WorldWideScience

Sample records for crystal inversion dimers

  1. Liquid crystal dimers

    CERN Document Server

    Kumar Pal, Santanu

    2017-01-01

    This book covers in-depth discussion of design principles, synthesis and thermal behavior of all types of liquid crystal (LC) dimers. The text presents recent advances in the field of LC dimers consisting of different mesogenic units such as calamitic, discotic and bent-core molecules. It starts with a chapter on the introduction of liquid crystal dimers, including their odd-even behavior, basic classification of dimers and common mesophases in dimers. The text shows how the molecular architectures are being used to develop new materials to study a range of interesting phenomena such as the biaxial nematic phase containing rod-like and disc-like mesogenic units. Finally, the text presents perspectives related to technological relevance of these dimers such as dopants in LC display mixtures exhibiting faster relaxation time, strong flexoelectric coupling and others to effect control over the properties of these materials.

  2. Evaluation of stability difference between asymmetric homochiral dimer in (S)-thalidomide crystal and symmetric heterochiral dimer in (RS)-thalidomide crystal

    Science.gov (United States)

    Suzuki, Toshiya; Tanaka, Masahito; Shiro, Motoo; Shibata, Norio; Osaka, Tetsuya; Asahi, Toru

    2010-03-01

    This article discusses differences in physicochemical properties such as solubility and melting point between (S)-thalidomide and (RS)-thalidomide based on crystal structures determined by X-ray diffraction experiments. Investigation of such differences is of great importance because thalidomide has attracted considerable attention again due to its wide-range bioactivity for intractable diseases. In this article, structures of hydrogen-bonded rings were compared between asymmetric homochiral dimers in (S)-thalidomide crystal and symmetric heterochiral dimers in (RS)-thalidomide crystal. The heterochiral dimer was evaluated to be more stable than the homochiral dimer by the energy calculations for hydrogen-bonded rings in those dimers. These results indicate that differences in physicochemical properties between enantiomeric and racemic thalidomides originate from the difference of structural stability between homochiral and heterochiral dimers.

  3. Elastic properties of the degenerate f.c.c. crystal of polydisperse soft dimers at zero temperature

    CERN Document Server

    Narojczyk, J W

    2015-01-01

    Elastic properties of soft, three-dimensional dimers, interacting through site-site n-inverse-power potential, are determined by computer simulations at zero temperature. The degenerate crystal of dimers exhibiting (Gaussian) size distribution of atomic diameters - i.e. size polydispersity - is studied at the molecular number density $1/\\sqrt{2}$; the distance between centers of atoms forming dimers is considered as a length unit. It is shown that, at the fixed number density of the dimers, increasing polydispersity causes, typically, an increase of pressure, elastic constants and Poisson's ratio; the latter is positive in most direction. A direction is found, however, in which the size polydispersity causes substantial decrease of Poisson's ratio, down to negative values for large $n$. Thus, the system is partially auxetic for large polydispersity and large n.

  4. Vortexlike topological defects in nematic colloids: chiral colloidal dimers and 2D crystals.

    Science.gov (United States)

    Tkalec, U; Ravnik, M; Zumer, S; Musevic, I

    2009-09-18

    We show that chiral ordering of the underlying complex fluid strongly influences defect formation and colloidal interactions. Nonsingular defect loops with a topological charge -2 are observed, with a cross section identical to hyperbolic vortices in magnetic systems. These loops are binding spontaneously formed pairs of colloidal particles and dimers, which are chiral objects. Chiral dimer-dimer interaction weakly depends on the chirality of dimers and leads to the assembly of 2D nematic colloidal crystals of pure or "mixed" chirality, intercalated with a lattice of nonsingular vortexlike defects.

  5. Dislocations and vacancies in two-dimensional mixed crystals of spheres and dimers

    KAUST Repository

    Gerbode, Sharon J.

    2010-10-15

    In colloidal crystals of spheres, dislocation motion is unrestricted. On the other hand, recent studies of relaxation in crystals of colloidal dimer particles have demonstrated that the dislocation dynamics in such crystals are reminiscent of glassy systems. The observed glassy dynamics arise as a result of dislocation cages formed by certain dimer orientations. In the current study, we use experiments and simulations to investigate the transition that arises when a pure sphere crystal is doped with an increasing concentration of dimers. Specifically, we focus on both dislocation caging and vacancy motion. Interestingly, we find that any nonzero fraction of dimers introduces finite dislocation cages, suggesting that glassy dynamics are present for any mixed crystal. However, we have also identified a vacancy-mediated uncaging mechanism for releasing dislocations from their cages. This mechanism is dependent on vacancy diffusion, which slows by orders of magnitude as the dimer concentration is increased. We propose that in mixed crystals with low dimer concentrations vacancy diffusion is fast enough to uncage dislocations and delay the onset of glassy dislocation dynamics. © 2010 The American Physical Society.

  6. Synthesis and mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Connecting two discotic mesogens via a spacer not only stabilizes the columnar mesophase but also leads to the formation of glass columnar phase, and therefore improves the physical properties of discotic liquid crystals as organic semiconductor. Here, we report the synthesis of eight diacetylene-bridged triphenylene discotic liquid crystal dimers, [C18H6(OCnH2n+1)4(OMe)O2C-C8H16-C≡≡ C-]2, 3(n), (n = 4-8), [C18H6(OC6H13)5O2C-C8H16-C≡≡ C-]2, 6 and [C18H6(OC6H13)5O-(CH2)m-C≡≡ C-]2, 8(m), (m = 1, 3) by Eglinton coupling reaction. The thermotropic liquid crystal properties were studied by differential scanning calorimetry and polarized optical microscopy. The results are showed as follows: the length of peripheral alkyl chains of triphenylene influenced properties of liquid crystal dimers; dimers 3(n) (n = 5-8) and 6 had glass columnar phase, and no crystallization was observed above -50℃ for all the triphenylene dimers; compared with 3(6), 6 showed higher molecular symmetry, more stable columnar mesophase and wider mesophase range. The connecting group, length and rigidity of spacer had important influence on the mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers.

  7. Synthesis and mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers

    Institute of Scientific and Technical Information of China (English)

    JI Hong; ZHAO KeQing; YU WenHao; WANG BiQin; HU Pin

    2009-01-01

    Connecting two discotic mesogens via a spacer not only stabilizes the columnar mesophase but also leads to the formation of glass columnar phase,and therefore improves the physical properties of discotic liquid crystals as organic semiconductor.Here,we report the synthesis of eight diacetylene-bridged triphenylene discotic liquid crystal dimers,[C18H6(OCnH2n+1)4(OMe)O2C-CsH16-C≡C-]2,3(n),(n=4-8),[C18H6(OC6H13)5O2C-C8H16-C≡C-]2,6 and [C18H6(OC6H13)5O-(CH2)m-C≡C-]2,8(m),(m=1,3) by Eglinton coupling reaction.The thermotropic liquid crystal properties were studied by differential scanning calorimetry and polarized optical microscopy.The results are showed as follows:the length of peripheral alkyl chains of triphenylene influenced properties of liquid crystal dimers;dimers 3(n) (n=5-8) and 6 had glass columnar phase,and no crystallization was observed above -50℃ for all the triphenylene dimers;compared with 3(6),6 showed higher molecular symmetry,more stable columnar mesophase and wider mesophase range.The connecting group,length and rigidity of spacer had important influence on the mesomorphism of diacetylene-bridged triphenylene discotic liquid crystal dimers.

  8. Time-programmed helix inversion in phototunable liquid crystals.

    Science.gov (United States)

    Asshoff, Sarah J; Iamsaard, Supitchaya; Bosco, Alessandro; Cornelissen, Jeroen J L M; Feringa, Ben L; Katsonis, Nathalie

    2013-05-14

    Doping cholesteric liquid crystals with photo-responsive molecules enables controlling the colour and polarisation of the light they reflect. However, accelerating the rate of relaxation of these photo-controllable liquid crystals remains challenging. Here we show that the relaxation rate of the cholesteric helix is fully determined by helix inversion of the molecular dopants.

  9. Novel Air Stable Organic Radical Semiconductor of Dimers of Dithienothiophene, Single Crystals, and Field-Effect Transistors.

    Science.gov (United States)

    Zhang, Hantang; Dong, Huanli; Li, Yang; Jiang, Wei; Zhen, Yonggang; Jiang, Lang; Wang, Zhaohui; Chen, Wei; Wittmann, Angela; Hu, Wenping

    2016-09-01

    Singly linked and vinyl-linked dimers of dithienothiophenes exhibit different electronic behaviors. Single crystals of the singly linked dimer show a high conductivity of 0.265 S cm(-1) , five orders of magnitude higher than that of the vinyl-linked dimer. The huge increase in the hole density of singly linked dimers results from the formation of radicals, which can be reversibly tuned by facile thermal de-doping.

  10. Novel modulated Hexatic Phases in Symmetric Liquid Crystal Dimers

    OpenAIRE

    Date, R; Luckhurst, G.; Shuman, M.; Seddon, J

    1995-01-01

    Homologues of the dimeric α,ω-bis(4-n-alkylanilinebenzylidene-4'-oxy)alkanes (m.OnO.m) have been synthesised with spacer lengths n ranging from 9 to 12 methylene units and with terminal alkyl chain lengths m of 10, 12 and 14. Characterisation of these materials has been carried out by X-ray diffraction, differential scanning calorimetry and optical microscopy. In six of these compounds a novel modulated tilted hexatic phase, denoted S1, has been identified, in which the smectic layers have a ...

  11. Fabrication of silicon inverse woodpile photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Hermatschweiler, Martin; Wegener, Martin [DFG-Center for Functional Nanostructures (CFN) and Institut fuer Angewandte Physik, Universitaet Karlsruhe (TH), 76131 Karlsruhe (Germany); Ozin, Geoffrey A. [Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 (Canada); Ledermann, Alexandra; Freymann, Georg von [Institut fuer Nanotechnologie, Forschungszentrum Karlsruhe in der Helmholtz-Gemeinschaft, 76021 Karlsruhe (Germany)

    2007-07-01

    We fabricate silicon inverse woodpile structures for the first time. Direct laser writing of polymeric templates and a novel silicon-singleinversion procedure lead to structures with gap/midgap ratios of 14.2% centered at 2.5 {mu}m wavelength. First, polymer templates are fabricated by direct laser writing or other means. Next, we deposit a thin silica coating via atomic layer deposition (ALD) on the polymer and - without removing the polymer - infiltrate the composite structure with Si via Si chemical vapor deposition (CVD). The silica shell provides sufficient and reliable stabilization for the high temperature CVD process. Finally, the silica is etched out and the polymer is calcined in air, leading to a Si inverse woodpile structure. Optical measurements and comparison to bandstructure and scattering-matrix calculations reveal a gap/midgap ratio of 14.2% centered at 2.5 {mu}m. An optimized structure could open a band gap with a gap/midgap ratio of up to 20.5%.

  12. Serum Potassium Levels Inversely Correlate with D-Dimer In Patients with Acute-Onset Atrial Fibrillation

    Energy Technology Data Exchange (ETDEWEB)

    Cervellin, Gianfranco, E-mail: gcervellin@ao.pr.it; Bonfanti, Laura; Picanza, Alessandra; Lippi, Giuseppe [1Academic Hospital of Parma (Italy)

    2015-03-15

    D-dimer values are frequently increased in patients with atrial fibrillation (AF) compared to subjects in sinus rhythm. Hypokalemia plays a role in several cardiovascular diseases, but little is known about the association with AF. D-dimer values are frequently increased in patients with atrial fibrillation (AF) compared with subjects in sinus rhythm. Hypokalemia plays a role in several cardiovascular diseases, but little is known about the association with AF. The aim of this study was to investigate correlations between D-dimer and serum potassium in acute-onset AF (AAF). To investigate the potential correlation between the values of serum potassium and D-dimer in patients with AAF, we retrospectively reviewed clinical and laboratory data of all emergency department visits for AAF in 2013. Among 271 consecutive AAF patients with D-dimer assessments, those with hypokalemia (n = 98) had significantly higher D-dimer values than normokalemic patients (139 versus 114 ng/mL, p = 0.004). The rate of patients with D-dimer values exceeding the diagnostic cut-off was higher in the group of patients with hypokalemia than in those with normal serum potassium (26.5% versus 16.2%; p = 0.029). An inverse and highly significant correlation was found between serum potassium and D-dimer (r = −0.21; p < 0.001), even after adjustments for age and sex (beta coefficient −94.8; p = 0.001). The relative risk for a positive D-dimer value attributed to hypokalemia was 1.64 (95% CI, 1.02 to 2.63; p = 0.040). The correlation remained statistically significant in patients free from antihypertensive drugs (r = −0.25; p = 0.018), but not in those taking angiotensin-receptor blockers, angiotensin-converting enzyme inhibitors, or diuretics. The inverse correlation between values of potassium and D-dimer in patients with AAF provides important and complementary information about the thromboembolic risk of these patients.

  13. High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

    KAUST Repository

    Saidaminov, Makhsud I.

    2015-07-06

    Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3+, X=Br− or I−) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process. Here we present a rapid crystal growth process to obtain MAPbX3 single crystals, an order of magnitude faster than previous reports. The process is based on our observation of the substantial decrease of MAPbX3 solubility, in certain solvents, at elevated temperatures. The crystals can be both size- and shape-controlled by manipulating the different crystallization parameters. Despite the rapidity of the method, the grown crystals exhibit transport properties and trap densities comparable to the highest quality MAPbX3 reported to date. The phenomenon of inverse or retrograde solubility and its correlated inverse temperature crystallization strategy present a major step forward for advancing the field on perovskite crystallization.

  14. High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

    Science.gov (United States)

    Saidaminov, Makhsud I.; Abdelhady, Ahmed L.; Murali, Banavoth; Alarousu, Erkki; Burlakov, Victor M.; Peng, Wei; Dursun, Ibrahim; Wang, Lingfei; He, Yao; Maculan, Giacomo; Goriely, Alain; Wu, Tom; Mohammed, Omar F.; Bakr, Osman M.

    2015-07-01

    Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3+, X=Br- or I-) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process. Here we present a rapid crystal growth process to obtain MAPbX3 single crystals, an order of magnitude faster than previous reports. The process is based on our observation of the substantial decrease of MAPbX3 solubility, in certain solvents, at elevated temperatures. The crystals can be both size- and shape-controlled by manipulating the different crystallization parameters. Despite the rapidity of the method, the grown crystals exhibit transport properties and trap densities comparable to the highest quality MAPbX3 reported to date. The phenomenon of inverse or retrograde solubility and its correlated inverse temperature crystallization strategy present a major step forward for advancing the field on perovskite crystallization.

  15. Packing interface energetics in different crystal forms of the λ Cro dimer.

    Science.gov (United States)

    Ahlstrom, Logan S; Miyashita, Osamu

    2014-07-01

    Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures.

  16. Patterning hierarchy in direct and inverse opal crystals.

    Science.gov (United States)

    Mishchenko, Lidiya; Hatton, Benjamin; Kolle, Mathias; Aizenberg, Joanna

    2012-06-25

    Biological strategies for bottom-up synthesis of inorganic crystalline and amorphous materials within topographic templates have recently become an attractive approach for fabricating complex synthetic structures. Inspired by these strategies, herein the synthesis of multi-layered, hierarchical inverse colloidal crystal films formed directly on topographically patterned substrates via evaporative deposition, or "co-assembly", of polymeric spheres with a silicate sol-gel precursor solution and subsequent removal of the colloidal template, is described. The response of this growing composite colloid-silica system to artificially imposed 3D spatial constraints of various geometries is systematically studied, and compared with that of direct colloidal crystal assembly on the same template. Substrates designed with arrays of rectangular, triangular, and hexagonal prisms and cylinders are shown to control crystallographic domain nucleation and orientation of the direct and inverse opals. With this bottom-up topographical approach, it is demonstrated that the system can be manipulated to either form large patterned single crystals, or crystals with a fine-tuned extent of disorder, and to nucleate distinct colloidal domains of a defined size, location, and orientation in a wide range of length-scales. The resulting ordered, quasi-ordered, and disordered colloidal crystal films show distinct optical properties. Therefore, this method provides a means of controlling bottom-up synthesis of complex, hierarchical direct and inverse opal structures designed for altering optical properties and increased functionality. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Dielectric relaxation and birefringence study of 7.O5O.7 dimeric liquid crystal compound

    Science.gov (United States)

    Bhattacharjee, Debanjan; Paul-Choudhury, Sandip; Alapati, Parameswara Rao; Bhattacharjee, Ayon

    2016-05-01

    Measurement of dielectric relaxation and birefringence phenomenon of dimeric liquid crystal compound with the dependence of temperature was reported in this paper. Homogeneous (HG) and homeotropic (HT) alignment of the cell are introduced to investigate the dielectric relaxation, activation energy and birefringence. Cole-Cole plots analyzed the dielectric relaxation of the dimeric compound. The observed Cole-Cole plots were semi-circular, and the relaxation mechanism obeys the non-Debye type of relaxation behaviour. Slater's perturbation equations have been used to analysis the activation energy of the compound. The birefringence of the compound has positively anisotropy and thin prism mechanism was used to study the anisotropy of the compound.

  18. Formation of H-type liquid crystal dimer at air-water interface

    Energy Technology Data Exchange (ETDEWEB)

    Karthik, C., E-mail: karthik.c@pilani.bits-pilani.ac.in; Gupta, Adbhut, E-mail: karthik.c@pilani.bits-pilani.ac.in; Joshi, Aditya, E-mail: karthik.c@pilani.bits-pilani.ac.in; Manjuladevi, V., E-mail: karthik.c@pilani.bits-pilani.ac.in; Gupta, Raj Kumar, E-mail: karthik.c@pilani.bits-pilani.ac.in [Department of Physics, Birla Institute of Technology and Science, Pilani, Rajasthan -333031 (India); Varia, Mahesh C.; Kumar, Sandeep [Raman Research Institute, Sadashivanagar, Bangalore - 560080 (India)

    2014-04-24

    We have formed the Langmuir monolayer of H-shaped Azo linked liquid crystal dimer molecule at the air-water interface. Isocycles of the molecule showed hysteresis suggesting the ir-reversible nature of the monolayer formed. The thin film deposited on the silicon wafer was characterized using Atomic Force Microscopy (AFM) and Field Emission Scanning Electron Microscopy (FESEM). The images showed uniform domains of the dimer molecule. We propose that these molecules tend to take book shelf configuration in the liquid phase.

  19. Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography.

    Science.gov (United States)

    Vu, Anh T; Wang, Xinying; Wickramasinghe, S Ranil; Yu, Bing; Yuan, Hua; Cong, Hailin; Luo, Yongli; Tang, Jianguo

    2015-08-01

    Hydrophobic interaction membrane chromatography has gained interest due to its excellent performance in the purification of humanized monoclonal antibodies. The membrane material used in hydrophobic interaction membrane chromatography has typically been commercially available polyvinylidene fluoride. In this contribution, newly developed inverse colloidal crystal membranes that have uniform pores, high porosity and, therefore, high surface area for protein binding are used as hydrophobic interaction membrane chromatography membranes for humanized monoclonal antibody immunoglobulin G purification. The capacity of the inverse colloidal crystal membranes developed here is up to ten times greater than commercially available polyvinylidene fluoride membranes with a similar pore size. This work highlights the importance of developing uniform pore size high porosity membranes in order to maximize the capacity of hydrophobic interaction membrane chromatography. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Giant Flexoelectro-optic Effect with Liquid Crystal Dimer CB7CB

    Science.gov (United States)

    Varanytsia, Andrii; Chien, Liang-Chy

    2017-01-01

    We demonstrate a giant flexoelectro-optic behavior of liquid crystal dimer CB7CB. Flexoelectric properties of CB7CB experimentally characterized by measured angle of an in-plane rotation of helical axis (HA) in polymer stabilized uniform lying helix cholesteric liquid crystal. The 45° rotation of HA providing full intensity modulation of transmitted through a pair of crossed polarizers light, is achieved with 4.5 V/μm with a sub-millisecond electro-optic switching time. Reported properties enable application of CB7CB in applications of the flexoelectric effect in fast switching photonic and electro-optic devices. PMID:28117429

  1. The TonB dimeric crystal structures do not exist in vivo.

    Science.gov (United States)

    Postle, Kathleen; Kastead, Kyle A; Gresock, Michael G; Ghosh, Joydeep; Swayne, Cheryl D

    2010-12-21

    The TonB system energizes transport of nutrients across the outer membrane of Escherichia coli using cytoplasmic membrane proton motive force (PMF) for energy. Integral cytoplasmic membrane proteins ExbB and ExbD appear to harvest PMF and transduce it to TonB. The carboxy terminus of TonB then physically interacts with outer membrane transporters to allow translocation of ligands into the periplasmic space. The structure of the TonB carboxy terminus (residues ~150 to 239) has been solved several times with similar results. Our previous results hinted that in vitro structures might not mimic the dimeric conformations that characterize TonB in vivo. To test structural predictions and to identify irreplaceable residues, the entire carboxy terminus of TonB was scanned with Cys substitutions. TonB I232C and N233C, predicted to efficiently form disulfide-linked dimers in the crystal structures, did not do so. In contrast, Cys substitutions positioned at large distances from one another in the crystal structures efficiently formed dimers. Cys scanning identified seven functionally important residues. However, no single residue was irreplaceable. The phenotypes conferred by changes of the seven residues depended on both the specific assay used and the residue substituted. All seven residues were synergistic with one another. The buried nature of the residues in the structures was also inconsistent with these properties. Taken together, these results indicate that the solved dimeric crystal structures of TonB do not exist. The most likely explanation for the aberrant structures is that they were obtained in the absence of the TonB transmembrane domain, ExbB, ExbD, and/or the PMF.

  2. The ballistic dimer resonance in the one-dimensional disordered photonic crystals

    Science.gov (United States)

    Khalfoun, H.; Bentata, S.; Bouamoud, M.; Henrard, L.; Vandenbem, C.

    2009-12-01

    The propagation of electromagnetic waves in one-dimensional disordered dielectric layer stack is studied theoretically using the transfer matrix formalism. The presence of the dimer unit cells inside a host photonic crystal, as the intentionally short range disorder correlation, provides predicted dimer resonances, leading to the break down of the Anderson localization. However while suitably adjusting the intrinsic defect unit cell parameters (i.e. the defect dielectric constants), the light can be transmitted on larger localization length through a ballistic canal, opening up possibilities for performing better tailored ballistic optical filters. Moreover, by increasing the rate of disorder (i.e. the defects concentration and/or the length of the system) the quality of the transmission around the ballistic resonance can be improved with the smoother corresponding allowed mini bands.

  3. Crystal Structure of a Dimerized Cockroach Allergen Bla g 2 Complexed with a Monoclonal Antibody

    Energy Technology Data Exchange (ETDEWEB)

    Li, Mi; Gustchina, Alla; Alexandratos, Jerry; Wlodawer, Alexander; Wünschmann, Sabina; Kepley, Christopher L.; Chapman, Martin D.; Pomes, Anna (INDOOR Bio.); (VCU); (NIH)

    2008-09-03

    The crystal structure of a 1:1 complex between the German cockroach allergen Bla g 2 and the Fab' fragment of a monoclonal antibody 7C11 was solved at 2.8-{angstrom} resolution. Bla g 2 binds to the antibody through four loops that include residues 60-70, 83-86, 98-100, and 129-132. Cation-{pi} interactions exist between Lys-65, Arg-83, and Lys-132 in Bla g 2 and several tyrosines in 7C11. In the complex with Fab', Bla g 2 forms a dimer, which is stabilized by a quasi-four-helix bundle comprised of an {alpha}-helix and a helical turn from each allergen monomer, exhibiting a novel dimerization mode for an aspartic protease. A disulfide bridge between C51a and C113, unique to the aspartic protease family, connects the two helical elements within each Bla g 2 monomer, thus facilitating formation of the bundle. Mutation of these cysteines, as well as the residues Asn-52, Gln-110, and Ile-114, involved in hydrophobic interactions within the bundle, resulted in a protein that did not dimerize. The mutant proteins induced less {beta}-hexosaminidase release from mast cells than the wild-type Bla g 2, suggesting a functional role of dimerization in allergenicity. Because 7C11 shares a binding epitope with IgE, the information gained by analysis of the crystal structure of its complex provided guidance for site-directed mutagenesis of the allergen epitope. We have now identified key residues involved in IgE antibody binding; this information will be useful for the design of vaccines for immunotherapy.

  4. Accelerating MP2C dispersion corrections for dimers and molecular crystals

    Science.gov (United States)

    Huang, Yuanhang; Shao, Yihan; Beran, Gregory J. O.

    2013-06-01

    The MP2C dispersion correction of Pitonak and Hesselmann [J. Chem. Theory Comput. 6, 168 (2010)], 10.1021/ct9005882 substantially improves the performance of second-order Møller-Plesset perturbation theory for non-covalent interactions, albeit with non-trivial computational cost. Here, the MP2C correction is computed in a monomer-centered basis instead of a dimer-centered one. When applied to a single dimer MP2 calculation, this change accelerates the MP2C dispersion correction several-fold while introducing only trivial new errors. More significantly, in the context of fragment-based molecular crystal studies, combination of the new monomer basis algorithm and the periodic symmetry of the crystal reduces the cost of computing the dispersion correction by two orders of magnitude. This speed-up reduces the MP2C dispersion correction calculation from a significant computational expense to a negligible one in crystals like aspirin or oxalyl dihydrazide, without compromising accuracy.

  5. Synthesis and Characterization of Nonsymmetric Liquid Crystal Dimer Containing Biphenyl and Azobenzene Moiety

    Directory of Open Access Journals (Sweden)

    S. Sandy Subala

    2013-01-01

    Full Text Available Calamitic liquid crystalline dimer containing azobenzene moiety and a decyloxy biphenyl linked by flexible spacers {4-[7-(4′-decyloxy-biphenyl-4-yloxy-alkyloxy]-phenyl}-(4-decyl-phenyl-diazene has been synthesized and characterized by spectroscopic methods. The transition temperatures and phase behaviours were studied by Differential Scanning Calorimeter (DSC and Polarizing Optical Microscope (POM. The synthesized compounds exhibited enantiotropic liquid crystal phase with higher spacer display nematic and smectic C phases while lower spacer shows nematic and smectic A phases.

  6. The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions.

    Science.gov (United States)

    Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

    2011-03-04

    Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion.

  7. Orientational order parameter studies in two symmetric dimeric liquid crystals - an optical study

    Science.gov (United States)

    Pardhasaradhi, P.; Datta Prasad, P. V.; Madhavi Latha, D.; Pisipati, V. G. K. M.; Padmaja Rani, G.

    2012-12-01

    The optical technique developed by [W. Kuczynski, B. Zywucki, and J. Malecki, Determination of orientational order parameter in various liquid-crystalline phases, Mol. Cryst. Liq. Cryst. 381 (2002), pp. 1-19; B.J. Zywucki and W. Kuczynski, IEEE transactions on optical phenomena - The orientational order in nematic liquid crystals from birefringence measurements, Dielectr. Electr. Insul. 8 (2001), pp. 512-515] is fabricated and used to determine the orientational order parameter in two dimeric liquid crystalline compounds nematic and SmA phases of α,ω-bis(4-alkylanilinebenzylidene-4‧-oxy)alkane (m.OnO.m) homologous series. The compounds studied are 5.O8O.5 and 5.O10O.5 which exhibit nematic and SmA, and nematic phases, respectively. The orientational order parameter in both the phases of nematic and SmA phases of the compound one and the nematic phase of the compound two are obtained using the principle of Newton's rings which gives directly the birefringence, δn of the liquid crystal dimer. The merits of the technique used are presented over the conventional techniques for the determination of orientational order parameter. The results for the two compounds are compared with those values estimated from n e, n o and density using the two internal field models due to Vuks and Neugebauer applicable to nematic phase.

  8. Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer.

    Science.gov (United States)

    Horikoshi, Naoki; Tachiwana, Hiroaki; Kagawa, Wataru; Osakabe, Akihisa; Matsumoto, Syota; Iwai, Shigenori; Sugasawa, Kaoru; Kurumizaka, Hitoshi

    2016-02-26

    The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the mechanism by which the CPD is accommodated within the nucleosome has remained unknown. We now report the crystal structure of a nucleosome containing CPDs. In the nucleosome, the CPD induces only limited local backbone distortion, and the affected bases are accommodated within the duplex. Interestingly, one of the affected thymine bases is located within 3.0 Å from the undamaged complementary adenine base, suggesting the formation of complementary hydrogen bonds in the nucleosome. We also found that UV-DDB, which binds the CPD at the initial stage of the NER pathway, also efficiently binds to the nucleosomal CPD. These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin.

  9. Non-Covalent Interactions and Impact of Charge Penetration Effects in Linear Oligoacene Dimers and Single Crystals

    KAUST Repository

    Ryno, Sean M

    2016-05-18

    Non-covalent interactions determine in large part the thermodynamic aspects of molecular packing in organic crystals. Using a combination of symmetry-adapted perturbation theory (SAPT) and classical multipole electrostatics, we describe the interaction potential energy surfaces for dimers of the oligoacene family, from benzene to hexacene. An analysis of these surfaces and a thorough assessment of dimers extracted from the reported crystal structures underline that high-order interactions (i.e., three-body non-additive interactions) must be considered in order to rationalize the details of the crystal structures. A comparison of the SAPT electrostatic energy with the multipole interaction energy demonstrates the importance of the contribution of charge penetration, which is shown to account for up to 50% of the total interaction energy in dimers extracted from the experimental single crystals; in the case of the most stable co-facial model dimers, this contribution is even larger than the total interaction energy. Our results highlight the importance of taking account of charge penetration in studies of the larger oligoacenes.

  10. Domain-inversion characteristics of congruent and stoichiometric LiNbO3 crystals

    Institute of Scientific and Technical Information of China (English)

    于金辉; 王明常; 周慧芬; 陆宾; 冯诚士

    2001-01-01

    The characteristics of the ferroelectxic domain inversion structures fabricated by applying voltage at room temperatture in Z-cut congruent LiNbO3 and stoichiometric LiNbO3 crystals were examined. The voltage required for domain reversal in congrueat crystals is about 2.8 times larger than the voltage for stoichiometric crystals. The periodicity of the sstoichiometric crystals are more uniforn than that of the congruent crystals.

  11. Insights into Strand Exchange in BTB Domain Dimers from the Crystal Structures of FAZF and Miz1

    Energy Technology Data Exchange (ETDEWEB)

    Stogios, Peter J.; Cuesta-Seijo, Jose Antonio; Chen, Lu; Pomroy, Neil C.; Privé, Gilbert G. (Toronto); (OCI)

    2010-09-22

    The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel {beta}-sheet with a strand from the other chain. We have solved the crystal structures of the BTB domains from Fanconi anemia zinc finger (FAZF) and Miz1 (Myc-interacting zinc finger 1) to resolutions of 2.0 {angstrom} and 2.6 {angstrom}, respectively. Unlike previous examples of BTB domain structures, the FAZF BTB domain is a nonswapped dimer, with each N-terminal {beta}-strand associated with its own chain. As a result, the dimerization interface in the FAZF BTB domain is about half as large as in the domain-swapped dimers. The Miz1 BTB domain resembles a typical swapped BTB dimer, although it has a shorter N-terminus that is not able to form the interchain sheet. Using cysteine cross-linking, we confirmed that the promyelocytic leukemia zinc finger (PLZF) BTB dimer is strand exchanged in solution, while the FAZF BTB dimer is not. A phylogenic tree of the BTB fold based on both sequence and structural features shows that the common ancestor of the BTB domain in BTB-ZF (bric a brac, tramtrack, broad-complex zinc finger) proteins was a domain-swapped dimer. The differences in the N-termini seen in the FAZF and Miz1 BTB domains appear to be more recent developments in the structural evolution of the domain.

  12. Emission studies on ZnO-inverse photonic crystals derived from self-assembly

    Indian Academy of Sciences (India)

    Sunita Kedia; R Vijaya; Alok K Ray; Sucharita Sinha; K Dasgupta

    2010-11-01

    Photonic crystals fabricated from the colloidal spheres of polymethyl methacrylate (PMMA) using the inward-growing self-assembly technique were subse-quently in-filled with zinc oxide (ZnO) prepared by the sol–gel process. The polymer template was removed by heat treatment and chemical method to get ZnO-inverse photonic crystal. The structural quality of the inverse photonic crystal obtained by the chemical method was found to be superior to that obtained by heat treatment. The ZnO-inverse photonic crystal obtained by the chemical method was further treated at an elevated temperature to ensure the crystalline nature of ZnO. Laser-induced emission tudies on ZnO-inverse photonic crystals were carried out at an excitation wavelength of 325 nm. The emission spectra showing UV and visible bands at collection angle of 45° from the direction of excitation helped to establish the role of crystalline ZnO.

  13. Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Jia; Tong, Liang

    2015-10-12

    Acetyl-CoA carboxylase (ACC) has crucial roles in fatty acid metabolism and is an attractive target for drug discovery against diabetes, cancer and other diseases1, 2, 3, 4, 5, 6. Saccharomyces cerevisiae ACC (ScACC) is crucial for the production of very-long-chain fatty acids and the maintenance of the nuclear envelope7, 8. ACC contains biotin carboxylase (BC) and carboxyltransferase (CT) activities, and its biotin is linked covalently to the biotin carboxyl carrier protein (BCCP). Most eukaryotic ACCs are 250-kilodalton (kDa), multi-domain enzymes and function as homodimers and higher oligomers. They contain a unique, 80-kDa central region that shares no homology with other proteins. Although the structures of the BC, CT and BCCP domains and other biotin-dependent carboxylase holoenzymes are known1, 9, 10, 11, 12, 13, 14, there is currently no structural information on the ACC holoenzyme. Here we report the crystal structure of the full-length, 500-kDa holoenzyme dimer of ScACC. The structure is remarkably different from that of the other biotin-dependent carboxylases. The central region contains five domains and is important for positioning the BC and CT domains for catalysis. The structure unexpectedly reveals a dimer of the BC domain and extensive conformational differences compared to the structure of the BC domain alone, which is a monomer. These structural changes reveal why the BC domain alone is catalytically inactive and define the molecular mechanism for the inhibition of eukaryotic ACC by the natural product soraphen A15, 16 and by phosphorylation of a Ser residue just before the BC domain core in mammalian ACC. The BC and CT active sites are separated by 80 Å, and the entire BCCP domain must translocate during catalysis.

  14. Crystal structure of dimeric heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme.

    Science.gov (United States)

    Sugishima, Masakazu; Hagiwara, Yoshinori; Zhang, Xuhong; Yoshida, Tadashi; Migita, Catharina T; Fukuyama, Keiichi

    2005-03-22

    Phycobiliproteins, light-harvesting proteins in cyanobacteria, red algae, and cryptophytes, contain phycobilin pigments. Phycobilins are synthesized from biliverdin, which is produced by the oxidative cleavage of the heme porphyrin ring catalyzed by heme oxygenase (HO). Two paralogs of ho (ho1 and ho2) have been identified in the genome of the cyanobacterium, Synechocystis sp. PCC 6803. The recombinant proteins of both paralogs (Syn HO-1 and Syn HO-2) possess in vitro heme degradation activity. We have determined the crystal structures of Syn HO-2 in complex with heme (heme-Syn HO-2) and its reduced and NO bound forms. The heme-Syn HO-2 crystal was a nonmerohedral twin, and detwinned diffraction data were used to refine the structure. Although heme-Syn HO-2 shares common folding with other HOs, the C-terminal segment is ordered and turns back to the heme-binding side. Gel-filtration chromatography analysis and molecular packing in the crystal indicate that heme-Syn HO-2 forms a homodimer, in which the C-terminal ordered segments interact with each other. Because Syn HO-2 is a monomer in the apo state, the dimeric interaction may aid in the selection of the reducing partner but likely does not interfere with heme binding. The heme iron is coordinated by a water molecule in the ferric form, but the distal water is absent in the ferrous form. In all of the Syn HO-2 structures, several water molecules form a hydrogen-bond network at the distal hemepocket, which is involved in HO activity. Upon NO binding, the side-chain conformation of Tyr 156 changes. Tyr 156 is located at the hydrophobic cluster, which interrupts the possible H(+) pathway from the molecular surface to the hemepocket. Thus, Tyr 156 may function as a H(+) shuttle by changing conformation.

  15. Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1: Insights into the molecular basis of formation of a dimer.

    Science.gov (United States)

    Tzeng, Ching-Ting; Huang, Yen-Hua; Huang, Cheng-Yang

    2016-09-23

    Dihydropyrimidinase, a tetrameric metalloenzyme, is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. In this paper, we report the crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.1 Å resolution. The structure of P. aeruginosa dihydropyrimidinase reveals a classic (β/α)8-barrel structure core embedding the catalytic dimetal center and a β-sandwich domain, which is commonly found in the architecture of dihydropyrimidinases. In contrast to all dihydropyrimidinases, P. aeruginosa dihydropyrimidinase forms a dimer, rather than a tetramer, both in the crystalline state and in the solution. Basing on sequence analysis and structural comparison of the C-terminal region and the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and Thermus sp. dihydropyrimidinase, we propose a working model to explain why this enzyme cannot be a tetramer.

  16. Time-programmed helix inversion in phototunable liquid crystals

    NARCIS (Netherlands)

    Asshoff, Sarah J.; Iamsaard, Supitchaya; Bosco, Alessandro; Cornelissen, Jeroen J. L. M.; Feringa, Ben L.; Katsonis, Nathalie

    2013-01-01

    Doping cholesteric liquid crystals with photo-responsive molecules enables controlling the colour and polarisation of the light they reflect. However, accelerating the rate of relaxation of these photo-controllable liquid crystals remains challenging. Here we show that the relaxation rate of the

  17. Time-programmed helix inversion in phototunable liquid crystals

    NARCIS (Netherlands)

    Asshoff, Sarah J.; Iamsaard, Supitchaya; Bosco, Alessandro; Cornelissen, Jeroen J. L. M.; Feringa, Ben L.; Katsonis, Nathalie

    2013-01-01

    Doping cholesteric liquid crystals with photo-responsive molecules enables controlling the colour and polarisation of the light they reflect. However, accelerating the rate of relaxation of these photo-controllable liquid crystals remains challenging. Here we show that the relaxation rate of the cho

  18. Dimerization of the D1 dopamine receptors is related with agonist and inverse agonist-induced receptor internalization

    Institute of Scientific and Technical Information of China (English)

    Yi-minTAO; Xue-junXU; Min-huaHONG; JieCHEN; Zhi-qiangCHI; Jing-genLIU

    2004-01-01

    AIM: To examine the relationship between D1 dopamine receptor dimer formation and ligand-induced receptor internalization. METHODS: FLAG-tagged D 1 dopamine receptor was transiently expressed in Sf9 cells. The cells were treated with SKF38393 or (+)butaclamol 1 μmol/L for different periods timeor at different doses for 30 min respectively. Western blot assaywas performed to assess dimer formation and flow evtomv.tv.r

  19. Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

    Directory of Open Access Journals (Sweden)

    Koh Eunhee

    2007-07-01

    Full Text Available Abstract Background EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information. Results Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1. Conclusion Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.

  20. Surface characterization and orientation interaction between diamond- like carbon layer structure and dimeric liquid crystals

    Science.gov (United States)

    Naradikian, H.; Petrov, M.; Katranchev, B.; Milenov, T.; Tinchev, S.

    2017-01-01

    Diamond-like carbon (DLC) and amorphous carbon films are very promising type of semiconductor materials. Depending on the hybridization sp2/sp3 ratio, the material’s band gap varies between 0.8 and 3 eV. Moreover carbon films possess different interesting for practice properties: comparable to the Silicon, Diamond like structure has 22-time better thermal conductivity etc. Here we present one type of implementation of such type nanostructure. That is one attempt for orientation of dimeric LC by using of pre-deposited DLC layer with different ratio of sp2/sp3 hybridized carbon content. It could be expected a pronounced π1-π2interaction between s and p orbital levels on the surface and the dimeric ring of LC. We present comparison of surface anchoring strengths of both orientation inter-surfaces DLC/dimeric LC and single wall carbon nanotubes (SWCNT)/dimeric LC. The mechanism of interaction of dimeric LC and activated surfaces with DLC or SWCNT will be discussed. In both cases we have π-π interaction, which in combination with hydrogen bonding, typical for the dimeric LCs, influence the LC alignment. The Raman spectroscopy data evidenced the presence of charge transfer between contacting hexagonal rings of DLC and the C = O groups of the LC molecules.

  1. Dimers of nineteen-electron sandwich compounds: Crystal and electronic structures, and comparison of reducing strengths

    KAUST Repository

    Mohapatra, Swagat Kumar

    2014-10-03

    The dimers of some Group 8 metal cyclopentadienyl/ arene complexes and Group 9 metallocenes can be handled in air, yet are strongly reducing, making them useful n-dopants in organic electronics. In this work, the Xray molecular structures are shown to resemble those of Group 8 metal cyclopentadienyl/pentadienyl or Group 9 metal cyclopentadienyl/diene model compounds. Compared to those of the model compounds, the DFT HOMOs of the dimers are significantly destabilized by interactions between the metal and the central C-C σ-bonding orbital, accounting for the facile oxidation of the dimers. The lengths of these C-C bonds (X-ray or DFT) do not correlate with DFT dissociation energies, the latter depending strongly on the monomer stabilities. Ru and Ir monomers are more reducing than their Fe and Rh analogues, but the corresponding dimers also exhibit much higher dissociation energies, so the estimated monomer cation/neutral dimer potentials are, with the exception of that of [RhCp2]2, rather similar (-1.97 to-2.15 V vs. FeCp2 +/0 in THF). The consequences of the variations in bond strength and redox potentials for the reactivity of the dimers are discussed.

  2. Pyroelectric electron emissions and domain inversion of LiNbO{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dong-Wook [Samsung Advanced Institute of Technology, U-Team, P.O. Box 111, Suwon, Kyongki 440-600 (Korea, Republic of)]. E-mail: Peterkim@ucsd.edu; Bourim, E.M. [Samsung Advanced Institute of Technology, U-Team, P.O. Box 111, Suwon, Kyongki 440-600 (Korea, Republic of); Jeong, Soo-Hwan [Samsung Advanced Institute of Technology, U-Team, P.O. Box 111, Suwon, Kyongki 440-600 (Korea, Republic of); Yoo, In K. [Samsung Advanced Institute of Technology, U-Team, P.O. Box 111, Suwon, Kyongki 440-600, Korea (Korea)

    2004-10-30

    We investigated the electron emissions from a congruent LiNbO{sub 3} single crystal with variation in temperature. When there was a small gap between the crystal and detector (<2 mm), we observed abrupt drops in the emission current and polarization domain inversion of the crystal. The current burst was distributed in tree-like patterns that suggested plasma generation. A sufficient gap and a crystal with a high coercive field appear to be factors that allow reproducible electron emissions from pyroelectric materials.

  3. Crystal Structure of the Nephila clavipes Major Ampullate Spidroin 1A N-terminal Domain Reveals Plasticity at the Dimer Interface.

    Science.gov (United States)

    Atkison, James H; Parnham, Stuart; Marcotte, William R; Olsen, Shaun K

    2016-09-02

    Spider dragline silk is a natural polymer harboring unique physical and biochemical properties that make it an ideal biomaterial. Artificial silk production requires an understanding of the in vivo mechanisms spiders use to convert soluble proteins, called spidroins, into insoluble fibers. Controlled dimerization of the spidroin N-terminal domain (NTD) is crucial to this process. Here, we report the crystal structure of the Nephila clavipes major ampullate spidroin NTD dimer. Comparison of our N. clavipes NTD structure with previously determined Euprosthenops australis NTD structures reveals subtle conformational alterations that lead to differences in how the subunits are arranged at the dimer interface. We observe a subset of contacts that are specific to each ortholog, as well as a substantial increase in asymmetry in the interactions observed at the N. clavipes NTD dimer interface. These asymmetric interactions include novel intermolecular salt bridges that provide new insights into the mechanism of NTD dimerization. We also observe a unique intramolecular "handshake" interaction between two conserved acidic residues that our data suggest adds an additional layer of complexity to the pH-sensitive relay mechanism for NTD dimerization. The results of a panel of tryptophan fluorescence dimerization assays probing the importance of these interactions support our structural observations. Based on our findings, we propose that conformational selectivity and plasticity at the NTD dimer interface play a role in the pH-dependent transition of the NTD from monomer to stably associated dimer as the spidroin progresses through the silk extrusion duct.

  4. Circuit-level simulation of the hysteresis inversion frequency of the ferroelectric liquid crystals

    Institute of Scientific and Technical Information of China (English)

    Wang Mengyao; Pan Wei; Luo Bin; Zhang Weili; Zou Xihua

    2009-01-01

    The V-shaped electro-optical properties control is investigated by an equivalent circuit model. Simulation results show that genuine V-shaped form is only observed at hysteresis inversion frequency, and below and above this frequency an anomalous and normal hysteresis are observed. And the inversion frequency decreases with the resistance of ferroelectric liquid crystal (FLC) layer following logfi=-alogRLC+b. The results are in good accordance with the reported experimental results.

  5. The Design and Investigation of Nanocomposites Containing Dimeric Nematogens and Liquid Crystal Gold Nanoparticles with Plasmonic Properties Showing a Nematic-Nematic Phase Transition (Nu-Nx/Ntb).

    Science.gov (United States)

    Tamba, Maria-Gabriela; Yu, Chih Hao; Tang, Bai Jia; Welch, Christopher; Kohlmeier, Alexandra; Schubert, Christopher P; Mehl, Georg H

    2014-04-30

    The construction of liquid crystal compositions consisting of the dimeric liquid crystal, CB_C9_CB (cyanobiphenyl dimer = 1'',9''-bis(4-cyanobiphenyl-4'-yl)nonane), and the range of nematic systems is explored. The materials include a laterally functionalized monomer, which was used to construct a phase diagram with CB_C9_CB, as well as one laterally linked dimer liquid crystal material and two liquid crystal gold nanoparticle (LC-Au-NPs) systems. For the Au-NP-LCs, the NP diameters were varied between ~3.3 nm and 10 nm. Stable mixtures that exhibit a nematic-nematic phase transition are reported and were investigated by POM (polarizing optical microscopy), DSC (differential scanning calorimetry) and X-ray diffraction studies.

  6. Modelling defect cavities formed in inverse three-dimensional rod-connected diamond photonic crystals

    Science.gov (United States)

    Taverne, M. P. C.; Ho, Y.-L. D.; Zheng, X.; Liu, S.; Chen, L.-F.; Lopez-Garcia, M.; Rarity, J. G.

    2016-12-01

    Defect cavities in 3D photonic crystal can trap and store light in the smallest volumes allowable in dielectric materials, enhancing non-linearities and cavity QED effects. Here, we study inverse rod-connected diamond (RCD) crystals containing point defect cavities using plane-wave expansion and finite-difference time domain methods. By optimizing the dimensions of the crystal, wide photonic bandgaps are obtained. Mid-bandgap resonances can then be engineered by introducing point defects in the crystal. We investigate a variety of single spherical defects at different locations in the unit cell focusing on high-refractive-index-contrast (3.3:1) inverse RCD structures; quality factors (Q-factors) and mode volumes of the resonant cavity modes are calculated. By choosing a symmetric arrangement, consisting of a single sphere defect located at the center of a tetrahedral arrangement, mode volumes < 0.06 cubic wavelengths are obtained, a record for high-index cavities.

  7. Modelling Defect Cavities Formed in Inverse Three-Dimensional Rod-Connected Diamond Photonic Crystals

    CERN Document Server

    Taverne, M P C; Zheng, X; Liu, S; Chen, L -F; Lopez-Garcia, M; Rarity, J G

    2016-01-01

    Defect cavities in 3D photonic crystal can trap and store light in the smallest volumes allowable in dielectric materials, enhancing non-linearities and cavity QED effects. Here, we study inverse rod-connected diamond (RCD) crystals containing point defect cavities using plane-wave expansion and finite-difference time domain methods. By optimizing the dimensions of the crystal, wide photonic band gaps are obtained. Mid-bandgap resonances can then be engineered by introducing point defects in the crystal. We investigate a variety of single spherical defects at different locations in the unit cell focusing on high-refractive-index contrast (3.3:1) inverse RCD structures; quality factors (Q-factors) and mode volumes of the resonant cavity modes are calculated. By choosing a symmetric arrangement, consisting of a single sphere defect located at the center of a tetrahedral arrangement, small mode volumes are obtained.

  8. Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan.

    Science.gov (United States)

    Scott, Paul G; McEwan, Paul A; Dodd, Carole M; Bergmann, Ernst M; Bishop, Paul N; Bella, Jordi

    2004-11-02

    Decorin is a ubiquitous extracellular matrix proteoglycan with a variety of important biological functions that are mediated by its interactions with extracellular matrix proteins, cytokines, and cell surface receptors. Decorin is the prototype of the family of small leucine-rich repeat proteoglycans and proteins (SLRPs), characterized by a protein core composed of leucine-rich repeats (LRRs), flanked by two cysteine-rich regions. We report here the crystal structure of the dimeric protein core of decorin, the best characterized member of the SLRP family. Each monomer adopts the curved solenoid fold characteristic of LRR domains, with a parallel beta-sheet on the inside interwoven with loops containing short segments of beta-strands, 3(10) helices, and polyproline II helices on the outside. Two main features are unique to this structure. First, decorin dimerizes through the concave surfaces of the LRR domains, which have been implicated previously in protein-ligand interactions. The amount of surface buried in this dimer rivals the buried surfaces of some of the highest-affinity macromolecular complexes reported to date. Second, the C-terminal region adopts an unusual capping motif that involves a laterally extended LRR and a disulfide bond. This motif seems to be unique to SLRPs and has not been observed in any other LRR protein structure to date. Possible implications of these features for decorin ligand binding and SLRP function are discussed.

  9. Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation

    KAUST Repository

    Kim, Jeong Joo

    2016-04-09

    Cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is a key regulator of smooth muscle and vascular tone and represents an important drug target for treating hypertensive diseases and erectile dysfunction. Despite its importance, its activation mechanism is not fully understood. To understand the activation mechanism, we determined a 2.5 Å crystal structure of the PKG I regulatory (R) domain bound with cGMP, which represents the activated state. Although we used a monomeric domain for crystallization, the structure reveals that two R domains form a symmetric dimer where the cGMP bound at high-affinity pockets provide critical dimeric contacts. Small-angle X-ray scattering and mutagenesis support this dimer model, suggesting that the dimer interface modulates kinase activation. Finally, structural comparison with the homologous cyclic AMP-dependent protein kinase reveals that PKG is drastically different from protein kinase A in its active conformation, suggesting a novel activation mechanism for PKG. Kim et al. obtain the first crystal structure of the PKG I R domain bound with cGMP representing its activated state. It reveals a symmetric R dimer where cGMP molecules provide dimeric contacts. This R-R interaction prevents the high-affinity inhibitory interaction between R-C domain and sustains activation. © 2016 Elsevier Ltd.

  10. The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jiahai; Liu, Chuan Yin; Back, Sung Hoon; Clark, Robert L.; Peisach, Daniel; Xu, Zhaohui; Kaufman, Randal J. (Michigan)

    2010-03-08

    The unfolded protein response (UPR) is an evolutionarily conserved mechanism by which all eukaryotic cells adapt to the accumulation of unfolded proteins in the endoplasmic reticulum (ER). Inositol-requiring kinase 1 (IRE1) and PKR-related ER kinase (PERK) are two type I transmembrane ER-localized protein kinase receptors that signal the UPR through a process that involves homodimerization and autophosphorylation. To elucidate the molecular basis of the ER transmembrane signaling event, we determined the x-ray crystal structure of the luminal domain of human IRE1{alpha}. The monomer of the luminal domain comprises a unique fold of a triangular assembly of {beta}-sheet clusters. Structural analysis identified an extensive dimerization interface stabilized by hydrogen bonds and hydrophobic interactions. Dimerization creates an MHC-like groove at the interface. However, because this groove is too narrow for peptide binding and the purified luminal domain forms high-affinity dimers in vitro, peptide binding to this groove is not required for dimerization. Consistent with our structural observations, mutations that disrupt the dimerization interface produced IRE1{alpha} molecules that failed to either dimerize or activate the UPR upon ER stress. In addition, mutations in a structurally homologous region within PERK also prevented dimerization. Our structural, biochemical, and functional studies in vivo altogether demonstrate that IRE1 and PERK have conserved a common molecular interface necessary and sufficient for dimerization and UPR signaling.

  11. Signature of a three-dimensional photonic band gap observed on silicon inverse woodpile photonic crystals

    CERN Document Server

    Huisman, Simon R; Woldering, Léon A; Leistikow, Merel D; Mosk, Allard P; Vos, Willem L

    2010-01-01

    We have studied the reflectivity of CMOS-compatible three-dimensional silicon inverse woodpile photonic crystals at near-infrared frequencies. Polarization-resolved reflectivity spectra were obtained from two orthogonal crystal surfaces corresponding to 1.88 pi sr solid angle. The spectra reveal broad peaks with high reflectivity up to 67 % that are independent of the spatial position on the crystals. The spectrally overlapping reflectivity peaks for all directions and polarizations form the signature of a broad photonic band gap with a relative bandwidth up to 16 %. This signature is supported with stopgaps in plane wave bandstructure calculations and with the frequency region of the expected band gap.

  12. Electrochromic effect in domain-inversion process in LiNbO3: Ru: Fe crystals

    Institute of Scientific and Technical Information of China (English)

    XI Qingxin; LIU De'an; ZHI Ya'nan; ZHU Luan; LIU Liren

    2005-01-01

    A reversible electrochromic effect accompanying domain-inversion during the electrical poling process in LiNbO3: Ru: Fe crystals at room temperature has been observed. In electrode area, both electrochromism and domain-inversion occur alternately, and electrochromism is also reversible during back-switch poling, which is experimentally verified and whose mechanism is briefly explained using a microstructure ferroelectric model. In addition, because of the enhancing elcctrochromic effect, different from the undoped LiNbO3 crystals, the coercive filed (21.0 kV/mm or so) measured in LiNbO3: Ru: Fe is lower than its breakdown field, thus providing a possible new technique for realizing the domain-inversion by constant electric field rather than a pulsed one.

  13. Polarons in endohedral Li+@C60- dimers and in 1D and 2D crystals

    Science.gov (United States)

    Kawazoe, Yoshiyuki; Belosludov, Vladimir R.; Zhdanov, Ravil K.; Belosludov, Rodion V.

    2017-10-01

    The electron charge distribution and polaron formation on the carbon sites of dimer clusters Li+@C60- and of 1D or 2D Li+@C60- periodic systems are studied with the use of the generalized Su-Schrieffer-Heeger model with respect to the intermolecular and intramolecular degrees of freedom. The charge distributions over the molecular surface and Jahn-Teller bond distortions of carbon atoms are calculated using the self-consistent iterative methods. Polarons formed in periodic 1D and 2D systems (chains and planar layers) as well as in dimer cluster system are examined. In the periodic systems polaron formation may be described by the cooperative Jahn-Teller effect. Orientation of the polarons on the molecule surface depends on the doping of the system, moreover, electron doping changes the energy levels in the system.

  14. Growth, Faraday and inverse Faraday characteristics of Tb2Ti2O7 crystal.

    Science.gov (United States)

    Guo, Feiyun; Sun, Yilin; Yang, Xiongsheng; Chen, Xin; Zhao, Bin; Zhuang, Naifeng; Chen, Jianzhong

    2016-03-21

    Tb2Ti2O7 (TTO) single crystal with dimensions of 20 × 20 × 16 mm3 was grown by the Czochralski method. Rietveld structure refinement of X-ray diffraction (XRD) data confirms that the compound crystallizes in the cubic system with pyrochlore structure. Transmission spectra, Magnetic circular dichroism (MCD) spectra, Faraday and inverse Faraday characteristics of TTO crystal have been measured and analyzed in detail. The results demonstrate that TTO crystal has high transmittance at 700-1400 nm waveband and a larger Verdat constant than that of TGG reported. Magnetic circular dichroism (MCD) spectra showed that the 4f→4f transitions of Tb3+ have significant contributions to the magneto-optical activity (MOA). In the time-resolved pump-probe spectroscopy, the rotation signals of the probe beam based on the inverse Faraday effect in magneto-optical crystal were observed at zero time delay, the full width at half maximum of the rotation and ellipticity signals can be as fast as ~500 fs, which indicates that TTO crystal can be a promising material for ultrafast all-optical magnetic switching.

  15. A High-Resolution Crystal Structure of a Psychrohalophilic α–Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface

    Energy Technology Data Exchange (ETDEWEB)

    Somalinga, Vijayakumar; Buhrman, Greg; Arun, Ashikha; Rose, Robert B.; Grunden, Amy M. (NCSU)

    2016-12-09

    Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s.

  16. Inverse-problem approach to designing photonic crystals for cavity QED experiments.

    Science.gov (United States)

    Geremia, J M; Williams, Jon; Mabuchi, Hideo

    2002-12-01

    Photonic band gap (PBG) materials are attractive for cavity QED experiments because they provide extremely small mode volumes and are monolithic, integratable structures. As such, PBG cavities are a promising alternative to Fabry-Perot resonators. However, the cavity requirements imposed by QED experiments, such as the need for high Q (low cavity damping) and small mode volumes, present significant design challenges for photonic band gap materials. Here, we pose the PBG design problem as a mathematical inversion and provide an analytical solution for a two-dimensional (2D) crystal. We then address a planar (2D crystal with finite thickness) structure using numerical techniques.

  17. PAM-PAA microgel inverse opal photonic crystal and pH response

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The colloidal crystal template or opal with a closed-packed face-centered cubic (fcc) lattice was prepared from monodisperse polystyrene (PS) spheres by vertical sedimentation. The template provided void space for infiltration of monomer precursor composed of acrylate acid, acrylamide and ammonium persulfate, as well as microgel from the subsequent copolymerization. The sample was immersed in dimethylbenzene for completely removing PS spheres to form PAM inverse opal hydrogels (IOHPAM) or PAM/PAA inverse opal hydrogels (IOHPAM/PAA) photonic crystals. The PS spheres were replaced by air spheres, which interconnected each other through the windows. The study of responses to pH show that there are two peaks for both IOHPAM and IOHPAM/PAA films, but the IOHPAM/PAA peaks shift to higher pH, and the peaks are independent with the AA content.

  18. High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

    OpenAIRE

    Saidaminov, Makhsud I.; Abdelhady, Ahmed L.; Murali, Banavoth; Alarousu, Erkki; Burlakov, Victor M.; Peng, Wei; Dursun, Ibrahim; Wang, Lingfei; He, Yao; Maculan, Giacomo; Goriely, Alain; Wu, Tom; Mohammed, Omar F.; Bakr, Osman M.

    2015-01-01

    Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3 +, X=Br− or I−) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process. Here we present a rapid crystal growth process to obtain MAPbX3 single crystals, an order of magnitude faster than previous reports. The process is based on our observation of the substantial decrease of MAPbX3 solubility, in certain solvents, at e...

  19. Influence of surface termination on inverse Goos-Hänchen shift of negatively refractive photonic crystals

    Science.gov (United States)

    Hu, Jinbing; Liang, Binming; Chen, Jiabi; Cai, Xiaoshu; Jiang, Qiang; Zhuang, Songlin

    2016-07-01

    The effect of surface termination on the inverse Goos-Hänchen (GH) shift of two-dimensional (2D) negatively refractive photonic crystals (NRPhCs) containing air holes arranged in a hexagonal lattice in a dielectric background is investigated for transverse magnetic (TM) polarization. Results show that the magnitude of the inverse GH shift of 2D-NRPhCs strongly depends on surface termination even for an incident beam with a fixed frequency and incidence angle. Calculation of dispersion of surface mode as a function of termination reveals that large inverse GH shift of 2D-NRPhCs results from the excitation of backward surface mode. In addition, the coupling coefficient of the incident field into the field of surface mode and energy flux around the interface are studied and demonstrate the above conclusion. This paper will provide technical information regarding the combination of various functional photonic elements in the design of integrated optical circuits.

  20. Light-Induced Domain Inversion in Mg-Doped near Stoichiometric Lithium Niobate Crystals

    Institute of Scientific and Technical Information of China (English)

    LIU Hong-De; KONG Yong-Fa; HU Qian; WU Ri-Wen; WANG Wen-Jie; LI Xiao-Chun; CHEN Shao-Lin; LIU Shi-Guo; XU Jing-Jun

    2007-01-01

    We investigate the influence of visible light on domain inversion in Mg-doped near stoichiometric lithium niobate crystals and find that the switching electric field decreases about 70% above a threshold light intensity. This effect helps us optically control domain switching and produce bulk domain structures on the micrometre scale. Finally, we introduce a model of photo-induced carriers to explain the origin of the reduction of switching electric field.

  1. Evaluation of crystallization behavior on the surface of nifedipine solid dispersion powder using inverse gas chromatography.

    Science.gov (United States)

    Miyanishi, Hideo; Nemoto, Takayuki; Mizuno, Masayasu; Mimura, Hisashi; Kitamura, Satoshi; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

    2013-02-01

    To investigate crystallization behavior on the surface of amorphous solid dispersion powder using inverse gas chromatography (IGC) and to predict the physical stability at temperatures below the glass transition temperature (T (g)). Amorphous solid dispersion powder was prepared by melt-quenching of a mixture of crystalline nifedipine and polyvinylpyrrolidon (PVP) K-30. IGC was conducted by injecting undecane (probe gas) and methane (reference gas) repeatedly to the solid dispersion at temperatures below T (g). Surface crystallization was evaluated by the retention volume change of undecane based on the observation that the surface of the solid dispersion with crystallized nifedipine gives an increased retention volume. On applying the retention volume change to the Hancock-Sharp equation, surface crystallization was found to follow a two-dimensional growth of nuclei mechanism. Estimation of the crystallization rates at temperatures far below T (g) using the Avrami-Erofeev equation and Arrhenius equation showed that, to maintain its quality for at least three years, the solid dispersion should be stored at -20°C (T (g) - 65°C). IGC can be used to evaluate crystallization behavior on the surface of a solid dispersion powder, and, unlike traditional techniques, can also predict the stability of the solid dispersion based on the surface crystallization behavior.

  2. Recent advances in fabrication of monolayer colloidal crystals and their inverse replicas

    Institute of Scientific and Technical Information of China (English)

    YE XiaoZhou; QI LiMin

    2014-01-01

    Monolayer colloidal crystals(MCCs)are two-dimensional(2D)colloidal crystals consisting of a monolayer of monodisperse colloidal particles arrayed with a 2D periodic order.In recent years,MCCs have attracted intensive interest because they can act as 2D photonic crystals and be used as versatile templates for fabrication of various 2D nanostructure arrays.In this review,we provide an overview of the recent progress in the controllable fabrication of MCCs and their inverse replicas.First,some newly-developed methods for the self-assembly of MCCs based on different strategies including interfacial assembly and convective assembly are introduced.Second,some representative novel methods regarding the fabrication of various functional2D inverse replicas of MCCs,such as 2D arrays of nanobowls,nanocaps,and hollow spheres,as well as 2D monolayer inverse opals(MIOs),are described.In addition,the potential applications of MCCs and their inverse replicas are discussed.

  3. The "Inverse Hall-Petch" effect on the impact response of single crystal copper

    Institute of Scientific and Technical Information of China (English)

    Zhen Chen; Shan Jiang; Yong Gan

    2012-01-01

    Based on the available experimental and computational capabilities,a phenomenological approach has been proposed to formulate a hypersurface in both spatial and temporal domains to predict combined specimen size and loading rate effects on the material properties [ 1-2].A systematic investigation is being performed to understand the combined size,rate and thermal effects on the properties and deformation patterns of representative materials with different nanostructures and under various types of loading conditions [3-16].The recent study on the single crystal copper response to impact loading has revealed the size-dependence of the Hugoniot curve.In this paper,the "inverse Hall-Petch" behavior as observed in the impact response of single crystal copper,which has not been reported in the open literature,is investigated by performing molecular dynamics simulations of the response of copper nanobeam targets subjected to impacts by copper nanobeam flyers with different impact velocities.It appears from the preliminary results that the "inverse Hall-Petch" behavior in single crystal copper is mainly due to the formation and evolution of disordered atoms and the interaction between ordered and disordered atoms,as compared with the physics behind the "inverse Hall-Petch"behavior as observed in nanocrystalline materials.

  4. Inverse gold photonic crystals and conjugated polymer coated opals for functional materials

    Energy Technology Data Exchange (ETDEWEB)

    Landon, P.B.; Gutierrez, Jose; Ferraris, John P.; Martinez, I.L.; Giridharagopal, Rajiv; Wu, Y.-C.; Lee, Sergey; Parikh, Kunjal; Gillespie, Jessica; Ussery, Geoffrey; Karimi, Behzad; Baughman, Ray; Zakhidov, Anvar; Glosser, R

    2003-10-01

    Inverse gold photonic crystals templated from synthetic opals with a face centered cubic (FCC) crystal lattice were constructed by heat converting gold chloride to metallic gold. Tetrahedral formations constructed of alternating large and small octahedrons oriented in the zinc sulfide structure were created by controlling the infiltration of gold chloride. Silica spheres were coated with polyanilinesulfonic acid, polypyrrole, poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) and 5 nm colloidal gold. Ordinary yeast cells were coated with polyanilinesulfonic acid, polypyrrole and 5 nm colloidal gold. Spheres coated with MEH-PPV were dispersed in H{sub 2}O and coated with polyelectrolytes which recharged and sterically stabilized the colloidal surfaces. The recharged spheres self-assembled by sedimentation with a FCC crystalline lattice possessing 500 {mu}m wide and 1 mm long crystallites. Silica spheres with diameters as large as 1500 {mu}m were self-assembled along the [1 0 0] direction of the FCC crystal lattice. Opals infiltrated with gold and opals constructed from polymer coated spheres were co-infiltrated with polypropylene yielding inverse polypropylene composite photonic crystals.

  5. Sign inversion of the spontaneous polarization in a "de Vries"-type ferroelectric liquid crystal.

    Science.gov (United States)

    Nonnenmacher, Dorothee; Lemieux, Robert P; Osipov, Mikhail A; Giesselmann, Frank

    2014-05-19

    In contrast to common ferroelectric smectic C* liquid crystals, the siloxane-terminated smectic mesogen E6 is characterized by an unusual temperature variation of the spontaneous polarization. The polarization starts to grow from nearly zero despite the first-order SmA*-SmC* transition, and increases faster than linearly over a large temperature interval while the tilt angle rapidly saturates. To study this behavior in more detail, binary mixtures of different concentrations of E6 in the achiral SmC material C8Cl, which has a similar chemical structure, were investigated. Surprisingly, all mixtures show a temperature dependent polarization sign inversion, which shifts towards the SmC*-SmA* transition with increasing E6 concentration. For the pure E6 the inversion temperature meets the SmA*-SmC* phase transition temperature. In a second binary mixture with E6 and a conventional material C9-2PhP we found out, that the dependence of the inversion temperature on the concentration of E6 changes qualitatively when the nanosegregation is partially destroyed. A molecular theory of the polarization sign inversion in smectics C* with strong polar intermolecular interactions is developed which enables one to explain the concentration dependence of the inversion temperature in both mixtures.

  6. Fabrication of BaTiO3 Inverse Opal Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    An XIANG; Jian Ping GAO; Hong Kui CHEN; Jiu Gao YU; Rui Xian LIU

    2004-01-01

    The colloidal crystal template or opal with a closed-packed face centered cubic (fcc) lattice, was prepared from monodisperse polystyrene (PS) spheres by gravity sedimentation. The template was used for the generation of photonic crystal. The template provided void space for infiltration of liquid precursor composed of titanium butyloxide, barium acetate, ethanol, and acetic acid. The opal composite was hydrolyzed, dried, sintered by heating for completely removing PS spheres to form BaTiO3 photonic crystals with inverse opal structure. The PS spheres were replaced by air spheres, which interconnected each other through the windows on the BaTiO3 wall. So both the BaTiO3 wall and air void constitute continuous phases.

  7. Crystal structure of nicotinic acid mononucleotide adenylyltransferase from Staphyloccocus aureus: structural basis for NaAD interaction in functional dimer.

    Science.gov (United States)

    Han, Seungil; Forman, Michael D; Loulakis, Pat; Rosner, Michelle H; Xie, Zhi; Wang, Hong; Danley, Dennis E; Yuan, Wei; Schafer, John; Xu, Zuoyu

    2006-07-21

    Bacterial nicotinic acid mononucleotide adenylyltransferase (NaMNAT; EC 2.7.7.18) encoded by the nadD gene, is essential for cell survival and is thus an attractive target for developing new antibacterial agents. The NaMNAT catalyzes the transfer of an adenylyl group of ATP to nicotinic acid mononucleotide (NaMN) to form nicotinic acid dinucleotide (NaAD). Two independently derived, high-resolution structures of Staphylococcus aureus NaMNAT-NaAD complexes establish the conserved features of the core dinucleotide-binding fold with other adenylyltransferases from bacteria to human despite a limited sequence conservation. The crystal structures reveal that the nicotinate carboxylates of NaAD are recognized by interaction with the main-chain amides of Thr85 and Tyr117, a positive helix dipole and two bridged-water molecules. Unlike other bacterial adenylyltransferases, where a partially conserved histidine residue interacts with the nicotinate ring, the Leu44 side-chain interacts with the nicotinate ring by van der Waals contact. Importantly, the S. aureus NaMNAT represents a distinct adenylyltransferase subfamily identifiable in part by common features of dimerization and substrate recognition in the loop connecting beta5 to beta6 (residues 132-146) and the additional beta6 strand. The unique beta6 strand helps orient the residues in the loop connecting beta5 to beta6 for substrate/product recognition and allows the beta7 strand structural flexibility to make key dimer interface interactions. Taken together, these structural results provide a molecular basis for understanding the coupled activity and recognition specificity for S. aureus NaMNAT and for rational design of selective inhibitors.

  8. The role of hydrogen bonding in the phase behaviour of supramolecular liquid crystal dimers

    Science.gov (United States)

    Martínez-Felipe, Alfonso; Imrie, Corrie T.

    2015-11-01

    The phase behaviour of equimolar mixtures of 4-octyloxybenzoic acid, OOBA, and either 1-(4-butylazobenzene-4‧-oxy)-6-(4-oxypyridine)pentane, BuABO5OPyr, or 1-(4-butylazobenzene-4‧-oxy)-6-(4-oxypyridine)hexane, BuABO6OPyr, is reported. OOBA exhibits enantiotropic smectic C and nematic phases, whereas BuABO5OPyr and BuABO6OPyr are not liquid crystalline. Both the OOBA/BuABO5OPyr and OOBA/BuABO6OPyr equimolar mixtures show an enantiotropic smectic A phase identified using X-ray diffraction and polarised light microscopy. The liquid crystallinty of the mixtures is attributed, in part, to the formation of a 1:1 hydrogen-bonded complex between OOBA and either BuABO5OPyr or BuABO6OPyr. Differences in the transitional properties of the mixtures are accounted for in terms of the average shapes of these 1:1 complexes. Temperature dependent FTIR spectroscopy shows, however, that the formation of the complex is not quantitative in the mixtures but instead a complex mixture exists over the complete temperature range studied, involving the 1:1 complex, both cyclic and open acid dimers, free acid and hence, free BuABOnOPyr molecules.

  9. Mechanism Analysis of the Inverse Doppler Effect in Two-Dimensional Photonic Crystal based on Phase Evolution

    Science.gov (United States)

    Jiang, Qiang; Chen, Jiabi; Wang, Yan; Liang, Binming; Hu, Jinbing; Zhuang, Songlin

    2016-04-01

    Although the inverse Doppler effect has been observed experimentally at optical frequencies in photonic crystal with negative effective refractive index, its explanation is based on phenomenological theory rather than a strict theory. Elucidating the physical mechanism underlying the inverse Doppler shift is necessary. In this article, the primary electrical field component in the photonic crystal that leads to negative refraction was extracted, and the phase evolution of the entire process when light travels through a moving photonic crystal was investigated using static and dynamic finite different time domain methods. The analysis demonstrates the validity of the use of np (the effective refractive index of the photonic crystal in the light path) in these calculations, and reveals the origin of the inverse Doppler effect in photonic crystals.

  10. Two Glass Transitions Associated to Different Dynamic Disorders in the Nematic Glassy State of a Non-Symmetric Liquid Crystal Dimer Dopped with g-Alumina Nanoparticles

    Directory of Open Access Journals (Sweden)

    Sergio Diez-Berart

    2015-06-01

    Full Text Available In the present work, the nematic glassy state of the non-symmetric LC dimer α-(4-cyanobiphenyl-4′-yloxy-ω-(1-pyrenimine-benzylidene-4′-oxy undecane is studied by means of calorimetric and dielectric measurements. The most striking result of the work is the presence of two different glass transition temperatures: one due to the freezing of the flip-flop motions of the bulkier unit of the dimer and the other, at a lower temperature, related to the freezing of the flip-flop and precessional motions of the cyanobiphenyl unit. This result shows the fact that glass transition is the consequence of the freezing of one or more coupled dynamic disorders and not of the disordered phase itself. In order to avoid crystallization when the bulk sample is cooled down, the LC dimer has been confined via the dispersion of γ-alumina nanoparticles, in several concentrations.

  11. Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation.

    Science.gov (United States)

    Kim, Jeong Joo; Lorenz, Robin; Arold, Stefan T; Reger, Albert S; Sankaran, Banumathi; Casteel, Darren E; Herberg, Friedrich W; Kim, Choel

    2016-05-03

    Cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is a key regulator of smooth muscle and vascular tone and represents an important drug target for treating hypertensive diseases and erectile dysfunction. Despite its importance, its activation mechanism is not fully understood. To understand the activation mechanism, we determined a 2.5 Å crystal structure of the PKG I regulatory (R) domain bound with cGMP, which represents the activated state. Although we used a monomeric domain for crystallization, the structure reveals that two R domains form a symmetric dimer where the cGMP bound at high-affinity pockets provide critical dimeric contacts. Small-angle X-ray scattering and mutagenesis support this dimer model, suggesting that the dimer interface modulates kinase activation. Finally, structural comparison with the homologous cyclic AMP-dependent protein kinase reveals that PKG is drastically different from protein kinase A in its active conformation, suggesting a novel activation mechanism for PKG.

  12. Enhancement of Tb-Yb quantum cutting emission by inverse opal photonic crystals

    Science.gov (United States)

    Wang, Qi; Qiu, Jianbei; Song, Zhiguo; Yang, Zhengwen; Yin, Zhaoyi; Zhou, Dacheng; Wang, Siqin

    2016-04-01

    Yb3+, Tb3+ co-doped YPO4 inverse opal photonic crystal was prepared directly by sol-gel technique in combination with self-assembly method. With the influence of the photonic band gap, quantum cutting emission of Tb3+, Yb3+ was investigated in photonic crystals by photoluminescence and fluorescence lifetime. The result clearly shows that, when the spontaneous emission of donor Tb3+ is inhibited by photonic band gap, Tb3+-Yb3+ quantum cutting quantum efficiency from Tb3+ to Yb3+ could be enhanced from 131.2% to 140.5%. The mechanisms for the influence of the photonic band gap on quantum cutting process of Tb3+ and Yb3+ are discussed. We believe that the present work will be valuable for the foundational study of quantum cutting energy transfer process and application of quantum cutting optical devices in spectral modification materials for silicon solar cells.

  13. A Crystal Structure of a Dimer of the Antibiotic Ramoplanin Illustrates Membrane Positioning and a Potential Lipid II Docking Interface

    Energy Technology Data Exchange (ETDEWEB)

    Hamburger, J.; Hoertz, A; Lee, A; Senturia, R; McCafferty, D; Loll, P

    2009-01-01

    The glycodepsipeptide antibiotic ramoplanin A2 is in late stage clinical development for the treatment of infections from Gram-positive pathogens, especially those that are resistant to first line antibiotics such as vancomycin. Ramoplanin A2 achieves its antibacterial effects by interfering with production of the bacterial cell wall; it indirectly inhibits the transglycosylases responsible for peptidoglycan biosynthesis by sequestering their Lipid II substrate. Lipid II recognition and sequestration occur at the interface between the extracellular environment and the bacterial membrane. Therefore, we determined the structure of ramoplanin A2 in an amphipathic environment, using detergents as membrane mimetics, to provide the most physiologically relevant structural context for mechanistic and pharmacological studies. We report here the X-ray crystal structure of ramoplanin A2 at a resolution of 1.4 {angstrom}. This structure reveals that ramoplanin A2 forms an intimate and highly amphipathic dimer and illustrates the potential means by which it interacts with bacterial target membranes. The structure also suggests a mechanism by which ramoplanin A2 recognizes its Lipid II ligand.

  14. Color Tunable and Upconversion Luminescence in Yb-Tm Co-Doped Yttrium Phosphate Inverse Opal Photonic Crystals.

    Science.gov (United States)

    Wang, Siqin; Qiu, Jianbei; Wang, Qi; Zhou, Dacheng; Yang, Zhengwen

    2016-04-01

    For this paper, YPO4: Tm, Yb inverse opals with the photonic band gaps at 475 nm and 655 nm were prepared by polystyrene colloidal crystal templates. We investigated the influence of photonic band gaps on the Tm-Yb upconversion emission which was in the YPO4: Tm Yb inverse opal photonic crystals. Comparing with the reference sample, significant suppression of both the blue and red upconversion luminescence of Tm3+ ions were observed in the inverse opals. The color purity of the blue emission was improved in the inverse opal by the suppression of red upconversion emission. Additionally, mechanism of upconversion emission in the inverse opal was discussed. We believe that the present work will be valuable for not only the foundational study of upconversion emission modification but also the development of new optical devices in upconversion lighting and display.

  15. Crystal structure of β-cyclodextrin-4-chlorobenzoic acid complex:Unusual C-Cl...π interaction between 4-chlorobenzoic acids in β-cyclodextrin dimer

    Institute of Scientific and Technical Information of China (English)

    En Ju Wang; Guang Ying Chen

    2011-01-01

    The inclusion complex of β-cyclodextrin (β-CD) with 4-chlorobenzoic acid was synthesized and its crystal structure was determined by single crystal X-ray diffraction under cryogenic condition. The complex contains two β-CDs, two 4-chlorobenzoic acids and twenty-nine water molecules in the asymmetric unit, and can be formulated as 2(C42H70O35)-2(C7H5O2Cl)·29(H2O). In the crystal lattice, two β-CDs form a face-to-face dimer jointed together through hydrogen bonding between the secondary hydroxyl groups of β-CDs. Two 4-chlorobenzoic acid molecules which contact by C-Cl…π interactions are included in the β-CD dimer cavity. The β-CD dimers are arranged in brickwork-like pattern along the crystallographic a-axis. The effect of guest molecule length on the inclusion geometry was discussed by comparative study of some β-CD complexes containing similar guests.

  16. Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.

    Science.gov (United States)

    Jones, Christopher P; Ferré-D'Amaré, Adrian R

    2014-11-18

    Cyclic diadenosine monophosphate (c-di-AMP) is a second messenger that is essential for growth and homeostasis in bacteria. A recently discovered c-di-AMP-responsive riboswitch controls the expression of genes in a variety of bacteria, including important pathogens. To elucidate the molecular basis for specific binding of c-di-AMP by a gene-regulatory mRNA domain, we have determined the co-crystal structure of this riboswitch. Unexpectedly, the structure reveals an internally pseudo-symmetric RNA in which two similar three-helix-junction elements associate head-to-tail, creating a trough that cradles two c-di-AMP molecules making quasi-equivalent contacts with the riboswitch. The riboswitch selectively binds c-di-AMP and discriminates exquisitely against other cyclic dinucleotides, such as c-di-GMP and cyclic-AMP-GMP, via interactions with both the backbone and bases of its cognate second messenger. Small-angle X-ray scattering experiments indicate that global folding of the riboswitch is induced by the two bound cyclic dinucleotides, which bridge the two symmetric three-helix domains. This structural reorganization likely couples c-di-AMP binding to gene expression.

  17. Synthesis, crystal structure, and fluorescence of two dimeric europium(Ⅲ) complexes with 2-(trifluoromethyl)benzoate

    Institute of Scientific and Technical Information of China (English)

    LI Yanqiu; LI Peizhou; LI Xia

    2008-01-01

    Two complexes [Eu2(2-TFMBA)6(2,2'-bipy)2].2H2O (1) and Eu2(2-TFMBA)6(1,10-phen)2 (2) (2-TFMBA=2-(Trifluoromethyl) benzoate; 2,2'-bipy=2,2'-bipyridine; 1,10-phen=1,10-phenanthroline) were synthesized by solvent method and determined by X-ray diffrac-tion analysis. Complex 1 crystallizes in monoclinic system with space group P21/c, whereas complex 2 crystallizes in triclinic system with space group P-1. Both are binuclear molecules with an inversion center. In complex 1, two center Eu3+ ions are linked together by four 2-TFMBA ligands in bidentate-bridging mode. Each Eu3+ion is eight-coordinated with six O atoms from five 2-TFMBA ligands and two N atoms from one 2,2'-bipy molecule. In complex 2, two center Eu3+ ions are linked together by four 2-TFMBA ligands in two modes, namely, bidentate-bridging and tridentate-bridging. Each Eu3+ ion is nine-coordinated with seven O atoms from five 2-TFMBA ligands and two N atoms from one 1,10-phen molecule. The two complexes both exhibited strong red fluorescence under ultraviolet light, and the 5D0→7Fj (j=0-4) transition emissions of Eu3+ ion were observed in their emission spectra.

  18. Routes to new hafnium(IV) tetraaryl porphyrins and crystal structures of unusual phosphate-, sulfate-, and peroxide-bridged dimers.

    Science.gov (United States)

    Falber, Alexander; Todaro, Louis; Goldberg, Israel; Favilla, Michael V; Drain, Charles Michael

    2008-01-21

    New routes for the synthesis of mono tetraaryl porphyrinato hafnium(IV) complexes, Hf(IV)Por(L)(2), are reported, where the secondary ligands, L, are determined by the method of purification. These synthetic routes cater to the solubility of the macrocycles and provide access to Hf(IV) complexes of meso tetraaryl porphyrins bearing diverse functional groups such as phenyl, tolyl, pyridyl, pentafluorophenyl, and carboxyphenyl. The latter three derivatives significantly expand the repertoire of hafnium porphyrinates. One route refluxes the porphyrin with HfCl(4) in 1-chloronaphthalene or in a mixed solvent of 1-chloronaphthalene and o-cresol. A second, solventless method is also reported wherein the porphyrin is mixed with Hf(cp)(2)Cl(2) and heated to give the metalated porphyrin in good yields. Simultaneous purification and formation of stable porphyrinato hafnium(IV) diacetate complexes, Hf(Por)OAc(2), is accomplished by elution over silica gel using 3-5% acetic acid in the eluent. Exchange of the acetate ligands for other oxo-bearing ligands can be nearly quantitative, such as p-aminobenzoate (PABA), pentanoate (pent), or octanoate (oct). Notably, we find that two to three of a variety of small multitopic dianions such as peroxo (O(2)(-2)), SO(4)(-2), and HPO(4)(-2) serve to bridge between two Hf(Por) moieties to form stable dimers. The crystal structures of this library of Hf(Por) complexes are reported, and we note that careful analysis of crystallography data reveals (Por)Hf(micro-eta(2)-O(2))(2)Hf(Por) rather than four bridging oxo or hydroxy ions.

  19. Photonic crystal heterostructures fabricated by TiO2 and ZnO inverse opals using colloidal crystal template with single kind of microspheres

    Science.gov (United States)

    Zhang, Yongna; Fu, Ming; Wang, Jigang; He, Dawei; Wang, Yongsheng

    2012-09-01

    The fabrication of photonic crystal heterostructures is important for the applications in the fields of integrated photonic crystal chips, multi-frequency optical Bragg filters or mirrors. However, multiple steps of self-assembly process of microspheres are always employed in the fabrication of photonic crystal heterostructures, which may produce lattice mismatches of colloidal crystals. Therefore, photonic crystal heterostructures fabricated by using colloidal crystal template with single kind of microspheres were investigated in this paper. A colloidal crystal template with uniform periodicity was firstly formed by monodispersed polystyrene microsphere. Then ZnO was electrodeposited into the interstices of the template. The thickness of ZnO was controlled to be less than the thickness of the template by varying the deposition time. After the TiO2 precursor was filled into the top voids in the template, the polystyrene colloidal crystal template was removed and photonic crystal heterostructures fabricated by ZnO and TiO2 were formed. Both the dielectric constant and the periodicity of the two parts of the heterostructures are different due to the shrinkage of the sol-gel process. The ZnO/TiO2 heterostructures have a broad photonic stop band which is the superposition of photonic stop bands of ZnO inverse opals and TiO2 inverse opals.

  20. Synthesis and Crystal Structure of an Inorganic-organic Hybrid [DMAPM]+[CdI3]-:The First Example of Cd2I62- Dimer

    Institute of Scientific and Technical Information of China (English)

    任鹏; 秦金贵; 张德清; 胡怀明

    2004-01-01

    A new inorganic-organic hybrid,[DMAPM]+[CdI3]-(DMAPM+ = p-dimethyla-mino-1-methyl-pyridinium),has been synthesized by the reaction of [DMAPM]+I-and CdI2,and characterized by IR and elemental analysis.The crystal structure was obtained via X-ray single-crystal diffraction with the following data: triclinic,space group P1,a = 8.0974(9),b = 9.6187(10),c = 10.5028(8)(A),α = 75.049(6),β = 86.321(3),γ = 87.791(3)o,V = 788.50(13)(A)3,Dc = 2.655 g/cm3,Z = 2,R = 0.0385 and Wr = 0.0976.In the structure,one cadmium and four iodine atoms form a tetrahedral geometry,and two of such tetrahedra are connected in a co-line way to constitute Cd2I62-dimer.To our knowledge,this is the first example of dimerized CdI4 tetrahedron.All of the dimers are packed in the same mode,while the [DMAPM]+ cations are anti-parallelly arrayed.

  1. Inverse design of third-order Dirac exceptional points in photonic crystals

    CERN Document Server

    Lin, Zin; Lončar, Marko; Rodriguez, Alejandro W

    2016-01-01

    We propose a novel inverse-design method that enables brute-force discovery of photonic crystal (PhC) structures with complex spectral degeneracies. As a proof of principle, we demonstrate PhCs exhibiting third-order Dirac points formed by the \\emph{accidental} degeneracy of modes of monopolar, dipolar, and quadrupolar nature. We show that under suitable conditions, these modes can coalesce and form a third-order exceptional point (EP3), leading to diverging Petermann factors. We show that the spontaneous emission (SE) rate of emitters at such EP3s, related to the local density of states, can be enhanced by a factor of 8 in purely lossy (passive) structures, with larger enhancements $\\sim \\sqrt{n^3}$ possible at exceptional points of higher order $n$ or in materials with gain.

  2. Inverse Opal Photonic Crystals as a Strategy to Improve Photocatalysis: Underexplored Questions.

    Science.gov (United States)

    Curti, Mariano; Schneider, Jenny; Bahnemann, Detlef W; Mendive, Cecilia B

    2015-10-01

    The structuring of materials in the form of photonic crystals for photocatalytic applications is a quite new strategy aiming to enhance the performance of the photocatalysts at wavelength ranges where their absorption is poor. It is of particular interest to successfully manufacture an efficient photocatalytic system that could make use of solar light. Thus, the key of the strategy is the "slow photon effect", occurring at the edges of a forbidden band for photons. In this Perspective we have chosen some questions that we consider of relevance and that are well worth being addressed both theoretically and experimentally. It is the aim of this discussion to eventually lead to a more productive use of inverse opals as photonic photocatalytic materials.

  3. Numerical Prediction of Turbulent Flow and Heat Transfer with Phase Change in Crystallizer of Inverse Casting

    Institute of Scientific and Technical Information of China (English)

    YanhuiFENG; XinxinZHANG; 等

    2000-01-01

    A two-dimensional mathematical model has been undertaken to describe coupled liquid steel's turbulent flow and beat transfer with solidification in the crystallizer of inverse casting.The solid-liquid phase change phenomena have been modeled by using the continuum formulations and considering the mush zone as porous media.The turbulence flow has been accounted for ,using a modified version of the low-Reynolds-number κ-εturbulence model.A well-known numerical procedure,SIMPLE,has been used to solve the control equations.The effects of some main parameters on the solidification behavior have been studied,such as the casting speed,the thickness and the initial temperature of mother sheet,the superheat degree of liquid steel.

  4. Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

    Energy Technology Data Exchange (ETDEWEB)

    Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in

    2014-07-18

    Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.

  5. Periodic order and defects in Ni-based inverse opal-like crystals on the mesoscopic and atomic scale

    NARCIS (Netherlands)

    Chumakova, A. V.; Valkovskiy, G. A.; Mistonov, A. A.; Dyadkin, V. A.; Grigoryeva, N. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Petukhov, Andrei V.; Grigoriev, S. V.

    2014-01-01

    The structure of inverse opal crystals based on nickel was probed on the mesoscopic and atomic levels by a set of complementary techniques such as scanning electron microscopy and synchrotron microradian and wide-angle diffraction. The microradian diffraction revealed the mesoscopic-scale face-cente

  6. H/D isotopic recognition and temperature effects in IR spectra of hydrogen-bonded cyclic dimers in crystals: 3-Methylcinnamic acid and 4-phenylbutyric acid

    Science.gov (United States)

    Hachuła, Barbara; Jabłońska-Czapla, Magdalena; Flakus, Henryk T.; Nowak, Maria; Kusz, Joachim

    2015-01-01

    In the present work, the experimental and theoretical study of the nature of the inter-hydrogen bond interactions in two different carboxylic acids, 3-methylcinnamic acid (3MCA) and 4-phenylbutyric acid (4PBA), were reported. The polarized IR spectra of 3MCA and 4PBA crystals were recorded at the frequency ranges of the νOsbnd H and νOsbnd D bands. The spectral properties of 3MCA and 4PBA interpreted with the aid of the calculations based on the "strong-coupling" model. The differences in the spectral properties of the two different dimeric systems in the crystals provide a valuable information about the existence of a direct relationship between the crystal spectral properties in IR and the electronic structure of the molecular systems. In 3MCA crystals strong vibrational exciton interactions favor a "tail-to-head" (TH)-type Davydov coupling widespread via the π-electrons, whereas in 4PBA crystals a weak "through-space" (SS) exciton coupling is responsible for a "side-to-side"-type coupling. The relative contribution of each individual exciton coupling mechanism in IR spectra generation strongly depends on temperature and molecular electronic structure. The H/D isotopic recognition effect, depending on a non-random distribution of protons and deuterons in the crystal hydrogen bridges, was also analyzed.

  7. Crystal electric field and dimer splitting in Cs{sub 3}Er{sub 2}X{sub 9} (X=Cl, Br)

    Energy Technology Data Exchange (ETDEWEB)

    Allenspach, P.; Furrer, A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Guedel, H.U.; Furer, N. [Bern Univ. (Switzerland); Buettner, H. [Institut Max von Laue - Paul Langevin, 75 - Paris (France)

    1997-09-01

    Inelastic neutron scattering technique was used to measure the crystal electric field (CEF) splitting of Cs{sub 3}Er{sub 2}Cl{sub 9}. Besides a low lying magnetic excitation at around 2 meV all the other transitions are in agreement with CEF transitions found in optical measurements. Similar additional low-lying magnetic transitions were found in Cs{sub 3}Er{sub 2}Br{sub 9}. While excitations of the rare-earth dimers most likely play a role, the size of the splitting and its absence in optical spectra still remain a mystery. (author) 2 figs., 5 refs.

  8. Simultaneous recognition of a carboxylate-containing ligand and an intramolecular surrogate ligand in the crystal structure of an asymmetric vancomycin dimer

    Energy Technology Data Exchange (ETDEWEB)

    Loll, P.J.; Bevivino, A.E.; Korty, B.D.; Axelsen, P.H. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)

    1997-02-19

    Vancomycin is one of the most important and commonly used antibiotics in hospitals. Despite numerous investigations, however, it is not clear how vancomycin recognizes its site of action in the bacterial cell wall. The increasing incidence of bacterial resistance to vancomycin makes it imperative to understand these recognition determinants so that alternative agents may be developed. Herein we report the first crystal structure of vancomycin. The structure resolves a long-standing controversy about carboxylate recognition by vancomycin, suggests a possible cooperative mechanism linking ligand binding and dimerization, and demonstrates the operation of a novel intramolecular flap which occupies the binding site in the absence of ligand. 45 refs., 5 figs., 1 tab.

  9. Novel disulfide bond-mediated dimerization of the CARD domain was revealed by the crystal structure of CARMA1 CARD.

    Directory of Open Access Journals (Sweden)

    Tae-ho Jang

    Full Text Available CARMA1, BCL10 and MALT1 form a large molecular complex known as the CARMA1 signalosome during lymphocyte activation. Lymphocyte activation via the CARMA1 signalosome is critical to immune response and linked to many immune diseases. Despite the important role of the CARMA1 signalosome during lymphocyte activation and proliferation, limited structural information is available. Here, we report the dimeric structure of CARMA1 CARD at a resolution of 3.2 Å. Interestingly, although CARMA1 CARD has a canonical six helical-bundles structural fold similar to other CARDs, CARMA1 CARD shows the first homo-dimeric structure of CARD formed by a disulfide bond and reveals a possible biologically important homo-dimerization mechanism.

  10. Molecular basis for homo-dimerization of the CIDE domain revealed by the crystal structure of the CIDE-N domain of FSP27.

    Science.gov (United States)

    Lee, Seung Mi; Jang, Tae-ho; Park, Hyun Ho

    2013-10-04

    FSP27 (CIDE-3 in humans) plays critical roles in lipid metabolism and apoptosis and is known to be involved in regulation of lipid droplet (LD) size and lipid storage and apoptotic DNA fragmentation. Given that CIDE-containing proteins including FSP27 are associated with many human diseases including cancer, aging, diabetes, and obesity, studies of FSP27 and other CIDE-containing proteins are of great biological importance. As a first step toward elucidating the molecular mechanisms of FSP27-mediated lipid droplet growth and apoptosis, we report the crystal structure of the CIDE-N domain of FSP27 at a resolution of 2.0 Å. The structure revealed a possible biologically important homo-dimeric interface similar to that formed by the hetero-dimeric complex, CAD/ICAD. Comparison with other structural homologues revealed that the PB1 domain of BEM1P, ubiquitin-like domain of BAG6 and ubiquitin are structurally similar proteins. Our homo-dimeric structure of the CIDE-N domain of FSP27 will provide important information that will enable better understanding of the function of FSP27.

  11. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.

    Science.gov (United States)

    Ellenberger, T E; Brandl, C J; Struhl, K; Harrison, S C

    1992-12-24

    The yeast transcriptional activator GCN4 is 1 of over 30 identified eukaryotic proteins containing the basic region leucine zipper (bZIP) DNA-binding motif. We have determined the crystal structure of the GCN4 bZIP element complexed with DNA at 2.9 A resolution. The bZIP dimer is a pair of continuous alpha helices that form a parallel coiled coil over their carboxy-terminal 30 residues and gradually diverge toward their amino termini to pass through the major groove of the DNA-binding site. The coiled-coil dimerization interface is oriented almost perpendicular to the DNA axis, giving the complex the appearance of the letter T. There are no kinks or sharp bends in either bZIP monomer. Numerous contacts to DNA bases and phosphate oxygens are made by basic region residues that are conserved in the bZIP protein family. The details of the bZIP dimer interaction with DNA can explain recognition of the AP-1 site by the GCN4 protein.

  12. Spontaneous emission of semiconductor quantum dots in inverse opal SiO2 photonic crystals at different temperatures.

    Science.gov (United States)

    Yang, Peng; Yang, Yingshu; Wang, Yinghui; Gao, Jiechao; Sui, Ning; Chi, Xiaochun; Zou, Lu; Zhang, Han-Zhuang

    2016-02-01

    The photoluminescence (PL) characteristics of CdSe quantum dots (QDs) infiltrated into inverse opal SiO2 photonic crystals (PCs) are systemically studied. The special porous structure of inverse opal PCs enhanced the thermal exchange rate between the CdSe QDs and their surrounding environment. Finally, inverse opal SiO2 PCs suppressed the nonlinear PL enhancement of CdSe QDs in PCs excited by a continuum laser and effectively modulated the PL characteristics of CdSe QDs in PCs at high temperatures in comparison with that of CdSe QDs out of PCs. The final results are of benefit in further understanding the role of inverse opal PCs on the PL characteristics of QDs.

  13. The crystal structure of the non-liganded 14-3-3σ protein: insights into determinants of isoform specific ligand binding and dimerization

    Institute of Scientific and Technical Information of China (English)

    Anne BENZINGER; Grzegorz M. POPOWICZ; Joma K. JOY; Sudipta MAJUMDAR; Tad A. HOLAK; Heiko HERMEKING

    2005-01-01

    Seven different, but highly conserved 14-3-3 proteins are involved in diverse signaling pathways in human cells. It is unclear how the 14-3-3σ isoform, a transcriptional target of p53, exerts its inhibitory effect on the cell cycle in the presence of other 14-3-3 isoforms, which are constitutively expressed at high levels. In order to identify structural differences between the 14-3-3 isoforms, we solved the crystal structure of the human 14-3-3σ protein at a resolution of 2.8 A and compared it to the known structures of 14-3-3ζ and 14-3-3τ. The global architecture of the 14-3-3σ fold is similar to the previously determined structures of 14-3-3ζ and 14-3-3τ: two 14-3-3σ molecules form a cup-shaped dimer. Significant differences between these 14-3-3 isoforms were detected adjacent to the amphipathic groove, which mediates the binding to phosphorylated consensus motifs in 14-3-3-1igands. Another specificity determining region is localized between amino-acids 203 to 215. These differences presumably select for the interaction with specific ligands,which may explain the different biological functions of the respective 14-3-3 isoforms. Furthermore, the two 14-3-3σ molecules forming a dimer differ by the spatial position of the ninth helix, which is shifted to the inside of the ligand interaction surface, thus indicating adaptability of this part of the molecule. In addition, 5 non-conserved residues are located at the interface between two 14-3-3σ proteins forming a dimer and represent candidate determinants of homoand hetero-dimerization specificity. The structural differences among the 14-3-3 isoforms described here presumably contribute to isoform-specific interactions and functions.

  14. Optically Biaxial, Re-entrant and Frustrated Mesophases in Chiral, Non-symmetric Liquid Crystal Dimers and Binary Mixtures.

    Science.gov (United States)

    Padmini, Vediappen; Babu, Palakurthy Nani; Nair, Geetha G; Rao, D S Shankar; Yelamaggad, Channabasaveshwar V

    2016-10-20

    Sixteen optically active, non-symmetric dimers, in which cyanobiphenyl and salicylaldimine mesogens are interlinked by a flexible spacer, were synthesized and characterized. While the terminal chiral tail, in the form of either (R)-2-octyloxy or (S)-2-octyloxy chain attached to salicylaldimine core, was held constant, the number of methylene units in the spacer was varied from 3 to 10 affording eight pairs of (R & S) enantiomers. They were probed for their thermal properties with the aid of orthoscopy, conoscopy, differential scanning calorimetry and X-ray powder diffraction. In addition, the binary mixture study was carried out using chiral and achiral dimers with the intensions of stabilizing optically biaxial phase/s, re-entrant phases and important phase sequences. Notably, one of the chiral dimers as well as some mixtures exhibited a biaxial smectic A (SmAb ) phase appearing between a uniaxial SmA and a re-entrant uniaxial SmA phases. The mesophases such as chiral nematic (N*) and frustrated phases viz., blue phases (BPs) and twist grain boundary (TGB) phases, were also found to occur in most of the dimers and mixtures. X-ray diffraction studies revealed that the dimers possessing oxybutoxy and oxypentoxy spacers show interdigitated (SmAd ) phase where smectic periodicity is over 1.4 times the molecular length; whereas in the intercalated SmA (SmAc ) phase formed by a dimer having oxydecoxy spacer the periodicity was found to be approximately half the molecular length. The handedness of the helical structure of the N* phases formed by two enantiomers was examined with the aid of CD measurements; as expected, these enantiomers showed optical activities of equal magnitudes but with opposite signs. Overall, it appears that the chiral dimers and mixtures presented herein may serve as model systems in design and developing novel materials exhibiting the apolar SmAb phase possessing D2h symmetry and nematic-type biaxiality. © 2016 Wiley-VCH Verlag GmbH & Co. KGa

  15. Gold nanoparticle incorporated inverse opal photonic crystal capillaries for optofluidic surface enhanced Raman spectroscopy.

    Science.gov (United States)

    Zhao, Xiangwei; Xue, Jiangyang; Mu, Zhongde; Huang, Yin; Lu, Meng; Gu, Zhongze

    2015-10-15

    Novel transducers are needed for point of care testing (POCT) devices which aim at facile, sensitive and quick acquisition of health related information. Recent advances in optofluidics offer tremendous opportunities for biological/chemical analysis using extremely small sample volumes. This paper demonstrates nanostructured capillary tubes for surface enhanced Raman spectroscopy (SERS) analysis in a flow-through fashion. The capillary tube integrates the SERS sensor and the nanofluidic structure to synergistically offer sample delivery and analysis functions. Inside the capillary tube, inverse opal photonic crystal (IO PhC) was fabricated using the co-assembly approach to form nanoscale liquid pathways. In the nano-voids of the IO PhC, gold nanoparticles were in situ synthesized and functioned as the SERS hotspots. The advantages of the flow-through SERS sensor are multifold. The capillary effect facilities the sample delivery process, the nanofluidic channels boosts the interaction of analyte and gold nanoparticles, and the PhC structure strengthens the optical field near the SERS hotspots and results in enhanced SERS signals from analytes. As an exemplary demonstration, the sensor was used to measure creatinein spiked in artificial urine samples with detection limit of 0.9 mg/dL.

  16. Direct band gap silicon crystals predicted by an inverse design method

    Science.gov (United States)

    Oh, Young Jun; Lee, In-Ho; Lee, Jooyoung; Kim, Sunghyun; Chang, Kee Joo

    2015-03-01

    Cubic diamond silicon has an indirect band gap and does not absorb or emit light as efficiently as other semiconductors with direct band gaps. Thus, searching for Si crystals with direct band gaps around 1.3 eV is important to realize efficient thin-film solar cells. In this work, we report various crystalline silicon allotropes with direct and quasi-direct band gaps, which are predicted by the inverse design method which combines a conformation space annealing algorithm for global optimization and first-principles density functional calculations. The predicted allotropes exhibit energies less than 0.3 eV per atom and good lattice matches, compared with the diamond structure. The structural stability is examined by performing finite-temperature ab initio molecular dynamics simulations and calculating the phonon spectra. The absorption spectra are obtained by solving the Bethe-Salpeter equation together with the quasiparticle G0W0 approximation. For several allotropes with the band gaps around 1 eV, photovoltaic efficiencies are comparable to those of best-known photovoltaic absorbers such as CuInSe2. This work is supported by the National Research Foundation of Korea (2005-0093845 and 2008-0061987), Samsung Science and Technology Foundation (SSTF-BA1401-08), KIAS Center for Advanced Computation, and KISTI (KSC-2013-C2-040).

  17. Crystal structure of a BCL-W domain-swapped dimer: implications for the function of BCL-2 family proteins.

    Science.gov (United States)

    Lee, Erinna F; Dewson, Grant; Smith, Brian J; Evangelista, Marco; Pettikiriarachchi, Anne; Dogovski, Con; Perugini, Matthew A; Colman, Peter M; Fairlie, W Douglas

    2011-10-12

    The prosurvival and proapoptotic proteins of the BCL-2 family share a similar three-dimensional fold despite their opposing functions. However, many biochemical studies highlight the requirement for conformational changes for the functioning of both types of proteins, although structural data to support such changes remain elusive. Here, we describe the X-ray structure of dimeric BCL-W that reveals a major conformational change involving helices α3 and α4 hinging away from the core of the protein. Biochemical and functional studies reveal that the α4-α5 hinge region is required for dimerization of BCL-W, and functioning of both pro- and antiapoptotic BCL-2 proteins. Hence, this structure reveals a conformational flexibility not seen in previous BCL-2 protein structures and provides insights into how these regulators of apoptosis can change conformation to exert their function.

  18. A crystal structure of the catalytic core domain of an avian sarcoma and leukemia virus integrase suggests an alternate dimeric assembly.

    Science.gov (United States)

    Ballandras, Allison; Moreau, Karen; Robert, Xavier; Confort, Marie-Pierre; Merceron, Romain; Haser, Richard; Ronfort, Corinne; Gouet, Patrice

    2011-01-01

    Integrase (IN) is an important therapeutic target in the search for anti-Human Immunodeficiency Virus (HIV) inhibitors. This enzyme is composed of three domains and is hard to crystallize in its full form. First structural results on IN were obtained on the catalytic core domain (CCD) of the avian Rous and Sarcoma Virus strain Schmidt-Ruppin A (RSV-A) and on the CCD of HIV-1 IN. A ribonuclease-H like motif was revealed as well as a dimeric interface stabilized by two pairs of α-helices (α1/α5, α5/α1). These structural features have been validated in other structures of IN CCDs. We have determined the crystal structure of the Rous-associated virus type-1 (RAV-1) IN CCD to 1.8 Å resolution. RAV-1 IN shows a standard activity for integration and its CCD differs in sequence from that of RSV-A by a single accessible residue in position 182 (substitution A182T). Surprisingly, the CCD of RAV-1 IN associates itself with an unexpected dimeric interface characterized by three pairs of α-helices (α3/α5, α1/α1, α5/α3). A182 is not involved in this novel interface, which results from a rigid body rearrangement of the protein at its α1, α3, α5 surface. A new basic groove that is suitable for single-stranded nucleic acid binding is observed at the surface of the dimer. We have subsequently determined the structure of the mutant A182T of RAV-1 IN CCD and obtained a RSV-A IN CCD-like structure with two pairs of buried α-helices at the interface. Our results suggest that the CCD of avian INs can dimerize in more than one state. Such flexibility can further explain the multifunctionality of retroviral INs, which beside integration of dsDNA are implicated in different steps of the retroviral cycle in presence of viral ssRNA.

  19. CH3NH3PbCl3 Single Crystals: Inverse Temperature Crystallization and Visible-Blind UV-Photodetector

    KAUST Repository

    Maculan, Giacomo

    2015-09-02

    Single crystals of hybrid perovskites have shown remarkably improved physical properties compared to their polycrystalline film counterparts, underscoring their importance in the further development of advanced semiconductor devices. Here we present a new method of sizeable CH3NH3PbCl3 single crystal growth based on retrograde solubility behavior of hybrid perovskites. We show, for the first time, the energy band structure, charge-carrier recombination and transport properties of single crystal CH3NH3PbCl3. The chloride-based perovskite crystals exhibit trap-state density, charge carriers concentration, mobility and diffusion length comparable with the best quality crystals of methylammonium lead iodide or bromide perovskites reported so far. The high quality of the crystal along with its suitable optical bandgap enabled us to design and build an efficient visible-blind UV-photodetector, demonstrating the potential of this material to be employed in optoelectronic applications.

  20. Correlation between steady-oscillatory flow transition and the interface inversion process during the Czochralski growth of semitransparent oxide crystal

    Science.gov (United States)

    Faiez, Reza; Rezaei, Yazdan

    2016-12-01

    In this paper, steady-oscillatory transition of the convective flow in a Czochralski (Cz) growth system was numerically studied. In this configuration, rapid variations in density across narrow region of the flow in the vicinity of the crystallization front leads to an unstable stratification of the flow in this region. Time-dependent, finite volume method calculation of the momentum and heat transport equations shows that an instability mechanism, giving rise to the formation of cold plumes beneath the phase boundary, might be associated with an irreversible change in the convexity of the front. Dynamics of the crystallization front was found to be correlated with the periodic oscillation of the flow. It was shown that the interface inversion process occurs at a critical Reynolds number significantly (˜25%) lower than that predicted by the steady-state Cz-oxide model analysis. Consistently, the time-averaged maximum value of stream function was found to be larger than its corresponding steady-state value. This indicates that the mechanism behind the oscillatory transition of the flow has a positive feedback on the intensity of forced convection flow. These numerical results were attributed to the baroclinic instability mechanism characterized by oscillations of a cold plume appearing at the crystal periphery and descending along the symmetry axis. The time period of oscillations was found to be considerably (30-40%) decreases and, simultaneously, the inclination angle of isopycnals increases (˜48%) at a critical rotation rate of the crystal for which the interface inversion occurs.

  1. Influence of surface termination on the inverse Goos-H\\"anchen shift of negatively refractive photonic crystals

    CERN Document Server

    Hu, Jinbing; Chen, Jiabi; Jiang, Qiang; Wang, Yan; Ma, Luming; Luo, Xuexue; Zhuang, Songlin

    2014-01-01

    The investigation of surface termination over the inverse Goos-H\\"anchen (GH) shift of two-dimensional (2D) negatively refractive photonic crystal (NRPhC), made by air holes arranged in hexagonal lattice in a dielectric background, shows that the magnitude of the inverse GH shift of 2D-NRPhC depends strongly on the surface termination even for an incident beam with fixed frequency and incidence angle, while the effective index of 2D-NRPhC remains. For surface termination with the outmost row of air holes complete, TM-polarized light is characterized by the inverse GH shift of more than tens of lattices and TE-polarized light by very tiny inverse GH shift. While for surface termination with the outmost row of air holes cut in quarter or so, the situation is just on the opposite. In addition, the reflectivity of 2D-NRPhC as a function of surface termination is also studied, and the result shows that the smaller the reflectivity the larger the inverse GH shifts. The results of this paper will provide technical i...

  2. Crystal structure of dimeric cardiac L-type calcium channel regulatory domains bridged by Ca[superscript 2+]·calmodulins

    Energy Technology Data Exchange (ETDEWEB)

    Fallon, Jennifer L.; Baker, Mariah R.; Xiong, Liangwen; Loy, Ryan E.; Yang, Guojun; Dirksen, Robert T.; Hamilton, Susan L.; Quiocho, Florante A.; (Baylor); (Rochester-Med)

    2009-11-10

    Voltage-dependent calcium channels (Ca(V)) open in response to changes in membrane potential, but their activity is modulated by Ca(2+) binding to calmodulin (CaM). Structural studies of this family of channels have focused on CaM bound to the IQ motif; however, the minimal differences between structures cannot adequately describe CaM's role in the regulation of these channels. We report a unique crystal structure of a 77-residue fragment of the Ca(V)1.2 alpha(1) subunit carboxyl terminus, which includes a tandem of the pre-IQ and IQ domains, in complex with Ca(2+).CaM in 2 distinct binding modes. The structure of the Ca(V)1.2 fragment is an unusual dimer of 2 coiled-coiled pre-IQ regions bridged by 2 Ca(2+).CaMs interacting with the pre-IQ regions and a canonical Ca(V)1-IQ-Ca(2+).CaM complex. Native Ca(V)1.2 channels are shown to be a mixture of monomers/dimers and a point mutation in the pre-IQ region predicted to abolish the coiled-coil structure significantly reduces Ca(2+)-dependent inactivation of heterologously expressed Ca(V)1.2 channels.

  3. Crystal structure of a dimeric Ser49- PLA₂-like myotoxic component of the Vipera ammodytes meridionalis venomics reveals determinants of myotoxicity and membrane damaging activity.

    Science.gov (United States)

    Georgieva, Dessislava; Coronado, Monika; Oberthür, Dominik; Buck, Friedrich; Duhalov, Deyan; Arni, Raghuvir K; Betzel, Christian

    2012-04-01

    Myotoxicity and membrane damage play a central role in the life-threatening effects of the viper envenomation. Myotoxins are an important part of the viper venomics. A Ser49 PLA₂-like myotoxin from the venom of Vipera ammodytes meridionalis, the most venomous snake in Europe, was crystallized and its three-dimensional structure determined. The toxin is devoid of phospholipolytic activity. The structure demonstrates a formation of dimers. In the dimers functionally important peptide segments, located on the protein surface, point in the same direction which can strengthen the pharmacological effect. This supports the hypothesis about the physiological importance of the toxin oligomerization for the myotoxicity and membrane damage. The crystallographic model revealed that the structural determinants of myotoxicity (a positively charged C-terminal region and a hydrophobic knuckle) are fully exposed on the protein surface and accessible for interactions with target membranes. Distortion of the catalytic site region explains the absence of enzymatic activity. The structure reveals anion-binding sites which can be considered as possible sites of interactions of the toxin with a negatively charged membrane surface. The high structural similarity of the Ser49 myotoxin and Asp49 PLA₂ from the same venom suggests an evolutionary relationship: probably, the Ser49 myotoxin is a product of evolution of the catalytically active phospholipase A₂. The first toxin lost the enzymatic activity which is not necessary for the myotoxicity but preserved the cytotoxicity and membrane damaging activity as important components of the venom toxicity.

  4. A neutron diffraction study from 6 to 293 K and a macroscopic-scale quantum theory of the hydrogen bonded dimers in the crystal of benzoic acid

    CERN Document Server

    Fillaux, François

    2011-01-01

    The crystal of benzoic acid is comprised of tautomeric centrosymmetric dimers linked through bistable hydrogen bonds. Statistical disorder of the bonding protons is excluded by neutron diffraction from 6 K to 293 K. In addition to diffraction data, vibrational spectra and relaxation rates measured with solid-state-NMR and quasi-elastic neutron scattering are consistent with wave-like, rather than particle-like protons. We present a macroscopic-scale quantum theory for the bonding protons represented by a periodic lattice of fermions. The adiabatic separation, the exclusion principle, and the antisymmetry postulate yield a static lattice-state immune to decoherence. According to the theory of quantum measurements, vibrational spectroscopy and relaxometry involve realizations of decoherence-free Bloch states for nonlocal symmetry species that did not exist before the measurement. The eigen states are fully determined by three temperature-independent parameters which are effectively measured: the energy differen...

  5. X-ray Crystal Structures of Monomeric and Dimeric Peptide Inhibitors in Complex with the Human Neonatal Fc Receptor, FcRn

    Energy Technology Data Exchange (ETDEWEB)

    Mezo, Adam R.; Sridhar, Vandana; Badger, John; Sakorafas, Paul; Nienaber, Vicki (Zenobia); (Biogen)

    2010-10-28

    The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A. R., McDonnell, K. A., Tan Hehir, C. A., Low, S. C., Palombella, V. J., Stattel, J. M., Kamphaus, G. D., Fraley, C., Zhang, Y., Dumont, J. A., and Bitonti, A. J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 2337-2342). Herein, the x-ray crystal structure of a representative monomeric peptide in complex with human FcRn was solved to 2.6 {angstrom} resolution. The structure shows that the peptide binds to human FcRn at the same general binding site as does the Fc domain of IgG. The data correlate well with structure-activity relationship data relating to how the peptide family binds to human FcRn. In addition, the x-ray crystal structure of a representative dimeric peptide in complex with human FcRn shows how the bivalent ligand can bridge two FcRn molecules, which may be relevant to the mechanism by which the dimeric peptides inhibit FcRn and increase IgG catabolism in vivo. Modeling of the peptide:FcRn structure as compared with available structural data on Fc and FcRn suggest that the His-6 and Phe-7 (peptide) partially mimic the interaction of His-310 and Ile-253 (Fc) in binding to FcRn, but using a different backbone topology.

  6. Synthesis and Crystal Structure of Cis-syn Cyclobutane 1-(Carboxyethyl)thymine Dimer Monopentyl Amide Monotryptophan Methyl Ester Amide

    Institute of Scientific and Technical Information of China (English)

    TANG Wen-Jian; SONG Hai-Bin; SONG Qin-Hua

    2007-01-01

    The crystal structure of the title compound (C34H47N7O9, Mr=697.79) has been determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21 with a=9.000(8), b=11.360(10), c=17.841(15)(A), β=97.083(14)°, V=1810(3) (A)3, Z=2, F(000)=744, Dc=1.280 g/cm3, μ=0.094 mm-1, the final R=0.0721 and wR=0.1942 for 2479 observed reflections with Ⅰ > 2σ(Ⅰ). The two methyl groups attached to the cyclobutane ring are cis oriented. An intramolecular hydrogen bond (N(6)-H(6)…O(8)) (A)ntroduces rigidity into the title molecule and the crystal structure is stabilized by intermolecular N-H…O hydrogen bonds.

  7. Universality in bosonic dimer-dimer scattering

    Energy Technology Data Exchange (ETDEWEB)

    Deltuva, A. [Centro de Fisica Nuclear, Universidade de Lisboa, P-1649-003 Lisboa (Portugal)

    2011-08-15

    Bosonic dimer-dimer scattering is studied near the unitary limit using momentum-space equations for the four-particle transition operators. The impact of the Efimov effect on the dimer-dimer scattering observables is explored, and a number of universal relations is established with high accuracy. The rate for the creation of Efimov trimers via dimer-dimer collisions is calculated.

  8. Crystal structure of 3-[(2-acetylphenoxycarbonyl]benzoic acid

    Directory of Open Access Journals (Sweden)

    Mohammad Shoaib

    2014-11-01

    Full Text Available In the title compound, C16H12O5, synthesized from isopthaloyl chloride and 2′-hydroxyacetophenone, the dihedral angle between the planes of the aromatic rings is 71.37 (9°. In the crystal, carboxylic acid inversion dimers generate R22(8 loops. The dimers are linked by C—H...O interactions, generating (101 sheets.

  9. Syntheses and crystal structures of two mixed-ligand dimeric zinc complexes containing a dithiol ligand and an open chain crown ether ligand with terminal quinolyl groups

    Science.gov (United States)

    Li, Cheng-Juan; Dou, Jian-Min; Li, Da-Cheng; Wang, Da-Qi

    2006-02-01

    Two mixed-ligand zinc complexes Zn(L)(H 2O)(mnt) ( 1) and Zn(L)(H 2O)(i-mnt) ( 2) (where L=2,6-bis(8'-quinoylyloxymethyl)pyridine, mnt =1,2-dicyanoethylene-1,2-ditholate and i-mnt =1,1-dicyanoethylene-2,2-ditholate) have been synthesized and characterized by elemental analysis, FT-IR spectra, and single-crystal X-ray diffraction. Complexes 1 and 2 both crystallize in the monoclinic system, space group C2/ c and each displays a distorted trigonal bipyramidal around zinc atom. The coordination sphere of Zn is NO 2S 2 type, where the dithiol ligand (mnt or i-mnt) and one terminal quinolyl group of L act as the chelate S, S and N, O donor sets, respectively, besides the coordination water molecules. Furthermore, there are intramolecular H-bonds occurred between the coordination water molecule and the N2, N3 atoms of the L and the molecules of 1 and 2 both form the dimers through the intermolecular π-π stacking interactions.

  10. Functional characterization and crystal structure of thermostable amylase from Thermotoga petrophila, reveals high thermostability and an unusual form of dimerization

    DEFF Research Database (Denmark)

    Hameed, Uzma; Price, Ian; Ikram-Ul-Haq

    2017-01-01

    Thermostable α-amylases have many industrial applications and are therefore continuously explored from novel sources. We present the characterization of a novel putative α-amylase gene product (Tp-AmyS) cloned from Thermotoga petrophila. The purified recombinant enzyme is highly thermostable and ...... of salivary amylase from a previous crystal structure, and thus could be a functional feature of some amylases....

  11. Band gap expansion, shear inversion phase change behaviour and low-voltage induced crystal oscillation in low-dimensional tin selenide crystals.

    Science.gov (United States)

    Carter, Robin; Suyetin, Mikhail; Lister, Samantha; Dyson, M Adam; Trewhitt, Harrison; Goel, Sanam; Liu, Zheng; Suenaga, Kazu; Giusca, Cristina; Kashtiban, Reza J; Hutchison, John L; Dore, John C; Bell, Gavin R; Bichoutskaia, Elena; Sloan, Jeremy

    2014-05-28

    In common with rocksalt-type alkali halide phases and also semiconductors such as GeTe and SnTe, SnSe forms all-surface two atom-thick low dimensional crystals when encapsulated within single walled nanotubes (SWNTs) with diameters below ∼1.4 nm. Whereas previous density functional theory (DFT) studies indicate that optimised low-dimensional trigonal HgTe changes from a semi-metal to a semi-conductor, low-dimensional SnSe crystals typically undergo band-gap expansion. In slightly wider diameter SWNTs (∼1.4-1.6 nm), we observe that three atom thick low dimensional SnSe crystals undergo a previously unobserved form of a shear inversion phase change resulting in two discrete strain states in a section of curved nanotube. Under low-voltage (i.e. 80-100 kV) imaging conditions in a transmission electron microscope, encapsulated SnSe crystals undergo longitudinal and rotational oscillations, possibly as a result of the increase in the inelastic scattering cross-section of the sample at those voltages.

  12. Design of a three-dimensional photonic band gap cavity in a diamondlike inverse woodpile photonic crystal

    Science.gov (United States)

    Woldering, Léon A.; Mosk, Allard P.; Vos, Willem L.

    2014-09-01

    We theoretically investigate the design of cavities in a three-dimensional (3D) inverse woodpile photonic crystal. This class of cubic diamondlike crystals has a very broad photonic band gap and consists of two perpendicular arrays of pores with a rectangular structure. The point defect that acts as a cavity is centered on the intersection of two intersecting perpendicular pores with a radius that differs from the ones in the bulk of the crystal. We have performed supercell band structure calculations with up to 5×5×5 unit cells. We find that up to five isolated and dispersionless bands appear within the 3D photonic band gap. For each isolated band, the electric-field energy is localized in a volume centered on the point defect, hence the point defect acts as a 3D photonic band gap cavity. The mode volume of the cavities resonances is as small as 0.8 λ3 (resonance wavelength cubed), indicating a strong confinement of the light. By varying the radius of the defect pores we found that only donorlike resonances appear for smaller defect radius, whereas no acceptorlike resonances appear for greater defect radius. From a 3D plot of the distribution of the electric-field energy density we conclude that peaks of energy are found in sharp edges situated at the point defect, similar to how electrons collect at such features. This is different from what is observed for cavities in noninverted woodpile structures. Since inverse woodpile crystals can be fabricated from silicon by CMOS-compatible means, we project that single cavities and even cavity arrays can be realized, for wavelength ranges compatible with telecommunication windows in the near infrared.

  13. A visual and organic vapor sensitive photonic crystal sensor consisting of polymer-infiltrated SiO2 inverse opal.

    Science.gov (United States)

    Zhang, Yuqi; Qiu, Jianhua; Hu, Rongrong; Li, Pei; Gao, Loujun; Heng, Liping; Tang, Ben Zhong; Jiang, Lei

    2015-04-21

    A photonic crystal (PC) sensor that can selectively detect organic vapors through visual color changes has been proposed. The sensor was fabricated by infiltrating a tetraphenylethene polymer (TPEP) into the voids of SiO2 inverse opal photonic crystal. When the sensor was exposed to tetrahydrofuran or acetone vapor, a red shift of the stopband of more than 50 nm could be clearly observed; meanwhile, the film's color changed from violet to cyan. Subsequently, when exposed to air, the stopband underwent a blue shift and the color returned to violet. The reason for the observed change is that a reversible adsorption-desorption process occurs on alternate exposure of the sensor to organic vapor and air, due to the high specific surface area of the inverse opal macroporous structure and the high affinity of TPEP to tetrahydrofuran and acetone. The adsorption of vapor analyte can increase the PC's effective refractive index, which will induce the stopband red shift and the resulting color change according to Bragg's Law. The reversible adsorption-desorption of organic vapors varied the effective refractive index of the sensor repeatedly, causing the reversible stopband shift and color change, and providing a general method for the design of visual vapor sensors.

  14. Energy flux pattern of inverse Goos-Hanchen shift in photonic crystals with negative index of refraction

    CERN Document Server

    Hu, Jinbing; Chen, Jiabi; Jiang, Qiang; Wang, Yan; Zhuang, Songlin

    2015-01-01

    The energy flux patterns of inverse Goos-Hanchen (GH) shift around the interface between air and negatively refractive photonic crystal (NRPhC) with different surface terminations is investigated. Results show that NRPhC exhibits inverse GH shift in TM and TE polarization, and the localization and pattern of energy flux differ in TM and TE polarizations and are strongly affected by surface termination. This is different to the condition of negative permittivity materials (i.e., metal), which only presents inverse GH shift in TM polarization. In the case of TE polarization, the energy flux pattern exhibits the flux of backward wave whose localization changes from the surface to inside of NRPhC with the variation of surface termination. In the case of TM polarization, the energy flux pattern is always confined within the surface of NRPhC, whereas its pattern changes from the flux of backward wave to vortices at the surface of NRPhC, which is different to the energy flux of TM polarization of metal. By properly ...

  15. Disorder of the dimeric TCNQ–TCNQ unit in the crystal structure of [Ni(bpy3]2(TCNQ–TCNQ(TCNQ2·6H2O (TCNQ is 7,7,8,8-tetracyanoquinodimethane

    Directory of Open Access Journals (Sweden)

    Juraj Černák

    2017-01-01

    Full Text Available Crystallization from an aqueous methanol system composed of Ni(NO32, 2,2′-bipyridine (bpy and LiTCNQ (TCNQ is 7,7,8,8-tetracyanoquinodimethane in a 1:3:2 molar ratio yielded single crystals of bis[tris(2,2′-bipyridine-κ2N,N′nickel(II] bis(7,7,8,8-tetracyanoquinodimethane radical anion bi[7,7,8,8-tetracyanoquinodimethanide] hexahydrate, [Ni(C10H8N23]2(C24H8N8(C12H4N42·6H2O or [Ni(bpy3]2(TCNQ–TCNQ(TCNQ2·6H2O. The crystal structure comprises [Ni(bpy3]2+ complex cations, two centrosymmetric crystallographically independent TCNQ·− anion radicals with π-stacked exo groups, and an additional dimeric TCNQ–TCNQ unit which comprises 75.3 (9% of a σ-dimerized (TCNQ–TCNQ2− dianion and 24.7 (9% of two TCNQ·− anion radicals with tightly π-stacked exo groups. The title complex represents the first example of an NiII complex containing a σ-dimerized (TCNQ–TCNQ2− dianion. Disordered solvent water molecules present in the crystal structure participate in hydrogen-bonding interactions.

  16. Crystal Structure of a Novel Dimeric Form of NS5A Domain I Protein from Hepatitis C Virus

    Energy Technology Data Exchange (ETDEWEB)

    Love, Robert A.; Brodsky, Oleg; Hickey, Michael J.; Wells, Peter A.; Cronin, Ciarán N.; Pfizer

    2009-07-10

    A new protein expression vector design utilizing an N-terminal six-histidine tag and tobacco etch virus protease cleavage site upstream of the hepatitis C virus NS5A sequence has resulted in a more straightforward purification method and improved yields of purified NS5A domain I protein. High-resolution diffracting crystals of NS5A domain I (amino acids 33 to 202) [NS5A(33-202)] were obtained by using detergent additive crystallization screens, leading to the structure of a homodimer which is organized differently from that published previously (T. L. Tellinghuisen, J. Marcotrigiano, and C. M. Rice, Nature 435:374-379, 2005) yet is consistent with a membrane association model for NS5A. The monomer-monomer interface of NS5A(33-202) features an extensive buried surface area involving the most-highly conserved face of each monomer. The two alternate structural forms of domain I now available may be indicative of the multiple roles emerging for NS5A in viral RNA replication and viral particle assembly.

  17. Design of a 3D photonic band gap cavity in a diamond-like inverse woodpile photonic crystal

    CERN Document Server

    Woldering, Léon A; Vos, Willem L

    2014-01-01

    We theoretically investigate the design of cavities in a three-dimensional (3D) inverse woodpile photonic crystal. This class of cubic diamond-like crystals has a very broad photonic band gap and consists of two perpendicular arrays of pores with a rectangular structure. The point defect that acts as a cavity is centred on the intersection of two intersecting perpendicular pores with a radius that differs from the ones in the bulk of the crystal. We have performed supercell bandstructure calculations with up to $5 \\times 5 \\times 5$ unit cells. We find that up to five isolated and dispersionless bands appear within the 3D photonic band gap. For each isolated band, the electric-field energy is localized in a volume centred on the point defect, hence the point defect acts as a 3D photonic band gap cavity. The mode volume of the cavities resonances is as small as 0.8 $\\lambda^{3}$ (resonance wavelength cubed), indicating a strong confinement of the light. By varying the radius of the defect pores we found that o...

  18. The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.

    Science.gov (United States)

    Nagano, Soshichiro; Scheerer, Patrick; Zubow, Kristina; Michael, Norbert; Inomata, Katsuhiko; Lamparter, Tilman; Krauß, Norbert

    2016-09-23

    Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion.

  19. Synthesis and phase transition studies on non-symmetric liquid crystal dimers: N-(4-(n-(4-(benzothiazol-2-yl)phenoxy)alkyloxy)-benzylidene)-4-chloroanilines

    Science.gov (United States)

    Yeap, Guan-Yeow; Al-Taifi, Elham A.; Ong, Chin-Hin; Kamil Mahmood, Wan Ahmad; Takeuchi, Daisuke; Ito, Masato M.

    2012-06-01

    A new series of non-symmetric liquid crystal dimers N-(4-(n-(4-(benzothiazol-2-yl)phenoxy)alkyloxy)benzylidene)-4-chloroaniline containing benzothiazole and benzylideneimine units connected by a flexible alkyl spacer, -(CH2) n -, with n ranging from 4 to 12 in even parity have been prepared. All five members of this homologous series exhibit an enantiotropic nematic phase. The compounds with greater n of 8-12 exhibit both nematic and smectic phases upon cooling. A notable feature among this series is that for the member with n = 10, the smectic-nematic transition is also present. The nematic-isotropic transition temperatures and associated entropy changes with respect to all compounds in this series exhibit a dramatic dependence on the length of the flexible spacer. A comparison of the transitional properties of this series with those of α-(4-benzylidenechloroaniline-4‧-oxy)-ω-[4-(thiophene-2-carboxyl)benzylideneaniline-4‧-oxy]alkanes reveals that replacing benzothiazole moiety at one side of the flexible alkyl spacer reduces the nematic-isotropic transition temperature.

  20. The dimer-approach to characterize opto-electronic properties of and exciton trapping and diffusion in organic semiconductor aggregates and crystals.

    Science.gov (United States)

    Engels, Bernd; Engel, Volker

    2017-05-24

    A fundamental understanding of photo-induced processes in opto-electronic thin film devices is a prerequisite for the rational design of improved organic semiconductor materials. Absorption and emission spectra provide important insights into the complicated electronic structure of and relaxation processes in organic semiconductor aggregates and crystals. They are of interest because they often limit the efficiencies of the devices. For an assignment of the spectra a close interplay between experiment and theory is essential because simulations are often necessary to entangle the various effects which determine the features of the spectra. In the present perspective we describe the so called dimer-approach and provide a few examples in which this approach could successfully deliver an atomistic picture of photo-induced relaxation effects in perylene-based materials and characterize their optical spectra. The model Hamiltonians of standard monomer-based approaches are also briefly discussed to reveal the differences between both methods and to shed some light on their strengths and shortcomings.

  1. Crystal structure of a chloride-bridged copper(II dimer: piperazine-1,4-dium bis(di-μ-chlorido-bis[(4-carboxypyridine-2-carboxylato-κ2N,O2chloridocuprate(II

    Directory of Open Access Journals (Sweden)

    Bassey Enyi Inah

    2017-02-01

    Full Text Available Crystals of a new dimeric chloride-bridged cuprate(II derived from pyridine-2,4-dicarboxylic acid were obtained solvothermally in the presence of piperazine and hydrochloric acid. The crystal structure determination of the title salt, (C4H12N2[Cu2(C7H4NO42Cl4], revealed one of the carboxyl groups of the original pyridine-2,4-dicarboxylic acid ligand to be protonated, whereas the other is deprotonated and binds together with the pyridine N atom to the CuII atom. The coordination environment of the CuII atom is distorted square-pyramidal. One of the chloride ligands bridges two metal cations to form a centrosymmetric dimer with two different Cu—Cl distances of 2.2632 (8 and 2.7853 (8 Å, whereby the longer distance is associated with the apical ligand. The remaining chloride ligand is terminal at one of the basal positions, with a distance of 2.2272 (9 Å. In the crystal, the dimers are linked by intermolecular O—H...O hydrogen bonds, together with N—H...O and N—H...Cl interactions involving the centrosymmetric organic cation, into a three-dimensional supramolecular network. Further but weaker C—H...O and C—H...Cl interactions consolidate the packing.

  2. Crystal structure of a chloride-bridged copper(II) dimer: piperazine-1,4-dium bis-(di-μ-chlorido-bis[(4-carboxypyridine-2-carboxyl-ato-κ(2)N,O(2))chlorido-cuprate(II)].

    Science.gov (United States)

    Inah, Bassey Enyi; Ayi, Ayi Anyama; Adhikary, Amit

    2017-02-01

    Crystals of a new dimeric chloride-bridged cuprate(II) derived from pyridine-2,4-di-carb-oxy-lic acid were obtained solvothermally in the presence of piperazine and hydro-chloric acid. The crystal structure determination of the title salt, (C4H12N2)[Cu2(C7H4NO4)2Cl4], revealed one of the carboxyl groups of the original pyridine-2,4-di-carb-oxy-lic acid ligand to be protonated, whereas the other is deprotonated and binds together with the pyridine N atom to the Cu(II) atom. The coordination environment of the Cu(II) atom is distorted square-pyramidal. One of the chloride ligands bridges two metal cations to form a centrosymmetric dimer with two different Cu-Cl distances of 2.2632 (8) and 2.7853 (8) Å, whereby the longer distance is associated with the apical ligand. The remaining chloride ligand is terminal at one of the basal positions, with a distance of 2.2272 (9) Å. In the crystal, the dimers are linked by inter-molecular O-H⋯O hydrogen bonds, together with N-H⋯O and N-H⋯Cl inter-actions involving the centrosymmetric organic cation, into a three-dimensional supra-molecular network. Further but weaker C-H⋯O and C-H⋯Cl inter-actions consolidate the packing.

  3. Periodic domain inversion in x-cut single-crystal lithium niobate thin film

    Science.gov (United States)

    Mackwitz, P.; Rüsing, M.; Berth, G.; Widhalm, A.; Müller, K.; Zrenner, A.

    2016-04-01

    We report the fabrication of periodically poled domain patterns in x-cut lithium niobate thin-film. Here, thin films on insulator have drawn particular attention due to their intrinsic waveguiding properties offering high mode confinement and smaller devices compared to in-diffused waveguides in bulk material. In contrast to z-cut thin film lithium niobate, the x-cut geometry does not require back electrodes for poling. Further, the x-cut geometry grants direct access to the largest nonlinear and electro-optical tensor element, which overall promises smaller devices. The domain inversion was realized via electric field poling utilizing deposited aluminum top electrodes on a stack of LN thin film/SiO2 layer/Bulk LN, which were patterned by optical lithography. The periodic domain inversion was verified by non-invasive confocal second harmonic microscopy. Our results show domain patterns in accordance to the electrode mask layout. The second harmonic signatures can be interpreted in terms of spatially, overlapping domain filaments which start their growth on the +z side.

  4. Tilt order parameters, polarity, and inversion phenomena in smectic liquid crystals.

    Science.gov (United States)

    Karahaliou, P K; Vanakaras, A G; Photinos, D J

    2002-03-01

    The order parameters for the phenomenological description of the smectic-A to smectic-C phase transition are formulated on the basis of molecular symmetry and structure. It is shown that, unless the long molecular axis is an axis of twofold or higher rotational symmetry, the ordering of the molecules in the smectic-C phase gives rise to more than one tilt order parameter and to one or more polar order parameters. The latter describe the indigenous polarity of the smectic-C phase, which is not related to molecular chirality but underlies the appearance of spontaneous polarization in chiral smectics. A phenomenological theory of the phase transition is formulated by means of a Landau expansion in two tilt order parameters (primary and secondary) and an indigenous polarity order parameter. The coupling among these order parameters determines the possibility of sign inversions in the temperature dependence of the spontaneous polarization and of the helical pitch observed experimentally for some chiral smectic-C* materials. The molecular interpretation of the inversion phenomena is examined in the light of this formulation.

  5. Crystal Structure of the Dimeric Oct6 (Pou3fl) POU Domain Bound to Palindromic MORE DNA

    Energy Technology Data Exchange (ETDEWEB)

    R Jauch; S Choo; C Ng; P Kolatkar

    2011-12-31

    POU domains (named after their identification in Pit1, Oct1 unc86) are found in around 15 transcription factors encoded in mammalian genomes many of which feature prominently as key regulators at development bifurcations. For example, the POU III class Octamer binding protein 6 (Oct6) is expressed in embryonic stem cells and during neural development and drives the differentia5tion of myelinated cells in the central and peripheral nervous system. Defects in oct6 expression levels are linked to neurological disorders such as schizophrenia. POU proteins contain a bi-partite DNA binding domain that assembles on various DNA motifs with differentially configured subdomains. Intriguingly, alternative configurations of POU domains on different DNA sites were shown to affect the subsequent recruitment of transcriptional coactivators. Namely, binding of Oct1 to a Palindromic Oct-factor Recognition Element (PORE) was shown to facilitate the recruitment of the OBF1 coactivator whereas More of PORE (MORE) bound Oct1 does not. Moreover, Pit1 was shown to recruit the corepressor N-CoR only when bound to a variant MORE motif with a 2 bp half-site spacing. Therefore, POU proteins are seen as a paradigm for DNA induced allosteric effects on transcription factors modulating their regulatory potential. However, a big unresolved conundrum for the POU class and for most if not all other transcription factor classes is how highly similar proteins regulate different sets of genes causing fundamentally different biological responses. Ultimately, there must be subtle features enabling those factors to engage in contrasting molecular interactions in the cell. Thus, the dissection of the molecular details of the transcription-DNA recognition in general, and the formation of multimeric regulatory complexes, in particular, is highly desirable. To contribute to these efforts they solved the 2.05 {angstrom} crystal structure of Oct6 bound as a symmetrical homodimer to palindromic MORE DNA.

  6. Structural and magnetic properties of inverse opal photonic crystals studied by x-ray diffraction, scanning electron microscopy, and small-angle neutron scattering

    NARCIS (Netherlands)

    Grigoriev, S.V.; Napolskii, K.S.; Grigoryeva, N.A.; Vasilieva, A.V.; Mistonov, A.A.; Chernyshov, D.Y.; Petukhov, A.V.; Belov, D.V.; Eliseev, A.A.; Lukashin, A.V.; Tretyakov, Y.D.; Sinitskii, A.S.; Eckerlebe, H.

    2009-01-01

    The structural and magnetic properties of nickel inverse opal photonic crystal have been studied by complementary experimental techniques, including scanning electron microscopy, wide-angle and small-angle diffraction of synchrotron radiation, and polarized neutrons. The sample was fabricated by ele

  7. Coupling of Ag Nanoparticle with Inverse Opal Photonic Crystals as a Novel Strategy for Upconversion Emission Enhancement of NaYF4: Yb(3+), Er(3+) Nanoparticles.

    Science.gov (United States)

    Shao, Bo; Yang, Zhengwen; Wang, Yida; Li, Jun; Yang, Jianzhi; Qiu, Jianbei; Song, Zhiguo

    2015-11-18

    Rare-earth-ion-doped upconversion (UC) nanoparticles have generated considerable interest because of their potential application in solar cells, biological labeling, therapeutics, and imaging. However, the applications of UC nanoparticles were still limited because of their low emission efficiency. Photonic crystals and noble metal nanoparticles are applied extensively to enhance the UC emission of rare earth ions. In the present work, a novel substrate consisting of inverse opal photonic crystals and Ag nanoparticles was prepared by the template-assisted method, which was used to enhance the UC emission of NaYF4: Yb(3+), Er(3+) nanoparticles. The red or green UC emissions of NaYF4: Yb(3+), Er(3+) nanoparticles were selectively enhanced on the inverse opal substrates because of the Bragg reflection of the photonic band gap. Additionally, the UC emission enhancement of NaYF4: Yb(3+), Er(3+) nanoparticles induced by the coupling of metal nanoparticle plasmons and photonic crystal effects was realized on the Ag nanoparticles included in the inverse opal substrate. The present results demonstrated that coupling of Ag nanoparticle with inverse opal photonic crystals provides a useful strategy to enhance UC emission of rare-earth-ion-doped nanoparticles.

  8. Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel evolutionary path selected by the Lewis epitope.

    Science.gov (United States)

    Hao, Ning; Chen, Yutao; Xia, Ming; Tan, Ming; Liu, Wu; Guan, Xiaotao; Jiang, Xi; Li, Xuemei; Rao, Zihe

    2015-02-01

    Human noroviruses (huNoVs) recognize histo-blood group antigens (HBGAs) as attachment factors, in which genogroup (G) I and GII huNoVs use distinct binding interfaces. The genetic and evolutionary relationships of GII huNoVs under selection by the host HBGAs have been well elucidated via a number of structural studies; however, such relationships among GI NoVs remain less clear due to the fact that the structures of HBGA-binding interfaces of only three GI NoVs with similar binding profiles are known. In this study the crystal structures of the P dimers of a Lewis-binding strain, the GI.8 Boxer virus (BV) that does not bind the A and H antigens, in complex with the Lewis b (Le(b)) and Le(y) antigens, respectively, were determined and compared with those of the three previously known GI huNoVs, i.e. GI.1 Norwalk virus (NV), GI.2 FUV258 (FUV) and GI.7 TCH060 (TCH) that bind the A/H/Le antigens. The HBGA binding interface of BV is composed of a conserved central binding pocket (CBP) that interacts with the β-galactose of the precursor, and a well-developed Le epitope-binding site formed by five amino acids, including three consecutive residues from the long P-loop and one from the S-loop of the P1 subdomain, a feature that was not seen in the other GI NoVs. On the other hand, the H epitope/acetamido binding site observed in the other GI NoVs is greatly degenerated in BV. These data explain the evolutionary path of GI NoVs selected by the polymorphic human HBGAs. While the CBP is conserved, the regions surrounding the CBP are flexible, providing freedom for changes. The loss or degeneration of the H epitope/acetamido binding site and the reinforcement of the Le binding site of the GI.8 BV is a typical example of such change selected by the host Lewis epitope.

  9. Enhanced rare earth photoluminescence in inverse opal photonic crystals and its application for pH sensing

    Science.gov (United States)

    Zhu, Yongsheng; Cui, Shaobo; Wang, Yinhua; Liu, Mao; Lu, Cheng; Mishra, Abhinay; Xu, Wen

    2016-10-01

    Concentration quenching effects of identical rare earth (RE) activator ions and energy transfer (ET) between different RE ions often compromise the photoluminescence (PL) quantum efficiency in RE based luminescence materials. Here, we demonstrate that in NaGd(WO4)2:Tb3+, Eu3+ inverse opal photonic crystals (IOPCs), the suppression of the emission line located in the photonic stop band (PSB) and a dramatic increase of the lifetimes of Eu3+ and Tb3+ ions are observed. More interestingly, the concentration quenching among Eu3+ ions and ET from Tb3+ to Eu3+ is significantly relieved owing to the periodic empty cavity structure of IOPCs. As a consequence, the luminescent quantum efficiency (QE) of the NaGd(WO4)2:Tb3+, Eu3+ IOPCs increases ˜2 times more than that of crushed NaGd(WO4)2:Tb3+, Eu3+ powder. In addition, a reusable pH sensor with good linear response (pH 5-10) has been designed based on the high surface-to-volume ratio, high connectivity, and enhanced luminescence of NaGd(WO4)2:Tb3+, Eu3+IOPCs, which could be applied to the dynamical detection of pH value.

  10. Calix[4]arene supported clusters: a dimer of [Mn(III)Mn(II)] dimers

    DEFF Research Database (Denmark)

    Taylor, Stephanie M; McIntosh, Ruaraidh D; Beavers, Christine M;

    2011-01-01

    Phosphinate ligands allow for the transformation of a calix[4]arene supported [Mn(III)(2)Mn(II)(2)] tetramer cluster motif into an unusual [Mn(III)Mn(II)](2) dimer of dimers; the clusters self-assemble in the crystal to form bi-layer arrays reminiscent of the typical packing of calixarene solvates....

  11. High-quality photonic crystals with a nearly complete band gap obtained by direct inversion of woodpile templates with titanium dioxide

    CERN Document Server

    Marichy, Catherine; Froufe-Pérez, Luis S; Scheffold, Frank

    2015-01-01

    Photonic crystal materials are based on a periodic modulation of the dielectric constant on length scales comparable to the wavelength of light. These materials can exhibit photonic band gaps; frequency regions for which the propagation of electromagnetic radiation is forbidden due to the depletion of the density of states. In order to exhibit a full band gap, 3D PCs must present a threshold refractive index contrast that depends on the crystal structure. In the case of the so-called woodpile photonic crystals this threshold is comparably low, approximately 1.9 for the direct structure. Therefore direct or inverted woodpiles made of high refractive index materials like silicon, germanium or titanium dioxide are sought after. Here we show that, by combining multiphoton lithography and atomic layer deposition, we can achieve a direct inversion of polymer templates into TiO$_{2}$ based photonic crystals. The obtained structures show remarkable optical properties in the near-infrared region with almost perfect sp...

  12. Adventures in Holographic Dimer Models

    Energy Technology Data Exchange (ETDEWEB)

    Kachru, Shamit; /Stanford U., Phys. Dept. /SLAC; Karch, Andreas; /Washington U., Seattle; Yaida, Sho; /Stanford U., Phys. Dept.

    2011-08-12

    We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

  13. The crystal structures of the calcium-bound con-G and con-T[K7gamma] dimeric peptides demonstrate a metal-dependent helix-forming motif.

    Science.gov (United States)

    Cnudde, Sara E; Prorok, Mary; Dai, Qiuyun; Castellino, Francis J; Geiger, James H

    2007-02-14

    Short peptides that have the ability to form stable alpha-helices in solution are rare, and a number of strategies have been used to produce them, including the use of metal chelation to stabilize folding of the backbone. However, no example exists of a structurally well-defined helix stabilized exclusively through metal ion chelation. Conantokins (con)-G and -T are short peptides that are potent antagonists of N-methyl-D-aspartate receptor channels. While con-G exhibits no helicity alone, it undergoes a structural transition to a helical conformation in the presence of a variety of multivalent cations, especially Mg2+ and Ca2+. This complexation also results in antiparallel dimerization of two peptide helices in the presence of Ca2+, but not Mg2+. A con-T variant, con-T[K7gamma], displays very similar behavior. We have solved the crystal structures of both Ca2+/con-G and Ca2+/con-T [K7gamma] at atomic resolution. These structures clearly show the nature of the metal-dependent dimerization and helix formation and surprisingly also show that the con-G dimer interface is completely different from the con-T[K7gamma] interface, even though the metal chelation is similar in the two peptides. This represents a new paradigm in helix stabilization completely independent of the hydrophobic effect, which we define as the "metallo-zipper."

  14. Slow light enhanced near infrared luminescence in CeO{sub 2}: Er{sup 3+}, Yb{sup 3+} inverse opal photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Zhengwen, E-mail: yangzw@kmust.edu.cn; Wu, Hangjun; Li, Jun; Shao, Bo; Qiu, Jianbei; Song, Zhiguo

    2015-08-25

    Highlights: • CeO{sub 2}: Er{sup 3+}, Yb{sup 3+} photonic crystals was prepared. • Near infrared emission in the CeO{sub 2}: Er{sup 3+}, Yb{sup 3+} inverse opal was obtained. • Near infrared emission was enhanced by slow light effect of photonic crystals. - Abstract: The surface plasmon resonances of metal nanoparticles and energy transfer between rare earth ions were used widely to enhance the near infrared emission of rare earth ions. In this paper, a new method for near infrared emission enhancement of rare-earth is reported. The CeO{sub 2}: Er{sup 3+}, Yb{sup 3+} inverse opals with the photonic band gaps at the 500 and 450 nm were prepared by using polystyrene colloidal crystal as templates, and their near infrared emission properties were investigated. The results show that the near infrared emission property of the CeO{sub 2}: Er{sup 3+}, Yb{sup 3+} inverse opals depends on the overlapped extend between the excited light and photonic band gap. The near infrared emission located at the 1540 nm of the CeO{sub 2}: Er{sup 3+}, Yb{sup 3+} inverse opals have been enhanced obviously when the wavelength of the excitation light overlapped with photonic band gaps edge, which is attributed to the slow light effect of photonic crystals. The enhancement of near infrared emission may be important for the development of infrared laser and amplifiers for optical communication.

  15. Energy transfer and visible-infrared quantum cutting photoluminescence modification in Tm-Yb codoped YPO(4) inverse opal photonic crystals.

    Science.gov (United States)

    Wang, Siqin; Qiu, Jianbei; Wang, Qi; Zhou, Dacheng; Yang, Zhengwen

    2015-08-01

    YPO4:  Tm, Yb inverse opal photonic crystals were successfully synthesized by the colloidal crystal templates method, and the visible-infrared quantum cutting (QC) photoluminescence properties of YPO4:  Tm, Yb inverse opal photonic crystals were investigated. We obtained tetragonal phase YPO4 in all the samples when the samples sintered at 950°C for 5 h. The visible emission intensity of Tm3+ decreased significantly when the photonic bandgap was located at 650 nm under 480 nm excitation. On the contrary, the QC emission intensity of Yb3+ was enhanced as compared with the no photonic bandgap sample. When the photonic bandgap was located at 480 nm, the Yb3+ and Tm3+ light-emitting intensity weakened at the same time. We demonstrated that the energy transfer between Tm3+ and Yb3+ is enhanced by the suppression of the red emission of Tm3+. Additionally, the mechanisms for the influence of the photonic bandgap on the energy transfer process of the Tm3+, Yb3+ codoped YPO4 inverse opal are discussed.

  16. Slow photon amplification of gas-phase ethanol photo-oxidation in titania inverse opal photonic crystals

    Science.gov (United States)

    Jovic, Vedran; Idriss, Hicham; Waterhouse, Geoffrey I. N.

    2016-11-01

    Here we describe the successful fabrication of six titania inverse opal (TiO2 IO) photocatalysts with fcc[1 1 1] pseudo photonic band gaps (PBGs) tuned to span the UV-vis region. Photocatalysts were fabricated by a colloidal crystal templating and sol-gel approach - a robust and highly applicable bottom-up scheme which allowed for precise control over the geometric and optical properties of the TiO2 IO photocatalysts. Optical properties of the TiO2 IO thin films were investigated in detail by UV-vis transmittance and reflectance measurements. The PBG along the fcc[1 1 1] direction in the TiO2 IOs was dependent on the inter-planar spacing in the [1 1 1] direction, the incident angle of light and the refractive index of the medium filling the macropores in the IOs, in agreement with a modified Bragg's law expression. Calculated photonic band structures for the photocatalysts revealed a PBG along the Γ → L direction at a/λ ∼ 0.74, in agreement with the experimental optical data. By coupling the low frequency edge of the PBG along the [1 1 1] direction with the electronic absorption edge of anatase TiO2, a two-fold enhancement in the rate of gas phase ethanol photo-oxidation in air was achieved. This enhancement appears to be associated with a 'slow photon' effect that acts to both enhance TiO2 absorption and inhibit spontaneous emission (i.e. suppress electron-hole pair recombination).

  17. Synthesis and Crystal Structure of an Azide Bridged Binuclear Zinc(Ⅱ) Dimer Containing Taurine Schiff Base [Zn2(C8H9N2O3S)2·(N3)2·(H2O)2]2·2H2O

    Institute of Scientific and Technical Information of China (English)

    JIANG Yi-Min; LI Jia-Ming; XIE Fu-Qing; WANG Yan-Fei

    2006-01-01

    The title complex [Zn2L2(N3)2(H2O)2]·2H2O (L = N-(2-pyridylmethylidene) taurine)has been synthesized in a methanol-water solution. The crystal belongs to monoclinic, space group P21/c with a = 15.8064(10), b = 10.5015(5), c = 17.3193(11) (A), β = 111.314(2)°, V = 2678.2(3) (A)3, C16H26N10O10S2Zn2, Mr = 713.33, Z = 4, Dc = 1.769 g/cm3, μ = 2.017 mm-1 and F(000) =1456. The asymmetric unit consists of two half-molecules of the complex and two water molecules.Four N and two O atoms form the coordination environment of each Zn atom, resulting in a distorted octahedral configuration. The two halves of each independent dimer are related by a crystallographic inversion centre, which lies at the centre of the ring formed by two Zn atoms and the coordinating the ac plane.

  18. Neutron scattering in dimers

    DEFF Research Database (Denmark)

    Gudel, H. U.; Furrer, A.; Kjems, Jørgen

    1986-01-01

    Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer excitati......Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer...

  19. Crystal structure of 3-(hydroxymethylchromone

    Directory of Open Access Journals (Sweden)

    Yoshinobu Ishikawa

    2015-07-01

    Full Text Available In the title compound, C10H8O3 (systematic name 3-hydroxymethyl-4H-chromen-4-one, the fused-ring system is slightly puckered [dihedral angle between the rings = 3.84 (11°]. The hydroxy O atom deviates from the heterocyclic ring by 1.422 (1 Å. In the crystal, inversion dimers linked by pairs of O—H...O hydrogen bonds generate R22(12 loops. The dimers are linked by aromatic π–π stacking [shortest centroid–centroid distance = 3.580 (3 Å], and C—H...O hydrogen bonds, generating a three-dimensional network.

  20. Tripod molecules build molecular networks and open-dimer capsules by weak interactions

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Three tripod molecules, tris(2-methoxy-5-nitrobenzyl)phosphine oxide (1), tris(2-butoxy-3-methyl-5-nitrobenzyl)phosphine oxide (2), and tris(3-nitrobenzyl)amine (TNBA), were synthesized and crystallized. The structures of 1, 2, and their comparison (TNBA) were determined by X-ray crystallography. It is noteworthy that compound 1 interacted with adjacent molecules via π-π stacking and C-H···π interactions to yield an open supramolecular network with the porosity P in 8.9%, whereas compound 2 gathered closely to form an open-dimer capsule by sixfold N-O···π and triple C-H···O interactions, which showed a rare example of a stable in, out-invertomer of phosphine inversion existing in open-dimers. A series of columns were built and arranged side by side by these weak interactions. By contrast, TNBA crystallized to form a 2D network maintained by C-H···O and C-H···πinteractions. It seems minor changes of the chemical structure may cause large differences in the crystal structure and interactions in crystal engineering.

  1. Synthesis, structural characterization and antimicrobial activities of diorganotin(IV) complexes with azo-imino carboxylic acid ligand: Crystal structure and topological study of a doubly phenoxide-bridged dimeric dimethyltin(IV) complex appended with free carboxylic acid groups

    Science.gov (United States)

    Roy, Manojit; Roy, Subhadip; Devi, N. Manglembi; Singh, Ch. Brajakishor; Singh, Keisham Surjit

    2016-09-01

    Diorganotin(IV) complexes appended with free carboxylic acids were synthesized by reacting diorganotin(IV) dichlorides [R2SnCl2; R = Me (1), Bu (2) and Ph (3)] with an azo-imino carboxylic acid ligand i.e. 2-{4-hydroxy-3-[(2-hydroxyphenylimino)methyl]phenylazo}benzoic acid in presence of triethylamine. The complexes were characterized by elemental analysis, IR and multinuclear NMR (1H, 13C and 119Sn) spectroscopy. The structure of 1 in solid state has been determined by X-ray crystallography. Crystal structure of 1 reveals that the compound crystallizes in monoclinic space group P21/c and is a dimeric dimethyltin(IV) complex appended with free carboxylic acid groups. In the structure of 1, the Sn(IV) atoms are hexacoordinated and have a distorted octahedral coordination geometry in which two phenoxy oxygen atoms and the azomethine nitrogen atom of the ligand coordinate to each tin atom. One of the phenoxy oxygen atom bridges the two tin centers resulting in a planar Sn2O2 core. Topological analysis is used for the description of molecular packing in 1. Tin NMR spectroscopy study indicates that the complexes have five coordinate geometry around tin atom in solution state. Since the complexes have free carboxylic acids, these compounds could be further used as potential metallo-ligands for the synthesis of other complexes. The synthesized diorganotin(IV) complexes were also screened for their antimicrobial activities and compound 2 showed effective antimicrobial activities.

  2. Synthesis, spectral, electrochemical, crystal structure studies of two novel di-μ-halo-bis[halo(2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline)cadmium(II)] dimer complexes and their thermolysis to nanometal oxides

    Science.gov (United States)

    Warad, Ismail; Abdoh, Muneer; Shivalingegowda, Naveen; Lokanath, Neartur Krishnappagowda; Salghi, Rachid; Al-Nuri, Mohammed; Jodeh, Shehdeh; Radi, Smaail; Hammouti, Belkheir

    2015-11-01

    Two new neutral dimer Cadmium(II) complexes, [Cd2(dmdphphen)2X4] and where X = Cl (complex 1), Br (complex 2), and dmdphphen = 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline, were synthesized and characterized by an elemental analysis, UV-Vis, IR, TG/DTA, CV and single crystal X-ray diffraction. Complex 1 crystallizes in the triclinic system with the space group P-1 with unit cell parameters a = 10.1124(8) Å, b = 10.8875(8) Å, c = 11.5730(9) Å, α = 108.323(3)°, β = 107.010(3)°, γ = 91.260(3)° V = 1147.51(15) Å3 and Z = 1. The Cd(II) ions are located in a slightly distorted square-pyramidal geometry. The complexes exhibit a quasi-reversible one electron response at -570 mV vs. Cp2Fe/Cp2Fe+, which has been assigned Cd(II)/Cd(III) couples. TG/DTA result shows that these complexes are very stable and decomposed through one step reaction. Calcination of Complex 1, revealed the formation of Cubic nanoparticle CdO.

  3. Crystal structure of 4,4'-(ethene-1,2-di-yl)dipyridinium bis-(3-carb-oxy-benzene-sulfonate).

    Science.gov (United States)

    Wu, Jing; Zhu, Long-Guan

    2014-11-01

    In the title mol-ecular salt, C12H12N2 (2+)·2C7H5O5S(-), the complete dication is generated by crystallographic inversion symmetry. In the anion, the sulfonic acid group is deprotonated and the dihedral angle between the planes of the carb-oxy-lic acid group and the benzene ring is 12.41 (11)°. In the crystal, the anions are linked into inversion dimers by pairs of O-H⋯O hydrogen bonds, which generate R 2 (2)(16) loops. The dications link the anion dimers into [10-2] chains via N-H⋯O hydrogen bonds.

  4. Integral equation study of soft-repulsive dimeric fluids

    Science.gov (United States)

    Munaò, Gianmarco; Saija, Franz

    2017-03-01

    We study fluid structure and water-like anomalies of a system constituted by dimeric particles interacting via a purely repulsive core-softened potential by means of integral equation theories. In our model, dimers interact through a repulsive pair potential of inverse-power form with a softened repulsion strength. By employing the Ornstein–Zernike approach and the reference interaction site model (RISM) theory, we study the behavior of water-like anomalies upon progressively increasing the elongation λ of the dimers from the monomeric case (λ =0 ) to the tangent configuration (λ =1 ). For each value of the elongation we consider two different values of the interaction potential, corresponding to one and two length scales, with the aim to provide a comprehensive description of the possible fluid scenarios of this model. Our theoretical results are systematically compared with already existing or newly generated Monte Carlo data: we find that theories and simulations agree in providing the picture of a fluid exhibiting density and structural anomalies for low values of λ and for both the two values of the interaction potential. Integral equation theories give accurate predictions for pressure and radial distribution functions, whereas the temperatures where anomalies occur are underestimated. Upon increasing the elongation, the RISM theory still predicts the existence of anomalies; the latter are no longer observed in simulations, since their development is likely precluded by the onset of crystallization. We discuss our results in terms of the reliability of integral equation theories in predicting the existence of water-like anomalies in core-softened fluids.

  5. Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2

    DEFF Research Database (Denmark)

    Broutin, Isabelle; Jomain, Jean-Baptiste; Tallet, Estelle;

    2010-01-01

    We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely relate...

  6. Reversible dimerization of C60 molecules in the crystal structure of the bis(arene)chromium fulleride [Cr(C7H8)]2C60.

    Science.gov (United States)

    Hönnerscheid, Andreas; Dinnebier, Robert; Jansen, Martin

    2002-06-01

    Bis(toluene)chromium fulleride, [Cr(C(7)H(8))(2)]C(60), has been synthesized as a black microcrystalline powder from C(60) and [Cr(C(7)H(8))(2)] in toluene. [Cr(C(7)H(8))(2)]C(60) is an ionic compound in which the fullerene is negatively charged and the bis(toluene)chromium molecule positively charged. At T = 250 K a reversible first-order phase transition from a primitive cubic high-temperature phase to a triclinic low-temperature phase occurs. The high-temperature phase [Pm3 macro m, a = 9.9840 (1) A, T = 295 K] is composed of dynamically disordered fulleride anions and bis(toluene)chromium(I) cations in a CsCl-type arrangement. The triclinic low-temperature modification [P1 macro, a = 13.6414 (8), b = 13.8338 (7), c = 13.8548 (7) A, alpha = 91.830 (3), beta = 116.776 (2), gamma = 119.333 (2) degrees, T = 235 K] consists of ordered C(60) dimers and two crystallographically distinct bis(toluene)chromium entities.

  7. Influence of normal and inverse upconversion processes on the continuous wave operation of the Er3+ 3 µm crystal laser

    NARCIS (Netherlands)

    Pollnau, M.; Lüthy, W.; Weber, H.P.; Chai, Bruce H.T.; Fan, Tso Yee

    1994-01-01

    A computer simulation of the dynamics of the Er3+ 3 µm cw crystal laser considering the full rate-equation scheme up to the 4F7/2 level has been performed. The influence of the important system parameters on lasing and the interaction of these parameters has been clarified with multiple-parameter va

  8. Synthesis, Dimeric Crystal Structure, and Biological Activities of N-(4-Methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N-(2-trifluoromethyl-phenyl)-guanidine

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The title compound, N-(4-methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N′-(2-trifluoromethyl-phenyl)-guanidine, was synthesized and its structure was confirmed by using IR, MS, 1H NMR, and elemental analysis. The single crystal structure of the title compound was determined by X-ray diffraction. The preliminary biological test showed that the synthesized compound has a weak herbicidal activity.

  9. Disorder of the dimeric TCNQ-TCNQ unit in the crystal structure of [Ni(bpy)3]2(TCNQ-TCNQ)(TCNQ)2·6H2O (TCNQ is 7,7,8,8-tetra-cyano-quinodi-methane).

    Science.gov (United States)

    Černák, Juraj; Kuchár, Juraj; Hegedüs, Michal

    2017-01-01

    Crystallization from an aqueous methanol system composed of Ni(NO3)2, 2,2'-bipyridine (bpy) and LiTCNQ (TCNQ is 7,7,8,8-tetra-cyano-quinodi-methane) in a 1:3:2 molar ratio yielded single crystals of bis-[tris-(2,2'-bi-pyridine-κ(2)N,N')nickel(II)] bis-(7,7,8,8-tetra-cyano-quinodi-methane radical anion) bi[7,7,8,8-tetra-cyano-quino-dimethanide] hexa-hydrate, [Ni(C10H8N2)3]2(C24H8N8)(C12H4N4)2·6H2O or [Ni(bpy)3]2(TCNQ-TCNQ)(TCNQ)2·6H2O. The crystal structure comprises [Ni(bpy)3](2+) complex cations, two centrosymmetric crystallographically independent TCNQ (·-) anion radicals with π-stacked exo groups, and an additional dimeric TCNQ-TCNQ unit which comprises 75.3 (9)% of a σ-dimerized (TCNQ-TCNQ)(2-) dianion and 24.7 (9)% of two TCNQ(·-) anion radicals with tightly π-stacked exo groups. The title complex represents the first example of an Ni(II) complex containing a σ-dimerized (TCNQ-TCNQ)(2-) dianion. Disordered solvent water mol-ecules present in the crystal structure participate in hydrogen-bonding inter-actions.

  10. Synthesis of cadmium complexes of 4'-chloro-terpyridine: From discrete dimer to 1D chain polymer, crystal structure and antibacterial activity

    Indian Academy of Sciences (India)

    Lotfali Saghatforoush; Laura Valencia Matarranz; Firoozeh Chalabian; Shahriare Ghammamy; Fatemeh Katouzian

    2012-05-01

    Two new Cd(II) complexes with the ligand 4'-chloro-2,2':6',2"-terpyridine (Cltpy), [Cd(Cltpy)(N3)(CH3COO)], 1, and [Cd(Cltpy)(NCS)(CH3COO)], 2, have been synthesized and characterized by CHN elemental analyses, 1HNMR-, 13C NMR-, IR spectroscopy and structurally analysed by X-ray singlecrystal diffraction. The single crystal X-ray analyses show that the coordination number in these complexes is seven with three terpyridine (Cltpy) N-donor atoms, two acetate oxygens and two anionic bridged ligands. The crystal structure of 2 comprises a one-dimensional polymeric network bridged by NCS− anions. The antibacterial activities of Cltpy and its Cd(II) complexes are tested against different bacteria. Both complexes have shown good activity against all the tested bacteria. Against Klebsiella pneumonia and Staphylococcus aureus, antibacterial activity of complexes is higher than Cltpy ligand. The higher activity of complexes may be explained on the basis of chelation theory.

  11. Crystal structure of N-(3-chloro-1-methyl-1H-indazol-5-yl-4-methoxybenzenesulfonamide

    Directory of Open Access Journals (Sweden)

    Hakima Chicha

    2014-09-01

    Full Text Available In the title compound, C15H14ClN3O3S, the dihedral angle between the planes of the indazole ring system (r.m.s. deviation = 0.007 Å and the benzene ring is 89.05 (7°. The methoxy C atom deviates from its attached ring by 0.196 (3 Å. In the crystal, inversion dimers linked by pairs of N—H...O hydrogen bonds generate R22(8 loops. The dimers are connected into [010] chains by C—H...O interactions.

  12. Crystal structure of S-octyl (E-3-(4-methoxybenzylidenedithiocarbazate

    Directory of Open Access Journals (Sweden)

    M. S. Begum

    2015-04-01

    Full Text Available As already observed in similar molecules, the dithiocarbazate group in the title compound, C17H26N2OS2, adopts an EE configuration with respect to the C=N bond of the benzylidene moiety. In the crystal, molecules are connected into inversion dimers by pairs of N—H...S hydrogen bonds. The dimers are linked by weak π–π interactions, with centroid-to-centroid distances of 3.723 (11 Å, forming chains parallel to [110].

  13. Crystal structure of 1,3-dicyclohexyl-1-[3-(pyren-1-ylpropanoyl]urea

    Directory of Open Access Journals (Sweden)

    Edgar González-Juárez

    2015-10-01

    Full Text Available In the title compound, C33H38N2O2, each of the cyclohexyl rings adopts a chair conformation. The two planes involving carbonyl groups, C—(C=O—N and N—(C=O—N, are oriented at a dihedral angle of 62.28 (10°. In the crystal, two neighboring molecules are linked by a pair of N—H...O interactions, generating an inversion dimer. The dimers are interconnected by C—H...O hydrogen bonds into a supramolecular chain along the a-axis direction.

  14. Studies on Inverse Opal and Two-Dimensional Nonlinear Photonic Crystals%反Opal及二维非线性光子晶体的研究

    Institute of Scientific and Technical Information of China (English)

    倪培根; 程丙英; 张道中

    2006-01-01

    通过向SiO2 Opal模板中填充钛酸乙酯制备TiO2光子晶体,观测到光子晶体带隙位置的移动达62nm,并发现光子晶体的有序度随填充率的升高而下降.向聚苯乙烯Opal模板中填充钛酸乙酯,制备成当时填充率最高、带隙最短的紫外波段TiO2反Opal光子晶体(中心波长~380nm),并根据测量的其透射谱估算出其填充率约为12%,即Opal模板孔隙的50%被填充.本文还对二维PPLN光子晶体进行了研究.建立了一套高压极化装置和电压数据采集装置,通过外加电场极化法成功制备出了具有正方形和矩形两种晶格形状二维PPLN光子晶体.利用二维PPLN的二阶准相位匹配,测量了其对1.064μm激光的二次谐波转换效率,并研究了晶体的温度、激光的入射角度及占空比对二次谐波转换效率的影响.利用矩形晶格实现了多方向、多波长倍频高效输出.%In this paper, we report some results on inverse opal photonic crystal and two-dimensional periodically poled lithium niobate photonic crystal. First, the process of infiltrating TiO2 into SiO2 Opal was systematically studied. Because of the infiltration of TiO2, the gap of SiO2 Opal was shifted to longer wavelength and a maximum shift of 62nm was observed. Furthermore, an inverse TiO2 Opal with larger filling fraction, ~ 12%, was fabricated, whose band gap in the Γ-L direction is located in the ultraviolet region ( ~ 380nm). Then two-dimensional nonlinear photonic crystals of lithium nlobate with uniform square lattices were fabricated by applying external electric fields. The variations of second-harmonic output with crystal temperatures, incident angles and reversed duty cycles were measured. Red, yellow,green, blue, and violet coherent radiations were generated in the nonlinear photonic crystal with rectangular lattice in the collinearly and non-collinearly quasi-phase matching geometries. The results showed that two-dimensional nonlinear photonic crystal

  15. Synthesis, Crystal Structure and Thermal Stability of a Saturated Dimeric Ce(Ⅲ)-chelated Complex Based on Benzoate and 1,10-Phenanthroline Ligands

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The title complex, [Ce(BA)3phen]2 (BA = benzoate, phen = 1,10-phenanthroline),was prepared by the reaction of Ce(NO3)3·6H2O, benzoic acid and 1,10-phenanthroline. The complex was characterized by single-crystal X-ray diffraction, elemental analysis, IR spectra and TG-DTG techniques. The results show that the crystal is of triclinic, space group P(1) with a =10.912(2), b = 11.962(3), c = 12.474(3)(A), a = 104.889(3), β = 93.523(3), γ = 113.332(3)°,C66H46Ce2N4O12, Mr = 1366.90, V= 1420.2(6) (A)3, Z = 1, Dc = 1.598 g/cm3,μ = 1.652 mm-1, S =1.024 and F(000) = 682. The final R = 0.0391 and wR = 0.0947 for 4878 observed reflections with I > 2σ(1). The structure of the title complex consists of two Ce(C6H5COO)3(C12H8N2) units,forming a binuclear molecule. Each Ce(Ⅲ) is coordinated by two O atoms of one bidentate chelating carboxylate group, five O atoms of two bidentate bridging and two tridentate chelating-bridging carboxylate groups, and two N atoms of one 1,10-phenanthroline molecule to complete a distorted monocapped square antiprism geometry. Its thermogravimetric analysis was determined by TG-DTG techniques.

  16. Protein dimerization. Inside job.

    Science.gov (United States)

    Metzger, H

    1994-04-01

    In a sophisticated combination of genetic engineering and organic synthesis, a general method for dimerizing recombinant intracellular proteins has been devised; the usefulness of the method should now be testable.

  17. Calcium-dependent Dimerization of Human Soluble Calcium Activated Nucleotidase: Characterization of the Dimer Interface

    Energy Technology Data Exchange (ETDEWEB)

    Yang,M.; Horii, K.; Herr, A.; Kirley, T.

    2006-01-01

    Mammals express a protein homologous to soluble nucleotidases used by blood-sucking insects to inhibit host blood clotting. These vertebrate nucleotidases may play a role in protein glycosylation. The activity of this enzyme family is strictly dependent on calcium, which induces a conformational change in the secreted, soluble human nucleotidase. The crystal structure of this human enzyme was recently solved; however, the mechanism of calcium activation and the basis for the calcium-induced changes remain unclear. In this study, using analytical ultracentrifugation and chemical cross-linking, we show that calcium or strontium induce noncovalent dimerization of the soluble human enzyme. The location and nature of the dimer interface was elucidated using a combination of site-directed mutagenesis and chemical cross-linking, coupled with crystallographic analyses. Replacement of Ile{sup 170}, Ser{sup 172}, and Ser{sup 226} with cysteine residues resulted in calcium-dependent, sulfhydryl-specific intermolecular cross-linking, which was not observed after cysteine introduction at other surface locations. Analysis of a super-active mutant, E130Y, revealed that this mutant dimerized more readily than the wild-type enzyme. The crystal structure of the E130Y mutant revealed that the mutated residue is found in the dimer interface. In addition, expression of the full-length nucleotidase revealed that this membrane-bound form can also dimerize and that these dimers are stabilized by spontaneous oxidative cross-linking of Cys{sup 30}, located between the single transmembrane helix and the start of the soluble sequence. Thus, calcium-mediated dimerization may also represent a mechanism for regulation of the activity of this nucleotidase in the physiological setting of the endoplasmic reticulum or Golgi.

  18. Crystal structure of 2-(2,3-dimethoxynaphthalen-1-yl-3-hydroxy-6-methoxy-4H-chromen-4-one

    Directory of Open Access Journals (Sweden)

    Seunghyun Ahn

    2015-11-01

    Full Text Available In the title compound, C22H18O6, the dimethoxy-substituted naphthalene ring system is twisted relative to the 4H-chromenon skeleton by 88.96 (3°. The two methoxy substituents are tilted from the naphthalene ring system by 1.4 (4 and 113.0 (2°, respectively. An intramolecular O—H...O hydrogen bond closes an S(5 ring motif. In the crystal, pairs of O—H...O hydrogen bonds form inversion dimers with R22(10 loops and C—H...O interactions connect the dimers into [010] chains.

  19. DLTS study of the oxygen dimer formation kinetics in silicon

    Science.gov (United States)

    Yarykin, Nikolai; Weber, Jörg

    2009-12-01

    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480∘ C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  20. DLTS study of the oxygen dimer formation kinetics in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Yarykin, Nikolai, E-mail: nay@iptm.r [Institute of Microelectronics Technology RAS, 142432 Chernogolovka, Moscow Region (Russian Federation); Weber, Joerg [Technische Universitaet Dresden, 01062 Dresden (Germany)

    2009-12-15

    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480 deg. C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  1. Crystal structure of 2-pentyloxybenzamide

    Directory of Open Access Journals (Sweden)

    Bernhard Bugenhagen

    2014-10-01

    Full Text Available In the title molecule, C12H17NO2, the amide NH2 group is oriented toward the pentyloxy substituent and an intramolecular N—H...O hydrogen bond is formed with the pentyloxy O atom. The benzene ring forms dihedral angles of 2.93 (2 and 5.60 (2° with the amide group and the pentyloxy group mean planes, respectively. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with their molecular planes parallel, but at an offset of 0.45 (1 Å to each other. These dimers are ordered into two types of symmetry-related columns extended along the a axis, with the mean plane of one set of dimers in a column approximately parallel to (121 and the other in a column approximately parallel to (1-21. The two planes form a dihedral angle of 85.31 (2°, and are linked via C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional framework structure.

  2. Highly improved upconversion luminescence in NaGd(WO₄)₂:Yb³⁺/Tm³⁺ inverse opal photonic crystals.

    Science.gov (United States)

    Wang, Yunfeng; Xu, Wen; Cui, Shaobo; Xu, Sai; Yin, Ze; Song, Hongwei; Zhou, Pingwei; Liu, Xiaoyan; Xu, Lin; Cui, Haining

    2015-01-28

    The upconversion luminescence (UCL) of rare earth (RE) ions doped nanomaterials has attracted extensive interest because of its wide and great potential applications. However, the lower UCL efficiency is still an obstacle for real applications. Photonic modulation is a novel way to improve the efficiency of UCL. In this work, NaGd(WO4)2:Yb(3+)/Tm(3+) inverse opal photonic crystals (IOPCs) were fabricated through the polymethylmethacrylate (PMMA) template and the modification of the IOPC structure on the emission spectra and dynamics of Tm(3+) ions was systemically studied. It is interesting to observe that in the IOPCs, the high-order UCL (1)D2-(3)H6/(3)F4 was relatively enhanced. At the same time, the local thermal effect induced by laser irradiation was suppressed. Furthermore, the overall intensity ratio of visible UCL to near-infrared (NIR) down-conversion luminescence (DCL) was 2.8-8 times improved than that of the grinded reference (REF) and independent of the photonic stop band (PSB). The studies on UCL dynamics indicated that the nonradiative transition rate of Tm(3+) was considerably suppressed. The facts above indicated that in the IOPCs the UCL efficiency of Tm(3+) was largely improved due to the periodic macroporous structure.

  3. Revealing the consequences and errors of substance arising from the inverse confusion between the crystal (ligand) field quantities and the zero-field splitting ones

    Energy Technology Data Exchange (ETDEWEB)

    Rudowicz, Czesław, E-mail: crudowicz@zut.edu.pl [Institute of Physics, West Pomeranian University of Technology, Al. Piastów 17, 70-310 Szczecin (Poland); Karbowiak, Mirosław [Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław (Poland)

    2015-01-01

    Survey of recent literature has revealed a doubly-worrying tendency concerning the treatment of the two distinct types of Hamiltonians, namely, the physical crystal field (CF), or equivalently ligand field (LF), Hamiltonians and the zero-field splitting (ZFS) Hamiltonians, which appear in the effective spin Hamiltonians (SH). The nature and properties of the CF (LF) Hamiltonians have been mixed up in various ways with those of the ZFS Hamiltonians. Such cases have been identified in a rapidly growing number of studies of the transition-ion based systems using electron magnetic resonance (EMR), optical spectroscopy, and magnetic measurements. These findings have far ranging implications since these Hamiltonians are cornerstones for interpretation of magnetic and spectroscopic properties of the single transition ions in various crystals or molecules as well as the exchange coupled systems (ECS) of transition ions, e.g. single molecule magnets (SMM) or single ion magnets (SIM). The seriousness of the consequences of such conceptual problems and related terminological confusions has reached a level that goes far beyond simple semantic issues or misleading keyword classifications of papers in journals and scientific databases. The prevailing confusion, denoted as the CF=ZFS confusion, pertains to the cases of labeling the true ZFS quantities as purportedly the CF (LF) quantities. Here we consider the inverse confusion between the CF (LF) quantities and the SH (ZFS) ones, denoted the ZFS=CF confusion, which consists in referring to the parameters (or Hamiltonians), which are the true CF (LF) quantities, as purportedly the ZFS (or SH) quantities. Specific cases of the ZFS=CF confusion identified in recent textbooks, reviews and papers, especially SMM- and SIM-related ones, are surveyed and the pertinent misconceptions are clarified. The serious consequences of the terminological confusions include misinterpretation of data from a wide range of experimental techniques and

  4. Superbackscattering nanoparticle dimers.

    Science.gov (United States)

    Liberal, Iñigo; Ederra, Iñigo; Gonzalo, Ramón; Ziolkowski, Richard W

    2015-07-10

    The theory and design of superbackscattering nanoparticle dimers are presented. We analytically derive the optimal configurations and the upper bound of their backscattering cross-sections. In particular, it is demonstrated that electrically small nanoparticle dimers can enhance the backscattering by a factor of 6.25 with respect to single dipolar particles. We demonstrate that optimal designs approaching this theoretical limit can be found by using a simple circuit model. The study of practical implementations based on plasmonic and high-permittivity particles has been also addressed. Moreover, the numerical examples reveal that the dimers can attain close to a fourfold enhancement of the single nanoparticle response even in the presence of high losses.

  5. Multicritical tensor models and hard dimers on spherical random lattices

    CERN Document Server

    Bonzom, Valentin

    2012-01-01

    Random tensor models which display multicritical behaviors in a remarkably simple fashion are presented. They come with entropy exponents \\gamma = (m-1)/m, similarly to multicritical random branched polymers. Moreover, they are interpreted as models of hard dimers on a set of random lattices for the sphere in dimension three and higher. Dimers with their exclusion rules are generated by the different interactions between tensors, whose coupling constants are dimer activities. As an illustration, we describe one multicritical point, which is interpreted as a transition between the dilute phase and a crystallized phase, though with negative activities.

  6. Superbackscattering Nanoparticle Dimers

    CERN Document Server

    Liberal, Iñigo; Gonzalo, Ramón; Ziolkoski, Richard W

    2015-01-01

    The theory and design of superbackscattering nanoparticle dimers are presented. We analytically derive the optimal configurations and the upper bound of their backscattering cross-sections. In particular, it is demonstrated that electrically small nanoparticle dimers can enhance the backscattering by a factor of 6.25 with respect to single dipolar particles. We demonstrate that optimal designs approaching this theoretical limit can be found by using a simple circuit model. The study of practical implementations based on plasmonic and high-permittivity particles reveal that fourfold enhancement factors might be attainable even with realistic losses.

  7. Disorder of the dimeric TCNQ–TCNQ unit in the crystal structure of [Ni(bpy)3]2(TCNQ–TCNQ)(TCNQ)2·6H2O (TCNQ is 7,7,8,8-tetra­cyano­quinodi­methane)

    Science.gov (United States)

    Černák, Juraj; Kuchár, Juraj; Hegedüs, Michal

    2017-01-01

    Crystallization from an aqueous methanol system composed of Ni(NO3)2, 2,2′-bipyridine (bpy) and LiTCNQ (TCNQ is 7,7,8,8-tetra­cyano­quinodi­methane) in a 1:3:2 molar ratio yielded single crystals of bis­[tris­(2,2′-bi­pyridine-κ2 N,N′)nickel(II)] bis­(7,7,8,8-tetra­cyano­quinodi­methane radical anion) bi[7,7,8,8-tetra­cyano­quino­dimethanide] hexa­hydrate, [Ni(C10H8N2)3]2(C24H8N8)(C12H4N4)2·6H2O or [Ni(bpy)3]2(TCNQ–TCNQ)(TCNQ)2·6H2O. The crystal structure comprises [Ni(bpy)3]2+ complex cations, two centrosymmetric crystallographically independent TCNQ·− anion radicals with π-stacked exo groups, and an additional dimeric TCNQ–TCNQ unit which comprises 75.3 (9)% of a σ-dimerized (TCNQ–TCNQ)2− dianion and 24.7 (9)% of two TCNQ·− anion radicals with tightly π-stacked exo groups. The title complex represents the first example of an NiII complex containing a σ-dimerized (TCNQ–TCNQ)2− dianion. Disordered solvent water mol­ecules present in the crystal structure participate in hydrogen-bonding inter­actions. PMID:28083123

  8. Crystal structure of 2-chloro-1-(6-fluoro-3,4-dihydro-2H-chromen-2-ylethanone

    Directory of Open Access Journals (Sweden)

    Zheng Shen

    2014-10-01

    Full Text Available In the title molecule, C11H10ClFO2, the benzene ring, the F atom and the O atom of the dihydropyran ring are essentially coplanar, with an r.m.s. deviation of 0.007 Å. The dihydropyran ring is in a half-chair conformation. In the crystal, molecules are linked by pairs of weak C—H...π hydrogen bonds, forming inversion dimers.

  9. Alkane dimers interaction

    DEFF Research Database (Denmark)

    Ferrighi, Lara; Madsen, Georg Kent Hellerup; Hammer, Bjørk

    2010-01-01

    The interaction energies of a series of n-alkane dimers, from methane to decane, have been investigated with Density Functional Theory (DFT), using the MGGA-M06-L density functional. The results are compared both to the available wavefunction-based values as well as to dispersion corrected DFT...

  10. Crystal structure of 2-benzylamino-4-(4-bromophenyl-6,7-dihydro-5H-cyclopenta[b]pyridine-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    R. A. Nagalakshmi

    2015-03-01

    Full Text Available In the title compound C22H18BrN3, the cyclopentane ring adopts an envelope conformation with the central methylene C atom as the flap. The dihedral angles between the central pyridine ring and the pendant benzyl and and bromobenzene rings are 82.65 (1 and 47.23 (1°, respectively. In the crystal, inversion dimers linked by pairs of N—H...Nn (n = nitrile hydrogen bonds generate R22(12 loops. These dimers are linked by weak π–π interactions [centroid–centroid distance = 3.7713 (14 Å] into a layered structure.

  11. Crystal structure of 4-[(E-(4-chlorobenzylideneamino]-3-(2-methylbenzyl-1H-1,2,4-triazole-5(4H-thione

    Directory of Open Access Journals (Sweden)

    Kamni

    2014-09-01

    Full Text Available In the title molecule, C17H15ClN4S, the benzene rings form dihedral angles of 16.6 (1 and 77.2 (1° with the triazole ring. The dihedral angle between the benzene rings is 86.6 (1°. In the crystal, pairs of N—H...S hydrogen bonds form inversion dimers with graph-set notation R22(8. Weak C—H...S hydrogen bonds link these dimers into layers parallel to (100. Weak intramolecular C—H...S and C—H...N contacts are observed.

  12. Crystal structure of a chloride-bridged copper(II) dimer: piperazine-1,4-dium bis­(di-μ-chlorido-bis[(4-carboxypyridine-2-carboxyl­ato-κ2 N,O 2)chlorido­cuprate(II)

    Science.gov (United States)

    Inah, Bassey Enyi; Adhikary, Amit

    2017-01-01

    Crystals of a new dimeric chloride-bridged cuprate(II) derived from pyridine-2,4-di­carb­oxy­lic acid were obtained solvothermally in the presence of piperazine and hydro­chloric acid. The crystal structure determination of the title salt, (C4H12N2)[Cu2(C7H4NO4)2Cl4], revealed one of the carboxyl groups of the original pyridine-2,4-di­carb­oxy­lic acid ligand to be protonated, whereas the other is deprotonated and binds together with the pyridine N atom to the CuII atom. The coordination environment of the CuII atom is distorted square-pyramidal. One of the chloride ligands bridges two metal cations to form a centrosymmetric dimer with two different Cu—Cl distances of 2.2632 (8) and 2.7853 (8) Å, whereby the longer distance is associated with the apical ligand. The remaining chloride ligand is terminal at one of the basal positions, with a distance of 2.2272 (9) Å. In the crystal, the dimers are linked by inter­molecular O—H⋯O hydrogen bonds, together with N—H⋯O and N—H⋯Cl inter­actions involving the centrosymmetric organic cation, into a three-dimensional supra­molecular network. Further but weaker C—H⋯O and C—H⋯Cl inter­actions consolidate the packing. PMID:28217352

  13. Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

    KAUST Repository

    Han, Yu

    2016-03-31

    The fabrication of asymmetric monometallic nanocrystals with novel properties for plasmonics, nanophotonics and nanoelectronics. Asymmetric monometallic plasmonic nanocrystals are of both fundamental synthetic challenge and practical significance. In an example, a thiol-ligand mediated growth strategy that enables the synthesis of unprecedented Au Nanorod-Au Nanoparticle (AuNR-AuNP) dimers from pre-synthesized AuNR seeds. Using high-resolution electron microscopy and tomography, crystal structure and three-dimensional morphology of the dimer, as well as the growth pathway of the AuNP on the AuNR seed, was investigated for this example. The dimer exhibits an extraordinary broadband optical extinction spectrum spanning the UV, visible, and near infrared regions (300 - 1300 nm). This unexpected property makes the AuNR-AuNP dimer example useful for many nanophotonic applications. In two experiments, the dimer example was tested as a surface- enhanced Raman scattering (SERS) substrate and a solar light harvester for photothermal conversion, in comparison with the mixture of AuNR and AuNP. In the SERS experiment, the dimer example showed an enhancement factor about 10 times higher than that of the mixture, when the excitation wavelength (660 nm) was off the two surface plasmon resonance (SPR) bands of the mixture. In the photothermal conversion experiment under simulated sunlight illumination, the dimer example exhibited an energy conversion efficiency about 1.4 times as high as that of the mixture.

  14. Family C 7TM receptor dimerization and activation

    DEFF Research Database (Denmark)

    Bonde, Marie Mi; Sheikh, Søren P; Hansen, Jakob Lerche

    2006-01-01

    The family C seven transmembrane (7TM) receptors constitutes a small and especially well characterized subfamily of the large 7TM receptor superfamily. Approximately 50% of current prescription drugs target 7TM receptors, this biologically important family represents the largest class of drug......-targets today. It is well established that family C 7TM receptors form homo- or hetero-dimers on the cell surface of living cells. The large extra-cellular domains (ECD) have been crystallized as a dimer in the presence and absence of agonist. Upon agonist binding, the dimeric ECD undergoes large conformational...... to be fully defined. This review presents the biochemical support for family C 7TM receptor dimerization and discusses its importance for receptor biosynthesis, surface expression, ligand binding and activation, since lessons learnt here may well be applicable to the whole superfamily of 7TM receptors....

  15. REVISITING THE PUTATIVE TCR Cα DIMERIZATION MODEL THROUGH STRUCTURAL ANALYSIS

    Directory of Open Access Journals (Sweden)

    Jia-huai eWang

    2013-01-01

    Full Text Available Despite major advances in T cell receptor (TCR biology and structure, how peptide-MHC complex (pMHC ligands trigger αβ TCR activation remains unresolved. Two views exist. One model postulates that monomeric TCR-pMHC ligation events are sufficient while a second proposes that TCR-TCR dimerization in cis via Cα domain interaction plus pMHC binding is critical. We scrutinized 22 known TCR/pMHC complex crystal structures, and did not find any predicted molecular Cα-Cα contacts in these crystals that would allow for physiological TCR dimerization. Moreover, the presence of conserved glycan adducts on the outer face of the Cα domain preclude the hypothesized TCR dimerization through the Cα domain. Observed functional consequences of Cα mutations are likely indirect, with TCR microclusters at the immunological synapse driven by TCR transmembrane/cytoplasmic interactions via signaling molecules, scaffold proteins and/or cytoskeletal elements.

  16. Dihydroxo-bridged dimeric Cu(II) system containing sandwiched non-coordinating phenylacetate anion: Crystal structure, spectroscopic, anti-bacterial, anti-fungal and DNA-binding studies of [(phen)(H2O)Cu(OH)2Cu(H2O)(phen)]2L.6H2O: (HL = phenylacetic acid; phen = 1,10-phenanthroline)

    Science.gov (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Shah, Naseer Ali

    2017-09-01

    This paper reports the synthesis, X-ray crystal structure, DNA-binding, antibacterial and antifungal studies of a rare dihydroxo-bridged dinuclear copper(II) complex including 1,10-phenanthroline (Phen) ligands and phenylacetate (L) anions, [Cu2(Phen)2(OH)2(H2O)2].2L.6H2O. Structural data revealed distorted square-pyramidal geometry for each copper(II) atom with the basal plane formed by the two nitrogen atoms of the phenantroline ligand and the oxygen atoms of two bridging hydroxyl groups. The apical positions are filled by the oxygen atom from a water molecule. This forms a centrosymmetric cationic dimer where the uncoordinated phenylacetate ligands serve to balance the electrical charge. The dimers interact by means of hydrogen bonds aided by the coordinated as well as uncoordinated water molecules and phenyl-acetate moieties in the crystal lattice. The binding ability of the complex with salmon sperm DNA was determined using cyclic voltammetry and absorption spectroscopy yielding binding constants 2.426 × 104 M-1 and 1.399 × 104 M-1, respectively. The complex was screened against two Gram-positive (Micrococcus luteus and Bacillus subtilis) and one Gram-negative (Escherichia coli) bacterial strains exhibiting significant activity against all the three strains. The complex exhibited significant, moderate and no activity against fungal strains Mucor piriformis, Helminthosporium solani and Aspergillus Niger, respectively. These preliminary tests indicate the competence of the complex towards the development of a potent biological drug.

  17. Synthesis and Structural Study of the (N,N,N′,N′-TetraethylethylenediamineCdFe(CO4 Dimer

    Directory of Open Access Journals (Sweden)

    Torsten Kolb

    2014-01-01

    Full Text Available The new [(teedaCdFe(CO4]2 complex has been isolated from the reaction of [(NH32CdFe(CO4]n with tetraethylethylenediamine. Unlike previous structural reports of ligand adducts of [L2CdFe(CO4]x complexes, which have all been trimeric species composed of six-membered Cd3Fe3 rings, the teeda complex crystallized as a dimer, analogous to [(2,2-bpyZnFe(CO4]2. As in the zinc dimer, significant distortion arises from steric interactions between the axial carbonyl ligands on opposing iron centers. The complex sits on an inversion center, leading to two independent Cd–Fe distances, 2.7244(6 and 2.7433(6 Å, and crystallizes in the monoclinic space group P21/a with a = 14.8546(2 Å, b = 15.1647(3 Å, c = 15.5252(3 Å, β = 90.9517(12°, and Dcalc = 1.719 g/cm3 at 150(1 K.

  18. The acrylonitrile dimer ion

    Science.gov (United States)

    Ervasti, Henri K.; Jobst, Karl J.; Burgers, Peter C.; Ruttink, Paul J. Ae; Terlouw, Johan K.

    2007-04-01

    Large energy barriers prohibit the rearrangement of solitary acrylonitrile ions, CH2CHCN+, into their more stable hydrogen-shift isomers CH2CCNH+ or CHCH-CNH+. This prompted us to examine if these isomerizations occur by self-catalysis in acrylonitrile dimer ions. Such ions, generated by chemical ionization experiments of acrylonitrile with an excess of carbon dioxide, undergo five dissociations in the [mu]s time frame, as witnessed by peaks at m/z 53, 54, 79, 80 and 105 in their metastable ion mass spectrum. Collision experiments on these product ions, deuterium labeling, and a detailed computational analysis using the CBS-QB3 model chemistry lead to the following conclusions: (i) the m/z 54 ions are ions CH2CHCNH+ generated by self-protonation in ion-dipole stabilized hydrogen-bridged dimer ions [CH2CHCN...H-C(CN)CH2]+ and [CH2CHCN...H-C(H)C(H)CN]+; the proton shifts in these ions are associated with a small reverse barrier; (ii) dissociation of the H-bridged ions into CH2CCNH+ or CHCH-CNH+ by self-catalysis is energetically feasible but kinetically improbable: experiment shows that the m/z 53 ions are CH2CHCN+ ions, generated by back dissociation; (iii) the peaks at m/z 79, 80 and 105 correspond with the losses of HCN, C2H2 and H, respectively. The calculations indicate that these ions are generated from dimer ions that have adopted the (much more stable) covalently bound "head-to-tail" structure [CH2CHCN-C(H2)C(H)CN]+; experiments indicate that the m/z 79 (C5H5N) and m/z 105 (C6H6N2) ions have linear structures but the m/z 80 (C4H4N2) ions consist of ionized pyrimidine in admixture with its stable pyrimidine-2-ylidene isomer. Acrylonitrile is a confirmed species in interstellar space and our study provides experimental and computational evidence that its dimer radical cation yields the ionized prebiotic pyrimidine molecule.

  19. Crystal structure of 3,4′-diphenyl-3′-p-tolyl-4′H-spiro[indan-2,5′-[1,2]oxazol]-1-one

    Directory of Open Access Journals (Sweden)

    Asmae Mahfoud

    2015-11-01

    Full Text Available In the title compound, C30H23NO2, the five-membered rings are both in envelope conformations with the same spiro C atom as the flap. The benzene ring and the two phenyl rings are inclined to the mean plane of the indene ring system by 83.98 (8, 81.46 (8 and 72.31 (7°. In the crystal, molecules are linked by pairs of C—H...O hydrogen bonds into inversion dimers. The dimers are further connected by C—H...N interactions, forming layers parallel to (10-1.

  20. Tetramerization reinforces the dimer interface of MnSOD.

    Directory of Open Access Journals (Sweden)

    Yuewei Sheng

    Full Text Available Two yeast manganese superoxide dismutases (MnSOD, one from Saccharomyces cerevisiae mitochondria (ScMnSOD and the other from Candida albicans cytosol (CaMnSODc, have most biochemical and biophysical properties in common, yet ScMnSOD is a tetramer and CaMnSODc is a dimer or "loose tetramer" in solution. Although CaMnSODc was found to crystallize as a tetramer, there is no indication from the solution properties that the functionality of CaMnSODc in vivo depends upon the formation of the tetrameric structure. To elucidate further the functional significance of MnSOD quaternary structure, wild-type and mutant forms of ScMnSOD (K182R, A183P mutant and CaMnSODc (K184R, L185P mutant with the substitutions at dimer interfaces were analyzed with respect to their oligomeric states and resistance to pH, heat, and denaturant. Dimeric CaMnSODc was found to be significantly more subject to thermal or denaturant-induced unfolding than tetrameric ScMnSOD. The residue substitutions at dimer interfaces caused dimeric CaMnSODc but not tetrameric ScMnSOD to dissociate into monomers. We conclude that the tetrameric assembly strongly reinforces the dimer interface, which is critical for MnSOD activity.

  1. Synthesis and Crystal Structures of Three Ladder Distannoxane Dimers [(PhCH2)2(Cl)SnOSn(X)(CH2Ph)2]2(X=Cl,OMe,OEt)

    Institute of Scientific and Technical Information of China (English)

    马春林; 李凤

    2003-01-01

    Three distannoxane dimers[(PhCH2)2(Cl)SnOSn(X)(CH2Ph)2]2(X=Cl,OMe,OEt)were prepared by the hydrolytic reaction of (PhCH2)2SnCl2 with sodium alkoxides.The compounds are assigned tetranuclear distannoxane structures in solid state.which contain the so-called ladder arrangement with a central planar Sn2O2 four-membered ring.The endo-and exo-cyclic Sn atoms are both five-coordinate,and have distorted trigonal bipyramidal geometries.A variety of hydrolyses of(PhCH2)2SnCl2 were performed and these dimers were characterized by IR,1H NMR spectroscopy and X-ray diffraction analysis.

  2. Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors.

    Science.gov (United States)

    Kaczor, Agnieszka A; Guixà-González, Ramon; Carrió, Pau; Poso, Antti; Dove, Stefan; Pastor, Manuel; Selent, Jana

    2015-04-01

    In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, κ opioid receptor dimer, β1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data.

  3. Inverse Limits

    CERN Document Server

    Ingram, WT

    2012-01-01

    Inverse limits provide a powerful tool for constructing complicated spaces from simple ones. They also turn the study of a dynamical system consisting of a space and a self-map into a study of a (likely more complicated) space and a self-homeomorphism. In four chapters along with an appendix containing background material the authors develop the theory of inverse limits. The book begins with an introduction through inverse limits on [0,1] before moving to a general treatment of the subject. Special topics in continuum theory complete the book. Although it is not a book on dynamics, the influen

  4. Dynamics of a bouncing dimer

    CERN Document Server

    Dorbolo, S; Tsimring, L S; Kudrolli, A

    2005-01-01

    We investigate the dynamics of a dimer bouncing on a vertically oscillated plate. The dimer, composed of two spheres rigidly connected by a light rod, exhibits several modes depending on initial and driving conditions. The first excited mode has a novel horizontal drift in which one end of the dimer stays on the plate during most of the cycle, while the other end bounces in phase with the plate. The speed and direction of the drift depend on the aspect ratio of the dimer. We employ event-driven simulations based on a detailed treatment of frictional interactions between the dimer and the plate in order to elucidate the nature of the transport mechanism in the drift mode.

  5. Monomers, dimers, and trimers of [Au(CN2]− in a Ba(diaza-18-crown-62+ coordination polymer

    Directory of Open Access Journals (Sweden)

    2009-03-01

    Full Text Available The structure of the title compound, poly[triaquatetra-μ-cyanido-tetracyanidobis(1,4,10,13-tetraoxa-7,16-diazacyclooctadecanedibarium(IItetragold(I], [Au4Ba2(CN8(C12H26N2O42(H2O3]n, displays O—H...N hydrogen bonding between water molecules and cyano ligands and an unusual pattern of aurophilic interactions that yields a monomer, dimer, and trimer of [Au(CN2]− within the same crystal structure. In two of the five Au positions, the atom resides on a center of inversion. The overall arrangement is that of a coordination polymer assisted by aurophilic and hydrogen-bonded interactions.

  6. Synthesis and polarized photoluminescence of novel phosphorescent cyclometalated platinum dimer

    Institute of Scientific and Technical Information of China (English)

    Shi Ping Jiang; Kai Jun Luo; Ying Han Wang; Xin Wang; Ying Jiang; Yan Yan Wei

    2011-01-01

    A novel phosphorescent cyclometalated platinum dimer with bis-[2-(p-dodecyloxyphenyl) pyridyl]-hexane-l,6-diol as ligand and 1,3-( 1-n-hexyl,3-n-heptadecyl) diketone as ancillary ligand was synthesized. The chemical structure and liquid crystal property of the dimer were characterized by 1H NMR, ESI-MS, polarizing optical microscopy (POM) and differential scanning calorimetry (DSC). The aligned film of title compound on the rubbed polyimide film is intensely emissive at room temperature with emission maximum at 516 nm. The luminescence dichroic ratio (I∥/ IL) at 516 nm is 3.1.

  7. Crystal structure of methyl 3′-benzamido-4′-(4-methoxyphenyl-1′-methylspiro[indeno[1,2-b]quinoxaline-11,2′-pyrrolidine]-3′-carboxylate

    Directory of Open Access Journals (Sweden)

    Kuppan Chandralekha

    2016-09-01

    Full Text Available In the title compound, C35H30N4O3, the spiro C atom connects the five-membered pyrrolidine ring and the indenoquinoxaline ring system. The pyrrolidine ring adopts a twist conformation. An intramolecular N—H...N interaction between the amino group and the pyrazine ring is observed. In the crystal, molecules are linked by a pairs of C—H...O hydrogen bonds, forming inversion dimers.

  8. Toxicological Evaluation of a Potential Immunosensitizer for Use as a Mucosal Adjuvant—Bacillus thuringiensis Cry1Ac Spore-Crystals: A Possible Inverse Agonist that Deserves Further Investigation

    Directory of Open Access Journals (Sweden)

    Bélin Poletto Mezzomo

    2015-12-01

    Full Text Available In addition to their applicability as biopesticides, Bacillus thuringiensis (Bt Cry1Ac spore-crystals are being researched in the immunology field for their potential as adjuvants in mucosal and parenteral immunizations. We aimed to investigate the hematotoxicity and genotoxicity of Bt spore-crystals genetically modified to express Cry1Ac individually, administered orally (p.o. or with a single intraperitoneal (i.p. injection 24 h before euthanasia, to simulate the routes of mucosal and parenteral immunizations in Swiss mice. Blood samples were used to perform hemogram, and bone marrow was used for the micronucleus test. Cry1Ac presented cytotoxic effects on erythroid lineage in both routes, being more severe in the i.p. route, which also showed genotoxic effects. The greater severity noted in this route, mainly at 6.75 mg/kg, as well as the intermediate effects at 13.5 mg/kg, and the very low hematotoxicity at 27 mg/kg, suggested a possible inverse agonism. The higher immunogenicity for the p.o. route, particularly at 27 mg/kg, suggested that at this dose, Cry 1Ac could potentially be used as a mucosal adjuvant (but not in parenteral immunizations, due to the genotoxic effects observed. This potential should be investigated further, including making an evaluation of the proposed inverse agonism and carrying out cytokine profiling.

  9. Reactions of Cu(I)Br with aziridine derivatives. Synthesis, characterization and crystal structures of monomeric, dimeric and hexameric aziridine (= az) complexes of the formal type [CuBr(az)2]n (n = 1, 2) and [CuBr(az)]6.

    Science.gov (United States)

    Bobka, Roman; Roedel, J Nicolas; Wirth, Stefan; Lorenz, Ingo-Peter

    2010-11-14

    The first syntheses of monomeric and oligomeric aziridine complexes of copper(I) are described. Cu(I)Br (1) reacts with a series of different aziridine derivatives (C(2)H(3)PhNH (2), C(2)H(2)Me(2)NH (3), C(2)H(2)Me(2)NC(2)H(2)Me(2)NH(2) (4)) to give the neutral dimeric complex [CuBr(C(2)H(3)PhNH)(2)](2) (5) and the ionic hexameric complex [Cu(6)Br(5)(C(2)H(2)Me(2)NH)(6)]Br (6) with terminal bound aziridine ligands as well as the neutral monomeric complex [CuBr(C(2)H(2)Me(2)NC(2)H(2)Me(2)NH(2))] (7) where the dimerized aziridine acts as a N,N'-chelating ligand. After purification, all of the complexes were fully characterized and their IR, (1)H and (13)C NMR spectra are reported and discussed. The single crystal structure analysis revealed distorted tetrahedral geometry for the copper(I) centres in the complexes 5 and 6 and a trigonal planar structure for complex 7. In the oligomers the copper centres are bridged by two μ(2)- (5) or two μ(3)- and three μ(4)-bromido ligands (6), respectively.

  10. Universal dimer-dimer scattering in lattice effective field theory

    CERN Document Server

    Elhatisari, Serdar; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam

    2016-01-01

    We consider two-component fermions with short-range interactions and large scattering length. This system has universal properties that are realized in many different fields including atomic, nuclear and particle physics. In the limit of large fermion-fermion scattering length $a_\\mathrm{ff}$ and zero range interaction, all properties of the system scale proportionally with the only length scale $a_\\mathrm{ff}$. We consider the case where there are bound dimers and calculate the scattering phase shifts for the two-dimer system near threshold using lattice effective field theory. From the scattering phase shifts, we extract the universal dimer-dimer scattering length $a_\\mathrm{dd}/a_\\mathrm{ff}=0.645(89)$ and effective range $r_\\mathrm{dd}/a_\\mathrm{ff}=-0.413(79)$.

  11. Optofluidic taming of a colloidal dimer with a silicon nanocavity

    Energy Technology Data Exchange (ETDEWEB)

    Pin, C.; Renaut, C. [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France); University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Cluzel, B., E-mail: benoit.cluzel@u-bourgogne.fr; Fornel, F. de [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); Peyrade, D. [University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Picard, E.; Hadji, E. [University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France)

    2014-10-27

    We report here the optical trapping of a heterogeneous colloidal dimer above a photonic crystal nanocavity used as an on-chip optical tweezer. The trapped dimer consists of a cluster of two dielectric microbeads of different sizes linked by van der Waals forces. The smallest bead, 1 μm in diameter, is observed to be preferentially trapped by the nanotweezer, leaving the second bead untrapped. The rotational nature of the trapped dimer Brownian motion is first evidenced. Then, in the presence of a fluid flow, control of its orientation and rotation is achieved. The whole system is found to show high rotational degrees of freedom, thereby acting as an effective flow-sensitive microscopic optical ball joint.

  12. Investigation on crystalline perfection, optical transmittance, birefringence, temperature-dependent refractive index, laser damage threshold and pyroelectric characteristics of inversely soluble lithium sulfate monohydrate single crystals

    Science.gov (United States)

    Silambarasan, A.; Rajesh, P.; Bhatt, Rajeev; Bhaumik, Indranil; Karnal, A. K.; Ramasamy, P.; Gupta, P. K.

    2016-08-01

    Bulk prismatic lithium sulfate monohydrate (LSMH) single crystals were grown by seed rotation with slow heating method from aqueous solution. Small FWHM obtained from high-resolution X-ray diffraction spectrum shows that the crystals grown by this method have less defects and absence of low-angle grain boundaries. The high transmittance and low reflectance nature of the grown crystal was observed using UV-Vis-NIR spectrometer. The principal refractive indices of a LSMH crystal have been measured by a prism coupling method for the wavelengths of 0.407, 0.532, 0.828, 1.064 and 1.551 µm at room temperature, and Sellmeier equations are determined from the fitting of the data point. The refractive index data confirm that LSMH crystal is negative biaxial and the optic axis lies in YZ plane with an angle (2 V y ) of 51.74° with respect to y axis at 532 nm wavelength. The thermo-optic coefficients were determined from the temperature-dependent refractive indices measured in the range of 30-125 °C for the wavelengths of 532 and 1064 nm. The surface laser damage threshold studies reveal the higher optical radiation stability against 532-nm laser. The pyroelectric coefficients and pyroelectric figure of merit were determined from the pyroelectric current measurement by the Byer and Roundy method.

  13. Protein Crystallization

    Science.gov (United States)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  14. Crystal structure of 14-methyl-11-(3-methyl-phen-yl)-12-oxa-8,14-di-aza-tetra-cyclo-[8.3.3.0(1,10).0(2,7)]hexa-deca-2(7),3,5-triene-9,13-dione.

    Science.gov (United States)

    Savithri, M P; Suresh, M; Raghunathan, R; Raja, R; SubbiahPandi, A

    2015-06-01

    In the title compound, C21H20N2O3, the lactone ring adopts an envelope conformation with the quaternary C atom bonded to two other C atoms as the flap. The fused pyrrolidine ring adopts a twisted conformation about the Cq-N (q = quaternary) bond. In the crystal, inversion dimers linked by pairs of N-H⋯O hydrogen bonds generate R 2 (2)(8) loops. The dimers are linked into [110] chains by pairs of C-H⋯O inter-actions, which generate R 2 (2)(14) loops.

  15. Structural insights into lipid-dependent reversible dimerization of human GLTP

    Energy Technology Data Exchange (ETDEWEB)

    Samygina, Valeria R.; Ochoa-Lizarralde, Borja [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain); Popov, Alexander N. [European Synchrotron Radiation Facility, 38043 Grenoble (France); Cabo-Bilbao, Aintzane; Goni-de-Cerio, Felipe [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain); Molotkovsky, Julian G. [Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997 (Russian Federation); Patel, Dinshaw J. [Memorial Sloan–Kettering Cancer Center, New York, NY 10021 (United States); Brown, Rhoderick E., E-mail: reb@umn.edu [University of Minnesota, Austin, MN 55912 (United States); Malinina, Lucy, E-mail: reb@umn.edu [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain)

    2013-04-01

    It is shown that dimerization is promoted by glycolipid binding to human GLTP. The importance of dimer flexibility in wild-type protein is manifested by point mutation that ‘locks’ the dimer while diversifying ligand/protein adaptations. Human glycolipid transfer protein (hsGLTP) forms the prototypical GLTP fold and is characterized by a broad transfer selectivity for glycosphingolipids (GSLs). The GLTP mutation D48V near the ‘portal entrance’ of the glycolipid binding site has recently been shown to enhance selectivity for sulfatides (SFs) containing a long acyl chain. Here, nine novel crystal structures of hsGLTP and the SF-selective mutant complexed with short-acyl-chain monoSF and diSF in different crystal forms are reported in order to elucidate the potential functional roles of lipid-mediated homodimerization. In all crystal forms, the hsGLTP–SF complexes displayed homodimeric structures supported by similarly organized intermolecular interactions. The dimerization interface always involved the lipid sphingosine chain, the protein C-terminus (C-end) and α-helices 6 and 2, but the D48V mutant displayed a ‘locked’ dimer conformation compared with the hinge-like flexibility of wild-type dimers. Differences in contact angles, areas and residues at the dimer interfaces in the ‘flexible’ and ‘locked’ dimers revealed a potentially important role of the dimeric structure in the C-end conformation of hsGLTP and in the precise positioning of the key residue of the glycolipid recognition centre, His140. ΔY207 and ΔC-end deletion mutants, in which the C-end is shifted or truncated, showed an almost complete loss of transfer activity. The new structural insights suggest that ligand-dependent reversible dimerization plays a role in the function of human GLTP.

  16. Collisional properties of weakly bound heteronuclear dimers

    NARCIS (Netherlands)

    Marcelis, B.; Kokkelmans, S.J.J.M.F.; Shlyapnikov, G.V.; Petrov, D.S.

    2008-01-01

    We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional stability due to an effective dimer-dimer repulsion originating

  17. Centrosymmetric dimer of quinuclidine betaine and squaric acid complex

    Science.gov (United States)

    Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.

    2012-12-01

    The complex of squaric acid (3,4-dihydroxy-3-cyclobuten-1,2-dion, H2SQ) with quinuclidine betaine (1-carboxymethyl-1-azabicyclo[2.2.2]octane inner salt, QNB), 1, has been characterized by single-crystal X-ray analysis, FTIR and NMR spectroscopies and by DFT calculations. In the crystal of 1, monoclinic space group P21/n, one proton from H2SQ is transferred to QNB. QNBH+ and HSQ- are linked together by a Osbnd H⋯O hydrogen bond of 2.553(2) Å. Two such QNBH+·HSQ- complexes form a centrosymmetric dimer bridged by two Osbnd H⋯O bonds of 2.536(2) Å. The FTIR spectrum is consistent with the X-ray results. The structures of monomer QNBH+·HSQ- (1a) and dimer [QNB·H2SQ]2 (2) have been optimized at the B3LYP/6-311++G(d,p) level of theory. Isolated dimer 2 optimized back to a molecular aggregate of H2SQ and QNB. The calculated frequencies for the optimized structure of dimer 2 have been used to explain the frequencies of the experimental FTIR spectrum. The interpretation of 1H and 13C NMR spectra has been based on the calculated GIAO/B3LYP/6-311++G(d,p) magnetic isotropic shielding constants for monomer 1a.

  18. Inverse disjuncties

    NARCIS (Netherlands)

    Malepaard, J.

    2007-01-01

    Balansschikkingen (of negatief gebonden of-constructies) zijn volgens de in dit artikel ontwikkelde hypothese inverse disjuncties (id's). Het zijn tweeledige zinnen waarvan het eerste lid een verplichte negatieve of minimaliserende constituent bevat en het tweede lid met of begint. Evenals

  19. Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes

    DEFF Research Database (Denmark)

    Diehl, Carl; Wisniewska, Magdalena; Frick, Inga-Maria;

    2016-01-01

    tetramers both in the crystal and in solution. The tetramers are composed of four helix-loop-helix motifs with the loop regions connecting the helices displaying a high degree of flexibility. Owing to interactions at the tetramer interface, the observed tetramer can be described as a dimer of dimers. We...

  20. Crystal structure of N-(1-acetyl-3-chloro-1H-indazol-6-yl-4-methoxybenzenesulfonamide

    Directory of Open Access Journals (Sweden)

    Yassine Hakmaoui

    2015-12-01

    Full Text Available In the title compound, C16H14ClN3O4S, the six-membered ring of the indazole group is connected to a sulfonamide group. The indazole system is essentially planar, with the greatest deviation from the mean plane being 0.007 (2 Å. The dihedral angle between the two six-membered rings is 74.99 (9°. The crystal structure exhibits inversion dimers in which molecules are linked by pairs of N—H...O and C—H...O hydrogen bonds.

  1. Crystal structure of 2-(4-chlorophenyl-3-(4-methoxyphenyl-3-(methylsulfanylacrylonitrile

    Directory of Open Access Journals (Sweden)

    Shamantha Kumar

    2014-11-01

    Full Text Available In the title compound, C17H14ClNOS, the aromatic rings are inclined to one another by 64.22 (9°. The acrylonitrile group (C=C—C[triple-bond]N is planar to within 0.003 (2 Å, with the S atom and the methyl C atom displaced from this plane by 0.2317 (6 and −0.637 (2 Å, respectively. In the crystal, molecules are linked via pairs of C—H...π interactions, forming inversion dimers. There are no other significant intermolecular interactions present.

  2. ZnS-opal与反opal结构ZnS光子晶体的组装%Fabrication and characterization of ZnS-opal and inverse opal ZnS photonic crystals

    Institute of Scientific and Technical Information of China (English)

    段涛; 彭同江; 唐永建

    2009-01-01

    以单分散SiO2微球为基元,在75%~80%湿度、30~45℃恒温密闭烘箱中垂直快速组装opal模板;以Zn(NO3)2(0.035mol/L)、TAA乙醇溶液(0.05mol/L)为前体,通过溶剂热法充填形成ZnS-opal复合光子晶体;ZnS-opal复合光子晶体在2%~5%的HF溶液中浸泡4~5 h后卸载模板,制得反opal结构ZnS基光子晶体;采用XRD、SEM、UV-Vis测试手段对反opal结构ZnS基光子晶体形貌、物相和光学性能进行了表征.结果表明:溶剂热法多次充填可使ZnS纳米晶在模板密堆积形成的空隙中均匀成核;经过酸处理的ZnS-opal中SiO2微球溶解、坍塌,形成蜂窝状三维有序介孔和反opal结构ZnS基光子晶体;相同粒径SiO2微球组装的opal模板、ZnS-opal以及反opal结构ZnS光子晶体均表现出光子带隙特性,但反opal结构ZnS光子晶体带隙位置相比前两者发生了蓝移.%Opal templates were rapidly assembled from monodisperse SiO2 microspheres as building blocks by vertical sedimentation in an airtight oven at 30-45 ℃ and in a certain humidity. With a precursor composed of 0.035mol/L Zn (NO3)2 and 0.05mol/L TAA ethanol solution, ZnS photortic crystals with opal structure were prepared by solvothermal synthesis method repeatly. ZnS photonic crystals with inverse opal structure were obtained by removing the opal template after immersing in 2%-5% HF acid for 4-5 h. The morphology, component and optical properties of the synthetic samples were tested and compared. Results of XRD, SEM, and UV-Vis indicated that ZnS nanocrystals can grow in and fill in the void of opal template, and SiO2 microspheres of templates are dissolved so as to form some three dimensional ordered porous structure and to form the inverse opal ZnS photonic crystals. Compared with opal templates, ZnS-opal and inverse opal ZnS photonic crystals assembled with SiO2 spheres in the same diameter show good optical properties and exhibited photonic band gap. The photonic band gap position of inverse

  3. Stabilization of the dimeric birch pollen allergen Bet v 1 impacts its immunological properties.

    Science.gov (United States)

    Kofler, Stefan; Ackaert, Chloé; Samonig, Martin; Asam, Claudia; Briza, Peter; Horejs-Hoeck, Jutta; Cabrele, Chiara; Ferreira, Fatima; Duschl, Albert; Huber, Christian; Brandstetter, Hans

    2014-01-03

    Many allergens share several biophysical characteristics, including the capability to undergo oligomerization. The dimerization mechanism in Bet v 1 and its allergenic properties are so far poorly understood. Here, we report crystal structures of dimeric Bet v 1, revealing a noncanonical incorporation of cysteine at position 5 instead of genetically encoded tyrosine. Cysteine polysulfide bridging stabilized different dimeric assemblies, depending on the polysulfide linker length. These dimers represent quaternary arrangements that are frequently observed in related proteins, reflecting their prevalence in unmodified Bet v 1. These conclusions were corroborated by characteristic immunologic properties of monomeric and dimeric allergen variants. Hereby, residue 5 could be identified as an allergenic hot spot in Bet v 1. The presented results refine fundamental principles in protein chemistry and emphasize the importance of protein modifications in understanding the molecular basis of allergenicity.

  4. Crystal structure of 2,2-dichloro-1-(piperidin-1-ylethanone

    Directory of Open Access Journals (Sweden)

    Markus Schwierz

    2015-01-01

    Full Text Available In the title compound, C7H11Cl2NO, the piperidine ring shows a chair conformation and the bond-angle sum at the N atom is 359.9°. The H atom of the dichloromethyl group is in an eclipsed conformation with respect to the carbonyl group (H—C—C=O = −5°. In the crystal, inversion dimers are linked by pairs of C—H...O hydrogen bonds between the dichloromethyl group and the carbonyl O atom, which generate R22(8 loops. The dimers are linked into a ladder-like structure propagating in the [100] direction by short O...Cl [3.1084 (9 Å] contacts.

  5. Crystal structure of 2,2-di-chloro-1-(piperidin-1-yl)ethanone.

    Science.gov (United States)

    Schwierz, Markus; Görls, Helmar; Imhof, Wolfgang

    2015-01-01

    In the title compound, C7H11Cl2NO, the piperidine ring shows a chair conformation and the bond-angle sum at the N atom is 359.9°. The H atom of the di-chloro-methyl group is in an eclipsed conformation with respect to the carbonyl group (H-C-C=O = -5°). In the crystal, inversion dimers are linked by pairs of C-H⋯O hydrogen bonds between the di-chloro-methyl group and the carbonyl O atom, which generate R 2 (2)(8) loops. The dimers are linked into a ladder-like structure propagating in the [100] direction by short O⋯Cl [3.1084 (9) Å] contacts.

  6. Crystal structure of (7-fluoro-2-oxo-2H-chromen-4-ylmethyl morpholine-4-carbodithioate

    Directory of Open Access Journals (Sweden)

    B. R. Anitha

    2015-12-01

    Full Text Available In the title compound, C15H14FNO3S2, the 2H-chromene ring system is close to being planar (r.m.s. deviation = 0.024 Å and the morpholine ring adopts a chair conformation. The dihedral angle between the 2H-chromene ring system and the morpholine ring (all atoms is 88.21 (11°. In the crystal, inversion dimers linked by pairs of very weak C—H...F hydrogen bonds generate R22(8 loops; C—H...O hydrogen bonds connect the dimers into [010] chains. Weak aromatic π–π stacking interactions between the pyran rings of the chromene systems [centroid–centroid distance = 3.6940 (16 Å] are also observed.

  7. Crystal structure of ethyl 2-(2,4,5-trimethoxyphenylquinoline-4-carboxylate

    Directory of Open Access Journals (Sweden)

    T. O. Shrungesh Kumar

    2015-07-01

    Full Text Available In the title compound, C21H21NO5, the dihedral angle between the quinoline ring system (r.m.s. deviation = 0.028 Å and the trimethoxybenzene ring is 43.38 (5°. The C atoms of the methoxy groups deviate from their attached benzene ring by −0.396 (2, −0.049 (2 and 0.192 (2 Å for the ortho-, meta- and para-substituents, respectively. The pendant ethyl chain is disordered over two orientations in a 0.527 (5:0.473 (5 ratio. A short intramolecular C—H...O contact closes an S(6 ring. In the crystal, inversion dimers linked by pairs of weak C—H...O interactions generate R22(6 loops. The dimers are linked by further C—H...O interactions to generate [1-10] chains.

  8. Crystal structure of diethyl 2-amino-6-[(thiophen-3-ylethynyl]azulene-1,3-dicarboxylate

    Directory of Open Access Journals (Sweden)

    Sebastian Förster

    2015-03-01

    Full Text Available The title compound, C22H19NO4S, has an almost planar geometry supported by intramolecular N—H...O and C—H...O hydrogen bonds. The thiophene ring is inclined to the azulene ring by 4.85 (16°, while the ethoxycarbonyl groups are inclined to the azulene ring by 7.0 (2 and 5.7 (2°. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked via C—H...π interactions, forming sheets parallel to (10-1.

  9. Crystal structure of β-benzyl dl-aspartate N-carb-oxyanhydride.

    Science.gov (United States)

    Kanazawa, Hitoshi; Inada, Aya

    2017-03-01

    In the title racemic compound, C12H11NO5 [systematic name: benzyl 2-(2,5-dioxooxazolidin-4-yl)acetate], the oxazolidine ring is planar, with an r.m.s. deviation of 0.03 Å. The benzyl ring is almost normal to the oxazolidine ring, making a dihedral angle of 80.11 (12)°. In the crystal, inversion dimers are formed between the l- and d-enanti-omers via pairs of N-H⋯O hydrogen bonds. This arrangement is favourable for the polymerization of the compound in the solid state. The dimers are linked by C-H⋯O hydrogen bonds, forming layers parallel to the ab plane.

  10. Crystal stucture of methyl 2-({[2-(methoxycarbonylphenyl]carbamoyl}aminobenzoate

    Directory of Open Access Journals (Sweden)

    Hasna Yassine

    2015-05-01

    Full Text Available In the title compound, C17H16N2O5, the dihedral angles between the central urea [N—C(=O—N] fragment and its attached benzene rings are 20.20 (14 and 24.24 (13°; the dihedral angle between the aromatic rings is 42.1 (1°. The molecular conformation is consolidated by two intramolecular N—H...O hydrogen bonds, which both generate S(6 rings. In the crystal, inversion dimers linked by pairs of C—H...O interactions generate R22(14 loops. The dimers are linked by further C—H...O interactions into (011 sheets.

  11. Hydrogen bonding in the crystal structure of the molecular salt of pyrazole-pyrazolium picrate.

    Science.gov (United States)

    Su, Ping; Song, Xue-Gang; Sun, Ren-Qiang; Xu, Xing-Man

    2016-06-01

    The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-tri-nitro-phenolate-1H-pyrazole (1/1)], H(C3H4N2)2 (+)·C6H2N3O7 (-), consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N-H⋯N hydrogen bond is disordered over both symmetry-unique pyrazole mol-ecules with occupancies of 0.52 (5) and 0.48 (5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N-H⋯(O,O) hydrogen bonds. In addition, weak C-H⋯O hydrogen bonds link inversion-related chains, forming columns along [100].

  12. 在单晶硅片上直接电化学沉积制备镍反opal光子晶体%Fabrication of Ni inverse opal photonic crystals on silicon wafer by electrodeposition

    Institute of Scientific and Technical Information of China (English)

    许静

    2012-01-01

    采用电化学沉积工艺直接向组装在单晶硅片上的聚苯乙烯胶体晶体中填充金属Ni,成功制备了Ni的反opal光子晶体.采用线性扫描伏安法研究了单晶硅表面的化学刻蚀对Ni的电化学沉积过程的影响,并采用扫描电子显微镜(SEM)、X射线衍射等对Ni反opal光子晶体的形貌和结构进行了观察分析,对其光学性能进行了初步研究.研究结果表明,对单晶硅片表面进行化学刻蚀有利于金属Ni的电化学沉积;在PS胶体晶体模板中电化学生长的金属Ni呈多晶状态,去除模板后形成了金属Ni的有序多孔结构.%Electrodeposition was used to fill the voids of PS colloidal crystals on silicon wafer with Ni and Ni inverse opal was obtained. The influence of chemical etching of silicon wafer on the electrodeposition of Ni was studied by using cyclic voltammetry scan. The resulted Ni inverse opal was characterized by scanning electron microscopy and X-ray diffraction. It showed that chemical etching of silicon surface is beneficial for the deposition of Ni on silicon wafer. Ni grown in the voids of PS colloidal crystals is the polycrystalline phase and the ordered porous structure of Ni is formed after the removing of the PS template.

  13. Crystal structure of methyl 2-hydroxy-5-[(4-oxo-4,5-dihydro-1,3-thiazol-2-ylamino]benzoate

    Directory of Open Access Journals (Sweden)

    Shaaban K. Mohamed

    2015-05-01

    Full Text Available The title compound, C11H10N2O4S, crystallized with two independent molecules (A and B in the asymmetric unit. They differ primarily in the rotational orientation of the five-membered heterocyclic ring. In molecule A this ring is inclined to the benzene ring by 48.17 (8°, while in molecule B the same dihedral angle is 23.07 (8°. In each molecule there is an intramolecular O—H...O hydrogen bond involving the adjacent hydroxyl group and the ester carbonyl O atom. In the crystal, the A molecules are linked via pairs of N—H...N hydrogen bonds, forming inversion dimers. These dimers are linked to the B molecules via N—H.·O, C—H...O and C—H...S hydrogen bonds forming corrugated sheets lying parallel to (102.

  14. Crystal structure of ethyl N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-di­hydro-1H-pyrazol-4-yl)carbamate

    Science.gov (United States)

    Danish, Muhammad; Tahir, Muhammad Nawaz; Anwar, Uzma; Raza, Muhammad Asam

    2015-01-01

    In the title compound, C14H17N3O3, the dihedral angle between the benzene ring and the five-membered di­hydro­pyrazole ring is 52.26 (9)°. The ethyl ester group is approximately planar (r.m.s. deviation 0.0568 Å) and subtends an angle 67.73 (8)° to the pyrazole ring. In the crystal, molecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with an R 2 2(10) ring motif. Weaker C—H⋯O contacts link these dimers into a three-dimensional network of mol­ecules stacked along the a-axis direction. Offset π–π stacking inter­actions between the benzene rings [centroid-to-centroid distance = 3.8832 (12) Å] further stabilize the crystal packing. PMID:26029449

  15. Crystal structure of ethyl N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-ylcarbamate

    Directory of Open Access Journals (Sweden)

    Muhammad Danish

    2015-04-01

    Full Text Available In the title compound, C14H17N3O3, the dihedral angle between the benzene ring and the five-membered dihydropyrazole ring is 52.26 (9°. The ethyl ester group is approximately planar (r.m.s. deviation 0.0568 Å and subtends an angle 67.73 (8° to the pyrazole ring. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(10 ring motif. Weaker C—H...O contacts link these dimers into a three-dimensional network of molecules stacked along the a-axis direction. Offset π–π stacking interactions between the benzene rings [centroid-to-centroid distance = 3.8832 (12 Å] further stabilize the crystal packing.

  16. 反蛋白石结构光子晶体及其应用的研究∗%Research and Application of Inverse Opal Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    单晶; 谭天亚; 张春玉; 步秋雨; 韩亚洲; 季亚楠; 张帆; 梅勇; 徐攀峰; 王绩伟

    2016-01-01

    反蛋白石结构光子晶体因具有完全光子带隙、制备材料广泛、特殊的周期结构、大的比表面积和连通的孔洞结构,近年来在自发辐射的调制、提高光催化反应速率和染料敏化太阳能电池反应速率等领域成为研究热点之一,并且在光、电、催化、传感、显示、检测等领域有着巨大的应用价值。介绍了反蛋白石结构光子晶体的基本概念及制备方法,阐述了反蛋白石结构在材料自发辐射的调制、能量传递的调制、促进物理化学反应、外界环境响应材料等方面的作用及其应用。%Inverse opal structure with the properties of complete photonic band gap,extensive preparation ma-terials,periodic structure,large specific surface area and connected holes has great importance in the domains of spon-taneous emission modulation,enhancing efficiency of photocatalysis and improving photielectric conversion efficiency of the dye sensitized cell in recent years.This structure has high value and huge potential in optics,electronics,catal-ysis,sensor,display,detection and so on.This paper introduces the basic concepts of inverse opal structure and de-scribes several applications of inverse opal structure,such as preparation method,spontaneous emission modulation, energy transfer modulation,promoting physical reactions,promoting chemical reactions and external environmental response materials.

  17. The Dimer Interface of the Membrane Type 1 Matrix Metalloproteinase Hemopexin Domain

    Science.gov (United States)

    Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

    2011-01-01

    Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion. PMID:21193411

  18. Tuning solubility and stability of hydrochlorothiazide co-crystals.

    Science.gov (United States)

    Sanphui, Palash; Rajput, Lalit

    2014-02-01

    Hydrochlorothiazide (HCT), C7H8ClN3O4S2, is a diuretic BCS (Biopharmaceutics Classification System) class IV drug which has primary and secondary sulfonamide groups. To modify the aqueous solubility of the drug, co-crystals with biologically safe co-formers were screened. Multi-component molecular crystals of HCT were prepared with nicotinic acid, nicotinamide, succinamide, p-aminobenzoic acid, resorcinol and pyrogallol using liquid-assisted grinding. The co-crystals were characterized by FT-IR spectroscopy, powder X-ray diffraction (PXRD) and differential scanning calorimetry. Single crystal structures were obtained for four of them. The N-H...O sulfonamide catemer synthons found in the stable polymorph of pure HCT are replaced in the co-crystals by drug-co-former heterosynthons. Isostructural co-crystals with nicotinic acid and nicotinamide are devoid of the common sulfonamide dimer/catemer synthons. Solubility and stability experiments were carried out for the co-crystals in water (neutral pH) under ambient conditions. Among the six binary systems, the co-crystal with p-aminobenzoic acid showed a sixfold increase in solubility compared with pure HCT, and stability up to 24 h in an aqueous medium. The co-crystals with nicotinamide, resorcinol and pyrogallol showed only a 1.5-2-fold increase in solubility and transformed to HCT within 1 h of the dissolution experiment. An inverse correlation is observed between the melting points of the co-crystals and their solubilities.

  19. Cationic zinc (II) dimers and one dimensional coordination polymer from ionic carboxylic acid

    Indian Academy of Sciences (India)

    Paladugu Suresh; Ganesan Prabusankar

    2014-09-01

    A rare example of chelating two tetra cationic paddle-wheel zinc dimers were synthesized from the reaction between flexible imidazolium carboxylate (LH2Br2) and corresponding zinc precursors. A zinc coordination polymer was synthesised by treating in situ generation of 2 in the presence of 4,4′-bipyridine. These new molecules, dimers and polymer, were characterized by FT-IR, NMR, UV-vis, fluorescent and single crystal X-ray diffraction techniques. Zinc polymer is the first example of 1D coordination polymer constructed by tetra cationic zinc dimer as a secondary building unit in coordination polymer.

  20. Dimeric α-Cobratoxin X-ray Structure

    Science.gov (United States)

    Osipov, Alexey V.; Rucktooa, Prakash; Kasheverov, Igor E.; Filkin, Sergey Yu.; Starkov, Vladislav G.; Andreeva, Tatyana V.; Sixma, Titia K.; Bertrand, Daniel; Utkin, Yuri N.; Tsetlin, Victor I.

    2012-01-01

    In Naja kaouthia cobra venom, we have earlier discovered a covalent dimeric form of α-cobratoxin (αCT-αCT) with two intermolecular disulfides, but we could not determine their positions. Here, we report the αCT-αCT crystal structure at 1.94 Å where intermolecular disulfides are identified between Cys3 in one protomer and Cys20 of the second, and vice versa. All remaining intramolecular disulfides, including the additional bridge between Cys26 and Cys30 in the central loops II, have the same positions as in monomeric α-cobratoxin. The three-finger fold is essentially preserved in each protomer, but the arrangement of the αCT-αCT dimer differs from those of noncovalent crystallographic dimers of three-finger toxins (TFT) or from the κ-bungarotoxin solution structure. Selective reduction of Cys26-Cys30 in one protomer does not affect the activity against the α7 nicotinic acetylcholine receptor (nAChR), whereas its reduction in both protomers almost prevents α7 nAChR recognition. On the contrary, reduction of one or both Cys26-Cys30 disulfides in αCT-αCT considerably potentiates inhibition of the α3β2 nAChR by the toxin. The heteromeric dimer of α-cobratoxin and cytotoxin has an activity similar to that of αCT-αCT against the α7 nAChR and is more active against α3β2 nAChRs. Our results demonstrate that at least one Cys26-Cys30 disulfide in covalent TFT dimers, similar to the monomeric TFTs, is essential for their recognition by α7 nAChR, although it is less important for interaction of covalent TFT dimers with the α3β2 nAChR. PMID:22223648

  1. Crystal structure of 2-cyano-N′-(cyclohexylideneacetohydrazide

    Directory of Open Access Journals (Sweden)

    William T. A. Harrison

    2014-09-01

    Full Text Available In the title compound, C9H13N3O, the cyclohexylidene ring adopts a chair conformation and the bond-angle sum at the C atom linked to the N atom is 359.6°. The cyanoacetohydrazide grouping is close to planar (r.m.s. deviation for the non-H atoms = 0.031 Å and subtends a dihedral angle of 64.08 (4° with the four C atoms forming the seat of the chair. The C=O and N—H groups are in a syn conformation (O—C—N—H = −5°. In the crystal, inversion dimers linked by pairs of N—H...O hydrogen bonds generate R22(8 loops; this dimer linkage is reinforced by a pair of C—H...O interactions, which generate R22(14 loops. The dimers are linked by C—H...Nc (c = cyanide interactions into [100] ladders, which feature C(4 chains and R44(20 loops.

  2. Evidence for the dimerization-mediated catalysis of methionine sulfoxide reductase A from Clostridium oremlandii.

    Science.gov (United States)

    Lee, Eun Hye; Lee, Kitaik; Kwak, Geun-Hee; Park, Yeon Seung; Lee, Kong-Joo; Hwang, Kwang Yeon; Kim, Hwa-Young

    2015-01-01

    Clostridium oremlandii MsrA (CoMsrA) is a natively selenocysteine-containing methionine-S-sulfoxide reductase and classified into a 1-Cys type MsrA. CoMsrA exists as a monomer in solution. Herein, we report evidence that CoMsrA can undergo homodimerization during catalysis. The monomeric CoMsrA dimerizes in the presence of its substrate methionine sulfoxide via an intermolecular disulfide bond between catalytic Cys16 residues. The dimeric CoMsrA is resolved by the reductant glutaredoxin, suggesting the relevance of dimerization in catalysis. The dimerization reaction occurs in a concentration- and time-dependent manner. In addition, the occurrence of homodimer formation in the native selenoprotein CoMsrA is confirmed. We also determine the crystal structure of the dimeric CoMsrA, having the dimer interface around the two catalytic Cys16 residues. A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. Collectively, our biochemical and structural analyses suggest a novel dimerization-mediated mechanism for CoMsrA catalysis that is additionally involved in CoMsrA regeneration by glutaredoxin.

  3. Synthesis and characterization of a chiral dimeric copper(II) complex: Crystal structure of [Cu2(-Cl)2(HL)2].H2O(H2L = -(-)-2-[(2-hydroxy-1-phenyl-ethylimino)-methyl]-phenol)

    Indian Academy of Sciences (India)

    Chullikkattil P Pradeep; Panthapally S Zacharias; Samar K Das

    2005-03-01

    Synthesis and characterization of an optically active binuclear dichloro-bridged copper(II) complex [Cu2(-Cl)2(HL)2]$\\cdot$H2O 1 (H2L = -(-)-2-[(2-hydroxy-1-phenyl-ethylimino)-methyl]-phenol) of a Schiff-base derived from salicylaldehyde and ()-(+)-2-phenylglycinol are described. Compound 1 crystallizes in the orthorhombic chiral P212121 space group with = 4, = 10.21(2), = 11.574(3), = 25.364(9). Each copper shows square pyramidal geometry with O2NCl2 coordination and the Cu2Cl2 core geometry adopts a butterfly shape. Crystals of 1 were further characterized by elemental analysis, IR, UV-visible and EPR spectroscopy and circular dichroism (CD) studies.

  4. Kinetics of DNA tile dimerization.

    Science.gov (United States)

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

  5. Riemann Zeros and the Inverse Phase Problem

    Science.gov (United States)

    Tourigny, David S.

    2013-10-01

    Finding a universal method of crystal structure solution and proving the Riemann hypothesis are two outstanding challenges in apparently unrelated fields. For centro-symmetric crystals however, a connection arises as the result of a statistical approach to the inverse phase problem. It is shown that parameters of the phase distribution are related to the non-trivial Riemann zeros by a Mellin transform.

  6. RIEMANN ZEROS AND THE INVERSE PHASE PROBLEM

    Science.gov (United States)

    TOURIGNY, DAVID S.

    2013-01-01

    Finding a universal method of crystal structure solution and proving the Riemann hypothesis are two outstanding challenges in apparently unrelated fields. For centrosymmetric crystals however, a connection arises as the result of a statistical approach to the inverse phase problem. It is shown that parameters of the phase distribution are related to the non-trivial Riemann zeros by a Mellin transform. PMID:24293780

  7. NMR Structural Studies on Alamethicin Dimers

    Institute of Scientific and Technical Information of China (English)

    李星

    2003-01-01

    15N labeled alamethicin dimer was synthesized. The structure and dynamics of alamethicin dimers were studied with nuclear magnetic resonance (NMR) spectroscopy. The data from 15N-labeled alamethicin dimer suggest little differences in conformation between the dimer and monomer in the Aib1-Pro14 region. Significant difference in the conformation of the C-terminus are manifest in the NH chemical shifts in the Val15-Pho20 region.

  8. Crystal structure of benzyl (E)-2-(3,4-di-meth-oxy-benzyl-idene)hydrazine-1-carbodi-thio-ate.

    Science.gov (United States)

    Tan, Yew-Fung; Break, Mohammed Khaled Bin; Tahir, M Ibrahim M; Khoo, Teng-Jin

    2015-02-01

    The title compound, C17H18N2O2S2, synthesized via a condensation reaction between S-benzyl di-thio-carbazate and 3,4-di-meth-oxy-benzaldehyde, crystallized with two independent mol-ecules (A and B) in the asymmetric unit. Both mol-ecules have an L-shape but differ in the orientation of the benzyl ring with respect to the 3,4-di-meth-oxy-benzyl-idine ring, this dihedral angle is 65.59 (8)° in mol-ecule A and 73.10 (8)° in mol-ecule B. In the crystal, the A and B mol-ecules are linked via pairs of N-H⋯S hydrogen bonds, forming dimers with an R 2 (2)(8) ring motif. The dimers are linked via pairs of C-H⋯O hydrogen bonds, giving inversion dimers of dimers. These units are linked by C-H⋯π inter-actions, forming ribbons propagating in the [100] direction.

  9. Crystal structure of (5Z-5-(5-bromo-2-hydroxybenzylidene-1,3-thiazolidine-2,4-dione

    Directory of Open Access Journals (Sweden)

    Joel T. Mague

    2015-12-01

    Full Text Available In the title compound, C10H6BrNO3S, the dihedral angle between the thiazolidine ring (r.m.s. deviation = 0.014 Å and the benzene ring is 5.78 (14°. The S atom of the heterocyclic ring is syn to the OH group attached to the benzene ring. In the crystal, inversion dimers linked by pairs of N—H...O hydrogen bonds generate R22(8 loops. The dimers are linked into [001] ribbons by pairwise O—H...O hydrogen bonds with R22(18 motifs. There are no short contacts involving the Br atom.

  10. Crystal structure of 1,3-dimethyl-3-phenylpyrrolidine-2,5-dione: a clinically used anticonvulsant

    Directory of Open Access Journals (Sweden)

    Carlos Ordonez

    2014-09-01

    Full Text Available In the title compound, C12H13NO2, the five-membered ring has an envelope conformation; the disubstituted C atom lies out of the mean plane through the four other ring atoms (r.m.s. deviation = 0.0038 Å by 0.1877 (18 Å. The plane of the phenyl substituent is practically perpendicular to that of the planar part of the five-membered ring, with a dihedral angle of 87.01 (5°. In the crystal, molecules are linked by weak C—H...O hydrogen bonds, forming inversion dimers. The dimers are linked by further C—H...O hydrogen bonds, as well as carbonyl–carbonyl attractive interactions [O...C = 3.2879 (19 Å], forming a three-dimensional framework structure.

  11. Bethe Ansatz Solutions of the Bose-Hubbard Dimer

    Directory of Open Access Journals (Sweden)

    Jon Links

    2006-12-01

    Full Text Available The Bose-Hubbard dimer Hamiltonian is a simple yet effective model for describing tunneling phenomena of Bose-Einstein condensates. One of the significant mathematical properties of the model is that it can be exactly solved by Bethe ansatz methods. Here we review the known exact solutions, highlighting the contributions of V.B. Kuznetsov to this field. Two of the exact solutions arise in the context of the Quantum Inverse Scattering Method, while the third solution uses a differential operator realisation of the su(2 Lie algebra.

  12. Rubidium dimers in paraffin-coated cells

    CERN Document Server

    Acosta, V M; Windes, D; Corsini, E; Ledbetter, M P; Karaulanov, T; Auzinsh, M; Rangwala, S A; Kimball, D F Jackson; Budker, D

    2010-01-01

    Measurements were made to determine the density of rubidium dimer vapor in paraffin-coated cells. The number density of dimers and atoms in similar paraffin-coated and uncoated cells was measured by optical spectroscopy. Due to the relatively low melting point of paraffin, a limited temperature range of 43-80 deg C was explored, with the lower end corresponding to a dimer density of less than 10^7 cm^(-3). With one-minute integration time, a sensitivity to dimer number density of better than 10^6 cm^(-3) was achieved. No significant difference in dimer density was observed between the cells.

  13. Dimerization effect of sucrose octasulfate on rat FGF1

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Artur

    2008-01-01

    Fibroblast growth factors (FGFs) constitute a family of at least 23 structurally related heparin-binding proteins that are involved in regulation of cell growth, survival, differentiation and migration. Sucrose octasulfate (SOS), a chemical analogue of heparin, has been demonstrated to activate FGF...... signalling pathways. The structure of rat FGF1 crystallized in the presence of SOS has been determined at 2.2 A resolution. SOS-mediated dimerization of FGF1 was observed, which was further supported by gel-filtration experiments. The major contributors to the sulfate-binding sites in rat FGF1 are Lys113......, Lys118, Arg122 and Lys128. An arginine at position 116 is a consensus residue in mammalian FGF molecules; however, it is a serine in rat FGF1. This difference may be important for SOS-mediated FGF1 dimerization in rat....

  14. Dimerization interface of 3-hydroxyacyl-CoA dehydrogenase tunes the formation of its catalytic intermediate.

    Directory of Open Access Journals (Sweden)

    Yingzhi Xu

    Full Text Available 3-Hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35 is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60-80 that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects.

  15. Fiber optic D dimer biosensor

    Science.gov (United States)

    Glass, Robert S.; Grant, Sheila A.

    1999-01-01

    A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy.

  16. Mechanism of FGF receptor dimerization and activation

    Science.gov (United States)

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-01-01

    Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increase FGFR phosphorylation. The observed effects due to the ligands fgf1 and fgf2 are very different. The fgf2-bound dimer structure ensures the smallest separation between the transmembrane (TM) domains and the highest possible phosphorylation, a conclusion that is supported by a strong correlation between TM helix separation in the dimer and kinase phosphorylation. The pathogenic A391E mutation in FGFR3 TM domain emulates the action of fgf2, trapping the FGFR3 dimer in its most active state. This study establishes the existence of multiple active ligand-bound states, and uncovers a novel molecular mechanism through which FGFR-linked pathologies can arise.

  17. The E2 Domains of APP and APLP1 Share a Conserved Mode of Dimerization

    Energy Technology Data Exchange (ETDEWEB)

    S Lee; Y Xue; J Hulbert; Y Wang; X Liu; B Demeler; Y Ha

    2011-12-31

    Amyloid precursor protein (APP) is genetically linked to Alzheimer's disease. APP is a type I membrane protein, and its oligomeric structure is potentially important because this property may play a role in its function or affect the processing of the precursor by the secretases to generate amyloid {beta}-peptide. Several independent studies have shown that APP can form dimers in the cell, but how it dimerizes remains controversial. At least three regions of the precursor, including a centrally located and conserved domain called E2, have been proposed to contribute to dimerization. Here we report two new crystal structures of E2, one from APP and the other from APLP1, a mammalian APP homologue. Comparison with an earlier APP structure, which was determined in a different space group, shows that the E2 domains share a conserved and antiparallel mode of dimerization. Biophysical measurements in solution show that heparin binding induces E2 dimerization. The 2.1 {angstrom} resolution electron density map also reveals phosphate ions that are bound to the protein surface. Mutational analysis shows that protein residues interacting with the phosphate ions are also involved in heparin binding. The locations of two of these residues, Arg-369 and His-433, at the dimeric interface suggest a mechanism for heparin-induced protein dimerization.

  18. 二聚体有机锡配合物{[n-Bu2Sn(O2CCH2CS2NC4H8)]2O}2的合成,表征及晶体结构%Synthesis,Characterization and Crystal Structure of the Dimeric Organotin Compound:{[n-Bu2Sn(O2CCH2CS2NC4H8)]2O}2

    Institute of Scientific and Technical Information of China (English)

    尹汉东; 薛绳才; 王其宝

    2004-01-01

    The title compound, {[n-Bu2Sn(O2CCH2CS2NC4H8)]2O}2, has been synthesized by the reaction of (tetrahydropyrrodithiolocarbamoylthio)acetic acid with the di-n-bubyltin oxide in 1:1 molar ratio. The complex has been characterized by elemental analysis, IR and NMR. The crystal structure of it has been determined by X-ray single crystal diffraction. And the results showed that the crystal belongs to triclinic system with space group P1- and some crystal parameters: a=1.220 2(9) nm, b=1.315 8(10) nm, c=1.3804(10) nm, α=111.215(9)°, β=99.357(9)°,The complex has a centrosymmetric dimer structure mode with a four-membered central endo-cyclic Sn2O2 unit in which two bridged oxygen atoms both connect with an exo-cyclic tin atom which has a distorted octahedron. Each of the endo-cyclic tin atoms exhibits a distorted trigonal bipyramid coordination geometry with an additional weak coordination carboxylate oxygen. Four carboxylate ligands are divided into two types. And two of them are bidentate and connecting to each of exo-cyclic tin atoms by using both oxygen atoms, whereas the others bridge to each pair of exo-and endo-cyclic tinatoms utilizing one oxygen atom only. CCDC: 220513.

  19. Topological inverse semigroups

    Institute of Scientific and Technical Information of China (English)

    ZHU Yongwen

    2004-01-01

    That the projective limit of any projective system of compact inverse semigroups is also a compact inverse semigroup,the injective limit of any injective system of inverse semigroups is also an inverse semigroup, and that a compact inverse semigroup is topologically isomorphic to a strict projective limit of compact metric inverse semigroups are proved. It is also demonstrated that Horn (S,T) is a topological inverse semigroup provided that S or T is a topological inverse semigroup with some other conditions. Being proved by means of the combination of topological semigroup theory with inverse semigroup theory,all these results generalize the corresponding ones related to topological semigroups or topological groups.

  20. 应变液晶的负压光效应和反式压光效应%Negative piezo-optical effect and the inverse mo de piezo-o ptical effect of stressed liquid crystals

    Institute of Scientific and Technical Information of China (English)

    范志新; 黎振远; 周璇; 张志东

    2014-01-01

    The concepts of polymer dispersed liquid crystal (PDLC) and stressed liquid crystal (SLC) are introduced;the three kinds of definitions, i.e., “positive piezo-optical effect”, “negative piezo-optical effect” and “inverse mode piezo-optical effect”of PDLC switchable glass are given. The new types of stressed switchable glass samples of negative piezo-optical effect and inverse mode piezo-optical effect are prepared. The experimental results show that the haze is above 90%in a scattering state and the transmittance is nearly 30% in a translucent state. The principle of piezo-optical effect is analyzed with polarization microscopy. The results show that the vertical surface pressure or stretching stress applied to the sample will result in the special reorientation of LC molecules in LC droplets, which causes the optical characteristics of the sample to change significantly. The mode of vertical stretched liquid crystal droplet is proposed, the computation results and graph plotting conform with the results from the micrographs of polarizing microscope very well, so that the experimental phenomena are reasonably explained. The research on SLC piezo-optical effect has the fundamental significance for studying the PDLC and the application value for developing non-electro-optic switchable glass.%介绍聚合物分散液晶和应变液晶概念,给出聚合物分散液晶调光玻璃的“正压光效应”、“负压光效应”和“反式压光效应”三种效应定义。实验制备出负压光效应和反式压光效应新型应变调光玻璃样品,测试样品散射态雾度90%以上,半透明态透光率接近30%。用偏光显微术研究压光效应原理,表明对样品施加垂面按压或拉伸的应力诱导作用会引起液晶微滴中液晶分子具有某些特殊排列方式,导致样品光学性质发生显著变化。建立垂面拉伸液晶微滴模型,计算模拟所绘出的图形与偏光显微镜照片独特花样十分

  1. Synthesis of steroidal dimers: Selective amine catalysed steroidal dimerization

    Indian Academy of Sciences (India)

    Shamsuzzaman; Mohd Gulfam Aalam; Tabassum Siddiqui

    2011-07-01

    Some new dimeric steroids namely cholest-5-en-3-spiro-[6',5'-oxa]-5'-cholest-3'-one (2), cholest-5-en-7-spiro-[4',5'-oxa]-5'-cholest-7'-one (4a) and 3-substitutedcholest-5-en-7-spiro-[4',5'-oxa]-3'-substituted-5'-cholestan-7'-ones (4b, c) are synthesized starting from cholest-5-en-3-one (1), cholest-5-en-7-one (3a) and 3-substituted-cholest-5-en-7-ones (3b, c) respectively by using DMAP and xylene. All the synthesized compounds were characterized by using IR, MS and 1H, 13C NMR spectral and elemental analysis.

  2. Crystal structure and Hirshfeld surface analysis of ethyl 5-phenylisoxazole-3-carboxylate

    Directory of Open Access Journals (Sweden)

    Althaf Shaik

    2017-04-01

    Full Text Available The title compound, C12H11NO3, is an intermediate used in the synthesis of many drug-like molecules. The molecule is almost planar, with the phenyl ring inclined to the isoxazole ring by 0.5 (1°. The ester moiety has an extended conformation and is almost in the same plane with respect to the isoxazole ring, as indicated by the O—C—C—N torsion angle of −172.86 (18°. In the crystal, molecules are linked via pairs of C—H...O hydrogen bonds with the same acceptor atom, forming inversion dimers with two R21(7 ring motifs. The molecules stack in layers lying parallel to (10-3. Analysis using Hirshfeld surface generation and two-dimensional fingerprint plots explores the distribution of weak intermolecular interactions in the crystal structure.

  3. Crystal structure of 6,6′-dimethyl-2H,2′H-3,4′-bichromene-2,2′-dione

    Directory of Open Access Journals (Sweden)

    Kiran K. Pujar

    2014-11-01

    Full Text Available In the title compound, C20H14O4, the dihedral angle between the two coumarin ring systems is 52.37 (19°, showing a gauche arrangement across the C—C bond which links the two units. The carbonyl groups of the two coumarin units adopt an s-trans arrangement. In the crystal, pairs of C—H...O hydrogen bonds and π–π interactions [centroid–centroid distance = 3.631 (2 Å] connect the molecules into inversion dimers.

  4. Crystal structure of 2-amino-4-(4-chlorophenyl-1-(4-methylphenyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    Shaaban K. Mohamed

    2015-12-01

    Full Text Available In the title compound, C23H20ClN3O, each of the cyclohexene and 1,4-dihydropyridine rings of the 1,4,5,6,7,8-hexahydroquinoline ring system adopts a twisted-boat conformation. The dihedral angle between the two benzene rings is 11.52 (7°. In the crystal, molecules are linked through a pair of amino–nitrile N—H...N hydrogen bonds, forming inversion dimers. These assemble into a three-dimensional network via C—H...O and C—H...π interactions.

  5. Smectic Phase Formed by DNA Dimers

    Science.gov (United States)

    Salamonczyk, Miroslaw; Gleeson, James; Jakli, Antal; Sprunt, Samuel; Dhont, Jan; Stiakakis, Emmanuel

    The rapidly expanding bio market is driving the development and characterization of new multifunctional materials. In particular, nucleic acids are under intense study for gene therapy, drug delivery and other bio-safe applications [1,2,3]. DNA is well-known to form a cholesteric nematic liquid crystal in its native form; however, much recent research has focused on self-assembly and mesomorphic behavior in concentrated solutions of short DNA helices [4]. Our work focuses on DNA dimers, consisting of 48 base-pair double-stranded helices connected by a 5 to 20 base flexible single strand, and suspended in a natural buffer. Depending on temperature, concentration and length of the flexible spacer, polarizing optical microscopy and small angle x-ray scattering reveal cholesteric nematic and, remarkably, smectic liquid crystalline phases. A model for smectic phase formation in this system will be presented. 1] J.-L. Lim et al., Int. J. of. Pharm. 490 (2015) 2652] D.-H. Kim et al., Nature Biotech. 23 (2005) 2223] K. Liu et al., Chem. Eur. J. 21 (2015) 48984] M. Nakata et al., Science 318 (2007) 1276 NSF DMR 1307674.

  6. Dimerization of Human Growth Hormone by Zinc

    Science.gov (United States)

    Cunningham, Brian C.; Mulkerrin, Michael G.; Wells, James A.

    1991-08-01

    Size-exclusion chromatography and sedimentation equilibrium studies demonstrated that zinc ion (Zn2+) induced the dimerization of human growth hormone (hGH). Scatchard analysis of 65Zn2+ binding to hGH showed that two Zn2+ ions associate per dimer of hGH in a cooperative fashion. Cobalt (II) can substitute for Zn2+ in the hormone dimer and gives a visible spectrum characteristic of cobalt coordinated in a tetrahedral fashion by oxygen- and nitrogen-containing ligands. Replacement of potential Zn2+ ligands (His18, His21, and Glu174) in hGH with alanine weakened both Zn2+ binding and hGH dimer formation. The Zn2+-hGH dimer was more stable than monomeric hGH to denaturation in guanidine-HCl. Formation of a Zn2+-hGH dimeric complex may be important for storage of hGH in secretory granules.

  7. Synthesis and Structural Characterization of a Molecular Plutonium(IV) Compound Constructed from Dimeric Building Blocks

    Energy Technology Data Exchange (ETDEWEB)

    Runde, Wolfgang; Brodnax, Lia F.; Goff, George S.; Peper, Shane M.; Taw, Felicia L.; Scott, Brian L.

    2007-04-01

    Single crystals of Na8Pu2(O2)2(CO3)6•12H2O, exhibiting mu2, eta2-O2 ligands in unprecedented Pu(IV) dimeric units, were obtained at ambient temperature from aqueous Plutonium(IV) peroxide carbonate solution.

  8. Dimer-tetramer transition between solution and crystalline states of streptavidin and avidin mutants.

    Science.gov (United States)

    Pazy, Yael; Eisenberg-Domovich, Yael; Laitinen, Olli H; Kulomaa, Markku S; Bayer, Edward A; Wilchek, Meir; Livnah, Oded

    2003-07-01

    The biotin-binding tetrameric proteins, streptavidin from Streptomyces avidinii and chicken egg white avidin, are excellent models for the study of subunit-subunit interactions of a multimeric protein. Efforts are thus being made to prepare mutated forms of streptavidin and avidin, which would form monomers or dimers, in order to examine their effect on quaternary structure and assembly. In the present communication, we compared the crystal structures of binding site W-->K mutations in streptavidin and avidin. In solution, both mutant proteins are known to form dimers, but upon crystallization, both formed tetramers with the same parameters as the native proteins. All of the intersubunit bonds were conserved, except for the hydrophobic interaction between biotin and the tryptophan that was replaced by lysine. In the crystal structure, the binding site of the mutated apo-avidin contains 3 molecules of structured water instead of the 5 contained in the native protein. The lysine side chain extends in a direction opposite that of the native tryptophan, the void being partially filled by an adjacent lysine residue. Nevertheless, the binding-site conformation observed for the mutant tetramer is an artificial consequence of crystal packing that would not be maintained in the solution-phase dimer. It appears that the dimer-tetramer transition may be concentration dependent, and the interaction among subunits obeys the law of mass action.

  9. Dimer models and Calabi-Yau algebras

    CERN Document Server

    Broomhead, Nathan

    2008-01-01

    In this thesis we study dimer models, as introduced in string theory, which give a way of writing down a class of non-commutative `superpotential' algebras. Some examples are 3-dimensional Calabi-Yau algebras, as defined by Ginzburg, and some are not. We consider two types of `consistency' condition on dimer models, and show that a `geometrically consistent' model is `algebraically consistent'. Finally we prove that the algebras obtained from algebraically consistent dimer models are 3-dimensional Calabi-Yau algebras.

  10. On Dimer Models and Closed String Theories

    OpenAIRE

    Sarkar, Tapobrata

    2007-01-01

    We study some aspects of the recently discovered connection between dimer models and D-brane gauge theories. We argue that dimer models are also naturally related to closed string theories on non compact orbifolds of $\\BC^2$ and $\\BC^3$, via their twisted sector R charges, and show that perfect matchings in dimer models correspond to twisted sector states in the closed string theory. We also use this formalism to study the combinatorics of some unstable orbifolds of $\\BC^2$.

  11. Dimerization of norbornene on zeolite catalysts

    Institute of Scientific and Technical Information of China (English)

    N. G. Grigor’eva; S. V. Bubennov; L. M. Khalilov; B. I. Kutepov

    2015-01-01

    The high activity and selectivity of H‐Beta and H‐ZSM‐12 zeolites in the dimerization of norbornene was established. The norbornene conversion reached 100%in chlorinated paraffin and argon gas medium, with a selectivity of dimer formation of 88%–98%. Four stereo‐isomers of the bis‐2,2’‐norbornylidene structure were identified in the dimer fraction, with the (Z)‐anti‐bis‐2,2’‐norbornylidene prevailing over the others.

  12. Enhanced Chiral Recognition by Cyclodextrin Dimers

    Directory of Open Access Journals (Sweden)

    Bart Jan Ravoo

    2011-07-01

    Full Text Available In this article we investigate the effect of multivalency in chiral recognition. To this end, we measured the host-guest interaction of a β-cyclodextrin dimer with divalent chiral guests. We report the synthesis of carbohydrate-based water soluble chiral guests functionalized with two borneol, menthol, or isopinocampheol units in either (+ or (– configuration. We determined the interaction of these divalent guests with a β-cyclodextrin dimer using isothermal titration calorimetry. It was found that—in spite of a highly unfavorable conformation—the cyclodextrin dimer binds to guest dimers with an increased enantioselectivity, which clearly reflects the effect of multivalency.

  13. Sputtering of dimers off a silicon surface

    Energy Technology Data Exchange (ETDEWEB)

    Nietiadi, Maureen L. [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Rosandi, Yudi [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Department of Physics, Universitas Padjadjaran, Jatinangor, Sumedang 45363 (Indonesia); Kopnarski, Michael [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Institut fuer Oberflaechen- und Schichtanalytik IFOS GmbH, Trippstadter Strasse 120, D-67663 Kaiserslautern (Germany); Urbassek, Herbert M., E-mail: urbassek@rhrk.uni-kl.de [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany)

    2012-10-15

    We present experimental and molecular-dynamics simulation results of the sputtering of a Si surface by 2 keV Ar ions. Results on both the monomer and dimer distributions are presented. In simulation, these distributions follow a generalized Thompson law with power exponent n=2 and n=3, respectively. The experimental data, obtained via plasma post-ionization in an SNMS (secondary neutral mass spectrometry) apparatus, show good agreement with respect to the dimer fraction, and the relative energy distributions of dimers and monomers. The consequences for the dimer sputtering mechanism are discussed.

  14. Crystal structure of 2-(2-bromophenyl-4-(1H-indol-3-yl-6-(thiophen-2-ylpyridine-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    R. Vishnupriya

    2014-09-01

    Full Text Available In the title compound, C24H14BrN3S, the dihedral angles between the planes of the pyridine ring and the pendant thiophene ring, the indole ring system (r.m.s. deviation = 0.022 Å and the bromobenzene ring are 9.37 (17, 21.90 (12 and 69.01 (15°, respectively. The approximate coplanarity of the central ring and the indole ring system is supported by two intramolecular C—H...N interactions. In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds generate R22(16 loops and the dimers are linked by C—H...π and aromatic π–π stacking [shortest centroid–centroid separation = 3.729 (3 Å] into a three-dimensional network.

  15. The crystal structure of 6-(4-chlorophenyl-2-(4-methylbenzylimidazo[2,1-b][1,3,4]thiadiazole-5-carbaldehyde

    Directory of Open Access Journals (Sweden)

    A. Sowmya

    2016-10-01

    Full Text Available In the title imidazo[2,1-b][1,3,4]thiadiazole derivative, C19H14ClN3OS, the 4-methylbenzyl and chlorophenyl rings are inclined to the planar imidazo[2,1-b][1,3,4]thiadiazole moiety (r.m.s. deviation = 0.012 Å by 64.5 (1 and 3.7 (1°, respectively. The molecular structure is primarily stabilized by a strong intramolecular C—H...O hydrogen bond, leading to the formation of a pseudo-seven-membered S(7 ring motif, and a short intramolecular C—H...N contact forming an S(5 ring motif. In the crystal, molecules are linked by pairs of C—H...S hydrogen bonds, forming inversion dimers. The dimers are linked by C—H...O and C—H...π interactions, forming chains propagating along [110].

  16. Crystal structure of 2-amino-3-cyano-4-(4-methoxyphenyl-4H-1-benzothieno[3,2-b]pyran

    Directory of Open Access Journals (Sweden)

    Mohamed Bakhouch

    2015-12-01

    Full Text Available The three fused five- and six-membered rings in the title compound, C19H14N2O2S, are virtually coplanar, with the maximum deviation from the mean plane being 0.060 (1 Å. This benzothieno[3,2-b]pyran ring system is nearly perpendicular to the plane of the 4-methoxyphenyl ring, forming a dihedral angle of 83.65 (5°. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds into inversion dimers. The dimeric units are further connected by an N—H...O hydrogen bond into a tape running along the b axis. The tapes are linked together by C—H...N and π–π interactions [centroid–centroid distance = 3.7743 (8 Å], forming a three-dimensional network.

  17. New investigations of the guanine trichloro cuprate(II) complex crystal

    Science.gov (United States)

    Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

    2017-01-01

    Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

  18. Synthesis and Structure of Mixed Distannoxane Dimers [ClR2SnOSnR'2Cl]2

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Mixed distannoxane dimers [ClR2SnOSnR'2Cl]2 were synthesized by the reaction of R2SnO (R = Bu, Pr) and R2SnCl2 (R = Me, Ph, Cy, Oct). The crystal structures of compound 1 and 5 show they are ladder-type dimers that contain a central planar Sn2O2 four-membered ring. Both endo- and exo-Sn atoms are five-coordinate.

  19. Structure of Cyclic Aryl Thiosester Dimer Based on o—Phthaloyl Dichloride and Bis(4—mercaptophenyl)Sulfide

    Institute of Scientific and Technical Information of China (English)

    郭庆中; 王红华; 陈天禄

    2003-01-01

    A Cyclic aryl thioester dimer was prepared by the reaction of o-phthaloyl dichloride and bis(4-mercaptophenyl)sulfide in good yield under pseudo-high dilution conditions via interfacial polycondensation.The structure of the cyclic dimer was confirmed by a conmbination of MALDI-TOF-Ms,FTIR,gel permeation chromatography and NMR analyses.The X-ray diffraction study of the single crystal of cyclic thioester dimer obtained form two sotutions reveals no severe internal strain on the cyclic structure.

  20. Dimeric Matrine-Type Alkaloids from the Roots of Sophora flavescens and Their Anti-Hepatitis B Virus Activities.

    Science.gov (United States)

    Zhang, Yu-Bo; Zhan, Li-Qin; Li, Guo-Qiang; Wang, Feng; Wang, Ying; Li, Yao-Lan; Ye, Wen-Cai; Wang, Guo-Cai

    2016-08-01

    Six unusual matrine-type alkaloid dimers, flavesines A-F (1-6, respectively), together with three proposed biosynthetic intermediates (7-9) were isolated from the roots of Sophora flavescens. Compounds 1-5 were the first natural matrine-type alkaloid dimers, and compound 6 represented an unprecedented dimerization pattern constructed by matrine and (-)-cytisine. Their structures were elucidated by NMR, MS, single-crystal X-ray diffraction, and a chemical method. The hypothetical biogenetic pathways of 1-6 were also proposed. Compounds 1-9 exhibited inhibitory activities against hepatitis B virus.

  1. Dimerization and heme binding are conserved in amphibian and starfish homologues of the microRNA processing protein DGCR8.

    Directory of Open Access Journals (Sweden)

    Rachel Senturia

    Full Text Available Human DiGeorge Critical Region 8 (DGCR8 is an essential microRNA (miRNA processing factor that is activated via direct interaction with Fe(III heme. In order for DGCR8 to bind heme, it must dimerize using a dimerization domain embedded within its heme-binding domain (HBD. We previously reported a crystal structure of the dimerization domain from human DGCR8, which demonstrated how dimerization results in the formation of a surface important for association with heme. Here, in an attempt to crystallize the HBD, we search for DGCR8 homologues and show that DGCR8 from Patiria miniata (bat star also binds heme. The extinction coefficients (ε of DGCR8-heme complexes are determined; these values are useful for biochemical analyses and allow us to estimate the heme occupancy of DGCR8 proteins. Additionally, we present the crystal structure of the Xenopus laevis dimerization domain. The structure is very similar to that of human DGCR8. Our results indicate that dimerization and heme binding are evolutionarily conserved properties of DGCR8 homologues not only in vertebrates, but also in at least some invertebrates.

  2. Cholesterol modulates the dimer interface of the β₂-adrenergic receptor via cholesterol occupancy sites.

    Science.gov (United States)

    Prasanna, Xavier; Chattopadhyay, Amitabha; Sengupta, Durba

    2014-03-18

    The β2-adrenergic receptor is an important member of the G-protein-coupled receptor (GPCR) superfamily, whose stability and function are modulated by membrane cholesterol. The recent high-resolution crystal structure of the β2-adrenergic receptor revealed the presence of possible cholesterol-binding sites in the receptor. However, the functional relevance of cholesterol binding to the receptor remains unexplored. We used MARTINI coarse-grained molecular-dynamics simulations to explore dimerization of the β2-adrenergic receptor in lipid bilayers containing cholesterol. A novel (to our knowledge) aspect of our results is that receptor dimerization is modulated by membrane cholesterol. We show that cholesterol binds to transmembrane helix IV, and cholesterol occupancy at this site restricts its involvement at the dimer interface. With increasing cholesterol concentration, an increased presence of transmembrane helices I and II, but a reduced presence of transmembrane helix IV, is observed at the dimer interface. To our knowledge, this study is one of the first to explore the correlation between cholesterol occupancy and GPCR organization. Our results indicate that dimer plasticity is relevant not just as an organizational principle but also as a subtle regulatory principle for GPCR function. We believe these results constitute an important step toward designing better drugs for GPCR dimer targets.

  3. Dimeric (isoquinoline)(N-salicylidene-D,L-glutamato)copper(II) ethanol solvate.

    Science.gov (United States)

    Langer, Vratislav; Gyepesová, Dalma; Kohútová, Mária; Valent, Aladár

    2009-05-01

    The title racemic complex, bis[mu-N-(2-oxidobenzylidene)-D,L-glutamato(2-)]bis[(isoquinoline)copper(II)] ethanol disolvate, [Cu(2)(C(12)H(11)NO(5))(2)(C(9)H(7)N)(2)].2C(2)H(6)O, adopts a square-pyramidal Cu(II) coordination mode with a tridentate N-salicylideneglutamato Schiff base dianion and an isoquinoline ligand bound in the basal plane. The apex of the pyramid is occupied by a phenolic O atom from the adjacent chelate molecule at an apical distance of 2.487 (3) A, building a dimer located on the crystallographic inversion center. The Cu...Cu spacing within the dimers is 3.3264 (12) A. The ethanol solvent molecules are hydrogen bonded to the dimeric complex molecules, forming infinite chains in the a direction. The biological activity of the title complex has been studied.

  4. An alternative RNA polymerase I structure reveals a dimer hinge.

    Science.gov (United States)

    Kostrewa, Dirk; Kuhn, Claus-D; Engel, Christoph; Cramer, Patrick

    2015-09-01

    RNA polymerase I (Pol I) is the central, 14-subunit enzyme that synthesizes the ribosomal RNA (rRNA) precursor in eukaryotic cells. The recent crystal structure of Pol I at 2.8 Å resolution revealed two novel elements: the `expander' in the active-centre cleft and the `connector' that mediates Pol I dimerization [Engel et al. (2013), Nature (London), 502, 650-655]. Here, a Pol I structure in an alternative crystal form that was solved by molecular replacement using the original atomic Pol I structure is reported. The resulting alternative structure lacks the expander but still shows an expanded active-centre cleft. The neighbouring Pol I monomers form a homodimer with a relative orientation distinct from that observed previously, establishing the connector as a hinge between Pol I monomers.

  5. Mahler Measure, Eisenstein Series and Dimers

    NARCIS (Netherlands)

    Stienstra, J.

    2007-01-01

    This note reveals a mysterious link between the partition function of certain dimer models on 2-dimensional tori and the L-function of their spectral curves. It also relates the partition function in certain families of dimer models to Eisenstein series. http://www.arxiv.org/abs/math.NT/0502197

  6. Dimeric assembly of enterocyte brush border enzymes

    DEFF Research Database (Denmark)

    Danielsen, E M

    1994-01-01

    temperature (20 degrees C) reduced the rate of, but did not prevent, dimerization. Maltase-glucoamylase (EC 3.2.1.20) only appeared as a dimer when extracted and analyzed under low salt conditions, suggesting a weak association between the two subunits. This finding is consistent with the electronmicroscopic...

  7. Potassium Hexacyanoferrate (III-Catalyzed Dimerization of Hydroxystilbene: Biomimetic Synthesis of Indane Stilbene Dimers

    Directory of Open Access Journals (Sweden)

    Jing-Shan Xie

    2015-12-01

    Full Text Available Using potassium hexacyanoferrate (III–sodium acetate as oxidant, the oxidative coupling reaction of isorhapontigenin and resveratrol in aqueous acetone resulted in the isolation of three new indane dimers 4, 6, and 7, together with six known stilbene dimers. Indane dimer 5 was obtained for the first time by direct transformation from isorhapontigenin. The structures and relative configurations of the dimers were elucidated using spectral analysis, and their possible formation mechanisms were discussed. The results indicate that this reaction could be used as a convenient method for the semi-synthesis of indane dimers because of the mild conditions and simple reaction products.

  8. Locally Inverse Semigroups with Inverse Transversals

    Institute of Scientific and Technical Information of China (English)

    SHAO Yong; ZHAO Xian Zhong

    2009-01-01

    Let S be a locally inverse semigroup with an inverse transversal S°. In this paper, we construct an amenable partial order on S by an R-cone. Conversely, every amenable partial order on S can be constructed in this way. We give some properties of a locally inverse semigroup with a Clifford transversal. In particular, if S is a locally inverse semigroup with a Clifford transversal, then there is an order-preserving bijection from the set of all amenable partial orders on S to the set of all R-cones of S.

  9. Proteolysis of truncated hemolysin A yields a stable dimerization interface

    Energy Technology Data Exchange (ETDEWEB)

    Novak, Walter R.P.; Bhattacharyya, Basudeb; Grilley, Daniel P.; Weaver, Todd M. (Wabash); (UW)

    2017-02-21

    Wild-type and variant forms of HpmA265 (truncated hemolysin A) fromProteus mirabilisreveal a right-handed, parallel β-helix capped and flanked by segments of antiparallel β-strands. The low-salt crystal structures form a dimeric structureviathe implementation of on-edge main-chain hydrogen bonds donated by residues 243–263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formedviamain-chain hydrogen bonds donated by residues 203–215 of adjacent monomers, and a previously unobserved tetramer is formed. In addition, an eight-stranded antiparallel β-sheet is formed from the flap regions of crystallographically related monomers in the high-salt structures. This new interface is possible owing to additional proteolysis of these variants after Tyr240. The interface formed in the high-salt crystal forms of hemolysin A variants may mimic the on-edge β-strand positioning used in template-assisted hemolytic activity.

  10. Statistical transmutation in doped quantum dimer models.

    Science.gov (United States)

    Lamas, C A; Ralko, A; Cabra, D C; Poilblanc, D; Pujol, P

    2012-07-06

    We prove a "statistical transmutation" symmetry of doped quantum dimer models on the square, triangular, and kagome lattices: the energy spectrum is invariant under a simultaneous change of statistics (i.e., bosonic into fermionic or vice versa) of the holes and of the signs of all the dimer resonance loops. This exact transformation enables us to define the duality equivalence between doped quantum dimer Hamiltonians and provides the analytic framework to analyze dynamical statistical transmutations. We investigate numerically the doping of the triangular quantum dimer model with special focus on the topological Z(2) dimer liquid. Doping leads to four (instead of two for the square lattice) inequivalent families of Hamiltonians. Competition between phase separation, superfluidity, supersolidity, and fermionic phases is investigated in the four families.

  11. Universal four-Boson states in ultracold molecular gases: resonant effects in dimer-dimer collisions.

    Science.gov (United States)

    D'Incao, J P; von Stecher, J; Greene, Chris H

    2009-07-17

    We study the manifestations of universal four-body physics in ultracold dimer-dimer collisions. We show that resonant features associated with three-body Efimov physics and dimer-dimer scattering lengths are universally related. The emergence of universal four-boson states allows for the tunability of the dimer-dimer interaction, thus enabling the future study of ultracold molecular gases with both attractive and repulsive interactions. Moreover, our study of the interconversion between dimers and Efimov trimers shows that B2+B2-->B3+B rearrangement reactions can provide an efficient trimer formation mechanism. Our analysis of the temperature dependence of this reaction provides an interpretation of the available experimental data and sheds light on the possible experimental realization of rearrangement processes in ultracold gases.

  12. Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization

    DEFF Research Database (Denmark)

    Vinther, Tine N.; Norrman, Mathias; Strauss, Holger M.;

    2012-01-01

    An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...... in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic ß-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization...... and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization...

  13. Unravelling Thiol’s Role in Directing Asymmetric Growth of Au Nanorod–Au Nanoparticle Dimers

    KAUST Repository

    Huang, Jianfeng

    2015-12-15

    Asymmetric nanocrystals have practical significance in nanotechnologies but present fundamental synthetic challenges. Thiol ligands have proven effective in breaking the symmetric growth of metallic nanocrystals but their exact roles in the synthesis remain elusive. Here, we synthesized an unprecedented Au nanorod-Au nanoparticle (AuNR-AuNP) dimer structure with the assistance of a thiol ligand. On the basis of our experimental observations, we unraveled for the first time that the thiol could cause an inhomogeneous distribution of surface strains on the seed crystals as well as a modulated reduction rate of metal precursors, which jointly induced the asymmetric growth of monometallic dimers. © 2015 American Chemical Society.

  14. L-Cysteine halogenides: A new family of salts with an L-cysteine⋯L-cysteinium dimeric cation

    Science.gov (United States)

    Ghazaryan, V. V.; Minkov, V. S.; Boldyreva, E. V.; Petrosyan, A. M.

    2016-10-01

    Two L-cysteinium-halogenides with (L-cysteine···L-cysteinium) dimeric cations have been obtained, (L-Cys⋯L-Cys+)·Cl-, and (L-Cys⋯L-Cys+)·Br-. Both salts crystallize in monoclinic space group P21. Although these salts have the same dimeric cations and isotypical halogen anions, crystal packing is different. The main difference between the two salts rests in the conformation of (L-Cys⋯L-Cys+) dimeric cation, which also differs from that of the dimeric cation in the previously reported compound L-Cys+(L-Cys⋯L-Cys+)·F-·(F-⋯HF). The dimeric cation is formed by a very short O-H⋯O hydrogen bond with d(O···O) of 2.449(2) Å and 2.435(11) Å in the chloride and bromide, respectively. In addition to crystal structure analysis, Infrared and Raman spectra have been registered and discussed with a particular focus on intermolecular interactions. The L-Cys+·Br-·H2O salt with a simple L-cysteinium cation was also obtained and the crystal structure solved. It resembles its chloride analogue, L-Cys+·Cl-·H2O.

  15. Crystal structure of (E-4-(acetoxyimino-N-allyl-3-isopropyl-2,6-diphenylpiperidine-1-carbothioamide

    Directory of Open Access Journals (Sweden)

    T. Mohandas

    2015-08-01

    Full Text Available The title compound, C26H31N3O2S, crystallizes with two molecules (A and B in the asymmetric unit. In each case, the piperidine ring exists in a twist-boat conformation. The dihedral angle between the phenyl rings is 46.16 (12° in molecule A and 44.95 (12° in molecule B. In both molecules, the allyl side chain is disordered over two orientations in a 0.649 (9:0.351 (9 ratio for molecule A and 0.826 (10:0.174 (10 ratio for molecule B. In the crystal, neither molecule forms a hydrogen bond from its N—H group, presumably due to steric hindrance. A+A and B+B inversion dimers are formed, linked by pairs of weak C—H...O hydrogen bonds enclosing R22(22 ring motifs.

  16. Crystal structure of ethyl (4R-2-amino-7-hydroxy-4-phenyl-4H-chromene-3-carboxylate

    Directory of Open Access Journals (Sweden)

    Joel T. Mague

    2015-07-01

    Full Text Available In the title compound, C18H17NO4, the dihedral angle between the phenyl ring and the fused six-membered ring is 77.65 (4°. The conformation of the molecule is determined in part by an intramolecular N—H...O hydrogen bond between the amino H atom and the carbonyl O atom, forming an S(6 motif. In the crystal, molecules are linked into N—H...O hydrogen-bonded inversion dimers which are then connected into chains along [001], forming a two-dimensional network parallel to (100 via O—H...O hydrogen bonds. C—H...O interactions further contribute to the crystal stability. The ethyl group is disordered over two sets of sites in a 0.801 (5:0.199 (5 ratio.

  17. Crystal structure of 4-(meth-oxy-carbon-yl)phenyl-boronic acid.

    Science.gov (United States)

    Flanagan, Keith J; Senge, Mathias O

    2015-10-01

    In the title compound, C8H9BO4, the meth-oxy-carbonyl group is rotated out of the plane of the benzene ring by 7.70 (6)°. In the crystal, mol-ecules are linked via pairs of O-H⋯O hydrogen bonds, involving the boronic acid OH groups, forming inversion dimers. The dimers are linked via O-H⋯O hydrogen bonds, involving a boronic acid OH group and the carbonyl O atom, forming undulating sheets parallel to (10-2). Within the sheets there are also C-H⋯O hydrogen bonds present, also involving the carbonyl O atom. The sheets are linked via C-H⋯π and offset face-to-face π-inter-actions between inversion-related mol-ecules [inter-centroid distance = 3.7843 (16) Å, inter-planar distance = 3.3427 (4) Å and offset = 1.744 Å], forming a three-dimensional structure.

  18. Crystal structure of chlorido{4,5-dimethoxy-2-[(2,3-η-2-prop-2-en-1-yl]phenyl-κC1}(piperidine-κNplatinum(II ethanol monosolvate

    Directory of Open Access Journals (Sweden)

    Peter Mangwala Kimpende

    2014-11-01

    Full Text Available In the title compound, [Pt(C11H13O2Cl(C5H11N]·C2H5OH, the PtII cation is pentacoordinated in a distorted square-planar geometry. In the crystal, inversion dimers showing C—H...Cl and C—H...π interactions are further stacked in columns along the a axis via C—H...π interactions. The ethanol solvate molecule interacts with neighbouring methoxy groups of methyleugenol through O—H...O hydrogen bonds.

  19. Crystal structures of (E-3-(furan-2-yl-2-phenyl-N-tosylacrylamide and (E-3-phenyl-2-(m-tolyl-N-tosylacrylamide

    Directory of Open Access Journals (Sweden)

    Dong Cheng

    2016-06-01

    Full Text Available In the title N-tosylacrylamide compounds, C20H17NO4S, (I, and C23H21NO3S, (II, the conformation about the C=C bond is E. The acrylamide groups, [–NH—C(=O—C=C–], are almost planar, with the N—C—C=C torsion angle being −170.18 (14° in (I and −168.01 (17° in (II. In (I, the furan, phenyl and 4-methylbenzene rings are inclined to the acrylamide mean plane by 26.47 (11, 69.01 (8 and 82.49 (9°, respectively. In (II, the phenyl, 3-methylbenzene and 4-methylbenzene rings are inclined to the acrylamide mean plane by 11.61 (10, 78.44 (10 and 78.24 (10°, respectively. There is an intramolecular C—H...π interaction present in compound (II. In the crystals of both compounds, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(8 ring motif. In (I, the dimers are reinforced by C—H...O hydrogen bonds and linked by C—H...π interactions, forming chains along [011]. In the crystal of (II, the dimers are linked via C—H...O hydrogen bonds, forming chains along [100]. The chains are further linked by C—H...π interactions, forming layers parallel to (010.

  20. Quantum dimer model for the pseudogap metal

    Science.gov (United States)

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-01-01

    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S=1/2, charge +e fermionic dimers. The model realizes a “fractionalized Fermi liquid” with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8×8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments. PMID:26195771

  1. Quantum dimer model for the pseudogap metal.

    Science.gov (United States)

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-08-04

    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S = 1/2, charge +e fermionic dimers. The model realizes a "fractionalized Fermi liquid" with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8 × 8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments.

  2. Critical behavior in the cubic dimer model at nonzero monomer density

    Science.gov (United States)

    Sreejith, G. J.; Powell, Stephen

    2014-01-01

    We study critical behavior in the classical cubic dimer model (CDM) in the presence of a finite density of monomers. With attractive interactions between parallel dimers, the monomer-free CDM exhibits an unconventional transition from a Coulomb phase to a dimer crystal. Monomers act as charges (or monopoles) in the Coulomb phase and, at nonzero density, lead to a standard Landau-type transition. We use large-scale Monte Carlo simulations to study the system in the neighborhood of the critical point, and find results in agreement with detailed predictions of scaling theory. Going beyond previous studies of the transition in the absence of monomers, we explicitly confirm the distinction between conventional and unconventional criticality, and quantitatively demonstrate the crossover between the two. Our results also provide additional evidence for the theoretical claim that the transition in the CDM belongs in the same universality class as the deconfined quantum critical point in the SU (2) JQ model.

  3. Model for growth hormone receptor activation based on subunit rotation within a receptor dimer

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Richard J.; Adams, Julian J.; Pelekanos, Rebecca A.; Wan, Yu; McKinstry, William J.; Palethorpe, Kathryn; Seeber, Ruth M.; Monks, Thea A.; Eidne, Karin A.; Parker, Michael W.; Waters, Michael J. (UWA); (St. Vincent); (Queensland)

    2010-07-13

    Growth hormone is believed to activate the growth hormone receptor (GHR) by dimerizing two identical receptor subunits, leading to activation of JAK2 kinase associated with the cytoplasmic domain. However, we have reported previously that dimerization alone is insufficient to activate full-length GHR. By comparing the crystal structure of the liganded and unliganded human GHR extracellular domain, we show here that there is no substantial change in its conformation on ligand binding. However, the receptor can be activated by rotation without ligand by inserting a defined number of alanine residues within the transmembrane domain. Fluorescence resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET) and coimmunoprecipitation studies suggest that receptor subunits undergo specific transmembrane interactions independent of hormone binding. We propose an activation mechanism involving a relative rotation of subunits within a dimeric receptor as a result of asymmetric placement of the receptor-binding sites on the ligand.

  4. Crystal structure of 5,5'-bis-(di-methyl-amino)-N,N'-(3-methyl-3-aza-pentane-1,5-di-yl)di(naphthalene-1-sulfonamide).

    Science.gov (United States)

    Horne, Toyketa V; Haque, Syed A; Barton, Adrianne; Hossain, Md Alamgir

    2015-12-01

    In the title compound, C29H37N5O4S2, two arms substituted with dansyl derivatives are connected to a central tertiary amine, where the dihedral angle between the planes of two dansyl units is 56.39 (4)°. Each arm contains a sulfonamide functional group and both N-H groups in the compound are pointed to the same side. The central part of the mol-ecule is disordered over three sets of sites with a refined occupancy ratio of 0.547 (4):0.328 (4):0.125 (3). No intra-molecular π-π or hydrogen-bonding inter-actions are observed. In the crystal, mol-ecules are linked via pairs of N-H⋯O inter-actions involving the same acceptor atom, forming inversion dimers. In addition, C-H⋯O inter-actions exist between molecules, providing further stabilization of dimers.

  5. Crystal structure of 26-(4-methylphenyl-8,11,14,17-tetraoxa-28-azatetracyclo[22.3.1.02,7.018,23]hexacosa-2,4,6,18(23,19,21,24(1,25,27-nonaene

    Directory of Open Access Journals (Sweden)

    T. Thanh Van Tran

    2016-05-01

    Full Text Available The title compound, C30H29NO4, is a tetracyclic system containing a 4-arylpyridine fragment, two benzene rings and an aza-17-crown-5 ether moiety, in a bowl-like arrangement. The pyridine ring is inclined to the 4-methylphenyl ring by 26.64 (6°, and by 57.43 (6 and 56.81 (6° to the benzene rings. The benzene rings are inclined to one another by 88.32 (6°. In the crystal, molecules are linked by pairs of C—H...N hydrogen bonds, forming inversion dimers with an R22(14 ring motif. The dimers are linked via a number of C—H...π interactions, forming a three-dimensional architecture.

  6. Crystal structure of 13-(2-methoxyphenyl-3,4-dihydro-2H-indazolo[1,2-b]phthalazine-1,6,11(13H-trione

    Directory of Open Access Journals (Sweden)

    Abdelmalek Bouraiou

    2015-08-01

    Full Text Available In the title compound, C22H18N2O4, the three fused rings of the pyrazolophthalazine moiety are coplanar (r.m.s. deviation = 0.027 Å. The cyclohexene ring fused to the pyrazolidine ring, so forming the indazolophthalazine unit, has a half-chair conformation. The benzene ring is almost normal to the mean plane of the pyrazolophthalazine moiety, with a dihedral angle of 87.21 (6° between their planes. In the crystal, molecules are linked by pairs of C—H...O hydrogen bonds forming inversion dimers. The dimers are linked via C—H...π interactions, forming slabs parallel to (100. Between the slabs there are weak π–π interactions [shortest inter-centroid distance = 3.6664 (9 Å], leading to the formation of a three-dimensional structure.

  7. Crystal structure of (E-2-benzylidene-4-[(3-phenyl-4,5-dihydroisoxazol-5-ylmethyl]-2H-benzo[b][1,4]thiazin-3(4H-one

    Directory of Open Access Journals (Sweden)

    Nada Kheira Sebbar

    2015-06-01

    Full Text Available In the title compound, C25H20N2O2S, the dihydroisoxazole ring exhibits an envelope conformation with the methine atom being the flap, while the 1,4-thiazine ring displays a screw-boat conformation. The six-membered ring fused to the 1,4-thiazine ring makes dihedral angles of 63.04 (2 and 54.7 (2° with the mean planes through the five-membered heterocycle and the attached phenyl ring, respectively. The phenyl group connected to the 1,4-thiazine ring is disordered over two sites [major component = 0.57 (2]. The most prominent interactions in the crystal structure are C—H...O hydrogen bonds that link molecules, forming inversion dimers, and C—H...N hydrogen bonds that link the dimers into columns parallel to the b axis.

  8. The Structure of the Poxvirus A33 Protein Reveals a Dimer of Unique C-Type Lectin-Like Domains

    Energy Technology Data Exchange (ETDEWEB)

    Su, Hua-Poo; Singh, Kavita; Gittis, Apostolos G.; Garboczi, David N. (NIH)

    2010-11-03

    The current vaccine against smallpox is an infectious form of vaccinia virus that has significant side effects. Alternative vaccine approaches using recombinant viral proteins are being developed. A target of subunit vaccine strategies is the poxvirus protein A33, a conserved protein in the Chordopoxvirinae subfamily of Poxviridae that is expressed on the outer viral envelope. Here we have determined the structure of the A33 ectodomain of vaccinia virus. The structure revealed C-type lectin-like domains (CTLDs) that occur as dimers in A33 crystals with five different crystal lattices. Comparison of the A33 dimer models shows that the A33 monomers have a degree of flexibility in position within the dimer. Structural comparisons show that the A33 monomer is a close match to the Link module class of CTLDs but that the A33 dimer is most similar to the natural killer (NK)-cell receptor class of CTLDs. Structural data on Link modules and NK-cell receptor-ligand complexes suggest a surface of A33 that could interact with viral or host ligands. The dimer interface is well conserved in all known A33 sequences, indicating an important role for the A33 dimer. The structure indicates how previously described A33 mutations disrupt protein folding and locates the positions of N-linked glycosylations and the epitope of a protective antibody.

  9. Crystal structure of 2-bromobenzoic acid at 120 K: a redetermination

    Directory of Open Access Journals (Sweden)

    Kornelia Kowalska

    2014-10-01

    Full Text Available The crystal structure of the title compound, C7H5BrO2, was originally studied using photographic data at room temperature with Cu Kα radiation [Ferguson & Sim (1962. Acta Cryst. 15, 346–350]. The present study was undertaken at 120 K with a CCD diffractometer using Cu Kα radiation, and resulted in improved geometrical parameters. In the molecule, the carboxy group is inclined to the benzene ring by 18.7 (2° and there is a close intramolecular Br...O contact of 3.009 (3 Å. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonds, forming inversion dimers with the classical R22(8 ring motif for carboxylic acids. Neighbouring dimers are linked by weak C—H...O hydrogen bonds, forming tapes propagating in [1-10]. Adjacent tapes interact by slipped parallel π–π interactions [inter-centroid distance = 3.991 (2, interplanar distance = 3.509 (2 Å, slippage = 1.900 Å] to form columns approximately along the b-axis direction. Neighbouring columns interact dispersively, forming a three-dimensional framework structure.

  10. Inverse anticipating chaos synchronization.

    Science.gov (United States)

    Shahverdiev, E M; Sivaprakasam, S; Shore, K A

    2002-07-01

    We derive conditions for achieving inverse anticipating synchronization where a driven time-delay chaotic system synchronizes to the inverse future state of the driver. The significance of inverse anticipating chaos in delineating synchronization regimes in time-delay systems is elucidated. The concept is extended to cascaded time-delay systems.

  11. Locative Inversion in Cantonese.

    Science.gov (United States)

    Mok, Sui-Sang

    This study investigates the phenomenon of "Locative Inversion" in Cantonese. The term "Locative Inversion" indicates that the locative phrase (LP) syntactic process in Cantonese and the appears at the sentence-initial position and its logical subject occurs postverbally. It is demonstrated that this Locative Inversion is a…

  12. Quantitative analysis of cyclic dimer fatty acid content in the dimerization product by proton NMR spectroscopy.

    Science.gov (United States)

    Park, Kyun Joo; Kim, Minyoung; Seok, Seunghwan; Kim, Young-Wun; Kim, Do Hyun

    2015-01-01

    In this work, (1)H NMR is utilized for the quantitative analysis of a specific cyclic dimer fatty acid in a dimer acid mixture using the pseudo-standard material of mesitylene on the basis of its structural similarity. Mesitylene and cyclic dimer acid levels were determined using the signal of the proton on the cyclic ring (δ=6.8) referenced to the signal of maleic acid (δ=6.2). The content of the cyclic dimer fatty acid was successfully determined through the standard curve of mesitylene and the reported equation. Using the linearity of the mesitylene curve, the cyclic dimer fatty acid in the oil mixture was quantified. The results suggest that the proposed method can be used to quantify cyclic compounds in mixtures to optimize the dimerization process.

  13. Carbon Inverse Opal Rods for Nonenzymatic Cholesterol Detection.

    Science.gov (United States)

    Zhong, Qifeng; Xie, Zhuoying; Ding, Haibo; Zhu, Cun; Yang, Zixue; Gu, Zhongze

    2015-11-18

    Carbon inverse opal rods made from silica photonic crystal rods are used for nonenzymatic cholesterol sensing. The characteristic reflection peak originating from the physical periodic structure works as sensing signals for quantitatively estimating cholesterol concentrations. Carbon inverse opal rods work both in cholesterol standard solutions and human serum. They are suitable for practical use in clinical diagnose.

  14. Synthesis and photonic bandgap characterization of polymer inverse opals

    Energy Technology Data Exchange (ETDEWEB)

    Miguez, H.; Meseguer, F.; Lopez, C. [Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Inst. de Ciencia de Materiales; Universidad Politecnica de Valencia (Spain). Centro Tecnologico de Ondas; Lopez-Tejeira, F.; Sanchez-Dehesa, J. [Universidad Autonoma de Madrid (Spain). Dept. de Fisica Teorica de la Materia Condensada

    2001-03-16

    Polymer inverse opals with long-range order have been fabricated and their photonic crystal behavior examined. Good agreement between band structure calculations and experiment is found. It is envisaged that these inverse opals could be used for the modification of the electronic properties of incorporated luminescent materials and as matrices for the synthesis of spherical colloidal particles. (orig.)

  15. Crystal structure of 4-(2-azidophenyl-5-benzoyl-2-(1H-indol-3-yl-1H-pyrrole-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    G. Vimala

    2015-05-01

    Full Text Available In the title compound, C26H16N6O, the dihedral angles between the central pyrrole ring and the pendant indole ring system (r.m.s. deviation = 0.027 Å and the azide-bearing benzene ring are 37.56 (8 and 51.62 (11°, respectively. The azide group is almost coplanar with its attached benzene ring [C—C—N—N = 3.8 (3°]. The benzoyl benzene ring is disordered over two orientations twisted with respect to each other by 9.29 (8° in a 0.514 (2:0.486 (2 ratio. In the crystal, inversion dimers linked by pairs of Np—H...O (p = pyrrole hydrogen bonds generate R22(10 loops. A second inversion dimer arises from a pair of Ni—H...Nc (i = indole and c = cyanide hydrogen bonds, which generates an R22(16 loop. Together, the hydrogen bonds lead to [011] chains in the crystal.

  16. Formation of cystine slipknots in dimeric proteins.

    Directory of Open Access Journals (Sweden)

    Mateusz Sikora

    Full Text Available We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.

  17. A New Dimeric Phthalide from Angelica sinensis

    Institute of Scientific and Technical Information of China (English)

    Ling YI; Ping LI; Zhi Ming BI

    2006-01-01

    A new dimeric phthalide named Z, Z'-3.3'a, 7.7'a-diligustilide was isolated from the roots of Angelica sinensis. Its structure was determined using spectroscopic methods and X-ray crystallographic diffraction analysis.

  18. The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase.

    Science.gov (United States)

    Wei, Ping; Fan, Keqiang; Chen, Hao; Ma, Liang; Huang, Changkang; Tan, Lei; Xi, Dong; Li, Chunmei; Liu, Ying; Cao, Aoneng; Lai, Luhua

    2006-01-20

    The 3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been proposed to be a key target for structural-based drug design against SARS. Accurate determination of the dimer dissociation constant and the role of the N-finger (residues 1-7) will provide more insights into the enzyme catalytic mechanism of SARS 3CL proteinase. The dimer dissociation constant of the wild-type protein was determined to be 14.0microM by analytical ultracentrifugation method. The N-finger fragment of the enzyme plays an important role in enzyme dimerization as shown in the crystal structure. Key residues in the N-finger have been studied by site-directed mutagenesis, enzyme assay, and analytical ultracentrifugation. A single mutation of M6A was found to be critical to maintain the dimer structure of the enzyme. The N-terminal octapeptide N8 and its mutants were also synthesized and tested for their potency as dimerization inhibitors. Peptide cleavage assay confirms that peptide N8 is a dimerization inhibitor with a K(i) of 2.20mM. The comparison of the inhibitory activities of N8 and its mutants indicates that the hydrophobic interaction of Met-6 and the electrostatic interaction of Arg-4 contribute most for inhibitor binding. This study describes the first example of inhibitors targeting the dimeric interface of SARS 3CL proteinase, providing a novel strategy for drug design against SARS and other coronaviruses.

  19. Designing Stable Antiparallel Coiled Coil Dimers

    Institute of Scientific and Technical Information of China (English)

    曾宪纲; 周海梦

    2001-01-01

    The history of antiparallel coiled coil dimer design is briefly reviewed and the main principles governing the successful designs are explained. They include analysis of the inter-subunit electrostatic repulsion for determining partners for dimerization and of the buried polar interaction for determining the relative orientation of the partners. A theory is proposed to explain the lack of antiparallel coiled coil homodimers in nature.

  20. Formation of Cystine Slipknots in Dimeric Proteins

    OpenAIRE

    Mateusz Sikora; Marek Cieplak

    2013-01-01

    We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dim...

  1. CtBP1/BARS Gly172-->Glu mutant structure: impairing NAD(H)-binding and dimerization.

    Science.gov (United States)

    Nardini, Marco; Valente, Carmen; Ricagno, Stefano; Luini, Alberto; Corda, Daniela; Bolognesi, Martino

    2009-03-27

    C-terminal binding proteins (CtBPs) are multi-functional proteins involved in nuclear transcriptional co-repression, Golgi membrane fission, and synaptic ribbon formation. Binding of NAD(H) to CtBPs promotes dimerization. CtBP dimers act as a scaffold for multimeric protein complex formation, thus bridging transcriptional repressors and their targets in the nucleus. Based on size-exclusion chromatography experiments and on the crystal structure of the NAD(H)-free G172E CtBP mutant, we show here that absence of NAD(H) induces flexibility/backbone conformational changes at the dimerization interface and at the CtBP interdomain region. The results presented shed first light on the correlation between NAD(H)-binding and functional CtBP dimerization.

  2. Role of Rydberg states in the photostability of heterocyclic dimers: the case of pyrazole dimer.

    Science.gov (United States)

    Zilberg, Shmuel; Haas, Yehuda

    2012-11-26

    A new route for the nonradiative decay of photoexcited, H-bonded, nitrogen-containing, heterocyclic dimers is offered and exemplified by a study of the pyrazole dimer. In some of these systems the N(3s) Rydberg state is the lowest excited singlet state. This state is formed by direct light absorption or by nonradiative transition from the allowed ππ* state. An isomer of this Rydberg state is formed by H atom transfer to the other component of the dimer. The newly formed H-bonded radical pair is composed of two radicals (a H-adduct of pyrazole, a heterocyclic analogue of the NH(4) radical) and the pyrazolium π-radical. It is calculated to have a shallow local minimum and is the lowest point on the PES of the H-pyrazole/pyrazolium radical pair. This species can cross back to the ground state of the original dimer through a relatively small energy gap and compete with the H-atom loss channel, known for the monomer. In both Rydberg dimers, an electron occupies a Rydberg orbital centered mostly on one of the two components of the dimer. This Rydberg Center Shift (RCS) mechanism, proposed earlier (Zilberg, S.; Kahan, A.; Haas, Y. Phys. Chem. Chem. Phys. 2012, 14, 8836), leads to deactivation of the electronically excited dimer while keeping it intact. It, thus, may explain the high photostability of the pyrazole dimer as well as other heterocyclic dimers.

  3. The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.

    Science.gov (United States)

    Schulte, Kathrin; Pawlowski, Nikolaus; Faelber, Katja; Fröhlich, Chris; Howard, Jonathan; Daumke, Oliver

    2016-03-02

    The immunity-related GTPases (IRGs) constitute a powerful cell-autonomous resistance system against several intracellular pathogens. Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. Further dimerization contacts involve switch II, the G4 helix and the trans stabilizing loop. The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. This study contributes important insights into the assembly and catalytic mechanisms of IRG proteins as prerequisite to understand their anti-microbial action.

  4. Structure of the dimerization domain of DiGeorge critical region 8

    Energy Technology Data Exchange (ETDEWEB)

    Senturia, R.; Faller, M.; Yin, S.; Loo, J.A.; Cascio, D.; Sawaya, M.R.; Hwang, D.; Clubb, R.T.; Guo, F. (UCLA)

    2010-09-27

    Maturation of microRNAs (miRNAs, {approx}22nt) from long primary transcripts [primary miRNAs (pri-miRNAs)] is regulated during development and is altered in diseases such as cancer. The first processing step is a cleavage mediated by the Microprocessor complex containing the Drosha nuclease and the RNA-binding protein DiGeorge critical region 8 (DGCR8). We previously reported that dimeric DGCR8 binds heme and that the heme-bound DGCR8 is more active than the heme-free form. Here, we identified a conserved dimerization domain in DGCR8. Our crystal structure of this domain (residues 298-352) at 1.7 {angstrom} resolution demonstrates a previously unknown use of a WW motif as a platform for extensive dimerization interactions. The dimerization domain of DGCR8 is embedded in an independently folded heme-binding domain and directly contributes to association with heme. Heme-binding-deficient DGCR8 mutants have reduced pri-miRNA processing activity in vitro. Our study provides structural and biochemical bases for understanding how dimerization and heme binding of DGCR8 may contribute to regulation of miRNA biogenesis.

  5. Self-assembly in a model colloidal mixture of dimers and spherical particles

    Science.gov (United States)

    Prestipino, Santi; Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo

    2017-02-01

    We investigate the structure of a dilute mixture of amphiphilic dimers and spherical particles, a model relevant to the problem of encapsulating globular "guest" molecules in a dispersion. Dimers and spheres are taken to be hard particles, with an additional attraction between spheres and the smaller monomers in a dimer. Using the Monte Carlo simulation, we document the low-temperature formation of aggregates of guests (clusters) held together by dimers, whose typical size and shape depend on the guest concentration χ. For low χ (less than 10%), most guests are isolated and coated with a layer of dimers. As χ progressively increases, clusters grow in size becoming more and more elongated and polydisperse; after reaching a shallow maximum for χ ≈50 % , the size of clusters again reduces upon increasing χ further. In one case only (χ =50 % and moderately low temperature) the mixture relaxed to a fluid of lamellae, suggesting that in this case clusters are metastable with respect to crystal-vapor separation. On heating, clusters shrink until eventually the system becomes homogeneous on all scales. On the other hand, as the mixture is made denser and denser at low temperature, clusters get increasingly larger until a percolating network is formed.

  6. Dynamic interplay between adhesive and lateral E-cadherin dimers

    DEFF Research Database (Denmark)

    Klingelhöfer, Jörg; Laur, Oscar Y; Troyanovsky, Regina B;

    2002-01-01

    M. The disappearance of adhesive dimers was counterbalanced by an increase in Trp156-dependent lateral dimers. Increasing the calcium concentration to a normal level rapidly restored the original balance between adhesive and lateral dimers. We also present evidence that E-cadherin dimers in vivo have a short lifetime...

  7. Adsorption of dimeric surfactants in lamellar silicates

    Energy Technology Data Exchange (ETDEWEB)

    Balcerzak, Mateusz; Pietralik, Zuzanna [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland); Domka, Ludwik [Department of Metalorganic Chemistry, Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland); Skrzypczak, Andrzej [Institute of Chemical Technology, Poznań University of Technology, Berdychowo 4, 60-965 Poznań (Poland); Kozak, Maciej, E-mail: mkozak@amu.edu.pl [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland)

    2015-12-01

    Highlights: • The intercalation of dimeric surfactants changed the morphology of MMT samples. • XRD indicated structures formed by surfactant molecules in interlayer space. • The four-step thermal decomposition of dimeric surfactant, confirms intercalation. - Abstract: The adsorption of different types of cationic surfactants in lamellar silicates changes their surface character from hydrophilic to hydrophobic. This study was undertaken to obtain lamellar silicates modified by a series of novel dimeric (gemini) surfactants of different length alkyl chains and to characterise these organophilised materials. Synthetic sodium montmorillonite SOMASIF® ME 100 (M) and enriched bentonite of natural origin (Nanoclay – hydrophilic bentonite®) were organophilised with dimeric (gemini) surfactants (1,1′-(1,4-butanediyl)bis(alkoxymethyl)imidazolium dichlorides). As a result of surfactant molecule adsorption in interlamellar space, the d-spacing (d{sub 001}) increased from 0.97 nm (for the anhydrous structure) to 2.04 nm. A Fourier transform infrared spectroscopy (FTIR) analysis of the modified systems reveals bands assigned to the stretching vibrations of the CH{sub 2} and CH{sub 3} groups and the scissoring vibrations of the NH group from the structure of the dimeric surfactants. Thermogravimetric (TG) and derivative thermogravimetric (DTG) studies imply a four-stage process of surfactant decomposition. Scanning electron microscopy (SEM) images provide information on the influence of dimeric surfactant intercalation into the silicate structures. Particles of the modified systems show a tendency toward the formation of irregularly shaped agglomerates.

  8. Formation of a new copper(II) dimer through heterocyclic ligand ring opening reaction: Supramolecular features and magnetic properties

    Science.gov (United States)

    Gonçalves, Bruna Lisboa; Gervini, Vanessa Carratu; Flores, Alex Fabiani Claro; Junior, Jorge Luiz Pimentel; Bortoluzzi, Adailton João; Burrow, Robert Alan; Duarte, Rafael; da Silva, Robson Ricardo; Vicenti, Juliano Rosa de Menezes

    2017-01-01

    Two new compounds were synthesized and characterized in this work: the heterocycle (Z)-1-(4-(hydroxyimino)-3,5-dimethyl-1-(methylcarbamothioyl)-4,5-dihydro-1H-pyrazol-5-yl)-4-methylthiosemicarbazide and a copper(II) thiosemicarbazonato dimeric complex. Green prismatic single crystals of the dimer were obtained by the reaction of the heterocycle with copper(II) chloride dihydrate. Both compounds were essentially characterized by spectroscopic methods and X-ray diffraction crystallography. The crystal structures revealed molecules connected through supramolecular hydrogen bond interactions and copper(II) centers in a slightly distorted square-pyramidal environment. SQUID magnetometry performed for the dimer revealed both ferromagnetic and antiferromagnetic interactions in the studied complex, presenting a critical temperature of 19 K.

  9. Crystal structures of 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(naphthalen-1-yl)acetamide and 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(4-fluoro­phen­yl)acetamide

    Science.gov (United States)

    Subasri, S.; Kumar, Timiri Ajay; Sinha, Barij Nayan; Jayaprakash, Venkatesan; Viswanathan, Vijayan; Velmurugan, Devadasan

    2017-01-01

    The title compounds, C16H15N5OS, (I), and C12H12FN5OS, (II), are [(di­amino­pyrimidine)­sulfan­yl]acetamide derivatives. In (I), the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1)°, while in (II), the pyrimidine ring is inclined to the benzene ring by 58.93 (8)°. In (II), there is an intra­molecular N—H⋯N hydrogen bond and a short C—H⋯O contact. In the crystals of (I) and (II), mol­ecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers with R 2 2(8) ring motifs. In the crystal of (I), the dimers are linked by bifurcated N—H⋯(O,O) and C—H⋯O hydrogen bonds, forming layers parallel to (100). In the crystal of (II), the dimers are linked by N—H⋯O hydrogen bonds, also forming layers parallel to (100). The layers are linked by C—H⋯F hydrogen bonds, forming a three-dimensional architecture.

  10. Structural, magnetic and optical properties of an Fe(III) dimer bridged by the meridional planar divergent N,N'-bis(salicyl)hydrazide and its photo- and electro-chemistry in solution.

    Science.gov (United States)

    Cheaib, Khaled; Martel, David; Clément, Nicolas; Eckes, Fabrice; Kouaho, Stéphanie; Rogez, Guillaume; Dagorne, Samuel; Kurmoo, Mohamedally; Choua, Sylvie; Welter, Richard

    2013-02-07

    {Fe(III)Cl(DMF)(2)}(2)(L) where L is N,N'-bis(salicyl)hydrazide has been synthesized as red crystals and characterized using single-crystal diffraction, infrared and UV-vis spectroscopies, and its magnetic properties studied. The dimeric unit in the structure is formed through the two meridional sets of divergent O, N, O coordinating atoms of the hexacoordinated and quadruply charged ligand. With the presence of the inversion symmetry the Fe atoms are strictly planar with the ligand. The magnetic exchange interaction is found to be antiferromagnetic with a J = -5.98(3) cm(-1) through the rare Fe-N-N-Fe pathway. Irradiation of the FeCl(3)/H(4)L red DMF solution in the visible region of the spectrum resulted in its complete discoloration and from which the unknown colorless salt [Fe(II)(DMF)(6)][Fe(II)Cl(4)] and the neutral ligand have been identified by single crystal diffraction. The UV-visible spectra of FeCl(3), H(4)L and their mixture in DMF solution indicate that the iron complex is the absorbing species and the presence of the free ligand in the irradiated solution suggests that the ligand is potentially acting as a catalyst to the photoreduction of Fe(III) to Fe(II), while electrochemistry points to a mixed-valent (Fe(II)-Fe(III)) intermediate in the process.

  11. Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization

    DEFF Research Database (Denmark)

    Vinther, Tine N.; Norrman, Mathias; Strauss, Holger M.

    2012-01-01

    An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...

  12. Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization.

    Directory of Open Access Journals (Sweden)

    Tine N Vinther

    Full Text Available An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic β-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization to form the structural equivalent of the classical hexamer. The covalently linked dimer neither bound to the insulin receptor, nor induced a metabolic response in vitro. However, it was extremely thermodynamically stable and did not form amyloid fibrils when subjected to mechanical stress, underlining the importance of oligomerization for insulin stability.

  13. On the structure of the Nx phase of symmetric dimers: inferences from NMR.

    Science.gov (United States)

    Hoffmann, Anke; Vanakaras, Alexandros G; Kohlmeier, Alexandra; Mehl, Georg H; Photinos, Demetri J

    2015-02-07

    NMR measurements on a selectively deuterated liquid crystal dimer CB-C9-CB, exhibiting two nematic phases, show that the molecules in the lower temperature nematic phase, N(X), experience a chiral environment and are ordered about a uniformly oriented director throughout the macroscopic sample. The results are contrasted with previous interpretations that suggested a twist-bend spatial variation of the director. A structural picture is proposed wherein the molecules are packed into highly correlated chiral assemblies.

  14. Molecular chirality and chiral capsule-type dimer formation of cyclic triamides via hydrogen-bonding interactions.

    Science.gov (United States)

    Fujimoto, Noriko; Matsumura, Mio; Azumaya, Isao; Nishiyama, Shizuka; Masu, Hyuma; Kagechika, Hiroyuki; Tanatani, Aya

    2012-05-18

    Chiral properties of bowl-shaped cyclic triamides bearing functional groups with hydrogen-bonding ability were examined. Chiral induction of cyclic triamide 3a was observed by addition of chiral amine in solution, and chiral separation was achieved by simple crystallization to afford chiral capsule-type dimer structure of 4a.

  15. Crystal structure of 2-fluoro-N-(1,3-thiazol-2-ylbenzamide

    Directory of Open Access Journals (Sweden)

    Rodolfo Moreno-Fuquen

    2015-11-01

    Full Text Available In the title compound, C10H7FN2OS, the mean plane of the central amide fragment (r.m.s. deviation = 0.048 Å makes dihedral angles of 35.28 (8 and 10.14 (12° with those of the fluorobenzene and thiazole rings, respectively. The thiazole S and amide O atoms lie to the same side of the molecule. In the crystal, pairs of N—H...N hydrogen bonds connect the molecules into inversion dimers with R22(8 motifs, and weak C—H...O interactions connect the molecules into C(6 [001] chains. Together, the N—H...N and C—H...O hydrogen bonds generate (100 sheets.

  16. Crystal structure of 5-chloro-2,7-dimethyl-3-[(4-methylphenylsulfonyl]-1-benzofuran

    Directory of Open Access Journals (Sweden)

    Hong Dae Choi

    2014-09-01

    Full Text Available In the title compound, C17H15ClO3S, the dihedral angle between the planes of the benzofuran ring system [r.m.s. deviation = 0.008 Å] and the 4-methylphenyl ring is 77.29 (4°. In the crystal, molecules are linked by π–π interactions between the benzene rings of neighbouring molecules [centroid–centroid distance = 3.847 (2 Å] and between the benzene and furan rings of neighbouring molecules [centroid–centroid distance = 3.743 (2 Å]. The molecules are stacked along the a-axis direction. In addition, pairs of C—H...O hydrogen bonds are observed between inversion-related dimers: these generate R22(12 loops.

  17. Crystal structure of (E-3-allyl-2-sulfanylidene-5-[(thiophen-2-ylmethylidene]thiazolidin-4-one

    Directory of Open Access Journals (Sweden)

    Rahhal El Ajlaoui

    2015-06-01

    Full Text Available Molecules of the title compound, C11H9NOS3, are built up by one thiophene and one 2-thioxathiazolidin-4-one ring which are connected by a methylene bridge. In addition, there is an allyl substituent attached to nitrogen. The two rings are almost coplanar, making a dihedral angle between them of 0.76 (11°. The allyl group is oriented perpendicular to the mean plane through both ring systems. The crystal structure exhibits inversion dimers in which molecules are linked by pairs of C—H...O hydrogen bonds. Additional π–π interactions between neighboring thiophene and 2-thioxathiazolidin-4-one rings [intercentroid distance = 3.694 (2 Å] lead to the formation of a three-dimensional network.

  18. Direct Waveform Inversion by Iterative Inverse Propagation

    CERN Document Server

    Schlottmann, R B

    2009-01-01

    Seismic waves are the most sensitive probe of the Earth's interior we have. With the dense data sets available in exploration, images of subsurface structures can be obtained through processes such as migration. Unfortunately, relating these surface recordings to actual Earth properties is non-trivial. Tomographic techniques use only a small amount of the information contained in the full seismogram and result in relatively low resolution images. Other methods use a larger amount of the seismogram but are based on either linearization of the problem, an expensive statistical search over a limited range of models, or both. We present the development of a new approach to full waveform inversion, i.e., inversion which uses the complete seismogram. This new method, which falls under the general category of inverse scattering, is based on a highly non-linear Fredholm integral equation relating the Earth structure to itself and to the recorded seismograms. An iterative solution to this equation is proposed. The res...

  19. Inverse Kinematics using Quaternions

    DEFF Research Database (Denmark)

    Henriksen, Knud; Erleben, Kenny; Engell-Nørregård, Morten

    In this project I describe the status of inverse kinematics research, with the focus firmly on the methods that solve the core problem. An overview of the different methods are presented Three common methods used in inverse kinematics computation have been chosen as subject for closer inspection....... suite, developed in this project and in [4]. Source code developed for this project includes the CCD method , improvements on the BFGS method and Jacobian inverse originally developed in [4]....

  20. Inverse periodic shadowing properties

    CERN Document Server

    Osipov, Alexey V

    2011-01-01

    We consider inverse periodic shadowing properties of discrete dynamical systems generated by diffeomorphisms of closed smooth manifolds. We show that the $C^1$-interior of the set of all diffeomorphisms having so-called inverse periodic shadowing property coincides with the set of $\\Omega$-stable diffeomorphisms. The equivalence of Lipschitz inverse periodic shadowing property and hyperbolicity of the closure of all periodic points is proved. Besides, we prove that the set of all diffeomorphisms that have Lipschitz inverse periodic shadowing property and whose periodic points are dense in the nonwandering set coincides with the set of Axiom A diffeomorphisms.

  1. Dimerization of inositol monophosphatase Mycobacterium tuberculosis SuhB is not constitutive, but induced by binding of the activator Mg2+

    Directory of Open Access Journals (Sweden)

    Nigou Jérôme

    2007-08-01

    Full Text Available Abstract Background The cell wall of Mycobacterium tuberculosis contains a wide range of phosphatidyl inositol-based glycolipids that play critical structural roles and, in part, govern pathogen-host interactions. Synthesis of phosphatidyl inositol is dependent on free myo-inositol, generated through dephosphorylation of myo-inositol-1-phosphate by inositol monophosphatase (IMPase. Human IMPase, the putative target of lithium therapy, has been studied extensively, but the function of four IMPase-like genes in M. tuberculosis is unclear. Results We determined the crystal structure, to 2.6 Å resolution, of the IMPase M. tuberculosis SuhB in the apo form, and analysed self-assembly by analytical ultracentrifugation. Contrary to the paradigm of constitutive dimerization of IMPases, SuhB is predominantly monomeric in the absence of the physiological activator Mg2+, in spite of a conserved fold and apparent dimerization in the crystal. However, Mg2+ concentrations that result in enzymatic activation of SuhB decisively promote dimerization, with the inhibitor Li+ amplifying the effect of Mg2+, but failing to induce dimerization on its own. Conclusion The correlation of Mg2+-driven enzymatic activity with dimerization suggests that catalytic activity is linked to the dimer form. Current models of lithium inhibition of IMPases posit that Li+ competes for one of three catalytic Mg2+ sites in the active site, stabilized by a mobile loop at the dimer interface. Our data suggest that Mg2+/Li+-induced ordering of this loop may promote dimerization by expanding the dimer interface of SuhB. The dynamic nature of the monomer-dimer equilibrium may also explain the extended concentration range over which Mg2+ maintains SuhB activity.

  2. A study of hydrogen bonded vibrational spectra of (R)-(+)-Methylsuccinic acid, as aided by DFT dimer analysis

    Science.gov (United States)

    Tonannavar, J.; Chavan, Yashaswita B.; Yenagi, Jayashree

    2016-05-01

    Infrared and Raman spectral measurements in the region 4000-400 cm- 1 have been carried out for (R)-(+)-Methylsuccinic acid. The vibrational band structures near 3100-3040 cm- 1 in the IR and near 1650 cm- 1 in the Raman spectra have indicated the presence of an inter-molecular hydrogen bonding. A DFT dimer model has been proposed that involves O-H ⋯ OC type of hydrogen bonding. The proposed dimer model has been derived from the three stable monomers computed at RHF/3-21G and B3LYP/6-311 + G(d,p) levels of theory. A total of six dimer structures have been considered with a Boltzmann population of 38% for the most stable dimer and 62% for the remaining five dimer populations. A Boltzmann population weighted vibration spectrum has predicted bands, among others, for O-H ⋯ OC group that are in very good agreement with experiment. All the dimers have the same structure in that the two pairs of -O-H and -OC form a closed cyclic structure with a local center of inversion. This dimer geometry has given rise to one asymmetric mode at 1683 and one symmetric -CO mode at 1637 cm- 1 corresponding to mutually exclusive an experimental IR band at 1700 and a Raman band at 1651 cm- 1. Further, the bond length, H ⋯ O, for the most stable dimer is 1.686 Å, being shorter than the sums of van der Waals radii, 2.72 Å and the angle between O-H and H ⋯ O is almost linear (179°) suggesting that the hydrogen bonding is fairly strong.

  3. Geometric Reid's recipe for dimer models

    CERN Document Server

    Bocklandt, Raf; Velez, Alexander Quintero

    2013-01-01

    Crepant resolutions of three-dimensional toric Gorenstein singularities are derived equivalent to noncommutative algebras arising from consistent dimer models. By choosing a special stability parameter and hence a distinguished crepant resolution $Y$, this derived equivalence generalises the Fourier-Mukai transform relating the $G$-Hilbert scheme and the skew group algebra $\\CC[x,y,z]\\ast G$ for a finite abelian subgroup of $\\SL(3,\\CC)$. We show that this equivalence sends the vertex simples to pure sheaves, except for the zero vertex which is mapped to the dualising complex of the compact exceptional locus. This generalises results of Cautis-Logvinenko and Cautis-Craw-Logvinenko to the dimer setting, though our approach is different in each case. We also describe some of these pure sheaves explicitly and compute the support of the remainder, providing a dimer model analogue of results from Logvinenko.

  4. Partition-DFT on the Water Dimer

    CERN Document Server

    Gómez, Sara; Restrepo, Albeiro; Wasserman, Adam

    2016-01-01

    As is well known, the ground-state symmetry group of the water dimer switches from its equilibrium $C_{s}$-character to $C_{2h}$-character as the distance between the two oxygen atoms of the dimer decreases below $R_{\\rm O-O}\\sim 2.5$ \\AA{}. For a range of $R_{\\rm O-O}$ between 1 and 5 \\AA{}, and for both symmetries, we apply Partition Density Functional Theory (PDFT) to find the unique monomer densities that sum to the correct dimer densities while minimizing the sum of the monomer energies. We calculate the work involved in deforming the isolated monomer densities and find that it is slightly larger for the $C_s$ geometry for all $R_{\\rm O-O}$. We discuss how the PDFT densities and the corresponding partition potentials support the orbital-interaction picture of hydrogen-bond formation.

  5. Photoionization of helium dimers; Photoionisation von Heliumdimeren

    Energy Technology Data Exchange (ETDEWEB)

    Havermeier, Tilo

    2010-06-09

    The helium dimer is one of the most weakly bound systems in the universe. This makes it an interesting quantum mechanical object for investigation. These Van der Waals Clusters can be produced in an expansion of a cryogenic gas jet through a small nozzle into vacuum. In the present experiment we examine the interaction of He dimers with synchrotron radiation at an energy range from 64 to 78 eV. We observed different pathways leading to single ionization of both He atoms of the dimer compound. This two close standing ions begin now to dissociate in cause of their coulomb potential. All charged fragments were detected in coincidence with a COLTRIMS system. Especially Interatomic Coulombic Decay (ICD) and the two step process (TS1) were clearly identified. Furthermore a distribution of the internuclear distance was obtained from the measured Kinetic Energy Release (KER). (orig.)

  6. Kosterlitz Thouless Universality in Dimer Models

    CERN Document Server

    Chandrasekharan, S; Chandrasekharan, Shailesh; Strouthos, Costas G.

    2003-01-01

    Using the monomer-dimer representation of strongly coupled U(N) lattice gauge theories with staggered fermions, we study finite temperature chiral phase transitions in (2+1) dimensions. A new cluster algorithm allows us to compute monomer-monomer and dimer-dimer correlations at zero monomer density (chiral limit) accurately on large lattices. This makes it possible to show convincingly, for the first time, that these models undergo a finite temperature phase transition which belongs to the Kosterlitz-Thouless universality class. We find that this universality class is unaffected even in the large N limit. This shows that the mean field analysis often used in this limit breaks down in the critical region.

  7. Crystal structure of 11-(2,3-di-meth-oxy-phen-yl)-14-methyl-12-oxa-8,14-di-aza-tetra-cyclo-[8.3.3.0(1,10).0(2,7)]hexa-deca-2(7),3,5-triene-9,13-dione.

    Science.gov (United States)

    Savithri, M P; Suresh, M; Raghunathan, R; Raja, R; SubbiahPandi, A

    2015-05-01

    The title compound, C22H22N2O5, contains two conformationally similar mol-ecules (A and B) in its the asymmetric unit (r.m.s. overlay fit for the 29 non-H atoms = 0.194 Å). In each mol-ecule, the lactone ring has an envelope conformation with the spiro C atom as the flap. In the crystal, A+A and B+B inversion dimers linked by pairs of N-H⋯O hydrgen bonds occur; in both cases, R 2 (2)(8) loops are generated. A weak C-H⋯O inter-action is also observed, which links the dimers into [010] chains.

  8. An asymmetric post-hydrolysis state of the ABC transporter ATPase dimer.

    Directory of Open Access Journals (Sweden)

    Anthony M George

    Full Text Available ABC transporters are a superfamily of enzyme pumps that hydrolyse ATP in exchange for translocation of substrates across cellular membranes. Architecturally, ABC transporters are a dimer of transmembrane domains coupled to a dimer of nucleotide binding domains (NBDs: the NBD dimer contains two ATP-binding sites at the intersubunit interface. A current controversy is whether the protomers of the NBD dimer separate during ATP hydrolysis cycling, or remain in constant contact. In order to investigate the ABC ATPase catalytic mechanism, MD simulations using the recent structure of the ADP+Pi-bound MJ0796 isolated NBD dimer were performed. In three independent simulations of the ADP+Pi/apo state, comprising a total of >0.5 µs, significant opening of the apo (empty active site was observed; occurring by way of intrasubunit rotations between the core and helical subdomains within both NBD monomers. In contrast, in three equivalent simulations of the ATP/apo state, the NBD dimer remained close to the crystal structure, and no opening of either active site occurred. The results thus showed allosteric coupling between the active sites, mediated by intrasubunit conformational changes. Opening of the apo site is exquisitely tuned to the nature of the ligand, and thus to the stage of the reaction cycle, in the opposite site. In addition to this, in also showing how one active site can open, sufficient to bind nucleotide, while the opposite site remains occluded and bound to the hydrolysis products ADP+Pi, the results are consistent with a Constant Contact Model. Conversely, they show how there may be no requirement for the NBD protomers to separate to complete the catalytic cycle.

  9. Understanding Pd-Pd bond length variation in (PNP)Pd-Pd(PNP) dimers.

    Science.gov (United States)

    Walensky, Justin R; Fafard, Claudia M; Guo, Chengyun; Brammell, Christina M; Foxman, Bruce M; Hall, Michael B; Ozerov, Oleg V

    2013-03-04

    Analysis of the structures of three (PNP)Pd-Pd(PNP) dimers [where PNP stands for anionic diarylamido/bis(phosphine) pincer ligands] has been carried out with the help of single-crystal X-ray diffractometry and density functional theory (DFT) calculations on isolated molecules. The three dimers under study possess analogous ancillary ligands; two of them differ only by an F versus Me substituent in a remote (five bonds away from Pd) position of the pincer ligand. Despite these close similarities, X-ray structural determinations revealed two distinct structural motifs: a highly symmetric molecule with a long Pd-Pd bond or a highly distorted molecule with Pd-Pd bonds ca. 0.14 Å shorter. DFT calculations on a series of (PNP)Pd-Pd(PNP) dimers (as molecules in the gas phase) confirmed the existence of these distinct minima for dimers carrying large isopropyl substituents on the P-donor atoms (as in the experimental structure). These minima are nearly isoergic conformers. Evidently, the electronically preferred symmetric structure for the dimer (with a square-planar environment about Pd and a linear N-Pd-Pd-N vector) is not sterically possible with the preferred Pd-Pd distance. Thus, the minima correspond to either a symmetric structure with a long Pd-Pd bond distance or a structure with a short Pd-Pd distance but with substantial distortions in the Pd coordination environment to alleviate steric conflict. This notion is supported by finding only a single minimum (symmetric and with short Pd-Pd bonds) for each of the dimers carrying smaller substituents (H or Me) on the P atoms, regardless of the remote substitution.

  10. Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

    Science.gov (United States)

    Marchewka, M. K.; Drozd, M.; Janczak, J.

    2011-08-01

    The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

  11. Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine--its vibrational spectra and theoretical calculations.

    Science.gov (United States)

    Marchewka, M K; Drozd, M; Janczak, J

    2011-08-15

    The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2(1)/c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H···O hydrogen bonds with O···O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H···O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double CC bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

  12. A Novel Dimer of α-Tocopherol

    Directory of Open Access Journals (Sweden)

    Anjan Patel

    2008-01-01

    Full Text Available Decomposition of the complex 4, formed between the α-tocopherol ortho-quinone methide (2 and NMMO, by fast heating from −78∘C to 70∘C in inert solvents produces a novel α-tocopherol dimer with 6H,12H-dibenzo[b,f][1,5]dioxocine structure (5 which—in contrast to the well-known spiro-dimer of α-tocopherol (3—is symmetrical. This is the first example of a direct reaction of the highly transient zwitterionic, aromatic precursor 2a in the formation of the ortho-quinone methide 2.

  13. Synthesis of Methoxyethyl Nucleoside Dimer Phosphoramidates

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Gi Weon; Kang, Yong Han [Hanyang University, Ansan (Korea, Republic of)

    2016-05-15

    Four types of methoxyethyl (MOE) nucleoside phosphoramidites, which are categorized as second-generation building blocks of antisense oligonucleotide drugs, were synthesized. Also, three types of MOE nucleoside dimer phosphoramidites were synthesized to increase the efficiency and oligomer purity in solid phase synthesis. The block-like dimer phosphoramidites can prevent or minimize the formation of the (N-1) mer impurity, thereby affording the fabrication of pure oligonucleotides and reducing the synthesis time by performing coupling reactions in the order of 2 + 2 + 2.

  14. Photon Propagation through Linearly Active Dimers

    Directory of Open Access Journals (Sweden)

    José Delfino Huerta Morales

    2017-06-01

    Full Text Available We provide an analytic propagator for non-Hermitian dimers showing linear gain or losses in the quantum regime. In particular, we focus on experimentally feasible realizations of the PT -symmetric dimer and provide their mean photon number and second order two-point correlation. We study the propagation of vacuum, single photon spatially-separable, and two-photon spatially-entangled states. We show that each configuration produces a particular signature that might signal their possible uses as photon switches, semi-classical intensity-tunable sources, or spatially entangled sources to mention a few possible applications.

  15. Refined conformal spectra in the dimer model

    CERN Document Server

    Rasmussen, Jorgen

    2012-01-01

    Working with Lieb's transfer matrix for the dimer model, we point out that the full set of dimer configurations may be partitioned into disjoint subsets (sectors) closed under the action of the transfer matrix. These sectors are labelled by an integer or half-integer quantum number we call the variation index. In the continuum scaling limit, each sector gives rise to a representation of the Virasoro algebra. We determine the corresponding conformal partition functions and their finitizations, and observe an intriguing link to the Ramond and Neveu-Schwarz sectors of the critical dense polymer model as described by a conformal field theory with central charge c=-2.

  16. Dynamical inverse problems

    CERN Document Server

    Gladwell, Graham ML

    2011-01-01

    The papers in this volume present an overview of the general aspects and practical applications of dynamic inverse methods, through the interaction of several topics, ranging from classical and advanced inverse problems in vibration, isospectral systems, dynamic methods for structural identification, active vibration control and damage detection, imaging shear stiffness in biological tissues, wave propagation, to computational and experimental aspects relevant for engineering problems.

  17. Glycine hydrogen fluoride: Remarkable hydrogen bonding in the dimeric glycine glycinium cation

    Science.gov (United States)

    Fleck, M.; Ghazaryan, V. V.; Petrosyan, A. M.

    2010-12-01

    Crystals of glycine hydrogen fluoride (Gly·HF) were prepared from an aqueous solution containing stoichiometric quantities of the components. The crystal structure of Gly·HF was determined, IR and Raman spectra were registered and are discussed. Gly·HF crystallizes in the orthorhombic space group Pbca with Z = 32. The most remarkable feature of the structure is the existence of symmetric dimeric glycine-glycinium cations with short hydrogen bonds (O⋯O distance of 2.446 Å), charge-counterbalanced by hydrogen bifluoride (F sbnd H⋯F) - anions - in addition to the expected glycinium cations and fluoride anions. These results were compared with previously published data on crystals grown in the system glycine-HF-H 2O.

  18. Inverse Symmetric Inflationary Attractors

    CERN Document Server

    Odintsov, S D

    2016-01-01

    We present a class of inflationary potentials which are invariant under a special symmetry, which depends on the parameters of the models. As we show, in certain limiting cases, the inverse symmetric potentials are qualitatively similar to the $\\alpha$-attractors models, since the resulting observational indices are identical. However, there are some quantitative differences which we discuss in some detail. As we show, some inverse symmetric models always yield results compatible with observations, but this strongly depends on the asymptotic form of the potential at large $e$-folding numbers. In fact when the limiting functional form is identical to the one corresponding to the $\\alpha$-attractors models, the compatibility with the observations is guaranteed. Also we find the relation of the inverse symmetric models with the Starobinsky model and we highlight the differences. In addition, an alternative inverse symmetric model is studied and as we show, not all the inverse symmetric models are viable. Moreove...

  19. 0-Semidistributive Inverse Semigroups

    Institute of Scientific and Technical Information of China (English)

    田振际

    2004-01-01

    @@ For an inverse semigroup S, the set L(S) of all inverse subsemigroups (including the empty set) of S forms a lattice with respect to intersection denoted as usual by ∩ and union, where the union is the inverse subsemigroup generated by inverse subsemigroups A, B of S. The set LF(S) of all full inverse subsemigroups of S forms a complete sublattice of L(S), with Es as zero element (Es is the set of all idempotent of S)(see [3,5,6]). Note, that if S a group, then LF(S)=L(S), its lattice of all subgroups of S. If S = G0 is a group with adjoined zero, then clearly LF(S) ≌ L(G).

  20. Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB.

    Science.gov (United States)

    Mack, Timothy R; Gao, Rong; Stock, Ann M

    2009-06-05

    Structural analysis of the Escherichia coli response regulator transcription factor PhoB indicates that the protein dimerizes in two different orientations that are both mediated by the receiver domain. The two dimers exhibit 2-fold rotational symmetry: one involves the alpha 4-beta 5-alpha 5 surface and the other involves the alpha1/alpha 5 surface. The alpha 4-beta 5-alpha 5 dimer is observed when the protein is crystallized in the presence of the phosphoryl analog BeF(3)(-), while the alpha1/alpha 5 dimer is observed in its absence. From these studies, a model of the inactive and active states of PhoB has been proposed that involves the formation of two distinct dimers. In order to gain further insight into the roles of these dimers, we have engineered a series of mutations in PhoB intended to perturb each of them selectively. Our results indicate that perturbation of the alpha 4-beta 5-alpha 5 surface disrupts phosphorylation-dependent dimerization and DNA binding as well as PhoB-mediated transcriptional activation of phoA, while perturbations to the alpha1/alpha 5 surface do not. Furthermore, experiments with a GCN4 leucine zipper/PhoB chimera protein indicate that PhoB is activated through an intermolecular mechanism. Together, these results support a model of activation of PhoB in which phosphorylation promotes dimerization via the alpha 4-beta 5-alpha 5 face, which enhances DNA binding and thus the ability of PhoB to regulate transcription.

  1. A p-quinodimethane-bridged porphyrin dimer.

    Science.gov (United States)

    Zeng, Wangdong; Ishida, Masatoshi; Lee, Sangsu; Sung, Young Mo; Zeng, Zebing; Ni, Yong; Chi, Chunyan; Kim, Dongho; Wu, Jishan

    2013-12-01

    A p-quinodimethane (p-QDM)-bridged porphyrin dimer 1 has been prepared for the first time. An unexpected Michael addition reaction took place when we attempted to synthesize compound 1 by reaction of the cross-conjugated keto-linked porphyrin dimers 8a and 8b with alkynyl/aryl Grignard reagents. Alternatively, compound 1 could be successfully prepared by intramolecular Friedel-Crafts alkylation of the diol-linked porphyrin dimer 14 with concomitant oxidation in air. Compound 1 shows intense one-photon absorption (OPA, λ(max)=955 nm, ε=45400 M(-1) cm(-1)) and a large two-photon absorption (TPA) cross-section (σ((2))(max)=2080 GM at 1800 nm) in the near-infrared (NIR) region due to its extended π-conjugation and quinoidal character. It also exhibits a short singlet excited-state lifetime of 25 ps. The cyclic voltammogram of 1 displays multiple redox waves with a small electrochemical energy gap of 0.86 eV. The ground-state geometry, electronic structure, and optical properties of 1 have been further studied by density functional theory (DFT) calculations and compared with those of the keto-linked dimer 8b. This research has revealed that incorporation of a p-QDM unit into the porphyrin framework had a significant impact on its optical and electronic properties, leading to a novel NIR OPA and TPA chromophore.

  2. Geometric Reid's recipe for dimer models

    NARCIS (Netherlands)

    Bocklandt, R.; Craw, A.; Quintero Vélez, A.

    2015-01-01

    Crepant resolutions of three-dimensional toric Gorenstein singularities are derived equivalent to noncommutative algebras arising from consistent dimer models. By choosing a special stability parameter and hence a distinguished crepant resolution Y, this derived equivalence generalises the Fourier-M

  3. The Diamagnetic Susceptibility of the Tubulin Dimer

    Directory of Open Access Journals (Sweden)

    Wim Bras

    2014-01-01

    Full Text Available An approximate value of the diamagnetic anisotropy of the tubulin dimer, Δχdimer, has been determined assuming axial symmetry and that only the α-helices and β-sheets contribute to the anisotropy. Two approaches have been utilized: (a using the value for the Δχα for an α-helical peptide bond given by Pauling (1979 and (b using the previously determined anisotropy of fibrinogen as a calibration standard. The Δχdimer≈4×10-27 JT−2 obtained from these measurements are similar to within 20%. Although Cotton-Mouton measurements alone cannot be used to estimate Δχ directly, the value we measured, CMdimer=1.41±0.03×10-8 T−2cm2mg−1, is consistent with the above estimate for Δχdimer. The method utilized for the determination of the tubulin dimer diamagnetic susceptibility is applicable to other proteins and macromolecular assemblies as well.

  4. A new lignan dimer from Mallotus philippensis.

    Science.gov (United States)

    Mai, Nguyen Thi; Cuong, Nguyen Xuan; Thao, Nguyen Phuong; Nam, Nguyen Hoai; Khoi, Nguyen Huu; Minh, Chau Van; Heyden, Yvan Vander; Thuan, Ngo Thi; Tuyen, Nguyen Van; Quetin-Leclercq, Joëlle; Kiem, Phan Van

    2010-03-01

    A new lignan dimer, bilariciresinol (1), was isolated from the leaves of Mallotus philippensis, along with platanoside (2), isovitexin (3), dihydromyricetin (4), bergenin (5), 4-O-galloylbergenin (6), and pachysandiol A (7). Their structures were elucidated by spectroscopic experiments including 1D and 2D NMR and FTICR-MS.

  5. Biological consequences of cyclobutane pyrimidine dimers

    NARCIS (Netherlands)

    Vink, A.A.; Roza, L.

    2001-01-01

    In the skin many molecules may absorb ultraviolet (UV) radiation upon exposure. In particular, cellular DNA strongly absorbs shorter wavelength solar UV radiation, resulting in various types of DNA damage. Among the DNA photoproducts produced the cyclobutane pyrimidine dimers (CPDs) are predominant.

  6. Synthesis of novel 15-membered macrolide dimers

    Institute of Scientific and Technical Information of China (English)

    Shu Tao Ma; Rui Xin Ma; Rui Qing Xian; Bo Jiao

    2009-01-01

    A series of novel dimers of 15-memhered macrolides was synthesized and evaluated. The directs exhibited excellent activity against erythromycin-susceptible S. pneumonia, but did not show any improved activity against erythromycin-resistant S. pneumoniae encoded by erm gene.

  7. Amplitude enhancement by a gold dimer

    Science.gov (United States)

    Hong, Xin; Wang, Jingxin; Jin, Zheng

    2016-10-01

    The unique optical properties such as brightness, non-bleaching, good bio-compatibility make gold particles ideal label candidates for molecular probes. Due to the strongly enhanced field, aggregation of gold nanoparticles finds themselves plenty of applications in bio-imaging. But limited by its small cross-section associated with nanometer sized particle, it is a big challenge to employ it in a single molecular detection. The field enhancement results from the effect of plasmonic coupling between two closely attached gold nanoparticle under the right excitation condition. With the aim to apply the gold dimer probe to find the molecules in our recently established optical detection method, we compared of the amplitude enhancement by the dimer relative to a single particle. The amplitude distribution under a highly focused illumination objective was calculated, whose results suggest that at the optimized excitation condition, the local field can be enhanced 190 fold. In consequence, experimental detection was carried out. Gold dimers were linked together by the hybridization of two single chain DNAs. Dimer and single particle probes were mixed together in one detection. Overwhelming contrast between these two kinds of probes were clearly exhibited in the experimental detection image. This method can provide a way to a high specific detection in early diagnosis.

  8. Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription

    Energy Technology Data Exchange (ETDEWEB)

    Vaidya, Anand T.; Chen, Chen-Hui; Dunlap, Jay C.; Loros, Jennifer J.; Crane, Brian R. (Dartmouth-MED); (Cornell)

    2012-10-25

    Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.

  9. Mapping of the dimer interface of the Escherichia coli mannitol permease by cysteine cross-linking.

    Science.gov (United States)

    van Montfort, Bart A; Schuurman-Wolters, Gea K; Wind, Joyce; Broos, Jaap; Robillard, George T; Poolman, Bert

    2002-04-26

    A cysteine cross-linking approach was used to identify residues at the dimer interface of the Escherichia coli mannitol permease. This transport protein comprises two cytoplasmic domains and one membrane-embedded C domain per monomer, of which the latter provides the dimer contacts. A series of single-cysteine His-tagged C domains present in the native membrane were subjected to Cu(II)-(1,10-phenanthroline)(3)-catalyzed disulfide formation or cysteine cross-linking with dimaleimides of different length. The engineered cysteines were at the borders of the predicted membrane-spanning alpha-helices. Two residues were found to be located in close proximity of each other and capable of forming a disulfide, while four other locations formed cross-links with the longer dimaleimides. Solubilization of the membranes did only influence the cross-linking behavior at one position (Cys(73)). Mannitol binding only effected the cross-linking of a cysteine at the border of the third transmembrane helix (Cys(134)), indicating that substrate binding does not lead to large rearrangements in the helix packing or to dissociation of the dimer. Upon mannitol binding, the Cys(134) becomes more exposed but the residue is no longer capable of forming a stable disulfide in the dimeric IIC domain. In combination with the recently obtained projection structure of the IIC domain in two-dimensional crystals, a first proposal is made for alpha-helix packing in the mannitol permease.

  10. G domain dimerization controls dynamin's assembly-stimulated GTPase activity

    Energy Technology Data Exchange (ETDEWEB)

    Chappie, Joshua S.; Acharya, Sharmistha; Leonard, Marilyn; Schmid, Sandra L.; Dyda, Fred (NIH); (Scripps)

    2010-06-14

    Dynamin is an atypical GTPase that catalyses membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin's basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0 {angstrom} resolution crystal structure of a human dynamin 1-derived minimal GTPase-GED fusion protein, which was dimeric in the presence of the transition state mimic GDP.AlF{sub 4}{sup -}. The structure reveals dynamin's catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GTPase-GED fusion protein dimer provides insight into the mechanisms underlying dynamin-catalysed membrane fission.

  11. Structural basis for ligand-dependent dimerization of phenylalanine hydroxylase regulatory domain.

    Science.gov (United States)

    Patel, Dipali; Kopec, Jolanta; Fitzpatrick, Fiona; McCorvie, Thomas J; Yue, Wyatt W

    2016-04-06

    The multi-domain enzyme phenylalanine hydroxylase (PAH) catalyzes the hydroxylation of dietary I-phenylalanine (Phe) to I-tyrosine. Inherited mutations that result in PAH enzyme deficiency are the genetic cause of the autosomal recessive disorder phenylketonuria. Phe is the substrate for the PAH active site, but also an allosteric ligand that increases enzyme activity. Phe has been proposed to bind, in addition to the catalytic domain, a site at the PAH N-terminal regulatory domain (PAH-RD), to activate the enzyme via an unclear mechanism. Here we report the crystal structure of human PAH-RD bound with Phe at 1.8 Å resolution, revealing a homodimer of ACT folds with Phe bound at the dimer interface. This work delivers the structural evidence to support previous solution studies that a binding site exists in the RD for Phe, and that Phe binding results in dimerization of PAH-RD. Consistent with our structural observation, a disease-associated PAH mutant impaired in Phe binding disrupts the monomer:dimer equilibrium of PAH-RD. Our data therefore support an emerging model of PAH allosteric regulation, whereby Phe binds to PAH-RD and mediates the dimerization of regulatory modules that would bring about conformational changes to activate the enzyme.

  12. Structural Basis of Dimerization-dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase

    Energy Technology Data Exchange (ETDEWEB)

    Li, Y.; Hao, B

    2010-01-01

    The F-box proteins are the substrate recognition subunits of the SCF (Skp1-Cul1-Rbx1-F-box protein) ubiquitin ligase complexes that control the stability of numerous regulators in eukaryotic cells. Here we show that dimerization of the F-box protein Fbx4 is essential for SCF{sup Fbx4} (the superscript denotes the F-box protein) ubiquitination activity toward the telomere regulator Pin2 (also known as TRF1). The crystal structure of Fbx4 in complex with an adaptor protein Skp1 reveals an antiparallel dimer configuration in which the linker domain of Fbx4 interacts with the C-terminal substrate-binding domain of the other protomer, whereas the C-terminal domain of the protein adopts a compact {alpha}/{beta} fold distinct from those of known F-box proteins. Biochemical studies indicate that both the N-terminal domain and a loop connecting the linker and C-terminal domain of Fbx4 are critical for the dimerization and activation of the protein. Our findings provide a framework for understanding the role of F-box dimerization in the SCF-mediated ubiquitination reaction.

  13. Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant

    Science.gov (United States)

    Merlino, Antonello; Avella, Giovanna; Di Gaetano, Sonia; Arciello, Angela; Piccoli, Renata; Mazzarella, Lelio; Sica, Filomena

    2009-01-01

    A specialized class of RNases shows a high cytotoxicity toward tumor cell lines, which is critically dependent on their ability to reach the cytosol and to evade the action of the ribonuclease inhibitor (RI). The cytotoxicity and antitumor activity of bovine seminal ribonuclease (BSRNase), which exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer, are peculiar properties of the swapped form. A dimeric variant (HHP2-RNase) of human pancreatic RNase, in which the enzyme has been engineered to reproduce the sequence of BSRNase helix-II (Gln28→Leu, Arg31→Cys, Arg32→Cys, and Asn34→Lys) and to eliminate a negative charge on the surface (Glu111→Gly), is also extremely cytotoxic. Surprisingly, this activity is associated also to the unswapped form of the protein. The crystal structure reveals that on this molecule the hinge regions, which are highly disordered in the unswapped form of BSRNase, adopt a very well-defined conformation in both subunits. The results suggest that the two hinge peptides and the two Leu28 side chains may provide an anchorage to a transient noncovalent dimer, which maintains Cys31 and Cys32 of the two subunits in proximity, thus stabilizing a quaternary structure, similar to that found for the noncovalent swapped dimer of BSRNase, that allows the molecule to escape RI and/or to enhance the formation of the interchain disulfides. PMID:19177350

  14. Polymeric architectures of bismuth citrate based on dimeric building blocks

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Four bismuth complexes, (H2En)[Bi2(cit)2(H2O)4/3]·(H2O)x (1), (H2En)3[Bi2(cit)2Cl4]·(H2O)x (2), (HPy)2[Bi2(cit)2(H2O)8/5]·(H2O)x (3) and (H2En)[Bi2(cit)2](H2O)x (4) [cit = citrate4-; En = ethylenediamine; Py = pyridine] have been synthesized and crystallized. The crystal structures reveal that the basic building blocks in all of these complexes are bismuth citrate dimeric units which combine to form polymeric architectures. The embedded protonated ethylenediamine and pyridine moieties in the polymeric frameworks have been identified by X-ray crystallography and solid-state cross polarization/magic angle spinning (CP/MAS) 13C NMR. Based on the framework of complex 1, a structural model of a clinically used antiulcer drug, ranitidine bismuth citrate (RBC) was generated. The behavior of the protonated amine-bismuth citrate complexes in acidic aqueous solution has been studied by electrospray ionization-mass spectrometry (ESI-MS).

  15. Universal bosonic tetramers of dimer-atom-atom structure

    OpenAIRE

    Deltuva, A.

    2012-01-01

    Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.

  16. Ultraviolet Spectrum And Chemical Reactivity Of CIO Dimer

    Science.gov (United States)

    Demore, William B.; Tschuikow-Roux, E.

    1992-01-01

    Report describes experimental study of ultraviolet spectrum and chemical reactivity of dimer of chlorine monoxide (CIO). Objectives are to measure absorption cross sections of dimer at near-ultraviolet wavelengths; determine whether asymmetrical isomer (CIOCIO) exists at temperatures relevant to Antarctic stratosphere; and test for certain chemical reactions of dimer. Important in photochemistry of Antarctic stratosphere.

  17. A Nove Asymmetric ent—Kauranoid Dimer from Isodon enanderianus

    Institute of Scientific and Technical Information of China (English)

    纳智; 黎胜红; 等

    2002-01-01

    Further investigation on the aerial parts of Isodon enanderianus afforded a novel asymmetric ent-kauranoid dimer,enanderi-nanin J(1).The structure of the dimer was elucidated by means of spectroscopic methods (including 2D NMR tecniques ),Enanderinanin J was a dimer of xerophilusin A and probably formed by [4+2] cycloaddition.

  18. A Novel Asymmetric ent-Kauranoid Dimer from Isodon enanderianus

    Institute of Scientific and Technical Information of China (English)

    NA,Zhi(纳智); LI,Sheng-Hong(黎胜红); XIANG,Wei(项伟); ZHAO,Ai-Hua(赵爱华); LI,Chao-Ming(李朝明); SUN,Han-Dong(孙汉董)

    2002-01-01

    Further investigation on the aerial parts of Isodon enanderianus afforded a novel asymmetric ent-kauranoid dimer, enanuderinaninJ (1). The structure of the dimer was elucidated by means of spectroscopic methods (including 2D NMR techniques ). Enanderinanin J was a dimer of xerophilusin A and probably formed by [ 4 + 2] cycloaddition.

  19. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair.

    Science.gov (United States)

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  20. On Generalized Inverse Transversals

    Institute of Scientific and Technical Information of China (English)

    Rong Hua ZHANG; Shou Feng WANG

    2008-01-01

    Let S be a regular semigroup,S° an inverse subsemigroup of S.S° is called a generalized inverse transversal of S,if V(x) ∩N S°≠φ.In this paper,some properties of this kind of semigroups are discussed.In particular,a construction theorem is obtained which contains some recent results in the literature as its special cases.

  1. Crystal structure of ethylenedioxytetrathiafulvalene-4,5-bis(thiolbenzoic acid 0.25-hydrate

    Directory of Open Access Journals (Sweden)

    Yuanyuan Zhang

    2017-09-01

    Full Text Available In the title compound (systematic name: 4,4′-{[2-(5,6-dihydro-[1,3]dithiolo[4,5-b][1,4]dioxin-2-ylidene-1,3-dithiole-4,5-diyl]bis(sulfanediyl}dibenzoic acid 0.25-hydrate, C22H14O6S6·0.25H2O, the tetrathiafulvalene (TTF core adopts a boat conformation, where the central S2C=CS2 plane makes dihedral angles of 31.34 (4 and 26.83 (6°, respectively, with the peripheral S2C=CS2 and S2C2O2 planes. In the crystal, the benzoic acid molecules are linked via O—H...O hydrogen bonds, forming inversion dimers with R22(8 motifs. The dimers are linked through weak C—H...O hydrogen bonds into a chain structure along [-101]. The chains stack along the a axis through S...S and S...C short contacts, forming layers parallel to the ac plane.

  2. Crystal structure of a photobiologically active brominated angular pyran-ocoumarin: bromo-hy-droxy-seselin.

    Science.gov (United States)

    Bauri, A K; Foro, Sabine; Rahman, A F M Mustafizur

    2017-03-01

    The title compound, C14H13BrO3 [systematic name: rac-(9S,10R)-9-bromo-10-hy-droxy-8,8-dimethyl-9,10-di-hydro-2H,8H-pyrano[2,3-f]chromen-2-one], is a substituted pyran-ocoumarin, obtained by bromination of seselin [8,8-dimethyl-2H,8H-pyrano[2,3-f]chromen-2-one], which was isolated from the Indian herb Trachyspermum stictocarpum (Aajmod). The pyrano ring has a distorted half-chair conformation and its mean plane is inclined to the coumarin mean plane by 1.6 (2)°. In the crystal, mol-ecules are linked by pairs of O-H⋯O hydrogen bonds, forming inversion dimers with an R(2)2(16) ring motif. The dimers stack along the a-axis direction and are linked by offset π-π inter-actions, forming columns [inter-centroid distance = 3.514 (4) Å].

  3. Crystal structure of a photobiologically active brominated angular pyranocoumarin: bromo-hydroxy-seselin

    Directory of Open Access Journals (Sweden)

    A. K. Bauri

    2017-03-01

    Full Text Available The title compound, C14H13BrO3 [systematic name: rac-(9S,10R-9-bromo-10-hydroxy-8,8-dimethyl-9,10-dihydro-2H,8H-pyrano[2,3-f]chromen-2-one], is a substituted pyranocoumarin, obtained by bromination of seselin [8,8-dimethyl-2H,8H-pyrano[2,3-f]chromen-2-one], which was isolated from the Indian herb Trachyspermum stictocarpum (Aajmod. The pyrano ring has a distorted half-chair conformation and its mean plane is inclined to the coumarin mean plane by 1.6 (2°. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonds, forming inversion dimers with an R22(16 ring motif. The dimers stack along the a-axis direction and are linked by offset π–π interactions, forming columns [intercentroid distance = 3.514 (4 Å].

  4. Quantum crystals and spin chains

    Energy Technology Data Exchange (ETDEWEB)

    Dijkgraaf, Robbert [KdV Institute for Mathematics, University of Amsterdam, Plantage Muidergracht 24, 1018 TV Amsterdam (Netherlands); Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands); Orlando, Domenico [Institut de Physique, Universite de Neuchatel, Rue Breguet 1, CH-2000 Neuchatel (Switzerland); Reffert, Susanne [Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands)], E-mail: sreffert@gmail.com

    2009-04-21

    In this article, we discuss the quantum version of the melting crystal corner in one, two, and three dimensions, generalizing the treatment for the quantum dimer model. Using a mapping to spin chains we find that the two-dimensional case (growth of random partitions) is integrable and leads directly to the Hamiltonian of the Heisenberg XXZ ferromagnet. The three-dimensional case of the melting crystal corner is described in terms of a system of coupled XXZ spin chains. We give a conjecture for its mass gap and analyze the system numerically.

  5. Quantum crystals and spin chains

    Science.gov (United States)

    Dijkgraaf, Robbert; Orlando, Domenico; Reffert, Susanne

    2009-04-01

    In this article, we discuss the quantum version of the melting crystal corner in one, two, and three dimensions, generalizing the treatment for the quantum dimer model. Using a mapping to spin chains we find that the two-dimensional case (growth of random partitions) is integrable and leads directly to the Hamiltonian of the Heisenberg XXZ ferromagnet. The three-dimensional case of the melting crystal corner is described in terms of a system of coupled XXZ spin chains. We give a conjecture for its mass gap and analyze the system numerically.

  6. The inverse electroencephalography pipeline

    Science.gov (United States)

    Weinstein, David Michael

    The inverse electroencephalography (EEG) problem is defined as determining which regions of the brain are active based on remote measurements recorded with scalp EEG electrodes. An accurate solution to this problem would benefit both fundamental neuroscience research and clinical neuroscience applications. However, constructing accurate patient-specific inverse EEG solutions requires complex modeling, simulation, and visualization algorithms, and to date only a few systems have been developed that provide such capabilities. In this dissertation, a computational system for generating and investigating patient-specific inverse EEG solutions is introduced, and the requirements for each stage of this Inverse EEG Pipeline are defined and discussed. While the requirements of many of the stages are satisfied with existing algorithms, others have motivated research into novel modeling and simulation methods. The principal technical results of this work include novel surface-based volume modeling techniques, an efficient construction for the EEG lead field, and the Open Source release of the Inverse EEG Pipeline software for use by the bioelectric field research community. In this work, the Inverse EEG Pipeline is applied to three research problems in neurology: comparing focal and distributed source imaging algorithms; separating measurements into independent activation components for multifocal epilepsy; and localizing the cortical activity that produces the P300 effect in schizophrenia.

  7. Generalized emissivity inverse problem.

    Science.gov (United States)

    Ming, DengMing; Wen, Tao; Dai, XianXi; Dai, JiXin; Evenson, William E

    2002-04-01

    Inverse problems have recently drawn considerable attention from the physics community due to of potential widespread applications [K. Chadan and P. C. Sabatier, Inverse Problems in Quantum Scattering Theory, 2nd ed. (Springer Verlag, Berlin, 1989)]. An inverse emissivity problem that determines the emissivity g(nu) from measurements of only the total radiated power J(T) has recently been studied [Tao Wen, DengMing Ming, Xianxi Dai, Jixin Dai, and William E. Evenson, Phys. Rev. E 63, 045601(R) (2001)]. In this paper, a new type of generalized emissivity and transmissivity inverse (GETI) problem is proposed. The present problem differs from our previous work on inverse problems by allowing the unknown (emissivity) function g(nu) to be temperature dependent as well as frequency dependent. Based on published experimental information, we have developed an exact solution formula for this GETI problem. A universal function set suggested for numerical calculation is shown to be robust, making this inversion method practical and convenient for realistic calculations.

  8. Crystal structure of rac-3-[2,3-bis(phenylsulfanyl-3H-indol-3-yl]propanoic acid

    Directory of Open Access Journals (Sweden)

    Wayland E. Noland

    2015-11-01

    Full Text Available The title compound, C23H19NO2S2, was obtained as an unexpected regioisomer from an attempted synthesis of an intermediate for a substituent-effect study on ergot alkaloids. This is the first report of a 1H-indole monothioating at the 2- and 3-positions to give a 3H-indole. In the crystal, the acid H atom is twisted roughly 180° from the typical carboxy conformation and forms centrosymmetric O—H...N hydrogen-bonded dimers with the indole N atom of an inversion-related molecule. Together with a weak C—H...O hydrogen bond involving the carbonyl O atom, chains are formed along [100].

  9. Crystal structure of ethyl 2-({[(4Z-3,5-dioxo-1-phenylpyrazolidin-4-ylidene]methyl}aminoacetate

    Directory of Open Access Journals (Sweden)

    Shaaban K. Mohamed

    2014-09-01

    Full Text Available The title compound, C14H15N3O4, is nearly planar, the dihedral angle between the planes of the phenyl and pyrazolidine rings being 1.13 (7 Å, and that between the plane of the pyrazolidine ring and the mean plane of the side chain [C—N—C–C(=O—O; r.m.s. deviation = 0.024 Å] being 2.52 (7°. This is due in large part to the presence of the intramolecular N—H...O and C—H...O hydrogen bonds. In the crystal, pairwise N—H...O hydrogen bonds form inversion dimers, which are further associated into layers, lying very close to plane (-120, via pairwise C—H...O hydrogen bonds. The layers are then weakly connected through C—H...O hydrogen bonds, forming a three-dimensional structure.

  10. Crystal structure of 4-(1H-indol-3-yl-2-(4-methoxyphenyl-6-phenylpyridine-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    R. Vishnupriya

    2014-10-01

    Full Text Available In the title compound, C27H19N3O, the dihedral angles between the plane of the pyridine ring and those of the indole (r.m.s. deviation = 0.018 Å, phenyl and methoxybenzene substituents are 33.60 (6, 25.28 (7 and 49.31 (7°, respectively. The N atom of the carbonitrile group is significantly displaced [0.288 (2 Å] from the plane of the pyridine ring, perhaps due to steric crowding. In the crystal, inversion dimers linked by pairs of N—H...Nn (n = nitrile hydrogen bonds generate R22(16 loops. Aromatic π–π stacking [centroid–centroid separation = 3.6906 (7 Å] and very weak C—H...π interactions are also observed".

  11. Crystal structure of (3-carb-oxy-prop-yl)tri-phenyl-phospho-nium hexa-fluorido-phosphate.

    Science.gov (United States)

    Hillesheim, Patrick C; Scipione, Kent A; Stokes, Sean L

    2014-11-01

    In the title mol-ecular salt, C22H22O2P(+)·PF6 (-), the side chain of the cation adopts an anti-gauche conformation [P-C-C-C and C-C-C-C torsion angles = -179.11 (10) and -77.18 (16)°, respectively]. In the crystal, the cations are linked into carb-oxy-lic acid inversion dimers by pairs of O-H⋯O hydrogen bonds. Weak C-H⋯F and C-H⋯(F,F) hydrogen bonds connect the components into a three-dimensional network, but there are no aromatic π-π stacking inter-actions.

  12. Crystal structure of trans-dichlorido(4-nitroaniline-κN1(piperidine-κNplatinum(II

    Directory of Open Access Journals (Sweden)

    Chi Nguyen Thi Thanh

    2015-06-01

    Full Text Available In the title complex, [PtCl2(C5H11N(C6H6N2O2], the PtII metal atom displays a slightly distorted trans-PtN2Cl2 square-planar coordination geometry. The dihedral angle between the mean plane of the benzene and piperidine rings is 89.03 (3°. In the crystal structure, inversion dimers are formed via N—H...Cl hydrogen-bond interactions, resulting in chains parallel to the [001] direction. The benzene rings within the chains show π–π stacking interactions [centroid-to-centroid distances of 3.801 (3 Å] and neighbouring chains interact via N—H...O hydrogen bonds.

  13. Crystal structure of (Z-3-allyl-5-(3-bromobenzylidene-2-sulfanylidene-1,3-thiazolidin-4-one

    Directory of Open Access Journals (Sweden)

    Rahhal El Ajlaoui

    2015-12-01

    Full Text Available In the title compound, C13H10BrNOS2, the rhodanine (systematic name: 2-sulfanylidene-1,3-thiazolidin-4-one and the 3-bromobenzylidene ring systems are inclined slightly, forming a dihedral angle of 5.86 (12°. The rhodanine moiety is linked to an allyl group at the N atom and to the 3-bromobenzylidene ring system. The allyl group, C=C—C, is nearly perpendicular to the mean plane through the rhodanine ring, maling a dihedral angle of 87.2 (5°. In the crystal, molecules are linked by pairs of C—H...O hydrogen bonds, forming inversion dimers with an R22(10 ring motif.

  14. Crystal structure of (Z-3-allyl-5-(4-chlorobenzylidene-2-sulfanylidene-1,3-thiazolidin-4-one

    Directory of Open Access Journals (Sweden)

    Rahhal El Ajlaoui

    2015-12-01

    Full Text Available In the title compound, C13H10ClNOS2, the dihedral angle between the rhodanine (r.m.s. deviation = 0.008 Å and 4-chlorobenzylidene rings is 1.79 (11°. The allyl group attached to the N atom, which lies almost perpendicular to the rhodanine ring, is disordered over two orientations in a 0.519 (13:0.481 (13 ratio. A short intramolecular C—H...S interaction closes an S(6 ring. In the crystal, molecules are linked by π–π stacking interactions [centroid–centroid separation = 3.600 (15 Å], generating inversion dimers.

  15. Crystal structures of two solvates of (18-crown-6potassium acetate

    Directory of Open Access Journals (Sweden)

    Phil Liebing

    2016-12-01

    Full Text Available The crystal and molecular strutures of two solvated forms of [K(18c6]OAc (18c6 = 18-crown-6 = 1,4,7,10,13,16-hexaoxacyclooctadecane and OAc = acetate were determined by single-crystal X-ray diffraction, namely (acetato-κ2O,O′(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium dihydrate, [K(CH3COO(C12H24O6]·2H2O (1 and (acetato-κ2O,O′aqua(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium acetic acid monosolvate [K(CH3COO(C12H24O6(H2O]·CH3COOH (2. In both compounds, the acetate anion is bonded to the potassium ion in a chelating fashion and the metal atom is consequently slightly displaced from the O6 plane of the crown ether. In the crystals, O—H...O hydrogen bonds lead to a polymeric ladder structure in the dihydrate 1, while the acetic acid hydrate 2 features inversion dimers.

  16. Crystal structures of two solvates of (18-crown-6)potassium acetate.

    Science.gov (United States)

    Liebing, Phil; Zaeni, Ahmad; Olbrich, Falk; Edelmann, Frank T

    2016-12-01

    The crystal and mol-ecular strutures of two solvated forms of [K(18c6)]OAc (18c6 = 18-crown-6 = 1,4,7,10,13,16-hexa-oxa-cyclo-octa-decane and OAc = acetate) were determined by single-crystal X-ray diffraction, namely (acetato-κ(2)O,O')(1,4,7,10,13,16-hexa-oxa-cyclo-octa-decane-κ(6)O)potassium dihydrate, [K(CH3COO)(C12H24O6)]·2H2O (1) and (acetato-κ(2)O,O')aqua-(1,4,7,10,13,16-hexa-oxa-cyclo-octa-decane-κ(6)O)potassium acetic acid monosolvate [K(CH3COO)(C12H24O6)(H2O)]·CH3COOH (2). In both compounds, the acetate anion is bonded to the potassium ion in a chelating fashion and the metal atom is consequently slightly displaced from the O6 plane of the crown ether. In the crystals, O-H⋯O hydrogen bonds lead to a polymeric ladder structure in the dihydrate 1, while the acetic acid hydrate 2 features inversion dimers.

  17. Construction of a ferritin dimer by breaking its symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, B; Uenuma, M; Uraoka, Y; Yamashita, I [Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)

    2010-11-05

    Ferritin has a mono-dispersed structure and biomineralization properties that allow it to form various kinds of nanoparticles and play an important role in modern nanotechnology. Independent nanoparticles synthesized in ferritin are valuable, but moreover a pair of nanoparticles can bring new properties different from those of the independent nanoparticles. In this study, by breaking ferritin's symmetry, we successfully produced ferritin dimers which provide real protein frameworks for nanoparticle dimer formation. Identical nickel hydro-oxide nanoparticle dimers were produced by simply biomineralizing ferritin dimers. The method presented here can produce multi-functional ferritin dimers with different kinds of nanoparticles.

  18. Large D-Dimer Fluctuation in Normal Pregnancy

    DEFF Research Database (Denmark)

    Hedengran, Katrine K; Andersen, Malene R; Stender, Steen

    2016-01-01

    pregnancies were recruited. D-dimer was repeatedly measured during pregnancy, at active labor, and on the first and second postpartum days. Percentiles for each gestational week were calculated. Each individual D-dimer was normalized by transformation into percentiles for the relevant gestational age......Introduction. D-dimer levels increase throughout pregnancy, hampering the usefulness of the conventional threshold for dismissing thromboembolism. This study investigates the biological fluctuation of D-dimer in normal pregnancy. Methods. A total of 801 healthy women with expected normal...... normal pregnancy, repeated D-dimer measurements are of no clinical use in the evaluation of thromboembolic events during pregnancy....

  19. Plasmonic rod dimers as elementary planar chiral meta-atoms

    CERN Document Server

    Zhukovsky, Sergei V; Chigrin, Dmitry N

    2011-01-01

    Electromagnetic response of metallic rod dimers is theoretically calculated for arbitrary planar arrangement of rods in the dimer. It is shown that dimers without an in-plane symmetry axis exhibit elliptical dichroism and act as "atoms" in planar chiral metamaterials. Due to a very simple geometry of the rod dimer, such planar metamaterials are much easier in fabrication than conventional split-ring or gammadion-type structures, and lend themselves to a simple analytical treatment based on coupled dipole model. Dependencies of metamaterial's directional asymmetry on the dimer's geometry are established analytically and confirmed in numerical simulations.

  20. Revisiting the Optical PT-Symmetric Dimer

    Directory of Open Access Journals (Sweden)

    José Delfino Huerta Morales

    2016-08-01

    Full Text Available Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of PT -symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical PT -symmetric dimer, a two-waveguide coupler where the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry-based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar N-waveguide couplers that are the optical realization of the Lorentz group in 2 + 1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of the Ehrenfest theorem.

  1. Revisiting the optical $PT$-symmetric dimer

    CERN Document Server

    Morales, J D Huerta; López-Aguayo, S; Rodríguez-Lara, B M

    2016-01-01

    Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of $\\mathcal{PT}$-symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical $\\mathcal{PT}$-symmetric dimer, a two-waveguide coupler were the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar $N$-waveguide couplers that are the optical realization of Lorentz group in 2+1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of Ehrenfest theorem.

  2. Fibrillar dimer formation of islet amyloid polypeptides

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Chi-cheng [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); de Pablo, Juan J. [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  3. Immunoglobulin Free Light Chain Dimers in Human Diseases

    Directory of Open Access Journals (Sweden)

    Batia Kaplan

    2011-01-01

    Full Text Available Immunoglobulin free light chain (FLC kappa (κ and lambda (λ isotypes exist mainly in monomeric and dimeric forms. Under pathological conditions, the level of FLCs as well as the structure of monomeric and dimeric FLCs and their dimerization properties might be significantly altered. The abnormally high fractions of dimeric FLCs were demonstrated in the serum of patients with multiple myeloma (MM and primary systemic amyloidosis (AL, as well as in the serum of anephric patients. The presence of tetra- and trimolecular complexes formed due to dimer-dimer and dimer-monomer interactions was detected in the myeloma serum. Analysis of the amyloidogenic light chains demonstrated mutations within the dimer interface, thus raising the possibility that these mutations are responsible for amyloidogenicity. Increased κ monomer and dimer levels, as well as a high κ/λ monomer ratio, were typically found in the cerebrospinal fluid from patients with multiple sclerosis (MS. In many MS cases, the elevation of κ FLCs was accompanied by an abnormally high proportion of λ dimers. This review focuses on the disease-related changes of the structure and level of dimeric FLCs, and raises the questions regarding their formation, function, and role in the pathogenesis and diagnosis of human diseases.

  4. Allosteric inhibitors of inducible nitric oxide synthase dimerization discovered via combinatorial chemistry

    Science.gov (United States)

    McMillan, Kirk; Adler, Marc; Auld, Douglas S.; Baldwin, John J.; Blasko, Eric; Browne, Leslie J.; Chelsky, Daniel; Davey, David; Dolle, Ronald E.; Eagen, Keith A.; Erickson, Shawn; Feldman, Richard I.; Glaser, Charles B.; Mallari, Cornell; Morrissey, Michael M.; Ohlmeyer, Michael H. J.; Pan, Gonghua; Parkinson, John F.; Phillips, Gary B.; Polokoff, Mark A.; Sigal, Nolan H.; Vergona, Ronald; Whitlow, Marc; Young, Tish A.; Devlin, James J.

    2000-01-01

    Potent and selective inhibitors of inducible nitric oxide synthase (iNOS) (EC 1.14.13.39) were identified in an encoded combinatorial chemical library that blocked human iNOS dimerization, and thereby NO production. In a cell-based iNOS assay (A-172 astrocytoma cells) the inhibitors had low-nanomolar IC50 values and thus were >1,000-fold more potent than the substrate-based direct iNOS inhibitors 1400W and N-methyl-l-arginine. Biochemical studies confirmed that inhibitors caused accumulation of iNOS monomers in mouse macrophage RAW 264.7 cells. High affinity (Kd ≈ 3 nM) of inhibitors for isolated iNOS monomers was confirmed by using a radioligand binding assay. Inhibitors were >1,000-fold selective for iNOS versus endothelial NOS dimerization in a cell-based assay. The crystal structure of inhibitor bound to the monomeric iNOS oxygenase domain revealed inhibitor–heme coordination and substantial perturbation of the substrate binding site and the dimerization interface, indicating that this small molecule acts by allosterically disrupting protein–protein interactions at the dimer interface. These results provide a mechanism-based approach to highly selective iNOS inhibition. Inhibitors were active in vivo, with ED50 values of <2 mg/kg in a rat model of endotoxin-induced systemic iNOS induction. Thus, this class of dimerization inhibitors has broad therapeutic potential in iNOS-mediated pathologies. PMID:10677491

  5. Entanglement and decoherence in a quantum dimer

    Institute of Scientific and Technical Information of China (English)

    Hou Xi-Wen; Hui Zi; Ding Rui-Min; Chen Xiao-Yang; Gao Yu

    2006-01-01

    The dynamical properties of quantum entanglement in an integrable quantum dimer are studied in terms of the reduced-density linear entropy with various coupling parameters and total boson numbers. The characteristic time of decoherence process in the early-time evolution of the linear entropy is obtained, indicating that the characteristic time and the corresponding entropy exhibit a maximum near the position of the corresponding classical separatrix energy.

  6. Influence of point mutations on the stability, dimerization and oligomerization of human cystatin C and its L68Q variant

    Directory of Open Access Journals (Sweden)

    Aneta eSzymanska

    2012-07-01

    Full Text Available Human cystatin C (hCC is a small but very intriguing protein. Produced by all nucleated cells is found in almost all tissues and body fluids where, at physiological conditions, plays a role of a very potent inhibitor of cysteine proteases. Biologically active hCC is a monomeric protein but during cellular trafficking it forms dimers, transiently loosing its inhibitory activity. In vitro, dimerization of cystatin C was observed for the mature protein during crystallization trials, revealing that the mechanism of this process is based on the three dimensional swapping of the protein domains. In our work we have focused on the impact of two proposed hot spots in cystatin C structure on its conformational stability. Encouraged by promising results of the theoretical calculations, we designed and produced several hCC hinge region point mutation variants that display a variety of conformational stability and propensity for dimerization and aggregation. A similar approach, i.e. rational mutagenesis, has been also applied to study the amyloidogenic L68Q variant to determine the contribution of hydrophobic interactions and steric effect on the stability of monomeric cystatin C. In this overview we would like to summarize the results of our studies. The impact of a particular mutation on the properties of the studied proteins will be presented in the context of their thermal and mechanical stability, in vitro dimerization tendency as well as the outcome of crystallization. Better understanding of the mechanism and, especially, factors affecting conformational stability of cystatin C and access to stable monomeric and dimeric versions of the protein opens new perspectives in explaining the role of dimers and the domain swapping process in hCC oligomerization, as well as designing potential inhibitors of this process.

  7. Path integrals for dimerized quantum spin systems

    Energy Technology Data Exchange (ETDEWEB)

    Foussats, Adriana, E-mail: afoussats@gmail.co [Facultad de Ciencias Exactas, Ingenieria y Agrimensura and Instituto de Fisica Rosario (UNR-CONICET), Av. Pellegrini 250, 2000 Rosario (Argentina); Greco, Andres [Facultad de Ciencias Exactas, Ingenieria y Agrimensura and Instituto de Fisica Rosario (UNR-CONICET), Av. Pellegrini 250, 2000 Rosario (Argentina); Muramatsu, Alejandro [Institut fuer Theoretische Physik III, Universitaet Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart (Germany)

    2011-01-11

    Dimerized quantum spin systems may appear under several circumstances, e.g. by a modulation of the antiferromagnetic exchange coupling in space, or in frustrated quantum antiferromagnets. In general, such systems display a quantum phase transition to a Neel state as a function of a suitable coupling constant. We present here two path-integral formulations appropriate for spin S=1/2 dimerized systems. The first one deals with a description of the dimers degrees of freedom in an SO(4) manifold, while the second one provides a path-integral for the bond-operators introduced by Sachdev and Bhatt. The path-integral quantization is performed using the Faddeev-Jackiw symplectic formalism for constrained systems, such that the measures and constraints that result from the algebra of the operators is provided in both cases. As an example we consider a spin-Peierls chain, and show how to arrive at the corresponding field-theory, starting with both an SO(4) formulation and bond-operators.

  8. Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction

    Science.gov (United States)

    Baker, Anna W.; Satyshur, Kenneth A.; Moreno Morales, Neydis

    2016-01-01

    ABSTRACT Bacteriophytochrome photoreceptors (BphPs) and their cognate response regulators make up two-component signal transduction systems which direct bacteria to mount phenotypic responses to changes in environmental light quality. Most of these systems utilize single-domain response regulators to transduce signals through unknown pathways and mechanisms. Here we describe the photocycle and autophosphorylation kinetics of RtBphP1, a red light-regulated histidine kinase from the desert bacterium Ramlibacter tataouinensis. RtBphP1 undergoes red to far-red photoconversion with rapid thermal reversion to the dark state. RtBphP1 is autophosphorylated in the dark; this activity is inhibited under red light. The RtBphP1 cognate response regulator, the R. tataouinensis bacteriophytochrome response regulator (RtBRR), and a homolog, AtBRR from Agrobacterium tumefaciens, crystallize unexpectedly as arm-in-arm dimers, reliant on a conserved hydrophobic motif, hFWAhL (where h is a hydrophobic M, V, L, or I residue). RtBRR and AtBRR dimerize distinctly from four structurally characterized phytochrome response regulators found in photosynthetic organisms and from all other receiver domain homodimers in the Protein Data Bank. A unique cacodylate-zinc-histidine tag metal organic framework yielded single-wavelength anomalous diffraction phases and may be of general interest. Examination of the effect of the BRR stoichiometry on signal transduction showed that phosphorylated RtBRR is accumulated more efficiently than the engineered monomeric RtBRR (RtBRRmon) in phosphotransfer reactions. Thus, we conclude that arm-in-arm dimers are a relevant signaling intermediate in this class of two-component regulatory systems. IMPORTANCE BphP histidine kinases and their cognate response regulators comprise widespread red light-sensing two-component systems. Much work on BphPs has focused on structural understanding of light sensing and on enhancing the natural infrared fluorescence of these

  9. Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction.

    Science.gov (United States)

    Baker, Anna W; Satyshur, Kenneth A; Moreno Morales, Neydis; Forest, Katrina T

    2016-04-01

    Bacteriophytochrome photoreceptors (BphPs) and their cognate response regulators make up two-component signal transduction systems which direct bacteria to mount phenotypic responses to changes in environmental light quality. Most of these systems utilize single-domain response regulators to transduce signals through unknown pathways and mechanisms. Here we describe the photocycle and autophosphorylation kinetics of RtBphP1, a red light-regulated histidine kinase from the desert bacterium Ramlibacter tataouinensis RtBphP1 undergoes red to far-red photoconversion with rapid thermal reversion to the dark state. RtBphP1 is autophosphorylated in the dark; this activity is inhibited under red light. The RtBphP1 cognate response regulator, the R. tataouinensis bacteriophytochrome response regulator (RtBRR), and a homolog, AtBRR from Agrobacterium tumefaciens, crystallize unexpectedly as arm-in-arm dimers, reliant on a conserved hydrophobic motif, hFWAhL (where h is a hydrophobic M, V, L, or I residue). RtBRR and AtBRR dimerize distinctly from four structurally characterized phytochrome response regulators found in photosynthetic organisms and from all other receiver domain homodimers in the Protein Data Bank. A unique cacodylate-zinc-histidine tag metal organic framework yielded single-wavelength anomalous diffraction phases and may be of general interest. Examination of the effect of the BRR stoichiometry on signal transduction showed that phosphorylated RtBRR is accumulated more efficiently than the engineered monomeric RtBRR (RtBRRmon) in phosphotransfer reactions. Thus, we conclude that arm-in-arm dimers are a relevant signaling intermediate in this class of two-component regulatory systems. BphP histidine kinases and their cognate response regulators comprise widespread red light-sensing two-component systems. Much work on BphPs has focused on structural understanding of light sensing and on enhancing the natural infrared fluorescence of these proteins, rather than

  10. Structural and biochemical studies on Vibrio cholerae Hsp31 reveals a novel dimeric form and Glutathione-independent Glyoxalase activity

    Science.gov (United States)

    Dey, Sanjay

    2017-01-01

    Vibrio cholerae experiences a highly hostile environment at human intestine which triggers the induction of various heat shock genes. The hchA gene product of V. cholerae O395, referred to a hypothetical intracellular protease/amidase VcHsp31, is one such stress-inducible homodimeric protein. Our current study demonstrates that VcHsp31 is endowed with molecular chaperone, amidopeptidase and robust methylglyoxalase activities. Through site directed mutagenesis coupled with biochemical assays on VcHsp31, we have confirmed the role of residues in the vicinity of the active site towards amidopeptidase and methylglyoxalase activities. VcHsp31 suppresses the aggregation of insulin in vitro in a dose dependent manner. Through crystal structures of VcHsp31 and its mutants, grown at various temperatures, we demonstrate that VcHsp31 acquires two (Type-I and Type-II) dimeric forms. Type-I dimer is similar to EcHsp31 where two VcHsp31 monomers associate in eclipsed manner through several intersubunit hydrogen bonds involving their P-domains. Type-II dimer is a novel dimeric organization, where some of the intersubunit hydrogen bonds are abrogated and each monomer swings out in the opposite directions centering at their P-domains, like twisting of wet cloth. Normal mode analysis (NMA) of Type-I dimer shows similar movement of the individual monomers. Upon swinging, a dimeric surface of ~400Å2, mostly hydrophobic in nature, is uncovered which might bind partially unfolded protein substrates. We propose that, in solution, VcHsp31 remains as an equilibrium mixture of both the dimers. With increase in temperature, transformation to Type-II form having more exposed hydrophobic surface, occurs progressively accounting for the temperature dependent increase of chaperone activity of VcHsp31. PMID:28235098

  11. Molecular interactions investigated with DFT calculations of QTAIM and NBO analyses: An application to dimeric structures of rice α-amylase/subtilisin inhibitor

    Science.gov (United States)

    Astani, Elahe K.; Hadipour, Nasser L.; Chen, Chun-Jung

    2017-03-01

    Characterization of the dimer interactions at the dimeric interface of the crystal structure of rice α-amylase/subtilisin inhibitor (RASI) were performed using the quantum theory of atoms in molecules (QTAIM) and natural bonding orbital (NBO) analyses at the density-functional theory (DFT) level. The results revealed that Gly27 and Arg151 of chain A are the main residues involved in hydrogen bonds, dipole-dipole, and charge-dipole interactions with Gly64, Ala66, Ala67 and Arg81 of chain B at the dimeric interface. Calcium ion of chain A plays the significant role in the stability of the dimeric structure through a strong charge-charge interaction with Ala66.

  12. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Du, Fengxia [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); Zhang, Minjie [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Xiaohua; Yang, Caiyun [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); Meng, Hao; Wang, Dong; Chang, Shuang [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Xu, Ye [Department of Radiation Oncology, Division of Genomic Stability, Dana Farber Cancer Institute, Harvard Medical School, MA 02134 (United States); Price, Brendan, E-mail: Brendan_Price@dfci.harvard.edu [Department of Radiation Oncology, Division of Genomic Stability, Dana Farber Cancer Institute, Harvard Medical School, MA 02134 (United States); Sun, Yingli, E-mail: sunyl@big.ac.cn [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-10-03

    Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  13. Sharp spatially constrained inversion

    DEFF Research Database (Denmark)

    Vignoli, Giulio G.; Fiandaca, Gianluca G.; Christiansen, Anders Vest C A.V.C.;

    2013-01-01

    We present sharp reconstruction of multi-layer models using a spatially constrained inversion with minimum gradient support regularization. In particular, its application to airborne electromagnetic data is discussed. Airborne surveys produce extremely large datasets, traditionally inverted...... by using smoothly varying 1D models. Smoothness is a result of the regularization constraints applied to address the inversion ill-posedness. The standard Occam-type regularized multi-layer inversion produces results where boundaries between layers are smeared. The sharp regularization overcomes......, the results are compatible with the data and, at the same time, favor sharp transitions. The focusing strategy can also be used to constrain the 1D solutions laterally, guaranteeing that lateral sharp transitions are retrieved without losing resolution. By means of real and synthetic datasets, sharp...

  14. MspA nanopores from subunit dimers.

    Directory of Open Access Journals (Sweden)

    Mikhail Pavlenok

    Full Text Available Mycobacterium smegmatis porin A (MspA forms an octameric channel and represents the founding member of a new family of pore proteins. Control of subunit stoichiometry is important to tailor MspA for nanotechnological applications. In this study, two MspA monomers were connected by linkers ranging from 17 to 62 amino acids in length. The oligomeric pore proteins were purified from M. smegmatis and were shown to form functional channels in lipid bilayer experiments. These results indicated that the peptide linkers did not prohibit correct folding and localization of MspA. However, expression levels were reduced by 10-fold compared to wild-type MspA. MspA is ideal for nanopore sequencing due to its unique pore geometry and its robustness. To assess the usefulness of MspA made from dimeric subunits for DNA sequencing, we linked two M1-MspA monomers, whose constriction zones were modified to enable DNA translocation. Lipid bilayer experiments demonstrated that this construct also formed functional channels. Voltage gating of MspA pores made from M1 monomers and M1-M1 dimers was identical indicating similar structural and dynamic channel properties. Glucose uptake in M. smegmatis cells lacking porins was restored by expressing the dimeric mspA M1 gene indicating correct folding and localization of M1-M1 pores in their native membrane. Single-stranded DNA hairpins produced identical ionic current blockades in pores made from monomers and subunit dimers demonstrating that M1-M1 pores are suitable for DNA sequencing. This study provides the proof of principle that production of single-chain MspA pores in M. smegmatis is feasible and paves the way for generating MspA pores with altered stoichiometries. Subunit dimers enable better control of the chemical and physical properties of the constriction zone of MspA. This approach will be valuable both in understanding transport across the outer membrane in mycobacteria and in tailoring MspA for nanopore

  15. Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa.

    Science.gov (United States)

    Whitney, John C; Whitfield, Gregory B; Marmont, Lindsey S; Yip, Patrick; Neculai, A Mirela; Lobsanov, Yuri D; Robinson, Howard; Ohman, Dennis E; Howell, P Lynne

    2015-05-15

    Pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. Among the proteins required for alginate production, Alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding activity post-translationally regulates alginate secretion. In this study, we report the 1.8 Å crystal structure of the cytoplasmic region of Alg44 in complex with dimeric self-intercalated c-di-GMP and characterize its dinucleotide-binding site using mutational analysis. The structure shows that the c-di-GMP binding region of Alg44 adopts a PilZ domain fold with a dimerization mode not previously observed for this family of proteins. Calorimetric binding analysis of residues in the c-di-GMP binding site demonstrate that mutation of Arg-17 and Arg-95 alters the binding stoichiometry between c-di-GMP and Alg44 from 2:1 to 1:1. Introduction of these mutant alleles on the P. aeruginosa chromosome show that the residues required for binding of dimeric c-di-GMP in vitro are also required for efficient alginate production in vivo. These results suggest that the dimeric form of c-di-GMP represents the biologically active signaling molecule needed for the secretion of an important virulence factor produced by P. aeruginosa.

  16. Limits to Nonlinear Inversion

    DEFF Research Database (Denmark)

    Mosegaard, Klaus

    2012-01-01

    For non-linear inverse problems, the mathematical structure of the mapping from model parameters to data is usually unknown or partly unknown. Absence of information about the mathematical structure of this function prevents us from presenting an analytical solution, so our solution depends on our......-heuristics are inefficient for large-scale, non-linear inverse problems, and that the 'no-free-lunch' theorem holds. We discuss typical objections to the relevance of this theorem. A consequence of the no-free-lunch theorem is that algorithms adapted to the mathematical structure of the problem perform more efficiently than...

  17. 'Inverse' temporomandibular joint dislocation.

    Science.gov (United States)

    Alemán Navas, R M; Martínez Mendoza, M G

    2011-08-01

    Temporomandibular joint (TMJ) dislocation can be classified into four groups (anterior, posterior, lateral, and superior) depending on the direction of displacement and the location of the condylar head. All the groups are rare except for anterior dislocation. 'Inverse' TMJ dislocation is a bilateral anterior and superior dislocation with impaction of the mandible over the maxilla; to the authors' knowledge only two cases have previously been reported in the literature. Inverse TMJ dislocation has unique clinical and radiographic findings, which are described for this case. Copyright © 2011 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  18. Carbene supported dimer of heavier ketenimine analogue with p and si atoms.

    Science.gov (United States)

    Roy, Sudipta; Dittrich, Birger; Mondal, Totan; Koley, Debasis; Stückl, A Claudia; Schwederski, Brigitte; Kaim, Wolfgang; John, Michael; Vasa, Suresh Kumar; Linser, Rasmus; Roesky, Herbert W

    2015-05-20

    A cyclic alkyl(amino) carbene (cAAC) stabilized dimer [(cAAC)Si(P-Tip)]2 (2) (Tip = 2,4,6-triisopropylphenyl) is reported. 2 can be considered as a dimer of the heavier ketenimine (R2C═C═N-R) analogue. The dark-red rod-shaped crystals of 2 were synthesized by reduction of the precursor, cAAC-dichlorosilylene-stabilized phosphinidene (cAAC)SiCl2→P-Tip with sodium napthalenide. The crystals of 2 are storable at room temperature for several months and stable up to 215 °C under an inert atmosphere. X-ray single-crystal diffraction revealed that 2 contains a cyclic nonplanar four-membered SiPSiP ring. Magnetic susceptibility measurements confirmed the singlet spin ground state of 2. Cyclic voltammetry of 2 showed a quasi-reversible one-electron reduction indicating the formation of the corresponding radical anion 2(•-), which was further characterized by EPR measurements in solution. The electronic structure and bonding of 2 and 2(•-) were studied by theoretical calculations. The experimentally obtained data are in good agreement with the calculated values.

  19. Locative Inversion in English

    NARCIS (Netherlands)

    Broekhuis, H.

    2005-01-01

    This article aims at reformulating in more current terms Hoekstra and Mulder’s (1990) analysis of the Locative Inversion (LI) construction. The new proposal is crucially based on the assumption that Small Clause (SC) predicates agree with their external argument in phi-features, which may be morphol

  20. Structural studies on MRG701 chromodomain reveal a novel dimerization interface of MRG proteins in green plants

    Directory of Open Access Journals (Sweden)

    Yanchao Liu

    2016-09-01

    Full Text Available Abstract MRG proteins are conserved during evolution in fungi, flies, mammals and plants, and they can exhibit diversified functions. The animal MRGs were found to form various complexes to activate gene expression. Plant MRG1/2 and MRG702 were reported to be involved in the regulation of flowering time via binding to H3K36me3-marked flowering genes. Herein, we determined the crystal structure of MRG701 chromodomain (MRG701CD. MRG701CD forms a novel dimerization fold both in crystal and in solution. Moreover, we found that the dimerization of MRG chromodomains is conserved in green plants. Our findings may provide new insights into the mechanism of MRGs in regulation of gene expression in green plants.

  1. Effects of Convective Solute and Impurity Transport in Protein Crystal Growth

    Science.gov (United States)

    Vekilov, Peter G.; Thomas, Bill R.; Rosenberger, Franz

    1998-01-01

    High-resolution optical interferometry was used to investigate the effects of forced solution convection on the crystal growth kinetics of the model protein lysozyme. Most experiments were conducted with 99.99% pure protein solutions. To study impurity effects, approx. 1% of lysozyme dimer (covalently bound) was added in some cases. We show that the unsteady kinetics, corresponding to bunching of growth steps, can be characterized by the Fourier components of time traces of the growth rate. Specific Fourier spectra are uniquely determined by the solution conditions (composition, temperature, and flow rate) and the growth layer source activity. We found that the average step velocity and growth rate increase by approx. I0% with increasing flow rate, as a result of the enhanced solute supply to the interface. More importantly, faster convective transport results in lower fluctuation amplitudes. This observation supports our rationale for system-dependent effects of transport on the structural perfection of protein crystals. We also found that solution flow rates greater than 500 microns/s result in stronger fluctuations while the average growth rate is decreased. This can lead to growth cessation at low supersaturations. With the intentionally contaminated solutions, these undesirable phenomena occurred at about half the flow rates required in pure solutions. Thus, we conclude that they are due to enhanced convective supply of impurities that are incorporated into the crystal during growth. Furthermore, we found that the impurity effects are reduced at higher crystal growth rates. Since the exposure time of terraces is inversely proportional to the growth rate, this observation suggests that the increased kinetics instability results from impurity adsorption on the interface. Finally, we provide evidence relating earlier observations of "slow protein crystal growth kinetics" to step bunch formation in response to nonsteady step generation.

  2. Bayesian seismic AVO inversion

    Energy Technology Data Exchange (ETDEWEB)

    Buland, Arild

    2002-07-01

    A new linearized AVO inversion technique is developed in a Bayesian framework. The objective is to obtain posterior distributions for P-wave velocity, S-wave velocity and density. Distributions for other elastic parameters can also be assessed, for example acoustic impedance, shear impedance and P-wave to S-wave velocity ratio. The inversion algorithm is based on the convolutional model and a linearized weak contrast approximation of the Zoeppritz equation. The solution is represented by a Gaussian posterior distribution with explicit expressions for the posterior expectation and covariance, hence exact prediction intervals for the inverted parameters can be computed under the specified model. The explicit analytical form of the posterior distribution provides a computationally fast inversion method. Tests on synthetic data show that all inverted parameters were almost perfectly retrieved when the noise approached zero. With realistic noise levels, acoustic impedance was the best determined parameter, while the inversion provided practically no information about the density. The inversion algorithm has also been tested on a real 3-D dataset from the Sleipner Field. The results show good agreement with well logs but the uncertainty is high. The stochastic model includes uncertainties of both the elastic parameters, the wavelet and the seismic and well log data. The posterior distribution is explored by Markov chain Monte Carlo simulation using the Gibbs sampler algorithm. The inversion algorithm has been tested on a seismic line from the Heidrun Field with two wells located on the line. The uncertainty of the estimated wavelet is low. In the Heidrun examples the effect of including uncertainty of the wavelet and the noise level was marginal with respect to the AVO inversion results. We have developed a 3-D linearized AVO inversion method with spatially coupled model parameters where the objective is to obtain posterior distributions for P-wave velocity, S

  3. Calculation of the inverse data space via sparse inversion

    KAUST Repository

    Saragiotis, Christos

    2011-01-01

    The inverse data space provides a natural separation of primaries and surface-related multiples, as the surface multiples map onto the area around the origin while the primaries map elsewhere. However, the calculation of the inverse data is far from trivial as theory requires infinite time and offset recording. Furthermore regularization issues arise during inversion. We perform the inversion by minimizing the least-squares norm of the misfit function by constraining the $ell_1$ norm of the solution, being the inverse data space. In this way a sparse inversion approach is obtained. We show results on field data with an application to surface multiple removal.

  4. Pseudo waveform inversion

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Chang Soo; Park, Keun Pil [Korea Inst. of Geology Mining and Materials, Taejon (Korea, Republic of); Suh, Jung Hee; Hyun, Byung Koo; Shin, Sung Ryul [Seoul National University, Seoul (Korea, Republic of)

    1995-12-01

    The seismic reflection exploration technique which is one of the geophysical methods for oil exploration became effectively to image the subsurface structure with rapid development of computer. However, the imagining of subsurface based on the conventional data processing is almost impossible to obtain the information on physical properties of the subsurface such as velocity and density. Since seismic data are implicitly function of velocities of subsurface, it is necessary to develop the inversion method that can delineate the velocity structure using seismic topography and waveform inversion. As a tool to perform seismic inversion, seismic forward modeling program using ray tracing should be developed. In this study, we have developed the algorithm that calculate the travel time of the complex geologic structure using shooting ray tracing by subdividing the geologic model into blocky structure having the constant velocity. With the travel time calculation, the partial derivatives of travel time can be calculated efficiently without difficulties. Since the current ray tracing technique has a limitation to calculate the travel times for extremely complex geologic model, our aim in the future is to develop the powerful ray tracer using the finite element technique. After applying the pseudo waveform inversion to the seismic data of Korea offshore, we can obtain the subsurface velocity model and use the result in bring up the quality of the seismic data processing. If conventional seismic data processing and seismic interpretation are linked with this inversion technique, the high quality of seismic data processing can be expected to image the structure of the subsurface. Future research area is to develop the powerful ray tracer of ray tracing which can calculate the travel times for the extremely complex geologic model. (author). 39 refs., 32 figs., 2 tabs.

  5. Crystals in crystals

    DEFF Research Database (Denmark)

    Christensen, Claus H.; Schmidt, I.; Carlsson, A.;

    2005-01-01

    A major factor governing the performance of catalytically active particles supported on a zeolite carrier is the degree of dispersion. It is shown that the introduction of noncrystallographic mesopores into zeolite single crystals (silicalite-1, ZSM-5) may increase the degree of particle dispersion...... of the zeolite particles, particularly after thermal treatment. When using mesoporous zeolites, the particles were evenly distributed throughout the mesopore system of the zeolitic support, even after calcination, leading to nanocrystals within mesoporous zeolite single crystals....

  6. In Search for Universal Models. Dimerization of Nitrosobenzenes and Investigation of Some Basic Chemical Concepts

    Directory of Open Access Journals (Sweden)

    Biljan, I.

    2012-09-01

    Full Text Available One of the most exploited approaches in scientific methodology is studying concepts by using a case study. In chemistry, a case study appears in finding a specific molecular and/or reaction system by which the investigated problem can be observed directly "on substance". Thus, the stu- died problem becomes a concrete system, rather than an abstract concept. Most case-study models are designed specifically to deepen one or another chemical problem. However, there exist (although rarely models, which afford their universality, i.e. could serve for modeling of qui- te different, and even epistemologically independent concepts. Systematic investigations of the chemistry of C-nitroso compounds performed in our Laboratory in last few years, have resulted in the discovery that such molecular system may be used as a model for studying a series of basic chemical concepts; selectivity, self-assembly, solid-state reaction mechanisms, photochromism and molecular logics. Since it is known that C-nitroso compounds under specific conditions dime- rize by forming new N=N bond (Scheme 1, the reaction can be used for studying selectivity in the formation of dimers between different nitroso monomers (Fig. 1 and Fig. 2. The system is very convenient for investigation of the structure-selectivity relations.6 It has already been established, especially in the work of Brian Gowenlock, that nitroso compounds in crystal form appear as di- mers. These discoveries inspired us to investigate the kinetics and mechanism of dimerization of nitroso monomers in solid state, because the freshly sublimed nitrosoaromatic compounds appear as crystals of monomers. Consequently, this molecular system is a perfect case-study model for concepts of solid-state reactions, self-organizations in the crystalline forms (Fig. 3, as well as for the8,13 Extending our research of self-organization of nitroso compounds to two-dimensional systems (Fig. 4, we have also de- monstrated the ability of

  7. A dimeric structure of PD-L1: functional units or evolutionary relics?

    OpenAIRE

    Chen, Yong; Liu, Peipei; Gao, Feng; Cheng, Hao; Qi, Jianxun; Gao, George F

    2010-01-01

    PD-L1 is a member of the B7 protein family, most of whose members so far were identified as dimers in a solution and crystalline state, either complexed or uncomplexed with their ligand(s). The binding of PD-L1 with its receptor PD-1 (CD279) delivers an inhibitory signal regulating the T cell function. Simultaneously with the Garboczi group, we successfully solved another structure of human PD-L1 (hPD-L1). Our protein crystallized in the space group of C2221 with two hPD-L1 molecules per asym...

  8. Metal enhanced fluorescence of Ag-nanoshell dimer

    Science.gov (United States)

    Liaw, Jiunn-Woei; Chen, Huang-Chih; Chen, Bae-Renn; Kuo, Mao-Kuen

    2014-04-01

    The plasmon modes of Ag-nanoshell dimer on metal enhanced fluorescence (MEF) are studied theoretically. The amplified excitation rate of a dimer (two identical Ag nanoshells) illuminated by a plane wave for exciting a molecule located at the gap center is calculated. Subsequently, the apparent quantum yield of the emission of the excited molecule affected by the dimer is investigated. The multiple multipole method is used for the both simulations. Finally, the enhancement factor of the dimer on the overall photoluminescence of the molecule in terms of the two parameters is evaluated. Our results show that Ag-nanoshell dimer is a dual-band photoluminescence enhancer for MEF at the bonding dipole and quadrupole modes. The former is broadband, and the latter narrowband. Both bands depend on the gap size. Moreover, the average enhancement factor of Ag-nanoshell dimer for MEF with a Stokes shift is discussed.

  9. Cytochrome P450 as dimerization catalyst in diketopiperazine alkaloid biosynthesis.

    Science.gov (United States)

    Saruwatari, Takayoshi; Yagishita, Fumitoshi; Mino, Takashi; Noguchi, Hiroshi; Hotta, Kinya; Watanabe, Kenji

    2014-03-21

    As dimeric natural products frequently exhibit useful biological activities, identifying and understanding their mechanisms of dimerization is of great interest. One such compound is (−)-ditryptophenaline, isolated from Aspergillus flavus, which inhibits substance P receptor for potential analgesic and anti-inflammatory activity. Through targeted gene knockout in A. flavus and heterologous yeast gene expression, we determined for the first time the gene cluster and pathway for the biosynthesis of a dimeric diketopiperazine alkaloid. We also determined that a single cytochrome P450, DtpC, is responsible not only for pyrroloindole ring formation but also for concurrent dimerization of N-methylphenylalanyltryptophanyl diketopiperazine monomers into a homodimeric product. Furthermore, DtpC exhibits relaxed substrate specificity, allowing the formation of two new dimeric compounds from a non-native monomeric precursor, brevianamide F. A radical-mediated mechanism of dimerization is proposed.

  10. Syntheses, crystal structure and properties of the dimeric[(CH3)4N]4[PW11O39H2La(H2O)4]2 · 3H2O%二聚结构[(CH3)4N]4[PW(11)O(39)H2La(H2O)4]2·3H2O的合成、结构及性质

    Institute of Scientific and Technical Information of China (English)

    张少伟; 马鹏涛; 陈幻妮; 王敬平; 牛景杨

    2011-01-01

    以α-Na7PW(11)O(39)·nH2O,LaCl3·7H2O和(CH3)4NCl为原料,利用常规水溶液方法合成了2:2型二聚的单缺位Keggin结构稀土衍生物[(CH3)4N]4[PW(11)O(39)H2La(H2O)4]2·3H2O(1).X射线单晶衍射结果表明,该晶体属三斜晶系,P-1空间群,晶胞参数:a=1.35383(10)nm,b=1.60687(12)nm,c=1.86958(13)nm,α=65.9630(10)°,β=83.1650(10)°,γ=83.6780(10)°,Z=1,R1=0.0589,wR2=0.1447.二聚阴离子{[(α-PW(11)O(39)H2)La(H2O)4]2}(4-)由2个[α-PW(11)O(39)](7-)缺位阴离子通过2个[La(H2O)4](3+)配离子连接形成,La(3+)离子占据[α-PW(11)O(39)](7-)阴离子的缺位位置,采用九配位单加冠四方反棱柱构型,相邻的2个单取代阴离子[α-PW(11)La(39)](4-)通过2个La-Ot-W桥连成二聚物.热重分析结果表明,化合物1在25-600℃范围内表现为两步失重;循环伏安行为表明,化合物1阴离子在pH4.3的水溶液中存在两步可逆的单电子还原过程.%2∶2-type dimeric [(CH3)4N]4[PW11O39H2La(H2O)4]2·3H2O was successfully synthesized by reaction of the monovacant Keggin structure α-Na7PW11O39· nH2O with LaCl3· 7H2O and (CH3)4NCl in aqueous solution. Single crystals of this compound were analyzed by X-ray crystallography and found to be in the triclinic space group P1 with the following parameters: a = 1.35383(10) nm, b = 1.60687(12) nm, c = 1.86958(13) nm, α = 65.9630(10)°,β= 83.1650(10)°,γ= 83.6780(10)°, Z = 1, R1 = 0.0589, wR2= 0.1447. The dimeric polyoxoanion [((α-PW11O39H2)La(H2O)4}2]4- consisted of two [α-PW11O39]7- subunits linked together by two [La(H2O)4]3+ cations. The nine-coordinate La3+ cation was incorporated in the vacant site of the [α-PW11 O39]7- subunit, which adopted monocapped square antiprismatic coordination geometry. Thermogravimetric analysis exhibited two weight loss steps between 25 and 600℃; cyclic voltammetry indicated that two reversible single-electron reductions of the synthesized compound occurred in aqueous solution at pH 4.3.

  11. Thermodynamic properties for the sodium dimer

    Science.gov (United States)

    Song, Xiao-Qin; Wang, Chao-Wen; Jia, Chun-Sheng

    2017-04-01

    We present a closed-form expression of the classical vibrational partition function for the improved Rosen-Morse potential energy model. We give explicit expressions for the vibrational mean energy, vibrational specific heat, vibrational free energy, and vibrational entropy for diatomic molecule systems. The properties of these thermodynamic functions for the Na2 dimer are discussed in detail. We find that the improved Rosen-Morse potential model is superior to the harmonic oscillator in calculating the heat capacity for the Na2 molecules.

  12. Thermodynamics of acetylene van der Waals dimerization

    Science.gov (United States)

    Colussi, A. J.; Sander, S. P.; Friedl, R. R.

    1991-01-01

    Integrated band intensities of the 620/cm absorption in (C2H2)2 are measured by FTIR spectroscopy at constant acetylene pressure between 198 and 273 K. These data, in conjunction with ab initio results for (C2H2)2, are used for the statistical evaluation of the equilibrium constant Kp(T) for acetylene-cluster dimerization. The present results are used to clarify the role of molecular clusters in chemical systems at or near equilibrium, in particular in Titan's stratosphere.

  13. The properties of dimers confined between two charged plates.

    Science.gov (United States)

    Hatlo, Marius M; Bohinc, Klemen; Lue, Leo

    2010-03-21

    We consider two like-charged planar surfaces immersed in solution of oppositely charged dimer counterions with a bond length l. To analyze this system, we extend and employ a self-consistent field theory that has been shown to be accurate from the weak to the intermediate through to the strong coupling regimes. In the limit of very short dimers, the results converge to the results for pointlike divalent ions. Near the surfaces, the dimers lie parallel to the charged plates. In the intermediate coupling regime, the dimers are aligned perpendicularly to the surface when they are a distance l from a surface. In the weak coupling regime, the interactions are only repulsive. At slightly higher couplings, there is a minimum in the variation of the free energy with distance at approximately the bond length of the dimers, which arises from bridging conformations of the dimers. In the intermediate coupling regime, an additional minimum in the free energy is observed at much smaller distances, which is due to the correlations between the dimers. For large dimer bond lengths, this minimum is metastable with respect to the previous minimum. However, as the bond length decreases, this minimum becomes the stable, while the minimum associated with the dimer bond length becomes metastable and eventually disappears. For shorter dimer bond length the attractive interaction is the result of correlations between counterions and charges on the surfaces. We find that dimers can mediate attractive interaction between like-charged surfaces in the intermediate coupling regime. The analysis of orientations confirms the bridging mechanism for sufficiently long dimers, whereas at high electrostatic couplings charge correlations contribute to the attraction.

  14. Magnons in the quantum dimer antiferromagnet Sr{sub 3}Cr{sub 2}O{sub 8}

    Energy Technology Data Exchange (ETDEWEB)

    Quintero-Castro, Diana Lucia; Lake, Bella [Helmholtz Zentrum Berlin, Berlin 14109 (Germany); Institut fuer Festkoerperphysik, Technische Universitaet Berlin, D-10623 Berlin (Germany); Wheeler, Elisa Maria; Islam, Nazmul [Helmholtz Zentrum Berlin, Berlin 14109 (Germany)

    2011-07-01

    Sr{sub 3}Cr{sub 2}O{sub 8} consists of a three-dimensional frustrated arrangement of antiferromagnetically coupled pairs of Cr ions or dimers. The Cr ions are in the unusual 5+ valence state resulting in one electron in the 3d shell and a spin value of 1/2 while a tetrahedral crystal field ensures that this electron occupies the doubly degenerate eg orbitals. Below room temperature Sr{sub 3}Cr{sub 2}O{sub 8} undergoes a cooperative Jahn Teller distortion that lifts the orbital degeneracy so that only the 3z{sup 2}-r{sup 2} orbital is occupied. The low temperature structure is characterized by monoclinic crystal symmetry and antiferro-orbital ordering. The transition also gives rise to spatially anisotropic exchange paths and results in three crystal twins. We have grown single crystals of Sr{sub 3}Cr{sub 2}O{sub 8} and have performed DC susceptibility measurements, high field magnetisation and powder and single crystal inelastic neutron scattering experiments. The data reveals a singlet ground state and gapped triplet excitations consisting of three modes, coming from the three crystal twins. Using a random phase approximation, we have extracted the magnetic exchange interactions within the dimer and between dimers. Sr{sub 3}Cr{sub 2}O{sub 8} is a candidate for the study of the critical properties in the quantum phase transition as the magnetic field can drive a Bose Einstein condensation of magnons.

  15. Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

    Energy Technology Data Exchange (ETDEWEB)

    Mani, Devendra; Arunan, E., E-mail: arunan@ipc.iisc.ernet.in [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012 (India)

    2014-10-28

    Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer [A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and “Atoms in Molecules” analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O–H⋯O, O–H⋯π, and C–H⋯π. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact.

  16. Synthesis of Symmetrical Biaryls via Rhodium Catalyzed Dimerization of Arylmercurials and Mechanism of the Dimerization

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A series of symmetrical biaryls was synthesized from arylmercuric chlorides and biarylmercurials in the presence of [ClRh(CO)2]2 in hexamethylphosphoramide(HMPA). The mechanism of the [ClRh(CO)2]2 catalyzed dimerization of biarylmercurials was studied, and shown to be mainly intermolecular reaction.

  17. Crystal structure of diaquatris(1-ethyl-1H-imidazole-κN3(sulfato-κOnickel(II

    Directory of Open Access Journals (Sweden)

    Tamas Holczbauer

    2016-03-01

    Full Text Available In the title complex, [Ni(SO4(C5H8N23(H2O2], the NiII ion is coordinated by three facial 1-ethyl-1H-imidazole ligands, one monodentate sulfate ligand and two water molecules in a slightly distorted octahedral coordination environment. In the crystal, two pairs of O—H...O hydrogen bonds link complex molecules, forming inversion dimers incorporating R24(8, R22(8 and R22(12 rings. The dimeric unit also contains two symmetry-unique intramolecular O—H...O hydrogen bonds. In addition, weak C—H...O hydrogen bonds, weak C—H...π interactions and π–π interactions with a centroid–centroid distance of 3.560 (2 Å combine to form a three-dimensional network. One of the ethyl groups is disordered over two sets of sites with occupancies in the ratio 0.586 (7:0.414 (7.

  18. The Inverse Problem for the Dipole Field

    CERN Document Server

    Epp, V

    2015-01-01

    The Inverse problem for an electromagnetic field produced by a dipole is solved. It is assumed that the field of an arbitrary changing dipole is known. Obtained formulae allow calculation of the position and dynamics of the dipole which produces the measured field. The derived results can be used in investigations on radiative process in solids caused by changing of the charge distribution. For example, generation of the electromagnetic field caused by oscillations of atoms or electron gas at the trace of a particle channeling in a crystal, or fields arising at solids cracking or dislocation formation -- in any case when one is interested in the details of the dipole field source.

  19. Assembly of Drosophila centromeric nucleosomes requires CID dimerization.

    Science.gov (United States)

    Zhang, Weiguo; Colmenares, Serafin U; Karpen, Gary H

    2012-01-27

    Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four-helix bundle, which mediates intranucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly.

  20. Disordered clusters of Bak dimers rupture mitochondria during apoptosis

    Science.gov (United States)

    Uren, Rachel T; O’Hely, Martin; Iyer, Sweta; Bartolo, Ray; Shi, Melissa X; Brouwer, Jason M; Alsop, Amber E; Dewson, Grant; Kluck, Ruth M

    2017-01-01

    During apoptosis, Bak and Bax undergo major conformational change and form symmetric dimers that coalesce to perforate the mitochondrial outer membrane via an unknown mechanism. We have employed cysteine labelling and linkage analysis to the full length of Bak in mitochondria. This comprehensive survey showed that in each Bak dimer the N-termini are fully solvent-exposed and mobile, the core is highly structured, and the C-termini are flexible but restrained by their contact with the membrane. Dimer-dimer interactions were more labile than the BH3:groove interaction within dimers, suggesting there is no extensive protein interface between dimers. In addition, linkage in the mobile Bak N-terminus (V61C) specifically quantified association between dimers, allowing mathematical simulations of dimer arrangement. Together, our data show that Bak dimers form disordered clusters to generate lipidic pores. These findings provide a molecular explanation for the observed structural heterogeneity of the apoptotic pore. DOI: http://dx.doi.org/10.7554/eLife.19944.001 PMID:28182867

  1. An Autoinhibited Dimeric Form of BAX Regulates the BAX Activation Pathway.

    Science.gov (United States)

    Garner, Thomas P; Reyna, Denis E; Priyadarshi, Amit; Chen, Hui-Chen; Li, Sheng; Wu, Yang; Ganesan, Yogesh Tengarai; Malashkevich, Vladimir N; Almo, Steve S; Cheng, Emily H; Gavathiotis, Evripidis

    2016-08-04

    Pro-apoptotic BAX is a cell fate regulator playing an important role in cellular homeostasis and pathological cell death. BAX is predominantly localized in the cytosol, where it has a quiescent monomer conformation. Following a pro-apoptotic trigger, cytosolic BAX is activated and translocates to the mitochondria to initiate mitochondrial dysfunction and apoptosis. Here, cellular, biochemical, and structural data unexpectedly demonstrate that cytosolic BAX also has an inactive dimer conformation that regulates its activation. The full-length crystal structure of the inactive BAX dimer revealed an asymmetric interaction consistent with inhibition of the N-terminal conformational change of one protomer and the displacement of the C-terminal helix α9 of the second protomer. This autoinhibited BAX dimer dissociates to BAX monomers before BAX can be activated. Our data support a model whereby the degree of apoptosis induction is regulated by the conformation of cytosolic BAX and identify an unprecedented mechanism of cytosolic BAX inhibition. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Role of a Putative gp41 Dimerization Domain in Human Immunodeficiency Virus Type 1 Membrane Fusion

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Deng, Y; Li, Q; Dey, A; Moore, J; Lu, M

    2010-01-01

    The entry of human immunodeficiency virus type 1 (HIV-1) into a target cell entails a series of conformational changes in the gp41 transmembrane glycoprotein that mediates the fusion of the viral and target cell membranes. A trimer-of-hairpins structure formed by the association of two heptad repeat (HR) regions of the gp41 ectodomain has been implicated in a late step of the fusion pathway. Earlier native and intermediate states of the protein are postulated to mediate the antiviral activity of the fusion inhibitor enfuvirtide and of broadly neutralizing monoclonal antibodies (NAbs), but the details of these structures remain unknown. Here, we report the identification and crystal structure of a dimerization domain in the C-terminal ectodomain of gp41 (residues 630 to 683, or C54). Two C54 monomers associate to form an asymmetric, antiparallel coiled coil with two distinct C-terminal {alpha}-helical overhangs. This dimer structure is conferred largely by interactions within a central core that corresponds to the sequence of enfuvirtide. The mutagenic alteration of the dimer interface severely impairs the infectivity of Env-pseudotyped viruses. Moreover, the C54 structure binds tightly to both the 2F5 and 4E10 NAbs and likely represents a potential intermediate conformation of gp41. These results should enhance our understanding of the molecular basis of the gp41 fusogenic structural transitions and thereby guide rational, structure-based efforts to design new fusion inhibitors and vaccine candidates intended to induce broadly neutralizing antibodies.

  3. Crystal structure of 3-methyl-1-phenyl-6-propylamino-1H-pyrazolo[3,4-b]pyridine-5-carbonitrile

    Directory of Open Access Journals (Sweden)

    Jerry P. Jasinski

    2015-10-01

    Full Text Available In the title compound, C17H17N5, the dihedral angle between the 1H-pyrazolo[3,4-b]pyridine ring system (r.m.s. deviation = 0.001 Å and the attached phenyl group is 2.56 (6°. The propylamino side chain has a contorted conformation [Car—N—C—C = −77.97 (16° and N—C—C—C = −57.37 (17°]. An intramolecular C—H...N interaction closes an S(6 ring. In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds generate R22(12 loops. Aromatic π–π stacking interactions [centroid–centroid distance = 3.5726 (8 Å] are also observed.

  4. Crystal structure of rac-3-[2,3-bis-(phenyl-sulfan-yl)-3H-indol-3-yl]propanoic acid.

    Science.gov (United States)

    Noland, Wayland E; Brown, Christopher D; Bisel, Amanda M; Schneerer, Andrew K; Tritch, Kenneth J

    2015-11-01

    The title compound, C23H19NO2S2, was obtained as an unexpected regioisomer from an attempted synthesis of an inter-mediate for a substituent-effect study on ergot alkaloids. This is the first report of a 1H-indole mono-thio-ating at the 2- and 3-positions to give a 3H-indole. In the crystal, the acid H atom is twisted roughly 180° from the typical carb-oxy conformation and forms centrosymmetric O-H⋯N hydrogen-bonded dimers with the indole N atom of an inversion-related mol-ecule. Together with a weak C-H⋯O hydrogen bond involving the carbonyl O atom, chains are formed along [100].

  5. Crystal structure of rac-3-[2,3-bis­(phenyl­sulfan­yl)-3H-indol-3-yl]propanoic acid

    Science.gov (United States)

    Noland, Wayland E.; Brown, Christopher D.; Bisel, Amanda M.; Schneerer, Andrew K.; Tritch, Kenneth J.

    2015-01-01

    The title compound, C23H19NO2S2, was obtained as an unexpected regioisomer from an attempted synthesis of an inter­mediate for a substituent-effect study on ergot alkaloids. This is the first report of a 1H-indole mono­thio­ating at the 2- and 3-positions to give a 3H-indole. In the crystal, the acid H atom is twisted roughly 180° from the typical carb­oxy conformation and forms centrosymmetric O—H⋯N hydrogen-bonded dimers with the indole N atom of an inversion-related mol­ecule. Together with a weak C—H⋯O hydrogen bond involving the carbonyl O atom, chains are formed along [100]. PMID:26594523

  6. Crystal structure of di-μ-iodido-bis-{[1,3-bis-(2,6-diiso-propyl-phen-yl)imidazol-2-yl-idene]lithium}.

    Science.gov (United States)

    Wan, Hui-Da; Hong, Jian-Quan

    2015-06-01

    In the title binuclear complex, [Li2(C27H36N2)2I2], the unique Li(I) cation is coordinated by two iodide anions and one yl-idene C atom from a 1,3-bis-(2,6-diiso-propyl-phen-yl)imidazol-2-yl-idene ligand in a distorted trigonal-planar geometry. The two symmetry-related iodide anions bridge two Li(I) cations, forming an inversion dimer in which the Li2I2 plane is nearly perpendicular to the imidazol-2-yl-idene ring, with a dihedral angle of 85.5 (3)°. No hydrogen bonding is observed in the crystal.

  7. Crystal structure of 4-(3-carb-oxy-pro-pan-amido)-2-hy-droxy-benzoic acid mono-hydrate.

    Science.gov (United States)

    Tahir, Muhammad Nawaz; Ahmed, Muhammad Naeem; Butt, Arshad Farooq; Shad, Hazoor Ahmad

    2014-12-01

    In the title hydrate, C11H11NO6·H2O, the organic mol-ecule is approximately planar (r.m.s. deviation for the non-H atoms = 0.129 Å) and an intra-molecular O-H⋯O hydrogen bond closes an S(6) ring. In the crystal, the benzoic acid group participates in an O-H⋯O hydrogen bond to the water mol-ecule and accepts a similar bond from another water mol-ecule. The other -CO2H group forms a carb-oxy-lic acid inversion dimer, thereby forming an R 2 (2)(8) loop. These bonds, along with N-H⋯O and C-H⋯O inter-actions, generate a three-dimensional network.

  8. Pathogenic Cysteine Removal Mutations in FGFR Extracellular Domains Stabilize Receptor Dimers and Perturb the TM Dimer Structure.

    Science.gov (United States)

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-10-09

    Missense mutations that introduce or remove cysteine residues in receptor tyrosine kinases are believed to cause pathologies by stabilizing the active receptor tyrosine kinase dimers. However, the magnitude of this stabilizing effect has not been measured for full-length receptors. Here, we characterize the dimer stabilities of three full-length fibroblast growth factor receptor (FGFR) mutants harboring pathogenic cysteine substitutions: the C178S FGFR1 mutant, the C342R FGFR2 mutant, and the C228R FGFR3 mutant. We find that the three mutations stabilize the FGFR dimers. We further see that the mutations alter the configuration of the FGFR transmembrane dimers. Thus, both aberrant dimerization and perturbed dimer structure likely contribute to the pathological phenotypes arising due to these mutations.

  9. Application of graph theory to the statistical thermodynamics of lattice polymers. I. Elements of theory and test for dimers

    Science.gov (United States)

    Brazhnik, Olga D.; Freed, Karl F.

    1996-07-01

    The lattice cluster theory (LCT) is extended to enable inclusion of longer range correlation contributions to the partition function of lattice model polymers in the athermal limit. A diagrammatic technique represents the expansion of the partition function in powers of the inverse lattice coordination number. Graph theory is applied to sort, classify, and evaluate the numerous diagrams appearing in higher orders. New general theorems are proven that provide a significant reduction in the computational labor required to evaluate the contributions from higher order correlations. The new algorithm efficiently generates the correction to the Flory mean field approximation from as many as eight sterically interacting bonds. While the new results contain the essential ingredients for treating a system of flexible chains with arbitrary lengths and concentrations, the complexity of our new algorithm motivates us to test the theory here for the simplest case of a system of lattice dimers by comparison to the dimer packing entropies from the work of Gaunt. This comparison demonstrates that the eight bond LCT is exact through order φ5 for dimers in one through three dimensions, where φ is the volume fraction of dimers. A subsequent work will use the contracted diagrams, derived and tested here, to treat the packing entropy for a system of flexible N-mers at a volume fraction of φ on hypercubic lattices.

  10. Crystal structure of 4-[benzylideneamino]-3-thiophen-2-yl-methyl-4,5-dihydro-1H-[1,2,4] triazole-5-one

    Energy Technology Data Exchange (ETDEWEB)

    Tanak, H., E-mail: hasantanak@gmail.com [Amasya University, Department of Physics, Faculty of Arts and Sciences (Turkey)

    2013-12-15

    The crystal structure of the title compound C{sub 14}H{sub 12}N{sub 4}OS was determined by the X-ray diffraction method. The compound crystallizes in the triclinic space group P-bar1 with Z = 2. The molecule is not planar: the dihedral angle between the triazole and thiophene rings is 73.98(2)°, and that between the triazole and benzene rings is 4.05(2)°. The thiophene ring is disordered over two positions, which are approximately parallel and oppositely oriented. The major component refined to a site-occupancy factor of 0.573(3). An intramolecular C-H...O hydrogen bond generates an S(6) ring motif. In the crystal, molecules are linked together by two pairs of N-H...O interactions (to the same O atom as acceptor), forming inversion dimers. The crystal packing is also stabilized by π-π interactions [centroid-centroid distance is 3.978 Å].

  11. Synthesis, spectroscopic characterization and crystal structure of 5-bromo-1-(2-cyano-pyridin-4-yl)-1 H-indazole-3-carboxylic acid diethylamide

    Science.gov (United States)

    Anuradha, G.; Vasuki, G.; Surendrareddy, G.; Veerareddy, A.; Dubey, P. K.

    2014-07-01

    The title compound 5-bromo-1-(2-cyano-pyridin-4-yl)-1 H-indazole-3-carboxylic acid diethylamide, C18H16BrN5O, is prepared from 5-bromoindazole-3-carboxylic acid methylester. N 1-arylation is carried out with 4-chloro-2-cyanopyridine and the resulting product is converted to diethylamide by reacting with thionyl chloride and diethylamine. The structure is identified from its FT-IR, 1H NMR, 13C NMR spectroscopy, elemental analysis data and unambiguously confirmed by single crystal X-ray diffraction studies. There are two symmetry independent molecules in the asymmetric unit with no significant differences in bond lengths and angles. The title compound crystallizes in the triclinic system, space group , with a = 11.2330(2); b = 11.6130(2); c = 15.4710(3) Å, α = 92.515(1)°; β = 109.956(1)°; γ = 107.199(1)°; V = 1788.45(6)Å3 and z = 4. An intramolecular C-H…N hydrogen bond forms an S(6) ring motif in one of the unique molecules. In the crystal, two molecules are linked about a center of inversion by C-H…O hydrogen bonded dimers generating an R {2/2}(16) ring motif. The crystal packing is stabilized by C-H…N, C-H…O hydrogen bonds and π…π stacking interactions.

  12. Dimeric Labdane Diterpenes: Synthesis and Antiproliferative Effects

    Directory of Open Access Journals (Sweden)

    Guillermo Schmeda-Hirschmann

    2013-05-01

    Full Text Available Several diterpenes with the labdane skeleton show biological activity, including antiproliferative effects. Most of the research work on bioactive labdanes has been carried out on naturally occurring diterpenes and semisynthetic derivatives, but much less is known on the effects of diterpene dimers. The aim of the present work was to synthesize dimeric diterpenes from the labdane imbricatolic acid using esters, ethers and the triazole ring as linkers. Some 18 new derivatives were prepared and the compounds were evaluated for antiproliferative activity on human normal fibroblasts (MRC-5 and the following human tumor cell lines: AGS, SK-MES-1, J82 and HL-60. The diethers 8–10, differing in the number of CH2 units in the linker, presented better antiproliferative activity with a maximum effect for the derivative 9. The best antiproliferative effect against HL-60 cells was found for compounds 3 and 17, with IC50 values of 22.3 and 23.2 μM, lower than that found for the reference compound etoposide (2.23 μM. The compounds 9, 17 and 11 were the most active derivatives towards AGS cells with IC50 values of 17.8, 23.4 and 26.1 μM. A free carboxylic acid function seems relevant for the effect as several of the compounds showed less antiproliferative effect after methylation.

  13. Water dimer absorption of visible light

    Directory of Open Access Journals (Sweden)

    J. Hargrove

    2007-07-01

    Full Text Available Laboratory measurements of water vapor absorption using cavity ring-down spectroscopy revealed a broad absorption at 405 nm with a quadratic dependence on water monomer concentration, a similar absorption with a linear component at 532 nm, and only linear absorption at 570 nm in the vicinity of water monomer peaks. D2O absorption is weaker and linear at 405 nm. Van't Hoff plots constructed at 405.26 nm suggest that for dimerization, Keq=0.056±0.02 atm−1, ΔH°301 K=−16.6±2 kJ mol−1 and ΔS°301 K=−80±10 J mol−1 K−1. This transition peaks at 409.5 nm, could be attributed to the 8th overtone of water dimer and the 532 nm absorption to the 6th overtone. It is possible that some lower overtones previously searched for are less enhanced. These absorptions could increase water vapor feed back calculations leading to higher global temperature projections with currently projected greenhouse gas levels or greater cooling from greenhouse gas reductions.

  14. Modelling study of dimerization in mammalian defensins

    Directory of Open Access Journals (Sweden)

    Verma Chandra

    2006-12-01

    Full Text Available Abstract Background Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are considered key factors for their action. Based on structural information on human β-defensin 2, we examine homologous defensins from various mammalian species for conserved functional physico-chemical characteristics. Results Based on homology greater than 40%, structural models of 8 homologs of HBD-2 were constructed. A conserved pattern of electrostatics and dynamics was observed across 6 of the examined defensins; models backed by energetics suggest that the defensins in these 6 organisms are characterized by dimerization-linked enhanced functional potentials. In contrast, dimerization is not energetically favoured in the sheep, goat and mouse defensins, suggesting that they function efficiently as monomers. Conclusion β-defensin 2 from some mammals may work as monomers while those in others, including humans, work as oligomers. This could potentially be used to design human defensins that may be effective at lower concentrations and hence have therapeutic benefits.

  15. Reduced Bayesian Inversion

    OpenAIRE

    Himpe, Christian; Ohlberger, Mario

    2014-01-01

    Bayesian inversion of models with large state and parameter spaces proves to be computationally complex. A combined state and parameter reduction can significantly decrease the computational time and cost required for the parameter estimation. The presented technique is based on the well-known balanced truncation approach. Classically, the balancing of the controllability and observability gramians allows a truncation of discardable states. Here the underlying model, being a linear or nonline...

  16. The Fukushima Inverse Problem

    OpenAIRE

    Martinez-Camara, Marta; Dokmanic, Ivan; Ranieri, Juri; Scheibler, Robin; Vetterli, Martin; STOHL Andreas

    2013-01-01

    Knowing what amount of radioactive material was released from Fukushima in March 2011 and at what time instants is crucial to assess the risk, the pollution, and to understand the scope of the consequences. Moreover, it could be used in forward simulations to obtain accurate maps of deposition. But these data are often not publicly available. We propose to estimate the emission waveforms by solving an inverse problem. Previous approaches have relied on a detailed expert guess of how the relea...

  17. Crystal science fundamentals

    OpenAIRE

    Ramachandran, V.; Halfpenny, PJ; Roberts, KJ

    2017-01-01

    The fundamentals of crystal science notably crystallography, crystal chemistry, crystal defects, crystal morphology and the surface chemistry of crystals are introduced with particular emphasis on organic crystals.

  18. Role of the EHD2 unstructured loop in dimerization, protein binding and subcellular localization.

    Directory of Open Access Journals (Sweden)

    Kriti Bahl

    Full Text Available The C-terminal Eps 15 Homology Domain proteins (EHD1-4 play important roles in regulating endocytic trafficking. EHD2 is the only family member whose crystal structure has been solved, and it contains an unstructured loop consisting of two proline-phenylalanine (PF motifs: KPFRKLNPF. In contrast, despite EHD2 having nearly 70% amino acid identity with its paralogs, EHD1, EHD3 and EHD4, the latter proteins contain a single KPF or RPF motif, but no NPF motif. In this study, we sought to define the precise role of each PF motif in EHD2's homo-dimerization, binding with the protein partners, and subcellular localization. To test the role of the NPF motif, we generated an EHD2 NPF-to-NAF mutant to mimic the homologous sequences of EHD1 and EHD3. We demonstrated that this mutant lost both its ability to dimerize and bind to Syndapin2. However, it continued to localize primarily to the cytosolic face of the plasma membrane. On the other hand, EHD2 NPF-to-APA mutants displayed normal dimerization and Syndapin2 binding, but exhibited markedly increased nuclear localization and reduced association with the plasma membrane. We then hypothesized that the single PF motif of EHD1 (that aligns with the KPF of EHD2 might be responsible for both binding and localization functions of EHD1. Indeed, the EHD1 RPF motif was required for dimerization, interaction with MICAL-L1 and Syndapin2, as well as localization to tubular recycling endosomes. Moreover, recycling assays demonstrated that EHD1 RPF-to-APA was incapable of supporting normal receptor recycling. Overall, our data suggest that the EHD2 NPF phenylalanine residue is crucial for EHD2 localization to the plasma membrane, whereas the proline residue is essential for EHD2 dimerization and binding. These studies support the recently proposed model in which the EHD2 N-terminal region may regulate the availability of the unstructured loop for interactions with neighboring EHD2 dimers, thus promoting

  19. [Total inversion of the uterus].

    Science.gov (United States)

    Novachkov, V; Baltadzhieva, B; Ilieva, A; Rachev, E

    2008-01-01

    Non puerperal inversion of the uterus is very uncommon. Patients may present with pelvic pain, vaginal bleeding or hemodynamic shock. We report a fifty five old woman with uterus inversion second stage.

  20. Highly dispersed spherical Bi{sub 3.25}La{sub 0.75}Ti{sub 3}O{sub 12} nanocrystals via topotactic crystallization of aggregation-free gel particles from an effective inverse miniemulsion sol–gel approach

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Aijun; Zeng, Yanwei, E-mail: zengyw-njut@126.com, E-mail: stephen-zeng@njtech.edu.cn, E-mail: stephen-zeng@163.com; Han, Longxiang; Ding, Chuan; Cao, Liangliang; Li, Rongjie [Nanjing Tech University, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Materials Science and Engineering (China)

    2015-09-15

    Aggregation-free spherical lanthanum-doped bismuth titanate (Bi{sub 3.25}La{sub 0.75}Ti{sub 3}O{sub 12}, BLT) gel particles with an average size of about 150 nm were successfully obtained from an inverse miniemulsion sol–gel process, with Span-80 acting as surfactant, n-butanol as co-surfactant, cyclohexane as continuous phase, and submicro-droplets of aqueous solution containing Bi{sup 3+}, La{sup 3+} and Ti{sup 4+} ions as dispersed phase, and then topotactically transformed into highly dispersed spherical BLT nanocrystals after an in situ crystallization at 600 °C for 8 h. It has been found that the BLT gel particles can be obtained via a moderate sol–gel reaction inside the miniemulsion droplets at 65 °C, but their morphology and aggregation degree are strongly affected by the relative amounts of Span-80 and n-butanol. The perfect spherical BLT gel particles with no aggregation can be achieved only under the condition of 3 wt% n-butanol relative to the mass of cyclohexane, with excessive amount of n-butanol leading to the formation of ill-gelled particles with irregular shapes, while insufficient addition of n-butanol resulting in terrible aggregation of gel particles. To understand the formation of aggregation-free spherical BLT gel particles, a tentative mechanism is proposed and discussed, which reveals that a well-coordinated oil–water interfacial film made up of Span-80 and n-butanol molecules and the appropriately enhanced evaporation of water from such interfaces should be responsible for the formation of aggregation-free spherical BLT gel particles. Graphical Abstract: Aggregation-free spherical BLT (Bi{sub 3.25}La{sub 0.75}Ti{sub 3}O{sub 12}) gel particles can be prepared from an effective inverse miniemulsion sol–gel process, and subsequently topotactically transformed into spherical BLT nanocrystals through an in situ crystallization.

  1. Structural characterization suggests models for monomeric and dimeric forms of full-length ezrin.

    Science.gov (United States)

    Phang, Juanita M; Harrop, Stephen J; Duff, Anthony P; Sokolova, Anna V; Crossett, Ben; Walsh, James C; Beckham, Simone A; Nguyen, Cuong D; Davies, Roberta B; Glöckner, Carina; Bromley, Elizabeth H C; Wilk, Krystyna E; Curmi, Paul M G

    2016-09-15

    Ezrin is a member of the ERM (ezrin-radixin-moesin) family of proteins that have been conserved through metazoan evolution. These proteins have dormant and active forms, where the latter links the actin cytoskeleton to membranes. ERM proteins have three domains: an N-terminal FERM [band Four-point-one (4.1) ERM] domain comprising three subdomains (F1, F2, and F3); a helical domain; and a C-terminal actin-binding domain. In the dormant form, FERM and C-terminal domains form a stable complex. We have determined crystal structures of the active FERM domain and the dormant FERM:C-terminal domain complex of human ezrin. We observe a bistable array of phenylalanine residues in the core of subdomain F3 that is mobile in the active form and locked in the dormant form. As subdomain F3 is pivotal in binding membrane proteins and phospholipids, these transitions may facilitate activation and signaling. Full-length ezrin forms stable monomers and dimers. We used small-angle X-ray scattering to determine the solution structures of these species. As expected, the monomer shows a globular domain with a protruding helical coiled coil. The dimer shows an elongated dumbbell structure that is twice as long as the monomer. By aligning ERM sequences spanning metazoan evolution, we show that the central helical region is conserved, preserving the heptad repeat. Using this, we have built a dimer model where each monomer forms half of an elongated antiparallel coiled coil with domain-swapped FERM:C-terminal domain complexes at each end. The model suggests that ERM dimers may bind to actin in a parallel fashion.

  2. Perturbation of the dimer interface of triosephosphate isomerase and its effect on Trypanosoma cruzi.

    Directory of Open Access Journals (Sweden)

    Vanesa Olivares-Illana

    Full Text Available BACKGROUND: Chagas disease affects around 18 million people in the American continent. Unfortunately, there is no satisfactory treatment for the disease. The drugs currently used are not specific and exert serious toxic effects. Thus, there is an urgent need for drugs that are effective. Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM. The homodimeric enzyme is catalytically active only as a dimer. Because there are significant differences in the interface of the enzymes from the parasite and humans, we searched for small molecules that specifically disrupt contact between the two subunits of the enzyme from Trypanosoma cruzi but not those of TIM from Homo sapiens (HTIM, and tested if they kill the parasite. METHODOLOGY/PRINCIPAL FINDINGS: Dithiodianiline (DTDA at nanomolar concentrations completely inactivates recombinant TIM of T. cruzi (TcTIM. It also inactivated HTIM, but at concentrations around 400 times higher. DTDA was also tested on four TcTIM mutants with each of its four cysteines replaced with either valine or alanine. The sensitivity of the mutants to DTDA was markedly similar to that of the wild type. The crystal structure of the TcTIM soaked in DTDA at 2.15 A resolution, and the data on the mutants showed that inactivation resulted from alterations of the dimer interface. DTDA also prevented the growth of Escherichia coli cells transformed with TcTIM, had no effect on normal E. coli, and also killed T. cruzi epimastigotes in culture. CONCLUSIONS/SIGNIFICANCE: By targeting on the dimer interface of oligomeric enzymes from parasites, it is possible to discover small molecules that selectively thwart the life of the parasite. Also, the conformational changes that DTDA induces in the dimer interface of the trypanosomal enzyme are unique and identify a region of the interface that could be targeted for drug discovery.

  3. Electric-field-induced intradimer charge disproportionation in the dimer-Mott insulator β'-(BEDT-TTF ) 2IC l2

    Science.gov (United States)

    Hattori, Yuma; Iguchi, Satoshi; Sasaki, Takahiko; Iwai, Shinichiro; Taniguchi, Hiromi; Kishida, Hideo

    2017-02-01

    Raman scattering spectra of the dimer-Mott insulator β'-(BEDT-TTF ) 2IC l2 [BEDT-TTF = bis(ethylenedithio)tetrathiafulvalene] under a static electric field are investigated. The application of the electric field induces two additional Raman peaks on both sides of the original peak position of the charge-sensitive Raman mode (ν2) in the spectra. At 10 kV/cm, the original peak almost disappears and only the newly emerging peaks are observed. The emergence of these peaks indicates the field-induced charge disproportionation within the dimer. The temporal change of the Raman signals with the inversion of the electric field suggests a macroscopic domain formation of the charge-disproportionate dimers. This picture is reinforced by the direct measurement of the polarization.

  4. Crystal structures of 2-benzylamino-4-(4-bromophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile and 2-benzylamino-4-(4-chlorophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    R. A. Nagalakshmi

    2015-01-01

    Full Text Available In the title compounds, C24H22BrN3, (I, and C24H22ClN3, (II, the 2-aminopyridine ring is fused with a cycloheptane ring, which adopts a half-chair conformation. The planes of the phenyl and benzene rings are inclined to that of the central pyridine ring [r.m.s. deviations = 0.0083 (1 and 0.0093 (1 Å for (I and (II, respectively] by 62.47 (17 and 72.51 (14°, respectively, in (I, and by 71.44 (9 and 54.90 (8°, respectively, in (II. The planes of the aromatic rings are inclined to one another by 53.82 (17° in (I and by 58.04 (9° in (II. In the crystals of both (I and (II, pairs of N—H...Nnitrile hydrogen bonds link the molecules, forming inversion dimers with R22(12 ring motifs. In (I, the resulting dimers are connected through C—H...Br hydrogen bonds, forming sheets parallel to (10-1, and π–π interactions [inter-centroid distance = 3.7821 (16 Å] involving inversion-related pyridine rings, forming a three-dimensional network. In (II, the resulting dimers are connected through π–π interactions [inter-centroid distance = 3.771 (2 Å] involving inversion-related pyridine rings, forming a two-dimensional network lying parallel to (001.

  5. Form, function and functionality of two dimeric toluene-2,4-diisocyanate polymorphs.

    Science.gov (United States)

    Vella-Zarb, Liana; Dinnebier, Robert E

    2012-04-01

    2,4-Dioxo-1,3-diazetidine-1,3-bis(methyl-m-phenylene) diisocyanate (dimerized toluene-2,4-diisocyanate, TDI) is one of the most widely used aromatic diisocyanates in the polymer industry, and it crystallizes in at least two polymorphic forms (form A and form B) depending on reaction conditions. The crystal structures of the two forms were determined from high-resolution laboratory X-ray powder diffraction data using simulated annealing and Rietveld refinement. In spite of a marked structural similarity between them, significant discrepancies in the physical properties of the two forms prompted analysis of their partitioned energy terms in an effort to better our understanding of the driving force behind such differences in behaviour.

  6. Parallel interactions at large horizontal displacement in pyridine-pyridine and benzene-pyridine dimers.

    Science.gov (United States)

    Ninković, Dragan B; Andrić, Jelena M; Zarić, Snežana D

    2013-01-14

    A study of crystal structures from the Cambridge Structural Database (CSD) and DFT calculations reveals that parallel pyridine-pyridine and benzene-pyridine interactions at large horizontal displacements (offsets) can be important, similar to parallel benzene-benzene interactions. In the crystal structures from the CSD preferred parallel pyridine-pyridine interactions were observed at a large horizontal displacement (4.0-6.0 Å) and not at an offset of 1.5 Å with the lowest calculated energy. The calculated interaction energies for pyridine-pyridine and benzene-pyridine dimers at a large offset (4.5 Å) are about 2.2 and 2.1 kcal mol(-1), respectively. Substantial attraction at large offset values is a consequence of the balance between repulsion and dispersion. That is, dispersion at large offsets is reduced, however, repulsion is also reduced at large offsets, resulting in attractive interactions.

  7. Hydrogen atom trapping in a self-organized one-dimensional dimer

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Takami

    2014-09-01

    Full Text Available Metal–organic frameworks (MOFs have attracted widespread attention owing to their unusual structure and properties produced by their nanospaces. However, many MOFs possess the similar three-dimensional frameworks, limiting their structural variety and operating capacity for hydrogen storage under ambient conditions. Here we report the synthesis and structural characterization of a single-crystal one-dimensional dimer whose structure, operating capacity, and physical mechanism contrast with those of existing MOFs. The hydrogen storage capacity of 2.6 wt.% is comparable to the highest capacity achieved by existing MOFs at room temperature. This exceptional storage capacity is realized by self-organization during crystal growth using a weak base.

  8. Crystal structure of 2-methylamino-4-(6-methyl-4-oxo-4H-chromen-3-yl-3-nitropyrano[3,2-c]chromen-5(4H-one with an unknown solvate

    Directory of Open Access Journals (Sweden)

    Rajamani Raja

    2015-09-01

    Full Text Available In the title compound, C23H16N2O7, the mean planes of the two chromene units (r.m.s. deviations = 0.031 and 0.064 Å are almost normal to one another with a dihedral angle of 85.59 (6°. The central six-membered pyran ring has a distorted envelope conformation, with the methine C atom at the flap. There is an intramolecular N—H...O hydrogen bond, which generates an S(6 ring motif. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked by pairs of C—H...O hydrogen bonds, enclosing R22(6 ring motifs, forming zigzag chains along [001]. The chains are linked by a second pair of C—H...O hydrogen bonds, forming slabs parallel to (110. Within the slabs there are C—H...π interactions present. A region of disordered electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015. Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as plausible solvent molecule(s. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s.

  9. Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer

    DEFF Research Database (Denmark)

    Christiansen, Peter Leth; Maniadis, P.; Tsironis, G.P.

    1998-01-01

    We present exact solutions for a nonlinear dimer system defined throught a discrete nonlinear Schrodinger equation that contains also an integrable Ablowitz-Ladik term. The solutions are obtained throught a transformation that maps the dimer into a double Sine-Gordon like ordinary nonlinear...... differential equation....

  10. Synthesis of novel organo-phosphorus C60 dimers

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Carbon bridged organophosphorus C60 dimers were obtained by the reaction of aminome- thylenebisphosphonate anion with C60 and fully characterized by 1HNMR, 31PNMR, 13CNMR, FT- MALDI-MS, FT-IR, UV-Vis, DEPT and HMBC, and the dimeric compounds undergo hydrolysis by using TMSI.

  11. Local field enhancement: comparing self-similar and dimer nanoantennas

    CERN Document Server

    Pellegrini, Giovanni; Finazzi, Marco; Biagioni, Paolo

    2016-01-01

    We study the local field enhancement properties of self-similar nanolenses and compare the obtained results with the performance of standard dimer nanoantennas. We report that, despite the additional structural complexity, self-similar nanolenses are unable to provide significant improvements over the field enhancement performance of standard plasmonic dimers.

  12. Synthesis,Characterization,and Electrochemical Property of Nanometer Porphyrin Dimer

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A nanometer porphyrin dimer was synthesized with fumaryl chloride as a bridge-linked reagent. The characterization was carried out with elemental analyses, 1H NMR, UV-Vis, and IR spectrometries, and then the electrochemical properties of the porphyrins were studied. The authors found that there was moderate electronic communication between the two porphyrin rings in the nanometer porphyrin dimer.

  13. Temperature dependence of the effective interdimer exchange interaction in a weakly coupled antiferromagnetic dimer copper compound

    Science.gov (United States)

    Calvo, Rafael; Santana, Vinicius T.; Nascimento, Otaciro R.

    2017-08-01

    We report a variation with temperature T of the effective interdimeric interaction Jeff' in the antiferromagnetic (AFM) copper dimeric organic compound Cu2[TzTs] 4 (N -thiazol-2-yl-toluenesulfonamidate CuII). This T dependence was obtained from measurements of the effects in the electron paramagnetic resonance (EPR) spectra of the proposed quantum phase transition associated with the exchange-narrowing processes. Cu2[TzTs] 4 contains exchange-coupled pairs of CuII spins SA and SB (S =1 /2 ), with intradimeric AFM exchange coupling J0=(-115 ±1 ) cm-1 (Hex=-J0SA.SB ). The variation of the EPR linewidth of single crystals with field orientation around a "magic angle" where the transitions intersect and the integrated signal intensity of the so-called U peak of the powder spectrum were measured as a function of T . Modeling these data using arguments of exchange narrowing in the adiabatic regime considering the angular variation of the single-crystal spectra and a geometric description, we find that the effective interdimeric coupling | Jeff'| associated with the exchange frequency ωex is negligible for T ≪| J0/kB| when the units are uncoupled and | Jeff'|=(0.080 ±0.005 ) cm-1 (| Jeff'/J0|=7.0 × 10-4 ) at 298 K. Within this T interval, two ranges of | Jeff'| with linear temperature variation but different slopes, with a kink at ˜80 K, are observed and discussed. This T dependence arises from the growing population of the triplet state, and its relevance to the properties of various arrays of dimeric units is discussed. Our experimental procedures and results are compared with those of previous works in ion radical salts and dimeric metal compounds. The relation between the effective coupling | Jeff'| and the real interdimeric exchange coupling | J'| related to the chemical paths connecting neighbor units is discussed.

  14. New isolable dialkylsilylene and its isolable dimer that equilibrate in solution.

    Science.gov (United States)

    Abe, Takashi; Tanaka, Ryoji; Ishida, Shintaro; Kira, Mitsuo; Iwamoto, Takeaki

    2012-12-12

    The new isolable dialkylsilylene 3 bearing a bidentate alkyl substituent was synthesized. Recrystallization of silylene 3 gave yellow crystals of 3 and orange-red crystals of tetraalkyldisilene 4, a dimer of 3. In the solid state, 3 exists as a monomer with a closest distance of 6.745 Å between dicoordinate silicon atoms, while disilene 4 has a remarkably long Si═Si double bond distance of 2.252 Å. An equilibrium between 3 and 4 in solution was observed by NMR and UV-vis spectroscopies, and the thermodynamic parameters of the equilibrium were estimated to be ΔH = -36 ± 3 kJ mol(-1) and ΔS = -170 ± 15 J mol(-1) K(-1). Analysis of the percent buried volume, a measure of the steric demand around the divalent silicon, showed that the flexible steric bulkiness of the alkyl substituent of 3 and 4 allows the reversible dimerization of silylene 3 to disilene 4 and the isolation of both species.

  15. Residue conservation and dimer-interface analysis of olfactory receptor molecular models

    Directory of Open Access Journals (Sweden)

    Ramanathan Sowdhamini

    2012-10-01

    Full Text Available Olfactory Receptors (ORs are members of the Class A rhodopsin like G-protein coupled receptors (GPCRs which are the initial players in the signal transduction cascade, leading to the generation of nerve impulses transmitted to the brain and resulting in the detection of odorant molecules. Despite the accumulation of thousands of olfactory receptor sequences, no crystal structures of ORs are known tο date. However, the recent availability of crystallographic models of a few GPCRs allows us to generate homology models of ORs and analyze their amino acid patterns, as there is a huge diversity in OR sequences. In this study, we have generated three-dimensional models of 100 representative ORs from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Sacharomyces cerevisiae which were selected on the basis of a composite classification scheme and phylogenetic analysis. The crystal structure of bovine rhodopsin was used as a template and it was found that the full-length models have more than 90% of their residues in allowed regions of the Ramachandran plot. The structures were further used for analysis of conserved residues in the transmembrane and extracellular loop regions in order to identify functionally important residues. Several ORs are known to be functional as dimers and hence dimer interfaces were predicted for OR models to analyse their oligomeric functional state.

  16. Mechanistic basis of Nek7 activation through Nek9 binding and induced dimerization

    Science.gov (United States)

    Haq, Tamanna; Richards, Mark W.; Burgess, Selena G.; Gallego, Pablo; Yeoh, Sharon; O'Regan, Laura; Reverter, David; Roig, Joan; Fry, Andrew M.; Bayliss, Richard

    2015-11-01

    Mitotic spindle assembly requires the regulated activities of protein kinases such as Nek7 and Nek9. Nek7 is autoinhibited by the protrusion of Tyr97 into the active site and activated by the Nek9 non-catalytic C-terminal domain (CTD). CTD binding apparently releases autoinhibition because mutation of Tyr97 to phenylalanine increases Nek7 activity independently of Nek9. Here we find that self-association of the Nek9-CTD is needed for Nek7 activation. We map the minimal Nek7 binding region of Nek9 to residues 810-828. A crystal structure of Nek7Y97F bound to Nek9810-828 reveals a binding site on the C-lobe of the Nek7 kinase domain. Nek7Y97F crystallizes as a back-to-back dimer between kinase domain N-lobes, in which the specific contacts within the interface are coupled to the conformation of residue 97. Hence, we propose that the Nek9-CTD activates Nek7 through promoting back-to-back dimerization that releases the autoinhibitory tyrosine residue, a mechanism conserved in unrelated kinase families.

  17. Loop groups, Clusters, Dimers and Integrable systems

    CERN Document Server

    Fock, V V

    2014-01-01

    We describe a class of integrable systems on Poisson submanifolds of the affine Poisson-Lie groups $\\widehat{PGL}(N)$, which can be enumerated by cyclically irreducible elements the co-extended affine Weyl groups $(\\widehat{W}\\times \\widehat{W})^\\sharp$. Their phase spaces admit cluster coordinates, whereas the integrals of motion are cluster functions. We show, that this class of integrable systems coincides with the constructed by Goncharov and Kenyon out of dimer models on a two-dimensional torus and classified by the Newton polygons. We construct the correspondence between the Weyl group elements and polygons, demonstrating that each particular integrable model admits infinitely many realisations on the Poisson-Lie groups. We also discuss the particular examples, including the relativistic Toda chains and the Schwartz-Ovsienko-Tabachnikov pentagram map.

  18. Pseudo-two-dimensional random dimer lattices

    Energy Technology Data Exchange (ETDEWEB)

    Naether, U., E-mail: naether@unizar.es [Instituto de Ciencia de Materiales de Aragón and Departamento de Física de la Materia Condensada, CSIC – Universidad de Zaragoza, 50009 Zaragoza (Spain); Mejía-Cortés, C.; Vicencio, R.A. [Departamento de Física and MSI – Nucleus for Advanced Optics, Center for Optics and Photonics (CEFOP), Facultad de Ciencias, Universidad de Chile, Santiago (Chile)

    2015-06-05

    We study the long-time wave transport in correlated and uncorrelated disordered 2D arrays. When a separation of dimensions is applied to the model, we find that the previously predicted 1D random dimer phenomenology also appears in so-called pseudo-2D arrays. Therefore, a threshold behavior is observed in terms of the effective size for eigenmodes, as well as in long-time dynamics. A minimum system size is required to observe this threshold, which is very important when considering a possible experimental realization. For the long-time evolution, we find that for correlated lattices a super-diffusive long-range transport is observed. For completely uncorrelated disorder 2D transport becomes sub-diffusive within the localization length and for random binary pseudo-2D arrays localization is observed.

  19. Dimerization and oligomerization of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Ryder, L Rebekka; Steinø, Anne;

    2003-01-01

    protein. Using PAGE, urea gradient gel electrophoresis, capillary electrophoresis and MS, we show that dimerization through the SH group can be induced by lowering the pH to 5-6, heating, or under conditions that favour partial unfolding such as urea concentrations above 2.6 m or SDS concentrations above...... 0.025%. Moreover, we show that calreticulin also has the ability to self-oligomerize through noncovalent interactions at urea concentrations above 2.6 m at pH below 4.6 or above pH 10, at temperatures above 40 degrees C, or in the presence of high concentrations of organic solvents (25%), conditions...... urea or 1% SDS, and heat-induced oligomerization could be inhibited by 8 m urea or 1% SDS when present during heating. Comparison of the binding properties of monomeric and oligomeric calreticulin in solid-phase assays showed increased binding to peptides and denatured proteins when calreticulin...

  20. Edge Magnon Excitation in Spin Dimer Systems

    Science.gov (United States)

    Sakaguchi, Ryo; Matsumoto, Masashige

    2016-10-01

    Magnetic excitation in a spin dimer system on a bilayer honeycomb lattice is investigated in the presence of a zigzag edge, where disordered and ordered phases can be controlled by a quantum phase transition. In analogy with the case of graphene with a zigzag edge, a flat edge magnon mode appears in the disordered phase. In an ordered phase, a finite magnetic moment generates a mean-field potential to the magnon. Since the potential is nonuniform on the edge and bulk sites, it affects the excitation, and the dispersion of the edge mode deviates from the flat shape. We investigate how the edge magnon mode evolves when the phase changes through the quantum phase transition and discuss the similarities to ordered spin systems on a monolayer honeycomb lattice.

  1. Inversion assuming weak scattering

    DEFF Research Database (Denmark)

    Xenaki, Angeliki; Gerstoft, Peter; Mosegaard, Klaus

    2013-01-01

    The study of weak scattering from inhomogeneous media or interface roughness has long been of interest in sonar applications. In an acoustic backscattering model of a stationary field of volume inhomogeneities, a stochastic description of the field is more useful than a deterministic description...... due to the complex nature of the field. A method based on linear inversion is employed to infer information about the statistical properties of the scattering field from the obtained cross-spectral matrix. A synthetic example based on an active high-frequency sonar demonstrates that the proposed...

  2. Inverse Degree and Connectivity

    Institute of Scientific and Technical Information of China (English)

    MA Xiao-ling; TIAN Ying-zhi

    2013-01-01

    Let G be a connected graph with vertex set V(G),order n =丨V(G)丨,minimum degree δ(G) and connectivity κ(G).The graph G is called maximally connected if κ(G) =δ(G).Define the inverse degree of G with no isolated vertices as R(G) =Σv∈V(G)1/d(v),where d(v) denotes the degree of the vertex v.We show that G is maximally connected if R(G) < 1 + 2/δ + n-2δ+1/(n-1)(n-3).

  3. Fractional decay of quantum dots in real photonic crystals

    DEFF Research Database (Denmark)

    Kristensen, Philip Trøst; Koenderink, A. Femius; Lodahl, Peter;

    2008-01-01

    We show that fractional decay may be observable in experiments using quantum dots and photonic crystals with parameters that are currently achievable. We focus on the case of inverse opal photonic crystals and locate the position in the crystal where the effect is most pronounced. Furthermore, we...

  4. Molecular Dynamics Simulation of Amyloid Beta Dimer Formation

    CERN Document Server

    Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V

    2004-01-01

    Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...

  5. Metal membrane with dimer slots as a universal polarizer

    DEFF Research Database (Denmark)

    Zhukovsky, Sergei; Zalkovskij, Maksim; Malureanu, Radu

    2014-01-01

    In this work, we show theoretically and confirm experimentally that thin metal membranes patterned with an array of slot dimers (or their Babinet analogue with metal rods) can function as a versatile spectral and polarization filter. We present a detailed covariant multipole theory...... for the electromagnetic response of an arbitrary dimer based on the Green functions approach. The theory confirms that a great variety of polarization properties, such as birefringence, chirality and elliptical dichroism, can be achieved in a metal layer with such slot-dimer patterning (i.e. in a metasurface). Optical...... properties of the metasurface can be extensively tuned by varying the geometry (shape and dimensions) of the dimer, for example, by adjusting the sizes and mutual placement of the slots (e.g. inter-slot distance and alignment angle). Three basic shapes of dimers are analyzed: II-shaped (parallel slots), V...

  6. Three types of couplings between asymmetric plasmonic dimers.

    Science.gov (United States)

    Chao, Yen-Chun; Tseng, Hsuan-Chi; Chang, Kao-Der; Chang, Chih-Wei

    2012-01-30

    We report extensive numerical studies on plasmonic dimers of different configurations and find that their coupling effects can be categorized into three types of phenomena. First, like ordinary mechanical systems, the plasmonic dimers can exhibit positive couplings that show anti-crossing behavior. Second, they can also be arranged to exhibit negative couplings that display opposite trends in resonant frequency shifts. Third, when there are surface currents in proximity to each other, the resonance frequencies of the dimers exhibit unusual redshifts that do not have any analogies in conventional systems. Our work suggests that in addition to the well-known electric and magnetic dipolar interactions, contributions from the inductance of displacement currents in the near field cannot be ignored. Overall, asymmetric plasmonic dimers exhibit better sensitivities than the symmetric counterparts and our extensive studies also enable us to identify the plasmonic dimer with the highest sensing capabilities.

  7. Bowman-Birk protease inhibitor from the seeds of Vigna unguiculata forms a highly stable dimeric structure.

    Science.gov (United States)

    Rao, K N; Suresh, C G

    2007-10-01

    Different protease inhibitors including Bowman-Birk type (BBI) have been reported from the seeds of Vigna unguiculata. Protease isoinhibitors of double-headed Bowman-Birk type from the seeds of Vigna unguiculata have been purified and characterized. The BBI from Vigna unguiculata (Vu-BBI) has been found to undergo self-association to form very stable dimers and more complex oligomers, by size-exclusion chromatography and SDS-PAGE in the presence of urea. Many BBIs have been reported to undergo self-association to form homodimers or more complex oligomers in solution. Only one dimeric crystal structure of a BBI (pea-BBI) is reported to date. We report the three-dimensional structure of a Vu-BBI determined at 2.5 A resolution. Although, the inhibitor has a monomer fold similar to that found in other known structures of Bowman-Birk protease inhibitors, its quaternary structure is different from that commonly observed in this family. The structural elements responsible for the stability of monomer molecule and dimeric association are discussed. The Vu-BBI may use dimeric or higher quaternary association to maintain the physiological state and to execute its biological function.

  8. DNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer.

    Science.gov (United States)

    Medvedev, D; Stuchebrukhov, A A

    2001-05-21

    Photolyase is an enzyme that catalyses photorepair of thymine dimers in UV damaged DNA by electron transfer reaction. The structure of the photolyase/DNA complex is unknown at present. Using crystal structure coordinates of the substrate-free enzyme from E. coli, we have recently built a computer molecular model of a thymine dimer docked to photolyase catalytic site and studied molecular dynamics of the system. In this paper, we present analysis of the electronic coupling and electron transfer pathway between the catalytic cofactor FADH(-) and the pyrimidine dimer by the method of interatomic tunneling currents. Electronic structure is treated in the extended Hückel approximation. The root mean square transfer matrix element is about 6 cm(-1), which is consistent with the experimentally determined rate of transfer. We find that electron transfer mechanism responsible for the repair utilizes an unusual folded conformation of FADH(-) in photolyases, in which the isoalloxazine ring of the flavin and the adenine are in close proximity, and the peculiar features of the docked orientation of the dimer. The tunneling currents show explicitly that despite of the close proximity between the donor and acceptor complexes, the electron transfer mechanism between the flavin and the thymine bases is not direct, but indirect, with the adenine acting as an intermediate. These calculations confirm the previously made conclusion based on an indirect evidence for such mechanism.

  9. (9E)-9-benzylidene-2-methylsulfanyl-5-phenyl-6,7,8,9-tetrahydropyrimido[4,5-b]quinolin-4(3H)-one: a hydrogen-bonded R2(2)(8) dimer.

    Science.gov (United States)

    Becerra, Diana; Insuasty, Braulio; Cobo, Justo; Glidewell, Christopher

    2013-12-15

    In the molecule of the title compound, C25H21N3OS, which was prepared by mild oxidation of the corresponding 5,6,7,8,9,10-hexahydro analogue, the fused carbocyclic ring adopts an envelope conformation. Pairs of molecules are linked into cyclic centrosymmetric dimers by pairs of inversion-related N-H···O hydrogen bonds.

  10. Adhesion of single crystals on modified surfaces in crystallization fouling

    Science.gov (United States)

    Mayer, Moriz; Augustin, Wolfgang; Scholl, Stephan

    2012-12-01

    In crystallization fouling it has been observed that during a certain initial phase the fouling is formed by a non-uniform layer consisting of a population of single crystals. These single crystals are frequently formed by inverse soluble salts such as CaCO3. During heterogeneous nucleation and heterogeneous growth an interfacial area between the crystal and the heat transfer surface occurs. The development of this interfacial area is the reason for the adhesion of each single crystal and of all individual crystals, once a uniform layer has been built up. The emerging interfacial area is intrinsic to the heterogeneous nucleation of crystals and can be explained by the thermodynamic principle of the minimum of the Gibbs free energy. In this study CaCO3 crystals were grown heterogeneously on untreated and on modified surfaces inside a flow channel. An untreated stainless steel (AISI 304) surface was used as a reference. Following surface modifications were investigated: enameled and electropolished stainless steel as well as diamond-like-carbon based coatings on stainless steel substrate. The adhesion was measured through a novel measurement technique using a micromanipulator to shear off single crystals from the substrate which was fixed to a spring table inside a SEM.

  11. NaGd(WO4)2∶Yb3+/Tm3+反蛋白石光子晶体的制备与上转换发光调制研究%Preparation and Modified Upconversion Luminescence In NaGd(WO4)2∶Yb3+/Tm3+ Inverse Opal Photonic Crystals

    Institute of Scientific and Technical Information of China (English)

    王运锋; 宋金璠; 唐晓燕; 胡冬梅

    2016-01-01

    Photonic crystal (PC) possesses long-scale periodicity and has been widely applied in modifying visible and near-infrared photonic band gap.One of the extraordinary properties of the PCs is the modulation on spontaneous emis sion of embedded luminescence centers.In this study,three-dimensional NaGd (WO4)2∶yb3+/Tm3+ inverse opal photonic crystals (IOPC) with highly oridered periodic structure were prepared by self-assembly method using PMMA as template.The modulation effect of PC on emission spectra and dynamics of Tm3+ ions were systemically studied.In NaGd (WO4)2∶yb3+/Tm3+ inverse opal photonic crystals,due to unique cavity structure and photonic band gap effect,the emission line of 1G4-3H6 transition decreases by ~45% and the spontaneous radiation rate is suppressed by ~30%.Meanwhile,the up-conversion local thermal effect is largely suppressed.This experimental analysis indicates that the IOPC structure is an effective device for improving efficiency of up-conversion luminescence.%三维光子晶体具有长程有序的结构特点,在可见和近红外光谱范围内有着广泛的应用.光子晶体的一个重要性质是其对嵌入其中的发光中心自发辐射具有调制作用.本研究利用自组装和模板辅助法制备高质量的三维NaGd(WO4)2∶Yb3+/Tm3+反蛋白石光子晶体,探究了光子带隙对Tm3+离子上转换荧光发射与发光动力学的调制作用.通过对比分析发现,由于反蛋白石光子晶体独特的周期性大孔结构和光子带隙效应,处于光子带隙内的Tm3+离子1G4-3H6的发光强度被抑制约45%,自发辐射速率(SDR)被抑制约30%,同时上转换局域热效应得到有效的调制.本实验结果对探索新型高效稀土掺杂上转换发光材料和提高上转换发光效率有指导意义.

  12. Threshold electron attachment and electron impact ionization involving oxygen dimers

    Science.gov (United States)

    Kreil, J.; Ruf, M.-W.; Hotop, H.; Ettischer, I.; Buck, U.

    1998-12-01

    Using two different crossed-beams machines we have carried out the first quantitative study of threshold electron attachment and electron impact-induced ionization and fragmentation involving oxygen dimers (O 2) 2. In the electron attachment experiment we study electron transfer from state-selected Ar **(20d) Rydberg atoms to O 2 molecules and dimers in a skimmed supersonic beam at variable nozzle temperatures ( T0) and stagnation pressures ( p0). The relative dimer density is determined through measurements of Penning ionization by metastable Ne *(3s 3P2,0) atoms and used to estimate the absolute cross-section for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 dimers to be nearly 10 -17 m 2, almost four orders of magnitude larger than that for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 monomers. The fragmentation of the oxygen cluster beam is quantitatively characterized by the transverse helium beam scattering method which allows us to spatially separate different clusters. It is shown that in 70 eV electron impact of (O 2) 2 only 3.6(4)% of the dimers are detected as dimer ions (O 2) 2+. In additional experiments involving SF 6 clusters we show that SF 6 dimers fragment nearly completely upon 70 eV electron impact, yielding SF 5+ ions (probability for (SF 6)·SF 5+ production at most 0.3%).

  13. Dark Radiative Inverse Seesaw

    CERN Document Server

    Ahriche, Amine; Nasri, Salah

    2016-01-01

    We present a minimal model that simultaneously accounts for neutrino masses and the origin of dark matter (DM) and where the electroweak phase transition is strong enough to allow for electroweak baryogenesis. The Standard Model is enlarged with a Majorana fermion, three generations of chiral fermion pairs, and a single complex scalar that plays a central role in DM production and phenomenology, neutrino masses, and the strength of the phase transition. All the new fields are singlets under the SM gauge group. Neutrino masses are generated via a new variant of radiative inverse seesaw where the required small mass term is generated via loops involving DM and no large hierarchy is assumed among the mass scales. The model offers all the advantage of low-scale neutrino mass models as well as a viable dark matter candidate that is testable with direct detection experiments.

  14. Assembly of a New Cyano-bridged 4f-3d Dimer Sm(DMSO)4-(H2O)3Cr(CN)6 and Crystal Structure of [K3(18-crown-6)3-(H2O)4] Cr(CN)6 ·3H2O

    Institute of Scientific and Technical Information of China (English)

    周北川; 王宏根; 等

    2003-01-01

    A new syano-bridged binuclear 4f-3d complex Sm(DMSO)4-(H2O)3Cr(CN)6 was synthesized and characterized by single crystal structure analysis.It crystallizes in monoclinic,space group P21 with a=0.9367(3)°and Z=2,In this binuclear complex,Sm atom is eight coordinated and linked to the Cr atom by a cyano bridge,The molecules packs to form 3D structure due to the hydrogen bonds among them. [K3(18-crown-6)3-(H2O)4] Cr(CN)6 ·3H2O(18-C-6 represents 18-crown-6-ether)that was synthesized as a byproduct in the preparation of a Gd-Cr complex is also structurally characterized.Crystal data:triclinic,space group p-1 with a=1.0496(7)nm,b=1.1567(14)nm,c=1.3530(13)nm,α=94.15(9)°,β=96.04(8)°,γ=95.25(9)° and Z=1, [K3(18-crown-6)3-(H2O)4] Cr(CN)6 ·3H2O consists of ionic [K3(18-crown-6)3-(H2O)4]3+ and [Cr(CN)6]3- pairs,of which the [K3(18-C-6)3(H2O)4]3+ ion is a trinuclear cluster connected by water,and K atome are eight coordinated by eight oxygen atoms of one 18-C-6 and two water molecules.

  15. Flavonoid dimers as bivalent modulators for pentamidine and sodium stiboglucanate resistance in leishmania.

    Science.gov (United States)

    Wong, Iris L K; Chan, Kin-Fai; Burkett, Brendan A; Zhao, Yunzhe; Chai, Yi; Sun, Hongzhe; Chan, Tak Hang; Chow, Larry M C

    2007-03-01

    Drug resistance by overexpression of ATP-binding cassette (ABC) transporters is an impediment in the treatment of leishmaniasis. Flavonoids are known to reverse multidrug resistance (MDR) in Leishmania and mammalian cancers by inhibiting ABC transporters. Here, we found that synthetic flavonoid dimers with three (compound 9c) or four (compound 9d) ethylene glycol units exhibited a significantly higher reversing activity than other shorter or longer ethylene glycol-ligated dimers, with approximately 3-fold sensitization of pentamidine and sodium stibogluconate (SSG) resistance in Leishmania, respectively. This modulatory effect was dosage dependent and not observed in apigenin monomers with the linker, suggesting that the modulatory effect is due to its bivalent nature. The mechanism of reversal activity was due to increased intracellular accumulation of pentamidine and total antimony in Leishmania. Compared to other MDR modulators such as verapamil, reserpine, quinine, quinacrine, and quinidine, compounds 9c and 9d were the only agents that can reverse SSG resistance. In terms of reversing pentamidine resistance, 9c and 9d have activities comparable to those of reserpine and quinacrine. Modulators 9c and 9d exhibited reversal activity on pentamidine resistance among LeMDR1(-/-), LeMDR1(+/+), and LeMDR1-overexpressed mutants, suggesting that these modulators are specific to a non-LeMDR1 pentamidine transporter. The LeMDR1 copy number is inversely related to pentamidine resistance, suggesting that it might be involved in importing pentamidine into the mitochondria. In summary, bivalency could be a useful strategy for the development of more potent ABC transporter modulators and flavonoid dimers represent a promising reversal agent for overcoming pentamidine and SSG resistance in parasite Leishmania.

  16. Inverse Queries For Multidimensional Spaces

    CERN Document Server

    Bernecker, Thomas; Kriegel, Hans-Peter; Mamoulis, Nikos; Renz, Matthias; Zhang, Shiming; Züfle, Andreas

    2011-01-01

    Traditional spatial queries return, for a given query object $q$, all database objects that satisfy a given predicate, such as epsilon range and $k$-nearest neighbors. This paper defines and studies {\\em inverse} spatial queries, which, given a subset of database objects $Q$ and a query predicate, return all objects which, if used as query objects with the predicate, contain $Q$ in their result. We first show a straightforward solution for answering inverse spatial queries for any query predicate. Then, we propose a filter-and-refinement framework that can be used to improve efficiency. We show how to apply this framework on a variety of inverse queries, using appropriate space pruning strategies. In particular, we propose solutions for inverse epsilon range queries, inverse $k$-nearest neighbor queries, and inverse skyline queries. Our experiments show that our framework is significantly more efficient than naive approaches.

  17. Opal shell structures: direct assembly versus inversion approach.

    Science.gov (United States)

    Deng, Tian-Song; Sharifi, Parvin; Marlow, Frank

    2013-09-16

    Opal shell structures can be fabricated in two ways: By direct assembly from hollow spheres (hs-opal) or by infiltration of precursors into opal templates and inversion. The resulting lattice disturbances were characterized by scanning electron microscopy (SEM), optical microscopy, and transmission spectra. The hs-opal system shows much lower disturbances, for example, a lower number of cracks and lattice deformations. The strong suppression of crack formation in one of these inverse opal structures can be considered as promising candidates for the fabrication of more perfect photonic crystals.

  18. Crystal structure of (E-N-{2-[2-(2-chlorobenzylidenehydrazin-1-yl]-2-oxoethyl}-4-methylbenzamide monohydrate

    Directory of Open Access Journals (Sweden)

    H. Purandara

    2015-07-01

    Full Text Available The title compound, C17H16ClN3O2·H2O, an acylhydrazone derivative, contains a glycine moiety and two substituted benzene rings on either end of the chain. It crystallized as a monohydrate. The molecules adopt an E conformation with respect to the C=N double bond, as indicated by the N—N=C—C torsion angle of 179.38 (14°. The molecule is twisted in such a way that the almost planar Car—C(=O—N(H—C(H2 and C(H2—C(=ON(H—N=C—Car [r.m.s deviations = 0.009 and 0.025 Å, respectively] segments are inclined to on another by 77.36 (8°, while the benzene rings are normal to one another, making a dihedral angle of 89.69 (9°. In the crystal, the water molecule links three molecules through two O—H...O and one N—H...O hydrogen bonds. The molecules are linked via pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(14 ring motif. The dimers are linked by O—H...O hydrogen bonds, involving two molecules of water, forming chains along [100], enclosing R22(14 and R22(18 ring motifs. The chains are linked through C—H...O interactions, forming sheets parallel to (010. Within the sheets, there are C—H...π and parallel slipped π–π stacking interactions present [inter-centroid distance = 3.6458 (12 Å].

  19. Captopril and its dimer captopril disulfide: comparative structural and conformational studies.

    Science.gov (United States)

    Bojarska, Joanna; Maniukiewicz, Waldemar; Fruziński, Andrzej; Sieroń, Lesław; Remko, Milan

    2015-03-01

    The crystal structures of captopril {systematic name: (2S)-1-[(2S)-2-methyl-3-sulfanylpropanoyl]pyrrolidine-2-carboxylic acid}, C(9)H(15)NO(3)S, (1), and its dimer disulfide metabolite, 1,1'-{disulfanediylbis[(2S)-2-methyl-1-oxopropane-3,1-diyl]}bis-L-proline, C(18)H(28)N(2)O(6)S(2), (2), were determined by single-crystal X-ray diffraction analysis. Compound (1) crystallizes in the orthorhombic space group P2(1)2(1)2(1), while compound (2) crystallizes in the monoclinic space group P2(1), both with one molecule per asymmetric unit. The molecular geometries of (1) and (2) are quite similar, but certain differences appear in the conformations of the five-membered proline rings and the side chains containing the sulfhydryl group. The proline ring adopts an envelope conformation in (1), while in (2) it exists in envelope and slightly deformed half-chair conformations. The conformation adopted by the side chain is extended in (1) and folded in (2). A minimum-energy conformational search using Monte Carlo methods in the aqueous phase reveals that the optimized conformations of the title compounds differ from those determined crystallographically, which depend on their immediate environment. Intermolecular O-H...O and relatively weak C-H...O interactions seem to be effective in both structures and, together with S-H...O and C-H...S contacts, they create three-dimensional networks.

  20. Crystal structure of (E-pent-2-enoic acid

    Directory of Open Access Journals (Sweden)

    Tim Peppel

    2015-05-01

    Full Text Available The molecule of the title compound, C5H8O2, a low-melting α,β-unsaturated carboxylic acid, is essentially planar [maximum displacement = 0.0239 (13 Å]. In the crystal, molecules are linked into centrosymmetric dimers via pairs of O—H...O hydrogen bonds.

  1. Chemically Patterned Inverse Opal Created by a Selective Photolysis Modification Process.

    Science.gov (United States)

    Tian, Tian; Gao, Ning; Gu, Chen; Li, Jian; Wang, Hui; Lan, Yue; Yin, Xianpeng; Li, Guangtao

    2015-09-01

    Anisotropic photonic crystal materials have long been pursued for their broad applications. A novel method for creating chemically patterned inverse opals is proposed here. The patterning technique is based on selective photolysis of a photolabile polymer together with postmodification on released amine groups. The patterning method allows regioselective modification within an inverse opal structure, taking advantage of selective chemical reaction. Moreover, combined with the unique signal self-reporting feature of the photonic crystal, the fabricated structure is capable of various applications, including gradient photonic bandgap and dynamic chemical patterns. The proposed method provides the ability to extend the structural and chemical complexity of the photonic crystal, as well as its potential applications.

  2. Stochastic optimization-based study of dimerization kinetics

    Indian Academy of Sciences (India)

    Srijeeta Talukder; Shrabani Sen; Ralf Metzler; Suman K Banik; Pinaki Chaudhury

    2013-11-01

    We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and combine it with three different optimization techniques (genetic algorithm, simulated annealing and parallel tempering) to obtain the rate constants involved in each reaction step. We find good convergence of the numerical scheme to the rate constants of the process. We also perform a sensitivity test on the reaction kinetic parameters to see the relative effects of the parameters for the associated profile of the monomer/dimer distribution.

  3. Subsurface dimerization in III-V semiconductor (001) surfaces

    DEFF Research Database (Denmark)

    Kumpf, C.; Marks, L.D.; Ellis, D.

    2001-01-01

    We present the atomic structure of the c(8 X 2) reconstructions of InSb-, InAs-, and GaAs-(001) surfaces as determined by surface x-ray diffraction using direct methods. Contrary to common belief, group III dimers are not prominent on the surface, instead subsurface dimerization of group m atoms ...... takes place in the second bilayer, accompanied by a major rearrangement of the surface atoms above the dimers to form linear arrays. By varying the occupancies of four surface sites the (001)-c(8 X 2) reconstructions of III-V semiconductors can be described in a unified model....

  4. Circular dimers of lambda DNA in infected, nonlysogenic Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Freifelder, D.; Baran, N.; Folkmanis, A.; Freifelder, D.L.R.

    1977-09-01

    Covalently closed circular dimerss of phage lambda DNA have been found in Escherichia coli infected with lambda. These dimers can be formed by either the lambda Red or Int systems, by a nonrecombinational replicative mechanism requiring the activity of the lambda O and P genes or by joining of the cohesive ends. Dimers mediated by the E. coli Rec system have not been observed. Those formed by the Int system often result from recombination between different DNA molecules; however, the Red-mediated dimer may be a result of replicative extension of a single DNA molecule. Trimers have also been observed but studied only briefly.

  5. Time resolved structural dynamics of butadiyne-linked porphyrin dimers.

    Science.gov (United States)

    Camargo, Franco V A; Hall, Christopher R; Anderson, Harry L; Meech, Stephen R; Heisler, Ismael A

    2016-03-01

    In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral) angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution.

  6. Time resolved structural dynamics of butadiyne-linked porphyrin dimers

    Directory of Open Access Journals (Sweden)

    Franco V. A. Camargo

    2016-03-01

    Full Text Available In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution.

  7. How to use D-dimer in acute cardiovascular care

    DEFF Research Database (Denmark)

    Giannitsis, Evangelos; Mair, Johannes; Christersson, Christina

    2015-01-01

    D-dimer testing is important to aid in the exclusion of venous thromboembolic events (VTEs), including deep venous thrombosis and pulmonary embolism, and it may be used to evaluate suspected aortic dissection. D-dimer is produced upon activation of the coagulation system with the generation and s...... testing. For the exclusion of pulmonary embolism/deep vein thrombosis, age-adjusted cut-offs are recommend. Clinicians must be aware of the validated use of their hospital's D-dimer assay to avoid inappropriate use of this biomarker in routine care....

  8. Third-Order Optical Nonlinearity in Novel Porphyrin Dimers

    Institute of Scientific and Technical Information of China (English)

    PEI Song-Hao; ZHAO Da-Peng; ZHANG Wei; ZHENG Wen-Qi; WANG Xing-Qiao; PENG Wei-Xian; SHI Guang; SONG Ying-Lin

    2008-01-01

    @@ We investigate the third-order optical nonlinearities in four novel porphyrin dimers (directs A to I)) and a monomeric porphyrin H2 CPTPP measured by using the single-beam z-scan technique with a pulsed Q-switched Nd:YAG nanosecond laser at 532nm.All the samples show strong excited state absorption (ESA) and high value of X(3) in the ns domain at this wavelength.We perform a comparison between dimer A and its monomer H2 CPTPP in their third-order optical nonlinearity, and discuss the relationships between the values of X(3) and the different bridging groups for all the dimers.

  9. Dimeric Surfactants: Promising Ingredients of Cosmetics and Toiletries

    Directory of Open Access Journals (Sweden)

    Naveen Kumar

    2013-11-01

    Full Text Available Surfactants are an essential ingredient for cosmetic, toiletries and personal care products for enhancing their performance. Dimeric surfactants demonstrate superiority compared to conventional surfactants in all areas of application. Dimeric surfactants are extremely promising for utilization in various cosmetic formulations viz. shampoo, lotions, creams, conditioners etc. These surfactants possess extremely unique surface properties viz. lower surface tension, unique micellization, low critical micelle concentration (CMC and antimicrobial activity, higher solubilization etc. Dimerics enhance the performances of cosmetics in an extraordinary manner and provide eco-friendly preparations for human epidermis.

  10. Crystal structure of 2-(5-bromo-2-hydroxybenzylidene-2,3-dihydro-1H-indene-1,3-dione

    Directory of Open Access Journals (Sweden)

    Joel T. Mague

    2015-05-01

    Full Text Available The title molecule, C16H9BrO3, deviates slightly from planarity. The benzene ring makes a dihedral angle of 1.02 (9° with the plane defined by the five-membered ring of the indandione moiety. The latter exhibits a minute twist indicated by the dihedral angle of 0.47 (9° between the planes of the five- and six-membered rings. An intramolecular C—H...O hydrogen bond between the attached benzene ring with one of the indandione carbonyl O atoms stabilizes the molecular conformation. In the crystal, the molecules form dimers across centres of inversion via pairwise O—H...O hydrogen bonds. The dimers form stacks running parallel to [010] and interact through π–π interactions between the five-membered ring of one molecule and the six-membered rings of the indandione moiety of an adjacent molecule [centroid-to-centroid distance = 3.5454 (10 Å].

  11. Crystal structure of 3-(3,4,5-trimethoxyphenyl-1,2,3,4-tetrahydrocyclopenta[b]indole-2-carboxylic acid

    Directory of Open Access Journals (Sweden)

    Daniara Fernandes

    2015-06-01

    Full Text Available In the title compound, C21H21NO5, obtained from a Morita–Baylis–Hillman adduct, the hydrogenated five-membered ring adopts a shallow envelope conformation, with the C atom bearing the carboxylic acid substituent deviating by 0.237 (1 Å from the mean plane of the other four atoms (r.m.s. deviation = 0.007 Å. The dihedral angle between the fused ring system (all atoms; r.m.s. deviation = 0.057 Å and the pendant trimethoxy benzene ring is 66.65 (3°. The C atoms of the meta-methoxy groups lie close to the plane of the benzene ring [deviations = 0.052 (1 and −0.083 (1 Å], whereas the C atom of the para-methoxy group is significantly displaced [deviation = −1.289 (1 Å]. In the crystal, carboxylic acid inversion dimers generate R22(8 loops. The dimers are connected by N—H...O hydrogen bonds, forming [011] chains. A C—H...O interaction is also observed.

  12. Collective sliding states for colloidal molecular crystals

    Energy Technology Data Exchange (ETDEWEB)

    Reichhardt, Charles [Los Alamos National Laboratory; Reichhardt, Cynthia [Los Alamos National Laboratory

    2008-01-01

    We study the driving of colloidal molecular crystals over periodic substrates such as those created with optical traps. The n-merization that occurs in the colloidal molecular crystal states produces a remarkably rich variety of distinct dynamical behaviors, including polarization effects within the pinned phase and the formation of both ordered and disordered sliding phases. Using computer simulations, we map the dynamic phase diagrams as a function of substrate strength for dimers and trimers on a triangular substrate, and correlate features on the phase diagram with transport signatures.

  13. Crystal structure of 4,6-diamino-2,2-dimethyl-3-[3-(2,4,5-trichlorophenoxypropoxy]-2,3-dihydro-1,3,5-triazin-1-ium chloride methanol monosolvate

    Directory of Open Access Journals (Sweden)

    Pattarapol Khongsuk

    2015-08-01

    Full Text Available In the title methanol-solvated salt, C14H19Cl3N5O2+·Cl−·CH3OH, the triazine molecule is protonated at one of the triazine N atoms. In the crystal, the triazine cations are linked through a pair of N—H...N hydrogen bonds, with graph-set R22(8, forming an inversion dimer. The protonated N atom and the 2- and 4-amino groups of the triazine cation interact with the chloride anion through N—H...Cl hydrogen bonds, leading to the formation of a tape structure running along the b-axis direction. A short Cl...Cl contact [3.2937 (9 Å] is observed in the tape. The methanol molecule is linked to the chloride anion and the triazine cation, respectively, by an O—H...Cl hydrogen bond and a C—H...O interaction.

  14. Crystal structure of (2-{[3,5-bis(1,1-dimethylethyl-4-hydroxyphenyl](5-methyl-2H-pyrrol-2-ylidenemethyl}-5-methyl-1H-pyrrolido-κ2N,N′difluoridoboron

    Directory of Open Access Journals (Sweden)

    Yukio Morimoto

    2015-09-01

    Full Text Available The title compound, C25H31BF2N2O, is a potential boron tracedrug in boron neutron capture therapy (BNCT, in which the B atom adopts a distorted BN2F2 tetrahedral geometry: it is soluble in dimethyl sulfoxide, dimethylformamide and methanol. The pyrrolylidenemethylpyrrole triple fused ring system is almost planar (r.m.s. deviation = 0.031 Å and subtends a dihedral angle of 47.09 (5° with the plane of the pendant phenol ring. The phenol –OH group is blocked from forming hydrogen bonds by the adjacent bulky tert-butyl groups. In the crystal, inversion dimers linked by pairs of very weak C—H...F interactions generate R22(22 loops.

  15. Approximation Theorems of Moore-Penrose Inverse by Outer Inverses

    Institute of Scientific and Technical Information of China (English)

    Qianglian Huang; Zheng Fang

    2006-01-01

    Let X and Y be Hilbert spaces and T a bounded linear operator from X into Y with a separable range. In this note, we prove, without assuming the closeness of the range of T, that the Moore-Penrose inverse T+ of T can be approximated by its bounded outer inverses T#n with finite ranks.

  16. Vibrations of the carbon dioxide dimer

    Science.gov (United States)

    Chen, Hua; Light, J. C.

    2000-03-01

    Fully coupled four-dimensional quantum-mechanical calculations are presented for intermolecular vibrational states of rigid carbon dioxide dimer for J=0. The Hamiltonian operator is given in collision coordinates. The Hamiltonian matrix elements are evaluated using symmetrized products of spherical harmonics for angles and a potential optimized discrete variable representation (PO-DVR) for the intermolecular distance. The lowest ten or so states of each symmetry are reported for the potential energy surface (PES) given by Bukowski et al. [J. Chem. Phys. 110, 3785 (1999)]. Due to symmetries, there is no interconversion tunneling splitting for the ground state. Our calculations show that there is no tunneling shift of the ground state within our computation precision (0.01 cm-1). Analysis of the wave functions shows that only the ground states of each symmetry are nearly harmonic. The van der Waals frequencies and symmetry adapted force constants are found and compared to available experimental values. Strong coupling between the stretching coordinates and the bending coordinates are found for vibrationally excited states. The interconversion tunneling shifts are discussed for the vibrationally excited states.

  17. Synthesis and Crystal Structure of a Novel Iadder-Bridge-Shaped Heterometallacylic Organooxotin Dimer,[(n-BuSn)6 (μ3-O)4 (C4 H3 SCO2)8 Cl2 ]%梯桥状有机锡氧杂环二聚体[(n-BuSn)6(μ3-O)4(C4 H3SCO2)8Cl2]的合成及结构

    Institute of Scientific and Technical Information of China (English)

    邝代治; 冯泳兰; 张复兴; 王剑秋; 彭雁; 庾江喜; 蒋伍玖; 朱小明

    2015-01-01

    A Novel dimeric compound,[(n-BuSn)6 (μ3-O)4 (C4 H 3 SCO2 )8 Cl2 ]has been obtained by the reaction of of n-BuSn(O) (OH)with 2-thiophenecarboxylic acid,and then treated with HCCl3 .The structures were characterized by IR,1 H NMR,ele-mental analysis and the molecular structure of compound was determined by X-ray analysis.The crystal belongs to triclinic sys-tem,space group P-1 with the cell parameters:a = 1.2484(3)nm,b = 1.3656(3)nm,c = 1.5224(3)nm,α = 67.94(3)°,β= 65.99(3)°,γ = 66.72(3)°,V = 2.1053(7)nm 3 ,Z = 2,Dc = 1.929g /cm 3 ,μ(MoKa)= 2.270mm-1 ,F(000)=1200, R1 = 0.041 5 and wR2 = 0.1 1 60.The compound is a cluster structure with Sn-O bond.The three tin atoms are held together by aμ3-oxygen atom,and the two tin atoms in each tritin are carboxyl-bridged.The compound having a centro-symmetric lad-der-bridge [Sn4 (μ3-O)4 ]and eight the six-membered (-CO2 Sn 2 O)ring,the compounds formed a like ladder-bridge-shaped structure.%2-噻吩甲酸和正丁基锡酸反应后经三氯甲烷处理,获得一结构新颖的有机锡氧杂环二聚体化合物[(n-BuSn)6(μ3-O)4(C4 H 3 SCO2)8 Cl2],经 IR、1 HNMR 和元素分析表征,并用 X-射线晶体衍射测定了分子结构,该化合物晶体属于三斜晶系,空间群 P-1,晶胞参数:a =1.2484(3)nm,b =1.3656(3)nm,c =1.5224(3)nm,α=67.94(3)°,β=65.99(3)°,γ=66.72(3)°,V =2.1053(7)nm3,Z =2,Dc =1.929g /cm3,μ(MoKa )=2.270mm-1,F(000)=1200,R 1=0.0415 and wR 2=0.1160.晶体结构分析表明,化合物通过μ3-O 与3个 Sn 原子配位和羧基氧桥联2个 Sn 原子,形成 Sn-O 键构筑的中心对称梯桥状[Sn4(μ3-O)4]结构和8个由羧基组装的锡氧六元杂环(-CO2 Sn2 O)支撑其梯桥的有机锡氧簇化合物.

  18. β-lactoglobulin's conformational requirements for ligand binding at the calyx and the dimer interphase: a flexible docking study.

    Directory of Open Access Journals (Sweden)

    Lenin Domínguez-Ramírez

    Full Text Available β-lactoglobulin (BLG is an abundant milk protein relevant for industry and biotechnology, due significantly to its ability to bind a wide range of polar and apolar ligands. While hydrophobic ligand sites are known, sites for hydrophilic ligands such as the prevalent milk sugar, lactose, remain undetermined. Through the use of molecular docking we first, analyzed the known fatty acid binding sites in order to dissect their atomistic determinants and second, predicted the interaction sites for lactose with monomeric and dimeric BLG. We validated our approach against BLG structures co-crystallized with ligands and report a computational setup with a reduced number of flexible residues that is able to reproduce experimental results with high precision. Blind dockings with and without flexible side chains on BLG showed that: i 13 experimentally-determined ligands fit the calyx requiring minimal movement of up to 7 residues out of the 23 that constitute this binding site. ii Lactose does not bind the calyx despite conformational flexibility, but binds the dimer interface and an alternate Site C. iii Results point to a probable lactolation site in the BLG dimer interface, at K141, consistent with previous biochemical findings. In contrast, no accessible lysines are found near Site C. iv lactose forms hydrogen bonds with residues from both monomers stabilizing the dimer through a claw-like structure. Overall, these results improve our understanding of BLG's binding sites, importantly narrowing down the calyx residues that control ligand binding. Moreover, our results emphasize the importance of the dimer interface as an insufficiently explored, biologically relevant binding site of particular importance for hydrophilic ligands. Furthermore our analyses suggest that BLG is a robust scaffold for multiple ligand-binding, suitable for protein design, and advance our molecular understanding of its ligand sites to a point that allows manipulation to control

  19. β-Lactoglobulin's Conformational Requirements for Ligand Binding at the Calyx and the Dimer Interphase: a Flexible Docking Study

    Science.gov (United States)

    Domínguez-Ramírez, Lenin; Del Moral-Ramírez, Elizabeth; Cortes-Hernández, Paulina; García-Garibay, Mariano; Jiménez-Guzmán, Judith

    2013-01-01

    β-lactoglobulin (BLG) is an abundant milk protein relevant for industry and biotechnology, due significantly to its ability to bind a wide range of polar and apolar ligands. While hydrophobic ligand sites are known, sites for hydrophilic ligands such as the prevalent milk sugar, lactose, remain undetermined. Through the use of molecular docking we first, analyzed the known fatty acid binding sites in order to dissect their atomistic determinants and second, predicted the interaction sites for lactose with monomeric and dimeric BLG. We validated our approach against BLG structures co-crystallized with ligands and report a computational setup with a reduced number of flexible residues that is able to reproduce experimental results with high precision. Blind dockings with and without flexible side chains on BLG showed that: i) 13 experimentally-determined ligands fit the calyx requiring minimal movement of up to 7 residues out of the 23 that constitute this binding site. ii) Lactose does not bind the calyx despite conformational flexibility, but binds the dimer interface and an alternate Site C. iii) Results point to a probable lactolation site in the BLG dimer interface, at K141, consistent with previous biochemical findings. In contrast, no accessible lysines are found near Site C. iv) lactose forms hydrogen bonds with residues from both monomers stabilizing the dimer through a claw-like structure. Overall, these results improve our understanding of BLG's binding sites, importantly narrowing down the calyx residues that control ligand binding. Moreover, our results emphasize the importance of the dimer interface as an insufficiently explored, biologically relevant binding site of particular importance for hydrophilic ligands. Furthermore our analyses suggest that BLG is a robust scaffold for multiple ligand-binding, suitable for protein design, and advance our molecular understanding of its ligand sites to a point that allows manipulation to control binding. PMID

  20. Tubular inverse opal scaffolds for biomimetic vessels

    Science.gov (United States)

    Zhao, Ze; Wang, Jie; Lu, Jie; Yu, Yunru; Fu, Fanfan; Wang, Huan; Liu, Yuxiao; Zhao, Yuanjin; Gu, Zhongze

    2016-07-01

    There is a clinical need for tissue-engineered blood vessels that can be used to replace or bypass damaged arteries. The success of such grafts depends strongly on their ability to mimic native arteries; however, currently available artificial vessels are restricted by their complex processing, controversial integrity, or uncontrollable cell location and orientation. Here, we present new tubular scaffolds with specific surface microstructures for structural vessel mimicry. The tubular scaffolds are fabricated by rotationally expanding three-dimensional tubular inverse opals that are replicated from colloidal crystal templates in capillaries. Because of the ordered porous structure of the inverse opals, the expanded tubular scaffolds are imparted with circumferentially oriented elliptical pattern microstructures on their surfaces. It is demonstrated that these tailored tubular scaffolds can effectively make endothelial cells to form an integrated hollow tubular structure on their inner surface and induce smooth muscle cells to form a circumferential orientation on their outer surface. These features of our tubular scaffolds make them highly promising for the construction of biomimetic blood vessels.There is a clinical need for tissue-engineered blood vessels that can be used to replace or bypass damaged arteries. The success of such grafts depends strongly on their ability to mimic native arteries; however, currently available artificial vessels are restricted by their complex processing, controversial integrity, or uncontrollable cell location and orientation. Here, we present new tubular scaffolds with specific surface microstructures for structural vessel mimicry. The tubular scaffolds are fabricated by rotationally expanding three-dimensional tubular inverse opals that are replicated from colloidal crystal templates in capillaries. Because of the ordered porous structure of the inverse opals, the expanded tubular scaffolds are imparted with circumferentially