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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. [Ribonuclease hydration and its heat stability in solutions of H2O and D2O].

    PubMed

    Mrevlishvili, G M; Lobyshev, V I; Dzhaparidze, G Sh; Sokhadze, V M; Tatishvili, D A

    1980-01-01

    Ribonuclease hydration in wide concentration and temperature range using differential scanning microcalorimetry and NMR technique was studied. The temperature- concentration equilibrium diagram for H2O--ribonuclease system was suggested. Protein hydration in D2O was shown to be higher than in ordinary water. NMR measurements in dilute protein solutions showed that cooperative temperature denaturation was followed by solvation changes. Models of globular protein hydration are discussed. PMID:6245723

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

    PubMed

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

    2014-03-26

    The development of deuterated biomass is essential for effective neutron scattering studies on biomass, which can provide key insights into the complex biomass conversion processes. A method for optimized production of deuterated annual ryegrass (Lolium multiflorum) was developed by growing the plants in 50% D2O in perfused hydroponic chambers. Deuterium incorporation of 36.9% was found in the annual rye grown in 50% D2O. Further, deuterium incorporation of 60% was achieved by germinating the rye seedlings in H2O and growing in 50% D2O inside the perfusion chambers. The characteristics related to enzymatic hydrolysis such as biomass composition, degree of polymerization, and cellulose crystallinity were compared with its control protiated counterpart. The cellulose molecular weight indicated slight variation while hemicellulose molecular weights and cellulose crystallinity remain unaffected with the deuteration.

  4. Nuclear and electronic relaxation in lanthanide solutions: (CH 3) 4N +/Gd 3+ repulsive ion pair in D 2O

    NASA Astrophysics Data System (ADS)

    Vigouroux, C.; Bardet, M.; Belorizky, E.; Fries, P. H.; Guillermo, A.

    1998-04-01

    The longitudinal relaxation rate and self-diffusion coefficient of the tetramethylammonium protons are investigated at 400 MHz in D 2O solutions of hydrated Gd 3+ paramagnetic impurities, without and with complexing NO 3- ions. The results are interpreted using the hypernetted chain approximation of the potential of mean force between the repulsive ions, approximated as charged hard spheres in discrete polar and polarizable water. The standard dipolar relaxation formalism of Solomon is valid for the Gd 3+ lanthanide, i.e. its electron relaxation time is much longer than the translational correlation time of the interionic Brownian diffusion. The coordination effect by NO 3- is analyzed.

  5. Entropic effects and slow kinetics revealed in titrations of D2O-H2O solutions with different D/H ratios.

    PubMed

    Katsir, Yael; Shapira, Yoash; Mastai, Yitzhak; Dimova, Rumiana; Ben-Jacob, Eshel

    2010-05-01

    There is much renewed interest in the arrangement and kinetic of hydrogen bonds in water and heavy water. D(2)O forms a higher average number of hydrogen bonds per molecule (10% more) compared to the case for H(2)O, which cause a larger entropic cost for solvating molecules in D(2)O. Here we used isothermal titration calorimetry (ITC) to investigate the enthalpy of titration of D(2)O-H(2)O solutions with different D/H isotope ratios. We found significant enthalpy deviations (exothermic contributions) relative to the computed enthalpy for the limit of ideal mixing both for dilution titration and for concentration titration (injection of solutions with lower D/H ratios into solutions with higher ratios and vice versa). We propose that the observed exothermic deviations might be connected to entropic effects associated with differences in the H and D arrangements that depend on the D/H ratio of the solutions. This ratio varies during the titration processes, leading to the entropy production beyond that of ideal mixing. We also used the ITC in the nonstirring mode to measure the titration kinetics and found long relaxation times of up to tens of minutes for the concentration titrations (but not for the dilution titrations). These observations are consistent with slow propagation of the reaction H(2)O + D(2)O <--> 2HDO that involves hopping of deuterium and rearrangements of the H and D bonding.

  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. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed

    Fernández, P; Jiménez-Barbero, J

    1993-10-01

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

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

    PubMed

    Fernández, P; Jiménez-Barbero, J

    1993-10-01

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

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

    PubMed

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

    2016-09-13

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

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

    PubMed

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

    2016-09-13

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-03-01

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

  16. 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.

  17. Neutron reflectivity study of the swollen structure of polyzwitterion and polyeletrolyte brushes in aqueous solution.

    PubMed

    Kobayashi, Motoyasu; Ishihara, Kazuhiko; Takahara, Atsushi

    2014-01-01

    The swollen brush structures of polycation and zwitterionic polymer brushes, such as poly(2-methacryloyloxyethyltrimethylammonium chloride) (PMTAC), poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC), and poly[3-(N-2-methacryloyloxyethyl-N,N-dimethyl)ammonatopropanesulfonate] (PMAPS), in aqueous solutions of various ionic strengths were characterized by neutron reflectivity (NR) measurements. A series of the polyelectrolyte brushes were prepared by surface-initiated controlled radical polymerization on silicon substrates. A high-graft-density PMTAC brush in salt-free water (D2O) adopted a two-region step-like structure consisting of a shrunk region near the Si substrate surface and a diffuse brush region with a relatively stretched chain structure at the solution interface. The diffuse region of PMTAC was reduced with increase in salt (NaCl) concentration. The PMAPS brush in D2O formed a collapsed structure due to the strong molecular interaction between betaine groups, while significant increase in the swollen thickness was observed in salt aqueous solution. In contrast, no change was observed in the depth profile of the swollen PMPC brush in D2O with various salt concentrations. The unique solution behaviors of zwitterionic polymer brushes were described. PMID:25178564

  18. Nucleation and Droplet Growth During Co-condensation of Nonane and D2O in a Supersonic Nozzle

    NASA Astrophysics Data System (ADS)

    Pathak, Harshad Narayan

    . The subsequent process of growth of the droplets can be sensitive to droplet temperatures T d. For pure nonane droplets, we observe that T d is not important enough to alter the growth rates unlike pure D 2O. The growth of D2O droplets is further affected by coagulation once condensation has slowed down. We also observe that when nonane and D 2O both are condensing, the presence of nonane inhibits D2O condensation even when D2O dominates the nucleation process. Prediction of the droplet structure of composite nonane-D2O droplets is challenging because the SAXS spectra of these droplets does not fit to standard shapes like spheres or core-shell structures. The small size of these droplets makes it possible to study them through molecular dynamics simulations. Our collaborators conduct simulations of these droplets and calculate the scattering behavior for those shapes. The SAXS spectra are fit to scattering from shapes derived from both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Although the 'lens-on-sphere' structures derived from MD simulations fits the scattering spectra better than all other structures which we tested, the overall composition from this structure predicts that the amount of D2O condensed is 30-40% less than that measured from FTIR.

  19. Solution structure of (+)-discodermolide.

    PubMed

    Smith, A B; LaMarche, M J; Falcone-Hindley, M

    2001-03-01

    [structure: see text]. The solution structure of (+)-discodermolide (1) has been determined via 1- and 2-D NMR techniques in conjunction with Monte Carlo conformational analysis. Taken together, the results demonstrate that in solution (+)-discodermolide occupies a helical conformation remarkably similar to the solid state conformation.

  20. Vibrational Anylasis on I(H{_2}O){^-} and I(D{_2}O){^-} Spectra

    NASA Astrophysics Data System (ADS)

    Huang, Meng; McCoy, Anne B.

    2013-06-01

    Hydrated halide clusters provide good systems for investigating the effect of the intramolecular hydrogen-bond on the spectrum of ions and molecules. In this work, the vibrational spectra of I(H{_2}O){^-} and I(D{_2}O){^-} were studied. We focused on the couplings between the two O-H stretch modes and the in-plane bending mode, which is the frustrated rotation of the water molecule in the plane of the complex. A reduced-dimensional analysis with these three modes was developed to investigate the effect of the couplings on the spectra. The model potential in the analysis was obtained from ab initio calculation with MP2/aug-cc-pVTZ-PP level of method and basis set. The doublet structure of the O-H stretch mode in the spectrum was attributed to the tunneling splitting from the in-plane bending mode double-well potential energy surface.

  1. Magnetization of AN S=1/2 and 1 Ferrimagnetic Chain NiCu(pba)(D2O)32D2O in High Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Hagiwara, M.; Narumi, Y.; Tatani, K.; Kindo, K.; Minami, K.

    2004-11-01

    We report the results of high field magnetization measurements on a powder sample of NiCu (pba)(D2O)32D2O (pba = 1,3-propylenebis(oxamato), C7H6N2O6) which is regarded as a ferrimagnetic chain composed of spins S = 1/2 and 1. From a fit of the susceptibility of this compound to numerical calculations (exact diagonalization for ten sites), we evaluated the exchange constant J/kB = 121 K. In the magnetization measurements at 10 K up to 50 T, we observed a magnetization plateau of about 1.1 μB/(formula unit) corresponding to about one-third of the saturated magnetization. The increase of the magnetization at low magnetic fields is discussed and compared with some calculations.

  2. 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.

  3. 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)

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

    NASA Astrophysics Data System (ADS)

    Nagai, Kenta; Watanabe, Kazuo

    2016-01-01

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

  5. 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.

  6. 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.

  7. 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.

  8. Hydron transfer catalyzed by triosephosphate isomerase. Products of isomerization of dihydroxyacetone phosphate in D2O.

    PubMed

    O'Donoghue, Annmarie C; Amyes, Tina L; Richard, John P

    2005-02-22

    The product distributions for the reactions of dihydroxyacetone phosphate (DHAP) in D(2)O at pD 7.9 catalyzed by triosephosphate isomerase (TIM) from chicken and rabbit muscle were determined by (1)H NMR spectroscopy using glyceraldehyde 3-phosphate dehydrogenase to trap the first-formed products of the thermodynamically unfavorable isomerization reaction, (R)-glyceraldehyde 3-phosphate (GAP) and [2(R)-(2)H]-GAP (d-GAP). Three products were observed from the reactions catalyzed by TIM: GAP from isomerization with intramolecular transfer of hydrogen (18% of the enzymatic products), d-GAP from isomerization with incorporation of deuterium from D(2)O into C-2 of GAP (43% of the enzymatic products), and [1(R)-(2)H]-DHAP (d-DHAP) from incorporation of deuterium from D(2)O into C-1 of DHAP (40% of the enzymatic products). The ratios of the yields of the deuterium-labeled products d-DHAP and d-GAP from partitioning of the intermediate of the TIM-catalyzed reactions of GAP and DHAP in D(2)O are 1.48 and 0.93, respectively. This provides evidence that the reaction of these two substrates does not proceed through a single, common, reaction intermediate but, rather, through distinct intermediates that differ in the bonding and arrangement of catalytic residues at the enediolate O-1 and O-2 oxyanions formed on deprotonation of GAP and DHAP, respectively.

  9. Stealth carriers for low-resolution structure determination of membrane proteins in solution.

    PubMed

    Maric, Selma; Skar-Gislinge, Nicholas; Midtgaard, Søren; Thygesen, Mikkel B; Schiller, Jürgen; Frielinghaus, Henrich; Moulin, Martine; Haertlein, Michael; Forsyth, V Trevor; Pomorski, Thomas Günther; Arleth, Lise

    2014-02-01

    Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial nanoscale bilayer disc carriers that mimic the native bilayer environment allows the handling of membrane proteins in solution. This enables the use of small-angle scattering techniques for fast and reliable structural analysis. The difficulty with this approach is that the carrier discs contribute to the measured scattering intensity in a highly nontrivial fashion, making subsequent data analysis challenging. Here, an elegant solution to circumvent the intrinsic complexity brought about by the presence of the carrier disc is presented. In combination with small-angle neutron scattering (SANS) and the D2O/H2O-based solvent contrast-variation method, it is demonstrated that it is possible to prepare specifically deuterated carriers that become invisible to neutrons in 100% D2O at the length scales relevant to SANS. These `stealth' carrier discs may be used as a general platform for low-resolution structural studies of membrane proteins using well established data-analysis tools originally developed for soluble proteins. PMID:24531466

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

    PubMed Central

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

    2015-01-01

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

  11. 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

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

    PubMed

    Rosales, Antonio; Rodríguez-García, Ignacio

    2016-01-01

    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

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

    PubMed

    Chatterjee, Basujit; Gunanathan, Chidambaram

    2015-10-01

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

  14. 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.

  15. 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.

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

    PubMed

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

    2015-08-01

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

  17. Myochrysine Solution Structure and Reactivity

    PubMed Central

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

    1994-01-01

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

  18. 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

  19. Hydrogen bonding and Raman, IR, and 2D-IR spectroscopy of dilute HOD in liquid D2O.

    PubMed

    Auer, B; Kumar, R; Schmidt, J R; Skinner, J L

    2007-09-01

    We present improvements on our previous approaches for calculating vibrational spectroscopy observables for the OH stretch region of dilute HOD in liquid D2O. These revised approaches are implemented to calculate IR and isotropic Raman spectra, using the SPC/E simulation model, and the results are in good agreement with experiment. We also calculate observables associated with three-pulse IR echoes: the peak shift and 2D-IR spectrum. The agreement with experiment for the former is improved over our previous calculations, but discrepancies between theory and experiment still exist. Using our proposed definition for hydrogen bonding in liquid water, we decompose the distribution of frequencies in the OH stretch region in terms of subensembles of HOD molecules with different local hydrogen-bonding environments. Such a decomposition allows us to make the connection with experiments and calculations on water clusters and more generally to understand the extent of the relationship between transition frequency and local structure in the liquid.

  20. 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.

  1. 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.

  2. 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.

  3. Effect of Mannosylerythritol lipid-A on light scattering of AOT/D2O/Octane

    NASA Astrophysics Data System (ADS)

    Sharifi, Soheil

    2016-09-01

    The light scattering technique is used for the study of interaction of Mannosylerythritol lipid-A on AOT/D2O/Octane. The collective diffusion of AOT/D2O droplets soluble in Octane mixed with lipid is founded from a correlation function of light scattering. We focus on the variation of the dynamic behavior of droplets as a function of the lipid concentrations and the size of droplets. The increase of concentration of Mannosylerythritol lipid-A on microemulsion decreases the dynamic of droplets. The SAXS experiment shows the size and the interaction of the droplets change by increase of Mannosylerythritol lipid-A concentration. A hard sphere model can describe the interaction of lipid with AOT/D2O droplets.

  4. 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.

  5. Myochrysine solution structure and reactivity.

    PubMed

    Elder, R C; Jones, W B; Zhao, Z; Dorsey, J G; Tepperman, K

    1994-01-01

    We have determined the framework structure of Myochrysine (disodium gold(I)thiomalate) in the solid state and extremely concentrated aqueous solution, previously. It consists of an open chain polymer with linear gold coordination to two thiolates from the thiomalic acid moieties which bridge between pairs of gold atoms providing an Au-S-Au angle of 95 degrees . The question remained: was this structure relevant to the dilute solutions of drugs administered and the still lower concentrations of gold found in the bodies of patients (typically 1 ppm Au in blood and urine or 5 muM in Au). We have provided an answer to that question using extended X-ray absorption spectroscopy (EXAFS) and capillary zone electrophoresis (CZE). EXAFS studies confirm that the polymeric structure with two sulfur atoms per gold atom persists from molar concentrations down to millimolar concentrations. CZE is able to separate and detect Myochrysine at millimolar levels. More importantly, at micromolar levels Myochrysine solutions exhibit identical CZE behavior to that measured at millimolar levels. Thus, aqueous solutions of the drug remain oligomeric at concentrations commensurate with those found in patient blood and urine.The reactivity of Myochrysine with cyanide, a species especially prevalent in smoking patients, was explored using CZE. Cyanide freely replaces thiomalic acid to form [Au(CN)(2)](-) and thiomalic acid via a mixed ligand intermediate. The overall apparent equilibrium constant (K(app)) for the reaction is 6x10(-4)M(-1). Further reaction of [Au(CN)(2)](-) with a large excess of L, where L is cysteine, N-acetylcysteine, or glutathione, shows that these amino acids readily replace cyanide to form [AuL(2)](-). These species are thus potential metabolites and could possibly be active forms of gold in vivo. That all of these species are readily separated and quantified using CZE demonstrates that capillary electrophoresis is an accessible and powerful tool to add to those used

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

    SciTech Connect

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

    2004-05-14

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

  7. 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.

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

    PubMed

    Wang, Xiao-Gang; Carrington, Tucker

    2015-07-14

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Gang; Carrington, Tucker

    2015-07-01

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

  10. 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%.

  11. 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%.

  12. Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r)

    NASA Astrophysics Data System (ADS)

    Boek, E. S.; Briels, W. J.

    1993-01-01

    Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary conditions are chosen properly, even after a very careful equilibration. The total nitrogen scattering function GN(r), calculated from these simulations, is in good agreement with neutron scattering experiments when both intra- and intermolecular correlations are considered and the experimental truncation ripples are introduced by a Fourier transform of GN(r) back and forth. The simple pair potential model that we used gives results in good agreement with experiments and with a much more involved potential model, recently described in the literature [J. Chem. Phys. 95, 8419 (1991)].

  13. 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

  14. 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

  15. Solution Accounts for Structural Damping

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  16. 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.

  17. Hydron transfer catalyzed by triosephosphate isomerase. Products of isomerization of (R)-glyceraldehyde 3-phosphate in D2O.

    PubMed

    O'Donoghue, Annmarie C; Amyes, Tina L; Richard, John P

    2005-02-22

    The product distributions for the reactions of (R)-glyceraldehyde 3-phosphate (GAP) in D(2)O at pD 7.5-7.9 catalyzed by triosephosphate isomerase (TIM) from chicken and rabbit muscle were determined by (1)H NMR spectroscopy. Three products were observed from the reactions catalyzed by TIM: dihydroxyacetone phosphate (DHAP) from isomerization with intramolecular transfer of hydrogen (49% of the enzymatic products), [1(R)-(2)H]-DHAP from isomerization with incorporation of deuterium from D(2)O into C-1 of DHAP (31% of the enzymatic products), and [2(R)-(2)H]-GAP from incorporation of deuterium from D(2)O into C-2 of GAP (21% of the enzymatic products). The similar yields of [1(R)-(2)H]-DHAP and [2(R)-(2)H]-GAP from partitioning of the enzyme-bound enediol(ate) intermediate between hydron transfer to C-1 and C-2 is consistent with earlier results, which showed that there are similar barriers for conversion of this intermediate to the alpha-hydroxy ketone and aldehyde products (Knowles, J. R., and Albery, W. J. (1977) Acc. Chem. Res. 10, 105-111). However, the observation that the TIM-catalyzed isomerization of GAP in D(2)O proceeds with 49% intramolecular transfer of the (1)H label from substrate to product DHAP stands in sharp contrast with the

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

    PubMed

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

    2008-02-01

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

  19. Automated MAD and MIR structure solution.

    PubMed

    Terwilliger, T C; Berendzen, J

    1999-04-01

    Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations. PMID:10089316

  20. Wildtype and engineered monomeric triosephosphate isomerase from Trypanosoma brucei: partitioning of reaction intermediates in D2O and activation by phosphite dianion.

    PubMed

    Malabanan, M Merced; Go, Maybelle K; Amyes, Tina L; Richard, John P

    2011-06-28

    Product yields for the reactions of (R)-glyceraldehyde 3-phosphate (GAP) in D2O at pD 7.9 catalyzed by wildtype triosephosphate isomerase from Trypanosoma brucei brucei (Tbb TIM) and a monomeric variant (monoTIM) of this wildtype enzyme were determined by (1)H NMR spectroscopy and were compared with the yields determined in earlier work for the reactions catalyzed by TIM from rabbit and chicken muscle [O'Donoghue, A. C., Amyes, T. L., and Richard, J. P. (2005), Biochemistry 44, 2610 - 2621]. Three products were observed from the reactions catalyzed by TIM: dihydroxyacetone phosphate (DHAP) from isomerization with intramolecular transfer of hydrogen, d-DHAP from isomerization with incorporation of deuterium from D2O into C-1 of DHAP, and d-GAP from incorporation of deuterium from D2O into C-2 of GAP. The yield of DHAP formed by intramolecular transfer of hydrogen decreases from 49% for the muscle enzymes to 40% for wildtype Tbb TIM to 34% for monoTIM. There is no significant difference in the ratio of the yields of d-DHAP and d-GAP for wildtype TIM from muscle sources and Trypanosoma brucei brucei, but partitioning of the enediolate intermediate of the monoTIM reaction to form d-DHAP is less favorable ((k(C1))(D)/(k(C2))(D) = 1.1) than for the wildtype enzyme ((k(C1))(D)/(k(C2))(D) = 1.7). Product yields for the wildtype Tbb TIM and monoTIM-catalyzed reactions of glycolaldehyde labeled with carbon-13 at the carbonyl carbon ([1-(13)C]-GA) at pD 7.0 in the presence of phosphite dianion and in its absence were determined by (1)H NMR spectroscopy [Go, M. K., Amyes, T. L., and Richard, J. P. (2009) Biochemistry 48, 5769-5778]. There is no detectable difference in the yields of the products of wildtype muscle and Tbb TIM-catalyzed reactions of [1-(13)C]-GA in D2O. The kinetic parameters for phosphite dianion activation of the reactions of [1-(13)C]-GA catalyzed by wildtype Tbb TIM are similar to those reported for the enzyme from rabbit muscle [Amyes, T. L. and Richard, J

  1. Intramembrane Water Associated with TOAC Spin-Labeled Alamethicin: Electron Spin-Echo Envelope Modulation by D2O

    PubMed Central

    Bartucci, R.; Guzzi, R.; Sportelli, L.; Marsh, D.

    2009-01-01

    Alamethicin is a 20-residue, hydrophobic, helical peptide, which forms voltage-sensitive ion channels in lipid membranes. The helicogenic, nitroxyl amino acid TOAC was substituted isosterically for Aib at residue positions 1, 8, or 16 in a F50/5 alamethicin analog to enable EPR studies. Electron spin-echo envelope modulation (ESEEM) spectroscopy was used to investigate the water exposure of TOAC-alamethicin introduced into membranes of saturated or unsaturated diacyl phosphatidylcholines that were dispersed in D2O. Echo-detected EPR spectra were used to assess the degree of assembly of the peptide in the membrane, via the instantaneous diffusion from intermolecular spin-spin interactions. The profile of residue exposure to water differs between membranes of saturated and unsaturated lipids. In monounsaturated dioleoyl phosphatidylcholine, D2O-ESEEM intensities decrease from TOAC1 to TOAC8 and TOAC16 but not uniformly. This is consistent with a transmembrane orientation for the protoassembled state, in which TOAC16 is located in the bilayer leaflet opposite to that of TOAC1 and TOAC8. Relative to the monomer in fluid bilayers, assembled alamethicin is disposed asymmetrically about the bilayer midplane. In saturated dimyristoyl phosphatidylcholine, the D2O-ESEEM intensity is greatest for TOAC8, indicating a more superficial location for alamethicin, which correlates with the difference in orientation between gel- and fluid-phase membranes found by conventional EPR of TOAC-alamethicin in aligned phosphatidylcholine bilayers. Increasing alamethicin/lipid ratio in saturated phosphatidylcholine shifts the profile of water exposure toward that with unsaturated lipid, consistent with proposals of a critical concentration for switching between the two different membrane-associated states. PMID:19186137

  2. 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.

  3. Superconductivity in epitaxial thin films of NaxCoO2•yD2O

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-07-01

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

  5. 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.

  6. Automated MAD and MIR structure solution

    SciTech Connect

    Terwilliger, Thomas C.; Berendzen, Joel

    1999-04-01

    A fully automated procedure for solving MIR and MAD structures has been developed using a scoring scheme to convert the structure-solution process into an optimization problem. Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

  7. Refined solution structure of human profilin I.

    PubMed Central

    Metzler, W. J.; Farmer, B. T.; Constantine, K. L.; Friedrichs, M. S.; Lavoie, T.; Mueller, L.

    1995-01-01

    Profilin is a ubiquitous eukaryotic protein that binds to both cytosolic actin and the phospholipid phosphatidylinositol-4,5-bisphosphate. These dual competitive binding capabilities of profilin suggest that profilin serves as a link between the phosphatidyl inositol cycle and actin polymerization, and thus profilin may be an essential component in the signaling pathway leading to cytoskeletal rearrangement. The refined three-dimensional solution structure of human profilin I has been determined using multidimensional heteronuclear NMR spectroscopy. Twenty structures were selected to represent the solution conformational ensemble. This ensemble of structures has root-mean-square distance deviations from the mean structure of 0.58 A for the backbone atoms and 0.98 A for all non-hydrogen atoms. Comparison of the solution structure of human profilin to the crystal structure of bovine profilin reveals that, although profilin adopts essentially identical conformations in both states, the solution structure is more compact than the crystal structure. Interestingly, the regions that show the most structural diversity are located at or near the actin-binding site of profilin. We suggest that structural differences are reflective of dynamical properties of profilin that facilitate favorable interactions with actin. The global folding pattern of human profilin also closely resembles that of Acanthamoeba profilin I, reflective of the 22% sequence identity and approximately 45% sequence similarity between these two proteins. PMID:7795529

  8. 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

  9. Measurements of Line Positions and Strengths of HD O-18 and D2 O-18 in the 2500-4280 cm(exp -1) Region

    NASA Technical Reports Server (NTRS)

    Toth, Robert A.

    2005-01-01

    Measurements of line positions and strengths of D2 O-18 and HD O-18 were obtained with a Fourier transform spectrometer. The data were analyzed to obtain energy levels of the (100), (020), and (001) vibrational states of HD O-18 and the (001) and (011) states of D2 O-18 and the vibrational bands of these states connected to the ground state covered the spectral region from 2500 to 4278 cm(exp -1). 456 absorption lines of D2 O-18 and 856 lines of HD O-18 were assigned from the spectra. The measurements were of oxygen-18 enriched samples of deuterated water vapor and the spectra also contained features of HD O-16, D2 O-16, H2 O-16, H2 O-17 and H2 O-18 of which several were used as frequency calibration standards.

  10. Complex structures – smart solutions

    PubMed Central

    2011-01-01

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

  11. 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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1991-03-01

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

  14. Solution structure of pyoverdin GM-II.

    PubMed

    Mohn, G; Koehl, P; Budzikiewicz, H; Lefèvre, J F

    1994-03-15

    The three-dimensional structure in solution of ferri-pyoverdin GM-II isolated from the culture medium of Pseudomonas fluorescens was determined by application of NMR methods to the Ga3+ analogue. Distance geometry calculations were performed with FILMAN using interproton distances and coupling constants as constraints. Further conformational analysis was carried out by energy minimization with MM2 and AMBER. Back-calculation of the NOESY spectra shows that the resulting structures are in agreement with the experimental data. PMID:8130197

  15. 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

  16. Anharmonic RRKM calculation for the dissociation of (H(2)O)(2)H(+) and its deuterated species (D(2)O)(2)D(+).

    PubMed

    Song, Di; Su, Hongmei; Kong, Fan-Ao; Lin, Sheng-Hsien

    2010-09-23

    Investigations on the dissociation kinetics of hydrated protonium ions, (H(2)O)(2)H(+) and their deuterated species (D(2)O)(2)D(+), are reported based on the harmonic and anharmonic oscillator model using the transition state theory and ab initio calculations. We find that the dissociation of (H(2)O)(2)H(+) and (D(2)O)(2)D(+) exhibits a distinct threshold behavior due to the existence of activation energies. Moreover, the deviation between the harmonic and anharmonic dissociation rate constants becomes larger in the high energy or temperature range, with the rate constants becoming unreasonably large under the harmonic oscillator model. The isotope effect is found to become more distinct but only in the case of the anharmonic oscillator model. These results show that the anharmonic Rice-Ramsperger-Kassel-Marcus (RRKM) theory can provide a reasonably good description for the dissociation of (H(2)O)(2)H(+) and (D(2)O)(2)D(+). Furthermore, a theoretical model to demonstrate the principle of vibrational predissociation spectroscopy (VPS) is established from the viewpoint of RRKM theory and applied in determining the experimental conditions and understanding the role of the dissociation rate constant k(E) played in the VPS experiment, using (H(2)O)(2)H(+) and (D(2)O)(2)D(+) as examples.

  17. 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.

  18. 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.

  19. 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

    2011-10-01

    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.

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

    PubMed

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

    2011-10-21

    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, (H(2)O)(2) (and also (D(2)O)(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 (H(2)O)(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 (H(2)O)(2) and (D(2)O)(2) mainly produces either fragment in the bending excited (010) state. The H(2)O(J) and D(2)O(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 (D(2)O)(2) providing an accurate zero-point energy of 7247 cm(-1), and thus, a benchmark D(0) of 1244 ± 5 cm(-1).

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

    NASA Astrophysics Data System (ADS)

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

    1996-02-01

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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. Structuring of polymer solutions upon solvent evaporation

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  7. 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.

  8. Solution structure of human sorting nexin 22.

    PubMed

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

    2007-05-01

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

  9. 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.

  10. 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.

  11. Concentration Dependent Structure of Block Copolymer Solutions

    NASA Astrophysics Data System (ADS)

    Choi, Soohyung; Bates, Frank S.; Lodge, Timothy P.

    2015-03-01

    Addition of solvent molecules into block copolymer can induce additional interactions between the solvent and both blocks, and therefore expands the range of accessible self-assembled morphologies. In particular, the distribution of solvent molecules plays a key role in determining the microstructure and its characteristic domain spacing. In this study, concentration dependent structures formed by poly(styrene-b-ethylene-alt-propylene) (PS-PEP) solution in squalane are investigated using small-angle X-ray scattering. This reveals that squalane is essentially completely segregated into the PEP domains. In addition, the conformation of the PS block changes from stretched to nearly fully relaxed (i.e., Gaussian conformation) as amounts of squalane increases. NRF

  12. Structure of aqueous sodium perchlorate solutions.

    PubMed

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

    2008-12-01

    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

  13. Refinement of the solution structure of a branched DNA three-way junction.

    PubMed

    Ouporov, I V; Leontis, N B

    1995-01-01

    We have refined the structure of the DNA Three-Way Junction complex, TWJ-TC, described in the companion paper by quantitative analysis of two 2D NOESY spectra (mixing times 60 and 200 ms) obtained in D2O solution. NOESY crosspeak intensities extracted from these spectra were used in two kinds of refinement procedure: 1) distance-restrained energy minimization (EM) and molecular dynamics (MD) and 2) full relaxation matrix back calculation refinement. The global geometry of the refined model is very similar to that of a published, preliminary model (Leontis, 1993). Two of the helical arms of the junction are stacked. These are Helix 1, defined by basepairs S1-G1/S3-C12 through S1-C5/S3-G8 and Helix 2, which comprises basepairs S1-C6/S2-G5 through S1-G10/S2-G1. The third helical arm (Helix 3), comprised of basepairs S2-C6/S3-G5 through S2-C10/S3-G1 extends almost perpendicularly from the axis defined by Helices 1 and 2. The bases S1-C5 and S1-C6 of Strand 1 are continuously stacked across the junction region. The conformation of this strand is close to that of B-form DNA along its entire length, including the S1-C5 to S1-C6 dinucleotide step at the junction. The two unpaired bases S3-T6 and S3-C7 lie outside of the junction along the minor groove of Helix 1 and largely exposed to solvent. Analysis of the refined structure reveals that the glycosidic bond of S3-T6 exists in the syn conformation, allowing the methyl group of this residue to contact the hydrophobic surface of the minor groove of Helix 1, at S3-G11. The helical parameters of the three helical arms of the structure exhibit only weak deviations from typical values for right-handed B-form DNA. Unusual dihedral angles are only observed for the sugarphosphate backbone joining the "hinge" residues, S2-G5 and S2-C6, and S3-G5 through S3-G8. The glycosidic bond of S3-G8also lies within the syn range, allowing favorable Watson-Crick base-pairing interactions with Si -C5. The stability of this structure was checked

  14. 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.

  15. Acid-induced unfolding and refolding transitions of cytochrome c: a three-state mechanism in H2O and D2O.

    PubMed

    Goto, Y; Hagihara, Y; Hamada, D; Hoshino, M; Nishii, I

    1993-11-01

    Whereas the salt-dependent conformational transition of acid-denatured horse ferricytochrome c at pH 2 is approximated by a two-state mechanism from the acid-unfolded state to the molten globule state [Kataoka, M., Hagihara, Y., Mihara, K., & Goto, Y. (1993) J. Mol. Biol. 229, 591-596], the corresponding transition in D2O has been proposed to involve a noncompact, alpha-helical intermediate state (the pre-molten globule state) [Jeng, M.-F., & Englander, S. W. (1991) J. Mol. Biol. 221, 1045-1061]. To examine the proposed difference in the conformational transitions, we carried out the HCl and DCl titrations of cytochrome c in H2O and D2O, respectively, measured by far-UV circular dichroism, tryptophan fluorescence, and Soret absorption. In both D2O and H2O, unfolding from the native state to the acid-unfolded state and subsequent refolding to the molten globule state were observed. In either solvent, the conformational transitions were well approximated by a minimal three-state mechanism consisting of the native, molten globule, and acid-unfolded states. Thus, our results did not substantiate the presence of a pre-molten globule state in D2O. Acetylation of amino groups of cytochrome c is known to stabilize the molten globule state at pH 2. On the basis of the three-state mechanism, we constructed a conformational phase diagram for the effect of pH and the degree of acetylation. This phase diagram was similar to that of the pH- and salt-dependent conformational transition of cytochrome c, suggesting that the effects of acetylation on the conformational states are similar to those of salt.

  16. HDO and D 2O Low Pressure, Long Path Spectra in the 600-3100 cm -1Region . I. HDO Line Positions and Strengths

    NASA Astrophysics Data System (ADS)

    Toth, Robert A.

    1999-05-01

    High-resolution spectra of gas mixtures of HDO, D2O, and H2O were obtained with a Fourier-transform spectrometer with path lengths up to 433 m. The spectra were analyzed to obtain line positions and strengths of over 6000 transitions of HDO and D2O. For HDO, these included the (000)-(000), (020)-(010), and (100)-(010) bands of HD16O and the (010)-(000) bands of HD16O, HD17O, and HD18O. Several of these assignments are reported for the first time. Of interest was the extended coverage of theA-type transitions of the (010)-(000) band of HD16O. This is the onlyA-type infrared band of any of the water vapor species (HDO, D2O, and H2O) that is not involved in interactions with other bands. By this token, theA-type dipole-moment expansion matrix elements can be tested without involving perturbation theory. The measured linestrengths of the interacting bands, (020)-(010) and (100)-(010), were analyzed using a full perturbation treatment. Strong localized Coriolis interactions affected only a few observed transitions.

  17. 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.

  18. Special quasirandom structures for perovskite solid solutions.

    PubMed

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

    2016-11-30

    Special quasirandom structures (SQS) are presently generated for disordered (A'1-x [Formula: see text] x )BX3 and A(B'1-x [Formula: see text] 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. PMID:27661191

  19. 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.

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

    PubMed

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

    2014-01-28

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

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

    PubMed

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

    2014-01-28

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

  2. 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.

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

    PubMed

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

    2016-05-19

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

  4. Isopentenyl diphosphate isomerase catalyzed reactions in D2O: product release limits the rate of this sluggish enzyme-catalyzed reaction.

    PubMed

    Jonnalagadda, Venkatadurga; Toth, Krisztina; Richard, John P

    2012-04-18

    The E. coli isopentenyl diphosphate isomerase (IDI) catalyzed reaction of isopentenyl diphosphate (IPP) in D(2)O gives a 66% yield of dimethylallyl diphosphate labeled with deuterium at the (E)-methyl group (d-DMAPP) and a 34% yield of IPP labeled with 1 mol of deuterium at C-2 (d-IPP). This shows that the release to D(2)O of the initial product of the IDI-catalyzed reaction (d-DMAPP) is slower than its conversion to d-IPP. Product dissociation is therefore rate determining for isomerization of IPP with a rate constant k(dis) ≈ k(cat) = 0.08 s(-1). The data provide an estimated rate constant of k(as) = 6 × 10(3) M(-1) s(-1) for binding of DMAPP to E. coli IDI that is similar to rate constants determined for the binding of N-protonated 2-amino ethyl diphosphate intermediate analogs to IDI from yeast [Reardon, J. E.; Abeles, R. H. Biochemistry1986, 25, 5609-5616]. We propose that ligand binding to IDI is relatively slow because there is a significant kinetic barrier to reorganization of the initial encounter complex between enzyme, substrate, and an essential Mg(2+) to form the Michaelis complex where the metal cation bridges the protein and the substrate diphosphate group.

  5. 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.

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

    SciTech Connect

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

    2008-01-01

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

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

    PubMed

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

    2014-03-01

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

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

    SciTech Connect

    Rao, L.

    2007-02-01

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

  9. 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.

  10. Isolation of Exosome-Like Vesicles from Plants by Ultracentrifugation on Sucrose/Deuterium Oxide (D2O) Density Cushions.

    PubMed

    Stanly, Christopher; Fiume, Immacolata; Capasso, Giovambattista; Pocsfalvi, Gabriella

    2016-01-01

    Exosomes are nanovesicles of endocytic origin that are about 30-100 nm in diameter, surrounded by a lipid bilayer membrane, and contain proteins, nucleic acids, and other molecules. Mammalian cells- and biological fluids-derived exosomes have become the subject for a wide range of investigations in biological and biomedical sciences. More recently, a new interest is on the verge of rising: the presence of nanovesicles in plants. Lipoprotein vesicles from apoplastic fluid and exosome-like vesicles (ELVs) from fruit juice have been isolated and shown that they could be loaded with drugs and uptaken by recipient cells. In order to explore and analyze the contents and functions of ELVs, they must be isolated and purified with intense care. Isolation of ELVs can be a tedious process and often characterized by the co-purification of undesired contaminants. Here we describe a method which isolates ELVs based on their buoyant density. The method utilizes differential centrifugation in step 1 and 1 and 2 M sucrose/deuterium oxide double-cushion ultracentrifugation in step 2, to purify two diverse ELV subpopulations. In this method fruit juice is used as an example of starting material, although this protocol can be used for the isolation of vesicles from apoplastic fluid too. The quality and the quantity of ELV preparations have been found appropriate for downstream biological and structural studies, like proteomics, transcriptomics, and lipidomics. PMID:27665565

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

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

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

  12. Vibrational normal modes and dynamical stability of DNA triplex poly(dA). 2poly(dT): S-type structure is more stable and in better agreement with observations in solution.

    PubMed Central

    Chen, Y Z; Powell, J W; Prohofsky, E W

    1997-01-01

    A normal-mode and statistical mechanical calculation was carried out to determine the vibrational normal modes, contribution of internal fluctuations to the free energy, and hydrogen bond disruption of DNA triplex poly(dA).2poly(dT). The calculation was performed on both the x-ray fiber diffraction model with a N-type sugar conformation, and a newly proposed model with a S-type sugar conformation. Our calculated normal modes for the S-type structure are in better agreement with observed IR spectra for samples in D2O solution. We also find that the contribution of internal fluctuations to free energy, premelting hydrogen bond disruption probability, and hydrogen bond melting temperatures for the Hoogsteen and Watson-Crick hydrogen bonds all show that the S-type structure is dynamically more stable than the N-type structure in a nominal solution environment. Therefore our calculation supports experimental findings that the triplex d(T)n.d(A)nd(T)n most likely adopts a S-type sugar conformation in solution or at high humidity. Our calculations, however, do not preclude the possibility of an N-type conformation at lower humidities. PMID:9138578

  13. Ions in water: The microscopic structure of concentrated hydroxide solutions

    NASA Astrophysics Data System (ADS)

    Imberti, S.; Botti, A.; Bruni, F.; Cappa, G.; Ricci, M. A.; Soper, A. K.

    2005-05-01

    Neutron-diffraction data on aqueous solutions of hydroxides, at solute concentrations ranging from 1 solute per 12 water molecules to 1 solute per 3 water molecules, are analyzed by means of a Monte Carlo simulation (empirical potential structure refinement), in order to determine the hydration shell of the OH- in the presence of the smaller alkali metal ions. It is demonstrated that the symmetry argument between H+ and OH- cannot be used, at least in the liquid phase at such high concentrations, for determining the hydroxide hydration shell. Water molecules in the hydration shell of K+ orient their dipole moment at about 45° from the K+-water oxygen director, instead of radially as in the case of the Li+ and Na+ hydration shells. The K+-water oxygen radial distribution function shows a shallower first minimum compared to the other cation-water oxygen functions. The influence of the solutes on the water-water radial distribution functions is shown to have an effect on the water structure equivalent to an increase in the pressure of the water, depending on both ion concentration and ionic radius. The changes of the water structure in the presence of charged solutes and the differences among the hydration shells of the different cations are used to present a qualitative explanation of the observed cation mobility.

  14. Ions in water: the microscopic structure of concentrated hydroxide solutions.

    PubMed

    Imberti, S; Botti, A; Bruni, F; Cappa, G; Ricci, M A; Soper, A K

    2005-05-15

    Neutron-diffraction data on aqueous solutions of hydroxides, at solute concentrations ranging from 1 solute per 12 water molecules to 1 solute per 3 water molecules, are analyzed by means of a Monte Carlo simulation (empirical potential structure refinement), in order to determine the hydration shell of the OH- in the presence of the smaller alkali metal ions. It is demonstrated that the symmetry argument between H+ and OH- cannot be used, at least in the liquid phase at such high concentrations, for determining the hydroxide hydration shell. Water molecules in the hydration shell of K+ orient their dipole moment at about 45 degrees from the K+-water oxygen director, instead of radially as in the case of the Li+ and Na+ hydration shells. The K+-water oxygen radial distribution function shows a shallower first minimum compared to the other cation-water oxygen functions. The influence of the solutes on the water-water radial distribution functions is shown to have an effect on the water structure equivalent to an increase in the pressure of the water, depending on both ion concentration and ionic radius. The changes of the water structure in the presence of charged solutes and the differences among the hydration shells of the different cations are used to present a qualitative explanation of the observed cation mobility.

  15. Structural cluster analysis of chemical reactions in solution

    NASA Astrophysics Data System (ADS)

    Gallet, Grégoire A.; Pietrucci, Fabio

    2013-08-01

    We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.

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

    NASA Astrophysics Data System (ADS)

    Guo, Baofeng; Zou, Zongyuan; Jin, Miao

    2016-04-01

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

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

    SciTech Connect

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

    2010-06-17

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

  18. 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.

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

    PubMed

    Beltz, Adriene M; Molenaar, Peter C M

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed

    Zasetsky, Alexander Y; Gaiduk, Vladimir I

    2007-06-28

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

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

    NASA Astrophysics Data System (ADS)

    van Harrevelt, Rob; van Hemert, Marc C.

    2000-04-01

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

  4. Solution structure of At3g28950 from Arabidopsis thaliana

    PubMed Central

    de la Cruz, Norberto B.; Peterson, Francis C.; Volkman, Brian F.

    2009-01-01

    We determined the solution structure of At3g28950 from A. thaliana, a homolog of At5g39720, whose structure we solved earlier. The secondary structure of the 165-aa protein consists of a 5-strand anti-parallel β-barrel domain flanked by two α-helices and a 2-strand β-sheet; an additional free C-terminal α-helix extends into solution. Bioinformatic searches and analyses suggest that members of this growing set of structurally related proteins have been recruited to serve a wide variety of functions ranging from γ-glutamyl cyclotransferase activity, to participation in plant responses to chemical and biotic stimuli. Expression of a human homolog is elevated in bladder cancer tissues. Expression patterns for At3g28950 and its Arabidopsis paralogs suggest that each one evolved different a physiological role. The At3g28950 structure was solved as part of a structural genomics effort, and the results demonstrate how such a project can further understanding of genome evolution in addition to sequence-structure and structure-function relationships. PMID:18214976

  5. Extended structure of rat islet amyloid polypeptide in solution.

    PubMed

    Wei, Lei; Jiang, Ping; Manimekalai, Malathy Sony Subramanian; Hunke, Cornelia; Grüber, Gerhard; Pervushin, Konstantin; Mu, Yuguang

    2015-01-01

    The process of islet amyloid polypeptide (IAPP) formation and the prefibrillar oligomers are supposed to be one of the pathogenic agents causing pancreatic β-cell dysfunction. The human IAPP (hIAPP) aggregates easily and therefore, it is difficult to characterize its structural features by standard biophysical tools. The rat version of IAPP (rIAPP) that differs by six amino acids when compared with hIAPP, is not prone to aggregation and does not form amyloid fibrils. Similar to hIAPP it also demonstrates random-coiled nature in solution. The structural propensity of rIAPP has been studied as a hIAPP mimic in recent works. However, the overall shape of it in solution still remains elusive. Using small angle X-ray scattering (SAXS) measurements combined with nuclear magnetic resonance (NMR) and molecular dynamics simulations (MD) the solution structure of rIAPP was studied. An unambiguously extended structural model with a radius of gyration of 1.83 nm was determined from SAXS data. Consistent with previous studies, an overall random-coiled feature with residual helical propensity in the N-terminus was confirmed. Combined efforts are necessary to unambiguously resolve the structural features of intrinsic disordered proteins.

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

    PubMed Central

    Chaudhuri, Barnali N

    2015-01-01

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

  7. Structure of graphene oxide membranes in solvents and solutions

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  8. 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.

  9. Structure of graphene oxide membranes in solvents and solutions.

    PubMed

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

    2015-10-01

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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Understanding the defect structure of solution grown zinc oxide

    SciTech Connect

    Liew, Laura-Lynn; Sankar, Gopinathan; Handoko, Albertus D.; Goh, Gregory K.L.; Kohara, Shinji

    2012-05-15

    Zinc oxide (ZnO) is a wide bandgap semiconducting oxide with many potential applications in various optoelectronic devices such as light emitting diodes (LEDs) and field effect transistors (FETs). Much effort has been made to understand the ZnO structure and its defects. However, one major issue in determining whether it is Zn or O deficiency that provides ZnO its unique properties remains. X-ray absorption spectroscopy (XAS) is an ideal, atom specific characterization technique that is able to probe defect structure in many materials, including ZnO. In this paper, comparative studies of bulk and aqueous solution grown ({<=}90 Degree-Sign C) ZnO powders using XAS and x-ray pair distribution function (XPDF) techniques are described. The XAS Zn-Zn correlation and XPDF results undoubtedly point out that the solution grown ZnO contains Zn deficiency, rather than the O deficiency that were commonly reported. This understanding of ZnO short range order and structure will be invaluable for further development of solid state lighting and other optoelectronic device applications. - Graphical abstract: Highlights: Black-Right-Pointing-Pointer ZnO powders have been synthesized through an aqueous solution method. Black-Right-Pointing-Pointer Defect structure studied using XAS and XPDF. Black-Right-Pointing-Pointer Zn-Zn correlations are less in the ZnO powders synthesized in solution than bulk. Black-Right-Pointing-Pointer Zn vacancies are present in the powders synthesized. Black-Right-Pointing-Pointer EXAFS and XPDF, when used complementary, are useful characterization techniques.

  16. Solution structure of the Legionella pneumophila Mip-rapamycin complex

    PubMed Central

    Ceymann, Andreas; Horstmann, Martin; Ehses, Philipp; Schweimer, Kristian; Paschke, Anne-Katrin; Steinert, Michael; Faber, Cornelius

    2008-01-01

    Background Legionella pneumphila is the causative agent of Legionnaires' disease. A major virulence factor of the pathogen is the homodimeric surface protein Mip. It shows peptidyl-prolyl cis/trans isomerase activty and is a receptor of FK506 and rapamycin, which both inhibit its enzymatic function. Insight into the binding process may be used for the design of novel Mip inhibitors as potential drugs against Legionnaires' disease. Results We have solved the solution structure of free Mip77–213 and the Mip77–213-rapamycin complex by NMR spectroscopy. Mip77–213 showed the typical FKBP-fold and only minor rearrangements upon binding of rapamycin. Apart from the configuration of a flexible hairpin loop, which is partly stabilized upon binding, the solution structure confirms the crystal structure. Comparisons to the structures of free FKBP12 and the FKBP12-rapamycin complex suggested an identical binding mode for both proteins. Conclusion The structural similarity of the Mip-rapamycin and FKBP12-rapamycin complexes suggests that FKBP12 ligands may be promising starting points for the design of novel Mip inhibitors. The search for a novel drug against Legionnaires' disease may therefore benefit from the large variety of known FKBP12 inhibitors. PMID:18366641

  17. Solution structure of the HIV gp120 C5 domain.

    PubMed

    Guilhaudis, Laure; Jacobs, Amy; Caffrey, Michael

    2002-10-01

    In HIV the viral envelope protein is processed by a host cell protease to form gp120 and gp41. The C1 and C5 domains of gp120 are thought to directly interact with gp41 but are largely missing from the available X-ray structure. Biophysical studies of the HIV gp120 C5 domain (residues 489-511 of HIV-1 strain HXB2), which corresponds to the carboxy terminal region of gp120, have been undertaken. CD studies of the C5 domain suggest that it is unstructured in aqueous solutions but partially helical in trifluoroethanol/aqueous and hexafluoroisopropanol/aqueous buffers. The solution structure of the C5 peptide in 40% trifluoroethanol/aqueous buffer was determined by NMR spectroscopy. The resulting structure is a turn helix structural motif, consistent with the CD results. Fluorescence titration experiments suggest that HIV C5 forms a 1 : 1 complex with the HIV gp41 ectodomain in the presence of cosolvent with an apparent Kd of approximately 1.0 micro m. The absence of complex formation in the absence of cosolvent indicates that formation of the turn-helix structural motif of C5 is necessary for complex formation. Examination of the C5 structure provides insight into the interaction between gp120 and gp41 and provides a possible target site for future drug therapies designed to disrupt the gp120/gp41 complex. In addition, the C5 structure lends insight into the site of HIV envelope protein maturation by the host enzymes furin and PC7, which provides other possible targets for drug therapies.

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

    SciTech Connect

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

    2010-12-01

    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.

  19. Proton trapping and defect energetics in ice from FT-IR monitoring of photoinduced isotopic exchange of isolated D2O

    NASA Astrophysics Data System (ADS)

    Wooldridge, Paul J.; Devlin, J. Paul

    1988-03-01

    The photoexcitation of 2-naphthol as a trace impurity in ice results in the injection of excess protons into the ice network. These protons are immobile at temperatures <100 K but warming to ˜120 K generates a near steady-state concentration of mobile protons which decays slowly. This behavior confirms the existence of shallow proton traps in ice which, following Kunst and Warman, are presumed to be intrinsic and, most probably, Bjerrum L defects. The quantity of mobile protons at a given temperature, in a pseudoequilibrium with immobile protons bound to the L defects, is controlled by the temperature coefficients of (a) the pseudoequilibrium constant and (b) the L-defect concentration. Since both the L and D defects are immobile below ˜130 K, the L-defect concentration can be taken to be temperature independent. Consequently, the temperature dependence of the rate at which D2O molecules isolated in H2O cubic ice are converted to (HOD)2 units by mobile protons is a direct measure of the binding energy between the excess protons and the L defects. This binding energy has been estimated at 10.0 kcal/mol. At the completion of each kinetic experiment at T<126 K, the predominant deuterated species is (HOD)2. Such samples are ideal for observation of the ice L-defect activity which is thermally activated by warming to above 130 K. By following the rate of conversion of (HOD)2 to isolated HOD for the range 134 to 150 K, the activation energy for the L-defect formation and mobility has been determined to be 12.2 kcal for cubic ice. This is close to the value of 12.0 kcal previously determined for cubic ice from isotopic exchange rates, but is less than the accepted value for hexagonal ice of 13.1 kcal/mol. Further, the enthalpy change for ice self-ionization has been estimated as 16.8 kcal from a combination of the activation energies for proton transport (9.5 kcal) and L-defect formation (7.8 kcal) with the L-defect-proton binding energy of 10.0 kcal.

  20. Solution structure of murine macrophage inflammatory protein-2.

    PubMed

    Shao, W; Jerva, L F; West, J; Lolis, E; Schweitzer, B I

    1998-06-01

    The solution structure of murine macrophage inflammatory protein-2 (MIP-2), a heparin-binding chemokine that is secreted in response to inflammatory stimuli, has been determined using two-dimensional homonuclear and heteronuclear NMR spectroscopy. Structure calculations were carried out by means of torsion-angle molecular dynamics using the program X-PLOR. The structure is based on a total of 2390 experimental restraints, comprising 2246 NOE-derived distance restraints, 44 distance restraints for 22 hydrogen bonds, and 100 torsion angle restraints. The structure is well-defined, with the backbone (N, Calpha, C) and heavy atom atomic rms distribution about the mean coordinates for residues 9-69 of the dimer being 0.57 +/- 0.16 A and 0.96 +/- 0.12 A, respectively. The N- and C-terminal residues (1-8 and 70-73, respectively) are disordered. The overall structure of the MIP-2 dimer is similar to that reported previously for the NMR structures of MGSA and IL-8 and consists of a six-stranded antiparallel beta-sheet (residue 25-29, 39-44, and 48-52) packed against two C-terminal antiparallel alpha-helices. A best fit superposition of the NMR structure of MIP-2 on the structures of MGSA, NAP-2, and the NMR and X-ray structures of IL-8 are 1.11, 1.02, 1.27, and 1.19 A, respectively, for the monomers, and 1.28, 1.10, 1.55, and 1.36 A, respectively, for the dimers (IL-8 residues 7-14 and 16-67, NAP-2 residues 25-84). At the tertiary level, the main differences between the MIP-2 solution structure and the IL-8, MGSA, and NAP-2 structures involve the N-terminal loop between residues 9-23 and the loops formed by residues 30-38 and residues 53-58. At the quaternary level, the difference between MIP-2 and IL-8, MGSA, or NAP-2 results from differing interhelical angles and separations.

  1. Solution structure of murine macrophage inflammatory protein-2.

    PubMed

    Shao, W; Jerva, L F; West, J; Lolis, E; Schweitzer, B I

    1998-06-01

    The solution structure of murine macrophage inflammatory protein-2 (MIP-2), a heparin-binding chemokine that is secreted in response to inflammatory stimuli, has been determined using two-dimensional homonuclear and heteronuclear NMR spectroscopy. Structure calculations were carried out by means of torsion-angle molecular dynamics using the program X-PLOR. The structure is based on a total of 2390 experimental restraints, comprising 2246 NOE-derived distance restraints, 44 distance restraints for 22 hydrogen bonds, and 100 torsion angle restraints. The structure is well-defined, with the backbone (N, Calpha, C) and heavy atom atomic rms distribution about the mean coordinates for residues 9-69 of the dimer being 0.57 +/- 0.16 A and 0.96 +/- 0.12 A, respectively. The N- and C-terminal residues (1-8 and 70-73, respectively) are disordered. The overall structure of the MIP-2 dimer is similar to that reported previously for the NMR structures of MGSA and IL-8 and consists of a six-stranded antiparallel beta-sheet (residue 25-29, 39-44, and 48-52) packed against two C-terminal antiparallel alpha-helices. A best fit superposition of the NMR structure of MIP-2 on the structures of MGSA, NAP-2, and the NMR and X-ray structures of IL-8 are 1.11, 1.02, 1.27, and 1.19 A, respectively, for the monomers, and 1.28, 1.10, 1.55, and 1.36 A, respectively, for the dimers (IL-8 residues 7-14 and 16-67, NAP-2 residues 25-84). At the tertiary level, the main differences between the MIP-2 solution structure and the IL-8, MGSA, and NAP-2 structures involve the N-terminal loop between residues 9-23 and the loops formed by residues 30-38 and residues 53-58. At the quaternary level, the difference between MIP-2 and IL-8, MGSA, or NAP-2 results from differing interhelical angles and separations. PMID:9622482

  2. Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes.

    PubMed Central

    Ashbaugh, H S; Garde, S; Hummer, G; Kaler, E W; Paulaitis, M E

    1999-01-01

    Conformational free energies of butane, pentane, and hexane in water are calculated from molecular simulations with explicit waters and from a simple molecular theory in which the local hydration structure is estimated based on a proximity approximation. This proximity approximation uses only the two nearest carbon atoms on the alkane to predict the local water density at a given point in space. Conformational free energies of hydration are subsequently calculated using a free energy perturbation method. Quantitative agreement is found between the free energies obtained from simulations and theory. Moreover, free energy calculations using this proximity approximation are approximately four orders of magnitude faster than those based on explicit water simulations. Our results demonstrate the accuracy and utility of the proximity approximation for predicting water structure as the basis for a quantitative description of n-alkane conformational equilibria in water. In addition, the proximity approximation provides a molecular foundation for extending predictions of water structure and hydration thermodynamic properties of simple hydrophobic solutes to larger clusters or assemblies of hydrophobic solutes. PMID:10423414

  3. Spatial structures in microtubular solutions requiring a sustained energy source

    NASA Astrophysics Data System (ADS)

    Tabony, J.; Job, D.

    1990-08-01

    MICROTUBULES are believed to be the principal organizers of the cell interior1. Cells respond to a variety of stimuli by modifying the spatial distribution of the microtubules. These effects are central to cell division and morphogenesis2, and embryo development3. During embryo development, macroscopic patterns are frequently observed3. Here we report that microtubular solutions spontaneously form alternating white and dark stripes about 1 mm wide and 1 cm long. Small-angle neutron scattering measurements show that in each segment the microtubules are aligned obliquely to the direction of the stripe, and that the white and dark stripes differ in having mutually orthogonal orientations. The formation of these structures requires an initial reservoir of organic phosphate. Phosphorus NMR measurements show that the process is accompanied by the energy-liberating conversion of organic to inorganic phosphate. These observations, together with similarities to the dissipative spatial structure formed by the Belousov-Zhabotinski reaction4-6, provide strong evidence that the observed structures are energy-dissipative in nature. Dissipative structures are thought to be critical to the appearence of complex living organisms7,8. Our results strongly suggest that microtubules are capable of forming such structures. Microtubular dissipative structures may occur during mitosis and embryo morphogenesis.

  4. The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

    PubMed

    Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

    2008-01-28

    To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

  5. 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.

  6. 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

  7. Solution structure of the human signaling protein RACK1

    PubMed Central

    2010-01-01

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

  8. New solution method for steady-state canopy structural loads

    SciTech Connect

    Sundberg, W.D.

    1986-08-01

    A new computer code has been written to perform structural analysis canopies. Although an existing code, CANO, has been available, the new code has better convergence reliability, is more understandably written, and is easier to use. The equations have been reformulated for the new solution method. The new code assumes a symmetric canopy, a steady-state condition, and no strength in the vertical direction. It computes the inflated shape, loads in the horizontal members, radial members, vent lines, and suspension lines, and total drag. Constructed geometry, material properties, dynamic pressure, and pressure distribution are required as input.

  9. 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.

  10. 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.

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

    PubMed

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

    2012-07-23

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

  12. 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

    2010-02-01

    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.

  13. Structure of polymer layers adsorbed from concentrated solutions

    NASA Astrophysics Data System (ADS)

    Auvray, Loïc; Auroy, Philippe; Cruz, Margarida

    1992-06-01

    We study by neutron scattering the interfacial strucuture of poly(dimethylsiloxane) layers irreversibly adsorbed from concentrated solutions or melts. We first measure the thickness h of the layers swollen by a good solvent as a function of the chain polymerisation index N and of the polymer volume fraction in the initial solution Φ. The relation h ≈ N^{0.8}Φ^{0.3}, recently predicted from an analogy between irreversibly adsorbed layers and grafted polymer brushes, describes well our results. We can therefore deduce that there is at least one large loop of about N monomers per adsorbed chain. We also study the shape of the polymer concentration profile in the layers by measuring on two samples the polymer-solid partial structure factor, that is proportional to the Fourier transform of the profile. The model of pseudobrushes predicts a concentration decay varying with the distance of the wall z as z^{-2/5}. This power law profile accounts quantitatively for the angular variation of the polymer-solid cross structure factor but it is difficult to distinguish it without anbiguity from less singular profiles. It implies that the adsorption of PDMS onto silica is sufficiently strong and fast to quench completely the loop distribution in the initial layer. Nous étudions par diffusion de neutrons la structure interfaciale de couches de poly(diméthylsiloxane) irréversiblement adsorbées sur de la silice à partir de solutions semidiluées et de fondus. Nous mesurons d'abord l'épaisseur h des couches gonflées par un bon solvant en fonction du degré de polymérisation des chaînes N et de la fraction volumique dans la solution initiale Φ. La relation h≈ N^{0.8}Φ^{0.3} récemment prédite à partir de l'analogie entre couches irréversiblement adsorbées et brosses de polymères greffés décrit bien nos résultats. Nous en déduisons qu'il existe au moins une grande boucle d'environ N monomères par chaîne adsorbée. Nous étudions aussi la forme du profil de

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

    PubMed

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

    2001-03-01

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

  15. Quaternary structure of carbonmonoxyhemoglobins in solution: structural changes induced by the allosteric effector inositol hexaphosphate.

    PubMed

    Gong, Qingguo; Simplaceanu, Virgil; Lukin, Jonathan A; Giovannelli, Janel L; Ho, Nancy T; Ho, Chien

    2006-04-25

    We have applied the residual dipolar coupling (RDC) method to investigate the solution quaternary structures of (2)H- and (15)N-labeled human normal adult recombinant hemoglobin (rHb A) and a low-oxygen-affinity mutant recombinant hemoglobin, rHb(alpha96Val-->Trp), both in the carbonmonoxy form, in the absence and presence of an allosteric effector, inositol hexaphosphate (IHP), using a stretched polyacrylamide gel as the alignment medium. Our recent RDC results [Lukin, J. A., Kontaxis, G., Simplaceanu, V., Yuan, Y., Bax, A., and Ho, C. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 517-520] indicate that the quaternary structure of HbCO A in solution is a dynamic ensemble between two previously determined crystal structures, R (crystals grown under high-salt conditions) and R2 (crystals grown under low-salt conditions). On the basis of a comparison of the geometric coordinates of the T, R, and R2 structures, it has been suggested that the oxygenation of Hb A follows the transition pathway from T to R and then to R2, with R being the intermediate structure [Srinivasan, R., and Rose, G. D. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 11113-11117]. The results presented here suggest that IHP can shift the solution quaternary structure of HbCO A slightly toward the R structure. The solution quaternary structure of rHbCO(alpha96Val-->Trp) in the absence of IHP is similar to that of HbCO A in the presence of IHP, consistent with rHbCO(alpha96Val-->Trp) having an affinity for oxygen lower than that of Hb A. Moreover, IHP has a much stronger effect in shifting the solution quaternary structure of rHbCO(alpha96Val-->Trp) toward the R structure and toward the T structure, consistent with IHP causing a more pronounced decrease in its oxygen affinity. The results presented in this work, as well as other results recently reported in the literature, clearly indicate that there are multiple quaternary structures for the ligated form of hemoglobin. These results also provide new insights

  16. 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.

  17. 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.

  18. The solution structure of the copper clioquinol complex.

    PubMed

    Pushie, M Jake; Nienaber, Kurt H; Summers, Kelly L; Cotelesage, Julien J H; Ponomarenko, Olena; Nichol, Helen K; Pickering, Ingrid J; George, Graham N

    2014-04-01

    Clioquinol (5-chloro-7-iodo-8-hydroxyquinoline) recently has shown promising results in the treatment of Alzheimer's disease and in cancer therapy, both of which also are thought to be due to clioquinol's ability as a lipophilic copper chelator. Previously, clioquinol was used as an anti-fungal and anti-protozoal drug that was responsible for an epidemic of subacute myelo-optic neuropathy (SMON) in Japan during the 1960s, probably a myeloneuropathy arising from a clioquinol-induced copper deficiency. Previous X-ray absorption spectroscopy of solutions of copper chelates of clioquinol suggested unusual coordination chemistry. Here we use a combination of electron paramagnetic, UV-visible and X-ray absorption spectroscopies to provide clarification of the chelation chemistry between clioquinol and copper. We find that the solution structures for the copper complexes formed with stoichiometric and excess clioquinol are conventional 8-hydroxyquinolate chelates. Thus, the promise of clioquinol in new treatments for Alzheimer's disease and in cancer therapy is not likely to be due to any novel chelation chemistry, but rather due to other factors including the high lipophilicity of the free ligand and chelate complexes.

  19. 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.

  20. 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.

  1. Analytical solution of thermal magnetization on memory stabilizer structures

    NASA Astrophysics Data System (ADS)

    Tomita, Yu; Viteri, C. Ricardo; Brown, Kenneth R.

    2010-10-01

    We return to the question of how the choice of stabilizer generators affects the preservation of information on structures whose degenerate ground state encodes a classical redundancy code. Controlled-not gates are used to transform the stabilizer Hamiltonian into a Hamiltonian consisting of uncoupled single spins and/or pairs of spins. This transformation allows us to obtain an analytical partition function and derive closed-form equations for the relative magnetization and susceptibility. These equations are in agreement with the numerical results presented in Viteri [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.042313 80, 042313 (2009)] for finite size systems. Analytical solutions show that there is no finite critical temperature, Tc=0, for all of the memory structures in the thermodynamic limit. This is in contrast to the previously predicted finite critical temperatures based on extrapolation. The mismatch is a result of the infinite system being a poor approximation even for astronomically large finite-size systems, where spontaneous magnetization still arises below an apparent finite critical temperature. We extend our analysis to the canonical stabilizer Hamiltonian. Interestingly, Hamiltonians with two-body interactions have a higher apparent critical temperature than the many-body Hamiltonian.

  2. The NMR solution structure of recombinant RGD-hirudin

    SciTech Connect

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

    2007-08-17

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

  3. Analytical solution of thermal magnetization on memory stabilizer structures

    SciTech Connect

    Tomita, Yu; Viteri, C. Ricardo; Brown, Kenneth R.

    2010-10-15

    We return to the question of how the choice of stabilizer generators affects the preservation of information on structures whose degenerate ground state encodes a classical redundancy code. Controlled-not gates are used to transform the stabilizer Hamiltonian into a Hamiltonian consisting of uncoupled single spins and/or pairs of spins. This transformation allows us to obtain an analytical partition function and derive closed-form equations for the relative magnetization and susceptibility. These equations are in agreement with the numerical results presented in Viteri et al. [Phys. Rev. A 80, 042313 (2009)] for finite size systems. Analytical solutions show that there is no finite critical temperature, T{sub c}=0, for all of the memory structures in the thermodynamic limit. This is in contrast to the previously predicted finite critical temperatures based on extrapolation. The mismatch is a result of the infinite system being a poor approximation even for astronomically large finite-size systems, where spontaneous magnetization still arises below an apparent finite critical temperature. We extend our analysis to the canonical stabilizer Hamiltonian. Interestingly, Hamiltonians with two-body interactions have a higher apparent critical temperature than the many-body Hamiltonian.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  6. 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.

  7. 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.

  8. Computational tools for analysing structural changes in proteins in solution.

    PubMed

    Noé, Frank; Schwarzl, Sonja M; Fischer, Stefan; Smith, Jeremy C

    2003-01-01

    Many important structural changes in proteins involve long-time dynamics, which are outside the timescale presently accessible by a straightforward integration of Newton's equations of motion. This problem is addressed with minimisation-based algorithms, which are applied on possible reaction pathways using atomic-detail models. For reasons of efficiency, an implicit treatment of solvent is imperative. We present the charge reparameterisation protocol, which is a method that approximates the interaction energies obtained by a numerical solution of the Poisson-Boltzmann equation. Furthermore, we present a number of methods that can be used to compute possible reaction pathways associated with a particular conformational change. Two of them, the self-penalty walk and the nudged elastic band method, define an objective function, which is minimised to find optimal paths. A third method, conjugate peak refinement, is a heuristic method, which finds minimum energy paths without the use of an explicit objective function. Finally, we discuss problems and limitations with these methods and give a perspective on future research.

  9. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

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

  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. 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

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

    PubMed

    Yang, Rui; Gudipati, Murthy S

    2014-03-14

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

  13. 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.

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

    PubMed

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

    2016-05-27

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

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

    PubMed Central

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

    1999-01-01

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

  16. 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

  17. 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

  18. Variation of persistence length with concentration in a hydrogen bonding polymer solution

    NASA Astrophysics Data System (ADS)

    Sukumaran, S.; Beaucage, G.

    2000-03-01

    Miscibility of some polymers in water is usually attributed to the ability of the polymer to hydrogen bond with water. Hydrogen bonding contributes a strong interaction component to the free energy that enhances mixing between the polymer and water. It is widely known that certain conformations of the polymer have significantly higher dipole moment and consequently higher affinity for water. If the solvent alters the bond rotation energetics of the polymer it is natural to expect the average local structure of the chain to be affected leading to a change in the persistence length. Small angle neutron scattering experiments were performed on aqueous (D2O) solutions of a polymer (PEO or PVME) at different concentrations to investigate the microscopic structure of these solutions. The persistence length was strongly dependent on concentration. A simple physical explanation for this phenomenon will be provided. Possible ramifications of such a phenomenon in understanding phase behavior will be indicated.

  19. The structure of ionic aqueous solutions at interfaces: an intrinsic structure analysis.

    PubMed

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

    2012-09-21

    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 k(B)T (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. PMID:22998280

  20. 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

  1. 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.

  2. Analytical solitary wave solutions of the nonlinear Kronig-Penney model in photonic structures.

    PubMed

    Kominis, Y

    2006-06-01

    A phase space method is employed for the construction of analytical solitary wave solutions of the nonlinear Kronig-Penney model in a photonic structure. This class of solutions is obtained under quite generic conditions, while the method is applicable to a large variety of systems. The location of the solutions on the spectral band gap structure as well as on the low dimensional space of system's conserved quantities is studied, and robust solitary wave propagation is shown.

  3. Controlling molecular ordering in solution-state conjugated polymers

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  4. 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.

  5. 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.

  6. Integrated Force Method Solution to Indeterminate Structural Mechanics Problems

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

  7. 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.

  8. NMR solution structure of the neurotrypsin Kringle domain.

    PubMed

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

    2008-11-25

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

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

    NASA Astrophysics Data System (ADS)

    Graver, Thomas; Inaudi, Daniele; Doornink, Justin

    2004-12-01

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

  10. Structure and symmetry of crystalline solid solutions: general revision

    SciTech Connect

    Vaida, M.; Shimon, L.J.W.; Weisinger-Lewin, Y.; Frolow, F.; Lahav, M.; Leiserowitz, L.; McMullan, R.K.

    1988-09-16

    Mixed single crystals composed of host and guest organic molecules of similar structure and shapes are shown to comprise sectors with different host-guest distributions and to have symmetries lower than that of the host crystal. These properties are determined by the structure of the guest and the surface structures of the crystal faces through which the guest molecules are occluded. This general concept is illustrated by studies of three mixed crystal systems, (E)-cinnamamide-(E)-2-thienylacrylamide, (E)-cinnamamide-(E)-3-thienylacrylamide, and (S)-asparagine-(S)-aspartic acid, with x-ray and neutron diffraction and solid-state photochemistry. 19 references, 4 figures, 2 tables.

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

    PubMed Central

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

    2010-01-01

    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 Cα 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 Å, 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. PMID:19927325

  12. Solution structures of europium(III) complexes of ethylenediaminetetraacetic acid

    SciTech Connect

    Latva, M.; Kankara, J.; Haapakka, K.

    1996-04-01

    Coordination of ethylenediaminetetraacetic acid (EDTA) with europium(III) has been studied at different concentrations in solution using {sup 7}F{sub 0}{yields}{sup 5}D{sub 0} excitation spectroscopy and excited-state lifetime measurements. EDTA forms with Eu(III) ion three different species in equimolar solutions at room temperature. At low pH values EuEDTAH is formed and at higher pH values than 1.5 two EuEDTA{sup -} complexes, which differ from each other with one water molecule in the first coordination sphere of the Eu(III) ion, total coordination number and coordination geometry, are also formed. When the concentration of EDTA is higher than the concentration of Eu(III), an EuEDTA(EDTAH){sup 4-} species where the second EDTA is weakly coordinated to EuEDTA{sup -}, is formed. If the concentration of Eu(III) ion is higher than EDTA, the extra Eu(III) ions associate with EuEDTA{sup -} and link to one of the carboxylate groups of EDTA thus causing a shortening of the excited-state lifetime of the EuEDTA{sup -} complex.

  13. 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.

  14. 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…

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

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  16. Effect of water structure on adsorption of thermosensitive polymer hydrogel in salt solutions

    SciTech Connect

    Nakano, Yoshio; Seida, Yoshimi

    1996-12-31

    Effects of temperature and additive salt on an adsorption property of thermosensitive polymer hydrogel were studied in terms of (1) phase transition temperature of the gel, (2) hydration structure of network of the gel in the various salt solutions, and (3) structure of water in the solutions. The adsorption properties of the gel were correlated fairly well with the phase transition temperature of the gel and the structure of water both on the network of the gel and in the bulk solution. 2 refs., 5 figs.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-03-01

    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.

  19. EDM-DEDM and protein crystal structure solution.

    PubMed

    Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Mazzone, Anna Maria; Siliqi, Dritan

    2009-05-01

    Electron-density modification (EDM) procedures are the classical tool for driving model phases closer to those of the target structure. They are often combined with automated model-building programs to provide a correct protein model. The task is not always performed, mostly because of the large initial phase error. A recently proposed procedure combined EDM with DEDM (difference electron-density modification); the method was applied to the refinement of phases obtained by molecular replacement, ab initio or SAD phasing [Caliandro, Carrozzini, Cascarano, Giacovazzo, Mazzone & Siliqi (2009), Acta Cryst. D65, 249-256] and was more effective in improving phases than EDM alone. In this paper, a novel fully automated protocol for protein structure refinement based on the iterative application of automated model-building programs combined with the additional power derived from the EDM-DEDM algorithm is presented. The cyclic procedure was successfully tested on challenging cases for which all other approaches had failed.

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

    PubMed

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

    2011-01-01

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

  1. 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)

  2. The solution structure of an anti-CRISPR protein

    PubMed Central

    Maxwell, Karen L.; Garcia, Bianca; Bondy-Denomy, Joseph; Bona, Diane; Hidalgo-Reyes, Yurima; Davidson, Alan R.

    2016-01-01

    Bacterial CRISPR–Cas adaptive immune systems use small guide RNAs to protect against phage infection and invasion by foreign genetic elements. We previously demonstrated that a group of Pseudomonas aeruginosa phages encode anti-CRISPR proteins that inactivate the type I-F and I-E CRISPR–Cas systems using distinct mechanisms. Here, we present the three-dimensional structure of an anti-CRISPR protein and map a functional surface that is critical for its potent inhibitory activity. The interaction of the anti-CRISPR protein with the CRISPR–Cas complex through this functional surface is proposed to prevent the binding of target DNA. PMID:27725669

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

    DOE PAGES

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

    2014-08-14

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

  4. 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.

  5. Structural Order of Water Molecules around Hydrophobic Solutes: Length-Scale Dependence and Solute-Solvent Coupling.

    PubMed

    Hande, Vrushali R; Chakrabarty, Suman

    2015-08-27

    It has been suggested that the structure and thermodynamics of the water molecules in the hydration layer of simple hydrophobic solutes undergo an order-disorder transition around a nanometer length-scale of the solute size. Using extensive atomistic molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulation studies, we have probed this order-disorder transition around model hydrophobic solutes of varying size and shape (spherical, planar, and linear), as well as flexible hydrophobic homopolymer chains (n-alkanes), where the conformational fluctuations are likely to create both spatial and temporal heterogeneity on the solvent accessible surface. We have explored the structural response of the water molecules in the hydration shell due to the local variations of the length-scale (or curvature) upon hydrophobic collapse and/or local conformational changes of these polymers. We have shown that the tetrahedral order of the water molecules in the hydration shell is practically independent of the polymer size in the extended state of the polymer due to the availability of a subnanometer cross-sectional length-scale, allowing the water molecules to form hydrogen bonds around the polymer chain. Beyond a certain length of the polymer chains, the collapsed states (associated with larger solute length-scale) start to induce disorder in the surface water molecules. We demonstrate that the local structure (both local number density and tetrahedral order) of the hydration layer is dynamically coupled to the local topology of the polymer. Thus, we envisage that in a flexible (bio)polymer, the hydration shell properties will be sensitive to the local conformational state of the molecule (both spatially and temporally), and the overall observed water structure and dynamics will be dependent on the topological/chemical heterogeneity, and the time-scale of fluctuations in the local curvature (length-scale) of the solvent accessible surface. Moreover, we have

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  7. 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.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Enright, W. H.

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  12. 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.

  13. 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.

  14. The density, viscosity and structural properties of aqueous ethambutol hydrochloride solutions

    NASA Astrophysics Data System (ADS)

    Deosarkar, S. D.; Puyad, A. L.; Kalyankar, T. M.

    2012-05-01

    Ethambutol (EMB) is a bacteriostatic antimycobacterial drug prescribed to treat tuberculosis. It is bacteriostatic against actively growing TB bacilli. The density and viscosity of aqueous ethambutol hydrochloride solutions have been studied at 298.15, 301.15 and 304.15 K and at different concentrations (0.255, 0.168, 0.128, 0.087, 0.041, and 0.023 mol dm-3). The apparent molar volume of these solutions for different temperatures and concentrations was calculated from the density data. The relative viscosities of drug solutions have been analysed by Jones-Dole equation. The limiting apparent molar volumes have been evaluated for different temperatures. The different properties have been used to study structural properties, structure formation and breaking properties of drug and solute-solvent interactions in solutions.

  15. 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.

  16. 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.

  17. Method for minimization of solution costs for transient dynamic analysis of nonlinear periodic structures

    SciTech Connect

    Van Kirk, J.S.; Bogard, W.T.; Wood, L.R.

    1982-01-01

    Techniques are described for the transient dynamic analysis of nonlinear periodic structures subjected to time history excitations. These techniques consider the special characteristics of periodic structures in conjunction with the psuedo-force approach in numerical integration to reduce computerized solution costs. A special purpose computer code, based on these techniques, is applied to a specific nonlinear periodic structure: the response of a pressurized water reactor core to a postulated main coolant pipe rupture. Comparisons with a general purpose finite element code, using consistent integration methods, demonstrate the savings in solution cost.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  19. 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.

  20. Nanoparticle imaging. 3D structure of individual nanocrystals in solution by electron microscopy.

    PubMed

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

    2015-07-17

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale. PMID:26185247

  1. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed

    Smulsky, Joseph J

    2015-01-01

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

  3. 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.

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

    PubMed Central

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

    2000-01-01

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

  6. A refined solution structure of hen lysozyme determined using residual dipolar coupling data.

    PubMed

    Schwalbe, H; Grimshaw, S B; Spencer, A; Buck, M; Boyd, J; Dobson, C M; Redfield, C; Smith, L J

    2001-04-01

    A high resolution NMR structure of hen lysozyme has been determined using 209 residual 1H-15N dipolar coupling restraints from measurements made in two different dilute liquid crystalline phases (bicelles) in conjunction with a data set of 1632 NOE distance restraints, 110 torsion angle restraints, and 60 hydrogen bond restraints. The ensemble of 50 low-energy calculated structures has an average backbone RMSD of 0.50+/-0.13A to the mean structure and of 1.49+/-0.10A to the crystal structure of hen lysozyme. To assess the importance of the dipolar coupling data in the structure determination, the final structures are compared with an ensemble calculated using an identical protocol but excluding the dipolar coupling restraints. The comparison shows that structures calculated with the dipolar coupling data are more similar to the crystal structure than those calculated without, and have better stereochemical quality. The structures also show improved quality factors when compared with additional dipolar coupling data that were not included in the structure calculations, with orientation-dependent 15N chemical shift changes measured in the bicelle solutions, and with T1/T2 values obtained from 15N relaxation measurements. Analysis of the ensemble of NMR structures and comparisons with crystal structures, 15N relaxation data, and molecular dynamics simulations of hen lysozyme provides a detailed description of the solution structure of this protein and insights into its dynamical behavior.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    SciTech Connect

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

    2008-09-15

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

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

    SciTech Connect

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

    2014-06-01

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

  10. Evaporation induced self-assembly of ordered structures from a capillary-held solution

    NASA Astrophysics Data System (ADS)

    Hong, Suck Won

    The use of spontaneous self-assembly as a lithography and external fields-free means to construct well-ordered, often intriguing structures has received much attention as a result of the ease of producing complex structures with small feature sizes. Self-assembly via irreversible solvent evaporation of a droplet containing nonvolatile solutes (polymers, nanoparticles, and colloids) represents one such case. However, the flow instabilities within the evaporating droplet often result in irregular dissipative structures (e.g., convection patterns and fingering instabilities). Therefore, fully utilizing evaporation as a simple tool for creating well-ordered structures that have numerous technological applications requires delicate control over several factors, including the evaporative flux, solution concentration, interfacial interaction between the solute and the substrate, etc. In this study, we developed a simple route to produce highly regular polymeric structures in an easily controllable, cost-effective, and reproducible manner simply by allowing a drop to evaporate in a confined geometry consisting of a sphere on a Si surface (i.e., a sphere-on-Si geometry). The confined geometry provides unique environment for controlling the flow within the evaporating droplet, which, in turn, regulates the structure formation. A variety of polymers, including poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV), poly(ferrocenyldimethylsilane) (PFS), polystyrene (PS), poly(methyl methacrylate) (PMMA), and polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA), are selected as nonvolatile solutes. A number of parameters are found to effectively mediate the structure formation, including the solution concentration, the interfacial interaction between the solute and the substrate, curvature and molecular effect. This simple, lithography-free route allows subsequent preparation of various metal, metal oxide, and carbon nanotube patterns with controlled spacing

  11. [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

  12. Structural determinants of protein stabilization by solutes. The important of the hairpin loop in rubredoxins.

    PubMed

    Pais, Tiago M; Lamosa, Pedro; dos Santos, Wagner; Legall, Jean; Turner, David L; Santos, Helena

    2005-02-01

    Despite their high sequence homology, rubredoxins from Desulfovibrio gigas and D. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon Archaeoglobus fulgidus[Lamosa P, Burke A, Peist R, Huber R, Liu M Y, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C and Santos H (2000) Appl Environ Microbiol66, 1974-1979]. The principal structural difference between these two proteins is the absence of the hairpin loop in the rubredoxin from D. desulfuricans. Therefore, mutants of D. gigas rubredoxin bearing deletions in the loop region were constructed to investigate the importance of this structural feature on protein intrinsic stability, as well as on its capacity to undergo stabilization by compatible solutes. The three-dimensional structure of the mutant bearing the largest deletion, Delta17/29, was determined by 1H-NMR, demonstrating that, despite the drastic deletion, the main structural features were preserved. The dependence of the NH chemical shifts on temperature and solute concentration (diglycerol phosphate or mannosylglycerate) provide evidence of subtle conformational changes induced by the solute. The kinetic stability (as assessed from the absorption decay at 494 nm) of six mutant rubredoxins was determined at 90 degrees C and the stabilizing effect exerted by both solutes was assessed. The extent of protection conferred by each solute was highly dependent on the specific mutant examined: while the half-life for iron release in the wild-type D. gigas rubredoxin increased threefold in the presence of 0.1 M diglycerol phosphate, mutant Delta23/29 was destabilized. This study provides evidence for solute-induced compaction of the protein structure and occurrence of weak, specific interactions with the protein surface. The relevance of these findings to our understanding of the molecular basis for protein stabilization is discussed.

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

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-01

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

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

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-01

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

  15. 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.

  16. Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein.

    PubMed

    Liepinsh, Edvards; Otting, Gottfried; Harding, Margaret M; Ward, Leanne G; Mackay, Joel P; Haymet, A D J

    2002-02-01

    The solution structure of a synthetic mutant type I antifreeze protein (AFP I) was determined in aqueous solution at pH 7.0 using nuclear magnetic resonance (NMR) spectroscopy. The mutations comprised the replacement of the four Thr residues by Val and the introduction of two additional Lys-Glu salt bridges. The antifreeze activity of this mutant peptide, VVVV2KE, has been previously shown to be similar to that of the wild type protein, HPLC6 (defined here as TTTT). The solution structure reveals an alphahelix bent in the same direction as the more bent conformer of the published crystal structure of TTTT, while the side chain chi1 rotamers of VVVV2KE are similar to those of the straighter conformer in the crystal of TTTT. The Val side chains of VVVV2KE assume the same orientations as the Thr side chains of TTTT, confirming the conservative nature of this mutation. The combined data suggest that AFP I undergoes an equilibrium between straight and bent helices in solution, combined with independent equilibria between different side chain rotamers for some of the amino acid residues. The present study presents the first complete sequence-specific resonance assignments and the first complete solution structure determination by NMR of any AFP I protein.

  17. 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.

  18. Direct biochemical measurements of microtubule assembly and disassembly in Chinese hamster ovary cells. The effect of intercellular contact, cold, D2O, and N6,O2'-dibutyryl cyclic adenosine monophosphate

    PubMed Central

    1975-01-01

    A study was undertaken to develop a means of quantitating the amount of tubulin present as a soluble pool and as intact microtubules in cultured Chinese hamster ovary cells. A procedure was developed in which these cells grown on monolayer culture in Petri dishes were placed in a "microtubule stabilizing medium" (MTM) consisting of 50% glycerol, 10% dimethylsulfoxide and sodium phosphate magnesium buffer, as described previously by Filner and Behnke. These cells then were homogenized and the homogenate was spun in the ultracentrifuge. Colchicine binding activity was then determined in the supernates and the pellets. The values, when compared with total colchicine binding activity present in replicate homogenates, were used to determine the percentage of tubulin present as intact microtubules. A statistical analysis of thin sections of cells treated with MTM revealed no statistically significant difference between MTM-treated cells and untreated controls. It was further discovered that the relative amount of colchicine binding activity recovered in the high speed pellet varied dramatically, depending upon the cell number of the culture being studied. Preconfluent cultures showed very low colchicine binding activity averaging less than 5%, while confluent and postconfluent cultures often possessed as high as 25% of their total colchicine binding activity in pelletable material. Although cold and D2O treatment had little or no effect on these values, N6,O2'-dibutyryl cyclic adenosine monophosphate increased them. It is hoped that this study will serve as the basis for a reliable quantitative procedure for measuring microtubule polymerization and depolymerization in vivo. PMID:162792

  19. Solution Structure of the PhoP DNA-Binding Domain from Mycobacterium tuberculosis

    PubMed Central

    Macdonald, Ramsay; Sarkar, Dibyendu; Amer, Brendan R.; Clubb, Robert T.

    2015-01-01

    Summary Tuberculosis caused by Mycobacterium tuberculosis is a leading cause of death world-wide. The PhoP protein is required for virulence and is part of the PhoPR two-component system that regulates gene expression. The NMR-derived solution structure of the PhoP C-terminal DNA-binding domain is reported. Residues 150 to 246 form a structured domain that contains a winged helix-turn-helix motif. We provide evidence that the transactivation loop postulated to contact RNA polymerase is partially disordered in solution, and that the polypeptide that connects the DNA-binding domain to the regulatory domain is unstructured. PMID:26209027

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  2. 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.

  3. Crystal and solution structures of a superantigen from Yersinia pseudotuberculosis reveal a jelly-roll fold.

    PubMed

    Donadini, Roberta; Liew, Chu Wai; Kwan, Ann H Y; Mackay, Joel P; Fields, Barry A

    2004-01-01

    Superantigens are a class of microbial proteins with the ability to excessively activate T cells by binding to the T cell receptor. The staphylococcal and streptococcal superantigens are closely related in structure and possess an N-terminal domain that resembles an OB fold and a C-terminal domain similar to a beta-grasp fold. Yersinia pseudotuberculosis produces superantigens, YPMa, YPMb, and YPMc, which have no significant amino acid similarity to other proteins. We have determined the crystal and solution structures of YPMa, which show that the protein has a jelly-roll fold. The closest structural neighbors to YPMa are viral capsid proteins and members of the tumor necrosis factor superfamily. In the crystal structure, YPMa packs as a trimer, another feature shared with viral capsid proteins and TNF superfamily proteins. However, in solution YPMa behaves as a monomer, and any functional relevance of the trimer observed in the crystals is yet to be established.

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

    NASA Astrophysics Data System (ADS)

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

    2001-05-01

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

  5. 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.

  6. 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.

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

    SciTech Connect

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

    2013-08-01

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

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

    PubMed

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

    2016-06-01

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

  9. Parallel-vector solution of large-scale structural analysis problems on supercomputers

    NASA Technical Reports Server (NTRS)

    Storaasli, Olaf O.; Nguyen, Duc T.; Agarwal, Tarun K.

    1989-01-01

    A direct linear equation solution method based on the Choleski factorization procedure is presented which exploits both parallel and vector features of supercomputers. The new equation solver is described, and its performance is evaluated by solving structural analysis problems on three high-performance computers. The method has been implemented using Force, a generic parallel FORTRAN language.

  10. 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".…

  11. 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.

  12. 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.

  13. 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

  14. 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.

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

    PubMed

    Yang, Pei-Kun; Lim, Carmay

    2008-09-01

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

  16. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

    PubMed

    Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

    2008-02-01

    We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

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

    PubMed

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

    1995-04-01

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

  18. Solution Structure and Dynamics of Human Hemoglobin in the Carbonmonoxy Form

    PubMed Central

    Fan, Jing-Song; Zheng, Yu; Choy, Wing-Yiu; Simplaceanu, Virgil; Ho, Nancy T.; Ho, Chien; Yang, Daiwen

    2014-01-01

    The solution structure of HbCO A was refined using stereospecifically assigned methyl groups and residual dipolar couplings based on our previous NMR structure. The tertiary structures of individual chains were found to be very similar to the X-ray structures, while the quaternary structures in solution with low-salt resembled the X-ray R structure more than the R2 structure. On the basis of chemical shift perturbation by inositol hexaphosphate (IHP) titration and docking, we identified five possible IHP binding sites in HbCO A. Amide-water proton exchange experiments demonstrated that αThr38 located in the α1β2 interface and several loop regions in both α- and β-chains were dynamic on the sub-second timescale. Side-chain methyl dynamics revealed that methyl groups in the α1β2 interface were dynamic, but those in the α1β1 interface were quite rigid on the ns-ps and ms-µs timescales. All the data strongly suggest a dynamic α1β2 interface that allows conformational changes among different forms (like T, R, and R2) easily in solution. Binding of IHP to HbCO A induced small structural and dynamics changes in the α1β2 interface and the regions around the hemes, but did not increase the conformational entropy of HbCO A. The binding also caused conformational changes on the ms timescale, very likely arising from the relative motion of the α1β1 dimer with respect to the α2β2 dimer. Heterotropic effectors like IHP may change the oxygen affinity of Hb through modulating the relative motion of the two dimers and then further altering the structure of heme binding regions. PMID:23901897

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

    PubMed

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

    2014-04-15

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

  20. 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.

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

    SciTech Connect

    Taylor, Seth T.

    2002-05-17

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

  2. 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

  3. Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis

    PubMed Central

    Allen, Mark D.; Christie, Mary; Jones, Peter; Porebski, Benjamin T.; Roome, Brendan; Freund, Stefan M.V.; Buckle, Ashley M.; Bycroft, Mark; Christ, Daniel

    2015-01-01

    We have previously reported a phage display method for the identification of protein domains on a genome-wide scale (shotgun proteolysis). Here we present the solution structure of a fragment of the Escherichia coli membrane protein yrfF, as identified by shotgun proteolysis, and determined by NMR spectroscopy. Despite the absence of computational predictions, the fragment formed a well-defined beta-barrel structure, distantly falling within the OB-fold classification. Our results highlight the potential of high-throughput experimental approaches for the identification of protein domains for structural studies. PMID:25877662

  4. Assessment of solvent effects: do weak alignment media affect the structure of the solute?

    PubMed

    Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G; Panosyan, Henry A; Sahakyan, Aleksandr B; Byeon, In-Ja L; Gronenborn, Angela M

    2007-07-01

    Alignment media used for measuring residual dipolar couplings, such as solutions of filamentous phages, phospholipid mixtures, polyacrylamide gels and various lyotropic liquid crystalline systems were investigated with respect to solvent effects on molecular structure. Structural parameters of the small rigid model compound 13C-acetonitrile were calculated from dipolar couplings and variations from expectation values were used for assessment of solvent effects. Only minor solvent effects were observed for most of the media employed and the measured structural data are in good agreement with microwave data and theoretical predictions. PMID:17534883

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

    NASA Astrophysics Data System (ADS)

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

    1998-06-01

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

  6. 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.

  7. Liquid-Structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution

    PubMed Central

    Hassan, Sergio A.

    2008-01-01

    Molecular interactions in solution are controlled by the bulk medium and by the forces originating in the structured region of the solvent close to the solutes. In this paper, a model of electrostatic and liquid-structure forces for dynamics simulations of biomolecules is presented. The model introduces information on the microscopic nature of the liquid in the vicinity of polar and charged groups and the associated non-pairwise character of the forces, thus improving upon conventional continuum representations. The solvent is treated as a polar and polarizable medium, with dielectric properties described by an inhomogeneous version of the Onsager theory. This treatment leads to an effective position-dependent dielectric permittivity that incorporates saturation effects of the electric field and the spatial variation of the liquid density. The non-pairwise additivity of the liquid-structure forces is represented by centers of force located at specific points in the liquid phase. These out-of-the-solute centers are positioned at the peaks of liquid density and exert local, external forces on the atoms of the solute. The density is calculated from a barometric law, using a Lennard-Jones-type solute–liquid effective interaction potential. The conceptual aspects of the model and its exact numerical solutions are discussed for single alkali and halide ions and for ion-pair interactions. The practical aspects of the model and the simplifications introduced for efficient computation of forces in molecular solutes are discussed in the context of polar and charged amino acid dimers. The model reproduces the contact and solvent-separated minima and the desolvation barriers of intermolecular potentials of mean force of amino acid dimers, as observed in atomistic dynamics simulations. Possible refinements based on an improved treatment of molecular correlations are discussed. PMID:17201447

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

    PubMed

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

    2013-11-01

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

  9. 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.

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

    SciTech Connect

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

    2011-12-09

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

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

    SciTech Connect

    Ovchinnikov, Yu. N.

    2013-09-15

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

  12. 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.

  13. Novel Microwave Thermodynamic Model for Alcohol with Clustering Structure in Nonpolar Solution.

    PubMed

    Sumi, Takuya; Dillert, Ralf; Horikoshi, Satoshi

    2015-11-12

    A solution containing ethanol as polar material and either benzene or n-dodecane as nonpolar solvent was heated by microwave irradiation employing a single-mode resonance microwave device. Although the microwave heating efficiency was expected from the just value of the relative dielectric constant (εr') or relative dielectric loss (εr″) for liquid system, it was revealed that the clustering structure of alcohol molecules expected from the excess parameter such as the excess relative dielectric loss is the important factor in the decision for efficiency of the microwave heating for the solution. This assumption and novel theory were strongly supported from the thermodynamic data such as vapor pressure and the partial enthalpy.

  14. 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.

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

    PubMed

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

    2016-01-01

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

  16. 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.

  17. 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.; Schmidt, Martin U.

    2016-01-01

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

  18. 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.

  19. 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.

  20. Structural change of water with solutes and temperature up to 100 degrees C in aqueous solutions as revealed by attenuated total reflectance infrared spectroscopy.

    PubMed

    Masuda, Kaori; Haramaki, Taishiro; Nakashima, Satoru; Habert, Bertrand; Martinez, Isabelle; Kashiwabara, Seiichi

    2003-03-01

    The attenuated total reflectance infrared (ATR-IR) spectra of several aqueous solutions have been measured by using a newly developed heatable rod-type ATR cell. The OH stretching bands showed systematic change with increasing solute concentrations and these changes can be explained by four different OH components based on curve-fitting results. NaCl solutions show longer H-bond distance character, while carbonate solutions present shorter ones. The Na2CO3 1 M solution conserves this shorter H-bond nature up to 100 degrees C. On the other hand, the loose nature of NaCl solutions becomes less pronounced at higher temperatures because of the dissociation of pure water clusters. These in situ observations of water structures are generally in agreement with the expected nature of fluids within the earth. PMID:14658618

  1. Solution structure of apamin determined by nuclear magnetic resonance and distance geometry

    SciTech Connect

    Pease, J.H.B.; Wemmer, D.E.

    1988-11-01

    The solution structure of the bee venom neurotoxin apamin has been determined with a distance geometry program using distance constraints derived from NMR. Twenty embedded structures were generated and refined by using the program DSPACE. After error minimization using both conjugate gradient and dynamics algorithms, six structures had very low residual error. Comparisons of these show that the backbone of the peptide is quite well-defined with the largest rms difference between backbone atoms in these structures of 1.34 /Angstrom/. The side chains have far fewer constraints and show greater variability in their positions. The structure derived here is generally consistent with the qualitative model previously described, with most differences occurring in the loop between the ..beta..-turn (residues 2-5) and the C-terminal ..cap alpha..-helix (residues 9-17). Comparisons are made with previously derived models from NMR data and other methods.

  2. Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2

    PubMed Central

    Ju, Tingting; Bocik, William; Majumdar, Ananya; Tolman, Joel R.

    2009-01-01

    Ube2g2 is an E2 enzyme which functions as part of the endoplasmic reticulum-associated degradation (ERAD) pathway responsible for identification and degradation of misfolded proteins in the endoplasmic reticulum. In tandem with a cognate E3 ligase, Ube2g2 assembles K48-linked polyubiquitin chains and then transfers them to substrate, leading ultimately to proteasomal degradation of the polyubiquitin-tagged substrate. We report here the solution structure and backbone dynamics of Ube2g2 solved by nuclear magnetic resonance spectroscopy. Although the solution structure agrees well with crystallographic structures for the E2 core, catalytically important loops (encompassing residues 95-107 and 130-135) flanking the active site cysteine are poorly defined. 15N spin relaxation and residual dipolar coupling analysis directly demonstrates that these two loops are highly dynamic in solution. These results suggest that Ube2g2 requires one or more of its protein partners, such as cognate E3, acceptor ubiquitin substrate or thiolester-linked donor ubiquitin, in order to assume its catalytically relevant conformation. Within the NMR structural ensemble, interactions were observed between His94 and the highly mobile loop residues Asp98 and Asp99, supporting a possible role for His94 as a general base activated by the carboxylate side-chains of Asp98 or Asp99. PMID:20014027

  3. 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.

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

    PubMed

    Labate, Giuseppe; Matekovits, Ladislau

    2016-08-22

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

  5. Finite difference approximations for measure-valued solutions of a hierarchically size-structured population model.

    PubMed

    Ackleh, Azmy S; Chellamuthu, Vinodh K; Ito, Kazufumi

    2015-04-01

    We study a quasilinear hierarchically size-structured population model presented in [4]. In this model the growth, mortality and reproduction rates are assumed to depend on a function of the population density. In [4] we showed that solutions to this model can become singular (measure-valued) in finite time even if all the individual parameters are smooth. Therefore, in this paper we develop a first order finite difference scheme to compute these measure-valued solutions. Convergence analysis for this method is provided. We also develop a high resolution second order scheme to compute the measure-valued solution of the model and perform a comparative study between the two schemes. PMID:25811433

  6. 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.

  7. 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.

  8. The NMR solution structure of the pheromone Er-11 from the ciliated protozoan Euplotes raikovi.

    PubMed Central

    Luginbühl, P.; Wu, J.; Zerbe, O.; Ortenzi, C.; Luporini, P.; Wüthrich, K.

    1996-01-01

    The NMR solution structure of the pheromone Er-11, a 39-residue protein from the ciliated protozoan Euplotes raikovi, was calculated with the distance geometry program DIANA from 449 NOE upper distance constraints and 97 dihedral angle constraints, and the program OPAL was employed for structure refinement by molecular mechanics energy minimization in a water bath. For a group of 20 conformers used to characterize the solution structure, the average of the pairwise RMS deviations from the mean structure calculated for the backbone heavy atoms N, C alpha, and C' of residues 2-38 was 0.30 A. The molecular architecture is dominated by an up-down-up bundle of three short helices with residues 2-9, 12-19, and 22-32, which is closely similar to the previously determined structures of the homologous pheromones Er-1, Er-2, and Er-10. This finding provides structural evidence for the capability shown by these pheromones to compete with each other in binding reactions to their cell-surface receptors. PMID:8844842

  9. The NMR solution structure of the pheromone Er-2 from the ciliated protozoan Euplotes raikovi.

    PubMed Central

    Ottiger, M.; Szyperski, T.; Luginbühl, P.; Ortenzi, C.; Luporini, P.; Bradshaw, R. A.; Wüthrich, K.

    1994-01-01

    The NMR structure of the pheromone Er-2 from the ciliated protozoan Euplotes raikovi has been determined in aqueous solution. The structure of this 40-residue protein was calculated with the distance geometry program DIANA from 621 distance constraints and 89 dihedral angle constraints; the program OPAL was employed for the energy minimization. For a group of 20 conformers used to characterize the solution structure, the average pairwise RMS deviation from the mean structure calculated for the backbone heavy atoms N, C alpha, and C' of residues 3-37 was 0.31 A. The molecular architecture is dominated by an up-down-up bundle of 3 short helices of residues 5-11, 14-20, and 23-33, which is similar to the structures of the homologous pheromones Er-1 and Er-10. Novel structural features include a well-defined N-cap on the first helix, a 1-residue deletion in the second helix resulting in the formation of a 3(10)-helix rather than an alpha-helix as found in Er-1 and Er-10, and the simultaneous presence of 2 different conformations for the C-terminal tetrapeptide segment, i.e., a major conformation with the Leu 39-Pro 40 peptide bond in the trans form and a minor conformation with this peptide bond in the cis form. PMID:7833811

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

    PubMed

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

    2016-07-19

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

  11. Influence of the organized structure of 1-alkyl-3-methylimidazolium tetrafluoroborates on the rotational diffusion of structurally similar nondipolar solutes.

    PubMed

    Gangamallaiah, V; Dutt, G B

    2014-11-26

    To understand how the organized structure of the ionic liquids influences the location and mobility of nondipolar solutes, rotational diffusion of 2,5-dimethyl-1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DMDPP) and 1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DPP) has been examined in 1-alkyl-3-methylimidazolium (alkyl = ethyl, butyl, hexyl, and octyl) tetrafluoroborates. Both the solutes are structurally similar-the sole difference being the two NCH3 groups of DMDPP are replaced by two NH groups in DPP. The rotational diffusion of DPP is found to be significantly slower than DMDPP due to specific interactions between the NH groups of the solute and the anion of the ionic liquid. It has been observed that for a given viscosity and temperature, the rotational diffusion of DMDPP becomes progressively faster with an increase in the length of the alkyl chain on the imidazolium cation. DMDPP resides in the nonpolar domains of these ionic liquids whose sizes increase with an increase in the length of the alkyl chain, and as a result it experiences microviscosity that is lower than the bulk viscosity. However, an increase in the length of the alkyl chain has no apparent effect on the rotational diffusion of DPP because specific interactions with tetrafluoroborate necessitate the solute to be located in the vicinity of the anion. The results of this work exemplify that despite having similar size and shape, the rotational diffusion of DMDPP and DPP is quite contrasting as their sites of solubilization and the nature of interactions with the surroundings are vastly different owing to subtle variations in their chemical structures.

  12. Numerical Solutions and Structures of Double Quantum Jet Solving by an Upwind Scheme

    NASA Astrophysics Data System (ADS)

    Lin, San-Yih

    2005-11-01

    The solutions of a double quantum jet are analyzed by solving the quantum fluid dynamical formulation (QFD) of the Schr"odinger equation. The QFD equations are obtained by expressing the Schr"odinger wave function as =ρ^1/2(iS/)and u=(u,v). In QFD, Q=-ρ-1/2δρ^1/2 is called as quantum potential. An upwind method is developed to solve the QFD equations. The method use a third-order upwind method to discrete convection terms and the central finite difference method to discrete the quantum potential. A fourth-order Runge-Kutta method is used for time marching. Two cases, one-dimensional free particle with external potential and two-dimensional free particle with external potential, are presented to illustrate the accuracy of the QFD solver. The computational results are compared well with the results obtained by solving the Schr"odinger equation. Finally, the QFD solver is applied to solve the solutions of a double quantum jet and to investigate its structures. First, a mathematical formulation is derived to describe the double quantum jet. The jet has the probability density equals 2 and the velocity equals 2 at the inlet of the jet. Then, the solutions are computed by the QFD solver. The structures of the solutions are affected by the strength of the quantum potential. The interesting phenomena of quantum clustering are found.

  13. The thermal characteristics of superlattice structures based on AlGaInN solid solution

    NASA Astrophysics Data System (ADS)

    Evseenkov, A. S.; Tarasov, S. A.; Solomonov, A. V.; Altimime, S. M.; Obukhova, A. S.

    2016-08-01

    The blue light-emitting structures based on solid solutions of the system AlGaInN that contained superlattices In0.9Ga0.1N/In0.99Ga0.01N and Al0.15Ga0.85N/GaN were investigated, and its basic parameters and characteristics were defined. The main difference between the samples was an "upper blocking layer" that formed by AlGaN solid solutions with a different stoichiometric composition or as a superlattice. Spectral and thermal investigations of samples were conducted, and the temperatures of the active region were calculated. The optimal types of structures for different operation modes were offered.

  14. [Spatial structure of cro-repressor in a solution. II. Effect of ionized groups].

    PubMed

    Kurochkin, A V; Kirpichnikov, M P

    1986-01-01

    The technique of 1H NMR spectroscopy and absorption UV spectroscopy were used to study the ionization of the tyrosine phenol cycles and the effect of ionizable groups on the chemical shifts of signals from protons in the side chains of several amino acid residues. The microenvironment of these residues was established by analysing the titration curves. The mutual orientation of two functionally important adjacent alpha-helical protein regions was determined in solution. The signals from methionine residues belonging to different regions of the secondary structure were assigned in the NMR spectrum. The results indicate that the spatial structure of the repressor is similar in solution an in the crystal. They confirm the model proposed for the cro repressor interaction with DNA and based on the data of X-ray diffraction analysis.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    Minakata, Hisakazu; Uchinami, Shoichi

    2010-04-01

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

  17. Solution structure and properties of AlgH from Pseudomonas aeruginosa.

    PubMed

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

    2015-06-01

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

  18. Solution Structure and Properties of AlgH from Pseudomonas aeruginosa

    PubMed Central

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

    2015-01-01

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

  19. 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.

  20. A theory for correlating the thermodynamic and structural properties of molten silicate solutions

    SciTech Connect

    Blander, M.; Bloom, I.

    1995-06-01

    A theory of molten silicates is presented which takes into account the dependence of the free energy of cutting Si-O-Si bridging bonds on local structures of the two silicons in the bond. Resultant equations describe the thermodynamic properties of primary silicate solutions containing a mixture of bridges and cut bridges, and should ultimately provide a realistic measure of the distribution of silicon species which have i cut bridges (i = 1,2,3,4) from analyses of thermodynamic data.

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

    NASA Astrophysics Data System (ADS)

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

    2004-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  3. 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.

  4. 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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  7. The confluence of structure and dynamics in lanthanide(III) chelates: how dynamics help define structure in solution.

    PubMed

    Webber, Benjamin C; Woods, Mark

    2014-01-01

    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 Eu(3+) 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/r(LnH)(6)) of the chelate. The hydration state has recently come to be expressed as two separate parameters q and r(LnH). 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.

  8. 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.

  9. Effective protein-protein interaction from structure factor data of a lysozyme solution

    NASA Astrophysics Data System (ADS)

    Abramo, M. C.; Caccamo, C.; Cavero, M.; Costa, D.; Pellicane, G.; Ruberto, R.; Wanderlingh, U.

    2013-08-01

    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.

  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. PMID:19828118

  11. Reversible pressure-induced structure changes in turbostratic BN-C solid solutions.

    PubMed

    Solozhenko, Vladimir L; Kurakevych, Oleksandr O

    2005-10-01

    The results obtained by Rietveld analysis and numerical modeling of B-C-N layered clusters with various types of lattice defects explain the evolution of diffraction patterns of turbostratic graphite-like BN-C solid solutions which are experimentally observed at room temperature at pressures up to 30 GPa. Above 20 GPa a reversible diffusionless transformation of the initial turbostratic structure takes place, giving a high-pressure phase formed by close-packed buckled layers having a diamond-like structure.

  12. 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

  13. The structure of nanochannels formed by block copolymer solutions confined in nanotubes.

    PubMed

    Chen, Houyang; Ruckenstein, Eli

    2009-09-21

    Monte Carlo simulations are employed to obtain information about the radius and the roughness of the inner surface of the channels, which are generated by a family of block copolymer solutions confined in nanotubes. The fluctuations of the above quantities also have been calculated. The simulations have been carried out by varying the interactions between various kinds of segments and those between segments and the wall of the nanotubes, as well as the chemical structure of the copolymer and the nanotube diameter. The present simulations provide insight regarding the structure of ionic and water channels formed by protein in the phospholipid bilayers of the cell membrane.

  14. Analysis of the structure of aqueous solutions of isopropanol based on optical, volumetric, and elastic data

    NASA Astrophysics Data System (ADS)

    Abramovich, A. I.; Lanshina, L. V.

    2015-07-01

    The curve of the concentration dependence of the total molecular light scattering coefficient of xC3H7OH-(1 - x)H2O solutions showed two sharp maxima (at x = 0.04 and 0.09) and a minimum at x = 0.06 mole fractions, suggesting a considerable rearrangement of the structure of the solutions near these concentrations. The concentration dependences of excess molar volume, adiabatic compressibility, and molar refraction showed negative deviations from the ideal with a minimum in the range x = 0.18-0.3. The structure of water was assumed to undergo a rearrangement at x = 0.04 accompanied by structural fluctuations, which dispersed at 0.04 < x < 0.06. At x = 0.06, associates of isopropanol molecules started to form, whose number and size increased linearly up to x = 0.13. In the 0.13 < x < 0.35 concentration range, some kind of an aqueous alcohol emulsion containing pure alcohol "nanodrops" formed and the solutions became microheterogeneous.

  15. 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. PMID:27560477

  16. Strain-induced structural phase transition of a Ni lattice through dissolving Ta solute atoms

    NASA Astrophysics Data System (ADS)

    Zhang, Q.; Lai, W. S.; Liu, B. X.

    2001-06-01

    The structural phase transition of a single-crystal Ni lattice upon dissolving Ta solute atoms is investigated by means of molecular-dynamics simulations with a realistic n-body Ni-Ta potential. It is found that when the solute concentration is within 9-19 at. % of Ta, the accumulated strain results in a martensitic phase transition, i.e., face-centered-cubic (fcc) Ni transforms into a face-centered-orthorhombic-(fco) like structure through shearing, and that when the solute concentration is over 21 at. % of Ta, the Ni lattice collapses and turns into an amorphous state. Comparatively, for the case of an initial hcp Ni lattice, the same martensitic and amorphization transitions also take place. The former hcp-fco transition, however, is mainly through atomic rearrangement as well as readjustment of lattice parameters, and the resultant state is almost perfect single crystal with no shearing bands. Besides, the above structural transitions are frequently in association with a dramatic softening in shear elastic moduli.

  17. 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.

  18. Structure and properties of novel regenerated cellulose fibers prepared in NaOH complex solution.

    PubMed

    Wang, Wencong; Zhang, Peng; Zhang, Shuai; Li, Faxue; Yu, Jianyong; Lin, Jinyou

    2013-10-15

    Novel spinning solution, prepared by dissolving hydroxyethyl cellulose (HEC) owning a low molar substitution (MS) into NaOH/urea/thiouea aqueous solution with a specific weight ratio of 8:8:6.5, was employed to fabricate a new type of regenerated fibers by wet-spun method. The structure and properties of the resultant HEC fibers were characterized by (13)C NMR, FTIR, synchrotron WAXS, SEM, and tensile tester. The results showed that HEC fibers exhibited structure identical with HEC because of the physical dissolution and coagulation processes, but quite different from native cellulose due to partial breakage of hydrogen bonds and crystal transformation from cellulose I to cellulose II during cellulose modification. The resultant HEC fibers with relatively dense and homogenous structure displayed good moisture related properties and stayed stable in alkali solution with low concentration. Moreover, the novel fibers owned good dry mechanical properties in spit of their slightly poor wet mechanical properties comparable to viscose rayon, showing great potential in substituting the traditional viscose fibers. PMID:23987444

  19. New structural insights into Golgi Reassembly and Stacking Protein (GRASP) in solution.

    PubMed

    Mendes, Luís F S; Garcia, Assuero F; Kumagai, Patricia S; de Morais, Fabio R; Melo, Fernando A; Kmetzsch, Livia; Vainstein, Marilene H; Rodrigues, Marcio L; Costa-Filho, Antonio J

    2016-01-01

    Among all proteins localized in the Golgi apparatus, a two-PDZ (PSD95/DlgA/Zo-1) domain protein plays an important role in the assembly of the cisternae. This Golgi Reassembly and Stacking Protein (GRASP) has puzzled researchers due to its large array of functions and relevance in Golgi functionality. We report here a biochemical and biophysical study of the GRASP55/65 homologue in Cryptococcus neoformans (CnGRASP). Bioinformatic analysis, static fluorescence and circular dichroism spectroscopies, calorimetry, small angle X-ray scattering, solution nuclear magnetic resonance, size exclusion chromatography and proteolysis assays were used to unravel structural features of the full-length CnGRASP. We detected the coexistence of regular secondary structures and large amounts of disordered regions. The overall structure is less compact than a regular globular protein and the high structural flexibility makes its hydrophobic core more accessible to solvent. Our results indicate an unusual behavior of CnGRASP in solution, closely resembling a class of intrinsically disordered proteins called molten globule proteins. To the best of our knowledge, this is the first structural characterization of a full-length GRASP and observation of a molten globule-like behavior in the GRASP family. The possible implications of this and how it could explain the multiple facets of this intriguing class of proteins are discussed. PMID:27436376

  20. 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

  1. A Method for Solution NMR Structural Studies of Large Integral Membrane Proteins: Reverse Micelle Encapsulation

    PubMed Central

    Kielec, Joseph M.; Valentine, Kathleen G.; Wand, A. Joshua

    2009-01-01

    The structural study of membrane proteins perhaps represents one of the greatest challenges of the post-genomic era. While membrane proteins comprise over 50% of current and potential drug targets, their structural characterization lags far behind that of soluble proteins. Nuclear magnetic resonance (NMR) offers great potential not only with respect to structural characterization of integral membrane proteins but may also provide the ability to study the details of small ligand interactions. However, the size limitations of solution NMR have restricted comprehensive structural characterization of membrane protein NMR structures to the relatively small β-barrel proteins or helical proteins of relatively simple topology. In an effort to escape the barriers presented by slow molecular reorientation of large integral membrane proteins solubilized by detergent micelles in water, we have adapted the reverse micelle encapsulation strategy originally developed for the study of large soluble proteins by solution NMR methods. Here we review a novel approach to the solubilization of large integral membrane proteins in reverse micelle surfactants dissolved in low viscosity alkane solvents. The procedure is illustrated with a 54 kDa construct of the homotetrameric KcsA potassium channel. PMID:19665988

  2. Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion.

    PubMed

    Sung, Tai-Ching; Li, Ching-Yu; Lai, Yei-Chen; Hung, Chien-Lun; Shih, Orion; Yeh, Yi-Qi; Jeng, U-Ser; Chiang, Yun-Wei

    2015-10-01

    Proapoptotic BAX protein is largely cytosolic in healthy cells, but it oligomerizes and translocates to mitochondria upon receiving apoptotic stimuli. A long-standing challenge has been the inability to capture any structural information beyond the onset of activation. Here, we present solution structures of an activated BAX oligomer by means of spectroscopic and scattering methods, providing details about the monomer-monomer interfaces in the oligomer and how the oligomer is assembled from homodimers. We show that this soluble oligomer undergoes a direct conversion into membrane-inserted oligomer, which has the ability of inducing apoptosis and structurally resembles a membrane-embedded oligomer formed from BAX monomers in lipid environment. Structural differences between the soluble and the membrane-inserted oligomers are manifested in the C-terminal helices. Our data suggest an alternative pathway of apoptosis in which BAX oligomer formation occurs prior to membrane insertion.

  3. 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.

  4. 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

  5. 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.

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

    PubMed

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

    2016-01-01

    Precise nanometre-scale imaging of soft structures at room temperature poses a major challenge to any type of microscopy because fast thermal fluctuations lead to significant motion blur if the position of the structure is measured with insufficient bandwidth. Moreover, precise localization is also affected by optical heterogeneities, which lead to deformations in the imaged local geometry, the severity depending on the sample and its thickness. Here we introduce quantitative thermal noise imaging, a three-dimensional scanning probe technique, as a method for imaging soft, optically heterogeneous and porous matter with submicroscopic spatial resolution in aqueous solution. By imaging both individual microtubules and collagen fibrils in a network, we demonstrate that structures can be localized with a precision of ∼10 nm and that their local dynamics can be quantified with 50 kHz bandwidth and subnanometre amplitudes. Furthermore, we show how image distortions caused by optically dense structures can be corrected for. PMID:27596919

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    PubMed

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

    2016-11-01

    During ultrasonication of chitosan AgNO3 solution (10mM), silver cubic structures were identified along with other dispersed silver nanoparticles. Temperature influenced the formation of the cubic structures. Formation of the silver cubic structures occurred via initial formation of 'four petal flower-like' structures that underwent transformation to the "cubic morphology" in the latter stages. Aging of the reaction mixture led to formation of complete dendrites. These dendrites comprised a large quantity of silver nanoparticles. Upon repetition of the experiment with starch instead of chitosan, the identified silver cubic structures were completely absent, indicating that formation of the 'silver cubic structures' is dependent on the polysaccharide used. It is believed that the structural features of chitosan facilitate the formation of 'silver cubic structures' under ultrasonic conditions. The phenomena occurring during the experiments were evaluated via scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), ultraviolet-visible (UV-vis) spectra, transmission electron microscopy (TEM), and selected area electron diffraction (SAED) analysis.

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

    PubMed

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

    2016-11-01

    During ultrasonication of chitosan AgNO3 solution (10mM), silver cubic structures were identified along with other dispersed silver nanoparticles. Temperature influenced the formation of the cubic structures. Formation of the silver cubic structures occurred via initial formation of 'four petal flower-like' structures that underwent transformation to the "cubic morphology" in the latter stages. Aging of the reaction mixture led to formation of complete dendrites. These dendrites comprised a large quantity of silver nanoparticles. Upon repetition of the experiment with starch instead of chitosan, the identified silver cubic structures were completely absent, indicating that formation of the 'silver cubic structures' is dependent on the polysaccharide used. It is believed that the structural features of chitosan facilitate the formation of 'silver cubic structures' under ultrasonic conditions. The phenomena occurring during the experiments were evaluated via scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), ultraviolet-visible (UV-vis) spectra, transmission electron microscopy (TEM), and selected area electron diffraction (SAED) analysis. PMID:27516304

  13. Structural Stability of Riemann Solutions for a Multiphase Kinematic Conservation Law Model that Changes Type.

    NASA Astrophysics Data System (ADS)

    Vinod, Vaidyanath

    We consider a model for 2-way traffic flow introduced by Bick and Newell in 1960 (2). The model problem is: p_{t} + (pu)_{x } = 0; quad q_{t} + (qv)_ {x} = 0.eqno(0.1)Here p and q are the densities of cars in the two directions of flow and u and v are the respective velocities in the p and q directions; a choice suggested in (2) is u = 1 - p - beta q, v = -1 + q + beta p.. In this model, beta is a measure of the interaction between the two directions of flow. For the problem to be physically feasible, we require 0<=beta<1.. Equation (0.1) is a conservation law that changes type. The domain of the solution is p>=0, q<=0, 1 - p - beta q>=0, and -1 + q + beta p>=0.. When beta = 0, there is no interaction between the two directions of flow and then the system (0.1) reduces to a system of scalar equation for which the Riemann problem (Cauchy problem) to (0.1) with initial data of the form: U(x,0) = cases{{U_0,quad x < 0} crcr{U_1,quad x > 0} cr}has a unique solution in the class of Lax entropy or admissible wave solutions. In this case, there is an open set of initial states (U_0, U_1) for which the solution exhibits the phenomenon of 'overlapping rarefaction waves'. These waves occupy the same position in the physical plane and they are stable. When beta>0, for the same initial values U_0 and U_1, these overlapping rarefaction solutions disappear due to the presence of an elliptic region. For these states, we introduce a new shock solution which we term a critical shock (this is qualitatively similar to a Buckley-Leverett shock). The strength of the shock goes to zero as beta tends to zero; and this solution approaches the overlapping wave solution. The main result of this thesis is that these constructed solutions are structurally stable as beta approaches zero (that is, the elliptic region shrinks to a line); and that they converge strongly in L^1. The construction might prove useful in solving other problems that change type, for example models for three-phase flow

  14. Structural stability of Riemann solutions for a multiphase kinematic conservation law model that changes type

    SciTech Connect

    Vinod, V.

    1992-01-01

    The authors consider a model for 2-way traffic flow introduced by Bick and Newell in 1960. The model problem is: pt + (pu)x = 0; qt + (qv)x = 0. Here p and q are the densities of cars in the two directions of flow and u and v are the respective velocities in the p and q directions; a choice suggested is u = 1 - p - [beta]q, v = [minus]1 + q + [beta]p. In this model, [beta] is a measure of the interaction between the two directions of flow. For the problem to be physically feasible, one requires 0 [le] [beta] [le] 1. Equation (0.1) is a conservation law that changes type. The domain of the solution is p [ge] 0,q [le] 0, 1 - p - [beta]q [ge] 0, and [minus]1 + q + [beta]p [ge] 0. When [beta] = 0, there is no interaction between the two directions of flow and then the system (0.1) reduces to a system of scalar equation for which the Riemann problem (Cauchy problem) to (0.1) with initial data of the form: U(x,0) = U[sub 0], x<0 U[sub 1], x>0 has a unique solution in the class of Lax entropy or admissible wave solutions. In this case, there is an open set of initial states (U[sub 0], U[sub 1]) for which the solution exhibits the phenomenon of [open quotes]overlapping rarefaction waves.[close quotes] These waves occupy the same position in the physical plane and they are stable. When [beta] > 0, for the same initial values U[sub o] and U[sub 1], these overlapping rarefaction solutions disappear due to the presence of an elliptic region. For these states, the authors introduce a new shock solution which they term a critical shock (this is qualitatively similar to a Buckley-Leverett shock). The strength of the shock goes to zero as [beta] tends to zero; and this solution approaches the overlapping wave solution. The main result of this thesis is that these constructed solutions are structurally stable as [beta] approaches zero (that is, the elliptic region shrinks to a line); and that they converge strongly in L[sup 1].

  15. 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.

  16. 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.

  17. Characterization of the solution structure of a neuroligin/beta-neurexin complex.

    PubMed

    Comoletti, Davide; Grishaev, Alexander; Whitten, Andrew E; Taylor, Palmer; Trewhella, Jill

    2008-09-25

    Neuroligins are post-synaptic cell adhesion molecules that promote synaptic maturation and stabilization upon binding with pre-synaptic partners, the alpha- and beta-neurexins. Using a combination of analytical ultracentrifugation, small angle X-ray, and neutron scattering, we have characterized the low-resolution three-dimensional structure of the extracellular domain of the neuroligins, free in solution, and in complex with beta-neurexin. The globular extracellular domain of the neuroligins forms stable homodimers through a four-helix bundle typical of the cholinesterases and other members of the alpha/beta-hydrolase fold family. The presence of the stalk region adds to the extracellular domain of neuroligin-1 an elongated structure, suggesting a rod-like nature of the stalk domain. Sedimentation equilibrium coupled with solution scattering data of the beta-neurexin/neuroligin-1 complex indicated a 2:2 stoichiometry where two beta-neurexin molecules bind to a neuroligin-1 dimer. Deuteration of neurexin allowed us to collect neutron scattering data that, in combination with other biochemical techniques, provide a basis for optimizing the positioning of each component in a detailed computational model of the neuroligin/neurexin complex. As several mutations of both neurexin and neuroligin genes have been linked to autism spectrum disorders and mental retardation, these new structures provide an important framework for the study of altered structure and function of these synaptic proteins.

  18. Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy.

    PubMed

    Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing; Di Cera, Enrico

    2016-08-26

    The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr(93) in kringle-1 onto Trp(547) in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. The open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase. PMID:27435675

  19. Structural-energy states of water and aqueous solutions under external influences

    NASA Astrophysics Data System (ADS)

    Gorlenko, Nikolay; Laptev, Boris; Sidorenko, Galina; Sarkisov, Yuri; Minakova, Tamara; Kylchenko, Anton; Zubkova, Olga

    2016-01-01

    Methods are proposed for evaluating changes in the structure of water or aqueous electrolyte solutions under the influence of temperature, magnetic field and surface material by means of determining the electrical capacity of the liquid and the quality factor of the anti-resonant circuit in the frequency range from 1 kHz to 3000 kHz. The condenser plates in different types of electrochemical cells are placed one in front of the other, each at a distance of more than 5 cm, or relative to each other in parallel planes, or in one plane in which case the liquid is located on the condenser plates. The current density on the plates in various cells ranged from 10 to 100 nA/cm2. When measuring the electrical capacity, the voltage applied to the plates was reduced in proportion to the increase in the frequency of oscillator. The apparatus allows us to increase the dynamic range of the signal change from an electrochemical cell, reduce the impact of measurements on the structure of liquids, and also evaluate the direction and extent of changes in the structure of water and aqueous solutions under various external influences. Criteria are proposed for evaluating the structure of fluids.

  20. Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2

    PubMed Central

    Wienk, Hans; Tomaselli, Simona; Bernard, Cédric; Spurio, Roberto; Picone, Delia; Gualerzi, Claudio O.; Boelens, Rolf

    2005-01-01

    IF2 is one of three bacterial translation initiation factors that are conserved through all kingdoms of life. It binds the 30S and 50S ribosomal subunits, as well as fMet-tRNAfMet. After these interactions, fMet-tRNAfMet is oriented to the ribosomal P-site where the first amino acid of the nascent polypeptide, formylmethionine, is presented. The C-terminal domain of Bacillus stearothermophilus IF2, which is responsible for recognition and binding of fMet-tRNAfMet, contains two structured modules. Previously, the solution structure of the most C-terminal module, IF2-C2, has been elucidated by NMR spectroscopy and direct interactions between this subdomain and fMet-tRNAfMet were reported. In the present NMR study we have obtained the spectral assignment of the other module of the C-terminal domain (IF2-C1) and determined its solution structure and backbone dynamics. The IF2-C1 core forms a flattened fold consisting of a central four-stranded parallel β-sheet flanked by three α-helices. Although its overall organization resembles that of subdomain III of the archaeal IF2-homolog eIF5B whose crystal structure had previously been reported, some differences of potential functional significance are evident. PMID:16081655

  1. Structural changes of nucleic acid base in aqueous solution as observed in X-ray absorption near edge structure (XANES)

    NASA Astrophysics Data System (ADS)

    Shimada, Hiroyuki; Fukao, Taishi; Minami, Hirotake; Ukai, Masatoshi; Fujii, Kentaro; Yokoya, Akinari; Fukuda, Yoshihiro; Saitoh, Yuji

    2014-01-01

    X-ray absorption near edge structure (XANES) spectra for adenine-containing nucleotides, adenosine 5‧-monophosphate (AMP) and adenosine 5‧-triphosphate (ATP) in aqueous solutions at the nitrogen K-edge region were measured. The two intense peaks in XANES spectra are assigned to transitions of 1s electrons to the π∗ orbitals of different types of N atoms with particular bonding characteristics. The difference between their spectra is ascribed to protonation of a particular N atom. Similarity observed in XANES spectra of guanosine 5‧-monophosphate (GMP) and ATP is also interpreted as similar bonding characters of the N atoms in the nucleobase moiety.

  2. Rotational dynamics of thiocyanate ions in highly concentrated aqueous solutions.

    PubMed

    Kim, Heejae; Park, Sungnam; Cho, Minhaeng

    2012-05-14

    The thiocyanate (SCN(-)) anion is known as one of the best denaturants, which is also capable of breaking the hydrogen-bond network of water and destabilizing native structures of proteins. Despite prolonged efforts to understand the underlying mechanism of such Hofmeister effects, detailed dynamics of the ions in a highly concentrated solution have not been fully elucidated yet. Here, we used a dispersive IR pump-probe spectroscopic method to study the dependence of vibrational lifetimes and rotational relaxation times of thiocyanate ions on KSCN concentration in D(2)O. The nitrile stretch mode is used as a vibrational probe for dispersed IR pump-probe and FTIR measurements. To avoid possible self-attenuation of the IR pump-probe signal by highly concentrated SCN(-) ions, we added a small amount of (13)C-isotope-labeled thiocyanate ions (S(13)CN(-)) and focused on the excited-state absorption contribution to the IR pump-probe signal of the (13)C-isotope-labeled nitrile stretch mode. Quite unexpectedly, the vibrational lifetime of S(13)CN(-) ions is independent of the total KSCN concentration in the range from 0.46 m (molality) to 11.8 m while the rotational relaxation time of S(13)CN(-) ions is linearly dependent on the total KSCN concentration. By combining the present experimental findings with the fact that the dissolved ions of KSCN salt have a strong tendency to form a large ion cluster in a highly concentrated aqueous solution, we believe that the ion clusters consisting of potassium and thiocyanate ion pairs in D(2)O behave like ionic liquids and the ions inside ion clusters are weakly bound by electrostatic Coulombic interactions. The ability of SCN(-) ions to form ion clusters in aqueous protein solutions seems to be a key to understand the Hofmeister ion effect. We anticipate that the present experimental results provide a clue for further elucidating the underlying mechanism of the Hofmeister ion effects on protein stability in the future. PMID:22407336

  3. 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.

  4. Biomimetic Branched Hollow Fibers Templated by Self-assembled Fibrous Polyvinylpyrrolidone (PVP) Structures in Aqueous Solution

    PubMed Central

    Qiu, Penghe; Mao, Chuanbin

    2010-01-01

    Branched hollow fibers are common in nature, but to form artificial fibers with a similar branched hollow structure is still a challenge. We discovered that polyvinylpyrrolidone (PVP) could self-assemble into branched hollow fibers in an aqueous solution after aging the PVP solution for about two weeks. Based on this finding, we demonstrated two approaches by which the self-assembly of PVP into branched hollow fibers could be exploited to template the formation of branched hollow inorganic fibers. First, inorganic material such as silica with high affinity against the PVP could be deposited on the surface of the branched hollow PVP fibers to form branched hollow silica fibers. To extend the application of PVP self-assembly in templating the formation of hollow branched fibers, we then adopted a second approach where the PVP molecules bound to inorganic nanoparticles (using gold nanoparticles as a model) co-self-assemble with the free PVP molecules in an aqueous solution, resulting in the formation of the branched hollow fibers with the nanoparticles embedded in the PVP matrix constituting the walls of the fibers. Heating the resultant fibers above the glass transition temperature of PVP led to the formation of branched hollow gold fibers. Our work suggests that the self-assembly of the PVP molecules in the solution can serve as a general method for directing the formation of branched hollow inorganic fibers. The branched hollow fibers may find potential applications in microfluidics, artificial blood vessel generation, and tissue engineering. PMID:20158250

  5. Ascorbic acid and BSA protein in solution and films: interaction and surface morphological structure.

    PubMed

    Maciel, Rafael R G; de Almeida, Adriele A; Godinho, Odin G C; Gorza, Filipe D S; Pedro, Graciela C; Trescher, Tarquin F; Silva, Josmary R; de Souza, Nara C

    2013-01-01

    This paper reports on the study of the interactions between ascorbic acid (AA) and bovine serum albumin (BSA) in aqueous solution as well as in films (BSA/AA films) prepared by the layer-by-layer technique. Regarding to solution studies, a hyperchromism (in the range of ultraviolet) was found as a function of AA concentration, which suggested the formation of aggregates from AA and BSA. Binding constant, K, determined for aggregates from BSA and AA was found to be about 10(2) M(-1), which indicated low affinity of AA with BSA. For the BSA/AA films, it was also noted that the AA adsorption process and surface morphological structures depended on AA concentration. By changing the contact time between the AA and BSA, a hypochromism was revealed, which was associated to decrease of accessibility of solvent to tryptophan due to formation of aggregates. Furthermore, different morphological structures of aggregates were observed, which were attributed to the diffusion-limited aggregation. Since most of studies of interactions of drugs and proteins are performed in solution, the analysis of these processes by using films can be very valuable because this kind of system is able to employ several techniques of investigation in solid state.

  6. Ascorbic Acid and BSA Protein in Solution and Films: Interaction and Surface Morphological Structure

    PubMed Central

    Maciel, Rafael R. G.; de Almeida, Adriele A.; Godinho, Odin G. C.; Gorza, Filipe D. S.; Pedro, Graciela C.; Trescher, Tarquin F.; Silva, Josmary R.; de Souza, Nara C.

    2013-01-01

    This paper reports on the study of the interactions between ascorbic acid (AA) and bovine serum albumin (BSA) in aqueous solution as well as in films (BSA/AA films) prepared by the layer-by-layer technique. Regarding to solution studies, a hyperchromism (in the range of ultraviolet) was found as a function of AA concentration, which suggested the formation of aggregates from AA and BSA. Binding constant, K, determined for aggregates from BSA and AA was found to be about 102 M−1, which indicated low affinity of AA with BSA. For the BSA/AA films, it was also noted that the AA adsorption process and surface morphological structures depended on AA concentration. By changing the contact time between the AA and BSA, a hypochromism was revealed, which was associated to decrease of accessibility of solvent to tryptophan due to formation of aggregates. Furthermore, different morphological structures of aggregates were observed, which were attributed to the diffusion-limited aggregation. Since most of studies of interactions of drugs and proteins are performed in solution, the analysis of these processes by using films can be very valuable because this kind of system is able to employ several techniques of investigation in solid state. PMID:23984366

  7. Ascorbic acid and BSA protein in solution and films: interaction and surface morphological structure.

    PubMed

    Maciel, Rafael R G; de Almeida, Adriele A; Godinho, Odin G C; Gorza, Filipe D S; Pedro, Graciela C; Trescher, Tarquin F; Silva, Josmary R; de Souza, Nara C

    2013-01-01

    This paper reports on the study of the interactions between ascorbic acid (AA) and bovine serum albumin (BSA) in aqueous solution as well as in films (BSA/AA films) prepared by the layer-by-layer technique. Regarding to solution studies, a hyperchromism (in the range of ultraviolet) was found as a function of AA concentration, which suggested the formation of aggregates from AA and BSA. Binding constant, K, determined for aggregates from BSA and AA was found to be about 10(2) M(-1), which indicated low affinity of AA with BSA. For the BSA/AA films, it was also noted that the AA adsorption process and surface morphological structures depended on AA concentration. By changing the contact time between the AA and BSA, a hypochromism was revealed, which was associated to decrease of accessibility of solvent to tryptophan due to formation of aggregates. Furthermore, different morphological structures of aggregates were observed, which were attributed to the diffusion-limited aggregation. Since most of studies of interactions of drugs and proteins are performed in solution, the analysis of these processes by using films can be very valuable because this kind of system is able to employ several techniques of investigation in solid state. PMID:23984366

  8. The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes

    PubMed Central

    Huang, Lin; Lilley, David M. J.

    2015-01-01

    With the growing number of crystal structures of RNA and RNA/protein complexes, a critical next step is understanding the dynamic behavior of these entities in solution in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the widespread RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA/protein complexes in solution and uncovers the behavior of an important RNA/protein motif. This type of information will be necessary to understand, predict, and engineer the behavior and function of RNAs and their protein complexes. PMID:26727239

  9. Structure and properties of novel fibers spun from cellulose in NaOH/thiourea aqueous solution.

    PubMed

    Ruan, Dong; Zhang, Lina; Zhou, Jinping; Jin, Huiming; Chen, Hui

    2004-12-15

    Cellulose was dissolved rapidly in a NaOH/thiourea aqueous solution (9.5:4.5 in wt.-%) to prepare a transparent cellulose solution, which was employed, for the first time, to spin a new class of regenerated cellulose fibers by wet spinning. The structure and mechanical properties of the resulting cellulose fibers were characterized, and compared with those of commercially available viscose rayon, cuprammonium rayon and Lyocell fibers. The results from wide angle X-ray diffraction and CP/MAS 13C NMR indicated that the novel cellulose fibers have a structure typical for a family II cellulose and possessed relatively high degrees of crystallinity. Scanning electron microscopy (SEM) and optical microscopy images revealed that the cross-section of the fibers is circular, similar to natural silk. The new fibers have higher molecular weights and better mechanical properties than those of viscose rayon. This low-cost technology is simple, different from the polluting viscose process. The dissolution and regeneration of the cellulose in the NaOH/thiourea aqueous solutions were a physical process and a sol-gel transition rather than a chemical reaction, leading to the smoothness and luster of the fibers. This work provides a potential application in the field of functional fiber manufacturing.

  10. Structure of human salivary histatin 5 in aqueous and nonaqueous solutions.

    PubMed

    Raj, P A; Marcus, E; Sukumaran, D K

    1998-01-01

    The solution structure of human salivary histatin 5 (D-S-H-A-K-R-H-H-G-Y-K-R-K-F-H-E-K-H-H-S-H-R-G-Y) was examined in water (pH 3.8) and dimethyl sulfoxide solutions using 500 MHz homo- and heteronuclear two-dimensional (2D) nmr. The resonance assignment of peptide backbone and side-chain protons was accomplished by 2D total correlated spectroscopy and nuclear Overhauser effect (NOE) spectroscopy. The high JNH-C alpha H values (> or = 7.4 Hz), absence of any characteristic NH-NH (i, i + 1) or C alpha H-C beta H (i, i + 3) NOE connectivities, high d delta/dT values (> or = 0.004 ppm K-1) and the fast 1H/2H amide exchange suggest that histatin 5 molecules remain unstructured in aqueous solution at pH 3.8. In contrast, histatin 5 prefers largely alpha-helical conformation in dimethyl sulfoxide solution as evident from the JNH-C alpha H values (< or = 6.4 Hz), slow 1H/2H exchange, low d delta/dT values (< or = 0.003 ppm K-1) observed for amide resonances of residues 6-24, and the characteristic NH-NH (i, i + 1) and C alpha H-C beta H (i, i + 3) NOE connectivities. All backbone amide 15N-1H connectivities fall within 6 ppm on the 15N scale in the 2D heteronuclear single quantum correlated spectrum, and the restrained structure calculations using DIANA suggest the prevalence of alpha-helical conformations stabilized by 19 (5-->1) intramolecular backbone amide hydrogen bonds in polar aprotic medium such as dimethyl sulfoxide. The interside-chain hydrogen bonding and salt-bridge type interactions that normally stabilize the helical structure of linear peptides in aqueous solutions are not observed. Histatin 5, unlike other naturally occurring antimicrobial polypeptides such as magainins, defensins, and tachyplesins, does not adopt amphiphilic structure, precluding its insertion into microbial membranes and formation of ion channels across membranes. Electrostatic (ionic type) and hydrogen bonding interactions of the positively charged and polar residues with the head

  11. Structure and flow properties of micelle-nanoparticle solutions from Molecular Dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sureshkumar, Radhakrishna; Dhakal, Subas; Sambasivam, Abhinanden

    2014-03-01

    In aqueous media, cationic surfactant molecules spontaneously self-assemble into diverse morphologies depending upon temperature, surfactant concentration and solution ionic strength. Spherical, cylindrical and long (~ microns) flexible wormlike structures with or without branches with distinct rheological properties are observed. Inclusion of nanoparticles (NPs) provides additional means to manipulate structure and create active ``nano-fluids'' that respond to optical, magnetic or electrical stimuli. We study self-assembly, dynamics and rheology of such fluids using coarse-grained Molecular Dynamics simulations in presence of explicit solvent and salt. Specifically, we will discuss the mechanisms underlying fascinating phenomenology observed experimentally such as the pronounced non-monotonic dependence of the zero shear viscosity on salt/NP concentration, shear-induced structure formation, and isotropic to nematic transitions. NSF grants 1049489, 1049454 for the financial support, and Pittsburg Super Computer Centre for providing HPC resources.

  12. Solution-based growth and structural characterization of homo- and heterobranched semiconductor nanowires.

    PubMed

    Dong, Angang; Tang, Rui; Buhro, William E

    2007-10-10

    Colloidal homobranched ZnSe nanowires (NWs) and heterobranched CdSe-ZnSe NWs are successfully synthesized by combining a sequential seeding strategy with the solution-liquid-solid (SLS) growth process. We have developed an efficient approach to deposit secondary bismuth nanoparticles onto the NW backbone to induce the subsequent SLS branch growth. The density, length, and diameter of branches are rationally controlled by varying reaction conditions. Structural characterization reveals that crystalline branches grow epitaxially from the backbone in both homo- and heterobranched NWs. Two different branching structures are observed in the CdSe-ZnSe heterobranched NWs, owing to the phase admixture, i.e., cubic and hexagonal crystal structures, coexisting in the CdSe NW backbones. These branched NWs with well-designed architectures are expected to have potential as three-dimensional building blocks in the fabrication of nanoscale electronics and photonics.

  13. An inverse strategy for relocation of eigenfrequencies in structural design. Part II: second order approximate solutions

    NASA Astrophysics Data System (ADS)

    Farahani, K.; Bahai, H.

    2004-07-01

    This paper extends the first order formulations presented in Part I to second order methods for relocation of structural natural frequencies from their initial design values to new modified frequencies. The method is based on an inverse formulation and solution algorithm of the eigenvalue problem. Using the second order Taylor's expansion series, the required parameter variation to achieve a desired natural frequency shift for the structure is computed through second order differential or binomial equations. The proposed technique can also incorporate the design constraints or objective functions in the system equations. The formulations are quite generic and applicable to all finite element structures. The accuracy of the proposed methods is tested by conducting several case studies, the results of which demonstrate the validity of the technique for a wide range of practical problems.

  14. Mechanism driven structural elucidation of forced degradation products from hydrocortisone in solution.

    PubMed

    Zhang, Fa; Zhou, Jay; Shi, Yiqun; Tavlarakis, Panagiotis; Karaisz, Kenneth

    2016-09-01

    Hydrocortisone degradation products 1, 2, 3, and 4 along with hemiacetal derivatives 5, 6, 7, and 8 were observed through stressed hydrocortisone in solution. Their structures were identified based on HPLC-UV, HPLC-MS, and HPLC-HRMS (high resolution/high accuracy mass spectrometry) analyses as well as reaction mechanistic investigation and synthesis for structural confirmation. 1 and 2 are a pair of E/Z isomers and they were generated through acid catalyzed tautomerization/dehydration of hydrocortisone. Incorporation of water to 1 and 2 resulted in the formation of 3. We also discovered new degradation product 4 which was converted from 3 by oxidation. The degradation products were synthesized by stressing hydrocortisone under the optimized conditions and their structures were characterized by NMR ((1)H/(13)C, COSY, HMBC, HSQC, NOESY) and HRMS analyses. The degradation pathway of hydrocortisone is postulated.

  15. 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.

  16. Mechanism driven structural elucidation of forced degradation products from hydrocortisone in solution.

    PubMed

    Zhang, Fa; Zhou, Jay; Shi, Yiqun; Tavlarakis, Panagiotis; Karaisz, Kenneth

    2016-09-01

    Hydrocortisone degradation products 1, 2, 3, and 4 along with hemiacetal derivatives 5, 6, 7, and 8 were observed through stressed hydrocortisone in solution. Their structures were identified based on HPLC-UV, HPLC-MS, and HPLC-HRMS (high resolution/high accuracy mass spectrometry) analyses as well as reaction mechanistic investigation and synthesis for structural confirmation. 1 and 2 are a pair of E/Z isomers and they were generated through acid catalyzed tautomerization/dehydration of hydrocortisone. Incorporation of water to 1 and 2 resulted in the formation of 3. We also discovered new degradation product 4 which was converted from 3 by oxidation. The degradation products were synthesized by stressing hydrocortisone under the optimized conditions and their structures were characterized by NMR ((1)H/(13)C, COSY, HMBC, HSQC, NOESY) and HRMS analyses. The degradation pathway of hydrocortisone is postulated. PMID:27328360

  17. A vibrational spectroscopy study on anserine and its aqueous solutions.

    PubMed

    Akkaya, Y; Balci, K; Goren, Y; Akyuz, S; Stricker, M C; Stover, D D; Ritzhaupt, G; Collier, W B

    2015-01-01

    In this study based on vibrational spectroscopic measurements and Density Functional Theory (DFT), we aimed for a reliable interpretation of the IR and Raman spectra recorded for anserine in the solid phase and water (H2O) and heavy water (D2O) solutions. Initial DFT calculations at the B3LYP/6-31G(d) searched possible conformers of the anserine zwitterion using a systematic conformational search. The corresponding equilibrium geometrical parameters and vibrational spectral data were determined for each of the stable conformers (in water) by the geometry optimization and hessian calculations performed at the same level of theory using the polarized continuum model (PCM). The same calculations were repeated to determine the most energetically preferred dimer structure for the molecule and the associated geometry, force field and vibrational spectral data. The harmonic force constants obtained from these calculations were scaled by the Scaled Quantum Mechanical Force Field (SQM) method and then used in the calculation of the refined wavenumbers, potential energy distributions, IR and Raman intensities. These refined theoretical data, which confirm the zwitterion structure for anserine in the solid phase or aqueous solvents, revealed the remarkable effects of intermolecular hydrogen bonding on the structural properties and observed IR and Raman spectra of this molecule. PMID:25997178

  18. 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).

  19. 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).

  20. Application of Fourier transform infrared spectroscopy to studies of aqueous protein solutions.

    PubMed

    Zuber, G; Prestrelski, S J; Benedek, K

    1992-11-15

    Modern protein Fourier transform infrared (FT-IR) spectroscopy has proven to be a versatile and sensitive technique, applicable to many aspects of protein characterization. The major practical drawback for the FT-IR spectroscopy of proteins is the large absorbance band of water, which overlaps the amide I resonances. D2O is often substituted for H2O in infrared experiments. Removal of water from protein samples can be complicated and tedious and potentially lead to denaturation, aggregation, or sample loss. Solvent removal by dialysis is difficult for suspensions and sols. A new method called the D2O dilution technique (Ddt) is described which simplifies the sample preparation step and improves the solvent subtraction. The effect of the D2O concentration on the IR spectrum of aqueous solutions of several model proteins was studied. Dilution of aqueous samples with D2O yields good quality spectra. The Ddt has been evaluated for quantitative analysis using standard proteins and its applicability to solutions and suspensions of a genetically engineered malaria antigen is demonstrated. Use of resolution-enhancement techniques with spectra in mixed solvents has also been investigated. PMID:1489088

  1. 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.

  2. Surface structure and electrical properties of solution processed lanthanum nickelate films

    NASA Astrophysics Data System (ADS)

    Pandya, Nirav C.; Joshi, U. S.

    2014-04-01

    Conducting oxides with perovskite crystal structure have many advantages over the simple Pt or Au, Pt based metal bottom electrodes (BE), particularly in fabrication of ferroelectric as well as resistive random access memory devices, if they possess smooth surface morphology. LaNiO3 (LNO) thin films were prepared by modified chemical solution deposition method. Precursor solutions were spin coated onto SiO2-substrates. Deposited layers were thermally treated in a pre-heated furnace at 550 °C and oxygenated up to 800 °C. Results of AFM and FESEM showed that films are very smooth (Ra = 1.69 nm), dense, crack-free and with monodispersed nanocrystallites. Growth conditions such as spinning rate, annealing rates and temperatures etc. have been optimized for mono dispersed crystallinity with very smooth surface morphology. Sheet resistivity, carrier concentration and RMS roughness were correlated with growth temperatures.

  3. 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

  4. Structure of water + acetonitrile solutions from acoustic and positron annihilation measurements

    NASA Astrophysics Data System (ADS)

    Jerie, Kazimierz; Baranowski, Andrzej; Koziol, Stan; Gliński, Jacek; Burakowski, Andrzej

    2005-03-01

    We report the results of acoustic and positron annihilation measurements in aqueous solutions of acetonitrile (CH 3CN). Hydrophobicity of the solute is discussed, as well as the possibility of describing the title system in terms of hydrophobic solvation. A new method of calculating the "ideal" positronium lifetimes is proposed, based on the mean volume of cavities (holes) in liquid structure available for positronium pseudoatom. The results are almost identical with those obtained from molar volumes using the concept of Levay et al. On the other hand, the same calculations performed using the "bubble" model of annihilation yield very different results. It seems that either acetonitrile forms with water clathrate-like hydrates of untypical architecture, or it is too weak hydrophobic agent to form clathrate-like hydrates at all. The former interpretation seems to be more probable.

  5. Structure of Aqueous Solutions of Acetonitrile Investigated by Acoustic and Positron Annihilation Measurements

    NASA Astrophysics Data System (ADS)

    Jerie, K.; Baranowski, A.; Koziol, S.; Burakowski, A.

    2005-05-01

    We report the results of acoustic and positron annihilation measurements in aqueous solutions of acetonitrile (CH3CN). Hydrophobicity of the solute is discussed, as well as the possibility of describing the title system in terms of hydrophobic solvation. The concept of Levay et al. of calculating the "ideal positronium lifetimes is applied, basing on the mean volume of cavities (holes) in liquid structure available for positronium pseudoatom. The same calculations performed using the Tao model of annihilation yield very different results. It can be concluded that either acetonitrile forms with water clathrate-like hydrates of untypical architecture, or it is too weak hydrophobic agent to form clathrate-like hydrates at all. The former interpretation seems to be more probable.

  6. REVIEWS OF TOPICAL PROBLEMS: Supermolecular liquid-crystalline structures in solutions of amphiphilic molecules

    NASA Astrophysics Data System (ADS)

    Vedenov, A. A.; Levchenko, E. B.

    1983-09-01

    This paper reviews the physical properties of liquid-crystalline phases arising in solutions containing molecules of amphiphilic substances. The basic characteristics of micelle formation in dilute solutions, models of sphere-disk or sphere-cylinder structural transformations, as well as phase transitions related to the appearance of lyotropic mesophases in the system, including nematic, lamellar, hexagonal, and others, are examined. The results of experimental and theoretical investigation of "solvation" forces acting between micelles in the solvent, as well as recently studied models of swelling of lamellar phases are presented. The phenomena occurring near the inversion point of microemulsions in amphiphile-oil-water systems are examined briefly. The role of liquid-crystalline ordering in some biological systems is discussed.

  7. Coordination chemistry and solution structure of Fe(II)-peplomycin. Two possible coordination geometries.

    PubMed

    Li, Yang; Lehmann, Teresa

    2012-06-01

    The solution structure of Fe(II)-peplomycin was determined from NMR data collected for this molecule. As found previously for Fe(II)- and Co(II)-bound bleomycin; the coordination sphere of the metal is composed of the primary and secondary amines in β-aminoalanine, the pyrimidine and imidazole rings in the pyrimidinylpropionamide, and β-hydroxyhistidine moieties, respectively, the amine nitrogen in β-hydroxyhistidine, and either the carbamoyl group in mannose or a solvent molecule. The two most discussed coordination geometries for the aforementioned ligands in metallo-bleomycins have been tested against the NMR data generated for Fe(II)-peplomycin. The interpretation of the experimental evidence obtained through molecular dynamics indicates that both geometries are equally likely in solution for this compound in the absence of DNA, but arguments are offered to explain why one of these geometries is preferred in the presence of DNA.

  8. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    NASA Astrophysics Data System (ADS)

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-08-01

    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.

  9. 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.

  10. Thermomechanical effects of co-solute on the structure formation of bovine serum albumin.

    PubMed

    George, Paul; Lundin, Leif; Kasapis, Stefan

    2014-08-15

    The effect of glucose syrup on the structural properties of bovine serum albumin has been addressed in preparations from low to high solids. Fifteen percent protein was mixed with the co-solute at concentrations up to 65% and subjected to thermal treatment to examine the changes in phase and state transitions. Thermomechanics were the working protocol being carried out with micro differential scanning calorimetry and small deformation dynamic oscillation. Results argue that protein molecules have been extensively stabilised by the addition of a co-solute, recorded via a delayed thermal denaturation. Further, increasing the glucose syrup enhanced polymer-polymer interactions leading to stronger networks following thermal denaturation of the globular protein. Condensed BSA/glucose syrup mixtures, i.e. at 80% solids, were cooled at subzero temperatures to exhibit a considerable state of vitrification. Molecular relaxation phenomena were successfully followed using theoretical concepts from synthetic polymer research to yield the mechanical glass transition temperature.

  11. Surface structure and electrical properties of solution processed lanthanum nickelate films

    SciTech Connect

    Pandya, Nirav C. Joshi, U. S.

    2014-04-24

    Conducting oxides with perovskite crystal structure have many advantages over the simple Pt or Au, Pt based metal bottom electrodes (BE), particularly in fabrication of ferroelectric as well as resistive random access memory devices, if they possess smooth surface morphology. LaNiO{sub 3} (LNO) thin films were prepared by modified chemical solution deposition method. Precursor solutions were spin coated onto SiO{sub 2}-substrates. Deposited layers were thermally treated in a pre-heated furnace at 550 °C and oxygenated up to 800 °C. Results of AFM and FESEM showed that films are very smooth (Ra = 1.69 nm), dense, crack-free and with monodispersed nanocrystallites. Growth conditions such as spinning rate, annealing rates and temperatures etc. have been optimized for mono dispersed crystallinity with very smooth surface morphology. Sheet resistivity, carrier concentration and RMS roughness were correlated with growth temperatures.

  12. Periodic solutions of a nonautonomous predator-prey system with stage structure and time delays

    NASA Astrophysics Data System (ADS)

    Xu, Rui; Wang, Zhiqiang

    2006-11-01

    A nonautonomous Lotka-Volterra type predator-prey model with stage structure and time delays is investigated. It is assumed in the model that the individuals in each species may belong to one of two classes: the immatures and the matures, the age to maturity is presented by a time delay, and that the immature predators do not feed on prey and do not have the ability to reproduce. By some comparison arguments we first discuss the permanence of the model. By using the continuation theorem of coincidence degree theory, sufficient conditions are derived for the existence of positive periodic solutions to the model. By means of a suitable Lyapunov functional, sufficient conditions are obtained for the uniqueness and global stability of the positive periodic solutions to the model.

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

    PubMed

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

    2016-06-28

    Curli, consisting primarily of major structural subunit CsgA, are functional amyloids produced on the surface of Escherichia coli, as well as many other enteric bacteria, and are involved in cell colonization and biofilm formation. CsgE is a periplasmic accessory protein that plays a crucial role in curli biogenesis. CsgE binds to both CsgA and the nonameric pore protein CsgG. The CsgG-CsgE complex is the curli secretion channel and is essential for the formation of the curli fibril in vivo. To better understand the role of CsgE in curli formation, we have determined the solution NMR structure of a double mutant of CsgE (W48A/F79A) that appears to be similar to the wild-type (WT) protein in overall structure and function but does not form mixed oligomers at NMR concentrations similar to the WT. The well-converged structure of this mutant has a core scaffold composed of a layer of two α-helices and a layer of three-stranded antiparallel β-sheet with flexible N and C termini. The structure of CsgE fits well into the cryoelectron microscopy density map of the CsgG-CsgE complex. We highlight a striking feature of the electrostatic potential surface in CsgE structure and present an assembly model of the CsgG-CsgE complex. We suggest a structural mechanism of the interaction between CsgE and CsgA. Understanding curli formation can provide the information necessary to develop treatments and therapeutic agents for biofilm-related infections and may benefit the prevention and treatment of amyloid diseases. CsgE could establish a paradigm for the regulation of amyloidogenesis because of its unique role in curli formation. PMID:27298344

  14. 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

  15. Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

    PubMed

    Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

    1998-02-01

    The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.

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

    PubMed Central

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

    2013-01-01

    Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ. PMID:23897477

  17. Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii

    PubMed Central

    Singarapu, Kiran K.; Otte, Michele M.; Tonelli, Marco; Westler, William M.; Escalante-Semerena, Jorge C.; Markley, John L.

    2015-01-01

    GTP:adenosylcobinamide-phosphate (AdoCbi-P) guanylyl transferase (CobY) is an enzyme that transfers the GMP moiety of GTP to AdoCbi yielding AdoCbi-GDP in the late steps of the assembly of Ado-cobamides in archaea. The failure of repeated attempts to crystallize ligand-free (apo) CobY prompted us to explore its 3D structure by solution NMR spectroscopy. As reported here, the solution structure has a mixed α/β fold consisting of seven β-strands and five α-helices, which is very similar to a Rossmann fold. Titration of apo-CobY with GTP resulted in large changes in amide proton chemical shifts that indicated major structural perturbations upon complex formation. However, the CobY:GTP complex as followed by 1H-15N HSQC spectra was found to be unstable over time: GTP hydrolyzed and the protein converted slowly to a species with an NMR spectrum similar to that of apo-CobY. The variant CobYG153D, whose GTP complex was studied by X-ray crystallography, yielded NMR spectra similar to those of wild-type CobY in both its apo- state and in complex with GTP. The CobYG153D:GTP complex was also found to be unstable over time. PMID:26513744

  18. 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

  19. Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

    PubMed

    Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

    1998-02-01

    The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions. PMID:9443977

  20. Conformational structure and energetics of 2-methylphenyl(2'-methoxyphenyl)iodonium chloride: evidence for solution clusters.

    PubMed

    Lee, Yong-Sok; Hodoscek, Milan; Chun, Joong-Hyun; Pike, Victor W

    2010-09-10

    Diaryliodonium salts allow the efficient incorporation of cyclotron-produced [(18)F]fluoride ions into electron-rich and electron-deficient arenes to provide potential radiotracers for molecular imaging in vivo with positron emission tomography (PET). This process (ArI(+)Ar'+(18)F(-)→Ar(18)F+Ar'I) is still not well understood mechanistically. To better understand this and similar reactions, it would be valuable to understand the structures of diaryliodonium salts in organic media, where the reactions are typically conducted. In this endeavor, the X-ray structure of a representative iodonium salt, 2-methylphenyl(2'-methoxyphenyl)iodonium chloride (1), was determined. Our X-ray structure analysis showed 1 to have the conformational M-P dimer as the unit cell with hypervalent iodine as a stereogenic center in each conformer. With the ab initio replica path method we constructed the inversion path between the two enantiomers of 1, thereby revealing two additional pairs of enantiomers that are likely to undergo fast interconversion in solution. Also LC-MS of 1 showed the presence of dimeric and tetrameric anion-bridged clusters in weak organic solution. This observation is consistent with the energetics of 1, both as monomeric and dimeric forms in MeCN, calculated at the B3LYP/DGDZVP level. These evidences of the existence of dimeric and higher order clusters of 1 in solution are relevant to achieve a deeper general understanding of the mechanism and outcome of reactions of diaryliodonium salts in organic media with nucleophiles, such as the [(18)F]fluoride ion.

  1. Structure of the Glycyl-L-histidyl-L-lysine--copper(II) complex in solution.

    PubMed

    Freedman, J H; Pickart, L; Weinstein, B; Mims, W B; Peisach, J

    1982-09-14

    Optical, electron paramagnetic resonance, and electron spin-echo envelope spectroscopies were used to examine the structure of the Cu(II) complex of glycyl-L-histidyl-L-lysine (GHL) in solution. At neutral pH, GHL forms a mononuclear 1:1 Cu(II) compound having an EPR spectrum resembling that of Cu(II) equatorially coordinated by two or three nitrogen atoms. Electron spin-echo studies demonstrate that one of these is located in the histidyl imidazole ring. A pH titration of Cu(II)-GHL shows three optical transitions with apparent pKs of 3.6, 9.2 and 11.4 and molecularities, with respect to protons, of 2, 2, and 1, respectively. At the lowest pK, GHL binds Cu(II), forming the species present at physiological pH. At elevated pH, spectroscopic experiments suggest that an alteration of the Cu(II) structure occurs, yet the bound imidazole is retained. These solution studies are consistent with nitrogen coordination of Cu(II) in Cu(II)-GHL, but the solid-state polymeric structure, with oxygen-bridged Cu(II) pairs as previously determined by X-ray crystallographic analysis [Pickart, L., Freedman, J. H., Loker, W. J., Peisach, J., Perkins, C. M., Steinkamp, R. E., & Weinstein, B. (1980) Nature (London) 288, 715-717; C. M. Perkins, N. J. Rose, R. E. Steinkamp, L. H. Jensen, B. Weinstein, and L. Pickart, unpublished results], does not exist in solution. PMID:6291585

  2. Understanding the structural disorganization of starch in water-ionic liquid solutions.

    PubMed

    Zhang, Binjia; Chen, Ling; Xie, Fengwei; Li, Xiaoxi; Truss, Rowan W; Halley, Peter J; Shamshina, Julia L; Rogers, Robin D; McNally, Tony

    2015-06-01

    Using synchrotron X-ray scattering analyses and Fourier transform infrared spectroscopy, this work provides insights into the solvent effects of water : [C2mim][OAc] solutions on the disorganization of a starch semi-crystalline structure. When a certain ratio (10.2 : 1 mol/mol) of water : [C2mim][OAc] solution is used, the preferential hydrogen bonding between starch hydroxyls and [OAc](-) anions results in the breakage of the hydrogen bonding network of starch and thus the disruption of starch lamellae. This greatly facilitates the disorganization of starch, which occurs much easier than in pure water. In contrast, when 90.8 : 1 (mol/mol) water : [C2mim][OAc] solution is used, the interactions between [OAc](-) anions and water suppress the solvent effects on starch, thereby making the disorganization of starch less easy than in pure water. All these differences can be shown by changes in the lamellar and fractal structures: firstly, a preferable increase in the thickness of the crystalline lamellae rather than that of the amorphous lamellae causes an overall increase in the thickness of the semi-crystalline lamellae; then, the amorphous lamellae start to decrease probably due to the out-phasing of starch molecules from them; this forms a fractal gel on a larger scale (than the lamellae) which gradually decreases to a stable value as the temperature increases further. It is noteworthy that these changes occur at temperatures far below the transition temperature that is thermally detectable as is normally described. This hints to our future work that using certain aqueous ionic liquids for destructuration of the starch semi-crystalline structure is the key to realize green processes to obtain homogeneous amorphous materials. PMID:25899721

  3. 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

  4. Analytical solution to a fracture problem in a tough layered structure

    NASA Astrophysics Data System (ADS)

    Hamamoto, Yukari; Okumura, Ko

    2008-08-01

    Nacre causes the shining beauty of pearl due to its remarkable layered structure, which is also strong. We reconsider a simplified layered model of nacre proposed previously [Okumura and de Gennes, Eur. Phys. J. E 4, 121 (2001)] and obtain an analytical solution to a fundamental crack problem. The result asserts that the fracture toughness is enhanced due to a large displacement around the crack tip (even if the crack-tip stress is not reduced). The derivation offers ideas for solving a number of boundary problems for partial differential equations important in many fields.

  5. 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.

  6. Colloidal structure and stabilization mechanism of aqueous solutions of unmodified fullerene C{sub 60}

    SciTech Connect

    Khokhryakov, A. A. Kyzyma, O. A.; Bulavin, L. A.; Len, A.; Avdeev, M. V.; Aksenov, V. L.

    2007-05-15

    Despite the inability of fullerenes to be directly dissolved in water, there are methods for preparing stable dispersions of fullerenes in water without any particular modifications of the fullerene or addition of stabilizers. The colloidal properties of such systems prepared by replacing the solvent and structural changes in them during coagulation have been studied. The coagulation dynamics has been investigated by spectroscopy and small-angle neutron scattering. The results obtained confirm the colloidal nature of such systems. During coagulation, particles retain a large volume of water around them, an indication of interaction between fullerene and water during solution stabilization.

  7. Electronic structure of trypsin inhibitor from squash seeds in aqueous solution

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    2000-10-01

    The electronic structure of the trypsin inhibitor from seeds of the squash Cucurbita maxima (CMTI-I) in aqueous solution is obtained by ab initio, all-electron, full-potential calculations using the self-consistent cluster-embedding (SCCE) method. The reactive site of the inhibitor is explained theoretically, which is in agreement with the experimental results. It is shown that the coordinates of oxygen atoms in the inhibitor, determined by nuclear magnetic resonance and combination of distance geometry and dynamical simulated annealing, are systematically less accurate than that of other kinds of heavy atoms.

  8. 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

  9. Nuclear magnetic resonance analysis of the solution and solvolysis of sulfur mustard in deuterium oxide.

    PubMed

    Logan, Thomas P; Sartori, David A

    2003-01-01

    Our laboratory performs in vitro experiments in which cell cultures are exposed to sulfur mustard (HD) to investigate the toxicity of this agent of chemical warfare. To perform these experiments, it is important to know the rate of hydrolysis of HD in order to calculate the concentrations of HD and its hydrolysis products during the experiment. Researchers have previously investigated the kinetics and mechanism of the hydrolysis of HD using a variety of methods. In the present study, we used nuclear magnetic resonance (NMR) spectroscopy and gas chromatography/mass spectrometry (GC/MS) to investigate HD's dissolution and solvolysis in deuterium oxide (D 2 O) at 2 mM. We followed activity in proton spectrums and determined the half-life (t 1/2) of HD to be 7.0 +/- 0.5 min in four experiments performed at 22 degrees C. In addition, we determined the t 1/2 of HD in D 2 O containing 0.17 M sodium chloride to be 24 +/- 1 min in three experiments performed at 22 degrees C. As further proof of the existence of HD dissolved into D 2 O, deutero-hexane was used to extract the D 2 O HD solution. The resulting deutero-hexane solution was studied by 1 H NMR and GC/MS. The results obtained match those received from a standard deutero-hexane HD solution. These results demonstrate that HD can be identified in D 2 O with proton NMR and that proton NMR data can be used to monitor the subsequent solvolysis of HD. PMID:20021164

  10. Multicomponent adsorption of alcohols onto silicalite-1 from aqueous solution: isotherms, structural analysis, and assessment of ideal adsorbed solution theory.

    PubMed

    Bai, Peng; Tsapatsis, Michael; Siepmann, J Ilja

    2012-11-01

    Configurational-bias Monte Carlo (CBMC) simulations in the isobaric-isothermal version of the Gibbs ensemble (GE) were carried out to probe the adsorption from aqueous solutions of methanol and/or ethanol onto silicalite-1. This methodology does require neither specification of the chemical potential nor any reference to activity models based on experimental data. The CBMC-GE methodology can be applied to the complete range of mixture compositions from pure water to pure alcohols and can also be used when multiple solute types are present at high concentration. The simulations demonstrate high selectivities for the alcohols (α(ethanol) > α(methanol)) almost over the entire composition range. The ideal adsorbed solution theory is found to substantially underpredict the amount of sorbed water and leads to very large errors for low alcohol solution concentrations. The simulations indicate that, at lower loadings, the adsorbed alcohol molecules can serve as seeds for water adsorption but, at higher loadings, alcohols displace water molecules from their preferred region.

  11. Nuclear Magnetic Resonance Solution Structure of DNA Featuring Clustered 2'-Deoxyribonolactone and 8-Oxoguanine Lesions.

    PubMed

    Zálešák, Jan; Constant, Jean-François; Jourdan, Muriel

    2016-07-19

    Ionizing radiation, free radicals, and reactive oxygen species produce hundreds of different DNA lesions. Clustered lesions are typical for ionizing radiation. They compromise the efficiency of the base excision repair (BER) pathway, and as a consequence, they are much more toxic and mutagenic than isolated lesions. Despite their biological relevance, e.g., in cancer radiotherapy and accidental exposure, they are not very well studied from a structural point of view, and while insights provided by structural studies contribute to the understanding of the repair process, only three nuclear magnetic resonance (NMR) studies of DNA containing clusters of lesions were reported. Herein, we report the first NMR solution structure of two DNAs containing a bistranded cluster with the 2'-deoxyribonolactone and 8-oxoguanine lesions. Both DNA duplexes feature a 2'-deoxyribonolactone site in the middle of the sequence of one strand and differ by the relative position of the 8-oxoguanine, staggered 3' or 5' side on the complementary strand at a three-nucleotide distance. Depending on its relative position, the repair of the 8-oxoguanine lesion by the base excision repair protein Fpg is either almost complete or inhibited. We found that the structures of the two DNAs containing a bistranded cluster of two lesions are similar and do not deviate very much from the standard B-form. As no obvious structural deformations were observed between the two duplexes, we concluded that the differences in Fpg activity are not due to differences in their global conformation. PMID:27322640

  12. Structure of human telomeric RNA (TERRA): stacking of two G-quadruplex blocks in K(+) solution.

    PubMed

    Martadinata, Herry; Phan, Anh Tuân

    2013-04-01

    Telomeric repeat-containing RNAs (TERRA) are transcription products of the telomeres. Human TERRA sequences containing UUAGGG repeats can form parallel-stranded G-quadruplexes. The stacking interaction of such structures was shown to be important for ligand targeting and higher-order arrangement of G-quadruplexes in long TERRA sequences. Here we report on the first high-resolution structure of a stacked G-quadruplex formed by the 10-nucleotide human TERRA sequence r(GGGUUAGGGU) in potassium solution. This structure comprises two dimeric three-layer parallel-stranded G-quadruplex blocks, which stack on each other at their 5'-ends. The adenine in each UUA loop is nearly coplanar with the 5'-end G-tetrad forming an A·(G·G·G·G)·A hexad, thereby increasing the stacking contacts between the two blocks. Interestingly, this stacking and loop conformation is different from all structures previously reported for the free human TERRA but resembles the structure previously determined for a complex between a human TERRA sequence and an acridine ligand. This stacking conformation is a potential target for drugs that recognize or induce the stacking interface.

  13. Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

    PubMed Central

    Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2012-01-01

    What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea. PMID:22303014

  14. Unexpected structural softening of interstitial boron solid solution WB{sub 3+x}

    SciTech Connect

    Wu, Hao; Sun, Hong E-mail: chen@physics.unlv.edu; Chen, Changfeng E-mail: chen@physics.unlv.edu

    2014-11-24

    Using first-principles calculations, we reveal an unexpected structural softening in a recently proposed WB{sub 3+x} structural model that tries to explain the X-ray diffraction, high resolution TEM, pressure dependence of the normalized lattice c/a ratio, and hardness experimental results of the synthesized tungsten boride compounds with a nominal composition WB{sub 4}. We show that the interstitial boron in WB{sub 3+x}, which was proposed to strengthen the covalent bonding network, unexpectedly weakens the atomic bonding, resulting in a large reduction of its indentation strength to well below that of WB{sub 3}. This is in direct contradiction to the experimental results showing that synthesized WB{sub 4} is harder than WB{sub 3}. The unusual structural softening is attributed to the unique three-center covalent bonding formed by the interstitial boron atoms that can easily deform under indentation. Our results show that the proposed interstitial boron solid solution WB{sub 3+x} structure is incompatible with experimental results, which calls for further investigations to determine the crystal structure of the synthesized WB{sub 4}.

  15. Definition of the switch surface in the solution structure of Cdc42Hs.

    PubMed

    Feltham, J L; Dötsch, V; Raza, S; Manor, D; Cerione, R A; Sutcliffe, M J; Wagner, G; Oswald, R E

    1997-07-22

    Proteins of the rho subfamily of ras GTPases have been shown to be crucial components of pathways leading to cell growth and the establishment of cell polarity and mobility. Presented here is the solution structure of one such protein, Cdc42Hs, which provides insight into the structural basis for specificity of interactions between this protein and its effector and regulatory proteins. Standard heteronuclear NMR methods were used to assign the protein, and approximately 2100 distance and dihedral angle constraints were used to calculate a set of 20 structures using a combination of distance geometry and simulated annealing refinement. These structures show overall similarity to those of other GTP-binding proteins, with some exceptions. The regions corresponding to switch I and switch II in H-ras are disordered, and no evidence was found for an alpha-helix in switch II. The 13-residue insertion, which is only present in rho-subtype proteins and has been shown to be an important mediator of binding of regulatory and target proteins, forms a compact structure containing a short helix lying adjacent to the beta4-alpha3 loop. The insert forms one edge of a "switch surface" and, unexpectedly, does not change conformation upon activation of the protein by the exchange of GTP analogs for GDP. These studies indicate the insert region forms a stable invariant "footrest" for docking of regulatory and effector proteins.

  16. [Application of nuclear magnetic resonance for the determination of the structure of proteins in solution].

    PubMed

    Charretier, E; Guéron, M

    1991-01-01

    Knowledge of three-dimensional structure is a key factor in protein engineering. It is useful, for example, in predicting and understanding the functional consequences of specific substitution of one or more amino acids of the polypeptide chain. It is also necessary for the design of new effectors or analogs of the substrates of enzymes and receptors. X-ray diffraction by crystals of the biomolecule was for a long time the only method of determining three-dimensional structures. In the last 5 years, it has been joined by a new technique, two-dimensional nuclear magnetic resonance (2D NMR), which can resolve the structure of middle-sized proteins (less than 10 kilodaltons). The technique is applied on solutions whose pH, ionic strength, and temperature can be chosen and changed. The two basic measurements, COSY and NOESY, detect respectively the systems of hydrogen nuclei, or protons, coupled through covalent bonds, and those in which the interproton distances are less than 0.5 nm. A systematic strategy leads from resonance assignments of the two-dimensional spectrum to molecular modeling with constraints and finally to the determination of the molecular structure in the solution. Much sophistication is needed even today for the first task, the assignment of the resonances. Each of the COSY and NOESY spectra is a two-dimensional map, where the diagonal line is the one-dimensional spectrum, and the off-diagonal peaks indicate connectives between protons. Peak assignment to a specific type of amino acid is based on the pattern of scalar couplings observed in the COSY spectrum. Next, the amino acids are positioned in the primary sequence, using the spatial proximities of polypeptide chain protons, as observed in the NOESY spectrum. The principal secondary structures (alpha helix, beta sheets, etc.) are then identified by their specific connectivities. The tertiary structure is detected by NOESY connectivities between protons of different amino acids which are far apart

  17. Effect of tannic acid solution on collagen structures for dental restoration.

    PubMed

    Natsir, N; Wakasa, K; Yoshida, Y; Satou, N; Shintani, H

    1999-08-01

    This study examined the effect of tannic acid solution on dissolution of dentine collagen and morphological aspects of tendon collagen. Using root dentine, which was cut off from bovine anterior tooth, dentine powders were obtained by the pulverization and lyophilization. They were subject to an application of 1, 3, 5 or 10% tannic acid (TA) solution for 1, 3, 6, 12 or 24 h. TA-treated dentine powders were treated with 40% phosphoric acid (PA) for 30 s at 20 degrees C and additionally with trypsin. Released hydroxyproline in Woessner's assay after a hydrolysis in 6 N HCl at 110 degrees C for 20 h was assumed to be dissolved dentine collagen. Released hydroxyproline in a control sample without acid treatment decreased from 100 to about 60% with increased TA concentration of 1 to 10%, and decreased with increased incubation times of 1 to 24 h when applied by 5% TA solution. Scanning electron microscopy results established the morphological effect of their surface characteristics due to such treatments as 40% PA for 30 s and 5% TA for 6 h, or 40% PA after 5% TA treatment, yielding collagen structures protected by TA to attack from phosphoric acid.

  18. Inverse solution technique of steady-state responses for local nonlinear structures

    NASA Astrophysics Data System (ADS)

    Wang, Xing; Guan, Xin; Zheng, Gangtie

    2016-03-01

    An inverse solution technique with the ability of obtaining complete steady-state primary harmonic responses of local nonlinear structures in the frequency domain is proposed in the present paper. In this method, the nonlinear dynamic equations of motion is first condensed from many to only one algebraic amplitude-frequency equation of relative motion. Then this equation is transformed into a polynomial form, and with its frequency as the unknown variable, the polynomial equation is solved by tracing all the solutions of frequency with the increase of amplitude. With this solution technique, some complicated dynamic behaviors such as sharp tuning, anomalous jumps, breaks in responses and detached resonance curves could be obtained. The proposed method is demonstrated and validated through a finite element beam under force excitations and a lumped parameter model with a local nonlinear element under base excitations. The phenomenon of detached resonance curves in the frequency response and its coupling effects with multiple linear modes in the latter example are observed.

  19. Structural Evidence for Inter-Residue Hydrogen Bonding Observed for Cellobiose in Aqueous Solution

    PubMed Central

    O'Dell, William B.; Baker, David C.; McLain, Sylvia E.

    2012-01-01

    The structure of the disaccharide cellulose subunit cellobiose (4-O-β-D-glucopyranosyl-D-glucose) in solution has been determined via neutron diffraction with isotopic substitution (NDIS), computer modeling and nuclear magnetic resonance (NMR) spectroscopic studies. This study shows direct evidence for an intramolecular hydrogen bond between the reducing ring HO3 hydroxyl group and the non-reducing ring oxygen (O5′) that has been previously predicted by computation and NMR analysis. Moreover, this work shows that hydrogen bonding to the non-reducing ring O5′ oxygen is shared between water and the HO3 hydroxyl group with an average of 50% occupancy by each hydrogen-bond donor. The glycosidic torsion angles φH and ψH from the neutron diffraction-based model show a fairly tight distribution of angles around approximately 22° and −40°, respectively, in solution, consistent with the NMR measurements. Similarly, the hydroxymethyl torsional angles for both reducing and non-reducing rings are broadly consistent with the NMR measurements in this study, as well as with those from previous measurements for cellobiose in solution. PMID:23056199

  20. 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. Solution NMR Structure Determination of Polytopic α-Helical Membrane Proteins: A Guide to Spin Label Paramagnetic Relaxation Enhancement Restraints.

    PubMed

    Columbus, Linda; Kroncke, Brett

    2015-01-01

    Solution nuclear magnetic resonance structures of polytopic α-helical membrane proteins require additional restraints beyond the traditional Nuclear Overhauser Effect (NOE) restraints. Several methods have been developed and this review focuses on paramagnetic relaxation enhancement (PRE). Important aspects of spin labeling, PRE measurements, structure calculations, and structural quality are discussed.

  2. Solid-State and Solution Structures of Glycinimine-Derived Lithium Enolates.

    PubMed

    Jin, Kyoung Joo; Collum, David B

    2015-11-18

    A combination of crystallographic, spectroscopic, and computational studies was applied to study the structures of lithium enolates derived from glycinimines of benzophenone and (+)-camphor. The solvents examined included toluene and toluene containing various concentrations of tetrahydrofuran, N,N,N',N'-tetramethylethylenediamine (TMEDA), (R,R)-N,N,N',N'-tetramethylcyclohexanediamine [(R,R)-TMCDA], and (S,S)-N,N,N',N'-tetramethylcyclohexanediamine [(S,S)-TMCDA]. Crystal structures show chelated monomers, symmetric disolvated dimers, S4-symmetric tetramers, and both S6- and D3d-symmetric hexamers. (6)Li NMR spectroscopic studies in conjunction with the method of continuous variations show how these species distribute in solution. Density functional theory computations offer insights into experimentally elusive details. PMID:26554898

  3. Effect of iron oxide loading on magnetoferritin structure in solution as revealed by SAXS and SANS.

    PubMed

    Melníková, L; Petrenko, V I; Avdeev, M V; Garamus, V M; Almásy, L; Ivankov, O I; Bulavin, L A; Mitróová, Z; Kopčanský, P

    2014-11-01

    Synthetic biological macromolecule of magnetoferritin containing an iron oxide core inside a protein shell (apoferritin) is prepared with different content of iron. Its structure in aqueous solution is analysed by small-angle synchrotron X-ray (SAXS) and neutron (SANS) scattering. The loading factor (LF) defined as the average number of iron atoms per protein is varied up to LF=800. With an increase of the LF, the scattering curves exhibit a relative increase in the total scattered intensity, a partial smearing and a shift of the match point in the SANS contrast variation data. The analysis shows an increase in the polydispersity of the proteins and a corresponding effective increase in the relative content of magnetic material against the protein moiety of the shell with the LF growth. At LFs above ∼150, the apoferritin shell undergoes structural changes, which is strongly indicative of the fact that the shell stability is affected by iron oxide presence.

  4. Solution structure and antiparasitic activity of scorpine-like peptides from Hoffmannihadrurus gertschi.

    PubMed

    Flores-Solis, David; Toledano, Yanis; Rodríguez-Lima, Oscar; Cano-Sánchez, Patricia; Ramírez-Cordero, Belen Ernestina; Landa, Abraham; Rodríguez de la Vega, Ricardo C; Del Rio-Portilla, Federico

    2016-07-01

    Scorpine-like peptides are two domain peptides found in different scorpion venoms displaying various antimicrobial, cytolytic, and potassium channel-blocking activities. The relative contribution of each domain to their different activities remains to be elucidated. Here, we report the recombinant production, solution structure, and antiparasitic activity of Hge36, first identified as a naturally occurring truncated form of a Scorpine-like peptide from the venom of Hoffmannihadrurus gertschi. We also show that removing the first four residues from Hge36 renders a molecule with enhanced potassium channel-blocking and antiparasitic activities. Our results are important to rationalize the structure-function relationships of a pharmacologically versatile molecular scaffold. PMID:27314815

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

    PubMed

    Rong, Xi; Kolpak, Alexie M

    2015-05-01

    The design of efficient, stable, and inexpensive catalysts for oxygen evolution and reduction is crucial for the development of electrochemical energy conversion devices such as fuel cells and metal-air batteries. Currently, such design is limited by challenges in atomic-scale experimental characterization and computational modeling of solid-liquid interfaces. Here, we begin to address these issues by developing a general-, first-principles-, and electrochemical-principles-based framework for prediction of catalyst surface structure, stoichiometry, and stability as a function of pH, electrode potential, and aqueous cation concentration. We demonstrate the approach by determining the surface phase diagram of LaMnO3, which has been studied for oxygen evolution and reduction and computing the reaction overpotentials on the relevant surface phases. Our results illustrate the critical role of solvated cation species in governing the catalyst surface structure and stoichiometry, and thereby catalytic activity, in aqueous solution.

  6. Structural Analysis of Hydrophobe-Uptake Micelle of an Amphiphilic Alternating Copolymer in Aqueous Solution.

    PubMed

    Morishima, Ken; Terao, Ken; Sato, Takahiro

    2016-08-01

    We investigated the structure of the hydrophobe-uptake micelle of an alternating amphiphilic copolymer in aqueous solutions, by combining light scattering and small-angle X-ray scattering (SAXS). When the copolymer micelle includes the hydrophobe (1-dodecanol), the unicore flower micelle transforms into the multicore flower necklace, and the flower necklace is slightly stiffer than the hydrophobe-free flower necklace of the same copolymer. Moreover, the hydrophobe is included not in the hydrophobic core region but in the intermingled region of the hydrophobic group and the loop chain of the unit flower micelle. Therefore, the structure of the hydrophobe-uptake micelle of the amphiphilic alternating copolymer is quite different from that of hydrophobe-uptake spherical micelles of low molar mass surfactants and of amphiphilic block copolymers, where the hydrophobe is included in the hydrophobic region of the micelles.

  7. Effect of polymer matrix on structure of Se particles formed in aqueous solutions during redox process

    SciTech Connect

    Suvorova, E. I. Klechkovskaya, V. V.

    2010-12-15

    Transmission electron microscopy and X-ray energy dispersive microanalysis study of the structure of particles formed during the reduction of Se(IV) to Se(0) in aqueous solutions in the presence of amphiphilic polymers showed the formation of Se/polymer composite particles. The content of carbon inside the particles can be as large as 80 at %. Polymers deeply influence the structure of particles. Depending on polymers, the composite particles may be unstable with time and they spontaneously evolve from Se/polymer composite particles to crystalline particles of monoclinic Se. For the stable ones, addition of bacterial cellulose Acetobacter xylinum gel-film can induce crystallization in the particles which expel the polymeric material. The Se/polymer composite particles and Se crystalline particles exhibit different sensitivity to electron irradiation and stiffness.

  8. Layer structured graphite oxide as a novel adsorbent for humic acid removal from aqueous solution.

    PubMed

    Hartono, Tri; Wang, Shaobin; Ma, Qing; Zhu, Zhonghua

    2009-05-01

    Layer structured graphite oxide (GO) was prepared from graphite using the Hummers-Offeman method, characterised using N(2) adsorption, XRD, XPS, SEM(TEM), and FT-IR, and tested for humic acid (HA) adsorption in aqueous solution. XRD, XPS, and FT-IR measurements indicate the formation of layered structure with strong functional groups of GO. It is also found that the GO exhibits strong and much higher adsorption capacity of HA than graphite. The maximum adsorption capacity of the GO from the Langmuir isotherm is 190 mg/g, higher than activated carbon. For the adsorption, several parameters will affect the adsorption such as solid loading and pH. HA adsorption will decrease with increasing pH and an optimum GO loading is required for maximum adsorption. PMID:19233379

  9. 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.

  10. Elliptical vortex solutions, integrable Ermakov structure, and Lax pair formulation of the compressible Euler equations.

    PubMed

    An, Hongli; Fan, Engui; Zhu, Haixing

    2015-01-01

    The 2+1-dimensional compressible Euler equations are investigated here. A power-type elliptic vortex ansatz is introduced and thereby reduction obtains to an eight-dimensional nonlinear dynamical system. The latter is shown to have an underlying integral Ermakov-Ray-Reid structure of Hamiltonian type. It is of interest to notice that such an integrable Ermakov structure exists not only in the density representations but also in the velocity components. A class of typical elliptical vortex solutions termed pulsrodons corresponding to warm-core eddy theory is isolated and its behavior is simulated. In addition, a Lax pair formulation is constructed and the connection with stationary nonlinear cubic Schrödinger equations is established.

  11. Solution Structure of Ribosomal Protein S28E From Methanobacterium Thermoautotrophicum

    SciTech Connect

    Wu, Bin; Yee, Adelinda; Pineda-Lucena, Antonio; Semesi, Anthony; Ramelot, Theresa A.; Cort, John R.; Jung, Jin-Won; Edwards, Aled M.; Lee, Weontae; Kennedy, Michael A.; Arrowsmith, Cheryl H.

    2003-12-01

    The ribosomal protein S28E from the archaeon Methanobacterium thermoautotrophicum is a component of the 30S ribosomal subunit. Sequence homologs of S28E are found only in archaea and eukaryotes. Here we report the three-dimensional solution structure of S28E by NMR spectroscopy. S28E contains a globular region and a long C-terminal tail protruding from the core. The globular region consists of four antiparallel {beta}-strands which are arranged in a Greek-key topology. Unique features of S28E include an extended loop L2-3 that folds back onto the protein and a 12-residue charged C-terminal tail with no regular secondary structure and greater flexibility relative to the rest of the protein.

  12. 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.

  13. Amyloid-β peptide structure in aqueous solution varies with fragment size

    NASA Astrophysics Data System (ADS)

    Wise-Scira, Olivia; Xu, Liang; Kitahara, Taizo; Perry, George; Coskuner, Orkid

    2011-11-01

    Various fragment sizes of the amyloid-β (Aβ) peptide have been utilized to mimic the properties of the full-length Aβ peptide in solution. Among these smaller fragments, Aβ16 and Aβ28 have been investigated extensively. In this work, we report the structural and thermodynamic properties of the Aβ16, Aβ28, and Aβ42 peptides in an aqueous solution environment. We performed replica exchange molecular dynamics simulations along with thermodynamic calculations for investigating the conformational free energies, secondary and tertiary structures of the Aβ16, Aβ28, and Aβ42 peptides. The results show that the thermodynamic properties vary from each other for these peptides. Furthermore, the secondary structures in the Asp1-Lys16 and Asp1-Lys28 regions of Aβ42 cannot be completely captured by the Aβ16 and Aβ28 fragments. For example, the β-sheet structures in the N-terminal region of Aβ16 and Aβ28 are either not present or the abundance is significantly decreased in Aβ42. The α-helix and β-sheet abundances in Aβ28 and Aβ42 show trends - to some extent - with the potential of mean forces but no such trend could be obtained for Aβ16. Interestingly, Arg5 forms salt bridges with large abundances in all three peptides. The formation of a salt bridge between Asp23-Lys28 is more preferred over the Glu22-Lys28 salt bridge in Aβ28 but this trend is vice versa for Aβ42. This study shows that the Asp1-Lys16 and Asp1-Lys28 regions of the full length Aβ42 peptide cannot be completely mimicked by studying the Aβ16 and Aβ28 peptides.

  14. 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

  15. 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

  16. The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

    PubMed

    Shi, Xuesong; Huang, Lin; Lilley, David M J; Harbury, Pehr B; Herschlag, Daniel

    2016-03-01

    With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes. PMID:26727239

  17. 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.

  18. General-Purpose Expression of Structural Connectivity in the Parallel Solution Scheme and Its Application

    NASA Astrophysics Data System (ADS)

    Isobe, Daigoro; Yagi, Atsushi; Sato, Shunsuke

    In this paper, an algorithm for the general-purpose expression of structural connectivity is developed and implemented into the parallel solution scheme, which was previously proposed and successively applied to the feed-forward control of link mechanisms under various boundary conditions. The parallel solution scheme calculates the inverse dynamics of link systems by using a matrix-form equation separated into individual terms of different parameters. Therefore, the connectivity of link members can be expressed explicitly by one of the matrices, the member length matrix. Generated forces for the control can also be considered, without using any Jacobian matrices, simply by adding the values into one of the components in the equation, the vector related to nodal forces. We describe the forming process of the member length matrix and verify the validity of the calculated torque values, by presenting simple numerical results and experimental results for a structure-varying link system. We also perform a force control experiment on a quick motion, two-arm link system holding an object, where both generated forces and dynamical effects should be considered. Numerical and experimental results show the validity and the extensive ability of the scheme.

  19. Structure of P3HT crystals, thin films, and solutions by UV/Vis spectral analysis.

    PubMed

    Böckmann, Marcus; Schemme, Thomas; de Jong, Djurre H; Denz, Cornelia; Heuer, Andreas; Doltsinis, Nikos L

    2015-11-21

    Optical absorption spectra of poly(3-hexylthiophene) (P3HT) are calculated in solution, spin-coated thin films, and the bulk crystal using a multiscale simulation approach. The structure of the amorphous thin film is obtained from coarse grained molecular dynamics (MD) simulations and subsequent back-mapping onto an atomistic force field representation. The absorption spectra are computed using TDDFT by statistically averaging over an ensemble of molecules taken from the MD simulations. Experimental UV/Vis spectra of spin-coated thin films and solutions are recorded with varying ratios of 'good' versus 'poor' solvent. The theoretical approach is able to faithfully predict the spectral position in the various phases and offers fundamental insight into the cause of any spectral shifts. The position of the main absorption peak is found to be chiefly determined by the level of torsion between the thiophene rings inside each molecule, while intermolecular effects are less important. Hence, optical absorption spectra hold valuable clues about the microscopic structure of disordered P3HT phases. PMID:26443229

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

    PubMed

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

    2016-01-01

    Interfacial liquid layers play a central role in a variety of phenomena ranging from friction to molecular recognition. Liquids near a solid surface form an interfacial layer where the molecular structure is different from that of the bulk. Here we report atomic resolution three-dimensional images of electrolyte solutions near a mica surface that demonstrate the existence of three types of interfacial structures. At low concentrations (0.01-1 M), cations are adsorbed onto the mica. The cation layer is topped by a few hydration layers. At higher concentrations, the interfacial layer extends several nanometres into the liquid. It involves the alternation of cation and anion planes. Fluid Density Functional calculations show that water molecules are a critical factor for stabilizing the structure of the interfacial layer. The interfacial layer stabilizes a crystal-like structure compatible with liquid-like ion and solvent mobilities. At saturation, some ions precipitate and small crystals are formed on the mica. PMID:27416784

  1. Solution structure of a DNA double helix with consecutive metal-mediated base pairs.

    PubMed

    Johannsen, Silke; Megger, Nicole; Böhme, Dominik; Sigel, Roland K O; Müller, Jens

    2010-03-01

    Metal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of Ag(i) ions, a duplex comprising three imidazole-Ag(+)-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from ¹J(¹⁵N,¹⁰⁷/¹⁰⁹Ag) couplings upon incorporation of ¹⁵N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs. PMID:21124482

  2. 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.

  3. 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

  4. Solution structure and backbone dynamics of the defunct domain of calcium vector protein.

    PubMed

    Théret, I; Baladi, S; Cox, J A; Gallay, J; Sakamoto, H; Craescu, C T

    2001-11-20

    CaVP (calcium vector protein) is a Ca(2+) sensor of the EF-hand protein family which is highly abundant in the muscle of Amphioxus. Its three-dimensional structure is not known, but according to the sequence analysis, the protein is composed of two domains, each containing a pair of EF-hand motifs. We determined recently the solution structure of the C-terminal domain (Trp81-Ser161) and characterized the large conformational and dynamic changes induced by Ca(2+) binding. In contrast, the N-terminal domain (Ala1-Asp86) has lost the capacity to bind the metal ion due to critical mutations and insertions in the two calcium loops. In this paper, we report the solution structure of the N-terminal domain and its backbone dynamics based on NMR spectroscopy, nuclear relaxation, and molecular modeling. The well-resolved three-dimensional structure is typical of a pair of EF-hand motifs, joined together by a short antiparallel beta-sheet. The tertiary arrangement of the two EF-hands results in a closed-type conformation, with near-antiparallel alpha-helices, similar to other EF-hand pairs in the absence of calcium ions. To characterize the internal dynamics of the protein, we measured the (15)N nuclear relaxation rates and the heteronuclear NOE effect in (15)N-labeled N-CaVP at a magnetic field of 11.74 T and 298 K. The domain is mainly monomeric in solution and undergoes an isotropic Brownian rotational diffusion with a correlation time of 7.1 ns, in good agreement with the fluorescence anisotropy decay measurements. Data analysis using a model-free procedure showed that the amide backbone groups in the alpha-helices and beta-strands undergo highly restricted movements on a picosecond to nanosecond time scale. The amide groups in Ca(2+) binding loops and in the linker fragment also display rapid fluctuations with slightly increased amplitudes. PMID:11705378

  5. 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

  6. 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

  7. Solution structure of the isolated histone H2A-H2B heterodimer.

    PubMed

    Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-Ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi

    2016-01-01

    During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1-β1-α2-β2-α3-αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {(1)H}-(15)N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27-34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506

  8. Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations.

    PubMed

    Weisz, K; Shafer, R H; Egan, W; James, T L

    1994-01-11

    The solution structure of the DNA decamer d(CATTTGCATC)-d(GATGCAAATG), comprising the octamer motif of immunoglobulin genes, is determined by restrained molecular dynamics (rMD) simulations. The restraint data set includes interproton distances and torsion angles for the deoxyribose sugar ring which were previously obtained by a complete relaxation matrix analysis of the two-dimensional nuclear Overhauser enhancement (2D NOE) intensities and by the quantitative simulation of cross-peaks in double-quantum-filtered correlated (2QF-COSY) spectra. The influence of torsion angles and the number of experimental distance restraints on the structural refinement has been systematically examined. Omitting part of the experimental NOE-derived distances results in reduced restraint violations and lower R factors but impairs structural convergence in the rMD refinement. Eight separate restrained molecular dynamics simulations were carried out for 20 ps each, starting from either energy-minimized A- or B-DNA. Mutual atomic root-mean-square (rms) differences among the refined structures are well below 1 A and comparable to the rms fluctuations of the atoms about their average position, indicating convergence to essentially identical structures. The average refined structure was subjected to an additional 100 ps of rMD simulations and analyzed in terms of average torsion angles and helical parameters. The B-type duplex exhibits clear sequence-dependent variations in its geometry with a narrow minor groove at the T3.A3 tract and a large positive roll at the subsequent TG.CA step. This is accompanied by a noticeable bend of the global helix axis into the major groove. There is also evidence of significant flexibility of the sugar-phosphate backbone with rapid interconversion among different conformers.

  9. 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

  10. Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

    SciTech Connect

    Lee, A L

    1996-05-01

    Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the {delta}-Al-{var_epsilon} activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a {beta}{alpha}{beta}-{beta}{alpha}{beta} pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel {beta}-sheet. In addition {sup 15}N T{sub 1}, T{sub 2}, and {sup 15}N/{sup 1}H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone {sup 1}H, {sup 13}C, and {sup 15}N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and {sup 15}N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

  11. Structure solution with ARCIMBOLDO using fragments derived from distant homology models.

    PubMed

    Sammito, Massimo; Meindl, Kathrin; de Ilarduya, Iñaki M; Millán, Claudia; Artola-Recolons, Cecilia; Hermoso, Juan A; Usón, Isabel

    2014-09-01

    Molecular replacement, one of the general methods used to solve the crystallographic phase problem, relies on the availability of suitable models for placement in the unit cell of the unknown structure in order to provide initial phases. ARCIMBOLDO, originally conceived for ab initio phasing, operates at the limit of this approach, using small, very accurate fragments such as polyalanine α-helices. A distant homolog may contain accurate building blocks, but it may not be evident which sub-structure is the most suitable purely from the degree of conservation. Trying out all alternative possibilities in a systematic way is computationally expensive, even if effective. In the present study, the solution of the previously unknown structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli, is described. The asymmetric unit contains a dimer of this 194 amino acid protein. The closest available homolog was the catalytic domain of Slt70 (PDB code 1QTE). Originally, this template was used omitting contiguous spans of aminoacids and setting as many ARCIMBOLDO runs as models, each aiming to locate two copies sequentially with PHASER. Fragment trimming against the correlation coefficient prior to expansion through density modification and autotracing in SHELXE was essential. Analysis of the figures of merit led to the strategy to optimize the search model against the experimental data now implemented within ARCIMBOLDO-SHREDDER (http://chango.ibmb.csic.es/SHREDDER). In this strategy, the initial template is systematically shredded, and fragments are scored against each unique solution of the rotation function. Results are combined into a score per residue and the template is trimmed accordingly.

  12. 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.

  13. Multiple solution of linear algebraic systems by an iterative method with recomputed preconditioner in the analysis of microstrip structures

    NASA Astrophysics Data System (ADS)

    Ahunov, Roman R.; Kuksenko, Sergey P.; Gazizov, Talgat R.

    2016-06-01

    A multiple solution of linear algebraic systems with dense matrix by iterative methods is considered. To accelerate the process, the recomputing of the preconditioning matrix is used. A priory condition of the recomputing based on change of the arithmetic mean of the current solution time during the multiple solution is proposed. To confirm the effectiveness of the proposed approach, the numerical experiments using iterative methods BiCGStab and CGS for four different sets of matrices on two examples of microstrip structures are carried out. For solution of 100 linear systems the acceleration up to 1.6 times, compared to the approach without recomputing, is obtained.

  14. Be2+ hydration in concentrated aqueous solutions of BeCl2.

    PubMed

    Mason, Philip E; Ansell, Stuart; Neilson, George W; Brady, John W

    2008-02-21

    Neutron diffraction experiments were carried out on concentrated aqueous solutions of beryllium chloride at three concentrations: 1.5, 3, and 6 molal. By working with a specific ("null") mixture of heavy water (D2O) and water (H2O), information on the local structure around Be2+ ions was extracted directly. For all three BeCl2 solutions, the results show that the Be2+ ion has a well-defined 4-fold coordination shell that is dominated by oxygen atoms. There is also a relatively small probability (10-15%) that there are direct contacts between Be2+ and Cl- at a distance of approximately 2.2 angstroms. The oxygen atoms of the highly structured Be2+ first hydration shell are found to be situated at 2.6 angstroms apart, and form a pyramidal structure, in agreement with recent MD simulation results. The Cl- ions have approximately seven oxygen atoms (water molecules) in their hydration shells sited at 3.2 angstroms.

  15. Solution Structural Analysis of the Single-Domain Parvulin TbPin1

    PubMed Central

    Sun, Lifang; Wu, Xueji; Peng, Yu; Goh, Jian Yuan; Liou, Yih-Cherng; Lin, Donghai; Zhao, Yufen

    2012-01-01

    Background Pin1-type parvulins are phosphorylation-dependent peptidyl-prolyl cis-trans isomerases. Their functions have been widely reported to be involved in a variety of cellular responses or processes, such as cell division, transcription, and apoptosis, as well as in human diseases including Alzheimer's disease and cancers. TbPin1 was identified as a novel class of Pin1-type parvulins from Trypanosoma brucei, containing a unique PPIase domain, which can catalyze the isomerization of phosphorylated Ser/Thr-Pro peptide bond. Methodology/Principal Findings We determined the solution structure of TbPin1 and performed 15N relaxation measurements to analyze its backbone dynamics using multi-dimensional heteronuclear NMR spectroscopy. The average RMSD values of the 20 lowest energy structures are 0.50±0.05 Å for backbone heavy atoms and 0.85±0.08 Å for all heavy atoms. TbPin1 adopts the typical catalytic tertiary structure of Pin1-type parvulins, which comprises a globular fold with a four-stranded anti-parallel β-sheet core surrounded by three α-helices and one 310-helix. The global structure of TbPin1 is relatively rigid except the active site. The 2D EXSY spectra illustrate that TbPin1 possesses a phosphorylation-dependent PPIase activity. The binding sites of TbPin1 for a phosphorylated peptide substrate {SSYFSG[p]TPLEDDSD} were determined by the chemical shift perturbation approach. Residues Ser15, Arg18, Asn19, Val21, Ser22, Val32, Gly66, Ser67, Met83, Asp105 and Gly107 are involved in substantial contact with the substrate. Conclusions/Significance The solution structure of TbPin1 and the binding sites of the phosphorylated peptide substrate on TbPin1 were determined. The work is helpful for further understanding the molecular basis of the substrate specificity for Pin1-type parvulin family and enzyme catalysis. PMID:22900083

  16. 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.

  17. Characterization of atomic structure of oxide films on carbon steel in simulated concrete pore solutions using EELS

    NASA Astrophysics Data System (ADS)

    Gunay, H. Burak; Ghods, Pouria; Isgor, O. Burkan; Carpenter, Graham J. C.; Wu, Xiaohua

    2013-06-01

    The atomic structure of oxide films formed on carbon steel that are exposed to highly alkaline simulated concrete pore solutions was investigated using Electron Energy Loss Spectroscopy (EELS). In particular, the effect of chloride exposure on film structure was studied in two types of simulated pore solutions: saturated calcium hydroxide (CH) and a solution prepared to represent typical concrete pore solutions (CP). It was shown that the films that form on carbon steel in simulated concrete pore solutions contained three indistinct layers. The inner oxide film had a structure similar to that of FeIIO, which is known to be unstable in the presence of chlorides. The outer oxide film mainly resembled Fe3O4 (FeIIO·Fe2IIIO3) in the CH solution and α-Fe2IIIO3/Fe3O4 in the CP solution. The composition of the transition layer between the inner and outer layers of the oxide film was mainly composed of Fe3O4 (FeIIO·Fe2IIIO3). In the presence of chloride, the relative amount of the FeIII/FeII increased, confirming that chlorides induce valence state transformation of oxides from FeII to FeIII, and the difference between the atomic structures of oxide film layers diminished.

  18. Insight into the Structure of Light Harvesting Complex II and its Stabilization in Detergent Solution

    SciTech Connect

    Cardoso, Mateus B; Smolensky, Dmitriy; Heller, William T; O'Neill, Hugh Michael

    2009-01-01

    The structure of spinach light-harvesting complex II (LHC II), stabilized in a solution of the detergent n-octyl-{beta}-d-glucoside (BOG), was investigated by small-angle neutron scattering (SANS). Physicochemical characterization of the isolated complex indicated that it was pure (>95%) and also in its native trimeric state. SANS with contrast variation was used to investigate the properties of the protein-detergent complex at three different H{sub 2}O/D{sub 2}O contrast match points, enabling the scattering properties of the protein and detergent to be investigated independently. The topological shape of LHC II, determined using ab initio shape restoration methods from the SANS data at the contrast match point of BOG, was consistent with the X-ray crystallographic structure of LHC II (Liu et al. Nature 2004 428, 287-292). The interactions of the protein and detergent were investigated at the contrast match point for the protein and also in 100% D{sub 2}O. The data suggested that BOG micelle structure was altered by its interaction with LHC II, but large aggregate structures were not formed. Indirect Fourier transform analysis of the LHC II/BOG scattering curves showed that the increase in the maximum dimension of the protein-detergent complex was consistent with the presence of a monolayer of detergent surrounding the protein. A model of the LHC II/BOG complex was generated to interpret the measurements made in 100% D{sub 2}O. This model adequately reproduced the overall size of the LHC II/BOG complex, but demonstrated that the detergent does not have a highly regular shape that surrounds the hydrophobic periphery of LHC II. In addition to demonstrating that natively structured LHC II can be produced for functional characterization and for use in artificial solar energy applications, the analysis and modeling approaches described here can be used for characterizing detergent-associated {alpha}-helical transmembrane proteins.

  19. Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

    PubMed Central

    Anfinrud, Philip

    2010-01-01

    We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02–2.5 Å-1, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 Å), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 Å3 volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume ∼2 Å3 larger than MbCO within ∼10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them. PMID:20406909

  20. 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.

  1. 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.

  2. Solution structure of the ubiquitin-binding domain in Swa2p from Saccharomyces cerevisiae.

    PubMed

    Chim, Nicholas; Gall, Walter E; Xiao, Jing; Harris, Mark P; Graham, Todd R; Krezel, Andrzej M

    2004-03-01

    The SWA2/AUX1 gene has been proposed to encode the Saccharomyces cerevisiae ortholog of mammalian auxilin. Swa2p is required for clathrin assembly/dissassembly in vivo, thereby implicating it in intracellular protein and lipid trafficking. While investigating the 287-residue N-terminal region of Swa2p, we found a single stably folded domain between residues 140 and 180. Using binding assays and structural analysis, we established this to be a ubiquitin-associated (UBA) domain, unidentified by bioinformatics of the yeast genome. We determined the solution structure of this Swa2p domain and found a characteristic three-helix UBA fold. Comparisons of structures of known UBA folds reveal that the position of the third helix is quite variable. This helix in Swa2p UBA contains a bulkier tyrosine in place of smaller residues found in other UBAs and cannot pack as close to the second helix. The molecular surface of Swa2p UBA has a mostly negative potential, with a single hydrophobic surface patch found also in the UBA domains of human protein, HHR23A. The presence of a UBA domain implicates Swa2p in novel roles involving ubiquitin and ubiquitinated substrates. We propose that Swa2p is a multifunctional protein capable of recognizing several proteins through its protein-protein recognition domains. PMID:14997574

  3. Solution structure of villin 14T, a domain conserved among actin-severing proteins.

    PubMed Central

    Markus, M. A.; Nakayama, T.; Matsudaira, P.; Wagner, G.

    1994-01-01

    The solution structure of the N-terminal domain of the actin-severing protein villin has been determined by multidimensional heteronuclear resonance spectroscopy. Villin is a member of a family of actin-severing proteins that regulate the organization of actin in the eukaryotic cytoskeleton. Members of this family are built from 3 or 6 homologous repeats of a structural domain of approximately 130 amino acids that is unrelated to any previously known structure. The N-terminal domain of villin (14T) contains a central beta-sheet with 4 antiparallel strands and a fifth parallel strand at one edge. This sheet is sandwiched between 2 helices on one side and a 2-stranded parallel beta-sheet with another helix on the other side. The strongly conserved sequence characteristic of the protein family corresponds to internal hydrophobic residues. Calcium titration experiments suggest that there are 2 binding sites for Ca2+, a stronger site near the N-terminal end of the longest helix, with a Kd of 1.8 +/- 0.4 mM, and a weaker site near the C-terminal end of the same helix, with a Kd of 11 +/- 2 mM. Mutational and biochemical studies of this domain in several members of the family suggest that the actin monomer binding site is near the parallel strand at the edge of the central beta-sheet. PMID:8142900

  4. 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.

  5. 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.

  6. Solution structure of the potassium channel inhibitor agitoxin 2: caliper for probing channel geometry.

    PubMed Central

    Krezel, A. M.; Kasibhatla, C.; Hidalgo, P.; MacKinnon, R.; Wagner, G.

    1995-01-01

    The structure of the potassium channel blocker agitoxin 2 was solved by solution NMR methods. The structure consists of a triple-stranded antiparallel beta-sheet and a single helix covering one face of the beta-sheet. The cysteine side chains connecting the beta-sheet and the helix form the core of the molecule. One edge of the beta-sheet and the adjacent face of the helix form the interface with the Shaker K+ channel. The fold of agitoxin is homologous to the previously determined folds of scorpion venom toxins. However, agitoxin 2 differs significantly from the other channel blockers in the specificity of its interactions. This study was thus focused on a precise characterization of the surface residues at the face of the protein interacting with the Shaker K+ channel. The rigid toxin molecule can be used to estimate dimensions of the potassium channel. Surface-exposed residues, Arg24, Lys27, and Arg31 of the beta-sheet, have been identified from mutagenesis studies as functionally important for blocking the Shaker K+ channel. The sequential and spatial locations of Arg24 and Arg31 are not conserved among the homologous toxins. Knowledge on the details of the channel-binding sites of agitoxin 2 formed a basis for site-directed mutagenesis studies of the toxin and the K+ channel sequences. Observed interactions between mutated toxin and channel are being used to elucidate the channel structure and mechanisms of channel-toxin interactions. PMID:8520473

  7. Structure and properties of alizarin complex formed with alkali metal hydroxides in methanol solution.

    PubMed

    Jeliński, Tomasz; Cysewski, Piotr

    2016-06-01

    Quantum chemical computations were used for prediction of the structure and color of alizarin complex with alkali metal hydroxides in methanolic solutions. The color prediction relying on the single Gaussian-like band once again proved the usefulness of the PBE0 density functional due to the observed smallest color difference between computed and experimentally derived values. It was found that the alkali metal hydroxide molecules can bind to the two oxygen atoms of both hydroxyl groups of alizarin or to one of these atoms and the oxygen atom from the keto group in a complex with three methanol molecules. This means that two electronic transitions need to be taken into account when considering the spectra of the studied complexes. The resulting bond lengths and angles are correlated with the properties of the alkali metal atoms. The molar mass, the atomic radius, and the Pauling electronegativity of studied metals are quite accurate predictors of the geometric properties of hydroxide complexes with alizarin in methanol solution. Graphical abstract The spectra of the neutral and monoanionic form of alizarin together with color changes resulting from addition of different metal hydroxides and represented in CIE color space. PMID:27178415

  8. Novel solution-phase structures of gallium-containing pyrogallol[4]arene scaffolds**

    PubMed Central

    Kumari, Harshita; Kline, Steven R.; Wycoff, Wei G.; Paul, Rick L.; Mossine, Andrew V.; Deakyne, Carol A.; Atwood, Jerry L.

    2012-01-01

    The variations in architecture of gallium-seamed (PgC4Ga) and gallium-zinc-seamed (PgC4GaZn) C-butylpyrogallol[4]arene nanoassemblies in solution (SANS/NMR) versus the solid state (XRD) have been investigated. Rearrangement from the solid-state spheroidal to the solution-phase toroidal shape differentiates the gallium-containing pyrogallol[4]arene nanoassemblies from all other PgCnM nanocapsules studied thus far. Different structural arrangements of the metals and arenes of PgC4Ga versus PgC4GaZn have been deduced from the different toroidal dimensions, C–H proton environments and guest encapsulation of the two toroids. PGAA of mixed-metal hexamers reveals a decrease in gallium-to-metal ratio as the second metal varies from cobalt to zinc. Overall, the combined study demonstrates the versatility of gallium in directing the self-assembly of pyrogallol[4]arenes into novel nanoarchitectures. PMID:22511521

  9. 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.

  10. Effects of 940 Hz EMF on luciferase solution: structure, function, and dielectric studies.

    PubMed

    Sefidbakht, Yahya; Hosseinkhani, Saman; Mortazavi, Mojtaba; Tavakkolnia, Iman; Khellat, Mohammad R; Shakiba-Herfeh, Mahdi; Saviz, Mehrdad; Faraji-Dana, Reza; Saboury, Ali A; Sheibani, Nader; Moosavi-Movahedi, Ali A

    2013-09-01

    We designed a rectangular waveguide exposure system to study the effects of mobile phone frequency (940 MHz) electromagnetic fields (EMF) on luciferase structure and activity. The luciferase activity of exposed samples was significantly higher than that of unexposed samples. Dynamic light scattering of the exposed samples showed smaller hydrodynamic radii compared to unexposed samples (20 nm vs. 47 nm ± 5%). The exposed samples also showed less tendency to form aggregates, monitored by turbidity measurements at l = 360 nm. A microwave dielectric measurement was performed to study the hydration properties of luciferase solutions with a precision network analyzer over frequency ranges from 0.2 to 20 GHz before and after exposure. The change in the dielectric properties of the exposed luciferase solution was related to the disaggregation potency of the applied field. Together, our results suggested that direct interactions with luciferase molecules and its dipole moment were responsible for the reduced aggregation and enhanced luciferase activity upon exposure to the EMF. PMID:23633149

  11. 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

  12. Structural Dynamics of Star-Shaped Weak Polyelectrolytes in Dilute Aqueous Solution

    NASA Astrophysics Data System (ADS)

    Qu, Chen; Zhu, Y. Elaine

    Weak polyelectrolyte (PE) bearing tunable charges along their backbones show great potential as ``smart'' polymer materials for diverse applications from drug delivery to energy storage. With the introduction of branched topology, the local counterion distribution in the vicinity to the polyelectrolyte segments becomes highly inhomogeneous. To experimentally investigate the interplay between structural dynamics and local electric environment of a branched polyelectrolyte, in this work we custom synthesized star-shaped poly(2-vinylpyridine) (P2VP) using reversible addition fragmentation chain transfer (RAFT) polymerization and labeled P2VP stars with pH-sensitive fluorophore precisely either in the center or periphery. By employing fluorescence correlation spectroscopy (FCS) with photon counts histogram (PCH) analysis, we observed gradual stretched-to-collapses conformational transition with increasing solution pH for both P2VP stars of different fluorophore labeling locations. However, the measured local pH, or local proton concentration, shows strong dependence of the fluorophore labeling locations. Higher electric potential yet lower ionization degree was observed in the core of P2VP star than that in the periphery. Ongoing work is carried out to examine the scaling behaviors of P2VP star sizes with varied number of arms, arm lengths and counterion concentrations in dilute aqueous solutions.

  13. Structure and properties of alizarin complex formed with alkali metal hydroxides in methanol solution.

    PubMed

    Jeliński, Tomasz; Cysewski, Piotr

    2016-06-01

    Quantum chemical computations were used for prediction of the structure and color of alizarin complex with alkali metal hydroxides in methanolic solutions. The color prediction relying on the single Gaussian-like band once again proved the usefulness of the PBE0 density functional due to the observed smallest color difference between computed and experimentally derived values. It was found that the alkali metal hydroxide molecules can bind to the two oxygen atoms of both hydroxyl groups of alizarin or to one of these atoms and the oxygen atom from the keto group in a complex with three methanol molecules. This means that two electronic transitions need to be taken into account when considering the spectra of the studied complexes. The resulting bond lengths and angles are correlated with the properties of the alkali metal atoms. The molar mass, the atomic radius, and the Pauling electronegativity of studied metals are quite accurate predictors of the geometric properties of hydroxide complexes with alizarin in methanol solution. Graphical abstract The spectra of the neutral and monoanionic form of alizarin together with color changes resulting from addition of different metal hydroxides and represented in CIE color space.

  14. Structural changes in axillary eccrine glands following long-term treatment with aluminium chloride hexahydrate solution.

    PubMed

    Hölzle, E; Braun-Falco, O

    1984-04-01

    Axillary skin biopsies from fifteen patients with axillary hyperhidrosis who had received long-term treatment with aqueous aluminium chloride solution were examined histologically. The apocrine glands were normal, but the eccrine glands showed conspicuous morphological changes of varying severity. These included vacuolization of the secretory epithelium, dilatation of eccrine acini with atrophy of secretory cells, and accumulation of PAS-positive, diastase-resistant material in the dilated lumen of the secretory coils. The histological changes correlated in most patients with decreased secretion of sweat. We conclude that long-term blockage of the distal acrosyringium due to aluminium salts may lead to functional and structural degeneration of the eccrine acini. PMID:6712884

  15. Solution growth of silicon on multicrystalline Si substrate: growth velocity, defect structure and electrical activity

    NASA Astrophysics Data System (ADS)

    Voigt, A.; Steiner, B.; Dorsch, W.; Krinke, J.; Albrecht, M.; Strunk, H. P.; Wagner, G.

    1996-09-01

    Thin silicon films, solution-grown on cast silicon wafers, are examined as an example of liquid phase epitaxy of silicon on a polycrystalline seed layer. We investigate the structural and electrical properties of grain boundaries in the epilayers by transmission electron microscopy and electron-beam-induced current measurements. We find that growth close to thermodynamic equilibrium leads to low electrical activity of defects and to a low-energy geometry of grain boundaries. Layers grown with different growth rates show no difference in electrical activity. Trenches at grain boundary sites are typical surface features of the epilayers. An increased growth rate leads to a reduction in trench depth, which is an advantage for the contact metallization of solar cells.

  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. X-ray structure analysis of a solid solution of milbemycins A3 and A4.

    PubMed

    Bizdena, E; Belyakov, S; Jure, M; Grinsteine, I; Kumpiņš, V; Turks, M

    2013-10-01

    Milbemycins A3 and A4 are pharmaceutically and agriculturally useful macrolides isolated from Streptomyces species. The molecular structures of the title compounds were unambiguously established by a single crystal X-ray analysis of the solid solution of both compounds. The crystals present trigonal system, space group P32 with Z = 3, unit cell dimensions: a = 12.2211(4), c = 17.5372(7) Å; V = 2268.4(1) Å(3), μ = 0.082 mm(- 1); d = 1.183 g cm(- 3). An interesting system of intramolecular hydrogen bonds and weak intermolecular CH…O type hydrogen bond was observed in the solid state.

  18. 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.

  19. Shear-induced structure evolution of carbon nanotubes dispersions in polyacrylonitrile-dimethylsulfoxide solution

    NASA Astrophysics Data System (ADS)

    Karpushkin, Evgeny; Lapshina, Maria; Sergeyev, Vladimir

    2015-04-01

    Rheological behavior of carbon nanotubes finely dispersed in polyacrylonitrile-dimethylsulfoxide solution has been studied as function of the applied pre-shear stress and discussed in view of possible structural changes induced by the pre-shearing of the samples. The observed effects can be ascribed to a combination of internal processes involving alignment and association of the macromolecules as well as orientation and association of carbon nanotubes. The effects caused by the macromolecules alignment and association are mainly observed at low concentration of the filler and at higher shear stress, whereas the processes involving carbon nanotubes reorganization are mainly observed at the higher filler content and at low pre-shear stress.

  20. Reverse micelles in integral membrane protein structural biology by solution NMR spectroscopy

    PubMed Central

    Kielec, Joseph M.; Valentine, Kathleen G.; Babu, Charles R.; Wand, A. Joshua

    2009-01-01

    SUMMARY Integral membrane proteins remain a significant challenge to structural studies by solution NMR spectroscopy. This is due not only to spectral complexity but also because the effects of slow molecular reorientation are exacerbated by the need to solublize the protein in aqueous detergent micelles. These assemblies can be quite large and require deuteration for use of the TROSY effect. In principle, another approach is to employ reverse micelle encapsulation to solublize the protein in a low viscosity solvent where the rapid tumbling of the resulting particle allows use of standard triple resonance methods. The preparation of such samples of membrane proteins is difficult. Using a 54 kDa construct of the homotetrameric potassium channel KcsA we demonstrate a strategy that employs a hybrid surfactant to transfer the protein to the reverse micelle system. PMID:19278649

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

    DOE PAGES

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

    2016-01-25

    Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

  2. Monitoring Solution Structures of Peroxisome Proliferator-Activated Receptor β/δ upon Ligand Binding.

    PubMed

    Schwarz, Rico; Tänzler, Dirk; Ihling, Christian H; Sinz, Andrea

    2016-01-01

    Peroxisome proliferator-activated receptors (PPARs) have been intensively studied as drug targets to treat type 2 diabetes, lipid disorders, and metabolic syndrome. This study is part of our ongoing efforts to map conformational changes in PPARs in solution by a combination of chemical cross-linking and mass spectrometry (MS). To our best knowledge, we performed the first studies addressing solution structures of full-length PPAR-β/δ. We monitored the conformations of the ligand-binding domain (LBD) as well as full-length PPAR-β/δ upon binding of two agonists. (Photo-) cross-linking relied on (i) a variety of externally introduced amine- and carboxyl-reactive linkers and (ii) the incorporation of the photo-reactive amino acid p-benzoylphenylalanine (Bpa) into PPAR-β/δ by genetic engineering. The distances derived from cross-linking experiments allowed us to monitor conformational changes in PPAR-β/δ upon ligand binding. The cross-linking/MS approach proved highly advantageous to study nuclear receptors, such as PPARs, and revealed the interplay between DBD (DNA-binding domain) and LDB in PPAR-β/δ. Our results indicate the stabilization of a specific conformation through ligand binding in PPAR-β/δ LBD as well as full-length PPAR-β/δ. Moreover, our results suggest a close distance between the N- and C-terminal regions of full-length PPAR-β/δ in the presence of GW1516. Chemical cross-linking/MS allowed us gaining detailed insights into conformational changes that are induced in PPARs when activating ligands are present. Thus, cross-linking/MS should be added to the arsenal of structural methods available for studying nuclear receptors.

  3. Monitoring Solution Structures of Peroxisome Proliferator-Activated Receptor β/δ upon Ligand Binding.

    PubMed

    Schwarz, Rico; Tänzler, Dirk; Ihling, Christian H; Sinz, Andrea

    2016-01-01

    Peroxisome proliferator-activated receptors (PPARs) have been intensively studied as drug targets to treat type 2 diabetes, lipid disorders, and metabolic syndrome. This study is part of our ongoing efforts to map conformational changes in PPARs in solution by a combination of chemical cross-linking and mass spectrometry (MS). To our best knowledge, we performed the first studies addressing solution structures of full-length PPAR-β/δ. We monitored the conformations of the ligand-binding domain (LBD) as well as full-length PPAR-β/δ upon binding of two agonists. (Photo-) cross-linking relied on (i) a variety of externally introduced amine- and carboxyl-reactive linkers and (ii) the incorporation of the photo-reactive amino acid p-benzoylphenylalanine (Bpa) into PPAR-β/δ by genetic engineering. The distances derived from cross-linking experiments allowed us to monitor conformational changes in PPAR-β/δ upon ligand binding. The cross-linking/MS approach proved highly advantageous to study nuclear receptors, such as PPARs, and revealed the interplay between DBD (DNA-binding domain) and LDB in PPAR-β/δ. Our results indicate the stabilization of a specific conformation through ligand binding in PPAR-β/δ LBD as well as full-length PPAR-β/δ. Moreover, our results suggest a close distance between the N- and C-terminal regions of full-length PPAR-β/δ in the presence of GW1516. Chemical cross-linking/MS allowed us gaining detailed insights into conformational changes that are induced in PPARs when activating ligands are present. Thus, cross-linking/MS should be added to the arsenal of structural methods available for studying nuclear receptors. PMID:26992147

  4. Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects.

    PubMed

    Hack, John; Grills, David C; Miller, John R; Mani, Tomoyasu

    2016-02-18

    Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent. PMID:26807492

  5. 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

  6. 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.

  7. 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

  8. Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.

    PubMed Central

    Gao, Y.; Kaluarachchi, K.; Giedroc, D. P.

    1998-01-01

    Retroviral nucleocapsid proteins (NCPs) are CCHC-type zinc finger proteins that mediate virion RNA binding activities associated with retrovirus assembly and genomic RNA encapsidation. Mason-Pfizer monkey virus (MPMV), a type D retrovirus, encodes a 96-amino acid nucleocapsid protein, which contains two Cys-X2-Cys-X4-His-X4-Cys (CCHC) zinc fingers connected by an unusually long 15-amino acid linker. Homonuclear, two-dimensional sensitivity-enhanced 15N-1H, three-dimensional 15N-1H, and triple resonance NMR spectroscopy have been used to determine the solution structure and residue-specific backbone dynamics of the structured core domain of MPMV NCP containing residues 21-80. Structure calculations and spectral density mapping of N-H bond vector mobility reveal that MPMV NCP 21-80 is best described as two independently folded, rotationally uncorrelated globular domains connected by a seven-residue flexible linker consisting of residues 42-48. The N-terminal CCHC zinc finger domain (residues 24-37) appears to adopt a fold like that described previously for HIV-1 NCP; however, residues within this domain and the immediately adjacent linker region (residues 38-41) are characterized by extensive conformational averaging on the micros-ms time scale at 25 degrees C. In contrast to other NCPs, residues 49-77, which includes the C-terminal CCHC zinc-finger (residues 53-66), comprise a well-folded globular domain with the Val49-Pro-Gly-Leu52 sequence and C-terminal tail residues 67-77 characterized by amide proton exchange properties and 15N R1, R2, and (1H-15N) NOE values indistinguishable to residues in the core C-terminal finger. Twelve refined structural models of MPMV NCP residues 49-80 (pairwise backbone RMSD of 0.77 A) reveal that the side chains of the conserved Pro50 and Trp62 are in van der Waals contact with one another. Residues 70-73 in the C-terminal tail adopt a reverse turn-like structure. Ile77 is involved in extensive van der Waals contact with the core

  9. Solution structure of spheniscin, a beta-defensin from the penguin stomach.

    PubMed

    Landon, Céline; Thouzeau, Cécile; Labbé, Henri; Bulet, Philippe; Vovelle, Françoise

    2004-07-16

    Recently two beta-defensins, named spheniscins, have been isolated from the stomach content of the king penguin (Aptenodytes patagonicus), which is capable of preserving food for several weeks during egg incubation (Thouzeau, C., Le Maho, Y., Froget, G., Sabatier, L., Le Bohec, C., Hoffmann, J. A., and Bulet, P. (2003) J. Biol. Chem. 278, 51053-51058). It has been proposed that, in combination with other antimicrobial peptides, spheniscins may be involved in this long term preservation of food in the bird's stomach. To draw some structure/function features, the three-dimensional structure in aqueous solution of the most abundant spheniscin (Sphe-2) was determined by two-dimensional NMR and molecular modeling techniques. The overall fold of Sphe-2 includes a three-stranded antiparallel beta-sheet stabilized by three disulfide bridges with a pairing typical of beta-defensins. In addition, the N-terminal segment shows helical features on most structures. Sphe-2 is highly cationic, and its surface displays a hydrophobic patch. Comparative modeling revealed that this patch is preserved in avian defensins. The activity of Sphe-2 against a pathogenic Gram-positive strain was retained in vitro in the conditions of osmolarity found in penguin stomach content and also in different salt concentrations and compositions up to those reported for seawater. Comparison with structurally related mammalian beta-defensins showed that the hydrophobic patch is not preserved in mammalian beta-defensins and that the high cationicity of Sphe-2 is presumably the critical factor for its retained activity in high salt concentrations. Such peculiarities, in addition to a broad activity spectrum, suggest that penguin defensins may represent interesting probes for the design of highly efficient antibiotics to fight off pathogens that develop in relatively salt-rich body fluids. PMID:15123713

  10. Solution structure of Gfi-1 zinc domain bound to consensus DNA.

    PubMed

    Lee, Soojin; Doddapaneni, Kiran; Hogue, Amber; McGhee, Laura; Meyers, Shari; Wu, Zhengrong

    2010-04-01

    Gfi-1 is a crucial transcriptional repressor for the precise regulation of cell proliferation and differentiation in hematopoiesis. Recently, this protein has also been demonstrated to be capable of restricting the proliferation of hematopoietic stem cells, a process that appears to be vital for the long-term competency of hematopoietic stem cells. These two seemingly opposite outcomes of regulation are likely to arise from its interactions with a variety of cellular partners. Such interactions can directly affect the genes that Gfi-1 recognizes through its DNA binding zinc-finger domain. In this work, we report the determination of the solution structure of Gfi-1 zinc fingers 3-5 in complex with a 16-mer consensus DNA using multidimensional NMR method. Unlike a proposed minor-groove binding model based on methylation interference experiments, our structure clearly shows that Gfi-1 zinc fingers 3-5 bind into the major groove of the target DNA reminiscent of canonical C(2)H(2) zinc-finger domains. The fourth and fifth zinc fingers recognize the AATC core sequence by forming base-specific hydrogen bonds between the side chains of Asn382, Gln379, and Asp354 and the bases of the invariant adenines and cytosine. Overall, the current work provides valuable insight into the structural determinants for DNA binding specificity, in particular for the TCA triplet that has not been observed in any other structures of zinc finger-DNA complexes, as well as molecular rationales for a naturally occurring mutation that causes acute myeloid leukemia. PMID:20153336

  11. 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

  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. Global structure stability of Riemann solutions of quasilinear hyperbolic systems of conservation laws: shocks and contact discontinuities

    NASA Astrophysics Data System (ADS)

    Kong, De-Xing

    In this paper, the author proves the global structure stability of the Lax's Riemann solution u=U( {x}/{t}) , containing only shocks and contact discontinuities, of general n× n quasilinear hyperbolic system of conservation laws. More precisely, the author proves the global existence and uniqueness of the piecewise C1 solution u= u( t, x) of a class of generalized Riemann problem, which can be regarded as a perturbation of the corresponding Riemann problem, for the quasilinear hyperbolic system of conservation laws; moreover, this solution has a global structure similar to that of the solution u=U( {x}/{t}) . Combining the results in Kong (Global structure instability of Riemann solutions of quasilinear hyperbolic systems of conservation laws: rarefaction waves, to appear), the author proves that the Lax's Riemann solution of general n× n quasilinear hyperbolic system of conservation laws is globally structurally stable if and only if it contains only non-degenerate shocks and contact discontinuities, but no rarefaction waves and other weak discontinuities.

  14. New era of molecular structure and dynamics from solution scattering experiments

    SciTech Connect

    Sosnick, Tobin; Woodson, Sarah

    2011-10-24

    Six contributions in this special issue of Biopolymers are devoted to the application of small angle scattering (SAS) to biological macromolecules. Biological applications of SAS have undergone a resurgence in the last 15 years. Although SAS cannot compete with the atomic level information provided by crystallographic and NMR-based methods, nonetheless SAS has advantages that make it an extremely useful component in the structural biologist's tool box. An obvious reason for the renewed popularity of scattering experiments is the increased access to SAS beamlines at synchrotron X-ray sources. These high intensity sources greatly reduce the sample requirements and accelerate data acquisition. However, improved access only partially explains the resurgence of SAS. As highlighted in the six papers in this special issue, creative applications of SAS are opening up new avenues for studying biological macromolecules which are not readily investigated using other structural methods. SAS excels at characterizing the global dimensions and shape of individual molecules, molecular complexes and even disordered states, particularly as a function of solvent condition and time, and can do so in a high throughput manner. In addition, SAS can provide information about the dynamics of molecular complexes in solution. These capabilities are highlighted in this special issue which illustrates how SAS is both a versatile technique in its own right and, when combined with other methods, capable of producing a more complete description of the conformational changes and dynamics of complicated biological processes.

  15. Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?

    PubMed

    Urzhumtsev, Alexandre; Urzhumtseva, Ludmila; Baumann, Ulrich

    2016-01-01

    Crystallographic molecular replacement method is the key tool to define an atomic structure of nucleic acids. Frequently nucleic acids are packed forming continuous helices in the crystal. This arrangement of individual molecules in "infinite" pseudo helical structures in crystal may be the reason why the molecular replacement fails to find a unique position of the search atomic model as the method requires. The Patterson function, calculated as a Fourier series with diffraction intensities, has auxiliary peaks for such a molecular packing. Those near the origin peak indicate the orientation of the helices. The coordinates of other peaks are related to the molecular position and the rotation angle between two such "infinite" helices. Thus, the peak analysis allows getting molecular position even without a search model. An intelligent selecting and averaging of the phase sets corresponding to multiple probable positions of the search model again result in a unique solution but in the form of a Fourier synthesis and not a model. This synthesis can be used then to build an atomic model as it is the case for usual phasing methods.

  16. Aggregation properties and structural studies of anticancer drug Irinotecan in DMSO solution based on NMR measurements

    NASA Astrophysics Data System (ADS)

    D'Amelio, N.; Aroulmoji, V.; Toraldo, A.; Sundaraganesan, N.; Anbarasan, P. M.

    2012-04-01

    Irinotecan is an antitumor drug mostly used in the treatment of colorectal cancer. Its efficacy is influenced by the chemical state of the molecule undergoing chemical equilibria, metabolic changes and photodegradation. In this work, we describe the chemical equilibria of the drug in dimethyl sulfoxide (DMSO). The energetic barrier for hindered rotation around the bond connecting the piperidino—piperidino moiety with the camptothecin-like fragment was evaluated. Furthermore, we showed how the molecule aggregates in DMSO solution forming dimeric species able to prevent its degradation. The equilibrium constant for self-aggregation was determined by NMR based on the assumption of the isodesmic model. The formation of a dimer was highlighted by NMR diffusion ordered spectroscopy (NMR-DOSY) experiments at the concentrations used. Structural features of the complex were inferred by NOE and 13C chemical shift data. Molecular modelling of the complex driven by experimental data, lead to a structure implying the formation of two hydrogen bonds involving the lactone ring whose opening is one of the main causes of drug degradation. This species is probably responsible for the improved stability of the drug at concentrations higher than 1 mM.

  17. The structure and properties of PEDOT synthesized by template-free solution method

    PubMed Central

    2014-01-01

    In this study, a simple one-step template-free solution method was developed for the preparation of poly(3,4-ethylenedioxythiophene) (PEDOTs) with different morphologies by adjusting various ratios of oxidant (FeCl3·6H2O) to monomer (3,4-ethylenedioxythiophene (EDOT)). The results from structural analysis showed that the structure of PEDOT was strongly affected by the oxidant/monomer ratio, and the polymerization degree, conjugation length, doping level, and crystallinity of PEDOT decreased with increasing of the oxidant/monomer ratio. The morphological analysis showed that PEDOT prepared from an oxidant/monomer ratio of 3:1 displayed a special coral-like morphology, and the branches of ‘coral’ would adjoin or grow together with increasing content of oxidant in the reaction medium; consequently, the morphology of PEDOT changed from coral to sheets (at an oxidant/monomer ratio of 9:1). The electrochemical analysis proved that the PEDOT prepared from an oxidant/monomer ratio of 3:1 had the lowest resistance and the highest specific capacitances (174 F/g) at a current density of 1 A/g with a capacity retention rate of 74% over 1,500 cycles, which indicated that the PEDOT with a coral-like morphology could be applied as a promising electrode material for supercapacitors. PMID:25317104

  18. 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, whereas proteins (~50 kDa) had ~9,000 collisions/sec and required about 10 sec (tortuosity ~ 2 to 2.5). These simulations help define physical processes during thrombosis and constraints for drug delivery to the thrombus. PMID:23423707

  19. Analysis of structure and orientation of adsorbed polymers in solution subject to a dynamic shear stress

    SciTech Connect

    Smith, G.; Baker, S.; Toprakcioglu, C.

    1996-09-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Polymer-based separation techniques rely on the ability of a binding portion of the polymer to interact with a specific molecule in a solution flowing past the polymer. The location of the binding site within or out of the entangled polymer chains is thus crucial to the effectiveness of these methods. For this reason, the details of flow induced deformation of the polymer chains is important in such applications as exclusion chromatography, waste water treatment, ultrafiltration, enhanced oil recovery and microbial adhesion. Few techniques exist to examine the structure and orientation of polymeric materials, and even fewer to examine systems in a dynamic fluid flow. The goal of this project was to understand the molecular structure and orientation of adsorbed polymers with and without active binding ligands as a function of solvent shear rate, solvent power, polymer molecular weight, surface polymer coverage and heterogeneity of the surface polymer chains by neutron reflectometry in a newly designed shear cell. Geometrical effects on binding of molecules in the flow was also studied subject to the same parameters.

  20. Speciation and structure of tin(II) in hyper-alkaline aqueous solution.

    PubMed

    Bajnóczi, Eva G; Czeglédi, Eszter; Kuzmann, Ernő; Homonnay, Zoltán; Bálint, Szabolcs; Dombi, György; Forgo, Péter; Berkesi, Ottó; Pálinkó, István; Peintler, Gábor; Sipos, Pál; Persson, Ingmar

    2014-12-28

    The identity of the predominating tin(ii)-hydroxide complex formed in hyper-alkaline aqueous solutions (0.2 ≤CNaOH≤ 12 mol dm(-3)) is determined by potentiometric titrations, Raman, Mössbauer and XANES spectroscopy, supplemented by quantum chemical calculations. Thermodynamic studies using a H2/Pt electrode up to free hydroxide concentrations of 1 mol dm(-3) showed the presence of a single monomeric complex with a tin(II) : hydroxide ratio of 1 : 3. This observation together with Raman and Mössbauer spectroscopic measurements supplemented by quantum mechanical calculations proved that the predominating complex is [Sn(OH)3](-), and that the presence of the other possible complex, [SnO(OH)](-), could not be proven with either experiments or simulations. The structure of the trihydroxidostannate(II) complex, [Sn(OH)3](-), was determined by EXAFS and was found to be independent of the applied hydroxide and tin(II) concentrations. The mean Sn-O bond distance is short, 2.078 Å, and in very good agreement with the only structure reported in the solid state. It is also shown that at pH values above 13 the speciation of the predominant trihydroxidostannate(II) complex is not affected by the presence of high concentrations of chloride ions.

  1. Solution structure of DinI provides insight into its mode of RecA inactivation.

    PubMed Central

    Ramirez, B. E.; Voloshin, O. N.; Camerini-Otero, R. D.; Bax, A.

    2000-01-01

    The Escherichia coli RecA protein triggers both DNA repair and mutagenesis in a process known as the SOS response. The 81-residue E. coli protein DinI inhibits activity of RecA in vivo. The solution structure of DinI has been determined by multidimensional triple resonance NMR spectroscopy, using restraints derived from two sets of residual dipolar couplings, obtained in bicelle and phage media, supplemented with J couplings and a moderate number of NOE restraints. DinI has an alpha/beta fold comprised of a three-stranded beta-sheet and two alpha-helices. The beta-sheet topology is unusual: the central strand is flanked by a parallel and an antiparallel strand and the sheet is remarkably flat. The structure of DinI shows that six negatively charged Glu and Asp residues on DinI's kinked C-terminal alpha-helix form an extended, negatively charged ridge. We propose that this ridge mimics the electrostatic character of the DNA phospodiester backbone, thereby enabling DinI to compete with single-stranded DNA for RecA binding. Biochemical data confirm that DinI is able to displace ssDNA from RecA. PMID:11152126

  2. Structure of steady state accretion shocks with several cooling functions: Closed integral-form solution

    NASA Technical Reports Server (NTRS)

    Wu, Kinwah; Chanmugam, G.; Shaviv, G.

    1994-01-01

    We present, for the first time, a closed integral-form solution to the accretion shock structures for the case where the cooling is due to optically thin bremsstrahlung emission and a series of power-law cooling functions of density and temperature. Our results can provide useful checks on numerical calculations and simple accurate estimates for valuable parameters such as the shock height. For the case where the cooling rate j = (2/3)Arho(exp 2)(P/rho)(exp 1/2)(1 + epsilon (sub s)(P/P(sub s)(exp alpha)(rho(sub s)/rho)(exp beta)), we find that a substantial amount of the accretion energy is released at the base of the accretion shock in the form of bremsstrahlung radiation. This implies that for a cyclotron-dominated shock (qualitatively given by alpha = 2.0, beta = 3.85, and epsilon(sub s) is much greater than 1), bremsstrahlung cooling still plays a crucial role in determining the shock structure. Our results are shown to be consistent with detailed numerical calculations.

  3. Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB

    SciTech Connect

    Tanabe, Mikio; Nimigean, Crina M.; Iverson, T.M.

    2010-06-25

    PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been determined to 2.3 {angstrom} resolution. Structural analysis and cocrystallization studies identify three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one transports cations nonselectively, and one facilitates the specific uptake of sugars. During infection, PorB likely binds host mitochondrial ATP, and cocrystallization with the ATP analog AMP-PNP suggests that binding of nucleotides regulates these translocation pathways both by partial occlusion of the pore and by restricting the motion of a putative voltage gating loop. PorB is located on the surface of N. meningitidis and can be recognized by receptors of the host innate immune system. Features of PorB suggest that Toll-like receptor mediated recognition outer membrane proteins may be initiated with a nonspecific electrostatic attraction.

  4. Structurally colored biopolymer thin films for detection of dissolved metal ions in aqueous solution

    NASA Astrophysics Data System (ADS)

    Cathell, Matthew David

    Natural polymers, such as the polysaccharides alginate and chitosan, are noted sorbents of heavy metals. Their polymer backbone structures are rich in ligands that can interact with metal ions through chelation, electrostatics, ion exchange and nonspecific mechanisms. These water-soluble biopolymer materials can be processed into hydrogel thin films, creating high surface area interfaces ideal for binding and sequestering metal ions from solution. By virtue of their uniform nanoscale dimensions (with thicknesses smaller than wavelengths of visible light) polymer thin films exhibit structure-based coloration. This phenomenon, frequently observed in nature, causes the transparent and essentially colorless films to reflect light in a wide array of colors. The lamellar film structures act as one-dimensional photonic crystals, allowing selective reflection of certain wavelengths of light while minimizing other wavelengths by out-of-phase interference. The combination of metal-binding and reflective properties make alginate and chitosan thin films attractive candidates for analyte sensing. Interactions with metal ions can induce changes in film thicknesses and refractive indices, thus altering the path of light reflected through the film. Small changes in dimensional or optical properties can lead to shifts in film color that are perceivable by the unaided eye. These thin films offer the potential for optical sensing of toxic dissolved materials without the need for instrumentation, external power or scientific expertise. With the use of a spectroscopic ellipsometer and a fiber optic reflectance spectrometer, the physical and optical characteristics of biopolymer thin films have been characterized in response to 50 ppm metal ion solutions. It has been determined that metal interactions can lead to measurable changes in both film thicknesses and effective refractive indices. The intrinsic response behaviors of alginate and chitosan, as well as the responses of modified

  5. Improving the structural consistency of C-S-H solid solution thermodynamic models

    SciTech Connect

    Kulik, Dmitrii A.

    2011-05-15

    Simple aqueous-solid solution models of C-S-H (calcium silicate hydrate) are widely used in studies of cement hydration and waste-cement interactions. Even without a clear structural/mechanistic basis, such thermodynamic models yield a good description of solubility data in [Ca]-C/S space, while only satisfactory in [Si]-C/S, H{sub 2}O-C/S, [Ca]-[Si] spaces and in the 0.1 < C/S < 0.8 range. Here, using a multi-site (sublattice) concept, the ideal solid solution model of C-S-H is revised to make it consistent with the Richardson-Groves structural model of C-S-H and with the modern interpretation of spectroscopic ({sup 29}Si MAS NMR) and solubility data. Consideration of two site substitutions, (1) coupled H{sub 2}OCa{sup 2+} for SiO{sub 2}H{sub 2}{sup 2+} replacement in bridging tetrahedral and adjacent interlayer sites, and (2) substitution of interstitial Ca(OH){sub 2} for a vacancy, leads to a new CSHQ model of (A,B) (C,D)X type composed of two tobermorite-like and two jennite-like end members. Because this ideal sublattice SS model cannot fit solubility data well at 0.8 < C/S < 1.1, a simpler CSH3T model is constructed from a polymeric TobH (CaO){sub 2}(SiO{sub 2}){sub 3}(H{sub 2}O){sub 5}, a dimeric T2C (CaO){sub 3}(SiO{sub 2}){sub 2}(H{sub 2}O){sub 5}, and an ordered pentameric T5C (CaO){sub 2.5}(SiO{sub 2}){sub 2.5}(H{sub 2}O){sub 5} tobermorite-like end members. This solid solution model, limited to the range 0.67 < C/S < 1.5, has a correct built-in dependence of the mean silicate chain length on C/S, yields quite realistic fits to the solubility data, and provides a basis for extensions with foreign cations whose sites in the defect-tobermorite structure of C-S-H are known. To account for C-S-H compositions with C/S > 1.5, CSHQ end members were downscaled to one tetrahedral site and used within the simple mixing model. Despite some loss of structural consistency, the solubility and mean silicate chain length data can be reproduced well with this downscaled

  6. An adaptive grid method for computing time accurate solutions on structured grids

    NASA Technical Reports Server (NTRS)

    Bockelie, Michael J.; Smith, Robert E.; Eiseman, Peter R.

    1991-01-01

    The solution method consists of three parts: a grid movement scheme; an unsteady Euler equation solver; and a temporal coupling routine that links the dynamic grid to the Euler solver. The grid movement scheme is an algebraic method containing grid controls that generate a smooth grid that resolves the severe solution gradients and the sharp transitions in the solution gradients. The temporal coupling is performed with a grid prediction correction procedure that is simple to implement and provides a grid that does not lag the solution in time. The adaptive solution method is tested by computing the unsteady inviscid solutions for a one dimensional shock tube and a two dimensional shock vortex iteraction.

  7. Structural studies of bean pod mottle virus, capsid, and RNA in crystal and solution states by laser Raman spectroscopy

    SciTech Connect

    Li, Tiansheng; Thomas, G.J. Jr. ); Chen, Zhongguo; Johnson, J.E. )

    1990-05-29

    Structures of protein and RNA components of bean pod mottle virus (BPMV) have been investigated by use of laser Raman spectroscopy. Raman spectra were collected from both aqueous solutions and single crystals of BPMV capsids (top component) and virions (middle and bottom components, which package, respectively, small and large RNA molecules). Analysis of the data permits the assignment of conformation-sensitive Raman bands to viral protein and RNA constituents and observation of structural similarities and differences between solution and crystalline states of BPMV components. The Raman results show that the protein subunits of the empty capsid contain between 45% and 55% {beta}-strand and {beta}-turn secondary structure, in agreement with the recently determined X-ray crystal structure, and that this total {beta}-strand content undergoes a small increase with packaging of RNA. A comparison of Raman spectra of crystal and solution states of the BPMV middle component reveals only minor structural differences between the two, and these are restricted almost exclusively to Raman bands of RNA in the region of assigned phosphodiester conformation markers. Although in both the crystal and solution only C3{prime} endo/anti nucleosides are detected, the crystal exhibits a weaker 813-cm{sup {minus}1} band and strong 870-cm{sup {minus}1} band, which suggests that {approximately}8% of the nucleotides have O-P-O torsions configured differently in the crystal from that in the solution.

  8. Structure Formation in Salt-Free Solutions of Amphiphilic Sulfonated Polyelectrolytes

    NASA Astrophysics Data System (ADS)

    Bockstaller, Michael; Koehler, Werner

    2000-03-01

    Self-assembled systems have long attracted attention due to their practical importance in many technical and biological fields. Dodecyl-substituted poly(para-phenylen)sulfonates (abbreviated PPPS) are highly charged polyelectrolytes which in the uncharged state have been investigated extensively and an intrinsic persistence length of 15 nm has been reported. Due to their hydrophobic side chains, PPPS are compatible with water only as micellar aggregates and tend to form supramolecular structures even at concentrations as low as 10-5mol_mon.units/l. Because of the rodlike conformation of PPPS, this self-assembly leads to aggregates of anisotropic shape. Therefore, depolarized light scattering was employed to yield complementary information about structure and dynamics of these complex fluids. Aqueous solutions of PPPS at room temperature undergo a structural transition at a critical concentration of c_crit.=0.016 g/l. This transition is characterized by a strong increase of scattered intensity in forward direction and dynamic depolarized scattering. Above c_crit. the cylindrical micelles (L=310 nm, d=3.1 nm, N_radial=12) self assembly into large ellipsoidal clusters of size in the μ m range. Due to the strong increase of depolarized scattered intensity there has to be a preferential orientation of the micelles inside those clusters, which thus represent a lyotropic mesophase. By combining static and dynamic light scattering for the low q-range as well as small angle x-ray scattering for the higher q-range it is possible to determine size and shape of each aggregation step. Decreasing the molecular weight of the PPPS has profound influence on the micellar length and hence on c_crit. which is close to the overlap concentration (c ~ 1/L^3) allowing for the observation of the polyelectrolyte effect.

  9. NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels.

    PubMed

    Lippens, G; Najib, J; Wodak, S J; Tartar, A

    1995-01-10

    The solution structure of chlorotoxin, a small toxin purified from the venom of the Leiurus quinquestriatus scorpion, has been determined using 2D 1H NMR spectroscopy. Analysis of the NMR data shows that the structure consists of a small three-stranded antiparallel beta-sheet packed against an alpha-helix, thereby adopting the same fold as charybdotoxin and other members of the short scorpion toxin family [Arseniev et al. (1984) FEBS Lett. 165, 57-62; Martins et al. (1990) FEBS Lett. 260, 249-253; Bontems et al. (1991) Science 254, 1521-1523]. Three disulfide bonds of chlorotoxin (Cys5-Cys28, Cys16-Cys33, and Cys20-Cys35), cross-linking the alpha-helix to the beta-sheet, follow the common pattern found in the other short scorpion toxins. The fourth disulfide bridge (Cys2-Cys19) links the small N-terminal beta strand to the rest of the molecule, in contrast to charybdotoxin where this disulfide bridge is absent and the first strand interacts with the rest of the molecule by several contacts between hydrophobic residues. Another structural difference between chlorotoxin and charybdotoxin is observed at the level of the alpha-beta turn. This difference is accompanied by a change in the electrostatic potential surface, which is largely positive at the level of this turn in chlorotoxin, whereas no such positive potential surface can be found at the same position in charybdotoxin. In the latter protein, the positive surface is formed by different charged residues situated on the solvent-exposed site of the C-terminal beta-sheet.(ABSTRACT TRUNCATED AT 250 WORDS)

  10. Solution structure of the squash aspartic acid proteinase inhibitor (SQAPI) and mutational analysis of pepsin inhibition.

    PubMed

    Headey, Stephen J; Macaskill, Ursula K; Wright, Michele A; Claridge, Jolyon K; Edwards, Patrick J B; Farley, Peter C; Christeller, John T; Laing, William A; Pascal, Steven M

    2010-08-27

    The squash aspartic acid proteinase inhibitor (SQAPI), a proteinaceous proteinase inhibitor from squash, is an effective inhibitor of a range of aspartic proteinases. Proteinaceous aspartic proteinase inhibitors are rare in nature. The only other example in plants probably evolved from a precursor serine proteinase inhibitor. Earlier work based on sequence homology modeling suggested SQAPI evolved from an ancestral cystatin. In this work, we determined the solution structure of SQAPI using NMR and show that SQAPI shares the same fold as a plant cystatin. The structure is characterized by a four-strand anti-parallel beta-sheet gripping an alpha-helix in an analogous manner to fingers of a hand gripping a tennis racquet. Truncation and site-specific mutagenesis revealed that the unstructured N terminus and the loop connecting beta-strands 1 and 2 are important for pepsin inhibition, but the loop connecting strands 3 and 4 is not. Using ambiguous restraints based on the mutagenesis results, SQAPI was then docked computationally to pepsin. The resulting model places the N-terminal strand of SQAPI in the S' side of the substrate binding cleft, whereas the first SQAPI loop binds on the S side of the cleft. The backbone of SQAPI does not interact with the pepsin catalytic Asp(32)-Asp(215) diad, thus avoiding cleavage. The data show that SQAPI does share homologous structural elements with cystatin and appears to retain a similar protease inhibitory mechanism despite its different target. This strongly supports our hypothesis that SQAPI evolved from an ancestral cystatin.

  11. Nonlinear oscillatory rheology and structure of wormlike micellar solutions and colloidal suspensions

    NASA Astrophysics Data System (ADS)

    Gurnon, Amanda Kate

    this constitutive model are tested by comparison with experiments on model WLM solutions. Further comparisons to the nonlinear oscillatory shear responses measured from colloidal suspensions establishes this analysis as a promising, quantitative method for understanding the underlying mechanisms responsible for the nonlinear dynamic response of complex fluids. A new experimental technique is developed to measure the microstructure of complex fluids during steady and transient shear flow using small-angle neutron scattering (SANS). The Flow-SANS experimental method is now available to the broader user communities at the NIST Center for Neutron Research, Gaithersburg, MD and the Institut Laue-Langevin, Grenoble, France. Using this new method, a model shear banding WLM solution is interrogated under steady and oscillatory shear. For the first time, the flow-SANS methods identify new metastable states for shear banding WLM solutions, thus establishing the method as capable of probing new states not accessible using traditional steady or linear oscillatory shear methods. The flow-induced three-dimensional microstructure of a colloidal suspension under steady and dynamic oscillatory shear is also measured using these rheo- and flow-SANS methods. A new structure state is identified in the shear thickening regime that proves critical for defining the "hydrocluster" microstructure state of the suspension that is responsible for shear thickening. For both the suspensions and the WLM solutions, stress-SANS rules with the measured microstructures define the individual stress components arising separately from conservative and hydrodynamic forces and these are compared with the macroscopic rheology. Analysis of these results defines the crucial length- and time-scales of the transient microstructure response. The novel dynamic microstructural measurements presented in this dissertation provide new insights into the complexities of shear thickening and shear banding flow phenomena

  12. Speciation and the structure of lead(II) in hyper-alkaline aqueous solution.

    PubMed

    Bajnóczi, Eva G; Pálinkó, István; Körtvélyesi, Tamás; Bálint, Szabolcs; Bakó, Imre; Sipos, Pál; Persson, Ingmar

    2014-12-14

    The identity of the predominating lead(ii) species in hyper-alkaline aqueous solution has been determined by Raman spectroscopy, and ab initio quantum chemical calculations and its structure has been determined by EXAFS. The observed and calculated Raman spectra for the [Pb(OH)3](-) complex are in agreement while they are different for two-coordinated complexes and complexes containing Pb[double bond, length as m-dash]O double bonds. Predicted bond lengths are also consistent with the presence of [Pb(OH)3](-) and exclude the formation of Pb[double bond, length as m-dash]O double bond(s). These observations together with experimentally established analogies between lead(ii) and tin(ii) in hyper-alkaline aqueous solutions suggest that the last stepwise hydroxido complex of lead(ii) is [Pb(OH)3](-). The Pb-O bond distance in the [Pb(OH)3](-) complex as determined is remarkably short, 2.216 Å, and has low symmetry as no multiple back-scattering is observed. The [Pb(OH)3](-) complex has most likely trigonal pyramidal geometry as all reported three-coordinated lead(ii) complexes in the solid state. From single crystal X-ray data, the bond lengths for O-coordinated lead(ii) complexes with low coordination numbers are spread over an unusually wide interval, 2.216-2.464 Å for N = 3. The Pb-O bond distance is at the short side and within the range of three coordinated complexes, as also observed for the trihydroxidostannate(ii) complex indicating that the hydroxide ion forms short bonds with d(10)s(2) metal ions with occupied anti-bonding orbitals.

  13. Calculation of the structures, stabilities, and vibrational spectra of arsenites, thioarsenites and thioarsenates in aqueous solution

    NASA Astrophysics Data System (ADS)

    Tossell, J. A.; Zimmermann, M. D.

    2008-11-01

    Structures, stabilities and vibrational spectra have been calculated using molecular quantum mechanical methods for As(OH) 3, AsO(OH) 3, As(SH) 3, AsS(SH) 3 and their conjugate bases and for several species with partial substitution of S for O. Properties for the neutral gas-phase molecules are calculated with state-of-the-art methods which yield As sbnd L distances within 0. 01 Å and As sbnd L stretching frequencies within 10 cm -1 of experiment. Similar accuracy is obtained for neutral molecules in solution using a polarizable continuum model (PCM). For monoanions such as AsO(OH)2- and AsS(SH)2-1 frequencies can be calculated to within 20 cm -1 of experiment using the polarizable continuum model. Multiply charged anions remain a challenge for accurate frequency calculations, but we have obtained results within the PCM model which at least semiquantitatively reproduce the available data. This allows us to assign the controversial features D, E and F in the Raman data of (Wood S. A., Tait C. D. and Janecky D. R. (2002) A Raman spectroscopic study of arsenite and thioarsenite species in aqueous solution at 25 °C. Geochem. Trans. 3, 31-39). To help in the assignment of the arsenic sulfide spectra we have also calculated energetics for the oxidation of As(III) to As(V) compounds by polysulfides, disproportionation of As(III) compounds and for the dissociation of the oxo- and thio-acids. We have determined that As(III) oxyacids can be transformed to thioacids which can in turn be oxidized to As(V) sulfides by polysulfides and that the p Ka1s of the acids involved can be ordered as follows: AsS(SH) 3 < As(SH) 3 < AsO(OH) 3 < As(OH) 3 in order of increasing p Ka1. We have also established from the calculated energies that the most stable form of the As(III) oxyacid in acidic aqueous solution is indeed As(OH) 3, consistent with previous assignments.

  14. Structure and dynamics of polymers: From bulk solutions to single polymer translocation

    NASA Astrophysics Data System (ADS)

    Guo, Lei

    This thesis covers the research work that has been done during my Ph.D. study, which focuses on studying polymeric systems by means of computational methods. The research topics include the study of the critical phase transition in ternary homopolymer solutions, the sol-gel transition of triblock copolymers, and single polymer translocation through nanopores. Specifically, the study of the critical phase transition in ternary solutions is aimed at verifying the theoretical predictions for such systems. Due to the finite polymer concentration, mean-field theory fails and the phase transition is described by a sophisticated renormalization approach. Phase separation also induces strong variation of the shape of linear chains, which is investigated as well. The study of the sol-gel transition of triblock copolymers aims to clarify the relationship between the structure and the dynamcal and mechanical properties of triblock copolymers. This is important for the design of new materials that have desired properties. Single DNA translocation through a nanopore presents another interesting and important problem. Understanding the DNA translocation process is beneficial for the design of an efficient DNA-sequencing device, the feasibility of which has been demonstrated in experiments. Moreover, simulations can reveal the complicated nature of the translocation dynamics, which is influenced by many factors, including the external driving force. Another interesting problem related to the translocation process is the distribution of ions and water molecules inside the nanopore, which is important for understanding the phenomena observed in the experiments, such as the screening of DNA inside the pore and the sometimes enhanced ionic current during translocation. It is of particular interest to study how the distribution of ions and water molecules is changed as the pore becomes polarizable, a feature displayed by certain types of nanopores. The thesis is organized as follows

  15. Raman Spectroscopy of Water-Ethanol Solutions: The Estimation of Hydrogen Bonding Energy and the Appearance of Clathrate-like Structures in Solutions.

    PubMed

    Dolenko, Tatiana A; Burikov, Sergey A; Dolenko, Sergey A; Efitorov, Alexander O; Plastinin, Ivan V; Yuzhakov, Viktor I; Patsaeva, Svetlana V

    2015-11-01

    The structure of aqueous alcohol solutions at the molecular level for many decades has remained an intriguing topic in numerous theoretical and practical investigations. The aberrant thermodynamic properties of water-alcohol mixtures are believed to be caused by the differences in energy of hydrogen bonding between water-water, alcohol-alcohol, and alcohol-water molecules. We present the Raman scattering spectra of water, ethanol, and water-ethanol solutions with 20 and 70 vol % of ethanol thoroughly measured and analyzed at temperatures varying from -10 to +70 °C. Application of the MCR-ALS method allowed for each spectrum to extract contributions of molecules with different strengths of hydrogen bonding. The energy (enthalpy) of formation/weakening of hydrogen bonds was calculated using the slope of Van't Hoff plot. The energy of hydrogen bonding in 20 vol % of ethanol was found the highest among all the samples. This finding further supports appearance of clathrate-like structures in water-ethanol solutions with concentrations around 20 vol % of ethanol. PMID:26465255

  16. Synthesis of BiFeO3 thin films by chemical solution deposition - Structural and magnetic studies

    NASA Astrophysics Data System (ADS)

    Angappane, S.; Kambhala, Nagaiah

    2012-06-01

    BiFeO3 thin films were deposited on Si (100) substrates by chemical solution deposition. A precursor solution of bismuth acetate and iron acetylacetonate dissolved in distilled water and acetic acid was spin coated on to silicon substrates at ambient conditions, followed by drying and annealing at 650 °C. The films were characterized by XRD and FESEM to study structural properties and morphology. The magnetic properties studied by SQUID magnetometer shows the ferromagnetic nature of the chemical solution deposited BiFeO3 films which are crucial for low cost device applications.

  17. X-Ray Structure of the Pestivirus NS3 Helicase and Its Conformation in Solution

    PubMed Centra