Waals stretching frequency is estimated to be ν(s) = 24.85 cm(-1) in the ground state and decreases to about 20.8 cm(-1) upon vibrational excitation of the D(2)O bend.

  14. 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.

  15. 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.

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

    PubMed

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

    2015-07-01

    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 (13)C 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-(13)C6]-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, (13)C: 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.

  17. 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

  18. The relaxation of OH (v=1) and OD (v=1) by H2O and D2O at temperatures from 251 to 390 K.

    PubMed

    McCabe, D C; Rajakumar, B; Marshall, P; Smith, I W M; Ravishankara, A R

    2006-10-21

    We report rate coefficients for the relaxation of OH(v=1) and OD(v=1) by H2O and D2O as a function of temperature between 251 and 390 K. All four rate coefficients exhibit a negative dependence on temperature. In Arrhenius form, the rate coefficients for relaxation (in units of 10(-12) cm3 molecule-1 s-1) can be expressed as: for OH(v=1)+H2O between 263 and 390 K: k=(2.4+/-0.9) exp((460+/-115)/T); for OH(v=1)+D2O between 256 and 371 K: k=(0.49+/-0.16) exp((610+/-90)/T); for OD(v=1)+H2O between 251 and 371 K: k=(0.92+/-0.16) exp((485+/-48)/T); for OD(v=1)+D2O between 253 and 366 K: k=(2.57+/-0.09) exp((342+/-10)/T). Rate coefficients at (297+/-1 K) are also reported for the relaxation of OH(v=2) by D2O and the relaxation of OD(v=2) by H2O and D2O. The results are discussed in terms of a mechanism involving the formation of hydrogen-bonded complexes in which intramolecular vibrational energy redistribution can occur at rates competitive with re-dissociation to the initial collision partners in their original vibrational states. New ab initio calculations on the H2O-HO system have been performed which, inter alia, yield vibrational frequencies for all four complexes: H2O-HO, D2O-HO, H2O-DO and D2O-DO. These data are then employed, adapting a formalism due to Troe (J. Troe, J. Chem. Phys., 1977, 66, 4758), in order to estimate the rates of intramolecular energy transfer from the OH (OD) vibration to other modes in the complexes in order to explain the measured relaxation rates-assuming that relaxation proceeds via the hydrogen-bonded complexes.

  19. Structure of aqueous sodium perchlorate solutions.

    PubMed

    General, Ignacio J; Asciutto, Eliana K; Madura, Jeffry D

    2008-12-04

    Salt solutions have been the object of study of many scientists through history, but one of the most important findings came along when the Hofmeister series were discovered. Their importance arises from the fact that they influence the relative solubility of proteins, and solubility is directly related to one of today's holy grails: protein folding. In this work we characterize one of the more-destabilizing salts in the series, sodium perchlorate, by studying it as an aqueous solution at various concentrations ranging from 0.08 to 1.60 mol/L. Molecular dynamics simulations at room temperature permitted a detailed study of the organization of solvent and cosolvent, in terms of its radial distribution functions, along with the study of the structure of hydrogen bonds in the ions' solvation shells. We found that the distribution functions have some variations in their shape as concentration changes, but the position of their peaks is mostly unaffected. Regarding water, the most salient fact is the noticeable (although small) change in the second hydration shell and even beyond, especially for g(O(w)***O(w)), showing that the locality of salt effects should not be restricted to considerations of only the first solvation shell. The perturbation of the second shell also appears in the study of the HB network, where the difference between the number of HBs around a water molecule and around the Na(+) cation gets much smaller as one goes from the first to the second solvation shell, yet the difference is not negligible. Nevertheless, the effect of the ions past their first hydration shell is not enough to make a noticeable change in the global HB network. The Kirkwood-Buff theory of liquids was applied to our system, in order to calculate the activity derivative of the cosolvent. This coefficient, along with a previously calculated preferential binding, allowed us to establish that if a folded AP peptide is immersed in the studied solution, becoming the solute, then

  20. [Photosensitized luminescence of singlet oxygen in aqueous solutions].

    PubMed

    Krasnovskiĭ, A A

    1979-01-01

    The photoluminescence of singlet oxygen has been observed in air saturated solutions of riboflavin in D2O and mixtures of D2O and H2O. The excitation spectrum coincides with the absorption spectrum of the pigment, the emission maximum lies at 1275 nm. In D2O the quantum yield is approximately 1,2 x 10(-7). H2O quenches the luminescence. Analysis of quenching has shown that the quantum yield in H2O is less than in D2O by the factor of 20.

  1. 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.

  2. 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.

  3. The Raman spectra and cross-sections of the ν2 band of H 2O, D 2O, and HDO

    NASA Astrophysics Data System (ADS)

    Avila, G.; Tejeda, G.; Fernández, J. M.; Montero, S.

    2004-02-01

    We report the experimental Raman spectra of the ν2 band of H 2O, D 2O, and HDO in the vapor phase at room temperature. A complete interpretation of the Raman intensities is carried out employing the variational rovibrational wavefunctions obtained from a Hamiltonian in Radau coordinates and an ab initio polarizability surface at 514.5 nm. We show the importance of the rotation-vibration coupling to obtain the correct line intensities. Several tables with the assignments of the individual rotational-vibrational transitions and their Raman scattering strengths are reported. From these tables, the ν2 Raman spectra can be simulated up to 2000 K for H 2O, and up to 300 K for D 2O and HDO.

  4. An efficient, compact pulsed D2O terahertz super-radiant laser pumped with a fundamental transverse mode transversely excited atmospheric pressure CO2 laser

    NASA Astrophysics Data System (ADS)

    Geng, Lijie; Ren, Deming; Zhao, Weijiang; Qu, Yanchen; Chen, Huiying; Du, Jun

    2013-02-01

    An efficient, compact pulsed D2O terahertz (THz) super-radiant laser pumped by a TEA (transversely excited atmospheric pressure) CO2 laser is presented. The pulse energy of the THz laser has been discussed as a function of CO2 laser pump energy, D2O gas pressure, and pump absorption. A pulse width of about 110 ns and the maximum pulse energy of about 1.3 mJ have been achieved at 385 μm, with pumping by a 378 mJ fundamental transverse mode TEA CO2 laser, and the photon conversion efficiency of 29% has been achieved. We have also studied the temporal behavior features such as the decay time, the full width at half-maximum, and the pulse broadening of the THz laser pulse compared with the pump pulse and the residual pump pulse at the optimum pressure.

  5. Special quasirandom structures for perovskite solid solutions

    NASA Astrophysics Data System (ADS)

    Jiang, Zhijun; Nahas, Yousra; Xu, Bin; Prosandeev, Sergey; Wang, Dawei; Bellaiche, Laurent

    2016-11-01

    Special quasirandom structures (SQS) are presently generated for disordered (A‧1-x {{\\text{A}}\\prime \\prime} x )BX3 and A(B‧1-x {{\\text{B}}\\prime \\prime} x )X3 perovskite solid solutions, with x  =  1/2 as well as 1/3 and 2/3. These SQS configurations are obtained by imposing that the so-called Cowley parameters are as close to zero as possible for the three nearest neighboring shells. Moreover, these SQS configurations are slightly larger in size than those available in the literature for x  =  1/2, mostly because of the current capabilities of atomistic techniques. They are used here within effective Hamiltonian schemes to predict various properties, which are then compared to those associated with large random supercells, in a variety of compounds, namely (Ba1-x Sr x )TiO3, Pb(Zr1-x Ti x )O3, Pb(Sc0.5Nb0.5)O3, Ba(Zr1-x Ti x )O3, Pb(Mg1/3Nb2/3)O3 and (Bi1-x Nd x )FeO3. It is found that these SQS configurations can reproduce many properties of large random supercells of most of these disordered perovskite alloys, below some finite material-dependent temperature. Examples of these properties are electrical polarization, anti-phase and in-phase octahedral tiltings, antipolar motions, antiferromagnetism, strain, piezoelectric coefficients, dielectric response, specific heat and even the formation of polar nanoregions (PNRs) in some relaxors. Some limitations of these SQS configurations are also pointed out and explained.

  6. Superbroadening in H2O and D2O by self-focused picosecond pulses from a YAlG:Nd laser

    NASA Technical Reports Server (NTRS)

    Smith, W. L.; Liu, P.; Bloembergen, N.

    1977-01-01

    The dielectric-breakdown intensity threshold, the critical power for self-focusing, and the power threshold for the production of spectral superbroadening have been measured in H2O and D2O. For bandwidth-limited pulses of 30 psec duration at 1.06 microns and of 21 psec duration at 0.53 micron, the superbroadening in water always required power levels sufficient for catastrophic self-focusing and intensities equal to the electric breakdown threshold.

  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. Millimeter Wave Spectra of the Internal Rotation Excited States of (o)H_2-H_2O and (o)H_2-D_2O

    NASA Astrophysics Data System (ADS)

    Harada, K.; Iwasaki, Y.; Giesen, T.; Tanaka, K.

    2013-06-01

    H_2-H_2O is a weakly bound complex and it has a various states according to the internal rotation for both H_2 and H_2O moieties. In our previous study, we have reported the pure rotational transitions of the (o)H_2 complex in the ground H_2O rotational state, 0_{00}(Σ), for both H_2-H_2O and H_2-D_2O, where (o)H_2 (j_{ H2} =1) is rotating perpendicular to the intermolecular axis to give the projection of j_{ H2} to the axis k_{ H2} to be zero (i.e. Σ state). In the present study, we have observed the rotational transitions for the 0_{00} (Π) states in the millimeter-wave region up to 220 GHz, where the (o)H_2 is rotating around the intermolecular axis to give the projection k_{ H2} to be one (i.e. Π state). The center of mass bond lengths derived from the observed rotational constants for 0_{00} (Π) are longer by 5 % than those for 0_{00} (Σ), while force constants for the intermolecular stretching for 0_{00} (Π) derived from centrifugal distortion constants are smaller by 23 % than those for 0_{00} (Σ), suggesting the Π and Σ substates have quite different structures. The recent theoretical calculation indicates that for 0_{00}(Σ), (o)H_2 is bound to the oxygen site of H_2O, while for the 0_{00} (Π) state, (o)H_2 to the hydrogen site of H_2O, and the 0_{00}(Σ) state is by 14 cm^{-1} more stable than the 0_{00} (Π) state. Observed molecular constants for 0_{00}(Σ) and (Π) are consistent with the structures given by the theoretical calculation. We also observed the rotational spectrum in the 1_{01} (Σ) and (Π) states, where Σ and Π correspond to the rotation of H_2O perpendicular and parallel to the intermolecular axis and (o)H_2 is calculated to be bound to the oxygen site of H_2O. The energy difference between the 1_{01} (Σ) and (Π) states will be discussed due to the Criolis interaction between these substates. C. J. Whitham, K. Tanaka, and K. Harada, The 56th OSU Symposium, RD08 (2001). Ad. van der Avoid and D. J. Nesbit, J. Chem. Phys

  9. High Repetition-Rate Neutron Generation by Several-mJ, 35 fs pulses interacting with Free-Flowing D2O

    NASA Astrophysics Data System (ADS)

    Hah, Jungmoo; Petrov, George; Nees, John; He, Zhaohan; Hammig, Mark; Krushelnick, Karl; Thomas, Alexander

    2016-10-01

    Recent advance in ultra-high power laser technology allows a development of laser-based neutron sources. Here we demonstrate heavy-water based neutron source. Using several-mJ energy pulses from a high-repetition rate (½kHz), ultrashort (35 fs) pulsed laser interacting with a 10 μm diameter stream of free-flowing heavy water (D2O), we get a 2.45 MeV neutron flux of 105/s. In the intentionally generated pre-plasma, laser pulse energy is efficiently absorbed, and energetic deuterons are generated. As a convertor, the bulk heavy water stream target and the large volume of low density D2O vapor near the target are collided with accelerated deuterons, generating neutron through d(d,n)3He reactions. As laser pulse energy increased from 6mJ to 12mJ, the neutron flux increased. From the 2D particle-in-cell simulation, comparable neutron fluxes are shown at the similar laser characteristics to the experiment. Also, simulation shows forward and backward moving deuterons, which are main distributing ions impinging upon D2O stream and vapor, respectively. This material is based upon work supported by the Air Force Office of Scien- tific Research under Award Numbers FA9550-12-1-0310 (Young Investigator Program) and FA9550-14-1-0282.

  10. 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.

  11. Protein folding, stability, and solvation structure in osmolyte solutions hydrophobicity

    NASA Astrophysics Data System (ADS)

    Montgomery Pettitt, B.

    2008-03-01

    The hydrophobic effect between solutes in aqueous solutions plays a central role in our understanding of recognition and folding of proteins and self assembly of lipids. Hydrophobicity induces nonideal solution behavior which plays a role in many aspects of biophysics. Work on the use of small biochemical compounds to crowd protein solutions indicates that a quantitative description of their non-ideal behavior is possible and straightforward. Here, we will show what the structural origin of this non-ideal solution behavior is from expression derived from a semi grand ensemble approach. We discuss the consequences of these findings regarding protein folding stability and solvation in crowded solutions through a structural analysis of the m-value or the change in free energy difference of a macromolecule in solution with respect to the concentration of a third component. This effect has recently been restudied and new mechanisms proposed for its origins in terms of transfer free energies and hydrophobicity.

  12. Protein Folding, Stability, and Solvation Structure in Osmolyte Solutions

    PubMed Central

    Rösgen, Jörg; Pettitt, B. Montgomery; Bolen, David Wayne

    2005-01-01

    An understanding of the impact of the crowded conditions in the cytoplasm on its biomolecules is of clear importance to biochemical, medical, and pharmaceutical science. Our previous work on the use of small biochemical compounds to crowd protein solutions indicates that a quantitative description of their nonideal behavior is possible and straightforward. Here, we show the structural origin of the nonideal solution behavior. We discuss the consequences of these findings regarding protein folding stability and solvation in crowded solutions through a structural analysis of the m-value or the change in free-energy difference of a macromolecule in solution with respect to the concentration of a third component. PMID:16113118

  13. Solution structure of nickel-peptide deformylase.

    PubMed

    Dardel, F; Ragusa, S; Lazennec, C; Blanquet, S; Meinnel, T

    1998-07-17

    In the accompanying paper, we report that zinc is unlikely to be the co-factor supporting peptide deformylase activity in vivo. In contrast, nickel binding promotes full enzyme activity. The three-dimensional structure of the resulting nickel-containing peptide deformylase (catalytic domain, residues 1 to 147) was solved by NMR using a 13C-15N-doubly labelled protein sample. A set of 2261 restraints could be collected, with an average of 15.4 per amino acid. The resolution, which shows a good definition for the position of most side-chains, is greatly improved compared to that previously reported for the zinc-containing, inactive form. A comparison of the two stuctures indicates however that both share the same 3D organization. This shows that the nature of the bound metal is the primary determinant of the hydrolytic activity of this enzyme. Site-directed mutagenesis enabled us to determine the conserved residues of PDF involved in the structure of the active site. In particular, a buried arginine appears to be critical for the positioning of Cys90, one of the metal ligands. Furthermore, the 3D structure of peptide deformylase was compared to thermolysin and metzincins. Although the structural folds are very different, they all display a common structural motif involving an alpha-helix and a three-stranded beta-sheet. These conserved structural elements build a common scaffold which includes the active site, suggesting a common hydrolytic mechanism for these proteases. Finally, an invariant glycine shared by both PDF and metzincins enables us to extend the conserved motif from HEXXH to HEXXHXXG.

  14. Solution Structure of Yeast Rpn9

    PubMed Central

    Hu, Yunfei; Wu, Yujie; Li, Qianwen; Zhang, Wenbo; Jin, Changwen

    2015-01-01

    The regulatory particle (RP) of the 26 S proteasome functions in preparing polyubiquitinated substrates for degradation. The lid complex of the RP contains an Rpn8-Rpn11 heterodimer surrounded by a horseshoe-shaped scaffold formed by six proteasome-COP9/CSN-initiation factor (PCI)-containing subunits. The PCI domains are essential for lid assembly, whereas the detailed molecular mechanisms remain elusive. Recent cryo-EM studies at near-atomic resolution provided invaluable information on the RP architecture in different functional states. Nevertheless, atomic resolution structural information on the RP is still limited, and deeper understanding of RP assembly mechanism requires further studies on the structures and interactions of individual subunits or subcomplexes. Herein we report the high-resolution NMR structures of the PCI-containing subunit Rpn9 from Saccharomyces cerevisiae. The 45-kDa protein contains an all-helical N-terminal domain and a C-terminal PCI domain linked via a semiflexible hinge. The N-terminal domain mediates interaction with the ubiquitin receptor Rpn10, whereas the PCI domain mediates interaction with the neighboring PCI subunit Rpn5. The Rpn9-Rpn5 interface highlights two structural motifs on the winged helix module forming a hydrophobic center surrounded by ionic pairs, which is a common pattern for all PCI-PCI interactions in the lid. The results suggest that divergence in surface composition among different PCI pairs may contribute to the modulation of lid assembly. PMID:25631053

  15. Solution processed organic microarray with inverted structure

    NASA Astrophysics Data System (ADS)

    Toglia, Patrick; Lewis, Jason; Lafalce, Evan; Jiang, Xiaomei

    2011-03-01

    We have fabricated inverted organic microarray using a novel solution-based technique. The array consists of 60 small (1 square mm) solar cells on a one inch by one inch glass substrate. The device utilizes photoactive materials such as a blend of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). Manipulation of active layer nanomorphology has been done by choice of solvents and annealing conditions. Detailed analysis of device physics including current voltage characteristics, external quantum efficiency and carrier recombinations will be presented and complimented by AFM images and glazing angle XRD of the active layer under different processing conditions. The procedure described here has the full potential for use in future fabrication of microarrays with single cell as small as 0.01 square mm for application in DC power supplies for electrostatic Microelectromechanical systems (MEMS) devices. This work was supported by New Energy Technology Inc. and Florida High Tech Corridor Matching Fund (FHT 09-18).

  16. Quantitative spectroscopic and theoretical study of the optical absorption spectra of H2O, HOD, and D2O in the 125-145 nm region.

    PubMed

    Cheng, Bing-Ming; Chung, Chao-Yu; Bahou, Mohammed; Lee, Yuan-Pern; Lee, L C; van Harrevelt, Rob; van Hemert, Marc C

    2004-01-01

    The room temperature absorption spectra of water and its isotopomers D2O and HOD have been determined in absolute cross section units in the 125 to 145 nm wavelength region using synchrotron radiation. The experimental results for these B band spectra are compared with results from quantum mechanical calculations using accurate diabatic ab initio potentials. A Monte Carlo sampling over the initial rotational states of the molecules is applied in order to calculate the cross sections at a temperature of 300 K. The overall rotation of the water molecule is treated exactly. Both for the experimental and for the theoretical spectrum an analysis is made in terms of a component attributed to rapid direct dissociation processes and a component attributed to longer-lived resonances. The agreement between the results from experiment and theory is excellent for H2O and D2O. In the case of HOD in the results of theory two more resonances are found at low energy. It is demonstrated that the width of the resonances of 0.04 eV is the result of overlapping and somewhat narrower resonances in the spectra of molecules differing in rotational ground state.

  17. The interaction of CCl4 with Ng (Ng = He, Ne, Ar), O2, D2O and ND3: rovibrational energies, spectroscopic constants and theoretical calculations.

    PubMed

    de Oliveira, Rhuiago M; Roncaratti, Luiz F; de Macedo, Luiz Guilherme M; Gargano, Ricardo

    2017-03-01

    This investigation generated rovibrational energies and spectroscopic constants for systems of CCl4 with Ng (Ng = He, Ne, Ar), O2, D2O and ND3 from scattering experimental data, and the results presented are of interest for microwave spectroscopy studies of small halogenated molecules. The rovibrational spectra were obtained through two different approaches (Dunham and DVR) within the improved Lennard Jones (ILJ) model. Spectra were also generated within ordinary Lennard Jones and deviations suggest that the ILJ model should be preferred due to interactions beyond dispersion forces presented in these systems. Data from the literature and additional high level quantum mechanical calculations presented in this work show that these systems should not be considered as van der Waals complexes due to halogen bonding (HB) interactions, and this is especially true for the CCl4-D2O and CCl4-ND3 complexes. The charge displacement from the latter systems are one order of magnitude higher than the values from literature for CCl4 and He, Ne, Ar and O2 systems, and show significant deviations between DFT and Hartree-Fock values not previously reported in the literature.

  18. Rapid structural analysis of nanomaterials in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Ryuzaki, Sou; Tsutsui, Makusu; He, Yuhui; Yokota, Kazumichi; Arima, Akihide; Morikawa, Takanori; Taniguchi, Masateru; Kawai, Tomoji

    2017-04-01

    Rapid structural analysis of nanoscale matter in a liquid environment represents innovative technologies that reveal the identities and functions of biologically important molecules. However, there is currently no method with high spatio-temporal resolution that can scan individual particles in solutions to gain structural information. Here we report the development of a nanopore platform realizing quantitative structural analysis for suspended nanomaterials in solutions with a high z-axis and xy-plane spatial resolution of 35.8 ± 1.1 and 12 nm, respectively. We used a low thickness-to-diameter aspect ratio pore architecture for achieving cross sectional areas of analyte (i.e. tomograms). Combining this with multiphysics simulation methods to translate ionic current data into tomograms, we demonstrated rapid structural analysis of single polystyrene (Pst) beads and single dumbbell-like Pst beads in aqueous 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. Product spin-orbit state resolved dynamics of the H+H2O and H+D2O abstraction reactions.

    PubMed

    Brouard, M; Burak, I; Marinakis, S; Rubio Lago, L; Tampkins, P; Vallance, C

    2004-12-01

    The product state-resolved dynamics of the reactions H+H(2)O/D(2)O-->OH/OD((2)Pi(Omega);v',N',f )+H(2)/HD have been explored at center-of-mass collision energies around 1.2, 1.4, and 2.5 eV. The experiments employ pulsed laser photolysis coupled with polarized Doppler-resolved laser induced fluorescence detection of the OH/OD radical products. The populations in the OH spin-orbit states at a collision energy of 1.2 eV have been determined for the H+H(2)O reaction, and for low rotational levels they are shown to deviate from the statistical limit. For the H+D(2)O reaction at the highest collision energy studied the OD((2)Pi(3/2),v'=0,N'=1,A') angular distributions show scattering over a wide range of angles with a preference towards the forward direction. The kinetic energy release distributions obtained at 2.5 eV also indicate that the HD coproducts are born with significantly more internal excitation than at 1.4 eV. The OD((2)Pi(3/2),v'=0,N'=1,A') angular and kinetic energy release distributions are almost identical to those of their spin-orbit excited OD((2)Pi(1/2),v'=0,N'=1,A') counterpart. The data are compared with previous experimental measurements at similar collision energies, and with the results of previously published quasiclassical trajectory and quantum mechanical calculations employing the most recently developed potential energy surface. Product OH/OD spin-orbit effects in the reaction are discussed with reference to simple models.

  1. Structural analysis of 5-fluorouracil and thymine solid solutions

    NASA Astrophysics Data System (ADS)

    Vogt, Frederick G.; Vena, Joseph A.; Chavda, Manisha; Clawson, Jacalyn S.; Strohmeier, Mark; Barnett, Maria E.

    2009-08-01

    Solid-state analysis with powder X-ray diffraction (PXRD), solid-state NMR (SSNMR), and other spectroscopic and physical methods can provide detailed structural information about organic and pharmaceutical cocrystals. In this study, a range of solid-state analysis methods are used to characterize co-crystallized solid solutions of 5-fluorouracil and thymine. 1H, 13C and 19F SSNMR and PXRD methods are used to study the structure and disorder present in a solid solution previously prepared by solution evaporation methods; here the solid solution is prepared over a wider stoichiometric range by solvent-drop grinding techniques. Long-range perturbations of key chemical shifts are detectable by SSNMR, indicating that the solid solution is not random. Cross-polarization and heteronuclear correlation SSNMR experiments between 1H, 13C, and 19F nuclei offer insight into the structure of this solid solution, and density functional theory (DFT) methods are applied to calculate lattice energies and NMR properties in order to understand the population of the two primary disordered sites in the crystal structure. In addition, a second solid solution of 5-fluorouracil and thymine is reported and analyzed. This solid solution, which was produced by solvent-drop grinding experiments and characterized by SSNMR and powder X-ray diffraction methods, is determined to be an isostructural phase to that of anhydrous thymine with the inclusion of 5-fluorouracil defects. A similar effect does not occur under excess 5-fluorouracil conditions; instead, phase-separated Form 1 of 5-fluorouracil and anhydrous thymine are obtained. DFT calculations are applied to offer a possible explanation for this disparity.

  2. [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.

  3. 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.

  4. On the structure of an aqueous propylene glycol solution

    NASA Astrophysics Data System (ADS)

    Rhys, Natasha H.; Gillams, Richard J.; Collins, Louise E.; Callear, Samantha K.; Lawrence, M. Jayne; McLain, Sylvia E.

    2016-12-01

    Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.

  5. On the structure of an aqueous propylene glycol solution.

    PubMed

    Rhys, Natasha H; Gillams, Richard J; Collins, Louise E; Callear, Samantha K; Lawrence, M Jayne; McLain, Sylvia E

    2016-12-14

    Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.

  6. Structures and stability of salt-bridge in aqueous solution.

    PubMed

    Sagarik, Kritsana; Chaiyapongs, Supaporn

    2005-09-01

    Structures and stability of salt-bridges in aqueous solutions were investigated using a complex formed from the guanidinium (Gdm+) and formate (FmO-) ions as a model system. The Test-particle model (T-model) potentials to describe the interactions in the Gdm+-H2O, FmO(-)-H2O and Gdm+-FmO- complexes were constructed, tested and applied in molecular dynamics (MD) simulations of the aqueous solutions at 298 K. The three-dimensional structures and energetic of the hydrogen bond (H-bond) networks of water in the first hydration shells of the Gdm+ and FmO- ions, as well as the Gdm+-FmO- complex, were visualized and analyzed using various probability distribution (PD) maps. The structures of the average potential energy landscapes at the H-bond networks were employed to characterize the stability and dynamic behavior of water molecules in the first hydration shells of the solutes. It was observed that water molecules in the first hydration shell of the close-contact Gdm+-FmO- complex form associated H-bond networks, which introduce a net stabilization effect to the ion-pair, whereas those in the interstitial H-bond network destabilize and break the solvent-separated Gdm+-FmO- complex. The present results showed that, in order to provide complete insights into the structures and stability of ion-pairs in aqueous solutions, explicit water molecules have to be included in the model calculations.

  7. Solution structures of nanoassemblies based on pyrogallol[4]arenes.

    PubMed

    Kumari, Harshita; Deakyne, Carol A; Atwood, Jerry L

    2014-10-21

    Nanoassemblies of hydrogen-bonded and metal-seamed pyrogallol[4]arenes have been shown to possess novel solution-phase geometries. Further, we have demonstrated that both guest encapsulation and structural rearrangements may be studied by solution-phase techniques such as small-angle neutron scattering (SANS) and diffusion NMR. Application of these techniques to pyrogallol[4]arene-based nanoassemblies has allowed (1) differentiation among spherical, ellipsoidal, toroidal, and tubular structures in solution, (2) determination of factors that control the preferred geometrical shape and size of the nanoassemblies, and (3) detection of small variations in metric dimensions distinguishing similarly and differently shaped nanoassemblies in a given solution. Indeed, we have shown that the solution-phase structure of such nanoassemblies is often quite different from what one would predict based on solid-state studies, a result in disagreement with the frequently made assumption that these assemblies have similar structures in the two phases. We instead have predicted solid-state architectures from solution-phase structures by combining the solution-phase analysis with solid-state magnetic and elemental analyses. Specifically, the iron-seamed C-methylpyrogallol[4]arene nanoassembly was found to be tubular in solution and predicted to be tubular in the solid state, but it was found to undergo a rearrangement from a tubular to spherical geometry in solution as a function of base concentration. The absence of metal within a tubular framework affects its stability in both solution and the solid state; however, this instability is not necessarily characteristic of hydrogen-bonded capsular entities. Even metal seaming of the capsules does not guarantee similar solid-state and solution-phase architectures. The rugby ball-shaped gallium-seamed C-butylpyrogallol[4]arene hexamer becomes toroidal on dissolution, as does the spherically shaped gallium/zinc-seamed C-butylpyrogallol[4

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

    PubMed

    Chaudhuri, Barnali N

    2015-03-01

    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.

  9. Crystal structure solution from experimentally determined atomic pair distribution functions

    SciTech Connect

    Juhas, P.; Granlund, L.; Gujarathi, S.R.; Duxbury, P.M.; Billinge, S.J.L.

    2010-05-25

    An extension of the Liga algorithm for structure solution from atomic pair distribution functions (PDFs), to handle periodic crystal structures with multiple elements in the unit cell, is described. The procedure is performed in three separate steps. First, pair distances are extracted from the experimental PDF. In the second step the Liga algorithm is used to find unit-cell sites consistent with these pair distances. Finally, the atom species are assigned over the cell sites by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron X-ray PDF data from 16 test samples. The structure solution was successful for 14 samples, including cases with enlarged supercells. The algorithm success rate and the reasons for the failed cases are discussed, together with enhancements that should improve its convergence and usability.

  10. Structural and Spectroscopic Properties of Water Around Small Hydrophobic Solutes

    PubMed Central

    Montagna, Maria; Sterpone, Fabio; Guidoni, Leonardo

    2013-01-01

    We investigated the structural, dynamical and spectroscopic properties of water molecules around a solvated methane by means of Car-Parrinello molecular dynamics simulations. Despite their mobility, in the first-shell water molecules are dynamically displaced in a clathrate-like cage around the hydrophobic solute. No significant differences in water geometrical parameters, in molecular dipole moments or in hydrogen bonding properties are observed between in-shell and out-shell molecules, indicating that liquid water can accommodate a small hydrophobic solute without altering its structural properties. The calculated contribution of the first shell water molecules to the infrared spectra does not show significant differences with respect the bulk signal once the effects of the missing polarization of second-shell molecules has been taken into account. Small fingerprints of the clathrate-like structure appear in the vibrational density of states in the libration and OH stretching regions. PMID:22946539

  11. Solution superstructures: truncated cubeoctahedron structures of pyrogallol[4]arene nanoassemblies.

    PubMed

    Kumari, Harshita; Kline, Steven R; Fowler, Drew A; Mossine, Andrew V; Deakyne, Carol A; Atwood, Jerry L

    2014-01-04

    Giant nanocapsules: the solution-phase structures of PgC1Ho and PgC3Ho have been investigated using in situ neutron scattering measurements. The SANS results show the presence of spherical nanoassemblies of radius 18.2 Å, which are larger than the previously reported metal-seamed PgC3 hexamers (radius = 10 Å). The spherical architectures conform to a truncated cubeoctahedron geometry, indicating formation of the first metal-containing pyrogallol[4]arene-based dodecameric nanoassemblies in solution.

  12. 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.

  13. 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.

  14. Relationship between solution structure and phase behavior: a neutron scattering study of concentrated aqueous hexamethylenetetramine solutions.

    PubMed

    Burton, R C; Ferrari, E S; Davey, R J; Finney, J L; Bowron, D T

    2009-04-30

    The water-hexamethylenetetramine system displays features of significant interest in the context of phase equilibria in molecular materials. First, it is possible to crystallize two solid phases depending on temperature, both hexahydrate and anhydrous forms. Second, saturated aqueous solutions in equilibrium with these forms exhibit a negative dependence of solubility (retrograde) on temperature. In this contribution, neutron scattering experiments (with isotopic substitution) of concentrated aqueous hexamethylenetetramine solutions combined with empirical potential structure refinement (EPSR) were used to investigate the time-averaged atomistic details of this system. Through the derivation of radial distribution functions, quantitative details emerge of the solution coordination, its relationship to the nature of the solid phases, and of the underlying cause of the solubility behavior of this molecule.

  15. What happens to the structure of water in cryoprotectant solutions?

    PubMed

    Towey, James J; Soper, Alan K; Dougan, Lorna

    2013-01-01

    Cryoprotectant molecules are widely utilised in basic molecular research through to industrial and biomedical applications. The molecular mechanisms by which cryoprotectants stabilise and protect molecules and cells, along with suppressing the formation of ice, are incompletely understood. To gain greater insight into these mechanisms, we have completed an experimental determination of the structure of aqueous glycerol. Our investigation combines neutron diffraction experiments with isotopic substitution and computational modelling to determine the atomistic level structure of the glycerol-water mixtures, across the complete concentration range at room temperature. We examine the local structure of the system focusing on water structure. By comparing our data with that from other studies of cryoprotectant solutions, we attempt to find general rules for the action of cryoprotectants on water structure. We also discuss how these molecular scale interactions may be related to the macroscopic properties of the system.

  16. Flow-induced structured phase in nonionic micellar solutions.

    PubMed

    Cardiel, Joshua J; Tonggu, Lige; de la Iglesia, Pablo; Zhao, Ya; Pozzo, Danilo C; Wang, Liguo; Shen, Amy Q

    2013-12-17

    In this work, we consider the flow of a nonionic micellar solution (precursor) through an array of microposts, with focus on its microstructural and rheological evolution. The precursor contains polyoxyethylene(20) sorbitan monooleate (Tween-80) and cosurfactant monolaurin (ML). An irreversible flow-induced structured phase (NI-FISP) emerges after the nonionic precursor flows through the hexagonal micropost arrays, when subjected to strain rates ~10(4) s(-1) and strain ~10(3). NI-FISP consists of close-looped micellar bundles and multiconnected micellar networks as evidenced by transmission electron microscopy (TEM) and cryo-electron microscopy (cryo-EM). We also conduct small-angle neutron scattering (SANS) measurements in both precursor and NI-FISP to illustrate the structural transition. We propose a potential mechanism for the NI-FISP formation that relies on the micropost arrays and the flow kinematics in the microdevice to induce entropic fluctuations in the micellar solution. Finally, we show that the rheological variation from a viscous precursor solution to a viscoelastic micellar structured phase is associated with the structural evolution from the precursor to NI-FISP.

  17. Travelling Wave Solutions in Multigroup Age-Structured Epidemic Models

    NASA Astrophysics Data System (ADS)

    Ducrot, Arnaut; Magal, Pierre; Ruan, Shigui

    2010-01-01

    Age-structured epidemic models have been used to describe either the age of individuals or the age of infection of certain diseases and to determine how these characteristics affect the outcomes and consequences of epidemiological processes. Most results on age-structured epidemic models focus on the existence, uniqueness, and convergence to disease equilibria of solutions. In this paper we investigate the existence of travelling wave solutions in a deterministic age-structured model describing the circulation of a disease within a population of multigroups. Individuals of each group are able to move with a random walk which is modelled by the classical Fickian diffusion and are classified into two subclasses, susceptible and infective. A susceptible individual in a given group can be crisscross infected by direct contact with infective individuals of possibly any group. This process of transmission can depend upon the age of the disease of infected individuals. The goal of this paper is to provide sufficient conditions that ensure the existence of travelling wave solutions for the age-structured epidemic model. The case of two population groups is numerically investigated which applies to the crisscross transmission of feline immunodeficiency virus (FIV) and some sexual transmission diseases.

  18. Isotope effects in liquid water by infrared spectroscopy. II. Factor analysis of the temperature effect on H2O and D2O

    NASA Astrophysics Data System (ADS)

    Larouche, Pascal; Max, Jean-Joseph; Chapados, Camille

    2008-08-01

    Some 500 infrared (IR) spectra of light and heavy waters were obtained between 29 and 93 °C in order to identify the species present in liquid water. Factor analysis of these gives two species for each type of water with their IR spectra and abundance curves. Using an orthogonalization procedure, we obtained the temperature factor limits of -22 and +118 °C (+/-5 °C) that we coined cold and hot factors, respectively. Within experimental error, these limits are the same for light and heavy waters. The spectra of the orthogonalized factors presented show a decrease of the OH (OD) stretch band integrated intensities of almost 36% from the cold to the hot factors. No ``free'' OH (OD) group is present or formed in the temperature ramp. This indicates that all water molecules in the bulk are made of an oxygen atom surrounded with four hydrogen atoms, two covalently bonded, and two hydrogen bonded. This is consistent with the previous study of mixtures of H2O and D2O [part I: J.-J. Max and C. Chapados, J. Chem. Phys. 116, 4626 (2002)]. To maintain the ordinary liquid within the limits of 0 and 100 °C at atmospheric pressure, a fraction of the cold and hot factors are necessary. With the spectra of the cold and hot factors and the abundance curves, one can generate the spectrum at any temperature between -22 and +118 °C of light and heavy liquid waters.

  19. 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.

  20. 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.

  1. 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.

  2. Water structure around peptide fragments in aqueous solutions

    SciTech Connect

    McLain, Sylvia E; Soper, Alan K; Watts, Prof Anthony

    2008-01-01

    The bulk water structure around small peptide fragments - glycyl-L-alanine, glycyl-L-proline and L-alanyl-L-proline - has been determined by a combination of neutron diffraction with isotopic substitution and empirical potential structural refinement techniques. The addition of each of the dipeptides to water yields a decreased water-water coordination in the surrounding water solvent. Additionally both the Ow-Ow radial distribution functions and the water-water spatial density functions in all of the solutions indicate an electrostrictive effect in the second water coordination shell of the bulk water network. This effect is not observed in similar experiments on the amino acid L-proline alone in solution, which is one component of two of the peptides measured here.

  3. 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

  4. 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.

  5. Solution structures of antimalarial drug-heme complexes.

    PubMed

    Leed, Alison; DuBay, Kateri; Ursos, Lyann M B; Sears, Devin; De Dios, Angel C; Roepe, Paul D

    2002-08-13

    Paramagnetic metal centers [such as Fe(III) found within ferriprotoporphyrin IX heme (FPIX)] exert through space effects on the relaxation rate of nearby proton spins that depend critically on the metal-proton distance. We have measured these effects for all protons of several antimalarial drugs that bind to FPIX by systematically varying the drug:heme molar ratio in high field NMR experiments. These measurements allow us to determine precise FPIX Fe-drug H distances for the solution structures of noncovalent complexes formed between FPIX mu-oxo dimers and the antimalarial drugs chloroquine (CQ), quinine (QN), and quinidine (QD). Using these distances, we then performed distance restraint calculations to determine the lowest-energy solution structures of these complexes. Structures were solved for neutral, monoprotic (+1), and diprotic (+2) forms of the drugs. Analysis of these structures allows us to visualize for the first time the stereospecific differences between QN and QD binding to FPIX and the differences in populations of QN and QD solution structures upon changes in digestive vacuolar pH for drug resistant malarial parasites [Dzekunov, S. M., et al. (2000) Mol. Biochem. Parasitol. 110, 107-124]. The data indicate a previously unrecognized key role for the CQ aliphatic chain in stabilizing FPIX-CQ complexes, and suggest how lengthening or shortening the chain might perturb stability. We also define FPIX:drug stoichiometries of 2:1 for the complexes formed at physiological FPIX concentrations, in contrast to the 4:1 and 5:1 stoichiometries previously determined at higher FPIX concentrations [Dorn, A., et al. (1998) Biochem. Pharmacol. 55, 727-736]. These atomic resolution antimalarial drug-heme structures should help elucidate how these drugs inhibit formation of hemozoin during metabolism of heme within the malarial parasite Plasmodium falciparum and assist ongoing development of strategies for circumventing antimalarial drug resistance.

  6. 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.

  7. Magnetic order through super-superexchanges in the polar magnetoelectric organic-inorganic hybrid Cr[(D3N-(CH2)2-PO3)(Cl)(D2O)].

    PubMed

    Nénert, Gwilherm; Koo, Hyun-Joo; Colin, Claire V; Bauer, Elvira M; Bellitto, Carlo; Ritter, Clemens; Righini, Guido; Whangbo, Myung-Hwan

    2013-01-18

    The crystal and magnetic structures of the organic-inorganic hybrid compound Cr(II) ammoniumethylphosphonate chloride monohydrate, Cr[D(3)N-(CH(2))(2)-PO(3))(Cl)(D(2)O)] (1), have been studied by temperature-dependent neutron powder diffraction and superconducting quantum interference device (SQUID) magnetometry. The compound represents a rare example of a magnetoelectric polar organic-inorganic hybrid solid, containing high spin Cr(2+) ions (S = 2) and is a canted antiferromagnet (weak ferromagnet) below T(N) = 5.5 K. The neutron powder diffraction pattern recorded at T = 10 K, shows that the partially deuterated compound crystallizes in the same non centrosymmetric monoclinic space group P2(1) (No. 4) with the following unit-cell parameters: a = 5.24041(4) Å, b =13.93113(8) Å, c = 5.26081(4) Å, and β = 105.4347(5)°. Powder neutron diffraction of a partially deuterated sample has enabled us, for the first time, to locate the water molecule. At low temperature, the compound presents a canted antiferromagnetic state characterized by k = 0 resulting in the magnetic symmetry P2(1)'. This symmetry is in agreement with the previously reported large magnetodielectric effect. The crystal structure of (1) can be described as being built up of triangular lattice planes made up of [Cr(II)O(4)Cl] square pyramids which are separated by ammonium ethyl groups along the b axis. The transition from paramagnetic to weakly ferromagnetic state results from super-superexchanges only. Surprisingly, while the overall magnetic behavior is antiferromagnetic, the Cr(II)O(4)Cl planes are ferromagnetic, and the strongest antiferromagnetic coupling is via the ammonium ethyl groups. Our density functional calculations confirm these aspects of the spin exchange interactions of (1) and that the spin exchange interactions between Cr(II) ions are considerably weak compared with the single-ion anisotropy of Cr(II).

  8. The high-pressure phase diagram of synthetic epsomite (MgSO4·7H2O and MgSO4·7D2O) from ultrasonic and neutron powder diffraction measurements

    NASA Astrophysics Data System (ADS)

    Gromnitskaya, E. L.; Yagafarov, O. F.; Lyapin, A. G.; Brazhkin, V. V.; Wood, I. G.; Tucker, M. G.; Fortes, A. D.

    2013-03-01

    We present an ultrasonic and neutron powder diffraction study of crystalline MgSO4·7H2O (synthetic epsomite) and MgSO4·7D2O under pressure up to ~3 GPa near room temperature and up to ~2 GPa at lower temperatures. Both methods provide complementary data on the phase transitions and elasticity of magnesium sulphate heptahydrate, where protonated and deuterated counterparts exhibit very similar behaviour and properties. Under compression in the declared pressure intervals, we observed three different sequences of phase transitions: between 280 and 295 K, phase transitions occurred at approximately 1.4, 1.6, and 2.5 GPa; between 240 and 280 K, only a single phase transition occurred; below 240 K, there were no phase transformations. Overall, we have identified four new phase fields at high pressure, in addition to that of the room-pressure orthorhombic structure. Of these, we present neutron powder diffraction data obtained in situ in the three phase fields observed near room temperature. We present evidence that these high-pressure phase fields correspond to regions where MgSO4·7H2O decomposes to a lower hydrate by exsolving water. Upon cooling to liquid nitrogen temperatures, the ratio of shear modulus G to bulk modulus B increases and we observe elastic softening of both moduli with pressure, which may be a precursor to pressure-induced amorphization. These observations may have important consequences for modelling the interiors of icy planetary bodies in which hydrated sulphates are important rock-forming minerals, such as the large icy moons of Jupiter, influencing their internal structure, dynamics, and potential for supporting life.

  9. Flavin Adenine Dinucleotide Structural Motifs: From Solution to Gas Phase

    PubMed Central

    2015-01-01

    Flavin adenine dinucleotide (FAD) is involved in important metabolic reactions where the biological function is intrinsically related to changes in conformation. In the present work, FAD conformational changes were studied in solution and in gas phase by measuring the fluorescence decay time and ion-neutral collision cross sections (CCS, in a trapped ion mobility spectrometer, TIMS) as a function of the solvent conditions (i.e., organic content) and gas-phase collisional partner (i.e., N2 doped with organic molecules). Changes in the fluorescence decay suggest that FAD can exist in four conformations in solution, where the abundance of the extended conformations increases with the organic content. TIMS-MS experiments showed that FAD can exist in the gas phase as deprotonated (M = C27H31N9O15P2) and protonated forms (M = C27H33N9O15P2) and that multiple conformations (up to 12) can be observed as a function of the starting solution for the [M + H]+ and [M + Na]+molecular ions. In addition, changes in the relative abundances of the gas-phase structures were observed from a “stack” to a “close” conformation when organic molecules were introduced in the TIMS cell as collision partners. Candidate structures optimized at the DFT/B3LYP/6-31G(d,p) were proposed for each IMS band, and results showed that the most abundant IMS band corresponds to the most stable candidate structure. Solution and gas-phase experiments suggest that the driving force that stabilizes the different conformations is based on the interaction of the adenine and isoalloxazine rings that can be tailored by the “solvation” effect created with the organic molecules. PMID:25222439

  10. Solution structure and thermodynamics of 2',5' RNA intercalation.

    PubMed

    Horowitz, Eric D; Lilavivat, Seth; Holladay, Benjamin W; Germann, Markus W; Hud, Nicholas V

    2009-04-29

    As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.

  11. Ultrafast excited-state dynamics and vibrational cooling of 8-oxo-7,8-dihydro-2'-deoxyguanosine in D2O.

    PubMed

    Zhang, Yuyuan; Dood, Jordan; Beckstead, Ashley; Chen, Jinquan; Li, Xi-Bo; Burrows, Cynthia J; Lu, Zhen; Matsika, Spiridoula; Kohler, Bern

    2013-12-05

    Nguyen and Burrows recently demonstrated that UV-B irradiation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a signature product of oxidatively damaged DNA, can repair cyclobutane pyrimidine dimers in double-stranded DNA (J. Am. Chem. Soc. 2011, 133, 14586 - 14589). In order to test the hypothesis that repair occurs by photoinduced electron transfer, it is critical to determine basic photophysical parameters of 8-oxodG including the excited-state lifetime. Here, femtosecond transient absorption spectroscopy was used to study the ultrafast excited-state dynamics of 8-oxodG with excitation in the UV and probing at visible and mid-IR wavelengths. The excited-state lifetimes of both neutral and basic forms of 8-oxodG in D2O are reported for the first time by monitoring the disappearance of excited-state absorption at 570 nm. The lifetime of the first excited state of the neutral form is 0.9 ± 0.1 ps, or nearly twice as long as that of 2'-deoxyguanosine. The basic form of 8-oxodG exhibits a much longer excited-state lifetime of 43 ± 3 ps. Following ultrafast internal conversion by neutral 8-oxodG, a vibrationally hot ground state is created that dissipates its excess vibrational energy to the solvent on a time scale of 2.4 ± 0.4 ps. Femtosecond time-resolved IR experiments provide additional insights into excited-state dynamics and the vibrational relaxation of several modes in the fingerprint region.

  12. Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

    PubMed Central

    Mereghetti, Paolo; Gabdoulline, Razif R.; Wade, Rebecca C.

    2010-01-01

    The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments. PMID:21112303

  13. Structural studies of ammonia and metallic lithium-ammonia solutions.

    PubMed

    Thompson, Helen; Wasse, Jonathan C; Skipper, Neal T; Hayama, Shusaku; Bowron, Daniel T; Soper, Alan K

    2003-03-05

    The technique of hydrogen/deuterium isotopic substitution has been used to extract detailed information concerning the solvent structure in pure ammonia and metallic lithium-ammonia solutions. In pure ammonia we find evidence for approximately 2.0 hydrogen bonds around each central nitrogen atom, with an average N-H distance of 2.4 A. On addition of alkali metal, we observe directly significant disruption of this hydrogen bonding. At 8 mol % metal there remains only around 0.7 hydrogen bond per nitrogen atom. This value decreases to 0.0 for the saturated solution of 21 mol % metal, as all ammonia molecules have then become incorporated into the tetrahedral first solvation spheres of the lithium cations. In conjunction with a classical three-dimensional computer modeling technique, we are now able to identify a well-defined second cationic solvation shell. In this secondary shell the nitrogen atoms tend to reside above the faces and edges of the primary tetrahedral shell. Furthermore, the computer-generated models reveal that on addition of alkali metal the solvent molecules form voids of approximate radius 2.5-3.0 A. Our data therefore provide new insight into the structure of the polaronic cavities and tunnels, which have been theoretically predicted for lithium-ammonia solutions.

  14. Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution).

    PubMed

    Zhang, Weizhe; Zhang, Hongmin; Zhang, Tao; Fan, Haifu; Hao, Quan

    2015-07-01

    Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.

  15. The solution structure of acyl carrier protein from Mycobacterium tuberculosis.

    PubMed

    Wong, Hing C; Liu, Gaohua; Zhang, Yong-Mei; Rock, Charles O; Zheng, Jie

    2002-05-03

    Acyl carrier protein (ACP) performs the essential function of shuttling the intermediates between the enzymes that constitute the type II fatty acid synthase system. Mycobacterium tuberculosis is unique in producing extremely long mycolic acids, and tubercular ACP, AcpM, is also unique in possessing a longer carboxyl terminus than other ACPs. We determined the solution structure of AcpM using protein NMR spectroscopy to define the similarities and differences between AcpM and the typical structures. The amino-terminal region of the structure is well defined and consists of four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions similar to the structures of other bacterial ACPs. The unique carboxyl-terminal extension from helix IV has a "melted down" feature, and the end of the molecule is a random coil. A comparison of the apo- and holo-forms of AcpM revealed that the 4'-phosphopantetheine group oscillates between two states; in one it is bound to a hydrophobic groove on the surface of AcpM, and in another it is solvent-exposed. The similarity between AcpM and other ACPs reveals the conserved structural motif that is recognized by all type II enzymes. However, the function of the coil domain extending from helix IV to the carboxyl terminus remains enigmatic, but its structural characteristics suggest that it may interact with the very long chain intermediates in mycolic acid biosynthesis or control specific protein-protein interactions.

  16. 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.

  17. Structure and Dynamics of Interacting Nanoparticles in Semidilute Polymer Solutions

    DOE PAGES

    Pollng-Skutvik, Ryan; Mongcopa, Katrina Irene S.; Faraone, Antonio; ...

    2016-08-17

    We investigate the structure and dynamics of silica nanoparticles and polymer chains in semidilute solutions of high molecular weight polystyrene in 2-butanone to determine the effect of long-range interparticle interactions on the coupling between particle and polymer dynamics. Particles at concentrations of 1–10 wt % are well dispersed in the semidilute polymer solutions and exhibit long-range electrostatic repulsions between particles. Because the particles are comparably sized to the radius of gyration of the polymer, the particle dynamics is predicted to couple to that of the polymer. We verify that the polymer structure and dynamics are not significantly affected by themore » particles, indicating that the particle–polymer coupling does not change with increasing particle loading. We find that the coupling between the dynamics of comparably sized particles and polymer results in subdiffusive particle dynamics, as expected. Over the interparticle distance, however, the particle dynamics is hindered and not fully described by the relaxation of the surrounding polymer chains. Instead, the particle dynamics is inversely related to the structure factor, suggesting that physical particle–polymer coupling on short length scales and interparticle interactions on long length scales both present energetic barriers to particle motion that lead to subdiffusive dynamics and de Gennes narrowing, respectively.« less

  18. Structure and Dynamics of Interacting Nanoparticles in Semidilute Polymer Solutions

    SciTech Connect

    Pollng-Skutvik, Ryan; Mongcopa, Katrina Irene S.; Faraone, Antonio; Narayanan, Suresh; Conrad, Jacinta C.; Krishnamoorti, Ramanan

    2016-08-17

    We investigate the structure and dynamics of silica nanoparticles and polymer chains in semidilute solutions of high molecular weight polystyrene in 2-butanone to determine the effect of long-range interparticle interactions on the coupling between particle and polymer dynamics. Particles at concentrations of 1–10 wt % are well dispersed in the semidilute polymer solutions and exhibit long-range electrostatic repulsions between particles. Because the particles are comparably sized to the radius of gyration of the polymer, the particle dynamics is predicted to couple to that of the polymer. We verify that the polymer structure and dynamics are not significantly affected by the particles, indicating that the particle–polymer coupling does not change with increasing particle loading. We find that the coupling between the dynamics of comparably sized particles and polymer results in subdiffusive particle dynamics, as expected. Over the interparticle distance, however, the particle dynamics is hindered and not fully described by the relaxation of the surrounding polymer chains. Instead, the particle dynamics is inversely related to the structure factor, suggesting that physical particle–polymer coupling on short length scales and interparticle interactions on long length scales both present energetic barriers to particle motion that lead to subdiffusive dynamics and de Gennes narrowing, respectively.

  19. 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

  20. Lanthanide(III) complexes with a tetrapyridine pendant-armed macrocyclic ligand: 1H NMR structural determination in solution, X-ray diffraction, and density-functional theory calculations.

    PubMed

    Del C Fernandez-Fernandez, M; Bastida, R; Macías, A; Pérez-Lourido, P; Platas-Iglesias, C; Valencia, L

    2006-05-29

    Complexes between the tetrapyridyl pendant-armed macrocyclic ligand (L) and the trivalent lanthanide ions have been synthesized, and structural studies have been made both in the solid state and in aqueous solution. The crystal structures of the La, Ce, Pr, Gd, Tb, Er, and Tm complexes have been determined by single-crystal X-ray crystallography. In the solid state, all the cation complexes show a 10-coordinated geometry close to a distorted bicapped antiprism, with the pyridine pendants situated alternatively above and below the main plane of the macrocycle. The conformations of the two five-membered chelate rings present in the complexes change along the lanthanide series. The La(III) and Ce(III) complexes show a lambdadelta (or deltalambda) conformation, while the complexes of the heavier lanthanide ions present lambdalambda (or deltadelta) conformation. The cationic [Ln(L)]3+ complexes (Ln = La, Pr, Eu, Tb, and Tm) were also characterized by theoretical calculations at the density-functional theory (DFT) B3LYP level. The theoretical calculations predict a stabilization of the lambdalambda (or deltadelta) conformation on decreasing the ionic radius of the Ln(III) ion, in agreement with the experimental evidence. The solution structures show a good agreement with the calculated ones, as demonstrated by paramagnetic NMR measurements (lanthanide induced shifts and relaxation rate enhancements). The 1H NMR spectra indicate an effective D2 symmetry of the complexes in D2O solution. The 1H lanthanide induced shifts (LIS) observed for the Ce(III), Tm(III), and Yb(III) complexes can be fit to a theoretical model assuming that dipolar contributions are dominant for all protons. The resulting calculated values are consistent with highly rhombic magnetic susceptibility tensors with the magnetic axes being coincident with the symmetry axes of the molecule. In contrast with the solid-state structure, the analysis of the LIS data indicates that the Ce(III) complexes present a

  1. Ab initio solution of macromolecular crystal structures without direct methods.

    PubMed

    McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

    2017-04-04

    The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

  2. 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.

  3. 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.

  4. 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.

  5. Dilute-solution Structure of Charged Arborescent Graft Polymer

    SciTech Connect

    Yun, Seok; Briber, R M; Kee, R. Andrew; Gauthier, Mario

    2006-01-01

    The solutions of charged G1 arborescent polystyrene-graft-poly(2-vinylpyridine) copolymers in methanol-d4 and D{sub 2}O were investigated over a dilute concentration range {phi} = 0.005-0.05 ({phi}: mass fraction) using small-angle neutron scattering (SANS). Upon addition of acid (HCl) arborescent graft polymers became charged and a peak appeared in SANS data. The interparticle distance (d{sub exp}) calculated from a peak position corresponded to the expected value (d{sub uni}) for a uniform particle distribution. This indicates the formation of liquid-like ordering due to long-range Coulombic repulsions. The smaller dielectric constant of methanol-d4 resulted in long-range electrostatic repulsions persisting to lower polymer concentration than in D{sub 2}O. The slow mode scattering was observed by dynamic light scattering measurements for the same polymer solutions, indicating the presence of structural inhomogeneity in the solutions. Both the peak and slow mode disappeared by addition of NaCl or excess HCl into the solutions due to the screening of electrostatic interactions. The G1 polymer grafted with longer P2VP chains (M{sub w} {approx} 30,000 versus 5000 g mol) formed a gel on addition of HCl. This result reveals that molecular expansion is more significant for arborescent polymers with longer (M{sub w} {approx} 30,000) linear polyelectrolyte branches, resulting in gelation for {phi} > 0.01. Upon addition of NaCl or excess HCl a gel transformed back to a liquid resulted from the screening of electrostatic interactions.

  6. A use of Ramachandran potentials in protein solution structure determinations.

    PubMed

    Bertini, Ivano; Cavallaro, Gabriele; Luchinat, Claudio; Poli, Irene

    2003-08-01

    A strategy is developed to use database-derived phi-psi constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived phi-psi constraints are enforced for all amino acids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the phi-psi values for each residue are examined. In the second and final run, the database-derived phi-psi constraints are enforced only for those residues which in the first run have ended in one and the same favored phi-psi region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.

  7. Solution structures of rat amylin peptide: simulation, theory, and experiment.

    PubMed

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

    2010-02-03

    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 alpha-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 alpha-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.

  8. 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

  9. Solution structure of the HU protein from Bacillus stearothermophilus.

    PubMed

    Vis, H; Mariani, M; Vorgias, C E; Wilson, K S; Kaptein, R; Boelens, R

    1995-12-08

    The histone-like protein HU from Bacillus stearothermophilus is a dimer with a molecular mass of 19.5 kDa that is capable of bending DNA. An X-ray structure has been determined, but no structure could be established for a large part of the supposed DNA-binding beta-arms. Using distance and dihedral constraints derived from triple-resonance NMR data of a 13C/15N doubly-labelled HU protein 49 distance geometry structures were calculated, which were refined by means of restrained Molecular Dynamics. From this set a total of 25 refined structures were selected having low constraint energy and few constraint violations. The ensemble of 25 structures display a root-mea-square co-ordinate deviation of 0.36 A with respect to the average structure, calculated over the backbone heavy atoms of residues 2 to 54 and 75 to 90 (and residues 2' to 54' and 75' to 90' of the second monomer). The structure of the core is very similar to that observed in the X-ray structure, with a pairwise r.m.s.d. of 1.06 A. The structure of the beta-hairpin arm contains a double flip-over at the prolines in the two strands of the beta-arm. Strong 15N-NH heteronuclear nuclear Overhauser effects indicate that the beta-arm and especially the tip is flexible. This explains the disorder observed in the solution and X-ray structures of the beta-arm, in respect of the core of the protein. Overlayed onto itself the beta-arm is better defined, with an r.m.s.d. of 1.0 A calculated over the backbone heavy atoms of residues 54 to 59 and 69 to 74. The tip of the arm adopts a well-defined 4:6 beta-hairpin conformation similar to the iron co-ordinating beta-arms of rubredoxin.

  10. NMR solution structures of actin depolymerizing factor homology domains

    PubMed Central

    Goroncy, Alexander K; Koshiba, Seizo; Tochio, Naoya; Tomizawa, Tadashi; Sato, Manami; Inoue, Makato; Watanabe, Satoru; Hayashizaki, Yoshihide; Tanaka, Akiko; Kigawa, Takanori; Yokoyama, Shigeyuki

    2009-01-01

    Actin is one of the most conserved proteins in nature. Its assembly and disassembly are regulated by many proteins, including the family of actin-depolymerizing factor homology (ADF-H) domains. ADF-H domains can be divided into five classes: ADF/cofilin, glia maturation factor (GMF), coactosin, twinfilin, and Abp1/drebrin. The best-characterized class is ADF/cofilin. The other four classes have drawn much less attention and very few structures have been reported. This study presents the solution NMR structure of the ADF-H domain of human HIP-55-drebrin-like protein, the first published structure of a drebrin-like domain (mammalian), and the first published structure of GMF β (mouse). We also determined the structures of mouse GMF γ, the mouse coactosin-like domain and the C-terminal ADF-H domain of mouse twinfilin 1. Although the overall fold of the five domains is similar, some significant differences provide valuable insights into filamentous actin (F-actin) and globular actin (G-actin) binding, including the identification of binding residues on the long central helix. This long helix is stabilized by three or four residues. Notably, the F-actin binding sites of mouse GMF β and GMF γ contain two additional β-strands not seen in other ADF-H structures. The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF β and GMF γ. PMID:19768801

  11. [Solution structure and antibacterial mechanism of two synthetic antimicrobial peptides].

    PubMed

    Yang, Lin; Fan, Meihua; Liu, Xuezhu; Wu, Mei; Shi, Ge; Liao, Zhi

    2011-11-01

    Mytilin-derived-peptide-1 (MDP-1) and mytilin-derived-peptide-2 (MDP-2) are two truncated decapeptides with reversed sequence synthesized corresponding to the residues 20-29 of mytilin-1 (GenBank Accession No. FJ973154) from M. coruscus. The objective of this study is to characterize the structural basis of these two peptides for their antimicrobial activities and functional differences, and to investigate the inhibitory mechanism of MDPs on Escherichia coli and Sarcina lutea. The structures of MDP-1 and MDP-2 in solution were determined by 1H 2D NMR methods; the antibactericidal effects of MDPs on E. coli and S. lutea were observed by transmitted electron microscopy (TEM). Both MDP-1 and MDP-2 have a well-defined loop structure stabilized by two additional disulfide bridges, which resemble the-hairpin structure of mytilin-1 model. The surface profile of MDPs' structures was characterized by protruding charged residues surrounded by hydrophobic residues. TEM analysis showed that MDPs destroyed cytoplasmic membrane and cell wall of bacteria and the interface between the cell wall and membrane was blurred. Furthermore, some holes were observed in treated bacteria, which resulted in cell death. Structural comparison between MDP-1 and MDP-2 shows that the distribution of positively charged amino acids on the loop of MDPs is topologically different significantly, which might be the reason why MDP-2 has higher activity than MDP-1. Furthermore, TEM results suggested that the bactericidal mechanisms of MDPs against E. coli and S. lutea were similar. Both MDP-1 and MDP-2 could attach to the negatively charged bacterial wall by positively charged amino acid residues and destroy the bacteria membrane in a pore-forming manner, thus cause the contents of the cells to release and eventually cell death.

  12. Isothermal equation of state and high-pressure phase transitions of synthetic meridianiite (MgSO4·11D2O) determined by neutron powder diffraction and quasielastic neutron spectroscopy

    PubMed Central

    Fortes, A. Dominic; Fernandez-Alonso, Felix; Tucker, Matthew; Wood, Ian G.

    2017-01-01

    We have collected neutron powder diffraction data from MgSO4·11D2O (the deuterated analogue of meridianiite), a highly hydrated sulfate salt that is thought to be a candidate rock-forming mineral in some icy satellites of the outer solar system. Our measurements, made using the PEARL/HiPr and OSIRIS instruments at the ISIS neutron spallation source, covered the range 0.1 < P < 800 MPa and 150 < T < 280 K. The refined unit-cell volumes as a function of P and T are parameterized in the form of a Murnaghan integrated linear equation of state having a zero-pressure volume V 0 = 706.23 (8) Å3, zero-pressure bulk modulus K 0 = 19.9 (4) GPa and its first pressure derivative, K′ = 9 (1). The structure’s compressibility is highly anisotropic, as expected, with the three principal directions of the unit-strain tensor having compressibilities of 9.6 × 10−3, 3.4 × 10−2 and 3.4 × 10−3 GPa−1, the most compressible direction being perpendicular to the long axis of a discrete hexadecameric water cluster, (D2O)16. At high pressure we observed two different phase transitions. First, warming of MgSO4·11D2O at 545 MPa resulted in a change in the diffraction pattern at 275 K consistent with partial (peritectic) melting; quasielastic neutron spectra collected simultaneously evince the onset of the reorientational motion of D2O molecules with characteristic time-scales of 20–30 ps, longer than those found in bulk liquid water at the same temperature and commensurate with the lifetime of solvent-separated ion pairs in aqueous MgSO4. Second, at ∼ 0.9 GPa, 240 K, MgSO4·11D2O decomposed into high-pressure water ice phase VI and MgSO4·9D2O, a recently discovered phase that has hitherto only been formed at ambient pressure by quenching small droplets of MgSO4(aq) in liquid nitrogen. The fate of the high-pressure enneahydrate on further compression and warming is not clear from the neutron diffraction data, but its occurrence

  13. 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.

  14. Nanostructured Block Copolymer Solutions and Composites: Mechanical and Structural Properties

    NASA Astrophysics Data System (ADS)

    Walker, Lynn

    2015-03-01

    Self-assembled block copolymer templates are used to control the nanoscale structure of materials that would not otherwise order in solution. In this work, we have developed a technique to use close-packed cubic and cylindrical mesophases of a thermoreversible block copolymer (PEO-PPO-PEO) to impart spatial order on dispersed nanoparticles. The thermoreversible nature of the template allows for the dispersion of particles synthesized outside the template. This feature extends the applicability of this templating method to many particle-polymer systems, including proteins, and also permits a systematic evaluation of the impact of design parameters on the structure and mechanical properties of the nanocomposites. The criteria for forming co-crystals have been characterized using small-angle scatting and the mechanical properties of these soft crystals determined. Numerous crystal structures have been reported for the block copolymer system and we have taken advantage of several to generate soft co-crystals. The result of this templating is spatially ordered nanoparticle arrays embedded within the block copolymer nanostructure. These soft materials can be shear aligned into crystals with long range order and this shear alignment is discussed. Finally, the dynamics of nanoparticles within the nanostructured material are characterized with fluorescence recovery after photobleaching (FRAP). The applications and general behavior of these nanostructured hydrogels are outlined.

  15. 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.

  16. 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.

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

    PubMed

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

    2013-01-07

    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.

  18. Tertiary structure of conotoxin GIIIA in aqueous solution.

    PubMed

    Lancelin, J M; Kohda, D; Tate, S; Yanagawa, Y; Abe, T; Satake, M; Inagaki, F

    1991-07-16

    The three-dimensional structure of conotoxin GIIIA, an important constituent of the venom from the marine hunting snail Conus geographus L., was determined in aqueous solution by two-dimensional proton nuclear magnetic resonance and simulated annealing based methods. On the basis of 162 assigned nuclear Overhauser effect (NOE) connectivities obtained at the medium field strength frequency of 400 MHz, 74 final distance constraints of sequential and tertiary ones were derived and used together with 18 torsion angle (phi, chi 1) constraints and 9 distance constraints derived from disulfide bridges. A total of 32 converged structures were obtained from 200 runs of calculations. The atomic root-mean-square (RMS) difference about the mean coordinate positions (excluding the terminal residues 1 and 22) is 0.8 A for backbone atoms (N, C alpha, C). Conotoxin GIIIA is characterized by a particular folding of the 22 amino acid peptidic chain, which is stabilized by three disulfide bridges arranged in cage at the center of a discoidal structure of approximately 20-A diameter. The seven cationic side chains of lysine and arginine residues project radially into the solvent and form potential sites of interaction with the skeletal muscle sodium channel for which the toxin is a strong inhibitor. The present results provide a molecular basis to elucidate the remarkable physiological properties of this neurotoxin.

  19. 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.

  20. 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.

  1. Solution structures and molecular interactions of selective melanocortin receptor antagonists.

    PubMed

    Lee, Chul-Jin; Yun, Ji-Hye; Lim, Sung-Kil; Lee, Weontae

    2010-12-01

    The solution structures and inter-molecular interaction of the cyclic melanocortin antagonists SHU9119, JKC363, HS014, and HS024 with receptor molecules have been determined by NMR spectroscopy and molecular modeling. While SHU9119 is known as a nonselective antagonist, JKC363, HS014, and HS024 are selective for the melanocortin subtype-4 receptor (MC4R) involved in modulation of food intake. Data from NMR and molecular dynamics suggest that the conformation of the Trp9 sidechain in the three MC4R-selective antagonists is quite different from that of SHU9119. This result strongly supports the concept that the spatial orientation of the hydrophobic aromatic residue is more important for determining selectivity than the presence of a basic, "arginine-like" moiety responsible for biological activity. We propose that the conformation of hydrophobic residues of MCR antagonists is critical for receptor-specific selectivity.

  2. Structural dependence of MEH-PPV chromism in solution.

    PubMed

    de Magalhães, Carlos E T; Savedra, Ranylson M L; Dias, Karina S; Ramos, Rodrigo; Siqueira, Melissa F

    2017-03-01

    The chromism observed in the MEH-PPV polymer in tetrahydrofuran (THF) solution is discussed as a function of the structural morphology of the backbone chains. To evaluate this phenomenon, we carried out simulations employing a hybrid methodology using molecular dynamics and quantum mechanical approaches. Our results support the hypothesis that the morphological order-disorder transition is related to the change from red to blue phase observed experimentally. The morphological disorder is associated with total or partial twisted arrangements in the polymer backbone, which induces an electronic conjugation length more confined to shorter segments. In addition, the main band of the MEH-PPV UV-Vis spectrum at the lower wavelength is related to the blue phase, in contrast to the red phase found for the more planar backbone chains.

  3. Three-dimensional solution structure of Acanthamoeba profilin-I

    PubMed Central

    1993-01-01

    We have determined a medium resolution three-dimensional solution structure of Acanthamoeba profilin-I by multidimensional nuclear magnetic resonance spectroscopy. This 13-kD actin binding protein consists of a five stranded antiparallel beta sheet flanked by NH2- and COOH-terminal helices on one face and by a third helix and a two stranded beta sheet on the other face. Data from actin-profilin cross- linking experiments and the localization of conserved residues between profilins in different phyla indicate that actin binding occurs on the molecular face occupied by the terminal helices. The other face of the molecule contains the residues that differ between Acanthamoeba profilins-I and II and may be important in determining the difference in polyphosphoinositide binding between these isoforms. This suggests that lipids and actin bind to different faces of the molecule. PMID:8397216

  4. 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.

  5. Structure of carboxymyoglobin in crystals and in solution.

    PubMed Central

    Makinen, M W; Houtchens, R A; Caughey, W S

    1979-01-01

    The configuration of the heme-carbonyl group upon binding of carbon monoxide to sperm whale myoglobin (Mb) in crystals is evaluated on the basis of infrared spectroscopic methods. Multiplets of the totally symmetric C-O stretching mode are observed for the heme-bound ligand near 1933, 1944, and 1967 cm-1, corresponding to three different heme-carbonyl conformers. Variations in the relative proportions of these conformers can be induced by incorporation of small fractions of metMb or deoxyMb into MbCO crystals. The configuration of the iron-carbonyl with respect to the immediate coordination environment of the heme iron is assigned for each v(CO) stretching frequency on the basis of a detailed comparison of the three-dimensional structures of the heme environments of MbCO, metMb, and deoxyMb defined by crystallographic methods. The structures of the three heme-carbonyl conformers account for the v(CO) infrared absorption bands that can be observed for MbCO in solution. PMID:293700

  6. Solution structure and dynamics of ADF from Toxoplasma gondii.

    PubMed

    Yadav, Rahul; Pathak, Prem Prakash; Shukla, Vaibhav Kumar; Jain, Anupam; Srivastava, Shubhra; Tripathi, Sarita; Krishna Pulavarti, S V S R; Mehta, Simren; Sibley, L David; Arora, Ashish

    2011-10-01

    Toxoplasma gondii ADF (TgADF) belongs to a functional subtype characterized by strong G-actin sequestering activity and low F-actin severing activity. Among the characterized ADF/cofilin proteins, TgADF has the shortest length and is missing a C-terminal helix implicated in F-actin binding. In order to understand its characteristic properties, we have determined the solution structure of TgADF and studied its backbone dynamics from ¹⁵N-relaxation measurements. TgADF has conserved ADF/cofilin fold consisting of a central mixed β-sheet comprised of six β-strands that are partially surrounded by three α-helices and a C-terminal helical turn. The high G-actin sequestering activity of TgADF relies on highly structurally and dynamically optimized interactions between G-actin and G-actin binding surface of TgADF. The equilibrium dissociation constant for TgADF and rabbit muscle G-actin was 23.81 nM, as measured by ITC, which reflects very strong affinity of TgADF and G-actin interactions. The F-actin binding site of TgADF is partially formed, with a shortened F-loop that does not project out of the ellipsoid structure and a C-terminal helical turn in place of the C-terminal helix α4. Yet, it is more rigid than the F-actin binding site of Leishmania donovani cofilin. Experimental observations and structural features do not support the interaction of PIP2 with TgADF, and PIP2 does not affect the interaction of TgADF with G-actin. Overall, this study suggests that conformational flexibility of G-actin binding sites enhances the affinity of TgADF for G-actin, while conformational rigidity of F-actin binding sites of conventional ADF/cofilins is necessary for stable binding to F-actin.

  7. Visualization of the atomic structure of solid solutions with the NaCl structure

    NASA Astrophysics Data System (ADS)

    Babanov, Yu. A.; Ponomarev, D. A.; Ustinov, V. V.

    2015-04-01

    It has been shown how an atomic cluster for a solid solution with a rock salt structure can be constructed using the Pauling model. Simulation has been performed for 343000 ions of Ni x Zn1 - x O3 ( x = 0, 0.3, 0.5, 0.7, 1.0) oxide substitutional solid solutions. Coordinates of all cluster ions are obtained and distribution functions of ion pairs (Ni-O, Ni-Ni, Ni-Zn, Zn-Zn, Zn-O, O-O) are constructed as functions of distance. The shape of the normal distribution indicates the existence of bounded chaos in the system of oxide solid solutions. The width of the Gaussian distribution function is determined by the difference of metal ionic radii. The results are in agreement with both X-ray diffraction and EXAFS spectroscopy data.

  8. 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.

  9. 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.

  10. 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

  11. Laser trapping dynamics of 200 nm-polystyrene particles at a solution surface

    NASA Astrophysics Data System (ADS)

    Yuyama, Ken-ichi; Sugiyama, Teruki; Masuhara, Hiroshi

    2013-09-01

    We present laser trapping behaviors of 200 nm-polystyrene particles in D2O solution and at its surface using a focused continuous-wave laser beam of 1064 nm. Upon focusing the laser beam into the solution surface, the particles are gathered at the focal spot, and their assembly is expanded to the outside and becomes much larger than the focal volume. The resultant assembly is observed colored under halogen lamp illumination, which is due to a periodic structure like a colloidal crystal. This trapping behavior is much different compared to the laser irradiation into the inside of the solution where a particle-like assembly with a size similar to that of the focal volume is prepared. These findings provide us new insights to consider how radiation pressure of a focused laser beam acts on nanoparticles at a solution surface.

  12. Large-scale structures in tetrahydrofuran-water mixture with a trace amount of antioxidant butylhydroxytoluene (BHT).

    PubMed

    Li, Zhiyong; Cheng, He; Li, Junyu; Hao, Jinkun; Zhang, Li; Hammouda, Boualem; Han, Charles C

    2011-06-23

    Author: Because of the closed-loop phase diagram of tetrahydrofuran (THF)-water mixture, THF aqueous solution naturally exhibits concentration fluctuations near the phase boundary. Besides the fast mode induced by concentration fluctuations, the 4.5% mole fraction THF aqueous solution is also characterized by a slow mode. The existence of a trace amount of butylhydroxytoluene (BHT) antioxidant in commercial THF strongly influences the slow mode in 4.5% mole fraction THF aqueous solution. A core-shell structure with a BHT core and a shell made from THF-rich THF-D(2)O mixture was identified by the combination of dynamic laser light scattering (DLS) and small-angle neutron scattering (SANS). BHT is hydrophobic, stabilized by a THF-rich domain in THF aqueous solution and acts as a tracer to make the large-scale structure (slow mode) "visible" through SANS because of its larger contrast with the solvent. In contrast, this large-scale structure was almost not detectable by SANS when BHT was removed from the THF-D(2)O mixture. Combined UV-vis, DLS, and static light scattering (SLS) indicated that slow-moving objects do exist and that their sizes almost do not change, but their concentration decreases to a small but nonzero value at the infinite dilution limit. The origin of the elusive large-scale structure at zero BHT concentration is still not clear, but it might be associated with some hydrophobic impurities or nanobubbles. However, a polydisperse sphere model of ∼8.5% mole fraction THF-D(2)O mixture can fit the structure with a radius of ∼100 nm, which gives the temperature-dependent low-q SANS profiles of 4.5% mole fraction THF aqueous solution at zero BHT concentration.

  13. Structure of supersaturated solution and crystal nucleation induced by diffusion

    NASA Astrophysics Data System (ADS)

    Ooshima, Hiroshi; Igarashi, Koichi; Iwasa, Hideo; Yamamoto, Ren

    2013-06-01

    The effect of a seed crystal on nucleation of L-alanine from a quiescent supersaturated solution was investigated. When a seed crystal was not used, nucleation did not occur at least for 5 h. When a seed crystal was introduced into the supersaturated solution with careful attention to avoid convection of the solution, fine crystals appeared at the place far from the seed crystal. At that time, there was no convection at the place that fine crystals appeared. Namely, there was no possibility that those fine crystals came from the surface of seed crystal. We supposed that nucleation was induced by directional diffusion of solute molecules caused by growth of the seed crystal. In order to prove this hypothesis, we designed an experiment using an apparatus composed of two compartments divided by a dialysis membrane that L-alanine molecules could freely permeate. Two supersaturated solutions having a supersaturation ratio of 1.2 and a smaller ratio were placed in the two compartments in the absence of seed crystals. This apparatus allowed the directional diffusion of solute molecules between two solutions. Nucleation occurred within 30 min. The frequency of nucleation among 7-times repeated experiments was in proportion to the difference of supersaturation ratio between the two solutions. This result poses a new mechanism of the secondary nucleation that the directional diffusion caused by growth of existing crystals induces nucleation.

  14. 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.

  15. 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

  16. 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

  17. Air/Water-Stable Tridentate NHC-PdII Complex; Catalytic C-H Activation of Hydrocarbons via H/D Exchange Process in D2O

    PubMed Central

    Lee, Joo Ho; Yoo, Kyung Soo; Park, Chan Pil; Olsen, Janet M.; Sakaguchi, Satoshi; Surya Prakash, G. K.; Mathew, Thomas; Jung, Kyung Woon

    2009-01-01

    While developing novel catalysts for carbon-carbon or carbon-heteroatom coupling (N, O, or F), we were able to introduce tridentate NHC-amidate-alkoxide palladium(II) complexes. In aqueous solution, these NHC-Pd(II) complexes showed high ability for C-H activation of various hydrocarbons (cyclohexane, cyclopentane, dimethyl ether, THF, acetone, and toluene) under mild conditions. PMID:20221298

  18. Structure of concentrated aqueous solutions of scandium chloride

    NASA Astrophysics Data System (ADS)

    Smirnov, P. R.; Grechin, O. V.

    2017-03-01

    It is shown via X-ray diffraction that aqueous solutions of scandium chloride form ionic associates in a wide range of concentrations. It is established that the Sc3+ ion coordination number increases upon dilution to 8.2 at an unchanged Sc3+-OH2 distance of 0.215 nm. The second coordination sphere of the cation forms at an average distance of 0.420 nm. The number of solvent molecules in the sphere logically increases during dilution. It is concluded that the anion does not form its own sphere in highly concentrated solutions. This coordination sphere begins to form only in solutions with moderate concentrations at a distance of 0.315 nm, and it contains six water molecules in diluted solutions.

  19. On the coupling of solvent characteristics to the electronic structure of solute molecules.

    PubMed

    Bogatko, Stuart; Cauët, Emilie; Geerlings, Paul; De Proft, Frank

    2014-02-28

    We present the results of a theoretical investigation focusing on the solvent structure surrounding the -1, 0 and +1 charged species of F, Cl, Br and I halogen atoms and F2, Cl2, Br2 and I2 di-halogen molecules in a methanol solvent and its influence on the electronic structure of the solute molecules. Our results show a large stabilizing effect arising from the solute-solvent interactions. Well-formed first solvation shells are observed for all species, the structure of which is strongly influenced by the charge of the solute species. Detailed analysis reveals that coordination number, CN, solvent orientation, θ, and solute-solvent distance, d, are important structural characteristics which are coupled to changes in the electronic structure of the solute. We propose that the fundamental chemistry of any solute species is generally regulated by these solvent degrees of freedom.

  20. 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.

  1. Solvation structure of coumarin 1 in acetonitrile: role of the electrostatic solute solvent potential

    NASA Astrophysics Data System (ADS)

    Diraison, M.; Millie, P.; Pommeret, S.; Gustavsson, T.; Mialocq, J.-Cl

    1998-01-01

    A molecular dynamics simulation study of a coumarin 1 molecule solvated in acetonitrile, in its S 0 and S 1 electronic states, is presented. Three solute-solvent interaction potentials, all containing the same Lennard-Jones component but different electrostatic interactions, have been considered. The structure of the solvent around the large dye solute strongly depends on the electrostatic solute-solvent potential, illustrating the crucial role of the local electric field. An accurate description of the charge distribution of the solute is therefore necessary to describe correctly the solute-solvent structure and the solvation energy.

  2. 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

  3. Application of finite-element-based solution technologies for viscoplastic structural analyses

    NASA Technical Reports Server (NTRS)

    Arya, V. K.

    1990-01-01

    Finite-element solution technology developed for use in conjunction with advanced viscoplastic models is described. The development of such solution technology is necessary for performing stress/life analyses of engineering structural problems where the complex geometries and loadings make the conventional analytical solutions difficult. The versatility of the solution technology is demonstrated by applying it to viscoplastic models possessing different mathematical structures and encompassing isotropic and anisotropic material. The computational results qualitatively replicate deformation behavior observed in experiments on prototypical structural components.

  4. Effective Forces Between Diamagnetic and Paramagnetic Ions in D 2 O at Low and Moderate Ionic Strengths: An NMR Relaxation Study

    NASA Astrophysics Data System (ADS)

    Sacco, A.; Belorizky, E.; Jeannin, M.; Gorecki, W.; Fries, P. H.

    1997-09-01

    The dynamical behaviour of several pairs of dissociated, attractive and repulsive, ions is investigated in aqueous solutions for ionic strengths up to 1 mol l^{-1}. The experimental information is provided by the NMR longitudinal relaxation rates of the protons on the diamagnetic ions. The ionic solutions were chosen so that the main relaxation mechanism of these protons is due to the time fluctuations of their dipolar magnetic coupling with the electronic spins on the paramagnetic ions. This coupling strongly depends on the ion-ion potential of mean force (PMF) and on the ion self-diffusion coefficients. The interionic spatial correlations and the associated PMF are derived from a new approximation of the integral equations of the statistical mechanics of liquids. This formalism, which treats all the ions as discrete particles, rests on the infinite dilution PMF of the various ion pairs. It mixes a Born-Oppenheimer theory at infinite dilution with a sort of McMillan-Mayer approximation to take the ionic concentration into account. It goes beyond the Debye-Hückel screening theory, in which a continuous screening charge distribution approximates the effects of the discrete surrounding ions. It is related to the concept of the local dielectric constants which replace the usual macroscopic dielectric constant and depend on the interionic distances. The self-diffusion coefficients of the diamagnetic ions were measured by the NMR pulsed magnetic field gradient (PMFG) techniques applied to the resonant protons. In paramagnetic solutions, where several protonated species coexist, special caution is required and this is discussed in detail. For all the investigated solutions the theory well accounts for the observed variation of the NMR relaxation as a function of the ion charges, of the ionic strength and of the NMR proton resonance frequency. The relaxation results predicted by the new approximation of the ion-ion PMF are compared with those derived from the simple

  5. Solution structure of an antifreeze protein CfAFP-501 from Choristoneura fumiferana.

    PubMed

    Li, Congmin; Guo, Xianrong; Jia, Zongchao; Xia, Bin; Jin, Changwen

    2005-07-01

    Antifreeze proteins (AFPs) are widely employed by various organisms as part of their overwintering survival strategy. AFPs have the unique ability to suppress the freezing point of aqueous solution and inhibit ice recrystallization through binding to the ice seed crystals and restricting their growth. The solution structure of CfAFP-501 from spruce budworm has been determined by NMR spectroscopy. Our result demonstrates that CfAFP-501 retains its rigid and highly regular structure in solution. Overall, the solution structure is similar to the crystal structure except the N- and C-terminal regions. NMR spin-relaxation experiments further indicate the overall rigidity of the protein and identify a collection of residues with greater flexibilities. Furthermore, Pro91 shows a cis conformation in solution instead of the trans conformation determined in the crystal structure.

  6. Special quasirandom structure modeling of fluorite-structured oxide solid solutions with aliovalent cation substitutions

    NASA Astrophysics Data System (ADS)

    Wolff-Goodrich, Silas; Hanken, Benjamin E.; Solomon, Jonathan M.; Asta, Mark

    2015-07-01

    The accuracy of the special quasirandom structure (SQS) approach for modeling the structure and energetics of fluorite-structured oxide solid solutions with aliovalent cation substitutions is assessed in an ionic-pair potential study of urania and ceria based systems mixed with trivalent rare-earth ions. Mixing enthalpies for SQS supercells containing 96 and 324 lattice sites were calculated using ionic pair potentials for U0.5La0.5O1.75, U0.5Y0.5O1.75, Ce0.5La0.5O1.75, Ce0.5Y0.5O1.75, and Ce0.5Gd0.5O1.75, which all have stoichiometries of pyrochlores. The SQS results were compared to benchmark values for random substitutional disorder obtained using large supercell models. The calculations show significant improvement of the mixing enthalpy for the larger 324 site SQS, which is attributed to a better description of the structural distortions, as characterized by the radial distribution functions in relaxed systems.

  7. 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.

  8. 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.

  9. MUFOLD: A new solution for protein 3D structure prediction.

    PubMed

    Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

    2010-04-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Calpha or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 A, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8.

  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. Automatic protein structure solution from weak X-ray data

    PubMed Central

    Skubák, Pavol; Pannu, Navraj S.

    2013-01-01

    Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing. PMID:24231803

  12. Automatic protein structure solution from weak X-ray data

    NASA Astrophysics Data System (ADS)

    Skubák, Pavol; Pannu, Navraj S.

    2013-11-01

    Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

  13. Solution softening in magnesium alloys: the effect of solid solutions on the dislocation core structure and nonbasal slip.

    PubMed

    Tsuru, T; Udagawa, Y; Yamaguchi, M; Itakura, M; Kaburaki, H; Kaji, Y

    2013-01-16

    There is a pressing need to improve the ductility of magnesium alloys so that they can be applied as lightweight structural materials. In this study, a mechanism for enhancing the ductility of magnesium alloys has been pursued using the atomistic method. The generalized stacking fault (GSF) energies for basal and prismatic planes in magnesium were calculated by using density functional theory, and the effect of the GSF energy on the dislocation core structures was examined using a semidiscrete variational Peierls-Nabarro model. Yttrium was found to have an anomalous influence on the solution softening owing to a reduction in the GSF energy gradient.

  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. Solutions for Missing Data in Structural Equation Modeling

    ERIC Educational Resources Information Center

    Carter, Rufus Lynn

    2006-01-01

    Many times in both educational and social science research it is impossible to collect data that is complete. When administering a survey, for example, people may answer some questions and not others. This missing data causes a problem for researchers using structural equation modeling (SEM) techniques for data analyses. Because SEM and…

  16. 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

  17. 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.

  18. 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.

  19. Raman spectra and ab initio calculation of a structure of aqueous solutions of methanol

    NASA Astrophysics Data System (ADS)

    Hushvaktov, H. A.; Tukhvatullin, F. H.; Jumabaev, A.; Tashkenbaev, U. N.; Absanov, A. A.; Hudoyberdiev, B. G.; Kuyliev, B.

    2017-03-01

    Small amount of low molecular weight alcohols leads to appearance of some special properties of alcohol-water solutions. In the literature it is associated with structural changes in solution with changing concentration. However, the problem special properties and structure of solutions at low concentration of alcohol is not very clear. Accordingly, we carried out quantum-chemical calculations and experimental studies of aqueous solutions of methyl alcohol. The calculations performed for ten molecular alcohol-water mixtures showed that with a low concentration of methyl alcohol in water the solubility of alcohol is poor: the alcohol molecules are displaced from the water structure and should form a particular structure. Thus, with low concentration of alcohol in the aqueous solution there are two types of structures: the structure of water and the structure of alcohol that should lead to the presence of specific properties. At high concentration of alcohol the structure of water is destroyed and there is just the structure made of alcohol-water aggregates. This interpretation is consistent with the experimental data of Raman spectroscopy. The band of Csbnd O vibrations of alcohol is detected to be of complex character just in the region of the presence of specific properties. Formation of intermolecular H-bonds also complicates the Raman spectra of Osbnd H or O-D vibrations of pure alcohol: a non-coincidence of peak frequencies, a shift of the band towards low-frequency region, a strong broadening of the band.

  20. 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)

  1. Modelling size and structure of nanoparticles formed from drying of submicron solution aerosols

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Arpan A.; Pawar, Amol A.; Venkataraman, Chandra; Mehra, Anurag

    2015-01-01

    Drying of submicron solution aerosols, under controlled conditions, has been explored to prepare nanoparticles for drug delivery applications. A computational model of solution drop evaporation is developed to study the evolution of solute gradients inside the drop and predict the size and shell thickness of precipitating nanoparticles. The model considers evaporation as a two-stage process involving droplet shrinkage and shell growth. It was corroborated that droplet evaporation rate controls the solute distribution within a droplet and the resulting particle structure (solid or shell type). At higher gas temperatures, rapid build-up of solute near drop surface from high evaporation rates results in early attainment of critical supersaturation solubility and a steeper solute gradient, which favours formation of larger, shell-type particles. At lower gas temperatures, formation of smaller, solid nanoparticles is indicated. The computed size and shell thickness are in good agreement with experimentally prepared lipid nanoparticles. This study indicates that solid or shell structure of precipitated nanoparticles is strongly affected by evaporation rate, while initial solute concentration in the precursor solution and atomized droplet size affect shell thickness. For the gas temperatures considered, evaporative cooling leads to droplet temperature below the melting point of the lipid solute. Thus, we conclude that control over nanoparticle size and structure, of thermolabile precursor materials suitable for drug delivery, can be achieved by controlling evaporation rates, through selection of aerosol processing conditions.

  2. Solution Structure of the Conserved Hypothetical Protein Rv2302 from Mycobacterium tuberculosis.

    SciTech Connect

    Buchko, Garry W.; Kim, Chang Y.; Terwilliger, Thomas C.; Kennedy, Michael A.

    2006-08-01

    The hypothetical Mycobacterium tuberculosis protein RV2302 (80 residues, MW = 8.6 kDa) has been characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. Size exclusion chromatography and NMR spectroscopy suggest that RV2302 is as a monomer is solution. Circular dichroism spectroscopy indicates the protein is structured in solution, but, irreversible unfolds upon heating with an inflection point of {approx}48 C. Using NMR based methods we determined the solution structure of RV2302. The protein contains a five strand, anti-parallel b-sheet core with one C-terminal a-helix (A65-A75) nestled against its side. Dali searches using the structure closest to the average structure did not identify any high similarities to any other known protein structure. Consequently, the structure of Rv2302 may potentially represent a novel protein fold.

  3. Both Reversible Self-Association and Structural Changes Underpin Molecular Viscoelasticity of mAb Solutions.

    PubMed

    Sarangapani, Prasad S; Weaver, Justin; Parupudi, Arun; Besong, Tabot M D; Adams, Gary G; Harding, Stephen E; Manikwar, Prakash; Castellanos, Maria M; Bishop, Steven M; Pathak, Jai A

    2016-12-01

    The role of antibody structure (conformation) in solution rheology is probed. It is demonstrated here that pH-dependent changes in the tertiary structure of 2 mAb solutions lead to viscoelasticity and not merely a shear viscosity (η) increase. Steady shear flow curves on mAb solutions are reported over broad pH (3.0 ≤ pH ≤ 8.7) and concentration (2 mg/mL ≤ c ≤ 120 mg/mL) ranges to comprehensively characterize their rheology. Results are interpreted using size exclusion chromatography, differential scanning calorimetry, analytical ultracentrifugation, near-UV circular dichroism, and dynamic light scattering. Changes in tertiary structure with concentration lead to elastic yield stress and increased solution viscosity in solution of "mAb1." These findings are supported by dynamic light scattering and differential scanning calorimetry, which show increased hydrodynamic radius of mAb1 at low pH and a reduced melting temperature Tm, respectively. Conversely, another molecule at 120 mg/mL solution concentration is a strong viscoelastic gel due to perturbed tertiary structure (seen in circular dichroism) at pH 3.0, but the same molecule responds as a viscous liquid due to reversible self-association at pH 7.4 (verified by analytical ultracentrifugation). Both protein-protein interactions and structural perturbations govern pH-dependent viscoelasticity of mAb solutions.

  4. Anomalous variations of crystal habits and solution properties in the context of the crystallization medium structure

    NASA Astrophysics Data System (ADS)

    Kiryanova, E. V.; Ugolkov, V. L.; Pyankova, L. A.; Filatov, S. K.

    2009-12-01

    The effect of the real structure of solutions on crystallization is one of the basic issues of crystallogenesis, which is also important for resolving problems of genetic mineralogy. The study of the NaNO3-H2O and KNO3-H2O model systems yielded new data on anomalous characteristics of crystal-forming systems, including morphological and kinetic properties of crystals, crystal-solution equilibrium, and physical properties of solutions (light scattering, thermal properties, IR parameters, pH), providing information on the structure of solutions. The internally consistent data confirm the previously suggested variations in structural heterogeneity of solutions related to minor (2-4%) variations in their composition, which result in numerous disturbances of monotonicity (thermal-concentration oscillations) in the liquidus curves of salts. It is shown that these variations can be caused by variable size and composition of crystal hydrate clusters. The experimental data indicate that the effect of the real solution structure on crystal morphology and crystal-solution equilibrium is enhanced in multicomponent systems, including natural crystal-forming systems. Anomalous faceting and habit, zoning, a sectorial structure of crystals, and nonuniform entrapment of admixtures cannot be ruled out in these systems.

  5. 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

  6. AGGREGATES: Finding structures in simulation results of solutions.

    PubMed

    Bernardes, Carlos E S

    2017-04-15

    Molecular Dynamic and Monte-Carlo simulations are widely used to investigate the structure and physical properties of solids and liquids at a molecular level. Tools to extract the most relevant information from the obtained results are, however, in considerable demand. One such tool, the program AGGREGATES, is described in this work. Based on distance criteria, the program searches trajectory files for the presence of molecular clusters and computes several statistical and shape properties for these structures. Tools designed to investigate the local organization and the molecular conformations in the clusters are also available. Among these, it is introduced a new approach to perform a First Shell Analysis, by looking for the presence of atomic contacts between molecules. These elements are particularly useful to obtain information on molecular assembly processes (such as the nucleation of crystals or colloidal particles) or to investigate polymorphism in organic compounds. The program features are illustrated here through the investigation of the 4'-hydroxyacetophenone + ethanol system. © 2017 Wiley Periodicals, Inc.

  7. 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.

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

    DOE PAGES

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; ...

    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

  9. Solution structure of 3-oxo-delta5-steroid isomerase.

    PubMed

    Wu, Z R; Ebrahimian, S; Zawrotny, M E; Thornburg, L D; Perez-Alvarado, G C; Brothers, P; Pollack, R M; Summers, M F

    1997-04-18

    The three-dimensional structure of the enzyme 3-oxo-delta5-steroid isomerase (E.C. 5.3.3.1), a 28-kilodalton symmetrical dimer, was solved by multidimensional heteronuclear magnetic resonance spectroscopy. The two independently folded monomers pack together by means of extensive hydrophobic and electrostatic interactions. Each monomer comprises three alpha helices and a six-strand mixed beta-pleated sheet arranged to form a deep hydrophobic cavity. Catalytically important residues Tyr14 (general acid) and Asp38 (general base) are located near the bottom of the cavity and positioned as expected from mechanistic hypotheses. An unexpected acid group (Asp99) is also located in the active site adjacent to Tyr14, and kinetic and binding studies of the Asp99 to Ala mutant demonstrate that Asp99 contributes to catalysis by stabilizing the intermediate.

  10. 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.

  11. 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.

  12. 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.

  13. The interplay of network structure and dispatch solutions in power grid cascading failures.

    PubMed

    Reynolds-Barredo, Jose M; Newman, David E; Carreras, Benjamin A; Dobson, Ian

    2016-11-01

    For a given minimum cost of the electricity dispatch, multiple equivalent dispatch solutions may exist. We explore the sensitivity of networks to these dispatch solutions and their impact on the vulnerability of the network to cascading failure blackouts. It is shown that, depending on the heterogeneity of the network structure, the blackout statistics can be sensitive to the dispatch solution chosen, with the clustering coefficient of the network being a key ingredient. We also investigate mechanisms or configurations that decrease discrepancies that can occur between the different dispatch solutions.

  14. The interplay of network structure and dispatch solutions in power grid cascading failures

    NASA Astrophysics Data System (ADS)

    Reynolds-Barredo, Jose M.; Newman, David E.; Carreras, Benjamin A.; Dobson, Ian

    2016-11-01

    For a given minimum cost of the electricity dispatch, multiple equivalent dispatch solutions may exist. We explore the sensitivity of networks to these dispatch solutions and their impact on the vulnerability of the network to cascading failure blackouts. It is shown that, depending on the heterogeneity of the network structure, the blackout statistics can be sensitive to the dispatch solution chosen, with the clustering coefficient of the network being a key ingredient. We also investigate mechanisms or configurations that decrease discrepancies that can occur between the different dispatch solutions.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    PubMed Central

    Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; Raines, Kevin S.; Lane, Thomas J.; Schenk, Gundolf; Nelson, Garrett; Subramanian, Ganesh; Tono, Kensuke; Joti, Yasumasa; Yabashi, Makina; Ratner, Daniel; Doniach, Sebastian

    2016-01-01

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. It is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules. PMID:27840681

  20. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    DOE PAGES

    Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; ...

    2016-09-26

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlinedmore » for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.« less

  1. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    SciTech Connect

    Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; Raines, Kevin S.; Lane, Thomas J.; Schenk, Gundolf; Nelson, Garrett; Subramanian, Ganesh; Tono, Kensuke; Joti, Yasumasa; Yabashi, Makina; Ratner, Daniel; Doniach, Sebastian

    2016-09-26

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.

  2. 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.

  3. Charge distribution and local structure of americium-bearing thorium oxide solid solutions.

    PubMed

    Carvajal-Nunez, U; Prieur, D; Vitova, T; Somers, J

    2012-11-05

    The electronical and structural properties of Th(0.80)Am(0.20)O(2-x) materials have been studied by the coupling of X-ray diffraction and X-ray absorption spectroscopy techniques. A substoichiometric fluorite Th(IV)(0.80)Am(III)(0.20)O(1.90) solid solution is found following sintering in moisturized Ar-H(2). In contrast, heating of this sample in air leads to a nondefective fluorite Th(IV)(0.80)Am(IV)(0.20)O(2.00) solid solution. The structures of these solid solution compounds were fully characterized by assessing the interatomic distances, the coordination numbers, and the structural disorder. The effect of the sintering atmosphere on these crystallographical parameters and on the cation valences has been determined and the capability of ThO(2) to accommodate tri- and tetravalent actinides in the fluorite structure assessed.

  4. 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}.

  5. 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.

  6. Disproportionation and thermochemical sulfate reduction reactions in S-H2O-CH4 and S-D2O-CH4 systems from 200 to 340 °C at elevated pressures

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    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 (FSCCs). After a heating period ranging from 24 to 2160 h (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 (<200 °C) than those of any previous experiments; (3) the disproportionation and TSR reactions in the S-H2O-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.

  7. 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.

  8. 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.

  9. Nonlinear Localized Dissipative Structures for Long-Time Solution of Wave Equation

    DTIC Science & Technology

    2009-07-01

    Fatemi, E., Engquist, B., and Osher, S., " Numerical Solution of the High Frequency Asymptotic Expansion for the Scalar Wave Equation ", Journal of...FINAL REPORT Grant Title: Nonlinear Localized Dissipative Structures for Long-Time Solution of Wave Equation By Dr. John Steinhoff Grant number... numerical method, "Wave Confinement" (WC), is developed to efficiently solve the linear wave equation . This is similar to the originally developed

  10. [Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

    PubMed

    Abaturov, L V; Nosova, N G

    2013-01-01

    The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

  11. The cluster structure of dilute aqueous-alcoholic solutions and molecular light scattering in them

    NASA Astrophysics Data System (ADS)

    Malomuzh, N. P.; Slinchak, E. L.

    2007-11-01

    The structures, equations of state, and character of fluctuations of dilute water-glycerol solutions are discussed. Two or three glycerol and about ten water molecules were found to form a fairly stable molecular complex. We call this complex elementary cluster (pseudoparticle). In a certain region of state parameters, the system could be considered a solution of pseudoparticles (clusters). Its properties were modeled by the van der Waals equation. The character of interactions between clusters was analyzed. An anomalous increase in concentration and molecular light scattering fluctuations was caused by the approach to the solution “pseudospinodal.” The experimental data were found to be in quite satisfactory agreement with theoretical estimates.

  12. Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology.

    PubMed

    Horst, Reto; Wüthrich, Kurt

    2015-07-20

    Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [(2)H, (15)N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al., 2013). 2D [(15)N, (1)H]-correlation maps are used as "fingerprints" to assess the foldedness of the IMP in solution. For promising samples, these "inexpensive" data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer.

  13. Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology

    PubMed Central

    Horst, Reto; Wüthrich, Kurt

    2016-01-01

    Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [2H, 15N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al., 2013). 2D [15N, 1H]-correlation maps are used as “fingerprints” to assess the foldedness of the IMP in solution. For promising samples, these “inexpensive” data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer. PMID:27077076

  14. Linear structural evolution induced tunable photoluminescence in clinopyroxene solid-solution phosphors.

    PubMed

    Xia, Zhiguo; Zhang, Yuanyuan; Molokeev, Maxim S; Atuchin, Victor V; Luo, Yi

    2013-11-22

    Clinopyroxenes along the Jervisite (NaScSi2O6)-Diopside (CaMgSi2O6) join have been studied, and a solid-solution of the type (Na(1-x)Ca(x))(Sc(1-x)Mg(x))Si2O6 has been identified in the full range of 0 ≤ x ≤ 1. The powder X-ray patterns of all the phases indicate a structural similarity to the end compounds and show smooth variation of structural parameters with composition. The linear structural evolution of iso-structural (Na(1-x)Ca(x))(Sc(1-x)Mg(x))Si2O6 solid-solutions obeying Vegard's rule has also been examined and verified by high resolution transmission electron microscopy (HRTEM). The continuous solid-solutions show the same structural type, therefore the photoluminescence spectra of Eu(2+) doped samples possess the superposition of spectral features from blue-emitting component (CaMgSi2O6:Eu(2+)) and yellow-emitting one (NaScSi2O6:Eu(2+)). This indicates that the spectroscopic properties of (Na(1-x)Ca(x))(Sc(1-x)Mg(x))Si2O6 clinopyroxene solid-solutions are in direct relations with structural parameters, and it is helpful for designing color-tunable photoluminescence with predetermined parameters.

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

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-04

    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

  16. Mathieu function solutions for photoacoustic waves in sinusoidal one-dimensional structures.

    PubMed

    Wu, Binbin; Diebold, Gerald J

    2012-07-01

    The photoacoustic effect for a one-dimensional structure, the sound speed of which varies sinusoidally in space, is shown to be governed by an inhomogeneous Mathieu equation with the forcing term dependent on the spatial and temporal properties of the exciting optical radiation. New orthogonality relations, traveling wave Mathieu functions, and solutions to the inhomogeneous Mathieu equation are found, which are used to determine the character of photoacoustic waves in infinite and finite length phononic structures. Floquet solutions to the Mathieu equation give the positions of the band gaps, the damping of the acoustic waves within the band gaps, and the dispersion relation for photoacoustic waves. The solutions to the Mathieu equation give the photoacoustic response of the structure, show the space equivalent of subharmonic generation and acoustic confinement when waves are excited within band gaps.

  17. Small-angle x-ray scattering investigation of the solution structure of troponin C

    SciTech Connect

    Hubbard, S.R.; Hodgson, K.O.; Doniach, S.

    1988-03-25

    X-ray crystallographic studies of troponin C have revealed a novel protein structure consisting of two globular domains, each containing two Ca/sup 2 +/-binding sites, connected via a nine-turn alpha-helix, three turns of which are fully exposed to solvent. Since the crystals were grown at pH approximately 5, it is of interest to determine whether this structure is applicable to the protein in solution under physiological conditions. We have used small-angle x-ray scattering to examine the solution structure of troponin C at pH 6.8 and the effect of Ca/sup 2 +/ on the structure. The scattering data are consistent with an elongated structure in solution with a radius of gyration of approximately 23.0 A, which is quite comparable to that computed for the crystal structure. The experimental scattering profile and the scattering profile computed from the crystal structure coordinates do, however, exhibit differences at the 40-A level. A weak Ca/sup 2 +/-facilitated dimerization of troponin C was observed. The data rule out large Ca/sup 2 +/-induced structural changes, indicating rather that the molecule with Ca/sup 2 +/ bound is only slightly more compact than the Ca/sup 2 +/-free molecule.

  18. New insights into structural alteration of enamel apatite induced by citric acid and sodium fluoride solutions.

    PubMed

    Wang, Xiaojie; Klocke, Arndt; Mihailova, Boriana; Tosheva, Lubomira; Bismayer, Ulrich

    2008-07-24

    Attenuated total reflectance infrared spectroscopy and complementary scanning electron microscopy were applied to analyze the surface structure of enamel apatite exposed to citric acid and to investigate the protective potential of fluorine-containing reagents against citric acid-induced erosion. Enamel and, for comparison, geological hydroxylapatite samples were treated with aqueous solutions of citric acid and sodium fluoride of different concentrations, ranging from 0.01 to 0.5 mol/L for citric acid solutions and from 0.5 to 2.0% for fluoride solutions. The two solutions were applied either simultaneously or consecutively. The citric acid-induced structural modification of apatite increases with the increase in the citric acid concentration and the number of treatments. The application of sodium fluoride alone does not suppress the atomic level changes in apatite exposed to acidic agents. The addition of sodium fluoride to citric acid solutions leads to formation of surface CaF2 and considerably reduces the changes in the apatite P-O-Ca framework. However, the CaF2 globules deposited on the enamel surface seem to be insufficient to prevent the alteration of the apatite structure upon further exposure to acidic agents. No evidence for fluorine-induced recovery of the apatite structure was found.

  19. On the origin of mesoscale structures in aqueous solutions of tertiary butyl alcohol: the mystery resolved.

    PubMed

    Sedlák, Marián; Rak, Dmytro

    2014-03-13

    We have performed a detailed experimental study on aqueous solutions of tertiary butyl alcohol which were a subject of long-standing controversies regarding the puzzling presence of virtually infinitely stable large-scale structures in such solutions occurring at length scales exceeding appreciably dimensions of individual molecules, referred to also as mesoscale structures. A combination of static and dynamic light scattering yielding information on solution structure and dynamics and gas chromatography coupled with mass spectrometry yielding information on chemical composition was used. We show that tertiary butyl alcohol clearly exhibiting such structures upon mixing with water does not contain any propylene oxide, which was previously considered as a source of these structures (an impurity expected to be present in all commercial samples of TBA). More importantly, we show that no mesoscale structures are generated upon addition of propylene oxide to aqueous solutions of TBA. The ternary system TBA/water/propylene oxide exhibits homogeneous mixing of the components on mesoscales. We show that the source of the mesoscale structures is a mesophase separation of appreciably more hydrophobic compounds than propylene oxide. These substances are explicitly analytically identified as well as their disappearance upon filtering out the mesoscale structures by nanopore filtration. We clearly show which substances are disappearing upon filtration and which are not. This enables us to estimate with rather high probability the chemical composition of the mesoscale structures. Visualization of large-scale structures via nanoparticle tracking analysis is also presented. Video capturing the mesoscale particles as well as their Brownian motion can be found in the Supporting Information .

  20. Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches.

    PubMed

    Schmidt, J R; Corcelli, S A; Skinner, J L

    2004-11-08

    Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio vibrational frequencies for a solute in a cluster of solvent molecules to a linear combination of the electrostatic potentials on the solute atoms due to the charges on the solvent molecules. These authors applied their method to the N-methylacetamide-D/D(2)O system. We (S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, [J. Chem. Phys. 120, 8107 (2004)]) have recently explored a closely related method, where instead of the electrostatic potential, the solute vibrational frequencies are fit to the components of the electric fields on the solute atoms due to the solvent molecules. We applied our method to the HOD/D(2)O and HOD/H(2)O systems. In order to make a direct comparison of these two approaches, in this paper we apply their method to the water system, and our method to the N-methylacetamide system. For the water system we find that the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape. For the N-methylacetamide system the two methods are comparable.

  1. 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.

  2. Structural and magnetic properties of mechanically alloyed Co 20Cu 80 solid solution

    NASA Astrophysics Data System (ADS)

    Yoo, Y. G.; Yang, D. S.; Yu, S. C.; Kim, W. T.; M. Lee, J.

    1999-08-01

    Microstructural change during the mechanical alloying of Co 20Cu 80 has been studied by X-ray diffractometry (XRD) and extended X-ray absorption fine structure (EXAFS) techniques. EXAFS analysis shows clearly the formation of supersaturated Co 20Cu 80 solid solution with FCC crystal structure during mechanical alloying, which is in good agreement with XRD analysis. Magnetic properties also have been studied by SQUID magnetometer from 4 to 290 K. The supersaturated Co 20Cu 80 solid solution shows wide distribution in Co cluster size due to the continuous blocking of Co cluster as a function of temperature.

  3. SOLVE and RESOLVE: automated structure solution, density modification and model building.

    PubMed

    Terwilliger, Thomas

    2004-01-01

    The software SOLVE and RESOLVE can carry out all the steps in macromolecular structure solution, from scaling and heavy-atom location through phasing, density modification and model-building in the MAD, SAD and MIR cases. SOLVE uses scoring scheme to convert the decision-making in macromolecular structure solution to an optimization problem. RESOLVE carries out the identification of NCS, density modification and automated model-building. The procedure is fully automated and can function at resolutions as low as 3 A.

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

    PubMed

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

    2014-06-01

    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.

  5. Implementation of Lamarckian concepts in a Genetic Algorithm for structure solution from powder diffraction data

    NASA Astrophysics Data System (ADS)

    Turner, Giles W.; Tedesco, Emilio; Harris, Kenneth D. M.; Johnston, Roy L.; Kariuki, Benson M.

    2000-04-01

    Previous implementations of Genetic Algorithms in direct-space strategies for structure solution from powder diffraction data have employed the operations of mating, mutation and natural selection, with the fitness of each structure based on comparison between calculated and experimental powder diffraction patterns (we define fitness as a function of weighted-profile R-factor Rwp). We report an extension to this method, in which each structure generated in the Genetic Algorithm is subjected to local minimization of Rwp with respect to structural variables. This approach represents an implementation of Lamarckian concepts of evolution, and is found to give significant improvements in efficiency and reliability.

  6. Solution structures of calcium regulating proteins: A small-angle scattering study

    SciTech Connect

    Trewhella, J.; Heidorn, D.B.; Seeger, P.A.

    1987-11-01

    Small-angle X-ray scattering (SAXS) experiments have shown that the solution structures of two calcium-binding regulatory proteins, calmodulin and troponin C, are significantly different from their crystal structure forms. The structural differences occur in a region of calmodulin that is thought to bind to target enzymes;the calmodulin-enzyme complex is an initiator for many important biochemical processes. Calcium binding to calmodulin induces a conformational change that is a prerequisite for calmodulin binding to a target enzyme. SAXS data can characterize this conformational change and give insight into the mechanism of enzyme binding. Neutron resonance scattering promises to determine accurately the distances between calcium binding sites, thus providing important constraints on the structure of calmodulin in solution. 24 refs., 5 figs., 1 tab.

  7. 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.

  8. An efficient solution procedure for the thermoelastic analysis of truss space structures

    NASA Technical Reports Server (NTRS)

    Givoli, D.; Rand, O.

    1992-01-01

    A solution procedure is proposed for the thermal and thermoelastic analysis of truss space structures in periodic motion. In this method, the spatial domain is first descretized using a consistent finite element formulation. Then the resulting semi-discrete equations in time are solved analytically by using Fourier decomposition. Geometrical symmetry is taken advantage of completely. An algorithm is presented for the calculation of heat flux distribution. The method is demonstrated via a numerical example of a cylindrically shaped space structure.

  9. Structural aspects of glucans formed in solution and on the surface of hydroxyapatite.

    PubMed

    Kopec, L K; Vacca-Smith, A M; Bowen, W H

    1997-10-01

    Streptococcus mutans glucosyltransferases (GtfB, -C, and -D) and their products formed from sucrose, glucans, play an essential role in the pathogenesis of dental caries. Enzymatically active Gtf is found in whole human saliva (solution), and incorporated into the salivary pellicle that is formed on teeth in vivo (surface). GtfB glucans are predominantly 1,3-linked; however, surface-formed glucans from GtfB contain greater amounts of 3-linked glucose than glucans formed in solution. In contrast, the major linkage of glucans formed on the surface by GtfB in the presence of sucrose and starch hydrolysates in 4-linked glucose. GtfC-derived glucans in solution have a major linkage of 6-linked glucose, while surface-formed glucans from the same enzyme have 3-linked glucose as the major linkage. GtfD glucans formed either in solution or on the surface are predominantly 1,6-linked; however, surface-formed glucans contain more 6-linked glucose than solution-formed glucans. Digestion with the glucanohydrolases mutanase and dextranase shows differences in susceptibility among glucans formed either in solution or on the surface by each of the Gtf enzymes, and differences are also seen in the soluble end products from these digestions. Our results show that the same Gtf enzyme can form structurally distinct glucans in solution and on a surface. These observations are important in the study of naturally occurring microbial films.

  10. Structure and properties of regenerated Antheraea pernyi silk fibroin in aqueous solution.

    PubMed

    Tao, Wei; Li, Mingzhong; Zhao, Chunxia

    2007-04-10

    Antheraea pernyi silk fibroin fibers were dissolved by aqueous lithium thiocyanate to obtain regenerated A. pernyi silk fibroin solution. By means of circular dichroism, (13)C NMR and Raman spectroscopy, the molecular conformation of regenerated A. pernyi silk fibroin in aqueous solution was investigated. The relationship of environmental factors and sol-gel transformation behavior of regenerated A. pernyi silk fibroin was also studied. The molecular conformations of regenerated A. pernyi silk fibroin mainly were alpha-helix and random coil in solution. There also existed a little beta-sheet conformation. It was obviously different with Bombyx mori silk fibroin, whose molecular conformation in solution was only random coil but no alpha-helix existence. With the increase of temperature and solution concentration and with the decrease of solution pH value, the gelation velocity of regenerated A. pernyi silk fibroin solution increased. Especially, it showed that A. pernyi silk fibroin was more sensitive to temperature than B. mori silk fibroin during the sol-gel transformation. The velocity increased obviously when the temperature was above 30 degrees C. During the sol-gel transformation, the molecular conformation of regenerated A. pernyi silk fibroin changed from random coil to beta-sheet structure. The results of these studies provided important insight into the preparation of new biomaterials by silk fibroin protein.

  11. 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.

  12. 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.

  13. Structure and interactions of fish type III antifreeze protein in solution.

    PubMed

    Salvay, Andrés G; Gabel, Frank; Pucci, Bernard; Santos, Javier; Howard, Eduardo I; Ebel, Christine

    2010-07-21

    It has been suggested that above a critical protein concentration, fish Type III antifreeze protein (AFP III) self-assembles to form micelle-like structures that may play a key role in antifreeze activity. To understand the complex activity of AFP III, a comprehensive description of its association state and structural organization in solution is necessary. We used analytical ultracentrifugation, analytical size-exclusion chromatography, and dynamic light scattering to characterize the interactions and homogeneity of AFP III in solution. Small-angle neutron scattering was used to determine the low-resolution structure in solution. Our results clearly show that at concentrations up to 20 mg mL(-1) and at temperatures of 20 degrees C, 6 degrees C, and 4 degrees C, AFP III is monomeric in solution and adopts a structure compatible with that determined by crystallography. Surface tension measurements show a propensity of AFP III to localize at the air/water interface, but this surface activity is not correlated with any aggregation in the bulk. These results support the hypothesis that each AFP III molecule acts independently of the others, and that specific intermolecular interactions between monomers are not required for binding to ice. The lack of attractive interactions between monomers may be functionally important, allowing for more efficient binding and covering of the ice surface.

  14. 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".…

  15. 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.

  16. Structure and Interactions of Fish Type III Antifreeze Protein in Solution

    PubMed Central

    Salvay, Andrés G.; Gabel, Frank; Pucci, Bernard; Santos, Javier; Howard, Eduardo I.; Ebel, Christine

    2010-01-01

    Abstract It has been suggested that above a critical protein concentration, fish Type III antifreeze protein (AFP III) self-assembles to form micelle-like structures that may play a key role in antifreeze activity. To understand the complex activity of AFP III, a comprehensive description of its association state and structural organization in solution is necessary. We used analytical ultracentrifugation, analytical size-exclusion chromatography, and dynamic light scattering to characterize the interactions and homogeneity of AFP III in solution. Small-angle neutron scattering was used to determine the low-resolution structure in solution. Our results clearly show that at concentrations up to 20 mg mL−1 and at temperatures of 20°C, 6°C, and 4°C, AFP III is monomeric in solution and adopts a structure compatible with that determined by crystallography. Surface tension measurements show a propensity of AFP III to localize at the air/water interface, but this surface activity is not correlated with any aggregation in the bulk. These results support the hypothesis that each AFP III molecule acts independently of the others, and that specific intermolecular interactions between monomers are not required for binding to ice. The lack of attractive interactions between monomers may be functionally important, allowing for more efficient binding and covering of the ice surface. PMID:20643081

  17. 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.

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

    PubMed

    Yang, Pei-Kun; Lim, Carmay

    2008-09-04

    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.

  19. Disproportionation and Thermochemical Sulfate Reduction Reactions in S-H2O-CH4 and S-D2O-CH4 Systems from 200 to 340 °C at Elevated Pressures

    NASA Astrophysics Data System (ADS)

    Chou, I.; Yuan, S.; Burruss, R. C.

    2010-12-01

    Elemental sulfur plays significant roles in thermochemical sulfate reduction (TSR) reactions as a transient intermediate oxidation state compound, by-product, or catalyst. However, the mechanisms of the reactions in S-H2O-hydrocarbon 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. After a heating period ranging from one to 90 days, the quenched samples were analyzed by Raman spectroscopy. Our results showed that the disproportionation of sulfur in the S-H2O-CH4 system occurred at temperatures above 200 °C and produced H2S, SO42-, and HSO4-. We also observed that the amounts of SO42- and HSO4- decreased for the samples quenched from 250 and 340 °C, and at the same time the amounts of CO2 and H2S increased. To demonstrate that the observed consumption of SO42- and HSO4- in the S-H2O-CH4 system at 300 °C was due to TSR instead of the back reaction between SO42- (or HSO4-) and H2S to form S during and after quench, we introduced 1m ZnBr2 to remove H2S as a ZnS precipitate, as soon as it formed. In these experiments sulfate species decreased and CO2 and H2S increased consistent with TSR and no back reaction. When compared with previously published experiments, our temperatures between 250 and 340 °C are much closer to natural systems (<200 °C) with documented TSR. Also, to demonstrate the relationship between disproportionation and TSR reactions in the S-H2O-CH4 system, we conducted experiments in the S-D2O-CH4 system at 250 and 300 °C. Only small Raman signals for CO2 and no signals for H2S and D2S were detected in the sample quenched from 250 °C, indicating that both the disproportionation reaction and the TSR reaction were very slow at this temperature. After heating at 300 °C for 40 h, Raman signals of the quenched sample indicated significant amount of D2S was produced through the

  20. 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.

  1. X-ray absorption spectroscopic investigation of the electronic structure differences in solution and crystalline oxyhemoglobin

    PubMed Central

    Wilson, Samuel A.; Green, Evan; Mathews, Irimpan I.; Benfatto, Maurizio; Hodgson, Keith O.; Hedman, Britt; Sarangi, Ritimukta

    2013-01-01

    Hemoglobin (Hb) is the heme-containing O2 transport protein essential for life in all vertebrates. The resting high-spin (S = 2) ferrous form, deoxy-Hb, combines with triplet O2, forming diamagnetic (S = 0) oxy-Hb. Understanding this electronic structure is the key first step in understanding transition metal–O2 interaction. However, despite intense spectroscopic and theoretical studies, the electronic structure description of oxy-Hb remains elusive, with at least three different descriptions proposed by Pauling, Weiss, and McClure-Goddard, based on theory, spectroscopy, and crystallography. Here, a combination of X-ray absorption spectroscopy and extended X-ray absorption fine structure, supported by density functional theory calculations, help resolve this debate. X-ray absorption spectroscopy data on solution and crystalline oxy-Hb indicate both geometric and electronic structure differences suggesting that two of the previous descriptions are correct for the Fe–O2 center in oxy-Hb. These results support the multiconfigurational nature of the ground state developed by theoretical results. Additionally, it is shown here that small differences in hydrogen bonding and solvation effects can tune the ground state, tipping it into one of the two probable configurations. These data underscore the importance of solution spectroscopy and show that the electronic structure in the crystalline form may not always reflect the true ground-state description in solution. PMID:24062465

  2. 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.

  3. Fabrication of three-dimensional micro-nanofiber structures by a novel solution blow spinning device

    NASA Astrophysics Data System (ADS)

    Liang, Feng; Fang, Feiyu; Zeng, Jun; Wang, Zhifeng; Ou, Weijun; Chen, Xindu; Wu, Peixuan; Wang, Han; Zhang, Lin

    2017-02-01

    The fabrication of three-dimensional scaffolds has attracted more attention in tissue engineering. The purpose of this study is to explore a new method for the fabrication of three-dimensional micro-nanofiber structures by combining solution blow spinning and rotating collector. In this study, we successfully fabricated fibers with a minimum diameter of 200 nm and a three-dimensional structure with a maximum porosity of 89.9%. At the same time, the influence of various parameters such as the solvent volatility, the shape of the collector, the feed rate of the solution and the applied gas pressure were studied. It is found that solvent volatility has large effect on the formation of the three-dimensional shape of the structure. The shape of the collector affects the porosity and fiber distribution of the three-dimensional structure. The fiber diameter and fiber uniformity can be controlled by adjusting the solution feed rate and the applied gas pressure. It is feasible to fabricate high-quality three-dimensional micro-nanofiber structure by this new method, which has great potential in tissue engineering.

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

    SciTech Connect

    Taylor, Seth Thomas

    2002-01-01

    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.

  5. Physical and structural stability of the monoclonal antibody, trastuzumab (Herceptin®), intravenous solutions.

    PubMed

    Pabari, Ritesh M; Ryan, Benedict; Ahmad, Wazir; Ramtoola, Zebunnissa

    2013-01-01

    A major limitation of biological therapeutics is their propensity for degradation particularly in aqueous solutions hence resulting in their short shelf-life. In this study, the stability of trastuzumab (Herceptin®) intravenous (i.v.) solutions, an IgG1 monoclonal antibody (mAb), indicated for the treatment of HER2 positive breast cancer, stored under refrigerated conditions, was evaluated over 28 days. No change in visual appearance or average particle size was observed. The pH values of the trastuzumab i.v. solutions remained stable over time. Interestingly, no change in trastuzumab monomer concentration was observed throughout the 28-day study, as determined by SEC-HPLC. SDSPAGE showed only a monomer band corresponding to the molecular weight of trastuzumab. Circular dichroism spectra obtained following 28-day storage demonstrated integrity of the secondary structural conformation of trastuzumab. Results from this study show that trastuzumab i.v. solutions remain physically and structurally stable on storage at 2-8°C for 28 days. These findings suggest that trastuzumab in solution may not be as sensitive to degradation as expected for a mAb and therefore may have important implications in extending trastuzumab shelf life for clinical use and reducing associated healthcare cost.

  6. Thermodynamic behavior and structural properties of an aqueous sodium chloride solution upon supercooling.

    PubMed

    Corradini, D; Gallo, P; Rovere, M

    2008-06-28

    We present the results of a molecular dynamics simulation study of thermodynamic and structural properties upon supercooling of a low concentration sodium chloride solution in TIP4P water and the comparison with the corresponding bulk quantities. We study the isotherms and the isochores for both the aqueous solution and bulk water. The comparison of the phase diagrams shows that thermodynamic properties of the solution are not merely shifted with respect to the bulk. Moreover, from the analysis of the thermodynamic curves, both the spinodal line and the temperatures of maximum density curve can be calculated. The spinodal line appears not to be influenced by the presence of ions at the chosen concentration, while the temperatures of maximum density curve displays both a mild shift in temperature and a shape modification with respect to bulk. Signatures of the presence of a liquid-liquid critical point are found in the aqueous solution. By analyzing the water-ion radial distribution functions of the aqueous solution, we observe that upon changing density, structural modifications appear close to the spinodal. For low temperatures, additional modifications appear also for densities close to that corresponding to a low density configurational energy minimum.

  7. Structural Analysis of the Flagellar Component Proteins in Solution by Small Angle X-Ray Scattering.

    PubMed

    Lee, Lawrence K

    2017-01-01

    Small angle X-ray scattering is an increasingly utilized method for characterizing the shape and structural properties of proteins in solution. The technique is amenable to very large protein complexes and to dynamic particles with different conformational states. It is therefore ideally suited to the analysis of some flagellar motor components. Indeed, we recently used the method to analyze the solution structure of the flagellar motor protein FliG, which when combined with high-resolution snapshots of conformational states from crystal structures, led to insights into conformational transitions that are important in mediating the self-assembly of the bacterial flagellar motor. Here, we describe procedures for X-ray scattering data collection of flagellar motor components, data analysis, and interpretation.

  8. 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

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

    PubMed

    Benmouna, Farida; Zemmour, Samira; Benmouna, Mustapha

    2016-03-03

    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.

  10. Dynamic structure factor of a stiff polymer in a glassy solution.

    PubMed

    Glaser, J; Hallatschek, O; Kroy, K

    2008-01-01

    We provide a comprehensive overview of the current theoretical understanding of the dynamic structure factor of stiff polymers in semidilute solution based on the wormlike chain (WLC) model. We extend previous work by computing exact numerical coefficients and an expression for the dynamic mean square displacement (MSD) of a free polymer and compare various common approximations for the hydrodynamic interactions, which need to be treated accurately if one wants to extract quantitative estimates for model parameters from experimental data. A recent controversy about the initial slope of the dynamic structure factor is thereby resolved. To account for the interactions of the polymer with a surrounding (sticky) polymer solution, we analyze an extension of the WLC model, the glassy wormlike chain (GWLC), which predicts near power law and logarithmic long-time tails in the dynamic structure factor.

  11. Solution of quadratic matrix equations for free vibration analysis of structures.

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1973-01-01

    An efficient digital computer procedure and the related numerical algorithm are presented herein for the solution of quadratic matrix equations associated with free vibration analysis of structures. Such a procedure enables accurate and economical analysis of natural frequencies and associated modes of discretized structures. The numerically stable algorithm is based on the Sturm sequence method, which fully exploits the banded form of associated stiffness and mass matrices. The related computer program written in FORTRAN V for the JPL UNIVAC 1108 computer proves to be substantially more accurate and economical than other existing procedures of such analysis. Numerical examples are presented for two structures - a cantilever beam and a semicircular arch.

  12. 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

  13. Structure and intermolecular interactions in selected binary solutions studied by X-ray methods

    NASA Astrophysics Data System (ADS)

    Drozdowski, Henryk; Romaniuk, Anna; Błaszczak, Zdzisław

    2013-12-01

    The results of X-ray structural studies of liquid chloroanisole C6H4OCH3Cl and 10% solutions of chloroanisole in 1,4-dimethylbenzene C8H10 are presented. It is the first paper on an X-ray diffraction study of the liquid solutions of chloroanisole. The X-ray measurements were made at 293 K for the scattering angle range 2Θ varying from 6° to 120°. Averaged scattered X-ray angular distributions I¯(S) were determined. The angular distributions of the intensity of X-ray scattered by 10% solutions of chloroanisole in 1,4-dimethylbenzene were compared to the angular distributions obtained for liquid ortho-, meta- and para-chloroanisole. The differential radial distribution functions of electron density 4πr∑j,knK[ρk(r)-ρ0] were numerically found using the Fourier analysis from a modified Warren, Krutter and Morningstar equation. To the maxima of DRDFs, interatomic and intermolecular distances were assigned. The use of short-wave radiation from an X-ray tube with a molybdenum anode permitted determination of the spheres of intermolecular ordering in the studied liquids and their solutions. The experimental results were used to plot models of the most highly probable mutual disposition of the molecules in liquid chloroanisole and their solutions. The benzene rings of two molecules are situated in parallel plane what results in antiparallel setting of the dipole moments of the chloroanisole molecules. X-ray structural analysis was applied to determine the packing coefficients of chloroanisole molecules. The results obtained in this paper confirm the specific structural properties of the solutions studied.

  14. 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.

  15. Effect of different alkaline solutions on crystalline structure of cellulose at different temperatures.

    PubMed

    Keshk, Sherif M A S

    2015-01-22

    Effect of alkaline solutions such as 10% NaOH, NaOH/urea and NaOH/ethylene glycol solutions on crystalline structure of different cellulosic fibers (cotton linter and filter paper) was investigated at room temperature and -4°C. The highest dissolution of cotton linter and filter paper was observed in NaOH/ethylene glycol at both temperatures. X-ray patterns of treated cotton linter with different alkaline solutions at low temperature showed only two diffractions at 2θ=12.5° and 21.0°, which belonged to the crystalline structure of cellulose II. CP/MAS (13)C NMR spectra showed the doublet peaks at 89.2 ppm and 88.3 ppm representing C4 resonance for cellulose I at room temperature, Whereas, at low temperature the doublet peaks were observed at 89.2 ppm and 87.8 ppm representing C4 resonance for cellulose II. Degree of polymerization of cellulose plays an important role in cellulose dissolution in different alkaline solutions and temperatures, where, a low temperature gives high dissolutions percentage with change in crystalline structure from cellulose I to cellulose II forms.

  16. 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.

  17. 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.

  18. 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.

  19. Plasticity of CYP2B Enzymes: Structural and Solution Biophysical Methods

    PubMed Central

    Wilderman, P. Ross; Halpert, James R.

    2013-01-01

    In the past three years, major advances in understanding cytochrome P450 2B (CYP2B) structure-function relationships have been made through determination of multiple ligand-bound and one ligand-free X-ray crystal structure of CYP2B4 and one ligand-bound X-ray crystal structure of CYP2B6. These structures have provided insight into the features that provide the high degree of plasticity of the enzymes. A combination of a phenylalanine cluster that allows for concerted movement of helices F through G and a conserved set of electrostatic interactions involving Arg262 facilitates movement of this region to accommodate binding of ligands of various sizes without perturbing most of the P450 fold. Integrating solution based techniques such as NMR or deuterium exchange mass spectrometry (DXMS) with computational methods including molecular docking has provided further insight into enzyme behavior upon ligand binding. In addition, extended molecular dynamics simulations have provided a link between an open and a closed conformation of ligand-free CYP2B4 found in crystal structures. Other studies revealed the utility of rational engineering in improving stability of P450s to facilitate structural studies. The solution and computational results combined with the X-ray crystal structures yield a comprehensive picture of how these enzymes adopt different conformations to bind various ligands. PMID:22208531

  20. 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.

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

    DOE PAGES

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.; ...

    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

  2. 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.

  3. 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

  4. Ultraviolet (UV) Raman Spectroscopy Study of the Soret Effect in High-Pressure CO2-Water Solutions

    SciTech Connect

    Windisch, Charles F.; Maupin, Gary D.; McGrail, B. Peter

    2012-07-01

    Spatially resolved deep-UV Raman spectroscopy was applied to solutions of CO2 and H2O or D2O subject to a temperature gradient in a thermally regulated high-pressure concentric-tube Raman cell in an attempt to measure a Soret effect in the vicinity of the critical point of CO2. Although Raman spectra of solutions of CO2 dissolved in D2O, at 10 MPa and temperatures near the critical point of CO2, had adequate signal-to-noise and spatial resolution to observe a Soret effect with a Soret coefficient with magnitude |ST| > 0.03, no evidence for an effect of this size was obtained for applied temperature gradients up to 19 C. In contrast, the concentration of CO2 dissolved in H2O was shown to vary significantly across the temperature gradient when excess CO2 was present, but the results could be explained simply by the variation in CO2 solubility over the temperature range and not to kinetic factors. For mixtures of D2O dissolved in scCO2 at 10 MPa and temperatures close to the critical point of CO2, the Raman peaks for D2O were too weak to measure with confidence even at the limit of D2O solubility.

  5. 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.

  6. A novel class of cysteine protease inhibitors: solution structure of staphostatin A from Staphylococcus aureus.

    PubMed

    Dubin, Grzegorz; Krajewski, Marcin; Popowicz, Grzegorz; Stec-Niemczyk, Justyna; Bochtler, Matthias; Potempa, Jan; Dubin, Adam; Holak, Tad A

    2003-11-25

    A series of secreted proteases are included among the virulence factors documented for Staphylococcus aureus. In light of increasing antibiotic resistance of this dangerous human pathogen, these proteases are considered as suitable targets for the development of novel therapeutic strategies. The recent discovery of staphostatins, endogenous, highly specific, staphylococcal cysteine protease inhibitors, opened a possibility for structure-based design of low molecular weight analogues. Moreover, the crystal structure of staphostatin B revealed a distinct folding pattern and an unexpected, substrate-like binding mode. The solution structure of staphostatin A reported here confirms that staphostatins constitute a novel, distinct class of cysteine protease inhibitors. In addition, the structure knowledge-based mutagenesis studies shed light on individual structural features of staphostatin A, the inhibition mechanism, and the determinants of distinct specificity of staphostatins toward their target proteases.

  7. Solution secondary structure of calcium-saturated troponin C monomer determined by multidimensional heteronuclear NMR spectroscopy.

    PubMed Central

    Slupsky, C. M.; Reinach, F. C.; Smillie, L. B.; Sykes, B. D.

    1995-01-01

    The solution secondary structure of calcium-saturated skeletal troponin C (TnC) in the presence of 15% (v/v) trifluoroethanol (TFE), which has been shown to exist predominantly as a monomer (Slupsky CM, Kay CM, Reinach FC, Smillie LB, Sykes BD, 1995, Biochemistry 34, forthcoming), has been investigated using multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The 1H, 15N, and 13C NMR chemical shift values for TnC in the presence of TFE are very similar to values obtained for calcium-saturated NTnC (residues 1-90 of skeletal TnC), calmodulin, and synthetic peptide homodimers. Moreover, the secondary structure elements of TnC are virtually identical to those obtained for calcium-saturated NTnC, calmodulin, and the synthetic peptide homodimers, suggesting that 15% (v/v) TFE minimally perturbs the secondary and tertiary structure of this stably folded protein. Comparison of the solution structure of calcium-saturated TnC with the X-ray crystal structure of half-saturated TnC reveals differences in the phi/psi angles of residue Glu 41 and in the linker between the two domains. Glu 41 has irregular phi/psi angles in the crystal structure, producing a kink in the B helix, whereas in calcium-saturated TnC, Glu 41 has helical phi/psi angles, resulting in a straight B helix. The linker between the N and C domains of calcium-saturated TnC is flexible in the solution structure. PMID:7670371

  8. Structure and properties of the precipitates formed from condensed solutions of the revised simulated body fluid.

    PubMed

    Dorozhkina, Elena I; Dorozhkin, Sergey V

    2003-11-01

    Precipitation experiments with aqueous solutions of the Kokubo's revised simulated body fluid (rSBF) equal to 2, 4, 8, and 12 times the ionic concentration of human blood plasma were performed. Instead of Hepes, solution pH was adjusted to the desired value of 7.40 +/- 0.02 by either bubbling of CO2 or addition of HCl. The experiments were performed in tightly closed plastic vessels kept at 37.0 +/- 0.2 degrees C for 72 h under permanent shaking. Afterward, the suspensions were filtrated, and the precipitates were collected and analyzed. The results revealed that increasing the concentration of rSBF resulted in great changes in both the structure and the chemical composition of the precipitates. Phosphate substitution for carbonate (although the amounts of calcium and magnesium remained unchanged) and crystallinity decreasing were the most important modifications found in the precipitates formed from the highly condensed solutions of rSBF.

  9. 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.

  10. 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.

  11. Method of single expression: an exact solution for wavelength scale 1D photonic structure computer modeling

    NASA Astrophysics Data System (ADS)

    Baghdasaryan, Hovik V.; Knyazyan, Tamara M.

    2003-12-01

    The principles of the method of single expression (MSE) for boundary problems solution in classical electrodynamics are presented. In the MSE the solution of the Helmholtz's equation is presented in the special form of a single expression describing resultant amplitude and phase distributions in the medium. This form of solution presenation permits to pass over the restrictions of the superposition principle and to solve both linear and nonlinear problems with ths same ease. In the MSE the Helmholtz's equation is reformulated to the set of first order differential equations and the boundary problem is solved numerically. No approximations are implied either in Helmholtz's equation or in boundary conditions. Using the MSE steady-state boundary problems are modeled for wavelength scale multilayer and modulated 1D photonic structures including amplification and nonuniformity evoked by intense electromagnetic field.

  12. The analytic solution of the structural analysis problem and its use in structural synthesis

    NASA Astrophysics Data System (ADS)

    Fuchs, M. B.

    An overview is presented of the analytic expressions for the inverse of the stiffness matrix, the nodal displacements, and the internal forces in linear elastic redundant structures. The inverse of the stiffness matrix and the nodal displacements are obtained using Binet and Cauchy's theorem on the product of compound matrices. The formula for the internal forces is derived from the principles of structural mechanics. This approach is shown to apply to all framed structures via the unimodal stiffnesses of its elements. Approximate models are constructed which are exact at preselected points along a line in the analysis space. An argument is also made for the use of multilinear polynomials as an alternative to Taylor expansion-based approximations.

  13. 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.

  14. Solvent-induced changes in the structure and rheology of polyelectrolyte solutions.

    NASA Astrophysics Data System (ADS)

    Breedveld, Victor

    2006-03-01

    By integrating microfluidics and particle tracking microrheology, we have constructed a dialysis cell for microrheology, which provides unique opportunities for studying the dynamics of microstructural changes induced by changes in solvent composition. Such experiments are virtually impossible with mechanical rheometers. The concept and design of the microdialysis cell will be discussed, and data will be presented on the structural and rheological response of polyelectrolyte solutions to changes in ionic strength. Sulphonated polystyrene is a water-soluble polymer and its molecular conformation in solution strongly depends on ionic strength of the solution. It will be shown that quantitative measurements of transient solution viscosity during solvent exchange can be performed with the new dialysis cell. Experiments were also performed on amphiphilic block copolypeptide (BCP) hydrogels, which self-assemble into fibrillar structures due to a subtle balance between attractive and repulsive intermolecular forces. Electrostatic repulsion between the hydrophilic L-lysine blocks plays a key role. Therefore, changes in ionic strength have a significant effect on the self-assembled local structure and mechanical properties of the BCP gels, as was previously observed in rheometer experiments. Microrheology in the dialysis cell provided a much more complete picture, revealing the occurrence of microscopic phase separation upon the addition of salt. For example, in a K160L40 lysine-leucine block copolypeptide, the motion of tracer particles in the hydrogel is homogeneous in DI water. After the addition of salt, microrheology reveals the co-existence of populations of freely moving and immobilized particles. The changes in local microstructure were found to be reversible when the ionic strength of the solution was lowered again. Data will be presented on the dynamics of the morphological and rheological changes of various block copolypeptide hydrogels.

  15. 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.

  16. 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.

  17. The equilibrium structure of lithium salt solutions in ether-functionalized ammonium ionic liquids.

    PubMed

    Figueiredo, Pedro Henrique; Siqueira, Leonardo J A; Ribeiro, Mauro C C

    2012-10-11

    Molecular dynamics simulations have been performed for ionic liquids based on a ternary mixture of lithium and ammonium cations and a common anion, bis(trifluoromethylsulfonyl)imide, [Tf(2)N](-). We address structural changes resulting from adding Li(+) in ionic liquids with increasing length of an ether-functionalized chain in the ammonium cation. The calculation of static structure factors reveals the lithium effect on charge ordering and intermediate range order in comparison with the neat ionic liquids. The charge ordering is modified in the lithium solution because the coordination of [Tf(2)N](-) toward Li(+) is much stronger than ammonium cations. Intermediate range order is observed in neat ionic liquids based on ammonium cations with a long chain, but in the lithium solutions, there is also a nonhomogenous distribution of Li(+) cations. The presence of Li(+) enhances interactions between the ammonium cations due to correlations between the oxygen atom of the ether chain and the nitrogen atom of another ammonium cation.

  18. On the structure of solutions to a class of quasilinear elliptic Neumann problems. Part II

    PubMed Central

    Zhao, Chunshan; Li, Yi

    2010-01-01

    We continue our work (Y. Li, C. Zhao in J Differ Equ 212:208–233, 2005) to study the structure of positive solutions to the equation εm Δmu − um−1 + f(u) = 0 with homogeneous Neumann boundary condition in a smooth bounded domain of RN (N ≥ 2). First, we study subcritical case for 2 < m < N and show that after passing by a sequence positive solutions go to a constant in C1, α sense as ε → ∞. Second, we study the critical case for 1 < m < N and prove that there is a uniform upper bound independent of ε ∈ [1, ∞) for the least-energy solutions. Third, we show that in the critical case for 1 < m ≤ 2 the least energy solutions must be a constant if ε is sufficiently large and for 2 < m < N the least energy solutions go to a constant in C1, α sense as ε → ∞. PMID:20700388

  19. Organic solid solution composed of two structurally similar porphyrins for organic solar cells.

    PubMed

    Zhen, Yonggang; Tanaka, Hideyuki; Harano, Koji; Okada, Satoshi; Matsuo, Yutaka; Nakamura, Eiichi

    2015-02-18

    A solid solution of a 75:25 mixture of tetrabenzoporphyrin (BP) and dichloroacenaphtho[q]tribenzo[b,g,l]porphyrin (CABP) forms when they are generated in a matrix of (dimethyl(o-anisyl)silylmethyl)(dimethylphenylsilylmethyl)[60]fullerene. This solid solution provides structural and optoelectronic properties entirely different from those of either pristine compounds or a mixture at other blending ratios. The use of this BP:CABP solid solution for organic solar cell (OSC) devices resulted in a power conversion efficiency (PCE) value higher by 16 and 300% than the PCE values obtained for the devices using the single donor BP and CABP, respectively, in a planar heterojunction architecture. This increase originates largely from the increase in short circuit current density, and hence by enhanced charge carrier separation at the donor/acceptor interface, which was probably caused by suitable energy level for the solid solution state, where electronic coupling between the two porphyrins occurred. The results suggest that physical and chemical modulation in solid solution is beneficial as an operationally simple method to enhance OSC performance.

  20. Role of the surfactant structure in the behavior of hydrophobic ionic liquids within aqueous micellar solutions.

    PubMed

    Behera, Kamalakanta; Kumar, Vinod; Pandey, Siddharth

    2010-04-06

    The behavior of an ionic liquid (IL) within aqueous micellar solutions is governed by its unique property to act as both an electrolyte and a cosolvent. The influence of the surfactant structure on the properties of aqueous micellar solutions of zwitterionic SB-12, nonionic Brij-35 and TX-100, and anionic sodium dodecyl sulfate (SDS) in the presence of the "hydrophobic" IL 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF(6)]) is assessed along with the possibility of forming oil-in-water microemulsions in which the IL acts as the "oil" phase. The solubility of [bmim][PF(6)] within aqueous micellar solutions increases with increasing surfactant concentration. In contrast to anionic SDS, the zwitterionic and nonionic surfactant solutions solubilize more [bmim][PF(6)] at higher concentrations and the average aggregate size remains almost unchanged. The formation of IL-in-water microemulsions when the concentration of [bmim][PF(6)] is above its aqueous solubility is suggested for nonionic Brij-35 and TX-100 aqueous surfactant solutions.

  1. Structure and micromorphology of titanium dioxide nanoporous microspheres formed in water solution

    NASA Astrophysics Data System (ADS)

    Troitskaia, I. B.; Gavrilova, T. A.; Atuchin, V. V.

    TiO2 nanoporous microspheres of 20 μm diameter with good crystallinity have been obtained by precipitation from aqua solution of ammonium titanate with nitric acid at pH = 1 and T = 100oC. Pure rutile, space group P42/mnm, phase composition has been confirmed by XRD analysis of the precipitate. SEM observation of these microspheres shows developed nanoporous structure with pore diameter of 20-30 nm.

  2. Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; Schwegler, Eric

    2016-10-01

    Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na+, K+, and Cl- ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

  3. 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.

  4. 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.

  5. Solution structure of the main alpha-amylase inhibitor from amaranth seeds.

    PubMed

    Martins, J C; Enassar, M; Willem, R; Wieruzeski, J M; Lippens, G; Wodak, S J

    2001-04-01

    The most abundant alpha-amylase inhibitor (AAI) present in the seeds of Amaranthus hypochondriacus, a variety of the Mexican crop plant amaranth, is the smallest polypeptide (32 residues) known to inhibit alpha-amylase activity of insect larvae while leaving that of mammals unaffected. In solution, 1H NMR reveals that AAI isolated from amaranth seeds adopts a major trans (70%) and minor cis (30%) conformation, resulting from slow cis-trans isomerization of the Val15-Pro16 peptide bond. Both solution structures have been determined using 2D 1H-NMR spectroscopy and XPLOR followed by restrained energy refinement in the consistent-valence force field. For the major isomer, a total of 563 distance restraints, including 55 medium-range and 173 long-range ones, were available from the NOESY spectra. This rather large number of constraints from a protein of such a small size results from a compact fold, imposed through three disulfide bridges arranged in a cysteine-knot motif. The structure of the minor cis isomer has also been determined using a smaller constraint set. It reveals a different backbone conformation in the Pro10-Pro20 segment, while preserving the overall global fold. The energy-refined ensemble of the major isomer, consisting of 20 low-energy conformers with an average backbone rmsd of 0.29 +/- 0.19 A and no violations larger than 0.4 A, represents a considerable improvement in precision over a previously reported and independently performed calculation on AAI obtained through solid-phase synthesis, which was determined with only half the number of medium-range and long-range restraints reported here, and featured the trans isomer only. The resulting differences in ensemble precision have been quantified locally and globally, indicating that, for regions of the backbone and a good fraction of the side chains, the conformation is better defined in the new solution structure. Structural comparison of the solution structure with the X-ray structure of the

  6. 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.

  7. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

    PubMed Central

    Svergun, D I

    1999-01-01

    A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to find a configuration that fits the data while minimizing the interfacial area. Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data. PMID:10354416

  8. XtalView, protein structure solution and protein graphics, a short history.

    PubMed

    McRee, Duncan E; Israel, Mark

    2008-09-01

    From a user's point-of-view we are in the Golden Age of protein crystallographic software. In the past few decades, solving protein structures has gone from a task requiring man-months of effort to a process requiring minutes on an ordinary laptop with no human intervention required. The birth of XtalView coincided with the mainstream use of synchrotron radiation, seleno-Met phasing and it continues to be used in this age of robotic crystallization, Fed-Ex data collection and fully automated structure solution "pipelines". This article is a retrospective history of protein crystallographic computing and a discussion of the current state of the art.

  9. 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

  10. 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.

  11. 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

  12. The Anion Effect on Li(+) Ion Coordination Structure in Ethylene Carbonate Solutions.

    PubMed

    Jiang, Bo; Ponnuchamy, Veerapandian; Shen, Yuneng; Yang, Xueming; Yuan, Kaijun; Vetere, Valentina; Mossa, Stefano; Skarmoutsos, Ioannis; Zhang, Yufan; Zheng, Junrong

    2016-09-15

    Rechargeable lithium ion batteries are an attractive alternative power source for a wide variety of applications. To optimize their performances, a complete description of the solvation properties of the ion in the electrolyte is crucial. A comprehensive understanding at the nanoscale of the solvation structure of lithium ions in nonaqueous carbonate electrolytes is, however, still unclear. We have measured by femtosecond vibrational spectroscopy the orientational correlation time of the CO stretching mode of Li(+)-bound and Li(+)-unbound ethylene carbonate molecules, in LiBF4, LiPF6, and LiClO4 ethylene carbonate solutions with different concentrations. Surprisingly, we have found that the coordination number of ethylene carbonate in the first solvation shell of Li(+) is only two, in all solutions with concentrations higher than 0.5 M. Density functional theory calculations indicate that the presence of anions in the first coordination shell modifies the generally accepted tetrahedral structure of the complex, allowing only two EC molecules to coordinate to Li(+) directly. Our results demonstrate for the first time, to the best of our knowledge, the anion influence on the overall structure of the first solvation shell of the Li(+) ion. The formation of such a cation/solvent/anion complex provides a rational explanation for the ionic conductivity drop of lithium/carbonate electrolyte solutions at high concentrations.

  13. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    PubMed Central

    Shi, Ya-Zhou; Jin, Lei; Wang, Feng-Hua; Zhu, Xiao-Long; Tan, Zhi-Jie

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  14. Solution structure studies of monomeric human TIP47/perilipin-3 reveal a highly extended conformation

    PubMed Central

    Hynson, Robert M. G.; Jeffries, Cy M.; Trewhella, Jill; Cocklin, Simon

    2012-01-01

    Tail-interacting protein of 47 kDa (TIP47) has two putative functions: lipid biogenesis and mannose 6-phosphate receptor recycling. Progress in understanding the molecular details of these two functions has been hampered by the lack of structural data on TIP47, with a crystal structure of the C-terminal domain of the mouse homologue constituting the only structural data in the literature so far. Our studies have first provided a strategy to obtain pure monodisperse preparations of the full-length TIP47/perilipin-3 protein, as well as a series of N-terminal truncation mutants with no exogenous sequences. These constructs have then enabled us to obtain the first structural characterization of the full-length protein in solution. Our work demonstrates that the N-terminal region of TIP47/perilipin-3, in contrast to the largely helical C-terminal region, is predominantly β-structure with turns and bends. Moreover, we show that full-length TIP47/perilipin-3 adopts an extended conformation in solution, with considerable spatial separation of the N- and C-termini that would likely translate into a separation of functional domains. PMID:22508559

  15. 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

  16. Nanoscopic imaging of thick heterogeneous soft-matter structures in aqueous solution

    PubMed Central

    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

  17. Thorium nanochemistry: the solution structure of the Th(IV)-hydroxo pentamer.

    PubMed

    Walther, Clemens; Rothe, Jörg; Schimmelpfennig, Bernd; Fuss, Markus

    2012-08-28

    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 Th(5)(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.

  18. Atomically resolved three-dimensional structures of electrolyte aqueous solutions near a solid surface.

    PubMed

    Martin-Jimenez, Daniel; Chacon, Enrique; Tarazona, Pedro; Garcia, Ricardo

    2016-07-15

    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.

  19. 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.

  20. 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.

  1. Nanoscopic imaging of thick heterogeneous soft-matter structures in aqueous solution

    NASA Astrophysics Data System (ADS)

    Bartsch, Tobias F.; Kochanczyk, Martin D.; Lissek, Emanuel N.; Lange, Janina R.; Florin, Ernst-Ludwig

    2016-09-01

    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.

  2. NMR solution structure of the RED subdomain of the Sleeping Beauty transposase.

    PubMed

    Konnova, Tatiana A; Singer, Christopher M; Nesmelova, Irina V

    2017-03-27

    DNA transposons can be employed for stable gene transfer in vertebrates. The Sleeping Beauty (SB) DNA transposon has been recently adapted for human application and is being evaluated in clinical trials, however its molecular mechanism is not clear. SB transposition is catalyzed by the transposase enzyme, which is a multi-domain protein containing the catalytic and the DNA-binding domains. The DNA-binding domain of the SB transposase contains two structurally independent subdomains, PAI and RED. Recently, the structures of the catalytic domain and the PAI subdomain have been determined, however no structural information on the RED subdomain and its interactions with DNA has been available. Here, we used NMR spectroscopy to determine the solution structure of the RED subdomain and characterize its interactions with the transposon DNA.

  3. 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.

  4. Identification of silver cubic structures during ultrasonication of chitosan AgNO3 solution.

    PubMed

    Raghavendra, Gownolla Malegowd; Jung, Jeyoung; Kim, Dowan; Varaprasad, Kokkarachedu; Seo, Jongchul

    2016-11-05

    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.

  5. Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models

    PubMed Central

    Zhong, Yang; Warren, G. Lee; Patel, Sandeep

    2014-01-01

    We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be −5.6±0.2 kcal/mole, in respectable agreement with the experimental value of −5.1 kcal/mole. With respect to solution micro-structure, the present cluster analysis suggests that the micro-scale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bi-percolating network structure. PMID:18074339

  6. 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.

  7. 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.

  8. New lanthanide complexes for sensitized visible and near-IR light emission: synthesis, 1H NMR, and X-ray structural investigation and photophysical properties.

    PubMed

    Quici, Silvio; Marzanni, Giovanni; Forni, Alessandra; Accorsi, Gianluca; Barigelletti, Francesco

    2004-02-23

    We describe the syntheses, the 1H NMR studies in CD3OD and D2O as solvent, the X-ray characterization, and the luminescence properties in D2O solution of the two complexes Eu.1 and Er.1, where 1 is a dipartite ligand that includes (i) a 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (DO3A) unit serving as hosting site for the metal center; and (ii) a phenanthroline unit which plays the role of light antenna for the sensitization process of the metal centered luminescence. In a previous report (Inorg. Chem. 2002, 41, 2777), we have shown that for Eu.1 there are no water molecules within the first coordination sphere. X-ray and 1H NMR results reported here are consistent with full saturation of the nine coordination sites within the Eu.1 and Er.1 complexes. In addition, these studies provide important details regarding the conformations, square antiprism (SAP) and twisted square antiprism (TSAP), adopted in solution by these complexes. The luminescence results are consistent with both an effective intersystem crossing (ISC) at the light absorbing phenanthroline unit (lambda(exc) = 278 nm) and an effective energy transfer (en) process from the phenanthroline donor to the cation acceptor (with unit or close to unit efficiency for both steps). In D2O solvent, the overall sensitization efficiency, phi(se), is 0.3 and 5 x 10(-6), for Eu.1 (main luminescence peaks at 585, 612, 699 nm) and Er.1 (luminescence peak at 1530 nm), respectively. The photophysical properties of both complexes are discussed with reference to their structural features as elucidated by the obtained 1H NMR and X-ray results.

  9. Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41.

    PubMed Central

    Caffrey, M; Cai, M; Kaufman, J; Stahl, S J; Wingfield, P T; Covell, D G; Gronenborn, A M; Clore, G M

    1998-01-01

    The solution structure of the ectodomain of simian immunodeficiency virus (SIV) gp41 (e-gp41), consisting of residues 27-149, has been determined by multidimensional heteronuclear NMR spectroscopy. SIV e-gp41 is a symmetric 44 kDa trimer with each subunit consisting of antiparallel N-terminal (residues 30-80) and C-terminal (residues 107-147) helices connected by a 26 residue loop (residues 81-106). The N-terminal helices of each subunit form a parallel coiled-coil structure in the interior of the complex which is surrounded by the C-terminal helices located on the exterior of the complex. The loop region is ordered and displays numerous intermolecular and non-sequential intramolecular contacts. The helical core of SIV e-gp41 is similar to recent X-ray structures of truncated constructs of the helical core of HIV-1 e-gp41. The present structure establishes unambiguously the connectivity of the N- and C-terminal helices in the trimer, and characterizes the conformation of the intervening loop, which has been implicated by mutagenesis and antibody epitope mapping to play a key role in gp120 association. In conjunction with previous studies, the solution structure of the SIV e-gp41 ectodomain provides insight into the binding site of gp120 and the mechanism of cell fusion. The present structure of SIV e-gp41 represents one of the largest protein structures determined by NMR to date. PMID:9707417

  10. Design solutions for dome and main structure (mount) of giant telescopes

    NASA Astrophysics Data System (ADS)

    Murga, Gaizka; Bilbao, Armando; de Bilbao, Lander; Lorentz, Thomas E.

    2016-07-01

    During the last recent years, designs for several giant telescopes ranging from 20 to 40m in diameter are being developed: European Extremely Large Telescope Telescope (TMT). (E-ELT), Giant Magellan Telescope (GMT) and Thirty Meter It is evident that simple direct up-scaling of solutions that were more or less successful in the 8 to 10m class telescopes can not lead to viable designs for the future giant telescopes. New solutions are required to provide adequate load sharing, to cope with the large-scale derived deflections and to provide the required compliance, or to respond to structure-mechanism control interaction issues, among others. From IDOM experience in the development of the Dome and Main Structure of the European Extremely Large Telescope and our participation in some other giant telescopes, this paper reviews several design approaches for the main mechanisms and key structural parts of enclosures and mounts/main structures for giant telescopes, analyzing pros and cons of the different alternatives and outlining the preferred design schemes. The assessment is carried out mainly from a technical and performance-based angle but it also considers specific logistical issues for the assembly of these large telescopes in remote and space-limited areas, together with cost and schedule related issues.

  11. Solution structure of the HsapBK K+ channel voltage-sensor paddle sequence.

    PubMed

    Unnerståle, Sofia; Lind, Jesper; Papadopoulos, Evangelos; Mäler, Lena

    2009-06-30

    Voltage-gated potassium channels open and close in response to changes in the membrane potential. In this study, we have determined the NMR solution structure of the putative S3b-S4 voltage-sensor paddle fragment, the part that moves to mediate voltage gating, of the HsapBK potassium channel in dodecylphosphocholine (DPC) micelles. This paper presents the first structure of the S3b-S4 fragment from a BK channel. Diffusion coefficients as determined from PFG NMR experiments showed that a well-defined complex between the peptide and DPC molecules was formed. The structure reveals a helix-turn-helix motif, which is in agreement with crystal structures of other voltage-gated potassium channels, thus indicating that it is feasible to study the isolated fragment. The paddle motifs generally contain several basic residues, implicated in the gating. The critical Arg residues in this structure all reside on the surface, which is in agreement with crystal structures of K(v) channels. Similarities in the structure of the S3b-S4 fragment in BK and K(v) channels as well as important differences are seen, which may be important for explaining the details in paddle movement within a bilayer.

  12. Structural and Optical Properties Thin Film Copper Oxides Formed by Chemical Solution Deposition Process Technique

    SciTech Connect

    Lockman, Zainovia; Abidin, Noor Rehan Zainal; Hutagalung, Sabar Derita

    2007-05-09

    Cu2O films were prepared by chemical deposition process (CSD) using solutions of copper nitrate, dip-coated onto glass substrates. The precursor solutions were altered in an effort to seek the best solution for successful deposition. Organic additive of ethanolamine (EA) and (poly)ethylene glycol (PEG, H(OCH2CH2)nOH) was added to the solution and had shown positive effect in terms of the wetability and hence homogenous films resulted. Most films characterised by XRD gave (002) Cu2O, cuprite structure. To avoid films cracking and inhomogeneous coverage, multiple coatings were done with drying in between the successive coatings. Five to eight coatings were carried out for better coverage to ensure surface homogeneity. The microstructure of the surface oxides consisted of nanostructured oxides with uniform size distribution of 60-80nm. The optical transmittance of optimized Cu2O film reaches around 80% at wavelength of {approx} 700nm and the calculated direct optical band gaps were {approx} 2eV for the Cu2O films.

  13. The effect of liquid crystalline structures on antiseizure properties of aqueous solutions of ethoxylated alcohols.

    PubMed

    Sulek, Marian Wlodzimierz; Bak, Anna

    2010-01-12

    Aqueous solutions of ethoxylated alcohols which form lyotropic liquid crystals at high concentrations (40-80%) were selected as model lubricating substances. Microscopic studies under polarized light and viscosity measurements were carried out in order to confirm the presence of liquid crystalline structures in the case of alcohol solutions with ethoxylation degrees of 3, 5, 7 and 10. Microscopic images and viscosity coefficient values characteristic of various mesophases were obtained. As expected, the viscosity of LLCs decreases considerably with an increase in shearing rate which is characteristic of liquid crystals being non-Newtonian liquids. Antiseizure properties were determined by means of a four-ball machine (T-02 Tester) and characterized by scuffing load (P(t)), seizure load (P(oz)) and limiting pressure of seizure (p(oz)). Alcohol ethoxylates forming mesophases in aqueous solutions have the strongest effect on the P(t) values which are several times higher than those measured in the presence of water. Ethoxylates with higher degrees of ethoxylation exhibit higher values of scuffing load. Those changes have been interpreted as a result of higher cloud points at which those compounds lose their amphiphilic properties. In general, the presence of mesophases in the bulk phase and particularly in the surface phase may lead to the formation of a lubricant film which separates the frictionally cooperating elements of a friction pair. The antiseizure efficiency of alcohol solutions is highest up to the load value which does not exceed the scuffing load value.

  14. 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.

  15. Ion aggregation in high salt solutions. II. Spectral graph analysis of water hydrogen-bonding network and ion aggregate structures.

    PubMed

    Choi, Jun-Ho; Cho, Minhaeng

    2014-10-21

    Graph theory in mathematics and computer science is the study of graphs that are structures with pairwise connections between any objects. Here, the spectral graph theory and molecular dynamics simulation method are used to describe both morphological variation of ion aggregates in high salt solutions and ion effects on water hydrogen-bonding network structure. From the characteristic value analysis of the adjacency matrices that are graph theoretical representations of ion clusters, ion networks, and water H-bond structures, we obtained the ensemble average eigenvalue spectra revealing intricate connectivity and topology of ion aggregate structure that can be classified as either ion cluster or ion network. We further show that there is an isospectral relationship between the eigenvalue spectra of ion networks in high KSCN solutions and those of water H-bonding networks. This reveals the isomorphic relationship between water H-bond structure and ion-ion network structure in KSCN solution. On the other hand, the ion clusters formed in high NaCl solutions are shown to be graph-theoretically and morphologically different from the ion network structures in KSCN solutions. These observations support the bifurcation hypothesis on large ion aggregate growth mechanism via either ion cluster or ion network formation. We thus anticipate that the present spectral graph analyses of ion aggregate structures and their effects on water H-bonding network structures in high salt solutions can provide important information on the specific ion effects on water structures and possibly protein stability resulting from protein-water interactions.

  16. Self-interacting inelastic dark matter: a viable solution to the small scale structure problems

    NASA Astrophysics Data System (ADS)

    Blennow, Mattias; Clementz, Stefan; Herrero-Garcia, Juan

    2017-03-01

    Self-interacting dark matter has been proposed as a solution to the small-scale structure problems, such as the observed flat cores in dwarf and low surface brightness galaxies. If scattering takes place through light mediators, the scattering cross section relevant to solve these problems may fall into the non-perturbative regime leading to a non-trivial velocity dependence, which allows compatibility with limits stemming from cluster-size objects. However, these models are strongly constrained by different observations, in particular from the requirements that the decay of the light mediator is sufficiently rapid (before Big Bang Nucleosynthesis) and from direct detection. A natural solution to reconcile both requirements are inelastic endothermic interactions, such that scatterings in direct detection experiments are suppressed or even kinematically forbidden if the mass splitting between the two-states is sufficiently large. Using an exact solution when numerically solving the Schrödinger equation, we study such scenarios and find regions in the parameter space of dark matter and mediator masses, and the mass splitting of the states, where the small scale structure problems can be solved, the dark matter has the correct relic abundance and direct detection limits can be evaded.

  17. Role of solution structure in self-assembly of conjugated block copolymer thin films

    DOE PAGES

    Brady, Michael A.; Ku, Sung -Yu; Perez, Louis A.; ...

    2016-10-24

    Conjugated block copolymers provide a pathway to achieve thermally stable nanostructured thin films for organic solar cells. We characterized the structural evolution of poly(3-hexylthiophene)-block-poly(diketopyrrolopyrrole–terthiophene) (P3HT-b-DPPT-T) from solution to nanostructured thin films. Aggregation of the DPPT-T block of P3HT-b-DPPT-T was found in solution by small-angle X-ray scattering with the P3HT block remaining well-solvated. The nanostructure in thin films was determined using a combination of wide and small-angle X-ray scattering techniques as a function of processing conditions. The structure in solution controlled the initial nanostructure in spin-cast thin films, allowing subsequent thermal annealing processes to further improve the ordering. In contrast tomore » the results for thin films, nanostructural ordering was not observed in the bulk samples by small-angle X-ray scattering. Finally, these results suggest the importance of controlling solvent induced aggregation in forming nanostructured thin films of conjugated block copolymers.« less

  18. Role of solution structure in self-assembly of conjugated block copolymer thin films

    SciTech Connect

    Brady, Michael A.; Ku, Sung -Yu; Perez, Louis A.; Cochran, Justin E.; Schmidt, Kristin; Weiss, Thomas M.; Toney, Michael F.; Ade, Harald; Hexemer, Alexander; Wang, Cheng; Hawker, Craig J.; Kramer, Edward J.; Chabinyc, Michael L.

    2016-10-24

    Conjugated block copolymers provide a pathway to achieve thermally stable nanostructured thin films for organic solar cells. We characterized the structural evolution of poly(3-hexylthiophene)-block-poly(diketopyrrolopyrrole–terthiophene) (P3HT-b-DPPT-T) from solution to nanostructured thin films. Aggregation of the DPPT-T block of P3HT-b-DPPT-T was found in solution by small-angle X-ray scattering with the P3HT block remaining well-solvated. The nanostructure in thin films was determined using a combination of wide and small-angle X-ray scattering techniques as a function of processing conditions. The structure in solution controlled the initial nanostructure in spin-cast thin films, allowing subsequent thermal annealing processes to further improve the ordering. In contrast to the results for thin films, nanostructural ordering was not observed in the bulk samples by small-angle X-ray scattering. Finally, these results suggest the importance of controlling solvent induced aggregation in forming nanostructured thin films of conjugated block copolymers.

  19. Solution structure and excitation energy transfer in phycobiliproteins of Acaryochloris marina investigated by small angle scattering.

    PubMed

    Golub, M; Combet, S; Wieland, D C F; Soloviov, D; Kuklin, A; Lokstein, H; Schmitt, F-J; Olliges, R; Hecht, M; Eckert, H-J; Pieper, J

    2017-04-01

    The structure of phycobiliproteins of the cyanobacterium Acaryochloris marina was investigated in buffer solution at physiological temperatures, i.e. under the same conditions applied in spectroscopic experiments, using small angle neutron scattering. The scattering data of intact phycobiliproteins in buffer solution containing phosphate can be well described using a cylindrical shape with a length of about 225Å and a diameter of approximately 100Å. This finding is qualitatively consistent with earlier electron microscopy studies reporting a rod-like shape of the phycobiliproteins with a length of about 250 (M. Chen et al., FEBS Letters 583, 2009, 2535) or 300Å (J. Marquart et al., FEBS Letters 410, 1997, 428). In contrast, phycobiliproteins dissolved in buffer lacking phosphate revealed a splitting of the rods into cylindrical subunits with a height of 28Å only, but also a pronounced sample aggregation. Complementary small angle neutron and X-ray scattering experiments on phycocyanin suggest that the cylindrical subunits may represent either trimeric phycocyanin or trimeric allophycocyanin. Our findings are in agreement with the assumption that a phycobiliprotein rod with a total height of about 225Å can accommodate seven trimeric phycocyanin subunits and one trimeric allophycocyanin subunit, each of which having a height of about 28Å. The structural information obtained by small angle neutron and X-ray scattering can be used to interpret variations in the low-energy region of the 4.5K absorption spectra of phycobiliproteins dissolved in buffer solutions containing and lacking phosphate, respectively.

  20. Structures in solid state and solution of dimethoxy curcuminoids: regioselective bromination and chlorination

    PubMed Central

    2013-01-01

    Background Several papers described the structure of curcumin and some other derivatives in solid and in solution. In the crystal structure of curcumin, the enol H atom is located symmetrically between both oxygen atoms of the enolone fragment with an O···O distance of 2.455 Å, which is characteristic for symmetrical H-bonds. In the solution, the geometry of the enolone fragment is attributed to the inherent disorder of the local environment, which solvates one of the basic sites better than the other, stabilizing one tautomer over the other. In this paper, how the position of methoxy groups in dimethoxy curcuminoids influence the conformation of molecules and how the halogen atoms change it when they are bonded at α-position in keto-enol part of molecules is described. Results Six isomers of dimethoxy curcuminoids were prepared. Conformations in solid state, which were determined by X-ray single crystallography and 1H MAS and 13C CPMAS NMR measurements, depend on the position of methoxy groups in curcuminoid molecules. In solution, a fast equilibrium between both keto-enol forms exists. A theoretical calculation finding shows that the position of methoxy groups changes the energy of HOMO and LUMO. An efficient protocol for the highly regioselective bromination and chlorination leading to α-halogenated product has been developed. All α-halogenated compounds are present mainly in cis keto-enol form. Conclusions The structures in solid state of dimethoxy curcuminoids depend on the position of methoxy groups. The NMR data of crystalline solid samples of 3,4-diOCH3 derivative, XRD measurements and X-ray structures lead us to the conclusion that polymorphism exists in solids. The same conclusion can be done for 3,5-diOCH3 derivative. In solution, dimethoxy curcuminoids are present in the forms that can be described as the coexistence of two equivalent tautomers being in fast equilibrium. The position of methoxy groups has a small influence on the enolic hydrogen

  1. Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models.

    PubMed

    Zhong, Yang; Warren, G Lee; Patel, Sandeep

    2008-05-01

    We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be -5.6 +/- 0.2 kcal/mol, in respectable agreement with the experimental value of -5.1 kcal/mol. With respect to solution microstructure, the present cluster analysis suggests that the microscale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bipercolating network structure.

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

    SciTech Connect

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

    2014-01-01

    A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies. 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.

  3. Small-angle x-ray scattering study of polymer structure: Carbosilane dendrimers in hexane solution

    NASA Astrophysics Data System (ADS)

    Shtykova, E. V.; Feigin, L. A.; Volkov, V. V.; Malakhova, Yu. N.; Streltsov, D. R.; Buzin, A. I.; Chvalun, S. N.; Katarzhanova, E. Yu.; Ignatieva, G. M.; Muzafarov, A. M.

    2016-09-01

    The three-dimensional organization of monodisperse hyper-branched macromolecules of regular structure—carbosilane dendrimers of zero, third, and sixth generations—has been studied by small-angle X-ray scattering (SAXS) in solution. The use of modern methods of SAXS data interpretation, including ab initio modeling, has made it possible to determine the internal architecture of the dendrimers in dependence of the generation number and the number of cyclosiloxane end groups (forming the shell of dendritic macromolecules) and show dendrimers to be spherical. The structural results give grounds to consider carbosilane dendrimers promising objects for forming crystals with subsequent structural analysis and determining their structure with high resolution, as well as for designing new materials to be used in various dendrimer-based technological applications.

  4. Solution structure of the cold-shock-like protein from Rickettsia rickettsii.

    PubMed

    Gerarden, Kyle P; Fuchs, Andrew M; Koch, Jonathan M; Mueller, Melissa M; Graupner, David R; O'Rorke, Justin T; Frost, Caleb D; Heinen, Heather A; Lackner, Emily R; Schoeller, Scott J; House, Paul G; Peterson, Francis C; Veldkamp, Christopher T

    2012-11-01

    Rocky Mountain spotted fever is caused by Rickettsia rickettsii infection. R. rickettsii can be transmitted to mammals, including humans, through the bite of an infected hard-bodied tick of the family Ixodidae. Since the R. rickettsii genome contains only one cold-shock-like protein and given the essential nature of cold-shock proteins in other bacteria, the structure of the cold-shock-like protein from R. rickettsii was investigated. With the exception of a short α-helix found between β-strands 3 and 4, the solution structure of the R. rickettsii cold-shock-like protein has the typical Greek-key five-stranded β-barrel structure found in most cold-shock domains. Additionally, the R. rickettsii cold-shock-like protein, with a ΔG of unfolding of 18.4 kJ mol(-1), has a similar stability when compared with other bacterial cold-shock proteins.

  5. Structure and aggregation proclivity of C12E3 in aqueous solution

    NASA Astrophysics Data System (ADS)

    Zahariev, Ts.; Ivanova, A.; Velinova, M.; Tadjer, A.

    2013-01-01

    Olygo(ethylene glycol) alkyl ethers - CxEy are well known for their high surface activity and rich phase behavior. These substances exhibit some unusual aggregation characteristics in aqueous solution even at concentrations well below CMC attributed to the formation of pre-aggregates of small size, e.g., dimers. To verify this, a series of C12E3 dimers with initial geometries taken from coarse-grained molecular dynamics simulations is subject to geometry optimization with two quantum chemical methods: DFT and ONIOM in implicit water solvent. The resulting structures are classified into groups based on structural parameters. Their stability is assessed by relative and binding energy and rationalized in terms of molecular characteristics. All studied dimers are stable and various mutual alignments of the surfactants therein are feasible. The loss of surface area is outlined as the predominant stabilizing factor. Substantial number of the structures is suitable for further aggregation.

  6. Elucidating the structure of merocyanine dyes with the ASEC-FEG method. Phenol blue in solution

    NASA Astrophysics Data System (ADS)

    Franco, Leandro R.; Brandão, Idney; Fonseca, Tertius L.; Georg, Herbert C.

    2016-11-01

    The electronic structure of phenol blue (PB) was investigated in several protic and aprotic solvents, in a wide range of dielectric constants, using atomistic simulations. We employed the sequential QM/MM and the free energy gradient methods to optimize the geometry of PB in each solvent at the MP2/aug-cc-pVTZ level. The ASEC mean field is used to include the ensemble average of the solute-solvent interaction into the molecular hamiltonian, both for the geometry optimization and for the calculations of the electronic properties. We found that the geometry of PB changes considerably, from a polyene-like structure in nonpolar solvents to a cyanine-like in water. Moreover, and quite interestingly, in protic solvents with higher dielectric constant than water, the structure of the molecule is less affected and lies in an intermediate state. The results illustrate the important role played by hydrogen bonds in the conformation of merocyanine dyes.

  7. Modifying Cadzow's algorithm to generate the optimal TLS-solution for the structured EIV-Model of a similarity transformation

    NASA Astrophysics Data System (ADS)

    Schaffrin, B.; Neitzel, F.; Uzun, S.; Mahboub, V.

    2012-01-01

    In 2005, Felus and Schaffrin discussed the problem of a Structured Errors-in-Variables (EIV) Model in the context of a parameter adjustment for a classical similarity transformation. Their proposal, however, to perform a Total Least-Squares (TLS) adjustment, followed by a Cadzow step to imprint the proper structure, would not always guarantee the identity of this solution with the optimal Structured TLS solution, particularly in view of the residuals. Here, an attempt will be made to modify the Cadzow step in order to generate the optimal solution with the desired structure as it would, for instance, also result from a traditional LS-adjustment within an iteratively linearized Gauss-Helmert Model (GHM). Incidentally, this solution coincides with the (properly) Weighted TLS solution which does not need a Cadzow step.

  8. Retention of fluoride ions from aqueous solution using porous hydroxyapatite. Structure and conduction properties.

    PubMed

    Hammari, L E L; Laghzizil, A; Barboux, P; Lahlil, K; Saoiabi, A

    2004-10-18

    Synthetic porous calcium hydroxyapatite (noted p-HAp) treated with different fluoride concentrations at room temperature in the presence of carbonate, sodium chloride and phosphate-rich media was investigated. The fluoridation rate of the porous calcium hydroxyapatite was 89% using 1 mol/L [F(-)] solution compared with 30% for crystalline hydroxyapatite (c-HAp). The high specific surface area of p-HAp (235 m(2)g(-1)) compared with c-HAp sample (47 m(2)g(-1)) has an important effect on the removal of fluoride ions from aqueous solution, when p-HAp was treated with high fluoride concentration to produce calcium fluorohydroxyapatite materials. Fluoride adsorption on porous hydroxyapatites (p-HAp) modified their structural and conduction properties.

  9. On a numerical solution of the plastic buckling problem of structures

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1978-01-01

    An automated digital computer procedure is presented for the accurate and efficient solution of the plastic buckling problem of structures. This is achieved by a Sturm sequence method employing a bisection strategy, which eliminates the need for having to solve the buckling eigenvalue problem at each incremental (decremental) loading stage that is associated with the usual solution techniques. The plastic buckling mode shape is determined by a simple inverse iteration process, once the buckling load has been established. Numerical results are presented for plate problems with various edge conditions. The resulting computer program written in FORTRAN V for the JPL UNIVAC 1108 machine proves to be most economical in comparison with other existing methods of such analysis.

  10. Structure and magnetic properties of metastable Co-Cu solid solution nanowire arrays fabricated by electrodeposition

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Li, Fashen; Wang, Ying; Song, Lijing

    2006-08-01

    Nanowire arrays of the metastable Cox Cu1-x (0.20 x 0.85) solid solution system which can not be obtained by equilibrium methods, were prepared by electrodeposition in pores of anodic aluminum oxide (AAO) template, and subsequently annealed at different temperatures. The as-deposited samples all show single phase of fcc structure, and lattice parameters decrease with the increase of Co content and fundamentally accord with Vegard's law. The phase transition with heat treatment was investigated by X-ray diffraction and differential thermal analysis (DTA) which further confirmed the formation of solid solution. With Co content increasing, the coercivity along nanowire axis for as-deposited samples increases, but it decreases for the annealed samples at 700 °C. This phenomenon was explained considering the interaction of Co particles through Cu in nanowires after phase separation.

  11. Numerical solution of singular ODE eigenvalue problems in electronic structure computations

    NASA Astrophysics Data System (ADS)

    Hammerling, Robert; Koch, Othmar; Simon, Christa; Weinmüller, Ewa B.

    2010-09-01

    We put forward a new method for the solution of eigenvalue problems for (systems of) ordinary differential equations, where our main focus is on eigenvalue problems for singular Schrödinger equations arising for example in electronic structure computations. In most established standard methods, the generation of the starting values for the computation of eigenvalues of higher index is a critical issue. Our approach comprises two stages: First we generate rough approximations by a matrix method, which yields several eigenvalues and associated eigenfunctions simultaneously, albeit with moderate accuracy. In a second stage, these approximations are used as starting values for a collocation method which yields approximations of high accuracy efficiently due to an adaptive mesh selection strategy, and additionally provides reliable error estimates. We successfully apply our method to the solution of the quantum mechanical Kepler, Yukawa and the coupled ODE Stark problems.

  12. 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.

  13. Small molecule solution-processed bulk heterojunction solar cells with inverted structure using porphyrin donor

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takaki; Hatano, Junichi; Nakagawa, Takafumi; Yamaguchi, Shigeru; Matsuo, Yutaka

    2013-01-01

    Utilizing tetraethynyl porphyrin derivative (TE-Por) as a small molecule donor material, we fabricated a small molecule solution-processed bulk heterojunction (BHJ) solar cell with inverted structure, which exhibited 1.6% power conversion efficiency (JSC (short-circuit current) = 4.6 mA/cm2, VOC (open-circuit voltage) = 0.90 V, and FF (fill factor) = 0.39) in the device configuration indium tin oxide/TiOx (titanium sub-oxide)/[6,6]-phenyl-C61-butyric acid methyl ester:TE-Por (5:1)/MoOx (molybdenum sub-oxide)/Au under AM1.5 G illumination at 100 mW/cm2. Without encapsulation, the small molecule solution-processed inverted BHJ solar cell also showed remarkable durability to air, where it kept over 73% of its initial power conversion efficiency after storage for 28 days under ambient atmosphere in the dark.

  14. 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

  15. Integration of structural health monitoring solutions onto commercial aircraft via the Federal Aviation Administration structural health monitoring research program

    NASA Astrophysics Data System (ADS)

    Swindell, Paul; Doyle, Jon; Roach, Dennis

    2017-02-01

    The Federal Aviation Administration (FAA) started a research program in structural health monitoring (SHM) in 2011. The program's goal was to understand the technical gaps of implementing SHM on commercial aircraft and the potential effects on FAA regulations and guidance. The program evolved into a demonstration program consisting of a team from Sandia National Labs Airworthiness Assurance NDI Center (AANC), the Boeing Corporation, Delta Air Lines, Structural Monitoring Systems (SMS), Anodyne Electronics Manufacturing Corp (AEM) and the FAA. This paper will discuss the program from the selection of the inspection problem, the SHM system (Comparative Vacuum Monitoring-CVM) that was selected as the inspection solution and the testing completed to provide sufficient data to gain the first approved use of an SHM system for routine maintenance on commercial US aircraft.

  16. Properties of solid solutions, doped film, and nanocomposite structures based on zinc oxide

    NASA Astrophysics Data System (ADS)

    Lashkarev, G. V.; Shtepliuk, I. I.; Ievtushenko, A. I.; Khyzhun, O. Y.; Kartuzov, V. V.; Ovsiannikova, L. I.; Karpyna, V. A.; Myroniuk, D. V.; Khomyak, V. V.; Tkach, V. N.; Timofeeva, I. I.; Popovich, V. I.; Dranchuk, N. V.; Khranovskyy, V. D.; Demydiuk, P. V.

    2015-02-01

    A study of the properties of materials based on the wide bandgap zinc oxide semiconductor, which are promising for application in optoelectronics, photovoltaics and nanoplasmonics. The structural and optical properties of solid solution Zn1-xCdxO films with different cadmium content, are studied. The samples are grown using magnetron sputtering on sapphire backing. Low-temperature photoluminescence spectra revealed emission peaks associated with radiative recombination processes in those areas of the film that have varying amounts of cadmium. X-ray phase analysis showed the presence of a cadmium oxide cubic phase in these films. Theoretical studies of the solid solution thermodynamic properties allowed for a qualitative interpretation of the observed experimental phenomena. It is established that the growth of the homogeneous solid solution film is possible only at high temperatures, whereas regions of inhomogeneous composition can be narrowed through elastic deformation, caused by the mismatch of the film-backing lattice constants. The driving forces of the spinodal decomposition of the Zn1-xCdxO system are identified. Fullerene-like clusters of Znn-xCdxOn are used to calculate the bandgap and the cohesive energy of ZnCdO solid solutions. The properties of transparent conductive ZnO films, doped with Group III donor impurities (Al, Ga, In), are examined. It is shown that oxygen vacancies are responsible for the hole trap centers in the zinc oxide photoconductivity process. We also examine the photoluminescence properties of metal-ZnO nanocomposite structures, caused by surface plasmons.

  17. Oligomerization process of Bcl-2 associated X protein revealed from intermediate structures in solution.

    PubMed

    Shih, Orion; Yeh, Yi-Qi; Liao, Kuei-Fen; Sung, Tai-Ching; Chiang, Yun-Wei; Jeng, U-Ser

    2017-03-15

    Upon apoptotic stress, Bcl-2 associated X (BAX) protein undergoes conformational changes and oligomerizes, leading to the mitochondrial membrane permeabilization and cell death. While structures of the resultant oligomer have been extensively studied, little is known about the intermediates that describe the reaction pathway from the inactive monomers to activated oligomers. Here we characterize the intermediate structures of BAX using combined small-angle X-ray scattering (SAXS) with on-line gel-filtration and electron spin resonance (ESR). The intermediates, including monomers, dimers, and tetramers, are reconstructed via integrating the SAXS-envelopes and ESR-determined skeleton structures. The hence revealed structures suggest a linear oligomerization of BAX utilizing the extended dimers with the two flexible α6 chains protruded out as ditopic ligands. The results of molecular dynamics simulation also support the ditopic dimer conformation with mobile α6. The ditopic dimers could further wind into a helical rod structure with three dimers in one helical turn. Our results not only reveal the on-pathway intermediates, but also suggest a ditopic oligomerization mechanism that may bridge the observed intermediate structures in solution to the large BAX assemblies lately observed on mitochondria.

  18. Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation

    PubMed Central

    Shu, Qin; Krezel, Andrzej M.; Cusumano, Zachary T.; Pinkner, Jerome S.; Klein, Roger; Hultgren, Scott J.; Frieden, Carl

    2016-01-01

    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

  19. 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

  20. Solution structure of alpha t alpha, a helical hairpin peptide of de novo design.

    PubMed Central

    Fezoui, Y.; Connolly, P. J.; Osterhout, J. J.

    1997-01-01

    alpha t alpha is a 38-residue peptide designed to adopt a helical hairpin conformation in solution (Fezoui Y, Weaver DL Osterhout JJ, 1995, Protein Sci 4:286-295). A previous study of the carboxylate form of alpha t alpha by CD and two-dimensional NMR indicated that the peptide was highly helical and that the helices associated in approximately the intended orientation (Fezoui Y, Weaver DL, Osterhout JJ, 1994, Proc Natl Acad Sci USA 91:3675-3679). Here, the solution structure of alpha t alpha as determined by two-dimensional NMR is reported. A total of 266 experimentally derived distance restraints and 20 dihedral angle restraints derived from J-couplings were used. One-hundred initial structures were generated by distance geometry and refined by dynamical simulated annealing. Twenty-three of the lowest-energy structures consistent with the experimental restraints were analyzed. The results presented here show that alpha t alpha is comprised of two associating helices connected by a turn region. PMID:9300486

  1. Solution structure and dynamics of the outer membrane cytochrome OmcF from Geobacter sulfurreducens.

    PubMed

    Dantas, Joana M; Silva, Marta A; Pantoja-Uceda, David; Turner, David L; Bruix, Marta; Salgueiro, Carlos A

    2017-04-01

    Gene knock-out studies on Geobacter sulfurreducens cells showed that the outer membrane-associated monoheme cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI). In addition, microarray analysis of an OmcF-deficient mutant revealed that many of the genes with decreased transcript level were those whose expression is up-regulated in cells grown with a graphite electrode as electron acceptor, suggesting that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electricity production by G. sulfurreducens in microbial fuel cells. (15)N,(13)C-labeled OmcF was produced and NMR spectroscopy was used to determine the solution structure of the protein in the fully reduced state and the pH-dependent conformational changes. In addition, (15)N relaxation NMR experiments were used to characterize the overall and internal backbone dynamics of OmcF. The structure obtained is well defined, with an average pairwise root mean square deviation of 0.37 Å for the backbone atoms and 0.98 Å for all heavy atoms. For the first time a solution structure and the protein motions were determined for an outer membrane cytochrome from G. sulfurreducens, which constitutes an important step to understand the extracellular electron transfer mechanism in Geobacter cells.

  2. 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

  3. Beat structure in the solution of scattering problems with nondecaying sources*

    NASA Astrophysics Data System (ADS)

    Ambrosio, Marcelo J.; Ancarani, Lorenzo U.; Gómez, Antonio I.; Gasaneo, Gustavo; Mitnik, Darío M.

    2017-03-01

    In this contribution we study mathematical properties of scattering solutions of Schrödinger-type equations with nondecaying, outgoing type, driven terms. We analyze in some details the two-body frame, where an analytical treatment is possible, and find how the scattering solution is expected to contain a beating type structure. The analytical formulation is first presented, and then fully and successfully confirmed with two numerical implementations: the Exterior Complex Scaling and the Generalized Sturmian Functions methods. Our results illustrate the underlying mathematical structure that can be found in, for example, the photoionization of atoms or molecules, in the case when several photons are absorbed or in second order calculations for a single photon absorption. A test case within the three-body frame is also presented, illustrating numerically the presence of beat structures in separately the single and double continuum channels. Contribution to the Topical Issue "Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces", edited by A.N. Grum-Grzhimailo, E.V. Gryzlova, Yu V. Popov, and A.V. Solov'yov.

  4. Solution structure of the cytoplasmic domain of phopholamban: phosphorylation leads to a local perturbation in secondary structure.

    PubMed

    Mortishire-Smith, R J; Pitzenberger, S M; Burke, C J; Middaugh, C R; Garsky, V M; Johnson, R G

    1995-06-13

    Peptides representing the N-terminal domain (Ia) of the cardiac sarcoplasmic reticulum protein phospholamban (residues 1-25 [PLB(1-25)] and a phosphorylated form [pPLB(1-25)]) were synthesized and their conformations examined using circular dichroism and nuclear magnetic resonance spectroscopy. In aqueous solution, both PLB(1-25) and pPLB(1-25) adopt a primarily disordered conformation. In 30% trifluoroethanol/10 mM phosphate, PLB(1-25) exhibits a CD spectrum consistent with 60% helical structure. This value decreases to 27% for the phosphorylated peptide. CD spectra in 2% SDS indicate 40% alpha-helix for PLB(1-25) and 20% for pPLB(1-25). Full chemical shift assignments were obtained by conventional homonuclear NMR methodologies for both PLB(1-25) and pPLB(1-25) in 30% trifluoroethanol/water and 300 mM SDS. The solution structure of PLB(1-25) in 30% TFE/water was determined from distance geometry calculations using 54 NOE distance constraints and 17 torsion angle constraints. In the family of 20 calculated conformers, the root mean square deviation from the mean structure is 0.79 A for backbone heavy atoms of residues 1-17. The structure comprises a regular alpha-helix extending from M1 to S16 with the remaining C-terminal residues disordered. The calculated structure is supported by analysis of C alpha H secondary shifts which are significantly negative for residues 1-16. Chemical shift degeneracy is substantially more extensive in the phospho form and precludes a direct comparison of calculated structures. However, the magnitudes of upfield secondary shifts are decreased by 20% in residues 1-11 and are not significantly helical for residues 12-16 according to the criteria of Wishart et al. [(1992) Biochemistry 31, 1647-1651]. 3JHN alpha coupling constants measured for I12, R13, A15, and S16 also suggest that residues 12-16 undergo a local unwinding of the helix upon phosphorylation. Similar results are obtained for PLB(1-25) and pPLB(1-25) in 300 mM perdeuterated

  5. Solution Structural Ensembles of Substrate-Free Cytochrome P450cama,b

    PubMed Central

    Asciutto, Eliana K.; Young, Matthew J.; Madura, Jeffry; Pochapsky, Susan Sondej; Pochapsky, Thomas C.

    2012-01-01

    Removal of substrate (+)-camphor from the active site of cytochrome P450cam (CYP101A1) results in nuclear magnetic resonance-detected perturbations in multiple regions of the enzyme. The 1H,15N correlation map of substrate-free diamagnetic Fe(II) CO-bound CYP101A permits these perturbations to be mapped onto the solution structure of the enzyme. Residual dipolar couplings (RDCs) were measured for 15N-1H amide pairs in two independent alignment media for the substrate-free enzyme and used as restraints in solvated molecular dynamics (MD) simulations to generate an ensemble of best-fit structures of the substrate-free enzyme in solution. NMR-detected chemical shift perturbations reflect changes in the electronic environment of the NH pairs, such as hydrogen bonding and ring current shifts, and are observed for residues in the active site as well as in hinge regions between secondary structural features. RDCs provide information regarding relative orientations of secondary structures, and RDC-restrained MD simulations indicate that portions of a β-rich region adjacent to the active site shift so as to partially occupy the vacancy left by removal of substrate. The accessible volume of the active site is reduced in the substrate-free enzyme relative to the substrate-bound structure calculated using the same methods. Both symmetric and asymmetric broadening of multiple resonances observed upon substrate removal as well as localized increased errors in RDC fits suggest that an ensemble of enzyme conformations are present in the substrate-free form. PMID:22468842

  6. 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

  7. Computational study of polymorphic structures of α- and β- chitin and chitosan in aqueous solution.

    PubMed

    Faria, Roberto Ribeiro; Guerra, Renan Faria; de Sousa Neto, Lourival Rodrigues; Motta, Luiz Frederico; Franca, Eduardo de Faria

    2016-01-01

    Chitin is a natural biopolymer and the second most abundant after cellulose. This polysaccharide can be found in the biomass in different polymorphic forms. Chitosan is one of the most important derivatives obtained from the deacetylation of chitin. In this work, Molecular Dynamics simulations of chitin and chitosan nanoparticles enabled us to evaluate their different conformation and solubility properties. The Molecular Dynamics simulations show that the arrangement of the chains of chitin and chitosan significantly affects the structural behavior of these biopolymers in aqueous solution.

  8. High-resolution /sup 1/H NMR study of the solution structure of alamethicin

    SciTech Connect

    Esposito, G.; Carver, J.A.; Boyd, J.; Campbell, I.D.

    1987-02-24

    A /sup 1/H NMR study of the peptide alamethicin, which forms voltage-gated ion channels in membranes, is described. The molecule was studied in methanol as a function of temperature and pH. A complete assignment of the spectra is given, including several stereospecific assignments. Alamethicin was found to have a structure substantially similar to the crystal although, in solution, the C-terminal dipeptide adopts a somewhat extended conformation. The overall conformation was insensitive to the ionization of the side chain of the ionizable group, Glu-18.

  9. Crystal and solution structural studies of mouse phospholipid hydroperoxide glutathione peroxidase 4

    PubMed Central

    Janowski, Robert; Scanu, Sandra; Niessing, Dierk; Madl, Tobias

    2016-01-01

    The mammalian glutathione peroxidase (GPx) family is a key component of the cellular antioxidative defence system. Within this family, GPx4 has unique features as it accepts a large class of hydroperoxy lipid substrates and has a plethora of biological functions, including sperm maturation, regulation of apoptosis and cerebral embryogenesis. In this paper, the structure of the cytoplasmic isoform of mouse phospholipid hydroperoxide glutathione peroxidase (O70325-2 GPx4) with selenocysteine 46 mutated to cysteine is reported solved at 1.8 Å resolution using X-ray crystallography. Furthermore, solution data of an isotope-labelled GPx protein are presented. PMID:27710939

  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. 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.

  12. The behavior of Gliclazide in solution and in the solid state: a case of organic compound presenting a solid-solution structure.

    PubMed

    Santa María, Dolores; Claramunt, Rosa M; Alkorta, Ibon; Elguero, José

    2009-06-01

    The structure of the hypoglycemic agent Gliclazide has been studied by (1)H, (13)C, and (15)N NMR in solution (CDCl(3) and DMSO-d(6)) and in the solid state. In the solid state, the compound crystallizes as an EZ isomer without dynamic properties. In CDCl(3) solution, the structure is still EZ but with a slow nitrogen inversion about the pyrrolidine nitrogen: two invertomers have been observed and characterized. In DMSO-d(6), the rate is faster and only averaged signals were observed. GIAO calculated absolute shieldings were used to confirm the nature of the observed species. In the solid state, Gliclazide presents the phenomenon of solid-solution with two disordered conformations present in the crystal at a 90:10 ratio.

  13. A hexaaza macrocyclic ligand containing acetohydrazide pendants for Ln(III) complexation in aqueous solution. Solid-state and solution structures and DFT calculations.

    PubMed

    Núñez, Cristina; Bastida, Rufina; Macías, Alejandro; Mato-Iglesias, Marta; Platas-Iglesias, Carlos; Valencia, Laura

    2008-08-07

    Lanthanide complexes of a hexaaza macrocyclic ligand containing acetohydrazide pendants (L) have been synthesised (Ln = La-Er, except Pm), and structural studies have been carried out both in the solid state and in aqueous solution. Attempts to isolate the complexes of the heaviest Ln(iii) ions (Ln = Tm-Lu) were unsuccessful. The crystal structures of the ligand and its lanthanum complex have been determined by single-crystal X-ray crystallography. The X-ray crystal structure of [La(L)](3+) shows the metal ion being ten-coordinate, with the acetohydrazide pendants situated alternatively above and below the plane of the macrocycle. The two five membered chelate rings formed by the ethylenediamine moieties adopt (deltadelta) [or (lambdalambda)] conformations. The [Ln(L)](3+) complexes have been characterised by means of density-functional theory (DFT) calculations (B3LYP model). The structures obtained from these theoretical calculations are in very good agreement with the experimental solution structures, as obtained from paramagnetic NMR measurements on the Ce(iii), Pr(III), Nd(III) and Eu(III) complexes. The complexes adopt in aqueous solution a D(2) structure with the ligand adopting a (deltadelta) [or (lambdalambda)] conformation.

  14. Temperature evolution of the crystal structure of Bi1 - xPrxFeO3 solid solutions

    NASA Astrophysics Data System (ADS)

    Karpinsky, D. V.; Troyanchuk, I. O.; Sikolenko, V. V.; Efimov, V.; Efimova, E.; Silibin, M. V.; Chobot, G. M.; Willinger, E.

    2014-11-01

    The crystal structure of solid solutions in the Bi1 - xPrxFeO3 system near the structural transition between the rhombohedral and orthorhombic phases (0.125 ≤ x ≤ 0.15) has been studied. The structural phase transitions induced by changes in the concentration of praseodymium ions and in the temperature have been investigated using X-ray diffraction, transmission electron microscopy, and differential scanning calorimetry. It has been established that the sequence of phase transformations in the crystal structure of Bi1 - xPrxFeO3 solid solutions with variations in the temperature differs significantly from the evolution of the crystal structure of the BiFeO3 compounds with the substitution of other rare-earth elements for bismuth ions. The regions of the existence of the single-phase structural state and regions of the coexistence of the structural phases have been determined in the investigation of the crystal structure of the Bi1 - xPrxFeO3 solid solutions. A three-phase structural state has been revealed for the solid solution with x = 0.125 at temperatures near 400°C. The specific features of the structural phase transitions of the compounds in the vicinity of the morphotropic phase boundary have been determined by analyzing the obtained results. It has been found that the solid solutions based on bismuth ferrite demonstrate a significant improvement in their physical properties.

  15. Solution structure of robustoxin, the lethal neurotoxin from the funnel-web spider Atrax robustus.

    PubMed

    Pallaghy, P K; Alewood, D; Alewood, P F; Norton, R S

    1997-12-15

    The solution structure of robustoxin, the lethal neurotoxin from the Sydney funnel-web spider Atrax robustus, has been determined from 2D 1H NMR data. Robustoxin is a polypeptide of 42 residues cross-linked by four disulphide bonds, the connectivities of which were determined from NMR data and trial structure calculations to be 1-15, 8-20, 14-31 and 16-42 (a 1-4/2-6/3-7/5-8 pattern). The structure consists of a small three-stranded, anti-parallel beta-sheet and a series of interlocking gamma-turns at the C-terminus. It also contains a cystine knot, thus placing it in the inhibitor cystine knot motif family of structures, which includes the omega-conotoxins and a number of plant and animal toxins and protease inhibitors. Robustoxin contains three distinct charged patches on its surface, and an extended loop that includes several aromatic and non-polar residues. Both of these structural features may play a role in its binding to the voltage-gated sodium channel.

  16. Solution structure of the RecQ C-terminal domain of human Bloom syndrome protein.

    PubMed

    Park, Chin-Ju; Ko, Junsang; Ryu, Kyoung-Seok; Choi, Byong-Seok

    2014-02-01

    RecQ C-terminal (RQC) domain is known as the main DNA binding module of RecQ helicases such as Bloom syndrome protein (BLM) and Werner syndrome protein (WRN) that recognizes various DNA structures. Even though BLM is able to resolve various DNA structures similarly to WRN, BLM has different binding preferences for DNA substrates from WRN. In this study, we determined the solution structure of the RQC domain of human BLM. The structure shares the common winged-helix motif with other RQC domains. However, half of the N-terminal has unstructured regions (α1-α2 loop and α3 region), and the aromatic side chain on the top of the β-hairpin, which is important for DNA duplex strand separation in other RQC domains, is substituted with a negatively charged residue (D1165) followed by the polar residue (Q1166). The structurally distinctive features of the RQC domain of human BLM suggest that the DNA binding modes of the BLM RQC domain may be different from those of other RQC domains.

  17. On the tree-like structure of rings in dense solutions.

    PubMed

    Michieletto, D

    2016-11-28

    One of the most challenging problems in polymer physics is providing a theoretical description for the behaviour of rings in dense solutions and melts. Although it is nowadays well established that the overall size of a ring in these conditions scales like that of a collapsed globule, there is compelling evidence that rings may exhibit ramified and tree-like conformations. In this work I show how to characterise these local tree-like structures by measuring the local writhing of the rings' segments and by identifying the patterns of intra-chain contacts. These quantities reveal two major topological structures: loops and terminal branches which strongly suggest that the strictly double-folded "lattice animal" picture for rings in the melt may be replaced by a more relaxed tree-like structure accommodating loops. In particular, I show that one can identify hierarchically looped structures whose degree increases linearly with the size of a ring, and that terminal branches are found to store about 30% of the whole ring mass, irrespectively of its length. Finally, I draw an analogy between rings in the melt and slip-linked chains, where contact points are enforced by mobile slip-links and for which a field-theoretic treatment can be employed to get some insight into their typical conformations. These findings are ultimately discussed in the light of recent works on the static structure of rings and on the existence of inter-ring threadings.

  18. NMR Solution Structure of a Cyanovirin Homolog from Wheat Head Blight Fungus

    PubMed Central

    Matei, Elena; Louis, John M.; Jee, JunGoo; Gronenborn, Angela M.

    2011-01-01

    Members of the cyanovirin-N homolog (CVNH) lectin family are found in bacteria, fungi and plants. As part of our ongoing work on CVNH structure-function studies, we determined the high-resolution NMR solution structure of the homolog from the wheat head blight disease causing ascomycetous fungus Gibberella zeae (or Fusarium graminearum), hereafter called GzCVNH. Like cyanovirin-N (CV-N), GzCVNH comprises two tandem sequence repeats and the protein sequence exhibits 30% identity with CV-N. The overall structure is similar to those of other members of the CVNH family, with the conserved pseudo-symmetric halves of the structure, domains A and B, closely resembling recently determined structures of Tuber borchii, Neurospora crassa and Ceratopteris richardii CVNH proteins. Although GzCVNH exhibits a similar glycan recognition profile to CV-N and specifically binds to Manα(1–2)Manα, its weak carbohydrate binding affinity to only one binding site is insufficient for conferring anti-HIV activity. PMID:21365681

  19. CSBB-ConeExclusion, adapting structure based solution virtual screening to libraries on solid support.

    PubMed

    Shave, Steven; Auer, Manfred

    2013-12-23

    Combinatorial chemical libraries produced on solid support offer fast and cost-effective access to a large number of unique compounds. If such libraries are screened directly on-bead, the speed at which chemical space can be explored by chemists is much greater than that addressable using solution based synthesis and screening methods. Solution based screening has a large supporting body of software such as structure-based virtual screening tools which enable the prediction of protein-ligand complexes. Use of these techniques to predict the protein bound complexes of compounds synthesized on solid support neglects to take into account the conjugation site on the small molecule ligand. This may invalidate predicted binding modes, the linker may be clashing with protein atoms. We present CSBB-ConeExclusion, a methodology and computer program which provides a measure of the applicability of solution dockings to solid support. Output is given in the form of statistics for each docking pose, a unique 2D visualization method which can be used to determine applicability at a glance, and automatically generated PyMol scripts allowing visualization of protein atom incursion into a defined exclusion volume. CSBB-ConeExclusion is then exemplarically used to determine the optimum attachment point for a purine library targeting cyclin-dependent kinase 2 CDK2.

  20. 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.

  1. 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.

  2. Solution structure of Q388A3 PDZ domain from Trypanosoma brucei.

    PubMed

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

    2016-05-01

    PDZ domains are abundant protein interaction modules that often recognize short amino acid motifs at the C-termini of target proteins and regulate multiple biological processes. So far, no PDZ domain in Trypanosoma brucei, an eukaryotic parasite causing sleeping sickness, has been studied. Q388A3, conserved in the related kinetoplastid parasites, is a 1634-residue protein containing a PDZ domain at its C-terminus. In this work, the solution structure of Q388A3 PDZ domain was solved by NMR spectroscopy. Q388A3 PDZ domain adopts a PDZ-like fold composed by a five-stranded β-sheet capped by two α-helices, which is similar to the PDZ domains from HtrA family proteins. Meanwhile, Q388A3 PDZ domain shows some structural features quite different from HtrA PDZ domain.

  3. Ab Initio Approach for Prediction of Oxide Surface Structure, Stoichiometry, and Electrocatalytic Activity in Aqueous Solution.

    PubMed

    Rong, Xi; Kolpak, Alexie M

    2015-05-07

    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.

  4. Structure of the hydrated and dimethyl sulfoxide solvated rubidium ions in solution.

    PubMed

    D'Angelo, Paola; Persson, Ingmar

    2004-05-31

    The structure of the hydrated and the dimethyl sulfoxide solvated rubidium ions in solution has been determined by means of large-angle X-ray scattering (LAXS) and extended X-ray absorption fine structure (EXAFS) studies. The models of the hydrated and dimethyl sulfoxide solvated rubidium ions fitting the experimental data best are square antiprisms with Rb-O bond distances of 2.98(2) and 2.98(3) A, respectively. The EXAFS data show a significant asymmetry in the Rb-O bond distance distribution with C(3) values of 0.0076 and 0.015 A(3), respectively. No second hydration sphere is observed around the hydrated rubidium ion. The dimethyl sulfoxide solvated rubidium ion displays a Rb-O-S bond angle of ca. 130 degrees, which is typical for a medium hard electron acceptor such as rubidium.

  5. An explicit solution to the optimal LQG problem for flexible structures with collocated rate sensors

    NASA Technical Reports Server (NTRS)

    Balakrishnan, A. V.

    1993-01-01

    We present a class of compensators in explicit form (not requiring numerical computer calculations) for stabilizing flexible structures with collocated rate sensors. They are based on the explicit solution, valid for both Continuum and FEM Models, of the LQG problem for minimizing mean square rate. They are robust with respect to system stability (will not destabilize modes even with mismatch of parameters), can be instrumented in state space form suitable for digital controllers, and can be specified directly from the structure modes and mode 'signature' (displacement vectors at sensor locations). Some simulation results are presented for the NASA LaRC Phase-Zero Evolutionary Model - a modal Trust model with 86 modes - showing damping ratios attainable as a function of compensator design parameters and complexity.

  6. Solution structure of FK506-binding protein 12 from Aedes aegypti.

    PubMed

    Chakraborty, Goutam; Shin, Joon; Nguyen, Quoc Toan; Harikishore, Amaravadhi; Baek, Kwanghee; Yoon, Ho Sup

    2012-10-01

    Dengue remains one of the major public concerns as the virus eludes the immune response. Currently, no vaccines or antiviral therapeutics are available for dengue prevention or treatment. Immunosuppressive drug FK506 shows an antimalarial activity, and its molecular target, FK506-binding protein (FKBP), was identified in human Plasmodium parasites. Likewise, a conserved FKBP family protein has also been identified in Aedes aegypti (AaFKBP12), which is expected to play a similar role in the life cycle of Aedes aegypti, the primary vector of dengue virus infection. As FKBPs belong to a highly conserved class of immunophilin family and are involved in key biological regulations, they are considered as attractive pharmacological targets. In this study, we have determined the nuclear magnetic resonance solution structure of AaFKBP12, a novel FKBP member from Aedes aegypti, and presented its structural features, which may facilitate the design of potential inhibitory ligands against the dengue-transmitting mosquitoes.

  7. PHENIX: a comprehensive Python-based system for macromolecular structure solution

    PubMed Central

    Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor; Chen, Vincent B.; Davis, Ian W.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Kapral, Gary J.; Grosse-Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

    2010-01-01

    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 macromolecular crystallo­graphic structure solution with an emphasis on the 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. PMID:20124702

  8. Structural characterization of the molten globule of alpha-lactalbumin by solution X-ray scattering.

    PubMed Central

    Kataoka, M.; Kuwajima, K.; Tokunaga, F.; Goto, Y.

    1997-01-01

    A compact denatured state is often observed under a mild denaturation condition for various proteins. A typical example is the alpha-lactalbumin molten globule. Although the molecular compactness and shape are the essential properties for defining the molten globule, there have been ambiguities of these properties for the molten globule of alpha-lactalbumin. Using solution X-ray scattering, we have examined the structural properties of two types of molten globule of alpha-lactalbumin, the apo-protein at neutral pH and the acid molten globule. The radius of gyration for the native holo-protein was 15.7 A, but the two different molten globules both had a radius of gyration of 17.2 A. The maximum dimension of the molecule was also increased from 50 A for the native state to 60 A for the molten globule. These values clearly indicate that the molten globule is not as compact as the native state. The increment in the radius of gyration was less than 10% for the alpha-lactalbumin molten globule, compared with up to 30% for the molten globules of other globular proteins. Intramolecular disulfide bonds restrict the molecular expansion of the molten globule. The distance distribution function of the alpha-lactalbumin molten globule is composed of a single peak suggesting a globular shape, which is simply swollen from the native state. The scattering profile in the high Q region of the molten globule indicates the presence of a significant amount of tertiary fold. Based on the structural properties obtained by solution X-ray scattering, general and conceptual structural images for the molten globules of various proteins are described and compared with the individual, detailed structural model obtained by nuclear magnetic resonance. PMID:9041645

  9. Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA.

    PubMed

    Bourbigot, Sarah; Dock-Bregeon, Anne-Catherine; Eberling, Pascal; Coutant, Jérôme; Kieffer, Bruno; Lebars, Isabelle

    2016-12-01

    The small nuclear 7SK RNA regulates RNA polymerase II (RNA Pol II) transcription, by sequestering and inhibiting the positive transcription elongation factor b (P-TEFb). P-TEFb is stored in the 7SK ribonucleoprotein (RNP) that contains the three nuclear proteins Hexim1, LaRP7, and MePCE. P-TEFb interacts with the protein Hexim1 and the 7SK RNA. Once P-TEFb is released from the 7SK RNP, it activates transcription by phosphorylating the C-terminal domain of RNA Pol II. P-TEFb also plays a crucial role in the replication of the human immunodeficiency virus HIV-1, through its recruitment by the viral transactivator Tat. Previous work demonstrated that the protein Tat promotes the release of P-TEFb from the 7SK RNP through direct binding to the 7SK RNA. Hexim1 and Tat proteins both comprise conserved and similar arginine-rich motifs that were identified to bind the 7SK RNA at a repeated GAUC site located at the top of the 5'-terminal hairpin (HPI). Here, we report the solution structure of this region as determined by nuclear magnetic resonance, to identify HPI structural features recognized by Hexim1 and Tat. The HPI solution structure displays an elongated shape featuring four helical segments interrupted by one internal loop and three bulges with distinct folds. In particular, the repeated GAUC motif adopts a pre-organized geometry. Our results suggest that the binding of Hexim1 and Tat to the 7SK RNA could originate from a conformational selection of this motif, highlighting how RNA local structure could lead to an adaptive recognition of their partners.

  10. 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

  11. 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).

  12. 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 shape, were broadly 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 the interface between TiO2 and the pore was not sharp. A density gradient of around 40 ~ 60 at the pore wall (i.e. interface between the pore and the TiO2 matrix) was estimated using both constant and semi-sigmoidal interface models. This may be due to the presence of fluorine and carbon partially absorbed by the pore wall from the fluoride-containing electrolyte and 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 vol/vol 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, S/V, was around 939 ~ 1003 m2/cm3 (283~ 302m2/g).

  13. 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.

  14. Molecular dynamics analysis of HIV-1 matrix protein: clarifying differences between crystallographic and solution structures.

    PubMed

    Verli, Hugo; Calazans, Alexandre; Brindeiro, Rodrigo; Tanuri, Amilcar; Guimarães, Jorge A

    2007-07-01

    One of the main structural features of the mature HIV-1 virion is the matrix protein (p17). This partially globular protein presents four helixes centrally organized and a fifth one, H5, projecting away from the packed bundle of helixes. Comparison between solution and crystallographic data of p17 indicates a 6 A displacement of a short 3(10) helix and a partial unfolding of H5 in solution related to crystal. While the behavior of the 3(10) helix has been previously addressed to virion assembly, the relevance and origin of H5 partial unfolding is possibly related to the contacts between p17 and other viral elements, such as p24. In this context, we present a 40 ns conformational sampling of monomeric p17 using molecular dynamics simulations. The performed simulations presented a progressive conversion of the p17 crystallographic structure to the NMR conformation, suggesting that the biological form of this protein may have its C-terminal portion partially unfolded.

  15. 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.

  16. Agarose gel shift assay reveals that calreticulin favors substrates with a quaternary structure in solution.

    PubMed

    Boelt, Sanne Grundvad; Houen, Gunnar; Højrup, Peter

    2015-07-15

    Here we present an agarose gel shift assay that, in contrast to other electrophoresis approaches, is loaded in the center of the gel. This allows proteins to migrate in either direction according to their isoelectric points. Therefore, the presented assay enables a direct visualization, separation, and prefractionation of protein interactions in solution independent of isoelectric point. We demonstrate that this assay is compatible with immunochemical methods and mass spectrometry. The assay was used to investigate interactions with several potential substrates for calreticulin, a chaperone that is involved in different biological aspects through interaction with other proteins. The current analytical assays used to investigate these interactions are mainly spectroscopic aggregation assays or solid phase assays that do not provide a direct visualization of the stable protein complex but rather provide an indirect measure of interactions. Therefore, no interaction studies between calreticulin and substrates in solution have been investigated previously. The results presented here indicate that calreticulin has a preference for substrates with a quaternary structure and primarily β-sheets in their secondary structure. It is also demonstrated that the agarose gel shift assay is useful in the study of other protein interactions and can be used as an alternative method to native polyacrylamide gel electrophoresis.

  17. The structure of neuronal calcium sensor-1 in solution revealed by molecular dynamics simulations.

    PubMed

    Bellucci, Luca; Corni, Stefano; Di Felice, Rosa; Paci, Emanuele

    2013-01-01

    Neuronal calcium sensor-1 (NCS-1) is a protein able to trigger signal transduction processes by binding a large number of substrates and re-shaping its structure depending on the environmental conditions. The X-ray crystal structure of the unmyristoilated NCS-1 shows a large solvent-exposed hydrophobic crevice (HC); this HC is partially occupied by the C-terminal tail and thus elusive to the surrounding solvent. We studied the native state of NCS-1 by performing room temperature molecular dynamics (MD) simulations starting from the crystal and the solution structures. We observe relaxation to a state independent of the initial structure, in which the C-terminal tail occupies the HC. We suggest that the C-terminal tail shields the HC binding pocket and modulates the affinity of NCS-1 for its natural targets. By analyzing the topology and nature of the inter-residue potential energy, we provide a compelling description of the interaction network that determines the three-dimensional organization of NCS-1.

  18. 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

  19. 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.

  20. 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

  1. [Influence of low-intensity laser radiation on the formation of liquid crystalline structures in a solution of glycoproteins].

    PubMed

    Skopinov, S A; Iakovleva, S V; Denisova, E A; Vazina, A A; Zheleznaia, L A

    1989-01-01

    Liquid-crystalline structure formation in glycoprotein solutions irradiated by helium-neon laser in the presence of hydrogen peroxide was observed by both polarizing microscopy and spectrophotometry. High molecular weight (2.10(6) Da) and heavily glycosylated (about 80%) glycoprotein was isolated from the mucus layer of pig small intestine. Remarkable changes of both optic parameters of the solutions and the morphology of liquid-crystalline structures were detected in irradiated samples compared to the non-irradiated ones.

  2. 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

  3. Solution structure of the zinc finger HIT domain in protein FON

    PubMed Central

    He, Fahu; Umehara, Takashi; Tsuda, Kengo; Inoue, Makoto; Kigawa, Takanori; Matsuda, Takayoshi; Yabuki, Takashi; Aoki, Masaaki; Seki, Eiko; Terada, Takaho; Shirouzu, Mikako; Tanaka, Akiko; Sugano, Sumio; Muto, Yutaka; Yokoyama, Shigeyuki

    2007-01-01

    The zinc finger HIT domain is a sequence motif found in many proteins, including thyroid hormone receptor interacting protein 3 (TRIP-3), which is possibly involved in maturity-onset diabetes of the young (MODY). Novel zinc finger motifs are suggested to play important roles in gene regulation and chromatin remodeling. Here, we determined the high-resolution solution structure of the zinc finger HIT domain in ZNHIT2 (protein FON) from Homo sapiens, by an NMR method based on 567 upper distance limits derived from NOE intensities measured in three-dimensional NOESY spectra. The structure yielded a backbone RMSD to the mean coordinates of 0.19 Å for the structured residues 12–48. The fold consists of two consecutive antiparallel β-sheets and two short C-terminal helices packed against the second β-sheet, and binds two zinc ions. Both zinc ions are coordinated tetrahedrally via a CCCC-CCHC motif to the ligand residues of the zf-HIT domain in an interleaved manner. The tertiary structure of the zinc finger HIT domain closely resembles the folds of the B-box, RING finger, and PHD domains with a cross-brace zinc coordination mode, but is distinct from them. The unique three-dimensional structure of the zinc finger HIT domain revealed a novel zinc-binding fold, as a new member of the treble clef domain family. On the basis of the structural data, we discuss the possible functional roles of the zinc finger HIT domain. PMID:17656577

  4. NMR solution structure of Ole e 6, a major allergen from olive tree pollen.

    PubMed

    Treviño, Miguel Angel; García-Mayoral, María Flor; Barral, Patricia; Villalba, Mayte; Santoro, Jorge; Rico, Manuel; Rodríguez, Rosalía; Bruix, Marta

    2004-09-10

    Ole e 6 is a pollen protein from the olive tree (Olea europaea) that exhibits allergenic activity with a high prevalence among olive-allergic individuals. The three-dimensional structure of Ole e 6 has been determined in solution by NMR methods. This is the first experimentally determined structure of an olive tree pollen allergen. The structure of this 50-residue protein is based on 486 upper limit distance constraints derived from nuclear Overhauser effects and 24 torsion angle restraints. The global fold of Ole e 6 consists of two nearly antiparallel alpha-helices, spanning residues 3-19 and 23-33, that are connected by a short loop and followed by a long, unstructured C-terminal tail. Viewed edge-on, the structured N terminus has a dumbbell-like shape with the two helices on the outside and with the hydrophobic core, mainly composed of 3 aromatic and 6 cysteine residues, on the inside. All the aromatic rings lie on top of and pack against the three disulfide bonds. The lack of thermal unfolding, even at 85 degrees C, indicates a high conformational stability. Based on the analysis of the molecular surface, we propose five plausible epitopes for IgE recognition. The results presented here provide the structural foundation for future experiments to verify the antigenicity of the proposed epitopes, as well as to design novel hypoallergenic forms of the protein suitable for diagnosis and treatment of type-I allergies. In addition, three-dimensional structure features of Ole e 6 are discussed to provide a basis for future functional studies.

  5. 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.

  6. Structural correspondence between uranyl chloride complexes in solution and their stability constants.

    PubMed

    Soderholm, L; Skanthakumar, S; Wilson, Richard E

    2011-05-19

    Pair-distribution functions (PDF)s were obtained from high-energy X-ray scattering (HEXS) data on a series of uranyl solutions as a function of chloride ion concentration. Analyses reveal that chloride forms only inner-sphere complexes with the uranyl, replacing inner-sphere waters such that the total uranyl coordination number decreases from 4.7 waters at [Cl(-)] = 0 m to 4.4 (1.7 water and 2.7 Cl(-)) at [Cl(-)] = 6.8 m. Some of the second-coordination sphere waters reorient upon uranyl inner-sphere chloride complexation in order to hydrogen bond with the bound anion. Similar data obtained on a series of solutions maintained at constant ionic strength are used to confirm structural assignments through determining stability constants for the addition of chloride to uranyl and comparison with published values. The stability constants, β(1) = 1.5(10) m(-1), β(2) = 0.8(4) m(-2), and β(3) = 0.4(1) m(-3), obtained in a series of solutions with constant ionic strength of 5.3 m, are in reasonable agreement with previously published results determined by solvent extraction. The agreement of stability constants supports our peak assignments for the PDF and thus our structural model for uranyl chloride complexes in solution. Using coordination numbers and speciation determined here as a function of chloride ion concentration, the monochloro species is found to have four coordinating waters in the uranyl equatorial plane, the dichoro species is found to be an equilibrium of three and two coordinating waters, and the trichloro species has only a single water in the equatorial plane. These values correspond to total average coordination numbers of 5, 4.3, and 4 for the mono-, di-, and trichlorouranyl complexes. From the equilibrium value of the dichloro species, it can be further estimated that ΔG = -0.5 kcal/mol for the conversion of five to four coordinate species. Overall, the HEXS data support the assertion that uranyl chloride correlations do exist and the results are

  7. Structure of the UO[subscript 2][superscript 2+]-SO[subscript 4][superscript 2-] Ion Pair in Aqueous Solution

    SciTech Connect

    Neuefeind, J.; Skanthakumar, S.; Soderholm, L.

    2010-11-16

    The structure of the ion pairs formed in aqueous uranyl sulfate solutions has been investigated with high-energy X-ray scattering. Sulfate binds to the uranyl as a monodentate ligand in equimolar solutions. The geometry of the ion pair is very similar to configurations found in crystalline structures; in particular, the U-O-S angle is bent in solution as well as in the solid state. It can therefore be concluded that an U-O-S angle of 143{sup o} is an intrinsic property of the uranyl sulfate bond and not due to packing effects or interaction with the water in the primary solvation shell.

  8. 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.

  9. Structure of the mammalian kinetochore.

    PubMed

    Ris, H; Witt, P L

    1981-01-01

    The structure of the mammalian trilaminar kinetochore was investigated using stereo electron microscopy of chromosomes in hypotonic solutions which unraveled the chromosome but maintained microtubules. Mouse and Chinese hamster ovary cells were arrested in Colcemid and allowed to reform microtubules after Colcemid was removed. Recovered cells were then swelled, lysed or spread in hypotonic solutions which contained D2O to preserve microtubules. The chromosomes were observed in thin and thick sections and as whole mounts using high voltage electron microscopy. Bundles of microtubules were seen directly attached to chromatin, indicating that the kinetochore outer layer represents a differential arrangement of chromatin, continuous with the body of the chromosome. In cells fixed wihout pretreatment, the outer layer could be seen to be composed of hairpin loops of chromatin stacked together to form a solid layer. The hypotonically-induced unraveling of the outer layer was found to be reversible, and the typical 300 nm thick disk reformed when cells were returned to isotonic solutions. Short microtubules, newly nucleated after Colcemid removal, were found not to be attached to the kinetochore out layer, but were situated in the fibrous corona on the external surface of the outer layer. This was verified by observation of thick sections in stereo which made it possible to identify microtubules ends within the section. Thus, kinetochore microtubules are nucleated within the fibrous corona, and subsequently become attached to the outer layer.

  10. NMR Solution Structure, Stability, and Interaction of the Recombinant Bovine Fibrinogen αC-Domain Fragment†

    PubMed Central

    Burton, Robert A.; Tsurupa, Galina; Hantgan, Roy R.; Tjandra, Nico; Medved, Leonid

    2008-01-01

    According to the current hypothesis, in fibrinogen, the COOH-terminal portions of two Aα chains are folded into compact αC-domains that interact intramolecularly with each other and with the central region of the molecule; in fibrin, the αC-domains switch to an intermolecular interaction resulting in αC polymers. In agreement, our recent NMR study identified within the bovine fibrinogen Aα374-538 αC-domain fragment an ordered compact structure including a β-hairpin restricted at the base by a 423–453 disulfide linkage. To establish the complete structure of the αC-domain and to further test the hypothesis, we expressed a shorter αC-fragment, Aα406-483, and performed detailed analysis of its structure, stability, and interactions. NMR experiments on the Aα406-483 fragment identified a second loose β-hairpin formed by residues 459–476, yielding a structure consisting of an intrinsically unstable mixed parallel/anti-parallel β-sheet. Size-exclusion chromatography and sedimentation velocity experiments revealed that the Aα406-483 fragment forms soluble oligomers whose fraction increases with increasing concentration. This was confirmed by sedimentation equilibrium analysis, which also revealed that the addition of each monomer to an assembling αC oligomer substantially increases its stabilizing free energy. In agreement, unfolding experiments monitored by CD established that oligomerization of Aα406-483 results in increased thermal stability. Altogether, these experiments establish the complete NMR solution structure of the Aα406-483 αC-domain fragment, provide direct evidence for the intra- and intermolecular interactions between the αC-domains, and confirm that these interactions are thermodynamically driven. PMID:17590019

  11. 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.

  12. The Solution Structure of Heparan Sulfate Differs from That of Heparin

    PubMed Central

    Khan, Sanaullah; Rodriguez, Elizabeth; Patel, Rima; Gor, Jayesh; Mulloy, Barbara; Perkins, Stephen J.

    2011-01-01

    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 degree of polymerization 6–18 (dp6–dp18) and 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 radius of gyration (RG) values from 1.03 to 2.82 nm, cross-sectional radius 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 5000–8000 conformationally randomized HS structures gave best fit dp6–dp16 molecular structures that were longer and more bent than their equivalents in heparin. No fits were obtained for HS dp18 or dp24, indicating their higher flexibility. We conclude that HS displays an extended bent conformation that is 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:21576246

  13. 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

  14. 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.

  15. Microstructure and Rheology of a Flow-Induced Structured Phase in Wormlike Micellar Solutions

    SciTech Connect

    Cardiel Rivera, Joshua J.; Dohnalkova, Alice; Dubash, Neville; Zhao, Ya; Cheung, Perry; Shen, Amy

    2013-04-30

    Surfactant molecules found in soaps and detergents can self-assemble into a great variety of morphologies (e.g., spherical micelles, cylindrical micelles, and lamellar phases). The resulting morphology is highly affected by ionic strength, temperature, and flow conditions. In particular, cylindrical micelles in the presence of inorganic or organic salts can self-assemble into large flexible and elongated wormlike micelles. In equilibrium, the wormlike micelles transition from slightly entangled to branched and, finally, to multi-connected structures with increasing salt concentration. In our work, by introducing external flow conditions via microfluidics, these micellar structures can follow very different trajectories on the phase map and new nanoporous structures can be created. This flow induced approach offers great potential to create novel materials and nanoporous scaffolds from wormlike micelles under ambient temperature and pressure, without any chemical and thermal means (1). As a result, this work provides attractive solutions for synthesizing new biocompatible materials under ambient conditions with biosensing, encapsulation, catalysis, photonics, and self-healing applications.

  16. Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine

    PubMed Central

    Atkinson, Sarah C.; Dogovski, Con; Downton, Matthew T.; Pearce, F. Grant; Reboul, Cyril F.; Buckle, Ashley M.; Gerrard, Juliet A.; Dobson, Renwick C. J.; Wagner, John; Perugini, Matthew A.

    2012-01-01

    Dihydrodipicolinate synthase (DHDPS) catalyzes the rate limiting step in lysine biosynthesis in bacteria and plants. The structure of DHDPS has been determined from several bacterial species and shown in most cases to form a homotetramer or dimer of dimers. However, only one plant DHDPS structure has been determined to date from the wild tobacco species, Nicotiana sylvestris (Blickling et al. (1997) J. Mol. Biol. 274, 608–621). Whilst N. sylvestris DHDPS also forms a homotetramer, the plant enzyme adopts a ‘back-to-back’ dimer of dimers compared to the ‘head-to-head’ architecture observed for bacterial DHDPS tetramers. This raises the question of whether the alternative quaternary architecture observed for N. sylvestris DHDPS is common to all plant DHDPS enzymes. Here, we describe the structure of DHDPS from the grapevine plant, Vitis vinifera, and show using analytical ultracentrifugation, small-angle X-ray scattering and X-ray crystallography that V. vinifera DHDPS forms a ‘back-to-back’ homotetramer, consistent with N. sylvestris DHDPS. This study is the first to demonstrate using both crystal and solution state measurements that DHDPS from the grapevine plant adopts an alternative tetrameric architecture to the bacterial form, which is important for optimizing protein dynamics as suggested by molecular dynamics simulations reported in this study. PMID:22761676

  17. Structural and electrical characteristics of solution processed P3HT-carbon nanotube composite

    NASA Astrophysics Data System (ADS)

    Mahakul, Prakash Chandra; Mahanandia, Pitamber

    2017-02-01

    Organic semiconductors have been identified as a fascinating class of low cost and flexible novel semiconductor materials that have the electrical and optical properties which can be easily processed. Due to their interesting physical properties, organic semiconductors have attracted tremendous research attention for next generation electronics and optoelectronics. Multiwalled carbon nanotubes (MWCNT) incorporated Poly[3-hexylthiophene-2,5-diyl] (P3HT) hybrid nano-composite film have been fabricated by solution processing technique followed by spin coating method using 1,2-dichlorobenzene as an intermediate solvent. Structural and morphological characteristics of the composite film have been studied by x-ray diffraction (XRD) and scanning electron microscope (SEM). The MWCNTs were observed to be well dispersed in the polymer matrix. Crystallites were found to be more ordered barely affecting the lamellar structure of P3HT in the nano-composite film. Structural and functional characteristics of P3HT and its hybrid nano-composite have been studied by UV-Visible (UV-Vis), Fourier transform infrared (FTIR) and Raman spectroscopic characterization. Excellent electrical properties have been observed from I-V and cyclic-voltammetric characterization of the well dispersed MWCNT in the P3HT composite. Improvement in electrical properties can be attributed to the higher carrier mobility of MWCNTs in the composites.

  18. 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.

  19. Magnetism and structure of Fe Cu binary solid solutions obtained by high-energy ball milling

    NASA Astrophysics Data System (ADS)

    Gorria, P.; Martínez-Blanco, D.; Blanco, J. A.; Pérez, M. J.; González, M. A.; Campo, J.

    2006-10-01

    Martensitic phase transformation is found in various metals, alloys, ceramics and even biological systems. This paper reports on the Fe segregated anomalous α- γ martensitic transformation observed in Fe xCu 100-x binary solid solutions ( x=25 and 50) after subsequent heating-cooling processes. A characteristic observable feature of a martensitic transformation is the microstructure it produces, thermal hysteresis, evolution and metastability. We have analysed the microstructure using neutron thermo-diffraction experiments up to 1100 K. The structural changes of the Fe segregated phase, from bcc to fcc crystal structures, have been followed in detail. The most relevant feature is that the onset of martensite transformation is observed, on heating, more than 100 K below the expected temperature for pure bcc-Fe (1183 K), while the reverse transformation occurs below 900 K on cooling. This anomalous behaviour for the α- γ transformation depends on sample composition, being more important for low Fe contents. Besides that, magnetisation vs. temperature measurements show a clear correlation with structure changes, thus exhibiting thermal hysteresis on heating-cooling cycles. Moreover, a magnetisation enhancement above 550 K is observed on heating, this fact can be attributed to thermal-induced ferromagnetism on isolated γ-Fe precipitates via strong magneto-volume coupling.

  20. Solution structure of a tethered Lmo2LIM2/Ldb1LID complex

    PubMed Central

    Dastmalchi, Siavoush; Wilkinson-White, Lorna; Kwan, Ann H; Gamsjaeger, Roland; Mackay, Joel P; Matthews, Jacqueline M

    2012-01-01

    LIM-only protein 2, Lmo2, is a regulatory protein that is essential for hematopoietic development and inappropriate overexpression of Lmo2 in T-cells contributes to T-cell leukemia. It exerts its functions by mediating protein–protein interactions and nucleating multicomponent transcriptional complexes. Lmo2 interacts with LIM domain binding protein 1 (Ldb1) through the tandem LIM domains of Lmo2 and the LIM interaction domain (LID) of Ldb1. Here, we present the solution structure of the LIM2 domain of Lmo2 bound to Ldb1LID. The ordered regions of Ldb1 in this complex correspond well with binding hotspots previously defined by mutagenic studies. Comparisons of this Lmo2LIM2–Ldb1LID structure with previously determined structures of the Lmo2/Ldb1LID complexes lead to the conclusion that modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions and/or conformational changes in both proteins. PMID:22936624

  1. 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.

  2. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.

    PubMed

    Guillière, Florence; Danioux, Chloé; Jaubert, Carole; Desnoues, Nicole; Delepierre, Muriel; Prangishvili, David; Sezonov, Guennadi; Guijarro, J Iñaki

    2013-01-01

    While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.

  3. Solution structure of a tethered Lmo2(LIM2) /Ldb1(LID) complex.

    PubMed

    Dastmalchi, Siavoush; Wilkinson-White, Lorna; Kwan, Ann H; Gamsjaeger, Roland; Mackay, Joel P; Matthews, Jacqueline M

    2012-11-01

    LIM-only protein 2, Lmo2, is a regulatory protein that is essential for hematopoietic development and inappropriate overexpression of Lmo2 in T-cells contributes to T-cell leukemia. It exerts its functions by mediating protein-protein interactions and nucleating multicomponent transcriptional complexes. Lmo2 interacts with LIM domain binding protein 1 (Ldb1) through the tandem LIM domains of Lmo2 and the LIM interaction domain (LID) of Ldb1. Here, we present the solution structure of the LIM2 domain of Lmo2 bound to Ldb1(LID) . The ordered regions of Ldb1 in this complex correspond well with binding hotspots previously defined by mutagenic studies. Comparisons of this Lmo2(LIM2) -Ldb1(LID) structure with previously determined structures of the Lmo2/Ldb1(LID) complexes lead to the conclusion that modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions and/or conformational changes in both proteins.

  4. Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA.

    PubMed

    Liu, Lei; Qin, Su; Zhang, Jiahai; Ji, Peng; Shi, Yunyu; Wu, Jihui

    2012-10-01

    Plant homeodomain (PHD) finger is found to be a versatile reader that functions in recruiting transcription factors and chromatin modification complexes. Bromodomain- and PHD finger-containing (BRPF) proteins are identified as scaffold component in a couple of histone acetyltransferase (HATs) complexes but the biological function of PHD fingers, composing the motif called PZPM (PHD/Zn-knuckle/PHD Motif), in BRPF proteins is far from being well understood. Here we report the three-dimensional solution structure of the second PHD finger of PZPM in human BRPF2. According to the structure, BRPF2 PHD2 possesses a two-strand β sheet which is different from any other PHD fingers. Functionally, this PHD finger can potentially bind DNA non-specifically with an evolutionarily conserved and positively charged surface. We provide the structural and interaction information of this atypical PHD finger and categorize this BRPF2 PHD2 into a new subset of PHD finger. Moreover our work also shed light on the functional aspect of the PZPM.

  5. 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.

  6. Solution-phase monitoring of the structural evolution of a Molybdenum Blue nanoring.

    PubMed

    Miras, Haralampos N; Richmond, Craig J; Long, De-Liang; Cronin, Leroy

    2012-02-29

    The inorganic host-guest complex Na(22){[Mo(VI)(36)O(112)(H(2)O)(16)]⊂[Mo(VI)(130)Mo(V)(20)O(442)(OH)(10)(H(2)O)(61)]}·180H(2)O ≡ {Mo(36)}⊂{Mo(150)}, compound 1, has been isolated in its solid crystalline state via unconventional synthesis in a custom flow reactor. Carrying out the reaction under controlled flow conditions selected for the generation of {Mo(36)}⊂{Mo(150)} as the major product, allowing it to be reproducibly isolated in a moderate yield, as opposed to traditional "one-pot" batch syntheses that typically lead to crystallization of the {Mo(36)} and {Mo(150)} species separately. Structural and spectroscopic studies of compound 1 and the archetypal Molybdenum Blue (MB) wheel, {Mo(150)}, identified compound 1 as a likely intermediate in the {Mo(36)} templated synthesis of MB wheels. Further evidence illustrating the template effect of {Mo(36)} to MB wheel synthesis was indicated by an increase in the yield and rate of production of {Mo(150)} as a direct result of the addition of preformed {Mo(36)} to the reaction mixture. Dynamic light scattering (DLS) techniques were also used to corroborate the mechanism of formation of the MB wheels through observation of the individual cluster species in solution. DLS measurement of the reaction solutions from which {Mo(36)} and {Mo(150)} crystallized gave particle size distribution curves averaging 1.9 and 3.9 nm, consistent with the dimensions of the discrete clusters, which allowed the use of size as a possible distinguishing feature of these key species in the reduced acidified molybdate solutions and to observe the templation of the MB wheel by {Mo(36)} directly.

  7. Structural investigations of aroylhydrazones derived from nicotinic acid hydrazide in solid state and in solution

    NASA Astrophysics Data System (ADS)

    Galić, Nives; Brođanac, Ivan; Kontrec, Darko; Miljanić, Snežana

    2013-04-01

    Structural forms of aroylhydrazones derived from nicotinic acid hydrazide have been studied in the solid state by FT-IR spectroscopy and in solution by NMR, UV-Vis and ATR spectroscopy. The studied compounds were N'-benzylidene-3-pyridinecarbohydrazide (1), N'-(2,4-dihydroxyphenylmethylidene)-3-pyridinecarbohydrazide (2), N'-(5-chloro-2-hydroxyphenylmethylidene)-3-pyridinecarbohydrazide (3), and N'-(3,5-dichloro-2-hydroxymethoxyphenylmethylidene)-3-pyridinecarbohydrazide (4). The compound 1 adopted the most stable ketoamine form (form I, sbnd COsbnd NHsbnd Ndbnd Csbnd ) in the solid state as well as in various organic solvents. In mixtures of organic solvents with water the UV-Vis and ATR spectra implied intermolecular hydrogen bonding of 1 with water molecules. The presence of both tautomeric forms I and II (form II, sbnd COHdbnd Nsbnd Ndbnd Csbnd ) was proposed for the solid substance and highly concentrated solutions of 2, whereas form I was detected as the predominant one in diluted solutions. For compounds 3 and 4 a coexistence of forms I and III (form III, sbnd COsbnd NHsbnd NHsbnd Cdbnd Csbnd COsbnd ) was noticed in the solid state and in polar protic organic solvents. The conversion to form III was induced by increasing the water content in the solvent mixtures. This process was the most pronounced for compound 4. When exposed to daylight, an appearance of a new band was observed during time in the UV-Vis spectrum of 4 in organic solvent/water 1/1 mixtures, which implied that tautomeric interconversion was most likely followed by E/Z isomerisation.

  8. Structure optimization via free energy gradient method: Application to glycine zwitterion in aqueous solution

    NASA Astrophysics Data System (ADS)

    Okuyama-Yoshida, Naoto; Kataoka, Ken; Nagaoka, Masataka; Yamabe, Tokio

    2000-09-01

    The free energy gradient method was applied to the multidimensional geometry optimization of glycine zwitterion (ZW) in aqueous solution in order not only to demonstrate its applicability, but also to examine its efficiency. The method utilizes force on the free energy surface that can be directly calculated by the molecular dynamics method and the free energy perturbation theory. Then, the most stable ZW structure in aqueous solution was obtained within the tolerance assumed, and it was found that the free energy (FE) and enthalpy changes of stabilization from the initial geometry optimized in the gas phase are -0.9 and -3.5 kcal/mol, respectively, and the amino and carboxyl groups are spatially separated by each other due to their solvating with water molecules. Comparing the contributions of enthalpy and entropy to FE, the former is attributed to the main origin of FE stabilization during the optimization procedure, and it was found that solvation entropy prevents water molecules from solvating the ZW more strongly.

  9. 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

  10. Solution and Structural Investigations of Ligand Preorganization in Trivalent Lanthanide Complexes of Bicyclic Malonamides

    SciTech Connect

    Parks, Bevin W.; Gilbertson, Robert D.; Hutchison, J. E.; Rather Healey, Elisabeth; Weakley, Timothy J R; Rapko, Brian M.; Hay, Benjamin P.; Sinkov, Sergei I.; Broker, Grant A.; Rogers, Robin D.

    2006-02-20

    This report describes an investigation into the coordination chemistry of trivalentlanthanides in solution and the solid state with acyclic and preorganized bicyclic malonamide ligands. Two experimental investigations were performed: solution bindingaffinities were determined through single-phase spectrophotometric titrations and the extent of conformational change upon binding was investigated with single-crystal X-raycrystallography. Both experimental methods compare the bicyclic malonamide (BMA), which is designed to be preorganized for binding trivalent lanthanides, to an analogousacyclic malonamide. Results from the spectrophotometric titrations indicate that BMA exhibits a 10-100 times increase in binding affinity to Ln(III) over acyclic malonamide.In addition, BMA forms compounds with high ligand-metal ratios, even when competing with water and nitrate ligands for binding sites. The crystal structures exhibit nosignificant differences in the nature of the binding between Ln(III) and the BMA or acyclic malonamide. These results support the conclusion that rational ligand design canlead to compounds that enhance the binding affinities within a ligand class.

  11. 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.

  12. Synthesis and structure of solution-stable one-dimensional palladium wires.

    PubMed

    Campbell, Michael G; Powers, David C; Raynaud, Jean; Graham, Michael J; Xie, Ping; Lee, Eunsung; Ritter, Tobias

    2011-11-13

    One-dimensional metal wires are valuable materials because of their optical and electronic anisotropy, and they have potential utility in devices such as photovoltaic cells and molecular sensors. However, despite more than a century of research, only a few examples exist of well-defined one-dimensional (1D) metal wires that allow for the rational variation of conductivity. Herein we describe the first examples of 1D molecular wires supported by Pd-Pd bonds, the thin-film conductive properties of which can be altered by controlled molecular changes. Wires based on Pd(III) give semiconducting films with a modifiable bandgap, whereas wires based on Pd(2.5) give films that display metallic conductivity above 200 K: a metallic state has not been reported previously for any polymer composed of 1D metal wires. The wires are infinite in the solid state and maintain 1D structures in solution with lengths of up to 750 nm. Solution stability enables thin film coating, a requisite for device fabrication using molecular wires.

  13. Solution structure of a membrane-anchored ubiquitin-fold (MUB) protein from Homo sapiens.

    PubMed

    de la Cruz, Norberto B; Peterson, Francis C; Lytle, Betsy L; Volkman, Brian F

    2007-07-01

    The protein Bc059385, whose solution structure is reported here, is the human representative of a recently identified family of membrane-anchored ubiquitin-fold (MUB) proteins. Analysis of their similarity to ubiquitin indicates that homologous amino acid residues in MUBs form a hydrophobic surface very similar to the recognition patch surrounding Ile-44 in ubiquitin. This suggests that MUBs may interact with proteins containing an alpha-helical motif similar to those of some ubiquitin binding domains. A disordered loop common to MUBs may also provide a second protein interaction site. From the available data, it is probable that this protein is prenylated and associated with the membrane. With <20% identity to ubiquitin, the MUB family further expands the sequence space that maps to the beta-grasp fold, and adds membrane localization to its list of functional roles.

  14. Solution structure of the integral human membrane protein VDAC-1 in detergent micelles**

    PubMed Central

    Hiller, Sebastian; Garces, Robert G.; Malia, Thomas J.; Orekhov, Vladislav Y.; Colombini, Marco; Wagner, Gerhard

    2008-01-01

    The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with anti-apoptotic proteins from the Bcl-2 family and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the NMR solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded β-barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a belt-like fashion. In the presence of cholesterol recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-xL, for β-NADH and for cholesterol. Bcl-xL interacts with the VDAC barrel laterally at strands 17 and 18. PMID:18755977

  15. 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.

  16. NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds.

    PubMed

    Ortegón-Reyna, David; Garcías-Morales, Cesar; Padilla-Martínez, Itzia; García-Báez, Efren; Aríza-Castolo, Armando; Peraza-Campos, Ana; Martínez-Martínez, Francisco

    2013-12-31

    An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.

  17. Synthesis, Solution, and Structural Characterization of Tetrahydrofuranyl-2,2-Bisphosphonic Acid Disodium Salt

    PubMed Central

    Maltezou, Elena; Stylianou, Marios; Roy, Sudeshna; Drouza, Chryssoula; Keramidas, Anastasios D.

    2010-01-01

    Bisphosphonates are biologically relevant therapeutics for bone disorders and cancer. Reaction of γ-chlorobutyric acid, phosphorus acid, and phosphorus trichloride without the use of solvent gave the tetrahydrofuranyl-2,2-bisphosphonate sodium salt (Na2H2L). The Na2H2L was isolated, characterized in solution by 1H, 13C, and 31P NMR spectroscopy and in solid state by single X-Ray crystallography. The crystal structure showed that the Na2H2L forms in the crystal infinite two-dimensional sheets stacked one parallel to the other. A comparison of the chelating properties of H2L2− with similar hydroxyl bisphosphonate ligands shows that the strength of the Na–O(furanyl/hydroxyl) bond is directly related to the total charge of the ligand anion. PMID:20467558

  18. Structural and dynamical properties of a new family of solid solutions: ?

    NASA Astrophysics Data System (ADS)

    Bordallo, H. N.; Almairac, R.; Bulou, A.; Nouet, J.

    1996-07-01

    The new solid solutions 0953-8984/8/27/010/img8 have been investigated by different experimental methods in the temperature range 10 K - 300 K. X-ray and calorimetric measurements show that the incommensurate phase characteristic of 0953-8984/8/27/010/img9 is also observed for 0953-8984/8/27/010/img10. Raman spectra were obtained for 0953-8984/8/27/010/img11 and 0953-8984/8/27/010/img12. Two low-frequency, temperature-dependent bands were observed over the whole temperature range investigated. These results are discussed in connection with structural disorder and the presence of precursor effects of an incommensurate phase transition.

  19. 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.

  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. 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.

  2. Identification of ion-pair structures in solution by vibrational stark effects

    DOE PAGES

    Hack, John; Mani, Tomoyasu; Grills, David C.; ...

    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

  3. Identification of ion-pair structures in solution by vibrational stark effects

    SciTech Connect

    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) 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.

  4. 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

  5. Solution structural studies and low-resolution model of the Schizosaccharomyces pombe sap1 protein.

    PubMed

    Bada, M; Walther, D; Arcangioli, B; Doniach, S; Delarue, M

    2000-07-14

    Sap1 is a DNA-binding protein involved in controlling the mating type switch in fission yeast Schizosaccharomyces pombe. In the absence of any significant sequence similarity with any structurally known protein, a variety of biophysical techniques has been used to probe the solution low-resolution structure of the sap1 protein. First, sap1 is demonstrated to be an unusually elongated dimer in solution by measuring the translational diffusion coefficient with two independent techniques: dynamic light-scattering and ultracentrifugation. Second, sequence analysis revealed the existence of a long coiled-coil region, which is responsible for dimerization. The length of the predicted coiled-coil matches estimates drawn from the hydrodynamic experimental behaviour of the molecule. In addition, the same measurements done on a shorter construct with a coiled-coil region shortened by roughly one-half confirmed the localization of the long coiled-coil region. A crude T-shape model incorporating all these information was built. Third, small-angle X-ray scattering (SAXS) of the free molecule provided additional evidence for the model. In particular, the P(r) curve strikingly demonstrates the existence of long intramolecular distances. Using a novel 3D reconstruction algorithm, a low resolution 3D model of the protein has been independently constructed that matches the SAXS experimental data. It also fits the translation diffusion coefficients measurements and agrees with the first T-shaped model. This low-resolution model has clearly biologically relevant new functional implications, suggesting that sap1 is a bifunctional protein, with the two active sites being separated by as much as 120 A; a tetrapeptide repeated four times at the C terminus of the molecule is postulated to be of utmost functional importance.

  6. Structure and nature of manganese(II) imidazole complexes in frozen aqueous solutions.

    PubMed

    Un, Sun

    2013-04-01

    A common feature of a large majority of the manganese metalloenzymes, as well as many synthetic biomimetic complexes, is the bonding between the manganese ion and imidazoles. This interaction was studied by examining the nature and structure of manganese(II) imidazole complexes in frozen aqueous solutions using 285 GHz high magnet-field continuous-wave electron paramagnetic resonance (cw-HFEPR) and 95 GHz pulsed electron-nuclear double resonance (ENDOR) and pulsed electron-double resonance detected nuclear magnetic resonance (PELDOR-NMR). The (55)Mn hyperfine coupling and isotropic g values of Mn(II) in frozen imidazole solutions continuously decreased with increasing imidazole concentration. ENDOR and PELDOR-NMR measurements demonstrated that the structural basis for this behavior arose from the imidazole concentration-dependent distribution of three six-coordinate and two four-coordinate species: [Mn(H2O)6](2+), [Mn(imidazole)(H2O)5](2+), [Mn(imidazole)2(H2O)4](2+), [Mn(imidazole)3(H2O)](2+), and [Mn(imidazole)4](2+). The hyperfine and g values of manganese proteins were also fully consistent with this imidazole effect. Density functional theory methods were used to calculate the structures, spin and charge densities, and hyperfine couplings of a number of different manganese imidazole complexes. The use of density functional theory with large exact-exchange admixture calculations gave isotropic (55)Mn hyperfine couplings that were semiquantitative and of predictive value. The results show that the covalency of the Mn-N bonds play an important role in determining not only magnetic spin parameters but also the structure of the metal binding site. The relationship between the isotropic (55)Mn hyperfine value and the number of imidazole ligands provides a quick and easy test for determining whether a protein binds an Mn(II) ion using histidine residues and, if so, how many are involved. Application of this method shows that as much as 40% of the Mn(II) ions in

  7. Polyphosphate ions encapsulated in oxothiomolybdate rings: synthesis, structure, and behavior in solution.

    PubMed

    Cadot, Emmanuel; Pouet, Marie-José; Robert-Labarre, Chantal; du Peloux, Charlotte; Marrot, Jérôme; Sécheresse, Francis

    2004-07-28

    Cyclic oxothiomolybdates containing polyphosphate ions were prepared by simple reactions in aqueous medium of the corresponding polyphosphate ions and the cyclic precursor K(2)I(2)Mo(10)S(10)O(10)(OH)(10)(OH(2))(5).15H(2)O. K(5)[Cl(P(2)O(7)]Mo(12)S(12)O(12)(OH)(12)(H(2)O)(4)].22H(2)O (1) was isolated from concentrated chloride solution (2.5 mol.L(-1)). 1 reveals a remarkable complex containing two different substrates encapsulated in a dodecanuclear ring, a H-bonded Cl(-) ion, and a covalently bonded [P(2)O(7)] group. The chloride ion in 1 can be selectively removed for a monohydrogenophosphate group yielding K(6)[(HPO(4))(P(2)O(7))Mo(12)S(12)O(12)(OH)(12)(H(2)O)(2)].19H(2)O (2), a mixed species containing a [P(2)O(7)] and a [HPO(4)] group. The substitution is accompanied by a significant change of the ring, which adopts a "pear-shape" conformation. In the presence of triphosphate ion, the "heart-shaped" decanuclear ring Rb(3)[(H(2)P(3)O(10))Mo(10)S(10)O(10)(OH)(10)].17.5H(2)O (3) is formed containing a linear [P(3)O(10)] group intimately embedded in the inorganic cyclic host. The three compounds were structurally characterized by single-crystal X-ray diffraction. The behaviors of 1, 2, and 3 in solution were studied by (31)P NMR. Variable temperature experiments, supported by a two-dimensional COSY (31)P experiment, revealed that the supramolecular interaction existing between the chloride ion and the ring in solid 1 is maintained in solution. Nevertheless, 1 remains labile, and successive equilibria were evidenced and interpreted as an ion-pair association involving a halide ion (Cl, Br, or I), responsible for the conformational change of the [P(2)O(7)] group within the cavity. The influence of the nature of the halide guest (Cl(-), Br(-), and I(-)) on the successive equilibria was studied, and the thermodynamic constant related to the postulated equilibrium was determined. The stability of the supramolecular association decreases in the order Cl > Br > I. In

  8. Lower denticity leading to higher stability: structural and solution studies of Ln(III)-OBETA complexes.

    PubMed

    Negri, Roberto; Baranyai, Zsolt; Tei, Lorenzo; Giovenzana, Giovanni B; Platas-Iglesias, Carlos; Bényei, Attila C; Bodnár, Judit; Vágner, Adrienn; Botta, Mauro

    2014-12-01

    The heptadentate ligand OBETA (2,2'-oxybis(ethylamine)-N,N,N',N'-tetraacetic acid) was reported to form complexes with Ln(3+) ions more stable than those formed by the octadentate and more popular congener EGTA (ethylene glycol O,O'-bis(ethylamine)-N,N,N',N'-tetraacetic acid). The structural features leading to this puzzling coordination paradox were investigated by X-ray diffraction, solution state NMR, molecular modeling, and relaxometric studies. The stability constant of Gd(OBETA) (log KGdL = 19.37, 0.1 M KCl) is 2 orders of magnitude higher than that of the higher denticity analogue Gd(EGTA) (log KGdL = 17.66, 0.1 M KCl). The half-lives (t1/2) for the dissociation reactions of Gd(OBETA) and Gd(EGTA) ([Cu(2+)]tot = 0.2 mM, [Cit(3-)]tot = 0.5 mM, [PO4(3-)]tot = 1.0 mM, and [CO3(2-)]tot = 25 mM at pH = 7.4 and 25 °C in 0.1 M KCl solution) are 6.8 and 0.63 h, respectively, reflecting the much higher inertness of Gd(OBETA) near physiological conditions. NMR studies and DFT calculations using the B3LYP functional and a large-core ECP indicate that the [Gd(OBETA)(H2O)2](-) complex most likely exists in solution as the Δ(λλ)(δδδδ)A/Λ(δδ)(λλλλ)A enantiomeric pair, with an activation free energy for the enantiomerization process of ∼40 kJ·mol(-1). The metal ion is nine-coordinate by seven donor atoms of the ligand and two inner-sphere water molecules. The X-ray crystal structure of [C(NH2)3]3[Lu(OBETA)(CO3)]·2H2O is in agreement with the predictions of DFT calculations, the two coordinated water molecules being replaced by a bidentate carbonate anion. The (1)H NMRD and (17)O NMR study revealed that the two inner-sphere water molecules in Gd(OBETA) are endowed with a relatively fast water exchange rate (kex(298) = 13 × 10(6) s(-1)). The higher thermodynamic stability and inertness of Ln(OBETA) complexes, peaking in the center of the 4f series, combined with the presence of two coordinated water molecules suggests that Gd(OBETA) is a promising

  9. Spectroscopic evidence for the formation of four-stranded solution structure of oligodeoxycytidine phosphorothioate.

    PubMed

    Kanehara, H; Mizuguchi, M; Tajima, K; Kanaori, K; Makino, K

    1997-02-18

    Oligodeoxycytidine phosphorothioate (PS-dCn, n = chain length), known to show virus inhibition ability by a mechanism other than the antisense one when n approximately 20, was explored for its solution structure by circular dichroism (CD) and ultraviolet (UV) absorption spectroscopy. For PS-dC4, when the strand concentration was higher than 10 microM, the respective 288-nm positive and 265-nm negative peaks appeared in the CD spectra at slightly acidic pHs and 0 degree C in the absence of salt, which is indicative of a four-stranded structure (namely, the i-motif). Strand concentration-dependent CD spectroscopy indicated that intermolecular association is responsible for this i-motif. The formation or i-motif was also characterized by UV absorption spectroscopy, in which the dissociation of this structure caused a sharp increase in the absorbance at 275 nm and a decrease at 305 nm. By plotting this change, the Tn values were estimated to be ca. 11 and 13 degrees C at 20 and 50 microM strand concentrations, respectively. Stability of the i-motif was compared between PS-dC, P-chiral diastereoisomers, and the Sp configuration produced a more stable structure than Rp. PS-dC20 was also investigated at physiological temperature, and the respective 288-nm positive and 265-nm negative peaks appeared at slightly acidic pH: it has been suggested that intermolecular folding was predominant above ca. 1 microM and that intramolecular folding dominated at low strand concentrations such as 0.05 microM. Gel-filtration chromatography and nondenaturing gel electrophoresis provided the supporting data for the four-stranded folding of PS-dC20.

  10. Atomistic simulation of local structure and mixing properties of mineral solid solutions

    NASA Astrophysics Data System (ADS)

    Urusov, V. S.

    2009-04-01

    At present there are several ways to simulate solid solution structure and properties by using ab initio as well as semi-empirical (atomistic) approaches [1]. The main problem of each approach is a reasonable representation of random distribution of atoms substituting each other over common positions. A procedure in operation here used large supercells and generation of most disordered atomic configurations for some selected compositions of solid solution (1:1, 1:3, 3:1, 4:1, 1:4, etc.). The following binary systems were studied by such a way: NaCl - KCl [2, 3, 4], CaO - MgO, CaO - SrO, SrO - BaO (supercell 444, 512 atoms) [3], TiO2 - SnO2 (444, 384 atoms), Al2O3 - Cr2O3, Al2O3 - Fe2O3, Fe2O3 - Cr2O3 (441, 480 atoms) [5]. The calculation technique was based on the method of semi-empirical potentials using the GULP program [6]. Potential parameters of ionic (halides) or partially covalent (oxides) interatomic interactions were optimized by using of structural, thermodynamic and elastic properties of pure components. Calculated heat capacities and entropies as a function of temperature were in a good agreement with experimental data. Excess mixing properties (enthalpy, volume, bulk modulus, vibrational entropy) were calculated for different compositions of the solid solutions. This allowed to reproduce Gibbs energy as a function of temperature and composition and estimate critical temperature of decomposition and miscibility gap of a solid solution. Statistical analysis of bond lengths frequencies for the nearest and next-nearest neighbors in (Na0.5K0.5)Cl, (Ca0.5Mg0.5)O, (Ti0.5Sn0.5)O2, (Al1.0Cr1.0)O3 solid solutions revealed a detailed picture of the lattice relaxation. These results were compared with earlier predictions made by phenomenological crystal chemical models [7, 8] and available EXAFS data. References 1. V.S.Urusov. J.Solid State Chem. 2000. V.153. 357. 2. Urusov V.S., Petrova T.G., Leonenko E.V., Eremin N.N. Vestn. Mosc. Univ. 2008

  11. 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.

  12. Structural, dynamic, and transport properties of concentrated aqueous sodium chloride solutions under an external static electric field.

    PubMed

    Ren, Gan; Shi, Rui; Wang, Yanting

    2014-04-24

    In the absence of an external electric field, it has already been known that ion clusters are formed instantaneously in moderately concentrated ionic solutions. In this work, we use molecular dynamics (MD) simulations to investigate the changes of structural, dynamic, and transport properties in a sodium chloride solution under an external electric field from the ion cluster perspective. Our MD simulation results indicate that, with a strong external electric field E (≥0.1 V/nm) applied, ion clusters become smaller and less net charged, and the structures and dynamics as well as transport properties of the ion solution become anisotropic. The influence of the cluster structure and shell structure to transport properties was analyzed and the Einstein relation was found invalid in this system.

  13. 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

  14. Structures of plant viruses from vibrational circular dichroism.

    PubMed

    Shanmugam, Ganesh; Polavarapu, Prasad L; Kendall, Amy; Stubbs, Gerald

    2005-08-01

    Vibrational circular dichroism (VCD) spectra in the amide I and II regions have been measured for viruses for the first time. VCD spectra were recorded for films prepared from aqueous buffer solutions and also for solutions using D(2)O buffers at pH 8. Investigations of four filamentous plant viruses, Tobacco mosaic virus (TMV), Papaya mosaic virus, Narcissus mosaic virus (NMV) and Potato virus X (PVX), as well as a deletion mutant of PVX, are described in this paper. The film VCD spectra of the viruses clearly revealed helical structures in the virus coat proteins; the nucleic acid bases present in the single-stranded RNA could also be characterized. In contrast, the solution VCD spectra showed the characteristic VCD bands for alpha-helical structures in the coat proteins but not for RNA. Both sets of results clearly indicated that the coat protein conformations are dominated by helical structures, in agreement with earlier reports. VCD results also indicated that the coat protein structures in PVX and NMV are similar to each other and somewhat different from that of TMV. The present study demonstrates the feasibility of measuring VCD spectra for viruses and extracting structural information from these spectra.

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

    PubMed

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

    2014-01-10

    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.

  16. Simulation of intrathrombus fluid and solute transport using in vivo clot structures with single platelet resolution

    PubMed Central

    Voronov, Roman S.; Stalker, Timothy J.; Brass, Lawrence F.; Diamond, Scott L.

    2013-01-01

    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 cm2). Average wall shear stresses were 80–100 dyne/cm2 (peak values > 200 dyne/cm2) on the outer rough surface of the thrombus. Within the thrombus, small molecule tracers (0.1 kDa) experienced ~70,000 collisions/sec and penetrated/exited it in about 1 sec, wh