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Sample records for ru-cl bond covalency

  1. Athermal fracture of covalent bonds

    SciTech Connect

    Gilman, J.J.

    1999-08-01

    Most fracture is athermal. Either because it occurs at low temperatures or because it occurs too fast for thermal activation to be effective. Thus it must be directly activated by applied stresses. This can occur via quantum tunneling when the chemical bonding of a solid resides in localized (covalent) bonds. Then applied stresses can cause the bonding electrons to become delocalized (anti-bonded) through quantum tunneling. That is, the bonds become broken. The process is related to the Zener tunneling process that is thought to be responsible for dielectric breakdown in semiconductors. Under a driving force, bonding electrons tunnel at constant energy from their bonding states into anti-bonding states through the forbidden gap in the bonding energy spectrum.

  2. Functional systems with orthogonal dynamic covalent bonds.

    PubMed

    Wilson, Adam; Gasparini, Giulio; Matile, Stefan

    2014-03-21

    This review summarizes the use of orthogonal dynamic covalent bonds to build functional systems. Dynamic covalent bonds are unique because of their dual nature. They can be as labile as non-covalent interactions or as permanent as covalent bonds, depending on conditions. Examples from nature, reaching from the role of disulfides in protein folding to thioester exchange in polyketide biosynthesis, indicate how dynamic covalent bonds are best used in functional systems. Several synthetic functional systems that employ a single type of dynamic covalent bonds have been reported. Considering that most functional systems make simultaneous use of several types of non-covalent interactions together, one would expect the literature to contain many examples in which different types of dynamic covalent bonds are similarly used in tandem. However, the incorporation of orthogonal dynamic covalent bonds into functional systems is a surprisingly rare and recent development. This review summarizes the available material comprehensively, covering a remarkably diverse collection of functions. However, probably more revealing than the specific functions addressed is that the questions asked are consistently quite unusual, very demanding and highly original, focusing on molecular systems that can self-sort, self-heal, adapt, exchange, replicate, transcribe, or even walk and "think" (logic gates). This focus on adventurous chemistry off the beaten track supports the promise that with orthogonal dynamic covalent bonds we can ask questions that otherwise cannot be asked. The broad range of functions and concepts covered should appeal to the supramolecular organic chemist but also to the broader community. PMID:24287608

  3. Construct Polyoxometalate Frameworks through Covalent Bonds.

    PubMed

    Chen, Hong; Zhao, Huishuang; Yu, Zheng-Bao; Wang, Lei; Sun, Licheng; Sun, Junliang

    2015-09-01

    An emerging strategy for exploring the application of polyoxometalates (POMs) is to assemble POM clusters into open-framework materials, especially inorganic-organic hybrid three-dimensional (3D) open-framework materials, via the introduction of different organic linkers between the POM clusters. This strategy has yielded a few 3D crystalline POMs of which a typical class is the group of polyoxometalate metal-organic frameworks (POMMOFs). However, for reported POMMOFs, only coordination bonds are involved between the linkers and POM clusters, and it has not yet produced any covalently bonded polyoxometalate frameworks. Here, the concept of "covalently bonded POMs (CPOMs)" is developed. By using vanadoborates as an example, we showed that the 3D CPOMs can be obtained by a condensation reaction through the oxolation mechanism of polymer chemistry. In particular, suitable single crystals were harvested and characterized by single-crystal X-ray diffraction. This work forges a link among polymer science, POM chemistry, and open-framework materials by demonstrating that it is possible to use covalent bonds according to polymer chemistry principles to construct crystalline 3D open-framework POM materials. PMID:26286321

  4. Sharing in covalent and hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Perhacs, Pablo

    1998-11-01

    The sharing of a single electron between two spatial and spin coordinates ζ and ζsp/prime in a many electron system is discussed in terms of the single particle sharing amplitude, Covalent bonding is distinguished from non-bonding and anti- bonding. Molecules studied are the diatomics of seven of the first nine elements and the hydrides of the first row of eight elements. Analysis is extended to the complex of methane and hydrogen fluoride and to pairs of hydrogen fluoride, water, and ammonia. The behavior of bonded complexes, is shown to have all the characteristics of covalent bonding. The ammonia dimer is shown not to be hydrogen bonded.

  5. Magnetic and Crystal Structure of α-RuCl3

    NASA Astrophysics Data System (ADS)

    Sears, Jennifer

    The layered honeycomb material α-RuCl3 has been proposed as a candidate material to show significant bond-dependent Kitaev type interactions. This has prompted several recent studies of magnetism in this material that have found evidence for multiple magnetic transitions in the temperature range of 8-14 K. We will present elastic neutron scattering measurements collected using a co-aligned array of α-RuCl3 crystals, identifying zigzag magnetic order within the honeycomb planes with an ordering temperature of ~8 K. It has been reported that the ordering temperature depends on the c axis periodicity of the layered structure, with ordering temperatures of 8 and 14 K for three and two-layer periodicity respectively. While the in-plane magnetic order has been identified, it is clear that a complete understanding of magnetic ordering and interactions will depend on the three dimensional structure of the crystal. Evidence of a structural transition at ~150 K has been reported and questions remain about the structural details, in particular the stacking of the honeycomb layers. We will present x-ray diffraction measurements investigating the low and high temperature structures and stacking disorder in α-RuCl3. Finally, we will present inelastic neutron scattering measurements of magnetic excitations in this material. Work done in collaboration with K. W. Plumb (Johns Hopkins University), J. P. Clancy, Young-June Kim (University of Toronto), J. Britten (McMaster University), Yu-Sheng Chen (Argonne National Laboratory), Y. Qiu, Y. Zhao, D. Parshall, and J. W. Lynn (NCNR).

  6. The covalent bond in Particle Spectroscopy

    SciTech Connect

    Bugg, D. V.

    2010-08-05

    Meson resonances are linear combinations of qq-bar and meson-meson (MM) baryon resonances are combinations of qqq and meson-baryon. Mixing between these combinations arises via decays of confined states to meson-meson or meson-baryon. There is a useful analogy with the covalent bond in molecular physics. One eigenstate is lowered by the mixing. Cusps arise at thresholds. At sharp thresholds due to S-wave 2-particle decays, these cusps play a conspicuous role in many sets of data.

  7. Grade-12 Students' Misconceptions of Covalent Bonding and Structure.

    ERIC Educational Resources Information Center

    Peterson, Raymond F.; Treagust, David F.

    1989-01-01

    Describes a multiple choice, pencil and paper, diagnostic instrument used to measure student understanding of covalent bonding and structure concepts. Reports evidence of seven commonly held misconceptions. (MVL)

  8. Carbonyl derivatives of chloride-dimethyl sulfoxide-ruthenium(III) complexes: Synthesis, crystal structure, and reactivity of [(DMSO){sub 2}H][trans-RuCl{sub 4}(DMSO)(CO)] and mer,cis-RuCl{sub 3}(DMSO){sub 2}(CO)

    SciTech Connect

    Alessio, E.; Bolle, M.; Milani, B.

    1995-09-13

    [(DMSO){sub 2}{sub 2}H][trans-RuCl{sub 4}(DMSO){sub 2}] (1) and mer,trans-RuCl{sub 3}(DMSO){sub 2}(DMSO) (2) (DMSO = S-bonded dimethyl sulfoxide; DMSO = O-bonded dimethyl sulfoxide; DMSO = O bonded dimethyl sulfoxide) react with carbon monoxide at room temperature and atmospheric pressure to give [(DMSO){sub 2}H][trans-RuCl{sub 4}(DMSO)(CO)] (3) and mer,cis-RuCl{sub 3}(DMSO){sub 2-} (CO) (4), respectively. Coordination of carbon monoxide induces the S to O linkage iosmerization of the DMSO ligand trans to it. Compounds 3 and 4 represent the first example of Ru-(III) chloride-DMSO-carbonyl complexes. In both 3 and 4 the DMSO ligand trans to CO is weakly bonded and easily replaced by a nitrogen donor ligand.

  9. Covalent organic frameworks formed with two types of covalent bonds based on orthogonal reactions.

    PubMed

    Zeng, Yongfei; Zou, Ruyi; Luo, Zhong; Zhang, Huacheng; Yao, Xin; Ma, Xing; Zou, Ruqiang; Zhao, Yanli

    2015-01-28

    Covalent organic frameworks (COFs) are excellent candidates for various applications. So far, successful methods for the constructions of COFs have been limited to a few condensation reactions based on only one type of covalent bond formation. Thus, the exploration of a new judicious synthetic strategy is a crucial and emergent task for the development of this promising class of porous materials. Here, we report a new orthogonal reaction strategy to construct COFs by reversible formations of two types of covalent bonds. The obtained COFs consisting of multiple components show high surface area and high H2 adsorption capacity. The strategy is a general protocol applicable to construct not only binary COFs but also more complicated systems in which employing regular synthetic methods did not work. PMID:25581488

  10. Repeatable mechanochemical activation of dynamic covalent bonds in thermoplastic elastomers.

    PubMed

    Imato, Keiichi; Kanehara, Takeshi; Nojima, Shiki; Ohishi, Tomoyuki; Higaki, Yuji; Takahara, Atsushi; Otsuka, Hideyuki

    2016-08-18

    Repeated mechanical scission and recombination of dynamic covalent bonds incorporated in segmented polyurethane elastomers are demonstrated by utilizing a diarylbibenzofuranone-based mechanophore and by the design of the segmented polymer structures. The repeated mechanochemical reactions can accompany clear colouration and simultaneous fading. PMID:27424868

  11. How Cellulose Stretches: Synergism between Covalent and Hydrogen Bonding

    PubMed Central

    2014-01-01

    Cellulose is the most familiar and most abundant strong biopolymer, but the reasons for its outstanding mechanical performance are not well understood. Each glucose unit in a cellulose chain is joined to the next by a covalent C–O–C linkage flanked by two hydrogen bonds. This geometry suggests some form of cooperativity between covalent and hydrogen bonding. Using infrared spectroscopy and X-ray diffraction, we show that mechanical tension straightens out the zigzag conformation of the cellulose chain, with each glucose unit pivoting around a fulcrum at either end. Straightening the chain leads to a small increase in its length and is resisted by one of the flanking hydrogen bonds. This constitutes a simple form of molecular leverage with the covalent structure providing the fulcrum and gives the hydrogen bond an unexpectedly amplified effect on the tensile stiffness of the chain. The principle of molecular leverage can be directly applied to certain other carbohydrate polymers, including the animal polysaccharide chitin. Related but more complex effects are possible in some proteins and nucleic acids. The stiffening of cellulose by this mechanism is, however, in complete contrast to the way in which hydrogen bonding provides toughness combined with extensibility in protein materials like spider silk. PMID:24568640

  12. Covalent bonding modulated graphene-metal interfacial thermal transport

    NASA Astrophysics Data System (ADS)

    Jiang, Tao; Zhang, Xueqiang; Vishwanath, Suresh; Mu, Xin; Kanzyuba, Vasily; Sokolov, Denis A.; Ptasinska, Sylwia; Go, David B.; Xing, Huili Grace; Luo, Tengfei

    2016-05-01

    We report the covalent bonding enabled modulation of the interfacial thermal conductance between graphene and metals Cu, Al, and Pt by controlling the oxidation of graphene. By combining comprehensive X-ray photoelectron spectroscopy (XPS) analysis and time-domain thermoreflectance measurements, we quantify the effect of graphene oxidation on interfacial thermal conductance. It was found that thermal conductance increases with the degree of graphene oxidation until a peak value is obtained at an oxygen/carbon atom percentage of ~7.7%. The maximum enhancement in thermal conductance was measured to be 55%, 38%, and 49% for interfaces between oxidized graphene and Cu, Al, and Pt, respectively. In situ XPS measurements show that oxygen covalently binds to Cu and graphene simultaneously, forming a highly efficient bridge to enhance the thermal transport. Our molecular dynamics simulations verify that strong interfacial covalent bonds are the key to the thermal conductance enhancement. This work provides valuable insights into the mechanism of functionalization-induced thermal conductance enhancement and design guidelines for graphene-based devices.We report the covalent bonding enabled modulation of the interfacial thermal conductance between graphene and metals Cu, Al, and Pt by controlling the oxidation of graphene. By combining comprehensive X-ray photoelectron spectroscopy (XPS) analysis and time-domain thermoreflectance measurements, we quantify the effect of graphene oxidation on interfacial thermal conductance. It was found that thermal conductance increases with the degree of graphene oxidation until a peak value is obtained at an oxygen/carbon atom percentage of ~7.7%. The maximum enhancement in thermal conductance was measured to be 55%, 38%, and 49% for interfaces between oxidized graphene and Cu, Al, and Pt, respectively. In situ XPS measurements show that oxygen covalently binds to Cu and graphene simultaneously, forming a highly efficient bridge to enhance

  13. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  14. Fast and accurate predictions of covalent bonds in chemical space

    NASA Astrophysics Data System (ADS)

    Chang, K. Y. Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (˜1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H 2+ . Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  15. Covalent bonding modulated graphene-metal interfacial thermal transport.

    PubMed

    Jiang, Tao; Zhang, Xueqiang; Vishwanath, Suresh; Mu, Xin; Kanzyuba, Vasily; Sokolov, Denis A; Ptasinska, Sylwia; Go, David B; Xing, Huili Grace; Luo, Tengfei

    2016-06-01

    We report the covalent bonding enabled modulation of the interfacial thermal conductance between graphene and metals Cu, Al, and Pt by controlling the oxidation of graphene. By combining comprehensive X-ray photoelectron spectroscopy (XPS) analysis and time-domain thermoreflectance measurements, we quantify the effect of graphene oxidation on interfacial thermal conductance. It was found that thermal conductance increases with the degree of graphene oxidation until a peak value is obtained at an oxygen/carbon atom percentage of ∼7.7%. The maximum enhancement in thermal conductance was measured to be 55%, 38%, and 49% for interfaces between oxidized graphene and Cu, Al, and Pt, respectively. In situ XPS measurements show that oxygen covalently binds to Cu and graphene simultaneously, forming a highly efficient bridge to enhance the thermal transport. Our molecular dynamics simulations verify that strong interfacial covalent bonds are the key to the thermal conductance enhancement. This work provides valuable insights into the mechanism of functionalization-induced thermal conductance enhancement and design guidelines for graphene-based devices. PMID:27174416

  16. Synthesis of Polymers Containing Covalently Bonded NLO Chromophores

    NASA Technical Reports Server (NTRS)

    Denga, Xiao-Hua; Sanghadasa, Mohan; Walton, Connie; Penn, Benjamin B.; Amai, Robert L. S.; Clark, Ronald D.

    1998-01-01

    Polymers containing covalently bonded nonlinear optical (NLO) chromophores are expected to possess special properties such as greater stability, better mechanical processing, and easier film formation than their non-polymeric equivalent. For the present work, polymethylmethacrylate (PMMA) was selected as the basic polymer unit on which to incorporate different NLO chromophores. The NLO components were variations of DIVA {[2-methoxyphenyl methylidene]-propanedinitrile} which we prepared from vanillin derivatives and malononitrile. These were esterified with methacrylic acid and polymerized either directly or with methyl methacrylate to form homopolymers or copolymers respectively. Characterization of the polymers and NLO property studies are underway.

  17. Application of the Covalent Bond Classification Method for the Teaching of Inorganic Chemistry

    ERIC Educational Resources Information Center

    Green, Malcolm L. H.; Parkin, Gerard

    2014-01-01

    The Covalent Bond Classification (CBC) method provides a means to classify covalent molecules according to the number and types of bonds that surround an atom of interest. This approach is based on an elementary molecular orbital analysis of the bonding involving the central atom (M), with the various interactions being classified according to the…

  18. Covalent binding of sulfamethazine to natural and synthetic humic acids: assessing laccase catalysis and covalent bond stability.

    PubMed

    Gulkowska, Anna; Sander, Michael; Hollender, Juliane; Krauss, Martin

    2013-07-01

    Sulfonamide antibiotics form stable covalent bonds with quinone moieties in organic matter via nucleophilic addition reactions. In this work, we combined analytical electrochemistry with trace analytics to assess the catalytic role of the oxidoreductase laccase in the binding of sulfamethazine (SMZ) to Leonardite humic acid (LHA) and to four synthetic humic acids (SHAs) polymerized from low molecular weight precursors and to determine the stability of the formed bonds. In the absence of laccase, a significant portion of the added SMZ formed covalent bonds with LHA, but only a very small fraction (<0.4%) of the total quinone moieties in LHA reacted. Increasing absolute, but decreasing relative concentrations of SMZ-LHA covalent bonds with increasing initial SMZ concentration suggested that the quinone moieties in LHA covered a wide distribution in reactivity for the nucleophilic addition of SMZ. Laccase catalyzed the formation of covalent bonds by oxidizing unreactive hydroquinone moieties in LHA to reactive, electrophilic quinone moieties, of which a large fraction (5%) reacted with SMZ. Compared to LHA, the SHA showed enhanced covalent bond formation in the absence of laccase, suggesting a higher reactivity of their quinone moieties toward nucleophilic addition. This work supports that binding to soil organic matter (SOM) is an important process governing the fate, bioactivity, and extractability of sulfonamides in soils. PMID:23384282

  19. Isotopic Effects on Covalent Bond Confined in a Penetrable Sphere.

    PubMed

    Sarsa, Antonio; Alcaraz-Pelegrina, José M; Le Sech, Claude

    2015-11-12

    A model of confinement of the covalent bond by a finite potential beyond the Born-Oppenheimer approximation is presented. A two-electron molecule is located at the center of a penetrable spherical cavity. The Schrödinger equation has been solved by using the diffusion Monte Carlo method. Total energies, internuclear distances, and vibrational frequencies of the confined molecular system have been obtained. Even for confining potentials of a few electronvolts, a noticeable increase in the bond energy and the nuclear vibrational frequency is observed, and the internuclear distance is lowered. The gap between the zero point energy of different molecular isotopes increases with confinement. The confinement of the electron pair might play a role in chemical reactivity, providing an alternative explanation for the tunnel effect, when large values of primary kinetic isotopic effect are observed. The Swain-Schaad relation is still verified when confinement changes the zero point energy. A semiquantitative illustration is proposed using the data relative to an hydrogen transfer involving a C-H cleavage catalyzed by the bovine serum amine oxidase. Changes on the confining conditions, corresponding to a confinement/deconfinement process, result in a significant decrease in the activation energy of the chemical transformation. It is proposed that confinement/deconfinement of the electron-pair bonding by external electrostatic forces inside the active pocket of an enzyme could be one of the basic mechanisms of the enzyme catalysis. PMID:26484576

  20. Adaptive polymeric nanomaterials utilizing reversible covalent and hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Neikirk, Colin

    Adaptive materials based on stimuli responsive and reversible bonding moieties are a rapidly developing area of materials research. Advances in supramolecular chemistry are now being adapted to novel molecular architectures including supramolecular polymers to allow small, reversible changes in molecular and nanoscale structure to affect large changes in macroscale properties. Meanwhile, dynamic covalent chemistry provides a complementary approach that will also play a role in the development of smart adaptive materials. In this thesis, we present several advances to the field of adaptive materials and also provide relevant insight to the areas of polymer nanocomposites and polymer nanoparticles. First, we have utilized the innate molecular recognition and binding capabilities of the quadruple hydrogen bonding group ureidopyrimidinone (UPy) to prepare supramolecular polymer nanocomposites based on supramolecular poly(caprolactone) which show improved mechanical properties, but also an increase in particle aggregation with nanoparticle UPy functionalization. We also present further insight into the relative effects of filler-filler, filler-matrix, and matrix-matrix interactions using a UPy side-chain functional poly(butyl acrylate). These nanocomposites have markedly different behavior depending on the amount of UPy sidechain functionality. Meanwhile, our investigations of reversible photo-response showed that coumarin functionality in polymer nanoparticles not only facilitates light mediated aggregation/dissociation behavior, but also provides a substantial overall reduction in particle size and improvement in nanoparticle stability for particles prepared by Flash NanoPrecipitation. Finally, we have combined these stimuli responsive motifs as a starting point for the development of multiresponsive adaptive materials. The synthesis of a library of multifunctional materials has provided a strong base for future research in this area, although our initial

  1. Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments

    PubMed Central

    Elgabarty, Hossam; Khaliullin, Rustam Z.; Kühne, Thomas D.

    2015-01-01

    The concept of covalency is widely used to describe the nature of intermolecular bonds, to explain their spectroscopic features and to rationalize their chemical behaviour. Unfortunately, the degree of covalency of an intermolecular bond cannot be directly measured in an experiment. Here we established a simple quantitative relationship between the calculated covalency of hydrogen bonds in liquid water and the anisotropy of the proton magnetic shielding tensor that can be measured experimentally. This relationship enabled us to quantify the degree of covalency of hydrogen bonds in liquid water using the experimentally measured anisotropy. We estimated that the amount of electron density transferred between molecules is on the order of 10  m while the stabilization energy due to this charge transfer is ∼15 kJ mol−1. The physical insight into the fundamental nature of hydrogen bonding provided in this work will facilitate new studies of intermolecular bonding in a variety of molecular systems. PMID:26370179

  2. Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments.

    PubMed

    Elgabarty, Hossam; Khaliullin, Rustam Z; Kühne, Thomas D

    2015-01-01

    The concept of covalency is widely used to describe the nature of intermolecular bonds, to explain their spectroscopic features and to rationalize their chemical behaviour. Unfortunately, the degree of covalency of an intermolecular bond cannot be directly measured in an experiment. Here we established a simple quantitative relationship between the calculated covalency of hydrogen bonds in liquid water and the anisotropy of the proton magnetic shielding tensor that can be measured experimentally. This relationship enabled us to quantify the degree of covalency of hydrogen bonds in liquid water using the experimentally measured anisotropy. We estimated that the amount of electron density transferred between molecules is on the order of 10  m while the stabilization energy due to this charge transfer is ∼15 kJ mol(-1). The physical insight into the fundamental nature of hydrogen bonding provided in this work will facilitate new studies of intermolecular bonding in a variety of molecular systems. PMID:26370179

  3. Bond-bending isomerism of Au2I3-: Competition between covalent bonding and aurophilicity

    DOE PAGESBeta

    Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian; Lopez, Gary V.; Piazza, Zachary A.; Huang, Dao -Ling; Chen, Teng -Teng; Su, Jing; Yang, Ping; Chen, Xin; et al

    2015-10-13

    We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au2I3– cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI– structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature, only the obtuse isomermore » is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au2I3– reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.« less

  4. Interplay of olefin metathesis and multiple hydrogen bonding interactions: covalently cross-linked zippers.

    PubMed

    Zeng, Jisen; Wang, Wei; Deng, Pengchi; Feng, Wen; Zhou, Jingjing; Yang, Yuanyou; Yuan, Lihua; Yamato, Kazuhiro; Gong, Bing

    2011-08-01

    Hydrogen-bonded zippers bearing terminal alkene groups were treated with Grubbs' catalyst, leading to covalently cross-linked zippers without violating H-bonding sequence specificity. The yield of a cross-linked zipper depended on the stability of its H-bonded precursor, with a weakly associating pair giving reasonable yields only at high concentrations while strongly associating pairs showed nearly quantitative yields. The integration of thermodynamic (H-bonding) and kinetic (irreversible C═C bond formation) processes suggests the possibility of developing many different covalent association units for constructing molecular structures based on a self-assembling way. PMID:21699249

  5. The Mechanism of Covalent Bonding: Analysis within the Huckel Model of Electronic Structure

    ERIC Educational Resources Information Center

    Nordholm, Sture; Back, Andreas; Backsay, George B.

    2007-01-01

    The commonly used Huckel model of electronic structure is employed to study the mechanisms of covalent bonding, a quantum effect related to electron dynamics. The model also explains the conjugation and aromaticity of planar hydrocarbon molecules completely.

  6. Electronic Communication in Covalently vs. Non-Covalently Bonded Polyfluorene Systems: the Role of the Covalent Linker.

    NASA Astrophysics Data System (ADS)

    Uhler, Brandon; Reilly, Neil J.; Talipov, Marat R.; Ivanov, Maxim; Timerghazin, Qadir; Rathore, Rajendra; Reid, Scott

    2015-06-01

    The covalently linked polyfluorene molecules F1-F6 (see left) are prototypical molecular wires by virtue of their favorable electron/hole transport properties brought about by π-stacking. To understand the role of the covalent linker in facilitating electron transport in these systems, we have investigated several van der Waals (vdW) analogues by resonant mass spectroscopy. Electronic spectra and ion yield curves are reported for jet-cooled vdW clusters containing up to six fluorene units. The near-coincidence of the electronic band origins for the dimer and larger clusters suggests that a structure containing a central dimer chromophore is the predominant conformational motif. As for F1-F6, the threshold ionization potentials extracted from the ion yield measurements decrease linearly with inverse cluster size. Importantly, however, the rate of decrease is significantly smaller in the vdW clusters, indicating more efficient hole stabilization in the covalently bound systems. Results for similar vdW clusters that are locked into specific conformations by steric effects will also be reported.

  7. Moving beyond Definitions: What Student-Generated Models Reveal about Their Understanding of Covalent Bonding and Ionic Bonding

    ERIC Educational Resources Information Center

    Luxford, Cynthia J.; Bretz, Stacey Lowery

    2013-01-01

    Chemistry students encounter a variety of terms, definitions, and classification schemes that many instructors expect students to memorize and be able to use. This research investigated students' descriptions of ionic and covalent bonding beyond definitions in order to explore students' knowledge about chemical bonding. Using Johnstone's Multiple…

  8. Selection of direction of the ordered moments in Na2IrO3 and α -RuCl3

    NASA Astrophysics Data System (ADS)

    Sizyuk, Yuriy; Wölfle, Peter; Perkins, Natalia B.

    2016-08-01

    The magnetic orders in Na2IrO3 and α -RuCl3 , i.e., honeycomb systems with strong spin-orbit coupling and correlations, have been recently described by models with the dominant Kitaev interactions. In this work, we discuss how the orientation of the magnetic order parameter is selected in this class of models. We show that while the order-by-disorder mechanism in the models with solely Kitaev anisotropies always selects cubic axes as easy axes for magnetic ordering, the additional effect of other small bond-dependent anisotropies, such as, e.g., Γ terms, leads to a deviation of the order parameter from the cubic directions. We show that both the zigzag ground state and the face-diagonal orientation of the magnetic moments in Na2IrO3 can be obtained within the J1-K1-J2-K2-J3 model in the presence of perturbatively small Γ terms. We also show that the zigzag phase found in the nearest-neighbor Kitaev-Heisenberg model, relevant for α -RuCl3 , has some stability against the Γ term.

  9. Multi-responsive coordination polymers utilising metal-stabilised, dynamic covalent imine bonds.

    PubMed

    García, Fátima; Pelss, Janis; Zuilhof, Han; Smulders, Maarten M J

    2016-07-12

    We report how the combination of dynamic covalent imine bonds and coordination bonds in a single polymer material not only imparts enhanced stability to the final polymer, but also allows the material to be sensitive to a range of stimuli, offering more fine-grained control over its properties. PMID:26879208

  10. Persistence of Covalent Bonding in Liquid Silicon Probed by Inelastic X-Ray Scattering

    NASA Astrophysics Data System (ADS)

    Okada, J. T.; Sit, P. H.-L.; Watanabe, Y.; Wang, Y. J.; Barbiellini, B.; Ishikawa, T.; Itou, M.; Sakurai, Y.; Bansil, A.; Ishikawa, R.; Hamaishi, M.; Masaki, T.; Paradis, P.-F.; Kimura, K.; Ishikawa, T.; Nanao, S.

    2012-02-01

    Metallic liquid silicon at 1787 K is investigated using x-ray Compton scattering. An excellent agreement is found between the measurements and the corresponding Car-Parrinello molecular dynamics simulations. Our results show persistence of covalent bonding in liquid silicon and provide support for the occurrence of theoretically predicted liquid-liquid phase transition in supercooled liquid states. The population of covalent bond pairs in liquid silicon is estimated to be 17% via a maximally localized Wannier function analysis. Compton scattering is shown to be a sensitive probe of bonding effects in the liquid state.

  11. Magnetic Properties of Restacked 2D Spin 1/2 honeycomb RuCl3Nanosheets

    NASA Astrophysics Data System (ADS)

    Weber, Daniel; Schoop, Leslie M.; Duppel, Viola; Lippmann, Judith M.; Nuss, Jürgen; Lotsch, Bettina V.

    2016-06-01

    Spin $\\frac{1}{2}$ honeycomb materials have gained substantial interest due to their exotic magnetism and possible application in quantum computing. However, in all current materials out-of-plane interactions are interfering with the in-plane order, hence a true 2D magnetic honeycomb system is still of demand. Here, we report the exfoliation of the magnetic semiconductor $\\alpha$-RuCl$_3$ into the first halide monolayers and the magnetic characterization of the spin $\\frac{1}{2}$ honeycomb arrangement of turbostratically stacked RuCl$_3$ monolayers. The exfoliation is based on a reductive lithiation/hydration approach, which gives rise to a loss of cooperative magnetism due to the disruption of the spin $\\frac{1}{2}$ state by electron injection into the layers. After an oxidative treatment, cooperative magnetism similar to the bulk is restored. The oxidized pellets of restacked single layers feature a magnetic transition at T$_N$ = 7 K in the in-plane direction, while the magnetic properties in the out-of-plane direction vastly differ from bulk $\\alpha$-RuCl$_3$. The macroscopic pellets of RuCl$_3$ therefore behave like a stack of monolayers without any symmetry relation in the stacking direction. The deliberate introduction of turbostratic disorder to manipulate the spin structure of RuCl$_3$ is of interest for research in frustrated magnetism and complex magnetic order as predicted by the Kitaev-Heisenberg model.

  12. Magnetic Properties of Restacked 2D Spin 1/2 honeycomb RuCl3 Nanosheets.

    PubMed

    Weber, Daniel; Schoop, Leslie M; Duppel, Viola; Lippmann, Judith M; Nuss, Jürgen; Lotsch, Bettina V

    2016-06-01

    Spin 1/2 honeycomb materials have gained substantial interest due to their exotic magnetism and possible application in quantum computing. However, in all current materials out-of-plane interactions are interfering with the in-plane order, hence a true 2D magnetic honeycomb system is still in demand. Here, we report the exfoliation of the magnetic semiconductor α-RuCl3 into the first halide monolayers and the magnetic characterization of the spin 1/2 honeycomb arrangement of turbostratically stacked RuCl3 monolayers. The exfoliation is based on a reductive lithiation/hydration approach, which gives rise to a loss of cooperative magnetism due to the disruption of the spin 1/2 state by electron injection into the layers. The restacked, macroscopic pellets of RuCl3 layers lack symmetry along the stacking direction. After an oxidative treatment, cooperative magnetism similar to the bulk is restored. The oxidized pellets of restacked single layers feature a magnetic transition at TN = 7 K if the field is aligned parallel to the ab-plane, while the magnetic properties differ from bulk α-RuCl3 if the field is aligned perpendicular to the ab-plane. The deliberate introduction of turbostratic disorder to manipulate the magnetic properties of RuCl3 is of interest for research in frustrated magnetism and complex magnetic order as predicted by the Kitaev-Heisenberg model. PMID:27176463

  13. Covalent Bond between Ligand and Receptor Required for Efficient Activation in Rhodopsin*

    PubMed Central

    Matsuyama, Take; Yamashita, Takahiro; Imai, Hiroo; Shichida, Yoshinori

    2010-01-01

    Rhodopsin is an extensively studied member of the G protein-coupled receptors (GPCRs). Although rhodopsin shares many features with the other GPCRs, it exhibits unique features as a photoreceptor molecule. A hallmark in the molecular structure of rhodopsin is the covalently bound chromophore that regulates the activity of the receptor acting as an agonist or inverse agonist. Here we show the pivotal role of the covalent bond between the retinal chromophore and the lysine residue at position 296 in the activation pathway of bovine rhodopsin, by use of a rhodopsin mutant K296G reconstituted with retinylidene Schiff bases. Our results show that photoreceptive functions of rhodopsin, such as regiospecific photoisomerization of the ligand, and its quantum yield were not affected by the absence of the covalent bond, whereas the activation mechanism triggered by photoisomerization of the retinal was severely affected. Furthermore, our results show that an active state similar to the Meta-II intermediate of wild-type rhodopsin did not form in the bleaching process of this mutant, although it exhibited relatively weak G protein activity after light irradiation because of an increased basal activity of the receptor. We propose that the covalent bond is required for transmitting structural changes from the photoisomerized agonist to the receptor and that the covalent bond forcibly keeps the low affinity agonist in the receptor, resulting in a more efficient G protein activation. PMID:20042594

  14. Ab-initio study on crystal structure of α-RuCl3

    NASA Astrophysics Data System (ADS)

    Kee, Hae-Young; Kim, Heung-Sik

    α -RuCl3 was recently proposed as a candidate system for materialization of Kitaev model, but precise structural information of the compound has remained elusive. For the clarification of the full three-dimensional crystal structure of α-RuCl3, we performed ab-initio electronic structure calculations including effects of spin-orbit coupling (SOC) and electron correlations. We found that SOC prevents dimerization between Ru atoms, and keeps the system close to honeycomb lattice. The ground state crystal structure has monoclinic C 2 / m -type layer stacking, but trigonal P31 12 -and orthorhombic Cmc21 -type stacking orders are comparable to the C 2 / m structure in energy, so that stacking faults can be easily introduced. The electronic structure and the jeff=1/2 pseudospin exchange interactions and possible magnetic states in α-RuCl3 will be presented.

  15. Selective conversion of polyenes to monoenes by RuCl(3) -catalyzed transfer hydrogenation: the case of cashew nutshell liquid.

    PubMed

    Perdriau, Sébastien; Harder, Sjoerd; Heeres, Hero J; de Vries, Johannes G

    2012-12-01

    Cardanol, a constituent of cashew nutshell liquid (CNSL), was subjected to transfer hydrogenation catalyzed by RuCl(3) using isopropanol as a reductant. The side chain of cardanol, which is a mixture of a triene, a diene, and a monoene, was selectively reduced to the monoene. Surprisingly, it is the C8-C9 double bond that is retained with high selectivity. A similar transfer hydrogenation of linoleic acid derivatives succeeded only if the substrate contained an aromatic ring, such as a benzyl ester. TEM and a negative mercury test showed that the catalyst was homogeneous. By using ESI-MS, ruthenium complexes were identified that contained one, two, or even three molecules of substrate, most likely as allyl complexes. The interaction between ruthenium and the aromatic ring determines selectivity in the hydrogenation reaction. PMID:23060315

  16. Metal nanoparticles functionalized with metal-ligand covalent bonds

    NASA Astrophysics Data System (ADS)

    Kang, Xiongwu

    Metal-organic contact has been recognized to play important roles in regulation of optical and electronic properties of nanoparticles. In this thesis, significant efforts have been devoted into synthesis of ruthenium nanoparticles with various metal-ligand interfacial linkages and investigation of their electronic and optical properties. Ruthenium nanoparticles were prepared by the self-assembly of functional group onto bare Ru colloid surface. As to Ru-alkyne nanoparticles, the formation of a Ru-vinylidene (Ru=C=CH--R) interfacial bonding linkage was confirmed by the specific reactivity of the nanoparticles with imine derivatives and olefin at the metal-ligand interface, as manifested in NMR, photoluminescence, and electrochemical measurements. Interestingly, it was found the electronic coupling coefficient (beta)for strongly depend upon such metal-ligand interfacial bonding. Next, such metal-ligand interfacial bonding was extended to ruthenium-nitrene pi bonds on ruthenium colloids, which were investigated by XPS. The nanoparticles exhibited a 1:1 atomic ratio of nitrogen to sulfur, consistent with that of sulfonyl nitrene fragments. In addition, the nanoparticle-bound nitrene moieties behaved analogously to azo derivatives, as manifested in UV-vis and fluorescence measurements. Further testimony of the formation of Ru=N interfacial linkages was highlighted in the unique reactivity of the nanoparticles with alkenes by imido transfer. Extensive conjugation between metal-ligand interfacial bond results in remarkable intraparticle charge delocalization on Ru-alkynide nanoparticles, which was manipulated by simple chemical reduction or oxidation. Charging of extra electrons into the nanoparticle cores led to an electron-rich metal core and hence red-shift of the triple bond stretching mode, lower binding energy of sp hybridized C 1s and dimmed fluorescence of nanoparticles. Instead, chemical oxidation resulted in the opposite impacts on these properties. By taking

  17. In situ synthesis of polysulfides covalently bonded to silica.

    PubMed

    Ossenkamp, Gabriel C; Kemmitt, Tim; Johnston, Jim H

    2002-05-15

    Silanol groups, triple bond SiOH, on the surface of silica were esterified with unsaturated alcohols and long-chain alcohols bearing thiol groups. The modified silicas obtained were used as substrates for a vulcanization-analogous reaction with sulfur catalyzed by zinc dimethyldithiocarbamate. Surface-esterified thiols could be smoothly converted to bridged polysulfides bonded to the silica surface, whereas the use of surface-esterified unsaturated alcohols led to removal of the surface-esterified alcohol from the silica surface. The materials were characterized by solid-state NMR and thermal and microanalytical analysis. The linking of surface-esterified alkenols and thiols by sulfide bridges was investigated by a numerical model for a flat surface. This showed that for a typical density of 3-4 micromol/m(2) surface groups, a statistical maximum of 70-75% of groups could be linked by S(n) bridges (n=2-4). PMID:16290622

  18. Reactions of a sulfonamide antimicrobial with model humic constituents: assessing pathways and stability of covalent bonding.

    PubMed

    Gulkowska, Anna; Krauss, Martin; Rentsch, Daniel; Hollender, Juliane

    2012-02-21

    The mechanism of covalent bond formation of the model sulfonamide sulfathiazole (STZ) and the stronger nucleophile para-ethoxyaniline was studied in reactions with model humic acid constituents (quinones and other carbonyl compounds) in the absence and presence of laccase. As revealed by high resolution mass spectrometry, the initial bonding of STZ occurred by 1,2- and 1,4-nucleophilic additions of the aromatic amino group to quinones resulting in imine and anilinoquinone formation, respectively. Experiments using the radical scavenger tert-butyl-alcohol provided the same products and similar formation rates as those without scavenger indicating that probably not radical coupling reactions were responsible for the initial covalent bond formation. No addition with nonquinone carbonyl compounds occurred within 76 days except for a slow 1,4-addition to the β-unsaturated carbonyl 1-penten-3-one. The stability of covalent bonds against desorption and pressurized liquid extraction (PLE) was assessed. The recovery rates showed no systematic differences in STZ extractability between the two product types. This suggests that the strength of bonding is not controlled by the initial type of bond, but by the extent of subsequent incorporation of the reaction product into the formed polymer. This incorporation was monitored for (15)N aniline by (1)H-(15)N HMBC NMR spectroscopy. The initial 1,2- and 1,4-addition bonds were replaced by stronger heterocyclic forms with increasing incubation time. These processes could also hold true for soils, and a slow nonextractable residue formation with time could be related to a slow increase of the amount of covalently bound sulfonamide and the strength of bonding. PMID:22260423

  19. Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)

    PubMed Central

    Netzel, Jeanette; van Smaalen, Sander

    2009-01-01

    Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T ≃ 20 K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (l max = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C—C, C—N and C—O bonds, and for hydrogen bonds together with covalent C—H and N—H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H⋯O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997) ▶. An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds. PMID:19767685

  20. Monoclinic crystal structure of α -RuCl3 and the zigzag antiferromagnetic ground state

    NASA Astrophysics Data System (ADS)

    Johnson, R. D.; Williams, S. C.; Haghighirad, A. A.; Singleton, J.; Zapf, V.; Manuel, P.; Mazin, I. I.; Li, Y.; Jeschke, H. O.; Valentí, R.; Coldea, R.

    2015-12-01

    The layered honeycomb magnet α -RuCl3 has been proposed as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled jeff=1/2 Ru3 + magnetic moments. Here, we report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, in contrast with the currently assumed trigonal three-layer stacking periodicity. We report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the jeff=1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below TN≈13 K. The analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in pulsed field up to 60 T show a single transition around 8 T for in

  1. Self-Protecting Bactericidal Titanium Alloy Surface Formed by Covalent Bonding of Daptomycin Bisphosphonates

    PubMed Central

    Chen, Chang-Po; Wickstrom, Eric

    2010-01-01

    Infections are a devastating complication of titanium alloy orthopedic implants. Current therapy includes antibiotic-impregnated bone cement, and antibiotic-containing coatings. We hypothesized that daptomycin, a Gram-positive peptide antibiotic, could prevent bacterial colonization on titanium alloy surfaces if covalently bonded via a flexible, hydrophilic spacer. We designed and synthesized a series of daptomycin conjugates for bonding to the surface of 1.0 cm2 Ti6Al4V foils through bisphosphonate groups, reaching a maximum yield of 180 pmol /cm2. Daptomycin-bonded foils killed 53±5% of a high challenge dose of 3×105 cfu Staphylococcus aureus ATCC 29213. PMID:20949909

  2. Physical understanding through variational reasoning: electron sharing and covalent bonding.

    PubMed

    Ruedenberg, Klaus; Schmidt, Michael W

    2009-03-12

    Energy changes of stationary states resulting from geometric parameter changes in the Hamiltonian can be understood by variational reasoning in terms of the physical attributes of the kinetic and the potential energy functionals. In atoms as well as molecules, the energy minimization determines the ground state as the optimal compromise between the potential pull of the nuclear attractions and the localization-resisting kinetic pressure of the electron cloud. This variational competition is analyzed for the exact ab initio ground-state wave function of the hydrogen molecule ion to elucidate the formation of the bond. Its electronic wave function is shown to differ from the ground-state wave function of the hydrogen atom by polarization, sharing, and contraction, and the corresponding contributions to the binding energy are examined in detail. All told, the critical feature is that a molecular orbital, contracting (in the variational context) toward two nuclei simultaneously, can lower its potential energy while maintaining a certain degree of delocalization. As a consequence, its kinetic energy functional has a lower value than that of an orbital contracting toward a single nucleus equally closely. By contrast, the potential energy functional is lowered equally effectively whether the orbital contracts toward one nucleus or simultaneously toward two nuclei. Because of this weaker kinetic energy pressure, the electrostatic potential pull of the nuclei in the molecule is able to attach the orbital more tightly to each of the nuclei than the pull of the single nucleus in the atom is able to do. The role of the virial theorem is clarified. Generalizations to other molecules are discussed. PMID:19228050

  3. a Theoretical Investigation on 10-12 Potential of Hydrogen-Hydrogen Covalent Bond

    NASA Astrophysics Data System (ADS)

    Taneri, Sencer

    2013-05-01

    This is an analytical investigation of well-known 10-12 potential of hydrogen-hydrogen covalent bond. In this research, we will make an elaboration of the well-known 6-12 Lennard-Jones potential in case of this type of bond. Though the results are illustrated in many text books and literature, an analytical analysis for these potentials is missing almost everywhere. The power laws are valid for small radial distances, which are calculated to some extent. The internuclear separation as well as the binding energy of the hydrogen molecule are evaluated with success.

  4. Structure and magnetic ground states of spin-orbit coupled compound alpha-RuCl3

    NASA Astrophysics Data System (ADS)

    Banerjee, Arnab; Bridges, Craig; Yan, Jiaqiang; Mandrus, David; Stone, Matthew; Aczel, Adam; Li, Ling; Yiu, Yuen; Lumsden, Mark; Chakoumakos, Bryan; Tennant, Alan; Nagler, Stephen

    2015-03-01

    The layered material alpha-RuCl3 is composed of stacks of weakly coupled honeycomb lattices of octahedrally coordinated Ru3 + ions. The Ru ion ground state has 5 d electrons in the low spin state, with spin-orbit coupling very strong compared to other terms in the single ion Hamiltonian. The material is therefore an excellent candidate for investigating possible Heisenberg-Kitaev physics. In addition, this compound is very amenable to investigation by neutron scattering to explore the magnetic ground state and excitations in detail. In this talk, we discuss the synthesis of phase-pure alpha-RuCl3 and the characterization of the magnetization, susceptibility, and heat-capacity. We also report neutron diffraction on both powder and single crystal alpha-RuCl3, identifying the low temperature magnetic order observed in the material. The results, when compared to theoretical calculations, shed light on the relative importance of Kitaev and Heisenberg terms in the Hamiltonian. The research is supported by the DOE BES Scientific User Facility Division.

  5. Spin-orbit correlated magnetic order in honeycomb α-RuCl3

    NASA Astrophysics Data System (ADS)

    Venkataraman, Vijay Shankar; Kim, Heung-Sik; Kee, Hae-Young

    2015-03-01

    There has been a lot of recent interest in the combined effects of spin-orbit coupling (SOC) and electronic correlations in transition metal compounds. RuCl3 with layered honeycomb structure was proposed as a candidate material, where SOC boosts the electronic interaction, leading to an insulating phase. However, the role of SOC is not clear in materials with 4d-orbitals, since SOC strength is weaker than 5d-orbital materials. Here we study electronic band structures of honeycomb RuCl3 using ab-initio and tight binding methods, and estimate its SOC strength. We find that SOC in RuCl3 is not strong enough to justify an effective jeff = 1 / 2 single band unlike in the iridates. However, when electronic interactions are introduced, a magnetic order develops, and upper- and lower-Hubbard bands are characterized by jeff = 1 / 2 and 3 / 2 , respectively. Within a mean field theory with multi-orbital bands, we find that a zig-zag magnetic order is a ground state. Experimental implications are also discussed.

  6. Large Band Gap of alpha-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sinn, Soobin; Kim, Choong Hyun; Sandilands, Luke; Lee, Kyungdong; Won, Choongjae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

    The Kitaev honeycomb lattice model has attracted great attention because of its possibility to stabilize a quantum spin liquid ground state. Recently, it was proposed that alpha-RuCl3 is its material realization and the first 4 d relativistic Mott insulator from an optical spectrum and LDA + U + SO calculations. Here, we present photoemission and inverse photoemission spectra of alpha-RuCl3. The observed band gap is about 1.8 eV, which suggests that the previously assigned optical gap of 0.3 eV is misinterpreted, and that the strong peak at about 1.2 eV in the optical spectrum may be associated with an actual optical gap. Assuming a strong excitonic effect of 0.6 eV in the optical spectrum, all the structures except for the peak at 0.3 eV are consistent with our electronic spectra. When compared with LDA + U + SO calculations, the value of U should be considerably larger than the previous one, which implies that the spin-orbit coupling is not a necessary ingredient for the insulating mechanism of alpha-RuCl3. We also present angle-resolved photoemission spectra to be compared with LDA + U + SO and LDA +DMFT calculations.

  7. Nanoscale structural and electronic characterization of α-RuCl3 layered compound

    NASA Astrophysics Data System (ADS)

    Ziatdinov, Maxim; Maksov, Artem; Banerjee, Arnab; Zhou, Wu; Berlijn, Tom; Yan, Jiaqiang; Nagler, Stephen; Mandrus, David; Baddorf, Arthur; Kalinin, Sergei

    The exceptional interplay of spin-orbit effects, Coulomb interaction, and electron-lattice coupling is expected to produce an elaborate phase space of α-RuCl3 layered compound, which to date remains largely unexplored. Here we employ a combination of scanning transmission electron microscopy (STEM) and scanning tunneling microscopy (STM) for detailed evaluation of the system's microscopic structural and electronic orders with a sub-nanometer precision. The STM and STEM measurements are further supported by neutron scattering, X-Ray diffraction, density functional theory (DFT), and multivariate statistical analysis. Our results show a trigonal distortion of Cl octahedral ligand cage along the C3 symmetry axes in each RuCl3 layer. The lattice distortion is limited mainly to the Cl subsystem leaving the Ru honeycomb lattice nearly intact. The STM topographic and spectroscopic characterization reveals an intra unit cell electronic symmetry breaking in a spin-orbit coupled Mott insulating phase on the Cl-terminated surface of α-RuCl3. The associated long-range charge order (CO) pattern is linked to a surface component of Cl cage distortion. We finally discuss a fine structure of CO and its potential relation to variations of average unit cell geometries found in multivariate analysis of STEM data. The research was sponsored by the U.S. Department of Energy.

  8. Highly Conducting pi-Conjugated Molecular Junctions Covalently Bonded to Gold Electrodes

    SciTech Connect

    Chen, W.; Hybertsen, M.; Widawsky, J.R.; Vazquez, H.; Schneebeli, S.T.; Breslow, R.; Venkataraman, L.

    2011-11-02

    We measure electronic conductance through single conjugated molecules bonded to Au metal electrodes with direct Au-C covalent bonds using the scanning tunneling microscope based break-junction technique. We start with molecules terminated with trimethyltin end groups that cleave off in situ, resulting in formation of a direct covalent {sigma} bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated {pi} system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the {pi} system. The junctions formed with the prototypical example of 1,4-dimethylenebenzene show a conductance approaching one conductance quantum (G{sub 0} = 2e{sup 2}/h). Junctions formed with methylene-terminated oligophenyls with two to four phenyl units show a 100-fold increase in conductance compared with junctions formed with amine-linked oligophenyls. The conduction mechanism for these longer oligophenyls is tunneling, as they exhibit an exponential dependence of conductance on oligomer length. In addition, density functional theory based calculations for the Au-xylylene-Au junction show near-resonant transmission, with a crossover to tunneling for the longer oligomers.

  9. Consequences of ionic and covalent bonding in Ge-Sb-Te phase change materials

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Saikat; Sun, Jifeng; Subedi, Alaska; Siegrist, Theo; Singh, David

    Structural transformation of Ge2Sb2Te5 has attracted a great deal of research as it involves two states (crystalline and amorphous) that are stable at ambient temperature but with remarkably different physical properties, in particular, very different optical constants. The differences in physical properties in these states have been explained in terms of resonant bonding that has been generalized to the description of covalent systems with high symmetry structures such as benzene and graphite. However, given the local lattice distortions noted from both experimental and theoretical investigations, it is clear that the meaning of ``resonant bonding'' in GST is very different from that in graphite or benzene and the precise nature of bonding in this phase has not been fully established. In this talk, based on our first-principles calculations, we show that there is a strong competition between ionic and covalent bonding in the cubic phase, and establish a link between the origins of phase change memory properties and giant responses of piezoelectric materials.

  10. Tribromobenzene on Cu(111): Temperature-dependent formation of halogen-bonded, organometallic, and covalent nanostructures

    SciTech Connect

    Fan, Qitang; Wang, Tao; Zhu, Junfa; Liu, Liming; Zhao, Jin; Gottfried, J. Michael

    2015-03-14

    The temperature-controlled surface-assisted synthesis of halogen bonded, organometallic, and covalent nanostructures based on 1,3,5-tribromo-benzene (TriBB) was studied with scanning tunneling microscopy and X-ray photoemission spectroscopy in ultrahigh vacuum. Vapor deposition of TriBB onto a Cu(111) surface held at 90 K leads to the formation of large domains of a honeycomb-like organic monolayer structure stabilized by triangular nodes with Br⋯Br intermolecular bonds. Upon annealing the organic monolayer to ∼140 K, a new hexagonal close-packed structure with intact TriBB molecules connected by Cu adatoms is formed. Further warming up the sample to 300 K gives rise to the scission of C–Br bonds and formation of C–Cu–C bonds between phenyl fragments such that stable dendritic organometallic networks are formed. Larger islands of organometallic networks are obtained by maintaining the temperature of Cu(111) at 420 K during deposition of TriBB. Simultaneously, large islands of Br atoms are formed around the organometallic networks. Annealing the more extended organometallic network (prepared at 420 K) to 520 K leads to the formation of a branched covalent organic framework (COF) which comprises structural elements of porous graphene and is surrounded by Br islands. These organometallic networks and COFs appear as small dendritic and branched domains, most likely due to the steric influence exerted by the Br islands.

  11. Tribromobenzene on Cu(111): Temperature-dependent formation of halogen-bonded, organometallic, and covalent nanostructures

    NASA Astrophysics Data System (ADS)

    Fan, Qitang; Wang, Tao; Liu, Liming; Zhao, Jin; Zhu, Junfa; Gottfried, J. Michael

    2015-03-01

    The temperature-controlled surface-assisted synthesis of halogen bonded, organometallic, and covalent nanostructures based on 1,3,5-tribromo-benzene (TriBB) was studied with scanning tunneling microscopy and X-ray photoemission spectroscopy in ultrahigh vacuum. Vapor deposition of TriBB onto a Cu(111) surface held at 90 K leads to the formation of large domains of a honeycomb-like organic monolayer structure stabilized by triangular nodes with Br⋯Br intermolecular bonds. Upon annealing the organic monolayer to ˜140 K, a new hexagonal close-packed structure with intact TriBB molecules connected by Cu adatoms is formed. Further warming up the sample to 300 K gives rise to the scission of C-Br bonds and formation of C-Cu-C bonds between phenyl fragments such that stable dendritic organometallic networks are formed. Larger islands of organometallic networks are obtained by maintaining the temperature of Cu(111) at 420 K during deposition of TriBB. Simultaneously, large islands of Br atoms are formed around the organometallic networks. Annealing the more extended organometallic network (prepared at 420 K) to 520 K leads to the formation of a branched covalent organic framework (COF) which comprises structural elements of porous graphene and is surrounded by Br islands. These organometallic networks and COFs appear as small dendritic and branched domains, most likely due to the steric influence exerted by the Br islands.

  12. Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

    PubMed Central

    Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

    2016-01-01

    Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

  13. Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

    PubMed Central

    Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

    2015-01-01

    Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner. PMID:26337527

  14. Highly polar bonds and the meaning of covalency and ionicity--structure and bonding of alkali metal hydride oligomers.

    PubMed

    Bickelhaupt, F Matthias; Solà, Miquel; Guerra, Célia Fonseca

    2007-01-01

    The hydrogen-alkali metal bond is simple and archetypal, and thus an ideal model for studying the nature of highly polar element-metal bonds. Thus, we have theoretically explored the alkali metal hydride monomers, HM, and (distorted) cubic tetramers, (HM)4, with M = Li, Na, K, and Rb, using density functional theory (DFT) at the BP86/TZ2P level. Our objective is to determine how the structure and thermochemistry (e.g., H-M bond lengths and strengths, oligomerization energies, etc.) of alkali metal hydrides depend on the metal atom, and to understand the emerging trends in terms of quantitative Kohn-Sham molecular orbital (KS-MO) theory. The H-M bond becomes longer and weaker, both in the monomers and tetramers, if one descends the periodic table from Li to Rb. Quantitative bonding analyses show that this trend is not determined by decreasing electrostatic attraction but, primarily, by the weakening in orbital interactions. The latter become less stabilizing along Li-Rb because the bond overlap between the singly occupied molecular orbitals (SOMOs) of H* and M* radicals decreases as the metal ns atomic orbital (AO) becomes larger and more diffuse. Thus, the H-M bond behaves as a text-book electron-pair bond and, in that respect, it is covalent, despite a high polarity. For the lithium and sodium hydride tetramers, the H4 tetrahedron is larger than and surrounds the M4 cluster (i.e., H-H > M-M). Interestingly, this is no longer the case in the potassium and rubidium hydride tetramers, in which the H4 tetrahedron is smaller than and inside the M4 cluster (i.e., H-H < M-M). PMID:17328442

  15. Competition between Covalent and Noncovalent Bond Cleavages in Dissociation of Phosphopeptide-Amine Complexes

    SciTech Connect

    Laskin, Julia; Yang, Zhibo; Woods, Amina S.

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A3pXA3-NH2 (X=S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. We demonstrate that covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel

  16. A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta

    PubMed Central

    O’Meara, Matthew J.; Leaver-Fay, Andrew; Tyka, Mike; Stein, Amelie; Houlihan, Kevin; DiMaio, Frank; Bradley, Philip; Kortemme, Tanja; Baker, David; Snoeyink, Jack; Kuhlman, Brian

    2015-01-01

    Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at longer ranges the orientation preferences are lost, but significant electrostatic interactions between charged and partially charged atoms remain. To simultaneously model these two types of behavior, we refined an orientation dependent model of hydrogen bonds [Kortemme et al. 2003] used by the molecular modeling program Rosetta and then combined it with a distance-dependent Coulomb model of electrostatics. The functional form of the H-bond potential is physically motivated and parameters are fit so that H-bond geometries that Rosetta generates closely resemble H-bond geometries in high-resolution crystal structures. The combined potentials improve performance in a variety of scientific benchmarks including decoy discrimination, side chain prediction, and native sequence recovery in protein design simulations, and establishes a new standard energy function for Rosetta. PMID:25866491

  17. Colorful surface architectures with three different types of dynamic covalent bonds: integration of anthocyanins, tritylium ions and flavins.

    PubMed

    Zhang, Kang-Da; Sakai, Naomi; Matile, Stefan

    2015-08-28

    Although they combine the best of covalent and non-covalent bonds, dynamic covalent bonds are usually not used together. Building on pioneering examples for functional systems with two orthogonal dynamic covalent bonds, we herein elaborate on multicomponent surface architectures that operate with three different types of dynamic covalent bonds. Disulfide exchange under basic conditions is used to grow single π stacks directly on oxide surfaces, hydrazone exchange under acidic conditions to add a second string or stack, and boronic-ester exchange under neutral conditions to build the third one. In this study, we show that this synthetic approach to complex systems provides access to emergent properties, as exemplified with ordered stacks of anthocyanins, pyrocatchol violet and riboflavins. The integration of anthocyanins, the central component of the pigments of plant flowers, is interesting to protect the blue flavylium cation against deprotonation, deplanarization and degradation. The integration of pyrocatchol violet is of interest to stabilize the blue, disfavored tritylium cation. The red riboflavin stacks are attractive because they generate high photocurrent. These colorful examples hint at the potential of synthetic methods that use three different types of dynamic covalent bonds in concert to build complex systems with emergent properties. PMID:26179486

  18. Controlling Interfacial Dynamics: Covalent Bonding versus Physical Adsorption in Polymer Nanocomposites.

    PubMed

    Holt, Adam P; Bocharova, Vera; Cheng, Shiwang; Kisliuk, Alexander M; White, B Tyler; Saito, Tomonori; Uhrig, David; Mahalik, J P; Kumar, Rajeev; Imel, Adam E; Etampawala, Thusitha; Martin, Halie; Sikes, Nicole; Sumpter, Bobby G; Dadmun, Mark D; Sokolov, Alexei P

    2016-07-26

    It is generally believed that the strength of the polymer-nanoparticle interaction controls the modification of near-interface segmental mobility in polymer nanocomposites (PNCs). However, little is known about the effect of covalent bonding on the segmental dynamics and glass transition of matrix-free polymer-grafted nanoparticles (PGNs), especially when compared to PNCs. In this article, we directly compare the static and dynamic properties of poly(2-vinylpyridine)/silica-based nanocomposites with polymer chains either physically adsorbed (PNCs) or covalently bonded (PGNs) to identical silica nanoparticles (RNP = 12.5 nm) for three different molecular weight (MW) systems. Interestingly, when the MW of the matrix is as low as 6 kg/mol (RNP/Rg = 5.4) or as high as 140 kg/mol (RNP/Rg= 1.13), both small-angle X-ray scattering and broadband dielectric spectroscopy show similar static and dynamic properties for PNCs and PGNs. However, for the intermediate MW of 18 kg/mol (RNP/Rg = 3.16), the difference between physical adsorption and covalent bonding can be clearly identified in the static and dynamic properties of the interfacial layer. We ascribe the differences in the interfacial properties of PNCs and PGNs to changes in chain stretching, as quantified by self-consistent field theory calculations. These results demonstrate that the dynamic suppression at the interface is affected by the chain stretching; that is, it depends on the anisotropy of the segmental conformations, more so than the strength of the interaction, which suggests that the interfacial dynamics can be effectively tuned by the degree of stretching-a parameter accessible from the MW or grafting density. PMID:27337392

  19. Controlling Interfacial Dynamics: Covalent Bonding versus Physical Adsorption in Polymer Nanocomposites

    DOE PAGESBeta

    Holt, Adam P.; Bocharova, Vera; Cheng, Shiwang; Kisliuk, Alexander M.; White, B. Tyler; Saito, Tomonori; Uhrig, David; Mahalik, J. P.; Kumar, Rajeev; Imel, Adam E.; et al

    2016-06-23

    It is generally believed that the strength of the polymer nanoparticle interaction controls the modification of near-interface segmental mobility in polymer nanocomposites (PNCs). However, little is known about the effect of covalent bonding on the segmental dynamics and glass transition of matrix-free polymer-grafted nanoparticles (PGNs), especially when compared to PNCs. In this article, we directly compare the static and dynamic properties of poly(2-vinylpyridine)/silica-based nanocomposites with polymer chains either physically adsorbed (PNCs) or covalently bonded (PGNs) to identical silica nanoparticles (RNP = 12.5 nm) for three different molecular weight (MW) systems. Interestingly, when the MW of the matrix is as lowmore » as 6 kg/mol (RNP/Rg = 5.4) or as high as 140 kg/mol (RNP/Rg= 1.13), both small-angle X-ray scattering and broadband dielectric spectroscopy show similar static and dynamic properties for PNCs and PGNs. However, for the intermediate MW of 18 kg/mol (RNP/Rg = 3.16), the difference between physical adsorption and covalent bonding can be clearly identified in the static and dynamic properties of the interfacial layer. We ascribe the differences in the interfacial properties of PNCs and PGNs to changes in chain stretching, as quantified by self-consistent field theory calculations. These results demonstrate that the dynamic suppression at the interface is affected by the chain stretching; that is, it depends on the anisotropy of the segmental conformations, more so than the strength of the interaction, which suggests that the interfacial dynamics can be effectively tuned by the degree of stretching a parameter accessible from the MW or grafting density.« less

  20. Field induced phase transition in layered honeycomb spin system α-RuCl3 studied by thermal conductivity

    NASA Astrophysics Data System (ADS)

    Leahy, Ian; Bornstein, Alex; Choi, Kwang-Yong; Lee, Minhyea

    α -RuCl3, a quasi -two-dimensional honeycomb lattice is known to be a candidate material to realize the Heisenberg-Kitaev spin model of a highly anisotropic bond-dependent exchange interaction. We investigate in-plane thermal conductivity (κ) as a function of temperature (T) and in-plane applied field (H). At H = 0 , the onset of a strong increase in κ marks the spontaneous long range ordering temperature, Tc = 6 . 5 K , corresponding to ``zigzag'' antiferromagnetic ordering. A broad peak appearing below Tc in κ was found to be suppressed significantly as H increases up to ~ 7 T , implying the system undergoes a field-induced transition from ordered to a new spin-disordered state analogous to the transverse-field Ising model. Further increasing H above 7 . 1 T , the large field seems to begin polarizing spins thus increasing the phonon mean free path, resulting in a significant rise in κ. This tendency is clearly shown in the field dependence of κ below Tc, which has a pronounced minimum at Hmin = 7 . 1 T . We will discuss our scaling analysis to characterize this field-induced phase transition and compare to the transverse-field Ising spin system. Work at the University of Colorado was supported by the US DOE Basic Energy Sciences under Award No. DE-SC0006888.

  1. Assessing covalency in equatorial U-N bonds: density based measures of bonding in BTP and isoamethyrin complexes of uranyl.

    PubMed

    Di Pietro, Poppy; Kerridge, Andrew

    2016-06-22

    Calculations performed at the density functional level of theory have been used to investigate complexes of uranyl with the expanded porphyrin isoamethyrin and the bis-triazinyl-pyridine (BTP) ligands, the latter of which is well-known to be effective in the separation of trivalent lanthanides and actinides. Analysis has been performed using a range of density-based techniques, including the Quantum Theory of Atoms in Molecules (QTAIM), the Electron Localisation Function (ELF) and the reduced density gradient (RDG). The effects of peripheral alkyl substituents on UO2-isoamethyrin, known to be vital for proper replication of the experimental geometry, are considered. Evidence for comparable amounts of covalent character has been found in the largely ionic U-N bonds of UO2-isoamethyrin and [UO2(BTP)2](2+) and examination of the variation in the electronic characteristics of the uranyl unit upon complexation in both of these cases reveal striking similarities in the nature of the U-N bonding and the effect of this bonding on the U-Oyl interaction, as well as evidence of donation into the U-N bonding region from the uranyl unit itself. PMID:27279271

  2. A first-principles study on three-dimensional covalently-bonded hexagonal boron nitride nanoribbons.

    PubMed

    Lee, Sang-Hoon; Jhi, Seung-Hoon

    2015-02-25

    We studied three-dimensional honeycomb-structure boron nitride (BN) allotrope using first-principles calculations and the tight-binding method. Interconnected by sp(3)-bonding at the vertices, hexagonal BN nanoribbons construct highly-porous, covalently-bonded hexagonal BN nanoribbons (CBBNs). We investigated the structural and mechanical properties of CBBNs with various sizes, compared with those of carbon and other BN allotropes. The mechanical and thermal stabilities are also checked. Our calculations show that, despite the high porosity and low mass density, CBBNs are stable and mechanically hard materials as cubic BN. Moreover, our calculated results suggest that CBBNs can be regarded as a binary alloy of sp(2)- and sp(3)-bonded BNs following the Vegard's rule in average bond lengths and bulk moduli. Calculated band structures show that the band gap of CBBNs has similar variation upon increasing size as BN nanoribbons and is also limited by the second-neighbor interaction between the pz states of sp(2)-bonded atoms in adjacent nanoribbons. PMID:25629431

  3. Enhancement of chemical stability and crystallinity in porphyrin-containing covalent organic frameworks by intramolecular hydrogen bonds.

    PubMed

    Kandambeth, Sharath; Shinde, Digambar Balaji; Panda, Manas K; Lukose, Binit; Heine, Thomas; Banerjee, Rahul

    2013-12-01

    A strong bond: A strategy based on intramolecular hydrogen-binding interactions in 2D covalent organic frameworks (COFs) is shown to improve the crystallinity, porosity, and chemical stability of the material. The concept is validated by removing the hydrogen-bonding interaction in the methoxy analog which showed a lower stability and crystallinity. PMID:24127339

  4. Crystal structure and magnetism in α -RuCl3 : An ab initio study

    NASA Astrophysics Data System (ADS)

    Kim, Heung-Sik; Kee, Hae-Young

    2016-04-01

    α -RuCl3 has been proposed recently as an excellent playground for exploring Kitaev physics on a two-dimensional (2D) honeycomb lattice. However, structural clarification of the compound has not been completed, which is crucial in understanding the physics of this system. Here, using ab initio electronic structure calculations, we study a full three-dimensional (3D) structure of α -RuCl3 , including the effects of spin-orbit coupling (SOC) and electronic correlations. The three major results are as follows: (i) SOC suppresses dimerization of Ru atoms, which exists in other Ru compounds such as isostructural Li2RuO3 , and makes the honeycomb closer to an ideal one. (ii) The nearest-neighbor Kitaev exchange interaction between the jeff=1 /2 pseudospin strongly depends on the Ru-Ru distance and the Cl position, originating from the nature of the edge-sharing geometry. (iii) The optimized 3D structure without electronic correlations has P 3 ¯1 m space-group symmetry independent of SOC, but including electronic correlation changes the optimized 3D structure to either C 2 /m or C m c 21 within 0.1 meV per formula unit (f.u.) energy difference. The reported P 3112 structure is also close in energy. The interlayer spin-exchange coupling is a few percent of the in-plane spin-exchange terms, confirming that α -RuCl3 is close to a 2D system. We further suggest how to increase the Kitaev term via tensile strain, which sheds light in realizing the Kitaev spin-liquid phase in this system.

  5. XY-like frustrated magnetic phase transitions in α-RuCl3

    NASA Astrophysics Data System (ADS)

    Tanaka, Hidekazu

    It is known that a honeycomb-lattice antiferromagnet with the nearest-neighbor exchange interaction undergoes a conventional magnetic ordering even for the spin-1/2 case. However, when a certain amount of second-neighbor exchange interaction or anisotropic exchange interaction exists, the honeycomb-lattice quantum magnet exhibits an unusual ground state. In the last decade, spin-1/2 quantum magnets on honeycomb lattices have been attracting considerable attention from the viewpoints of the frustrated J1 -J2 model and the Kitaev-Heisenberg model, both of which can exhibit the spin liquid state in some parameter range. α-RuCl3 is a layered compound, in which magnetic Ru3+ ions with the 4d5 electronic state form a honeycomb lattice. We have investigated the magnetic properties of α-RuCl3 via magnetization and specific heat measurements using single crystals. It was observed that α-RuCl3 undergoes a structural phase transition at Tt ~= 150 K accompanied by fairly large hysteresis. The magnetizations and magnetic susceptibilities are strongly anisotropic, which mainly arise from the anisotropic g-factors. These g-factors and the obtained entropy indicate that the effective spin of Ru3+ is one-half, which results from the low-spin state. Specific heat data show that magnetic ordering occurs in four steps at zero magnetic field. The magnetic phase diagram is obtained. The successive magnetic phase transitions can be ascribed to the competition among exchange interactions. We discuss the strongly anisotropic g-factors and deduce that the exchange interaction is strongly XY-like. Main results of this talk was published in Phys. Rev. B 91, 094422 (2015).

  6. Development of the Bonding Representations Inventory to Identify Student Misconceptions about Covalent and Ionic Bonding Representations

    ERIC Educational Resources Information Center

    Luxford, Cynthia J.; Bretz, Stacey Lowery

    2014-01-01

    Teachers use multiple representations to communicate the concepts of bonding, including Lewis structures, formulas, space-filling models, and 3D manipulatives. As students learn to interpret these multiple representations, they may develop misconceptions that can create problems in further learning of chemistry. Interviews were conducted with 28…

  7. Characteristics of enzyme hydrolyzing natural covalent bond between RNA and protein VPg of encephalomyocarditis virus

    SciTech Connect

    Drygin, Yu.F.; Siyanova, E.Yu.

    1986-08-10

    The isolation and a preliminary characterization of the enzyme specifically hydrolyzing the phosphodiester bond between protein VPg and the RNA of encephalomyocarditis virus was the goal of the present investigation. The enzyme was isolated from a salt extract of Krebs II mouse ascites carcinoma cells by ion-exchange and affinity chromatography. It was found that the enzyme actually specifically cleaves the covalent bond between the RNA and protein, however, the isolation procedure does not free the enzyme from impurities which partially inhibit it. The enzyme cleaves the RNA-protein VPg complex of polio virus at a high rate, it is completely inactivated at 55/sup 0/C, and is partially inhibited by EDTA.

  8. Formation of Me-O-Si covalent bonds at the interface between polysilazane and stainless steel

    NASA Astrophysics Data System (ADS)

    Amouzou, Dodji; Fourdrinier, Lionel; Maseri, Fabrizio; Sporken, Robert

    2014-11-01

    In earlier works, we demonstrated the potential of polysilazane (PSZ) coatings for a use as insulating layers in Cu(In,Ga)Se2 (CIGS) solar cells prepared on steels substrates and showed a good adhesion between PSZ coatings and both AISI316 and AISI430 steels. In the present paper, spectroscopic techniques are used to elucidate the reason of such adhesion. X-ray Photoelectron Spectroscopy (XPS) was used to investigate surfaces for the two steel substrates and showed the presence of metal oxides and metal hydroxides at the top surface. XPS has been also used to probe interfaces between substrates and PSZ, and metallosiloxane (Me-O-Si) covalent bonds have been detected. These results were confirmed by Infra-Red Reflection Absorption Spectroscopy (IRRAS) analyses since vibrations related to Cr-O-Si and Fe-O-Si compounds were detected. Thus, the good adhesion between steel substrates and PSZ coatings was explained by covalent bonding through chemical reactions between PSZ precursors and hydroxide functional groups present on top surface of the two types of steel. Based on these results, an adhesion mechanism between steel substrates and PSZ coatings is proposed.

  9. Design of Lead(II) Metal-Organic Frameworks Based on Covalent and Tetrel Bonding.

    PubMed

    Servati Gargari, Masoumeh; Stilinović, Vladimir; Bauzá, Antonio; Frontera, Antonio; McArdle, Patrick; Van Derveer, Donald; Ng, Seik Weng; Mahmoudi, Ghodrat

    2015-12-01

    Three solid materials, [Pb(HL)(SCN)2 ]⋅CH3 OH (1), [Pb(HL)(SCN)2 ] (2), and [Pb(L)(SCN)]n (3), were obtained from Pb(SCN)2 and an unsymmetrical bis-pyridyl hydrazone ligand that can act both as a bridging and as a chelating ligand. In all three the lead center is hemidirectionally coordinated and is thus sterically optimal for participation in tetrel bonding. In the crystal structures of all three compounds, the lead atoms participate in short contacts with thiocyanate sulfur or nitrogen atoms. These contacts are shorter than the sums of the van der Waals radii (3.04-3.47 Å for Pb⋅⋅⋅S and 3.54 Å for Pb⋅⋅⋅N) and interconnect the covalently bonded units (monomers, dimers, and 2D polymers) into supramolecular assemblies (chains and 3D structures). DFT calculations showed these contacts to be tetrel bonds of considerable energy (6.5-10.5 kcal mol(-1) for Pb⋅⋅⋅S and 16.5 kcal mol(-1) for Pb⋅⋅⋅N). A survey of structures in the CSD showed that similar contacts often appear in crystals of Pb(II) complexes with regular geometries, which leads to the conclusion that tetrel bonding plays a significant role in the supramolecular chemistry of Pb(II) . PMID:26489982

  10. Nitrogen-Doping Enables Covalent-Like pi-pi Bonding between Graphenes

    SciTech Connect

    Tian, Yong-Hui; Huang, Jingsong; Sumpter, Bobby G; Kertesz, Prof. Miklos

    2015-01-01

    The neighboring layers in bi-layer (and few-layer) graphenes of both AA and AB stacking motifs are known to be separated at a distance corresponding to van der Waals (vdW) interactions. In this Letter, we present for the first time a new aspect of graphene chemistry in terms of a special chemical bonding between the giant graphene molecules . Through rigorous theoretical calculations, we demonstrate that the N-doped graphenes (NGPs) with various doping levels can form an unusual two-dimensional (2D) pi pi bonding in bi-layer NGPs bringing the neighboring NGPs to significantly reduced interlayer separations. The interlayer binding energies can be enhanced by up to 50% compared to the pristine graphene bi-layers that are characterized by only vdW interactions. Such an unusual chemical bonding arises from the pi pi overlap across the vdW gap while the individual layers maintain their in-plane pi-conjugation and are accordingly planar. The existence of the resulting interlayer covalent-like bonding is corroborated by electronic structure calculations and crystal orbital overlap population (COOP) analyses. In NGP-based graphite with the optimal doping level, the NGP layers are uniformly stacked and the 3D bulk exhibits metallic characteristics both in the in-plane and along the stacking directions.

  11. Nitrogen Doping Enables Covalent-Like π–π Bonding between Graphenes

    SciTech Connect

    Tian, Yong-Hui; Huang, Jingsong; Sheng, Xiaolan; Sumpter, Bobby G.; Yoon, Mina; Kertesz, Miklos

    2015-07-07

    In neighboring layers of bilayer (and few-layer) graphenes, both AA and AB stacking motifs are known to be separated at a distance corresponding to van der Waals (vdW) interactions. In this Letter, we present for the first time a new aspect of graphene chemistry in terms of a special chemical bonding between the giant graphene "molecules". Through rigorous theoretical calculations, we demonstrate that the N-doped graphenes (NGPs) with various doping levels can form an unusual two-dimensional (2D) pi-pi bonding in bilayer NGPs bringing the neighboring NGPs to significantly reduced interlayer separations. The interlayer binding energies can be enhanced by up to 50% compared to the pristine graphene bilayers that are characterized by only vdW interactions. Such an unusual chemical bonding arises from the pi-pi overlap across the vdW gap while the individual layers maintain their in-plane pi-conjugation and are accordingly planar. Moreover, the existence of the resulting interlayer covalent-like bonding is corroborated by electronic structure calculations and crystal orbital overlap population (COOP) analyses. In NGP-based graphite with the optimal doping level, the NGP layers are uniformly stacked and the 3D bulk exhibits metallic characteristics both in the in-plane and along the stacking directions.

  12. Nitrogen Doping Enables Covalent-Like π–π Bonding between Graphenes

    DOE PAGESBeta

    Tian, Yong-Hui; Huang, Jingsong; Sheng, Xiaolan; Sumpter, Bobby G.; Yoon, Mina; Kertesz, Miklos

    2015-07-07

    In neighboring layers of bilayer (and few-layer) graphenes, both AA and AB stacking motifs are known to be separated at a distance corresponding to van der Waals (vdW) interactions. In this Letter, we present for the first time a new aspect of graphene chemistry in terms of a special chemical bonding between the giant graphene "molecules". Through rigorous theoretical calculations, we demonstrate that the N-doped graphenes (NGPs) with various doping levels can form an unusual two-dimensional (2D) pi-pi bonding in bilayer NGPs bringing the neighboring NGPs to significantly reduced interlayer separations. The interlayer binding energies can be enhanced by upmore » to 50% compared to the pristine graphene bilayers that are characterized by only vdW interactions. Such an unusual chemical bonding arises from the pi-pi overlap across the vdW gap while the individual layers maintain their in-plane pi-conjugation and are accordingly planar. Moreover, the existence of the resulting interlayer covalent-like bonding is corroborated by electronic structure calculations and crystal orbital overlap population (COOP) analyses. In NGP-based graphite with the optimal doping level, the NGP layers are uniformly stacked and the 3D bulk exhibits metallic characteristics both in the in-plane and along the stacking directions.« less

  13. Lewis Acid Based Sorption of Trace Amounts of RuCl3 by Polyaniline.

    PubMed

    Harbottle, Allison M; Hira, Steven M; Josowicz, Mira; Janata, Jiří

    2016-08-23

    A sorption process of RuCl3 in phosphate buffer by polyaniline (PANI) powder chemically synthesized from phosphoric acid was spectrophotometrically monitored as a function of time. It was determined that the sorption process follows the Langmuir and Freundlich isotherms, and their constants were evaluated. It was determined that chemisorption was the rate-controlling step. By conducting detailed studies, we assigned the chemisorption to Lewis acid based interactions of the sorbent electron pair localized at the benzenoid amine (-NH2) and quinoid imine (═NH) groups, with the sorbate, RuCl3, as the electron acceptor. The stability of the interaction over a period of ∼1 week showed that the presence of the Ru(III) in the PANI matrix reverses its state from emeraldine base to emeraldine salt, resulting in a change of conductivity. The partial electron donor based charge transfer is a slow process as compared to the sorption process involving Brønsted acid doping. PMID:27479848

  14. Establishing the Two-Photon Linkage Isomerization Mechanism in the Nitrosyl Complex trans-[RuCl(NO)(py)4](2+) by DFT and TDDFT.

    PubMed

    Sanz García, Juan; Alary, Fabienne; Boggio-Pasqua, Martial; Dixon, Isabelle M; Malfant, Isabelle; Heully, Jean-Louis

    2015-09-01

    The density functional theory calculations presented in this work allow the first rationalization of the full linkage photoisomerization mechanism of trans-[RuCl(NO)(py)4](2+), in both the forward and reverse directions. These mechanisms are consistent with the experimental data establishing that blue-light irradiation triggers the forward process, while red or IR photons trigger the reverse process. Characterization of the singlet and lowest triplet potential energy surfaces shows that, despite the unfavorable thermodynamic character of the forward process, the topologies of the surfaces and particularly some crucial surface crossings enable the isomerization. In the forward Ru-NO → Ru-ON direction, a sequential two-photon absorption mechanism is unraveled that involves a sideways-bonded metastable state. In contrast, in the reverse reaction, two mechanisms are proposed involving either one or two photons. PMID:26274397

  15. In situ metalation of free base phthalocyanine covalently bonded to silicon surfaces

    PubMed Central

    Lupo, Fabio; Tudisco, Cristina; Bertani, Federico; Dalcanale, Enrico

    2014-01-01

    Summary Free 4-undecenoxyphthalocyanine molecules were covalently bonded to Si(100) and porous silicon through thermic hydrosilylation of the terminal double bonds of the undecenyl chains. The success of the anchoring strategy on both surfaces was demonstrated by the combination of X-ray photoelectron spectroscopy with control experiments performed adopting the commercially available 2,3,9,10,16,17,23,24-octakis(octyloxy)-29H,31H-phthalocyanine, which is not suited for silicon anchoring. Moreover, the study of the shape of the XPS N 1s band gave relevant information on the interactions occurring between the anchored molecules and the substrates. The spectra suggest that the phthalocyanine ring interacts significantly with the flat Si surface, whilst ring–surface interactions are less relevant on porous Si. The surface-bonded molecules were then metalated in situ with Co by using wet chemistry. The efficiency of the metalation process was evaluated by XPS measurements and, in particular, on porous silicon, the complexation of cobalt was confirmed by the disappearance in the FTIR spectra of the band at 3290 cm−1 due to –NH stretches. Finally, XPS results revealed that the different surface–phthalocyanine interactions observed for flat and porous substrates affect the efficiency of the in situ metalation process. PMID:25551050

  16. Competing covalent and ionic bonding in Ge-Sb-Te phase change materials

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Saikat; Sun, Jifeng; Subedi, Alaska; Siegrist, Theo; Singh, David J.

    2016-05-01

    Ge2Sb2Te5 and related phase change materials are highly unusual in that they can be readily transformed between amorphous and crystalline states using very fast melt, quench, anneal cycles, although the resulting states are extremely long lived at ambient temperature. These states have remarkably different physical properties including very different optical constants in the visible in strong contrast to common glass formers such as silicates or phosphates. This behavior has been described in terms of resonant bonding, but puzzles remain, particularly regarding different physical properties of crystalline and amorphous phases. Here we show that there is a strong competition between ionic and covalent bonding in cubic phase providing a link between the chemical basis of phase change memory property and origins of giant responses of piezoelectric materials (PbTiO3, BiFeO3). This has important consequences for dynamical behavior in particular leading to a simultaneous hardening of acoustic modes and softening of high frequency optic modes in crystalline phase relative to amorphous. This different bonding in amorphous and crystalline phases provides a direct explanation for different physical properties and understanding of the combination of long time stability and rapid switching and may be useful in finding new phase change compositions with superior properties.

  17. Competing covalent and ionic bonding in Ge-Sb-Te phase change materials

    DOE PAGESBeta

    Subedi, Alaska; Siegrist, Theo; Singh, David J.; Mukhopadhyay, Saikat; Sun, Jifeng

    2016-05-19

    Ge2Sb2Te5 and related phase change materials are highly unusual in that they can be readily transformed between amorphous and crystalline states using very fast melt, quench, anneal cycles, although the resulting states are extremely long lived at ambient temperature. These states have remarkably different physical properties including very different optical constants in the visible in strong contrast to common glass formers such as silicates or phosphates. This behavior has been described in terms of resonant bonding, but puzzles remain, particularly regarding different physical properties of crystalline and amorphous phases. Here we show that there is a strong competition between ionicmore » and covalent bonding in cubic phase providing a link between the chemical basis of phase change memory property and origins of giant responses of piezoelectric materials (PbTiO3, BiFeO3). This has important consequences for dynamical behavior in particular leading to a simultaneous hardening of acoustic modes and softening of high frequency optic modes in crystalline phase relative to amorphous. As a result, this different bonding in amorphous and crystalline phases provides a direct explanation for different physical properties and understanding of the combination of long time stability and rapid switching and may be useful in finding new phase change compositions with superior properties.« less

  18. Competing covalent and ionic bonding in Ge-Sb-Te phase change materials

    PubMed Central

    Mukhopadhyay, Saikat; Sun, Jifeng; Subedi, Alaska; Siegrist, Theo; Singh, David J.

    2016-01-01

    Ge2Sb2Te5 and related phase change materials are highly unusual in that they can be readily transformed between amorphous and crystalline states using very fast melt, quench, anneal cycles, although the resulting states are extremely long lived at ambient temperature. These states have remarkably different physical properties including very different optical constants in the visible in strong contrast to common glass formers such as silicates or phosphates. This behavior has been described in terms of resonant bonding, but puzzles remain, particularly regarding different physical properties of crystalline and amorphous phases. Here we show that there is a strong competition between ionic and covalent bonding in cubic phase providing a link between the chemical basis of phase change memory property and origins of giant responses of piezoelectric materials (PbTiO3, BiFeO3). This has important consequences for dynamical behavior in particular leading to a simultaneous hardening of acoustic modes and softening of high frequency optic modes in crystalline phase relative to amorphous. This different bonding in amorphous and crystalline phases provides a direct explanation for different physical properties and understanding of the combination of long time stability and rapid switching and may be useful in finding new phase change compositions with superior properties. PMID:27193531

  19. Competing covalent and ionic bonding in Ge-Sb-Te phase change materials.

    PubMed

    Mukhopadhyay, Saikat; Sun, Jifeng; Subedi, Alaska; Siegrist, Theo; Singh, David J

    2016-01-01

    Ge2Sb2Te5 and related phase change materials are highly unusual in that they can be readily transformed between amorphous and crystalline states using very fast melt, quench, anneal cycles, although the resulting states are extremely long lived at ambient temperature. These states have remarkably different physical properties including very different optical constants in the visible in strong contrast to common glass formers such as silicates or phosphates. This behavior has been described in terms of resonant bonding, but puzzles remain, particularly regarding different physical properties of crystalline and amorphous phases. Here we show that there is a strong competition between ionic and covalent bonding in cubic phase providing a link between the chemical basis of phase change memory property and origins of giant responses of piezoelectric materials (PbTiO3, BiFeO3). This has important consequences for dynamical behavior in particular leading to a simultaneous hardening of acoustic modes and softening of high frequency optic modes in crystalline phase relative to amorphous. This different bonding in amorphous and crystalline phases provides a direct explanation for different physical properties and understanding of the combination of long time stability and rapid switching and may be useful in finding new phase change compositions with superior properties. PMID:27193531

  20. Mesoporous hybrids containing Eu 3+ complexes covalently bonded to SBA-15 functionalized: Assembly, characterization and photoluminescence

    NASA Astrophysics Data System (ADS)

    Li Kong, Li; Yan, Bing; Li, Ying

    2009-07-01

    A novel series of luminescent mesoporous organic-inorganic hybrid materials has been prepared by linking Eu 3+ complexes to the functionalized ordered mesoporous SBA-15 which was synthesis by a co-condensation process of 1,3-diphenyl-1,3-propanepione (DBM) modified by the coupling agent 3-(triethoxysilyl)-propyl isocyanate (TEPIC), tetraethoxysilane (TEOS), Pluronic P123 surfactant as a template. It was demonstrated that the efficient intramolecular energy transfer in the mesoporous material Eu(DBMSi-SBA-15) 3phen mainly occurred between the modified DBM (named as DBM-Si) and the central Eu 3+ ion. So the Eu(DBMSi-SBA-15) 3phen showed characteristic emission of Eu 3+ ion under UV irradiation with higher luminescence quantum efficiency. Moreover, the mesoporous hybrid materials exhibited excellent thermal stability as the lanthanide complex was covalently bonded to the mesoporous matrix.

  1. Atrazine removal by covalent bonding to piperazine functionalized PolyHIPEs.

    PubMed

    Pulko, Irena; Kolar, Mitja; Krajnc, Peter

    2007-11-01

    The removal of atrazine from water by a solid phase extraction technique using insoluble polymers is described. Porous crosslinked polymers bearing piperazine moieties were prepared in a one step reaction from the precursor 4-nitrophenylacrylate incorporating polymers (PolyHIPE type prepared by the polymerization of the continuous phase of a high internal phase emulsion and polymer beads prepared by suspension polymerization). Polymers were applied to sequester atrazine from aqueous solutions with a concentration of 33 ppb and irreversible covalent bonding to the polymers was achieved. GC/MS/MS was used to monitor the dynamics of atrazine uptake and it was found that almost complete removal of atrazine was accomplished with an excess of polymer after 48 hours at room temperature. For comparison, polymer beads of identical chemistry but lower porosity were also used and showed significantly slower action (near complete removal after 72 hours). PMID:17662371

  2. Reversible CO2 Capture by Conjugated Ionic Liquids through Dynamic Covalent Carbon-Oxygen Bonds.

    PubMed

    Pan, Mingguang; Cao, Ningning; Lin, Wenjun; Luo, Xiaoyan; Chen, Kaihong; Che, Siying; Li, Haoran; Wang, Congmin

    2016-09-01

    The strong chemisorption of CO2 is always accompanied by a high absorption enthalpy, and traditional methods to reduce the absorption enthalpy lead to decreased CO2 capacities. Through the introduction of a large π-conjugated structure into the anion, a dual-tuning approach for the improvement of CO2 capture by anion-functionalized ionic liquids (ILs) resulted in a high capacity of up to 0.96 molCO2  mol-1IL and excellent reversibility. The increased capacity and improved desorption were supported by quantum chemical calculations, spectroscopic investigations, and thermogravimetric analysis. The increased capacity may be a result of the strengthened dynamic covalent bonds in these π-electron-conjugated structures through anion aggregation upon the uptake of CO2 , and the improved desorption originates from the charge dispersion of interaction sites through the large π-electron delocalization. These results provide important insights into effective strategies for CO2 capture. PMID:27458723

  3. Strain rate effects on compressive behavior of covalently bonded CNT networks

    NASA Astrophysics Data System (ADS)

    Kirkayak, Levent

    2016-06-01

    In this study, strain rate effects on the compressive mechanical properties of randomly structured carbon nanotube (CNT) networks were examined. For this purpose, three-dimensional atomistic models of CNT networks with covalently-bonded junctions were generated. After that, molecular dynamics (MD) simulations of compressive loading were performed at five different strain rates to investigate the basic deformation characteristic mechanisms of CNT networks and determine the effect of strain rate on stress-strain curves. The simulation results showed that the strain rate of compressive loading increases, so that a higher resistance of specimens to deformation is observed. Furthermore, the local deformation characteristics of CNT segments, which are mainly driven by bending and buckling modes, and their prevalence are strongly affected by the deformation rate. It was also observed that CNT networks have superior features to metal foams such as metal matrix syntactic foams (MMSFs) and porous sintered fiber metals (PSFMs) in terms of energy absorbing capabilities.

  4. Dielectric spectroscopy of a polymerizing liquid and the evolution of molecular dynamics with increase in the number of covalent bonds

    NASA Astrophysics Data System (ADS)

    Parthun, M. G.; Johari, G. P.

    1995-07-01

    Dielectric spectroscopy and calorimetry studies of a low viscosity, initially monomeric liquid undergoing spontaneous chemical reaction, to form a linear chain polymer while maintaining isothermal conditions, have been used to determine how the number of covalent bonds formed during the growth of a linear chain affects the dielectric permittivity, relaxation time, and the spectral shape. During this reaction, the static permittivity decreased and the relaxation time increased towards limiting values. As the number of covalent bonds increased towards the Avogadro number, the change in the complex permittivity as measured for a fixed frequency was phenomenologically similar to that observed on varying the frequency, although the exact formalisms in both cases differed. In both cases the relaxation function could be well described by a stretched exponential or sum of exponentials, with a width that decreased as the liquid's state changed from monomeric liquid to a fully reacted chain polymer. The observed increase in the relaxation time with the number of bonds formed seems consistent with the decrease in the configurational entropy or the number of accessible configurations available to the structure, under isothermal conditions. It decreases progressively more slowly as the number of covalent bonds in the structure increases. As this occurs, a second relaxation process at higher frequencies is revealed. The dielectric manifestation of the irreversible process of covalent bond formation is remarkably similar to that observed on supercooling a molecular or polymeric liquid. The study demonstrates how negative feedback between molecular diffusion and chemical reaction vitrifies a liquid isothermally.

  5. Why Does Electron Sharing Lead to Covalent Bonding? A Variational Analysis

    SciTech Connect

    Ruedenberg, K.; Schmidt, M.

    2006-07-20

    Ground state energy differences between related systems can be elucidated by a comparative variational analysis of the energy functional, in which the concepts of variational kinetic pressure and variational electrostatic potential pull are found useful. This approach is applied to the formation of the bond in the hydrogen molecule ion. A highly accurate wavefunction is shown to be the superposition of two quasiatomic orbitals, each of which consists to 94% of the respective atomic 1s orbital, the remaining 6% deformation being 73% spherical and 27% nonspherical in character. The spherical deformation can be recovered to 99.9% by scaling the 1s orbital. These results quantify the conceptual metamorphosis of the free-atom wavefunction into the molecular wavefunction by orbital sharing, orbital contraction, and orbital polarization. Starting with the 1s orbital on one atom as the initial trial function, the value of the energy functional of the molecule at the equilibrium distance is stepwise lowered along several sequences of wavefunction modifications, whose energies monotonically decrease to the ground state energy of H{sub 2}{sup +}. The contributions of sharing, contraction and polarization to the overall lowering of the energy functional and their kinetic and potential components exhibit a consistent pattern that can be related to the wavefunction changes on the basis of physical reasoning, including the virial theorem. It is found that orbital sharing lowers the variational kinetic energy pressure and that this is the essential cause of covalent bonding in this molecule.

  6. Why does electron sharing lead to covalent bonding? A variational analysis.

    PubMed

    Ruedenberg, Klaus; Schmidt, Michael W

    2007-01-15

    Ground state energy differences between related systems can be elucidated by a comparative variational analysis of the energy functional, in which the concepts of variational kinetic pressure and variational electrostatic potential pull are found useful. This approach is applied to the formation of the bond in the hydrogen molecule ion. A highly accurate wavefunction is shown to be the superposition of two quasiatomic orbitals, each of which consists to 94% of the respective atomic 1s orbital, the remaining 6% deformation being 73% spherical and 27% nonspherical in character. The spherical deformation can be recovered to 99.9% by scaling the 1s orbital. These results quantify the conceptual metamorphosis of the free-atom wavefunction into the molecular wavefunction by orbital sharing, orbital contraction, and orbital polarization. Starting with the 1s orbital on one atom as the initial trial function, the value of the energy functional of the molecule at the equilibrium distance is stepwise lowered along several sequences of wavefunction modifications, whose energies monotonically decrease to the ground state energy of H2+. The contributions of sharing, contraction and polarization to the overall lowering of the energy functional and their kinetic and potential components exhibit a consistent pattern that can be related to the wavefunction changes on the basis of physical reasoning, including the virial theorem. It is found that orbital sharing lowers the variational kinetic energy pressure and that this is the essential cause of covalent bonding in this molecule. PMID:17143869

  7. A Rational Reconstruction of the Origin of the Covalent Bond and Its Implications for General Chemistry Textbooks.

    ERIC Educational Resources Information Center

    Niaz, Mansoor

    2001-01-01

    Develops a perspective based on the history and philosophy of science considerations (rational reconstruction) in order to understand the postulation of the covalent bond by Lewis. Formulates four criteria based on the perspective and evaluates of 27 textbooks based on the four criteria. Shows that most textbooks lacked a history and philosophy of…

  8. The Synthesis, Structures and Chemical Properties of Macrocyclic Ligands Covalently Bonded into Layered Arrays

    SciTech Connect

    Clearfield, Abraham

    2003-10-09

    OAK-B135 The immobilization of crown ethers tends to limit the leveling effect of solvents making the macrocycles more selective. In addition immobilization has the added advantage of relative ease of recovery of the otherwise soluble crown. We have affixed CH2PO3H2 groups to azacrown ethers. The resultant phosphorylated macrocycles may spontaneously aggregate into crystalline supramolecular linear arrays or contacted with cations produce layered or linear polymers. In the linear polymers the metal and phosphonic acids covalently bond into a central stem with the macrocyclic rings protruding from the stem as leaves on a twig. Two types of layered compounds were obtained with group 4 metals. Monoaza-crown ethers form a bilayer where the M4+ plus phosphonic acid groups build the layer and the rings fill the interlayer space. 1, 10-diazadiphosphonic acids cross-link the metal phosphonate layers forming a three-dimensional array of crown ethers. In order to improve diffusion into these 3-D arrays they are spaced by inclusion of phosphate or phosphate groups. Two series of azamacrocylic crown ethers were prepared containing rings with 20 to 32 atoms. These larger rings can complex two cations per ring. Methylene phosphonic acid groups have been bonded to the aza ring atoms to increase the complexing ability of these ligands. Our approach is to carry out acid-base titrations in the absence and presence of cations to determine the pKa values of the protons, both those bonded to aza groups and those associated with the phosphonic acid groups. From the differences in the titration curves obtained with and without the cations present we obtain the stoichiometry of complex formation and the complex stability constants. Some of the applications we are targeting include phase transfer catalysis, separation of cations and the separation of radioisotopes for diagnostic and cancer therapeutic purposes.

  9. Ions colliding with clusters of fullerenes-Decay pathways and covalent bond formations

    SciTech Connect

    Seitz, F.; Zettergren, H.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Schmidt, H. T.; Cederquist, H.; Rousseau, P.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Mery, A.; Maclot, S.; Adoui, L.; Wang, Y.; Martin, F.; Rangama, J.; Domaracka, A.; Vizcaino, V. [CIMAP, UMR 6252, CEA and others

    2013-07-21

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C{sub 60} molecules following collisions with Ar{sup 2+}, He{sup 2+}, and Xe{sup 20+} at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C{sub 60} monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C{sub 60}]{sub n}{sup +}{yields}C{sub 60}{sup +}+(n-1)C{sub 60} evaporation model. Excitation energies in the range of only {approx}0.7 eV per C{sub 60} molecule in a [C{sub 60}]{sub 13}{sup +} cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar{sup 2+} and He{sup 2+} collisions, we observe very efficient C{sub 119}{sup +} and C{sub 118}{sup +} formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C{sub 59}{sup +} or C{sub 58}{sup +} and C{sub 60} during cluster fragmentation. In the Ar{sup 2+} case, it is possible to form even smaller C{sub 120-2m}{sup +} molecules (m= 2-7), while no molecular fusion reactions are observed for the present Xe{sup 20+} collisions.

  10. Structure of covalently bonded materials: From the Peierls distortion to Phase-Change Materials

    NASA Astrophysics Data System (ADS)

    Gaspard, Jean-Pierre

    2016-03-01

    The relation between electronic structure and cohesion of materials has been a permanent quest of Jacques Friedel and his school. He developed simple models that are of great value as guidelines in conjunction with ab initio calculations. His local approach of bonding has both the advantages of a large field of applications including non-crystalline materials and a common language with chemists. Along this line, we review some fascinating behaviors of covalent materials, most of them showing a Peierls (symmetry breaking) instability mechanism, even in liquid and amorphous materials. We analyze the effect of external parameters such as pressure and temperature. In some temperature ranges, the Peierls distortion disappears and a negative thermal expansion is observed. In addition, the Peierls distortion plays a central role in Phase-Change Materials, which are very promising non-volatile memories. xml:lang="fr" Son approche locale de la liaison chimique s'applique à un vaste champ de systèmes, incluant les matériaux non cristallins et permis un langage commun avec les chimistes. Dans cet axe nous passons en revue quelques comportements fascinants des matériaux covalents, la plupart d'entre eux présentant un mécanisme d'instabilité de Peierls (brisure de symétrie), même les liquides et les amorphes, étonnamment. Nous analysons aussi l'effet de parame'tres externes tels que la pression et la température. Dans un certain domaine de température, la distorsion de Peierls disparaît et une dilatation thermique négative est observée. Enfin, la distorsion de Peierls joue un rôle central dans les matériaux à changement de phase (PC materials), qui sont très prometteurs pour la réalisation de mémoires non volatiles.

  11. Ab initio study of chemical bond interactions between covalently functionalized carbon nanotubes via amide, ester and anhydride linkages

    NASA Astrophysics Data System (ADS)

    Ben Doudou, Bessem; Chen, Jun; Vivet, Alexandre; Poilâne, Christophe

    2016-03-01

    In this paper, we have investigated the chemical bond interactions between covalently functionalized zigzag (5,0) and (8,0) SWCNT-SWCNT via various covalent linkages. Side-to-side junctions connected via amide, ester and anhydride linkages were particularly studied. The geometries and energy of the forming reaction were investigated using first-principles density functional theory. Furthermore, the band structures and the total density of states (DOS) of the junctions have also been analyzed. Our results show that several promising structures could be obtained by using chemical connection strategy and particularly the junctions formed by coupling amino functionalized SWCNT and carboxylic acid functionalized SWCNT was more favorable.

  12. A unique covalent bond in basement membrane is a primordial innovation for tissue evolution

    PubMed Central

    Fidler, Aaron L.; Vanacore, Roberto M.; Chetyrkin, Sergei V.; Pedchenko, Vadim K.; Bhave, Gautam; Yin, Viravuth P.; Stothers, Cody L.; Rose, Kristie Lindsey; McDonald, W. Hayes; Clark, Travis A.; Borza, Dorin-Bogdan; Steele, Robert E.; Ivy, Michael T.; Hudson, Julie K.; Hudson, Billy G.

    2014-01-01

    Basement membrane, a specialized ECM that underlies polarized epithelium of eumetazoans, provides signaling cues that regulate cell behavior and function in tissue genesis and homeostasis. A collagen IV scaffold, a major component, is essential for tissues and dysfunctional in several diseases. Studies of bovine and Drosophila tissues reveal that the scaffold is stabilized by sulfilimine chemical bonds (S = N) that covalently cross-link methionine and hydroxylysine residues at the interface of adjoining triple helical protomers. Peroxidasin, a heme peroxidase embedded in the basement membrane, produces hypohalous acid intermediates that oxidize methionine, forming the sulfilimine cross-link. We explored whether the sulfilimine cross-link is a fundamental requirement in the genesis and evolution of epithelial tissues by determining its occurrence and evolutionary origin in Eumetazoa and its essentiality in zebrafish development; 31 species, spanning 11 major phyla, were investigated for the occurrence of the sulfilimine cross-link by electrophoresis, MS, and multiple sequence alignment of de novo transcriptome and available genomic data for collagen IV and peroxidasin. The results show that the cross-link is conserved throughout Eumetazoa and arose at the divergence of Porifera and Cnidaria over 500 Mya. Also, peroxidasin, the enzyme that forms the bond, is evolutionarily conserved throughout Metazoa. Morpholino knockdown of peroxidasin in zebrafish revealed that the cross-link is essential for organogenesis. Collectively, our findings establish that the triad—a collagen IV scaffold with sulfilimine cross-links, peroxidasin, and hypohalous acids—is a primordial innovation of the ECM essential for organogenesis and tissue evolution. PMID:24344311

  13. A unique covalent bond in basement membrane is a primordial innovation for tissue evolution.

    PubMed

    Fidler, Aaron L; Vanacore, Roberto M; Chetyrkin, Sergei V; Pedchenko, Vadim K; Bhave, Gautam; Yin, Viravuth P; Stothers, Cody L; Rose, Kristie Lindsey; McDonald, W Hayes; Clark, Travis A; Borza, Dorin-Bogdan; Steele, Robert E; Ivy, Michael T; Hudson, Julie K; Hudson, Billy G

    2014-01-01

    Basement membrane, a specialized ECM that underlies polarized epithelium of eumetazoans, provides signaling cues that regulate cell behavior and function in tissue genesis and homeostasis. A collagen IV scaffold, a major component, is essential for tissues and dysfunctional in several diseases. Studies of bovine and Drosophila tissues reveal that the scaffold is stabilized by sulfilimine chemical bonds (S = N) that covalently cross-link methionine and hydroxylysine residues at the interface of adjoining triple helical protomers. Peroxidasin, a heme peroxidase embedded in the basement membrane, produces hypohalous acid intermediates that oxidize methionine, forming the sulfilimine cross-link. We explored whether the sulfilimine cross-link is a fundamental requirement in the genesis and evolution of epithelial tissues by determining its occurrence and evolutionary origin in Eumetazoa and its essentiality in zebrafish development; 31 species, spanning 11 major phyla, were investigated for the occurrence of the sulfilimine cross-link by electrophoresis, MS, and multiple sequence alignment of de novo transcriptome and available genomic data for collagen IV and peroxidasin. The results show that the cross-link is conserved throughout Eumetazoa and arose at the divergence of Porifera and Cnidaria over 500 Mya. Also, peroxidasin, the enzyme that forms the bond, is evolutionarily conserved throughout Metazoa. Morpholino knockdown of peroxidasin in zebrafish revealed that the cross-link is essential for organogenesis. Collectively, our findings establish that the triad-a collagen IV scaffold with sulfilimine cross-links, peroxidasin, and hypohalous acids-is a primordial innovation of the ECM essential for organogenesis and tissue evolution. PMID:24344311

  14. Reaction injection molding and direct covalent bonding of OSTE+ polymer microfluidic devices

    NASA Astrophysics Data System (ADS)

    Sandström, N.; Shafagh, R. Z.; Vastesson, A.; Carlborg, C. F.; van der Wijngaart, W.; Haraldsson, T.

    2015-07-01

    In this article, we present OSTE+RIM, a novel reaction injection molding (RIM) process that combines the merits of off-stoichiometric thiol-ene epoxy (OSTE+) thermosetting polymers with the fabrication of high quality microstructured parts. The process relies on the dual polymerization reactions of OSTE+ polymers, where the first curing step is used in OSTE+RIM for molding intermediately polymerized parts with well-defined shapes and reactive surface chemistries. In the facile back-end processing, the replicated parts are directly and covalently bonded and become fully polymerized using the second curing step, generating complete microfluidic devices. To achieve unprecedented rapid processing, high replication fidelity and low residual stress, OSTE+RIM uniquely incorporates temperature stabilization and shrinkage compensation of the OSTE+ polymerization during molding. Two different OSTE+ formulations were characterized and used for the OSTE+RIM fabrication of optically transparent, warp-free and natively hydrophilic microscopy glass slide format microfluidic demonstrator devices, featuring a storage modulus of 2.3 GPa and tolerating pressures of at least 4 bars.

  15. Covalent bonding of homochiral metal-organic framework in capillaries for stereoisomer separation by capillary electrochromatography.

    PubMed

    Ma, Jichao; Ye, Nengsheng; Li, Jian

    2016-02-01

    In this work, a [Cu(mal)(bpy)]⋅H2O (mal, L-(-)-malic acid; bpy, 4,4'-bipyridyl) homochiral metal-organic frameworks (MOFs) was synthesized and used for modifying the inner walls of capillary columns by utilizing amido bonds to form covalent links between the MOFs particles and capillary inner wall. The synthesized [Cu(mal)(bpy)]⋅H2 O and MOFs-modified capillary column were characterized by X-ray diffraction, thermogravimetric analysis, particle size distribution analysis, nitrogen absorption characterization, FTIR spectroscopy, SEM, and energy-dispersive X-ray spectroscopy (EDX). The MOFs-modified capillary column was used for the stereoisomer separation of some drugs. The LODs and LOQs of six analytes were 0.1 and 0.25 μg/mL, respectively. The linear range was 0.25-250 μg/mL for ephedrine, 0.25-250 μg/mL for pseudoephedrine, 0.25-180 μg/mL for D-penicillamine, 0.25-120 μg/mL for L-penicillamine, 0.25-180 μg/mL for D-phenylalanine, and 0.25-160 μg/mL for L-phenylalanine, all with R(2) > 0.999. Finally, the MOFs-modified capillary column was applied for the analysis of active ingredients in a real sample of the traditional Chinese medicine ephedra. PMID:26542186

  16. Mediatorless solar energy conversion by covalently bonded thylakoid monolayer on the glassy carbon electrode.

    PubMed

    Lee, Jinhwan; Im, Jaekyun; Kim, Sunghyun

    2016-04-01

    Light reactions of photosynthesis that take place in thylakoid membranes found in plants or cyanobacteria are among the most effective ways of utilizing light. Unlike most researches that use photosystem I or photosystem II as conversion units for converting light to electricity, we have developed a simple method in which the thylakoid monolayer was covalently immobilized on the glassy carbon electrode surface. The activity of isolated thylakoid membrane was confirmed by measuring evolving oxygen under illumination. Glassy carbon surfaces were first modified with partial or full monolayers of carboxyphenyl groups by reductive C-C coupling using 4-aminobenzoic acid and aniline and then thylakoid membrane was bioconjugated through the peptide bond between amine residues of thylakoid and carboxyl groups on the surface. Surface properties of modified surfaces were characterized by cyclic voltammetry, contact angle measurements, and electrochemical impedance spectroscopy. Photocurrent of 230 nA cm(-2) was observed when the thylakoid monolayer was formed on the mixed monolayer of 4-carboxylpheny and benzene at applied potential of 0.4V vs. Ag/AgCl. A small photocurrent resulted when the 4-carboxyphenyl full monolayer was used. This work shows the possibility of solar energy conversion by directly employing the whole thylakoid membrane through simple surface modification. PMID:26625272

  17. Schiff-base-functionalized mesoporous silica SBA-15: Covalently bonded assembly of blue nanophosphors

    NASA Astrophysics Data System (ADS)

    Li, Ying; Yan, Bing

    2009-05-01

    Two kinds of Schiff-base-functionalized organic-inorganic mesoporous luminescent hybrid materials have been obtained by co-condensation of tetraethyl orthosilicate and the organosilane in the presence of Pluronic P123 surfactant as a template. N, N'-Bis(salicylidene)-1,3-propanediamine (BSPA) and N, N', N″-tris(salicylidene)-(2-aminoethyl) amine (TSAEA), possessing two different representative structures, were firstly prepared and then functionalized with trialkoxylsilyl groups through the hydrogen transfer reactions between the active hydroxyl groups of the Schiff-base compounds and the internal ester group of isocyanate in 3-(triethoxysilyl)-propyl isocyanate (TESPIC). Schiff-base grafted to the coupling agent 3-(triethoxysilyl)-propyl isocyanate (TESPIC) was used as the precursor for the preparation of mesoporous materials. The luminescence properties of these resulting materials were characterized in detail, and the results reveal that they all have high surface area, uniformity in the mesostructure. The resulting materials (BSPA-SBA-15 and TSAEA-SBA-15) exhibit regular uniform microstructures and no phase separation happened because the organic and the inorganic compounds were covalently linked through Si-O bonds via a self-assembly process. Furthermore, these two materials have the similar luminescence range in the blue range.

  18. Structure, stability and electrochromic properties of polyaniline film covalently bonded to indium tin oxide substrate

    NASA Astrophysics Data System (ADS)

    Zhang, Wenzhi; Ju, Wenxing; Wu, Xinming; Wang, Yan; Wang, Qiguan; Zhou, Hongwei; Wang, Sumin; Hu, Chenglong

    2016-03-01

    Indium tin oxide (ITO) substrate was modified with 4-aminobenzylphosphonic acid (ABPA), and then the polyaniline (PANI) film covalently bonded to ITO substrate was prepared by the chemical oxidation polymerization. X-ray photoelectron spectroscopy (XPS), attenuated total reflection infrared (ATR-IR) spectroscopy, and atomic force microscopy (AFM) measurements demonstrated that chemical binding was formed between PANI and ABPA-modified ITO surface, and the maximum thickness of PANI layer is about 30 nm. The adhesive strength of PANI film on ITO substrate was tested by sonication. It was found that the film formed on the modified ITO exhibited a much better stability than that on bare one. Cyclic voltammetry (CV) and UV-vis spectroscopy measurements indicated that the oxidative potentials of PANI film on ABPA-modified ITO substrate were decreased and the film exhibited high electrochemical activities. Moreover, the optical contrast increased from 0.58 for PANI film (without ultrasound) to 1.06 for PANI film (after ultrasound for 60 min), which had an over 83% enhancement. The coloration time was 20.8 s, while the bleaching time was 19.5 s. The increase of electrochromic switching time was due to the lower ion diffusion coefficient of the large cation of (C4H9)4N+ under the positive and negative potentials as comparison with the small Li+ ion.

  19. The magnetic ground state and relationship to Kitaev physics in α-RuCl3

    NASA Astrophysics Data System (ADS)

    Banerjee, Arnab

    The 2D Kitaev candidate alpha-RuCl3 consists of stacked honeycomb layers weakly coupled by Van der Waals interactions. Here we report the measurements of bulk properties and neutron diffraction in both powder and single crystal samples. Our results show that the full three dimensional magnetic ground state is highly pliable with at least two dominant phases corresponding to two different out-of-plane magnetic orders. They have different Neel temperatures dependent on the stacking of the 2D layers, such as a broad magnetic transition at TN = 14 K as observed in phase-pure powder samples, or a sharp magnetic transition at a lower TN = 7 K as observed in homogeneous single crystals with no evidence for stacking faults. The magnetic refinements of the neutron scattering data will be discussed, which in all cases shows the in-plane magnetic ground state is the zigzag phase common in Kitaev related materials including the honeycomb lattice Iridates. Inelastic neutron scattering in all cases shows that this material consistently exhibit strong two-dimensional magnetic fluctuations leading to a break-down of the classical spin-wave picture. Work performed at ORNL is supported by U.S. Dept. of Energy, Office of Basic Energy Sciences and Office of User Facilities Division.

  20. Low-temperature crystal and magnetic structure of α -RuCl3

    NASA Astrophysics Data System (ADS)

    Cao, H. B.; Banerjee, A.; Yan, J.-Q.; Bridges, C. A.; Lumsden, M. D.; Mandrus, D. G.; Tennant, D. A.; Chakoumakos, B. C.; Nagler, S. E.

    2016-04-01

    Single crystals of the Kitaev spin-liquid candidate α -RuCl3 have been studied to determine the low-temperature bulk properties, the structure, and the magnetic ground state. Refinements of x-ray diffraction data show that the low-temperature crystal structure is described by space group C 2 /m with a nearly perfect honeycomb lattice exhibiting less than 0.2% in-plane distortion. The as-grown single crystals exhibit only one sharp magnetic transition at TN=7 K. The magnetic order below this temperature exhibits a propagation vector of k =(0 ,1 ,1 /3 ) , which coincides with a three-layer stacking of the C 2 /m unit cells. Magnetic transitions at higher temperatures up to 14 K can be introduced by deformations of the crystal that result in regions in the crystal with a two-layer stacking sequence. The best-fit symmetry-allowed magnetic structure of the as-grown crystals shows that the spins lie in the a c plane, with a zigzag configuration in each honeycomb layer. The three-layer repeat out-of-plane structure can be refined as a 120∘ spiral order or a collinear structure with a spin direction of 35∘ away from the a axis. The collinear spin configuration yields a slightly better fit and also is physically preferred. The average ordered moment in either structure is less than 0.45(5) μB per Ru3 + ion.

  1. FROM THE CURRENT LITERATURE: Radiation-induced states in crystals with ionic-covalent bonds

    NASA Astrophysics Data System (ADS)

    Kolontsova, E. V.

    1987-01-01

    Based on a review of data in the literature and on the results of a systematic investigation of the effect of various kinds of radiation on a number of crystals with ionic-covalent bonds (ICB crystals), the author describes mechanisms and regularities associated with the creation of radiation-induced structural states. A classification of these states is given, along with their characteristics and models of their behavior. The author proposes a criterion, tested on specially selected compounds, for high-temperature structural instability leading to the realization of a structural state, which in terms of the symmetry and parameters of the unit cell is close to the high-temperature modification of the unirradiated crystal. As a basis for choosing this special class of compounds thermodynamic parameters are adopted which determine the character of their thermal phase transitions. It is shown that, apart from amorphization and decomposition of the original compound, this is the only possible overall change in the structure of ICB crystals which extends throughout their entire volume. The author concludes that for the majority of ICB crystals in which such changes in crystal structure are observed, a decisive role is played by isolated point defects caused by radiation. She also investigates the influence of impurities, growth conditions and conditions of irradiation on the radiation hardness of a structure. In conclusion, she points out factors which determine the structural states of an irradiated ICB crystal, and analyzes the causes of discrepancies in the experimental data of various authors regarding the eifect of radiation on the structure of the same material.

  2. Enhancing Peptide Ligand Binding to Vascular Endothelial Growth Factor by Covalent Bond Formation

    PubMed Central

    Marquez, Bernadette V.; Beck, Heather E.; Aweda, Tolulope A.; Phinney, Brett; Holsclaw, Cynthia; Jewell, William; Tran, Diana; Day, Jeffrey J.; Peiris, Malalage N.; Nwosu, Charles; Lebrilla, Carlito; Meares, Claude F.

    2012-01-01

    Formation of a stable covalent bond between a synthetic probe molecule and a specific site on a target protein has many potential applications in biomedical science. For example, the properties of probes used as receptor-imaging ligands may be improved by increasing their residence time on the targeted receptor. Among the more interesting cases are peptide ligands, the strongest of which typically bind to receptors with micromolar dissociation constants, and which may depend on processes other than simple binding to provide images. The side chains of cysteine, histidine, or lysine are attractive for chemical attachment to improve binding to a receptor protein, and a system based on acryloyl probes attaching to engineered cysteine provides excellent positron emission tomographic images in animal models (Wei et al. (2008) J. Nucl. Med. 49, 1828-1835). In nature, lysine is a more common but less reactive residue than cysteine, making it an interesting challenge to modify. To seek practically useful cross-linking yields with naturally occurring lysine side chains, we have explored not only acryloyl but also other reactive linkers with different chemical properties. We employed a peptide-VEGF model system to discover that a 19mer peptide ligand, which carried a lysine-tagged dinitrofluorobenzene group, became attached stably and with good yield to a unique lysine residue on human vascular endothelial growth factor (VEGF), even in the presence of 70% fetal bovine serum. The same peptide carrying acryloyl and related Michael acceptors gave low yields of attachment to VEGF, as did the chloroacetyl peptide. PMID:22537066

  3. On-Surface Synthesis of Two-Dimensional Covalent Organic Structures versus Halogen-Bonded Self-Assembly: Competing Formation of Organic Nanoarchitectures.

    PubMed

    Peyrot, David; Silly, Fabien

    2016-05-24

    The competition between the on-surface synthesis of covalent nanoarchitectures and the self-assembly of star-shaped 1,3,5-Tris(4-iodophenyl)benzene molecules on Au(111) in vacuum is investigated using scanning tunneling microscopy above room temperature. The molecules form covalent polygonal nanoachitectures at the gold surface step edges and at the elbows of the gold reconstruction at low coverage. With coverage increasing two-dimensional halogen-bonded structures appear and grow on the surface terraces. Two different halogen-bonded nanoarchitectures are coexisting on the surface and hybrid covalent-halogen bonded structures are locally observed. At high coverage covalent nanoarchitectures are squeezed at the domain boundary of the halogen-bonded structures. The competitive growth between the covalent and halogen-bonded nanoarchitectures leads to formation of a two-layer film above one monolayer deposition. For this coverage, the covalent nanoarchitectures are propelled on top of the halogen-bonded first layer. These observations open up new opportunities for decoupling covalent nanoarchitectures from catalytically active and metal surfaces in vacuum. PMID:27158901

  4. A Macroscopic Reaction: Direct Covalent Bond Formation between Materials Using a Suzuki-Miyaura Cross-Coupling Reaction

    NASA Astrophysics Data System (ADS)

    Sekine, Tomoko; Kakuta, Takahiro; Nakamura, Takashi; Kobayashi, Yuichiro; Takashima, Yoshinori; Harada, Akira

    2014-09-01

    Cross-coupling reactions are important to form C-C covalent bonds using metal catalysts. Although many different cross-coupling reactions have been developed and applied to synthesize complex molecules or polymers (macromolecules), if cross-coupling reactions are realized in the macroscopic real world, the scope of materials should be dramatically broadened. Here, Suzuki-Miyaura coupling reactions are realized between macroscopic objects. When acrylamide gel modified with an iodophenyl group (I-gel) reacts with a gel possessing a phenylboronic group (PB-gel) using a palladium catalyst, the gels bond to form a single object. This concept can also be adapted for bonding between soft and hard materials. I-gel or PB-gel selectively bonds to the glass substrates whose surfaces are modified with an electrophile or nucleophile, respectively.

  5. A Macroscopic Reaction: Direct Covalent Bond Formation between Materials Using a Suzuki-Miyaura Cross-Coupling Reaction

    PubMed Central

    Sekine, Tomoko; Kakuta, Takahiro; Nakamura, Takashi; Kobayashi, Yuichiro; Takashima, Yoshinori; Harada, Akira

    2014-01-01

    Cross-coupling reactions are important to form C–C covalent bonds using metal catalysts. Although many different cross-coupling reactions have been developed and applied to synthesize complex molecules or polymers (macromolecules), if cross-coupling reactions are realized in the macroscopic real world, the scope of materials should be dramatically broadened. Here, Suzuki-Miyaura coupling reactions are realized between macroscopic objects. When acrylamide gel modified with an iodophenyl group (I-gel) reacts with a gel possessing a phenylboronic group (PB-gel) using a palladium catalyst, the gels bond to form a single object. This concept can also be adapted for bonding between soft and hard materials. I-gel or PB-gel selectively bonds to the glass substrates whose surfaces are modified with an electrophile or nucleophile, respectively. PMID:25231557

  6. Development and Application of a Diagnostic Instrument to Evaluate Grade-11 and -12 Students' Concepts of Covalent Bonding and Structure Following a Course of Instruction.

    ERIC Educational Resources Information Center

    Peterson, Raymond F.; And Others

    1989-01-01

    Outlines a procedure used to develop a written diagnostic instrument to identify misconceptions and misunderstandings of the chemistry topic. Reports the characteristic data for the instrument, and student understanding of covalent bonding and structure. (Author/YP)

  7. Design of polystyrene latex particles covered with polyoxometalate clusters via multiple covalent bonding.

    PubMed

    Chen, Xinyue; Li, Hui; Yin, Panchao; Liu, Tianbo

    2015-04-11

    Polyoxometalates (POMs) covalently functionalized with methyl methacrylate groups were applied as surfactants in the emulsion polymerization reaction of styrene. Due to the copolymerization of the methyl methacrylate groups and the styrene monomers, the polyoxometalate clusters are covalently grafted onto the surface of polystyrene latex nanoparticles. Such latex particles are fully covered with catalytic POM clusters and might serve as quasi-homogeneous catalysts. PMID:25743436

  8. Design of polystyrene latex particles covered with polyoxometalate clusters via multiple covalent bonding

    SciTech Connect

    Chen, Xinyue; Li, Hui; Yin, Panchao; Liu, Tianbo

    2015-02-27

    In this study, polyoxometalates (POMs) covalently functionalized with methyl methacrylate groups were applied as surfactants in the emulsion polymerization reaction of styrene. Due to the copolymerization of the methyl methacrylate groups and the styrene monomers, the polyoxometalate clusters are covalently grafted onto the surface of polystyrene latex nanoparticles. Finally, such latex particles are fully covered with catalytic POM clusters and might serve as quasi-homogeneous catalysts.

  9. Low-temperature crystal and magnetic structure of α – RuCl3

    DOE PAGESBeta

    Cao, Huibo B.; Yan, Jiaqiang; Bridges, Craig A.; Lumsden, Mark D.; Mandrus, D. G.; Chakoumakos, Bryan C.; Nagler, Stephen E.; Banerjee, A.; Tennant, D. A.

    2016-04-19

    Here, single crystals of the Kitaev spin-liquid candidate α – RuCl3 have been studied to determine the low-temperature bulk properties, the structure, and the magnetic ground state. Refinements of x-ray diffraction data show that the low-temperature crystal structure is described by space group C2/m with a nearly perfect honeycomb lattice exhibiting less than 0.2% in-plane distortion. The as-grown single crystals exhibit only one sharp magnetic transition at TN = 7 K. The magnetic order below this temperature exhibits a propagation vector of k=(0,1,1/3), which coincides with a three-layer stacking of the C2/m unit cells. Magnetic transitions at higher temperatures upmore » to 14 K can be introduced by deformations of the crystal that result in regions in the crystal with a two-layer stacking sequence. The best-fit symmetry-allowed magnetic structure of the as-grown crystals shows that the spins lie in the ac plane, with a zigzag configuration in each honeycomb layer. The three-layer repeat out-of-plane structure can be refined as a 120° spiral order or a collinear structure with a spin direction of 35° away from the a axis. The collinear spin configuration yields a slightly better fit and also is physically preferred. The average ordered moment in either structure is less than 0.45(5) μB per Ru3+ ion.« less

  10. Chlorophyll a Covalently Bonded to Organo-Modified Translucent Silica Xerogels: Optimizing Fluorescence and Maximum Loading.

    PubMed

    García-Sánchez, M A; Serratos, I N; Sosa, R; Tapia-Esquivel, T; González-García, F; Rojas-González, F; Tello-Solís, S R; Palacios-Enriquez, A Y; Esparza Schulz, J M; Arrieta, A

    2016-01-01

    Chlorophyll is a pyrrolic pigment with important optical properties, which is the reason it has been studied for many years. Recently, interest has been rising with respect to this molecule because of its outstanding physicochemical properties, particularly applicable to the design and development of luminescent materials, hybrid sensor systems, and photodynamic therapy devices for the treatment of cancer cells and bacteria. More recently, our research group has been finding evidence for the possibility of preserving these important properties of substrates containing chlorophyll covalently incorporated within solid pore matrices, such as SiO₂, TiO₂ or ZrO₂ synthesized through the sol-gel process. In this work, we study the optical properties of silica xerogels organo-modified on their surface with allyl and phenyl groups and containing different concentrations of chlorophyll bonded to the pore walls, in order to optimize the fluorescence that these macrocyclic species displays in solution. The intention of this investigation was to determine the maximum chlorophyll a concentration at which this molecule can be trapped inside the pores of a given xerogel and to ascertain if this pigment remains trapped as a monomer, a dimer, or aggregate. Allyl and phenyl groups were deposited on the surface of xerogels in view of their important effects on the stability of the molecule, as well as over the fluorescence emission of chlorophyll; however, these organic groups allow the trapping of either chlorophyll a monomers or dimers. The determination of the above parameters allows finding the most adequate systems for subsequent in vitro or in vivo studies. The characterization of the obtained xerogels was performed through spectroscopic absorption, emission and excitation spectra. These hybrid systems can be employed as mimics of natural systems; the entrapment of chlorophyll inside pore matrices indicates that it is possible to exploit some of the most physicochemical

  11. Characterization of irreversible kinase inhibitors by directly detecting covalent bond formation: a tool for dissecting kinase drug resistance.

    PubMed

    Klüter, Sabine; Simard, Jeffrey R; Rode, Haridas B; Grütter, Christian; Pawar, Vijaykumar; Raaijmakers, Hans C A; Barf, Tjeerd A; Rabiller, Matthias; van Otterlo, Willem A L; Rauh, Daniel

    2010-12-10

    Targeting protein kinases in cancer therapy with irreversible small-molecule inhibitors is moving to the forefront of kinase-inhibitor research and is thought to be an effective means of overcoming mutation-associated drug resistance in epidermal growth factor receptor kinase (EGFR). We generated a detection technique that allows direct measurements of covalent bond formation without relying on kinase activity, thereby allowing the straightforward investigation of the influence of steric clashes on covalent inhibitors in different resistant kinase mutants. The obtained results are discussed together with structural biology and biochemical studies of catalytic activity in both wild-type and gatekeeper mutated kinase variants to draw conclusions about the impact of steric hindrance and increased catalytic activity in drug-resistant kinase variants. PMID:21080395

  12. Porous solids arising from synergistic and competing modes of assembly: combining coordination chemistry and covalent bond formation.

    PubMed

    Dutta, Ananya; Koh, Kyoungmoo; Wong-Foy, Antek G; Matzger, Adam J

    2015-03-23

    Design and synthesis of porous solids employing both reversible coordination chemistry and reversible covalent bond formation is described. The combination of two different linkage modes in a single material presents a link between two distinct classes of porous materials as exemplified by metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). This strategy, in addition to being a compelling material-discovery method, also offers a platform for developing a fundamental understanding of the factors influencing the competing modes of assembly. We also demonstrate that even temporary formation of reversible connections between components may be leveraged to make new phases thus offering design routes to polymorphic frameworks. Moreover, this approach has the striking potential of providing a rich landscape of structurally complex materials from commercially available or readily accessible feedstocks. PMID:25678276

  13. Intriguing structures and magic sizes of heavy noble metal nanoclusters around size 55 governed by relativistic effect and covalent bonding.

    PubMed

    Zhao, X J; Xue, X L; Guo, Z X; Jia, Yu; Li, S F; Zhang, Zhenyu; Gao, Y F

    2015-11-01

    Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. By means of first-principles calculations within density functional theory, we find that heavy noble metal PtN nanoclusters around the size N = 55 begin to prefer an open configuration, rather than previously reported close-packed icosahedron or core-shell structures. Particularly, for PtN, the widely supposed icosahedronal magic cluster is changed to a three-atomic-layered structure with D6h symmetry, which can be well addressed by our recently established generalized Wulff construction principle (GWCP). However, the magic number of PtN clusters around 55 is shifted to a new odd number of 57. The high symmetric three-layered Pt57 motif is mainly stabilized by the enhanced covalent bonding contributed by both spin-orbital coupling effect and the open d orbital (5d(9)6s(1)) of Pt, which result in a delicate balance between the enhanced Pt-Pt covalent bonding of the interlayers and negligible d dangling bonds on the cluster edges. These findings about PtN clusters are also applicable to IrN clusters, but qualitatively different from their earlier neighboring element Os and their later neighboring element Au. The magic numbers for Os and Au are even, being 56 and 58, respectively. The findings of the new odd magic number 57 are the important supplementary of the recently established GWCP. PMID:26547165

  14. Intriguing structures and magic sizes of heavy noble metal nanoclusters around size 55 governed by relativistic effect and covalent bonding

    NASA Astrophysics Data System (ADS)

    Zhao, X. J.; Xue, X. L.; Guo, Z. X.; Jia, Yu; Li, S. F.; Zhang, Zhenyu; Gao, Y. F.

    2015-11-01

    Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. By means of first-principles calculations within density functional theory, we find that heavy noble metal PtN nanoclusters around the size N = 55 begin to prefer an open configuration, rather than previously reported close-packed icosahedron or core-shell structures. Particularly, for PtN, the widely supposed icosahedronal magic cluster is changed to a three-atomic-layered structure with D6h symmetry, which can be well addressed by our recently established generalized Wulff construction principle (GWCP). However, the magic number of PtN clusters around 55 is shifted to a new odd number of 57. The high symmetric three-layered Pt57 motif is mainly stabilized by the enhanced covalent bonding contributed by both spin-orbital coupling effect and the open d orbital (5d96s1) of Pt, which result in a delicate balance between the enhanced Pt-Pt covalent bonding of the interlayers and negligible d dangling bonds on the cluster edges. These findings about PtN clusters are also applicable to IrN clusters, but qualitatively different from their earlier neighboring element Os and their later neighboring element Au. The magic numbers for Os and Au are even, being 56 and 58, respectively. The findings of the new odd magic number 57 are the important supplementary of the recently established GWCP.

  15. Covalent functionalization of graphene by azobenzene with molecular hydrogen bonds for long-term solar thermal storage

    PubMed Central

    Feng, Yiyu; Liu, Hongpo; Luo, Wen; Liu, Enzuo; Zhao, Naiqin; Yoshino, Katsumi; Feng, Wei

    2013-01-01

    Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg−1 compared with RGO-ortho-AZO (149.6 kJ kg−1) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds. PMID:24247355

  16. Covalent functionalization of graphene by azobenzene with molecular hydrogen bonds for long-term solar thermal storage

    NASA Astrophysics Data System (ADS)

    Feng, Yiyu; Liu, Hongpo; Luo, Wen; Liu, Enzuo; Zhao, Naiqin; Yoshino, Katsumi; Feng, Wei

    2013-11-01

    Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg-1 compared with RGO-ortho-AZO (149.6 kJ kg-1) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds.

  17. Covalent functionalization of graphene by azobenzene with molecular hydrogen bonds for long-term solar thermal storage.

    PubMed

    Feng, Yiyu; Liu, Hongpo; Luo, Wen; Liu, Enzuo; Zhao, Naiqin; Yoshino, Katsumi; Feng, Wei

    2013-01-01

    Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg(-1) compared with RGO-ortho-AZO (149.6 kJ kg(-1)) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds. PMID:24247355

  18. Bond-bending isomerism of Au2I3-: Competition between covalent bonding and aurophilicity

    SciTech Connect

    Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian; Lopez, Gary V.; Piazza, Zachary A.; Huang, Dao -Ling; Chen, Teng -Teng; Su, Jing; Yang, Ping; Chen, Xin; Wang, Lai -Sheng; Li, Jun

    2015-10-13

    We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au2I3 cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature, only the obtuse isomer is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au2I3 reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.

  19. A stochastic description on the traction-separation law of an interface with non-covalent bonding

    NASA Astrophysics Data System (ADS)

    Wei, Yujie

    2014-10-01

    We formulate a stochastic description about the mechanical response of an interface composed of non-covalent bonds. In such interfaces, the evolution of bonding probability in response to deformation plays the central role in determining their traction-separation behavior. The model connects atomistic and molecular level bonding properties to meso-scale traction-separation relationship in an interface. In response to quasi-static loading, the traction-separation of a stochastic interface is the resultant of varying bonding probability as a function of separation, and the bonding probability follows the Boltzmann distribution. The quasi-static stochastic interface model is applied to understand the critical force while detaching a sphere from an infinite half space. We further show the kinetics of interfacial debonding in the context of the Bell model (1978) and two of its derivatives - the Evans-Richie model (1997) and the Freund model (2009). While subjected to constant force, an interface creeps and its separation-time curve shows typical characteristics seen during the creep of crystalline materials at high temperature. When we exert constant separation rate to an interface, interfacial traction shows strong rate-sensitivity with higher traction at faster separation rate. The model presented here may supply a guidance to bring the stochastic nature of interfacial debonding into theories on cracking initiation and growth during fatigue fracture.

  20. Locking covalent organic frameworks with hydrogen bonds: general and remarkable effects on crystalline structure, physical properties, and photochemical activity.

    PubMed

    Chen, Xiong; Addicoat, Matthew; Jin, Enquan; Zhai, Lipeng; Xu, Hong; Huang, Ning; Guo, Zhaoqi; Liu, Lili; Irle, Stephan; Jiang, Donglin

    2015-03-11

    A series of two-dimensional covalent organic frameworks (2D COFs) locked with intralayer hydrogen-bonding (H-bonding) interactions were synthesized. The H-bonding interaction sites were located on the edge units of the imine-linked tetragonal porphyrin COFs, and the contents of the H-bonding sites in the COFs were synthetically tuned using a three-component condensation system. The intralayer H-bonding interactions suppress the torsion of the edge units and lock the tetragonal sheets in a planar conformation. This planarization enhances the interlayer interactions and triggers extended π-cloud delocalization over the 2D sheets. Upon AA stacking, the resulting COFs with layered 2D sheets amplify these effects and strongly affect the physical properties of the material, including improving their crystallinity, enhancing their porosity, increasing their light-harvesting capability, reducing their band gap, and enhancing their photocatalytic activity toward the generation of singlet oxygen. These remarkable effects on the structure and properties of the material were observed for both freebase and metalloporphyin COFs. These results imply that exploration of supramolecular ensembles would open a new approach to the structural and functional design of COFs. PMID:25706112

  1. Non-covalent bonded 2D-3D supramolecular architectures based on 4-dimethylaminopyridine and organic acids

    NASA Astrophysics Data System (ADS)

    Zhang, Huan; Jin, Shouwen; Wen, Xianhong; Liu, Bin; Fang, Yang; Zhang, Yani; Wang, Daqi

    2015-07-01

    Studies concentrating on non-covalent weak interactions between the organic base of 4-dimethylaminopyridine, and acidic derivatives have led to an increased understanding of the role 4-dimethylaminopyridine has in binding with the organic acid derivatives. Here anhydrous and hydrous multicomponent organic acid-base adducts of 4-dimethylaminopyridine have been prepared with organic acids such as 1,3-benzodioxole-5-carboxylic acid, p-aminobenzoic acid, 2,4-dihydroxybenzoic acid, 3,5-dihydroxybenzoic acid, 5-chlorosalicylic acid, 5-bromosalicylic acid, 5-nitrosalicylic acid, and 5-sulfosalicylic acid. The 4-dimethylaminopyridine is only monoprotonated. All compounds are organic salts with the 1:1 ratio of the cation and the anion. For the 5-sulfosalicylic acid only one H is ionized to exhibit the valence number of -1. The eight crystalline complexes were characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. These structures adopted the hetero supramolecular synthons. Analysis of the crystal packing of 1-8 suggests that there are Nsbnd H⋯O, Osbnd H⋯O, and Osbnd H⋯S hydrogen bonds (charge assisted or neutral) between the organic acid and the 4-dimethylaminopyridine moieties in the studied compounds. Except the classical hydrogen bonding interactions, the secondary propagating interactions also play important roles in structure extension. For the synergistic effect of the various non-covalent interactions, the complexes displayed 2D-3D framework structures.

  2. Immobilization of collagen peptide on dialdehyde bacterial cellulose nanofibers via covalent bonds for tissue engineering and regeneration

    PubMed Central

    Wen, Xiaoxiao; Zheng, Yudong; Wu, Jian; Wang, Lu-Ning; Yuan, Zhenya; Peng, Jiang; Meng, Haoye

    2015-01-01

    Bacterial cellulose (BC) is an alternative nanostructured biomaterial to be utilized for a wide range of biomedical applications. Because of its low bioactivity, which restricted its practical application, collagen and collagen hydrolysate were usually composited into BC. It is necessary to develop a new method to generate covalent bonds between collagen and cellulose to improve the immobilization of collagen on BC. This study describes a facile dialdehyde BC/collagen peptide nanocomposite. BC was oxidized into dialdehyde bacterial cellulose (DBC) by regioselective oxidation, and then composited with collagen peptide (Col-p) via covalent bonds to form Schiff’s base type compounds, which was demonstrated by the results of microstructures, contact angle, Col-p content, and peptide-binding ratio. The peptide-binding ratio was further affected by the degree of oxidation, pH value, and zeta potential. In vitro desorption measurement of Col-p suggested a controlled release mechanism of the nanocomposite. Cell tests indicated that the prepared DBC/Col-p composite was bioactive and suitable for cell adhesion and attachment. This work demonstrates that the DBC/Col-p composite is a promising material for tissue engineering and regeneration. PMID:26229466

  3. Spin-orbit excitations and electronic structure of the putative Kitaev magnet α -RuCl3

    NASA Astrophysics Data System (ADS)

    Sandilands, Luke J.; Tian, Yao; Reijnders, Anjan A.; Kim, Heung-Sik; Plumb, K. W.; Kim, Young-June; Kee, Hae-Young; Burch, Kenneth S.

    2016-02-01

    Mott insulators with strong spin-orbit coupling have been proposed to host unconventional magnetic states, including the Kitaev quantum spin liquid. The 4 d system α -RuCl3 has recently come into view as a candidate Kitaev system, with evidence for unusual spin excitations in magnetic scattering experiments. We apply a combination of optical spectroscopy and Raman scattering to study the electronic structure of this material. Our measurements reveal a series of orbital excitations involving localized total angular momentum states of the Ru ion, implying that strong spin-orbit coupling and electron-electron interactions coexist in this material. Analysis of these features allows us to estimate the spin-orbit coupling strength, as well as other parameters describing the local electronic structure, revealing a well-defined hierarchy of energy scales within the Ru d states. By comparing our experimental results with density functional theory calculations, we also clarify the overall features of the optical response. Our results demonstrate that α -RuCl3 is an ideal material system to study spin-orbit coupled magnetism on the honeycomb lattice.

  4. Intriguing structures and magic sizes of heavy noble metal nanoclusters around size 55 governed by relativistic effect and covalent bonding

    SciTech Connect

    Zhao, X. J.; Xue, X. L.; Jia, Yu; Guo, Z. X.; Li, S. F.; Zhang, Zhenyu; Gao, Y. F.

    2015-11-07

    Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. By means of first-principles calculations within density functional theory, we find that heavy noble metal Pt{sub N} nanoclusters around the size N = 55 begin to prefer an open configuration, rather than previously reported close-packed icosahedron or core-shell structures. Particularly, for Pt{sub N}, the widely supposed icosahedronal magic cluster is changed to a three-atomic-layered structure with D{sub 6h} symmetry, which can be well addressed by our recently established generalized Wulff construction principle (GWCP). However, the magic number of Pt{sub N} clusters around 55 is shifted to a new odd number of 57. The high symmetric three-layered Pt{sub 57} motif is mainly stabilized by the enhanced covalent bonding contributed by both spin-orbital coupling effect and the open d orbital (5d{sup 9}6s{sup 1}) of Pt, which result in a delicate balance between the enhanced Pt–Pt covalent bonding of the interlayers and negligible d dangling bonds on the cluster edges. These findings about Pt{sub N} clusters are also applicable to Ir{sub N} clusters, but qualitatively different from their earlier neighboring element Os and their later neighboring element Au. The magic numbers for Os and Au are even, being 56 and 58, respectively. The findings of the new odd magic number 57 are the important supplementary of the recently established GWCP.

  5. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler.

    PubMed

    Shaffer, Christopher J; Andrikopoulos, Prokopis C; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

    2016-04-01

    Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific (13)C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)(+) ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H](+) ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase. Graphical Abstract ᅟ. PMID:26817657

  6. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

    NASA Astrophysics Data System (ADS)

    Shaffer, Christopher J.; Andrikopoulos, Prokopis C.; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

    2016-04-01

    Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific 13C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)+ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]+ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase.

  7. Strain shielding from mechanically activated covalent bond formation during nanoindentation of graphene delays the onset of failure.

    PubMed

    Kumar, Sandeep; Parks, David M

    2015-03-11

    Mechanical failure of an ideal crystal is dictated either by an elastic instability or a soft-mode instability. Previous interpretations of nanoindentation experiments on suspended graphene sheets,1,2 however, indicate an anomaly: the inferred strain in the graphene sheet directly beneath the diamond indenter at the measured failure load is anomalously large compared to the fracture strains predicted by both soft-mode and acoustic analyses. Through multiscale modeling combining the results of continuum, atomistic, and quantum calculations, and analysis of experiments, we identify a strain-shielding effect initiated by mechanochemical interactions at the graphene-indenter interface as the operative mechanism responsible for this anomaly. Transmission electron micrographs and a molecular model of the diamond indenter's tip suggest that the tip surface contains facets comprising crystallographic {111} and {100} planes. Ab initio and molecular dynamics (MD) simulations confirm that a covalent bond (weld) formation between graphene and the crystallographic {111} and {100} facets on the indenter's surface can be induced by compressive contact stresses of the order achieved in nanoindentation tests. Finite element analysis (FEA) and MD simulations of nanoindentation reveal that the shear stiction provided by the induced covalent bonding restricts relative slip of the graphene sheet at its contact with the indenter, thus initiating a local strain-shielding effect. As a result, subsequent to stress-induced bonding at the graphene-indenter interface, the spatial variation of continuing incremental strain is substantially redistributed, locally shielding the region directly beneath the indenter by limiting the buildup of strain while imparting deformation to the surrounding regions. The extent of strain shielding is governed by the strength of the shear stiction, which depends upon the level of hydrogen saturation at the indenter's surface. We show that at intermediate levels

  8. Intriguing structures and magic sizes of heavy noble metal nanoclusters around size 55 governed by relativistic effect and covalent bonding

    SciTech Connect

    Zhao, X. J.; Xue, X. L.; Guo, Z. X.; Jia, Yu; Li, S. F.; Zhang, Zhenyu; Gao, Y. F.

    2015-11-02

    Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. By means of first-principles calculations within density functional theory, we find that heavy noble metal PtN nanoclusters around the size N = 55 begin to prefer an open configuration, rather than previously reported close-packed icosahedron or core-shell structures. Particularly, for PtN, the widely supposed icosahedronal magic cluster is changed to a three-atomic-layered structure with D6h symmetry, which can be well addressed by our recently established generalized Wulff construction principle (GWCP). But, the magic number of PtN clusters around 55 is shifted to a new odd number of 57. The high symmetric three-layered Pt-57 motif is mainly stabilized by the enhanced covalent bonding contributed by both spin-orbital coupling effect and the open d orbital (5d96s1) of Pt, which result in a delicate balance between the enhanced Pt-Pt covalent bonding of the interlayers and negligible d dangling bonds on the cluster edges. Our findings about PtN clusters are also applicable to IrN clusters, but qualitatively different from their earlier neighboring element Os and their later neighboring element Au. The magic numbers for Os and Au are even, being 56 and 58, respectively. Finally, the findings of the new odd magic number 57 are the important supplementary of the recently established GWCP.

  9. Intriguing structures and magic sizes of heavy noble metal nanoclusters around size 55 governed by relativistic effect and covalent bonding

    DOE PAGESBeta

    Zhao, X. J.; Xue, X. L.; Guo, Z. X.; Jia, Yu; Li, S. F.; Zhang, Zhenyu; Gao, Y. F.

    2015-11-02

    Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. By means of first-principles calculations within density functional theory, we find that heavy noble metal PtN nanoclusters around the size N = 55 begin to prefer an open configuration, rather than previously reported close-packed icosahedron or core-shell structures. Particularly, for PtN, the widely supposed icosahedronal magic cluster is changed to a three-atomic-layered structure with D6h symmetry, which can be well addressed by our recently established generalized Wulff construction principle (GWCP). But, the magic number of PtN clusters around 55 ismore » shifted to a new odd number of 57. The high symmetric three-layered Pt-57 motif is mainly stabilized by the enhanced covalent bonding contributed by both spin-orbital coupling effect and the open d orbital (5d96s1) of Pt, which result in a delicate balance between the enhanced Pt-Pt covalent bonding of the interlayers and negligible d dangling bonds on the cluster edges. Our findings about PtN clusters are also applicable to IrN clusters, but qualitatively different from their earlier neighboring element Os and their later neighboring element Au. The magic numbers for Os and Au are even, being 56 and 58, respectively. Finally, the findings of the new odd magic number 57 are the important supplementary of the recently established GWCP.« less

  10. Covalently bonded single-molecule junctions with stable and reversible photoswitched conductivity.

    PubMed

    Jia, Chuancheng; Migliore, Agostino; Xin, Na; Huang, Shaoyun; Wang, Jinying; Yang, Qi; Wang, Shuopei; Chen, Hongliang; Wang, Duoming; Feng, Boyong; Liu, Zhirong; Zhang, Guangyu; Qu, Da-Hui; Tian, He; Ratner, Mark A; Xu, H Q; Nitzan, Abraham; Guo, Xuefeng

    2016-06-17

    Through molecular engineering, single diarylethenes were covalently sandwiched between graphene electrodes to form stable molecular conduction junctions. Our experimental and theoretical studies of these junctions consistently show and interpret reversible conductance photoswitching at room temperature and stochastic switching between different conductive states at low temperature at a single-molecule level. We demonstrate a fully reversible, two-mode, single-molecule electrical switch with unprecedented levels of accuracy (on/off ratio of ~100), stability (over a year), and reproducibility (46 devices with more than 100 cycles for photoswitching and ~10(5) to 10(6) cycles for stochastic switching). PMID:27313042

  11. Hydrogen-bond acidic functionalized carbon nanotubes (CNTs) with covalently-bound hexafluoroisopropanol groups

    SciTech Connect

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

    Fluorinated hydrogen-bond acidic groups are directly attached to the backbone of single walled carbon nanotubes (SWCNTs) without the introduction of intermediate electron donating surface groups. Hexafluoroalcohol functional groups are exceptionally strong hydrogen bond acids, and are added to the nanotube surface using the aryl diazonium approach to create hydrogen-bond acidic carbon nanotube (CNT) surfaces. These groups can promote strong hydrogen-bonding interactions with matrix materials in composites or with molecular species to be concentrated and sensed. In the latter case, this newly developed material is expected to find useful application in chemical sensors and in CNT-based preconcentrator devices for the detection of pesticides, chemical warfare agents and explosives.

  12. Covalently bonded three-dimensional carbon nanotube solids via boron induced nanojunctions

    SciTech Connect

    Sumpter, Bobby G; Meunier, Vincent; Terrones Maldonado, Humberto; Terrones Maldonado, Mauricio; Ajayan, Pullikel M; Hashim, Daniel; Romo Herrera, Jose M; Cullen, David; Munoz-Sandoval, Emilio; Smith, David J; Vajtai, Robert; Roy, Ajit K; Ganguli, Sabyasachi; Kelkhoff, Doug; Suttle, Joesph; Lezzi, Peter; Hahm, Gwan; Narayanan, Narayanan

    2012-01-01

    The establishment of covalent junctions between carbon nanotubes (CNTs) and the modification of their straight tubular morphology are two strategies needed to successfully synthesize nanotube-based three-dimensional (3D) frameworks exhibiting superior material properties. Engineering such 3D structures in scalable synthetic processes still remains a challenge. This work pioneers the bulk synthesis of 3D macroscale nanotube elastic solids directly via a boron-doping strategy during chemical vapor deposition, which influences the formation of atomic-scale elbow junctions and nanotube covalent interconnections. Detailed elemental analysis revealed that the elbow junctions are preferred sites for excess boron atoms, indicating the role of boron and curvature in the junction formation mechanism, in agreement with our first principle theoretical calculations. Exploiting this material s ultra-light weight, super-hydrophobicity, high porosity, thermal stability, and mechanical flexibility, the strongly oleophilic sponge-like solids are demonstrated as unique reusable sorbent scaffolds able to efficiently remove oil from contaminated seawater even after repeated use.

  13. Covalently bonded three-dimensional carbon nanotube solids via boron induced nanojunctions

    PubMed Central

    Hashim, Daniel P.; Narayanan, Narayanan T.; Romo-Herrera, Jose M.; Cullen, David A.; Hahm, Myung Gwan; Lezzi, Peter; Suttle, Joseph R.; Kelkhoff, Doug; Muñoz-Sandoval, E.; Ganguli, Sabyasachi; Roy, Ajit K.; Smith, David J.; Vajtai, Robert; Sumpter, Bobby G.; Meunier, Vincent; Terrones, Humberto; Terrones, Mauricio; Ajayan, Pulickel M.

    2012-01-01

    The establishment of covalent junctions between carbon nanotubes (CNTs) and the modification of their straight tubular morphology are two strategies needed to successfully synthesize nanotube-based three-dimensional (3D) frameworks exhibiting superior material properties. Engineering such 3D structures in scalable synthetic processes still remains a challenge. This work pioneers the bulk synthesis of 3D macroscale nanotube elastic solids directly via a boron-doping strategy during chemical vapour deposition, which influences the formation of atomic-scale “elbow” junctions and nanotube covalent interconnections. Detailed elemental analysis revealed that the “elbow” junctions are preferred sites for excess boron atoms, indicating the role of boron and curvature in the junction formation mechanism, in agreement with our first principle theoretical calculations. Exploiting this material’s ultra-light weight, super-hydrophobicity, high porosity, thermal stability, and mechanical flexibility, the strongly oleophilic sponge-like solids are demonstrated as unique reusable sorbent scaffolds able to efficiently remove oil from contaminated seawater even after repeated use. PMID:22509463

  14. Synthesis, characterization, and near-infrared luminescent properties of the ternary thulium complex covalently bonded to mesoporous MCM-41

    SciTech Connect

    Feng Jing; Song Shuyan; Xing Yan; Zhang Hongjie Li Zhefeng; Sun Lining; Guo Xianmin; Fan Weiqiang

    2009-03-15

    The crystal structure of a ternary Tm(DBM){sub 3}phen complex (DBM=dibenzoylmethane; phen=1, 10-phenanthroline) and the synthesis of hybrid mesoporous material in which the complex covalently bonded to mesoporous MCM-41 are reported. Crystal data: Tm(DBM){sub 3}phen C{sub 59}H{sub 47}N{sub 2}O{sub 7}Tm, monoclinic, P21/c, a=19.3216(12) A, b=10.6691(7) A, c=23.0165(15) A, {alpha}=90 deg., {beta}=91.6330(10) deg., {gamma}=90 deg., V=4742.8(5) A{sup 3}, Z=4. The properties of the Tm(DBM){sub 3}phen complex and the corresponding hybrid mesoporous material [Tm(DBM){sub 3}phen-MCM-41] have been studied. The results reveal that the Tm(DBM){sub 3}phen complex is successfully covalently bonded to MCM-41. Both Tm(DBM){sub 3}phen complex and Tm(DBM){sub 3}phen-MCM-41 display typical near-infrared (NIR) luminescence upon excitation at the maximum absorption of the ligands, which contributes to the efficient energy transfer from the ligands to the Tm{sup 3+} ion, an antenna effect. The full width at half maximum (FWHM) centered at 1474 nm in the emission spectrum of Tm(DBM){sub 3}phen-MCM-41 is 110 nm, which is the potential candidate of broadening amplification band from C band (1530-1560 nm) to S{sup +} band (1450-1480 nm) in optical area. - Graphical abstract: The crystal structure of Tm(DBM){sub 3}phen complex (DBM=dibenzoylmethane; phen=1, 10-phenanthroline). The complex is successfully covalently bonded to MCM-41 (Tm(DBM){sub 3}phen-MCM-41). After ligand-mediated excitation, the emission spectrum of Tm(DBM){sub 3}phen-MCM-41 shows the bands 802 and 1474 nm. The FWHM of the 1474-nm band for Tm(DBM){sub 3}phen-MCM-41 is 110 nm, such a broad spectrum enables a wide gain bandwidth for optical amplification.

  15. Molecular and environmental factors governing non-covalent bonding interactions and conformations of phosphorous functionalized γ-cyclodextrin hydrate systems.

    PubMed

    Ivanova, Bojidarka; Spiteller, Michael

    2016-06-01

    Recent strategies in molecular drugs-design shift efforts to nanomedicine. Large supra-molecular inclusion systems are implemented as therapeutics. The sophistication of design is based on major advances of cyclodextrins (CDs) as host molecules. They are friendly towards biological environment. CDs have good (bio)compatibility as well. CDs can form host-guest macromolecular systems incorporating small molecules with suitable shapes due to non-covalent interactions. Innovative strategies yield to polymeric nano-particles; micelles; linear polymers and/or CDs-functionalized dendrimeric nanostructures; nanofibers as well as hydrogels. Attractive are phosphorous containing (bio)matrerials, having high selectivity toward biological active molecules. The non-covalent interactions in aquatic CD-systems contribute to stability of host-guest systems under physiological conditions, determining conformational preferences of host-CD macromolecule and guest small molecular template. In this paper we have reported complementation application of mass spectrometric (MS) and quantum chemical analysis of phosphorous chemically substituted γ-cyclodextrin hydrates γ-CDPO/nH2O (n ∊ [0-14]), studying neutral and polynegatively charged molecules as an effort to describe realistic a representative scale of physiological conditions. The binding affinity and molecular conformations are discussed. The 250 neutral and charged systems (γ-CDPOHm/nH2O, n ∊ [10][0,14], m ∊ [0,15], γ-CDPOH-8/nH2O.8Na(+), and γ-CDPOH-16/nH2O.16Na(+)) in four main domains of non-covalent hydrogen bonding interactions are studied. PMID:26944657

  16. How covalent heme to protein bonds influence the formation and reactivity of redox intermediates of a bacterial peroxidase.

    PubMed

    Auer, Markus; Nicolussi, Andrea; Schütz, Georg; Furtmüller, Paul G; Obinger, Christian

    2014-11-01

    The most striking feature of mammalian peroxidases, including myeloperoxidase and lactoperoxidase (LPO) is the existence of covalent bonds between the prosthetic group and the protein, which has a strong impact on their (electronic) structure and biophysical and chemical properties. Recently, a novel bacterial heme peroxidase with high structural and functional similarities to LPO was described. Being released from Escherichia coli, it contains mainly heme b, which can be autocatalytically modified and covalently bound to the protein by incubation with hydrogen peroxide. In the present study, we investigated the reactivity of these two forms in their ferric, compound I and compound II state in a multi-mixing stopped-flow study. Upon heme modification, the reactions between the ferric proteins with cyanide or H2O2 were accelerated. Moreover, apparent bimolecular rate constants of the reaction of compound I with iodide, thiocyanate, bromide, and tyrosine increased significantly and became similar to LPO. Kinetic data are discussed and compared with known structure-function relationships of the mammalian peroxidases LPO and myeloperoxidase. PMID:25246525

  17. How Covalent Heme to Protein Bonds Influence the Formation and Reactivity of Redox Intermediates of a Bacterial Peroxidase*

    PubMed Central

    Auer, Markus; Nicolussi, Andrea; Schütz, Georg; Furtmüller, Paul G.; Obinger, Christian

    2014-01-01

    The most striking feature of mammalian peroxidases, including myeloperoxidase and lactoperoxidase (LPO) is the existence of covalent bonds between the prosthetic group and the protein, which has a strong impact on their (electronic) structure and biophysical and chemical properties. Recently, a novel bacterial heme peroxidase with high structural and functional similarities to LPO was described. Being released from Escherichia coli, it contains mainly heme b, which can be autocatalytically modified and covalently bound to the protein by incubation with hydrogen peroxide. In the present study, we investigated the reactivity of these two forms in their ferric, compound I and compound II state in a multi-mixing stopped-flow study. Upon heme modification, the reactions between the ferric proteins with cyanide or H2O2 were accelerated. Moreover, apparent bimolecular rate constants of the reaction of compound I with iodide, thiocyanate, bromide, and tyrosine increased significantly and became similar to LPO. Kinetic data are discussed and compared with known structure-function relationships of the mammalian peroxidases LPO and myeloperoxidase. PMID:25246525

  18. Effect of covalently bonded polysiloxane multilayers on the electrochemical behavior of graphite electrode in lithium ion batteries

    NASA Astrophysics Data System (ADS)

    Pan, Qinmin; Jiang, Yinghua

    Polysiloxane multilayers were covalently bonded to the surface of natural graphite particles via diazonium chemistry and silylation reaction. The as-prepared graphite exhibited excellent discharge-charge behavior as negative electrode materials in lithium ion batteries. The improvement in the electrochemical performance of the graphite electrodes was attributed to the formation of a stable and flexible passive film on their surfaces. It was also revealed that the chemical compositions of the multilayers exerted influence on the electrochemical behavior of the graphite electrodes. The result of this study presents a new strategy to the formation of elastic and strong passive film on the graphite electrode via molecular design. Owing to the diversity of polysilxoane multilayers, this method also enables researchers to control the surface chemistries of carbonaceous materials with flexibility.

  19. Methods of making non-covalently bonded carbon-titania nanocomposite thin films and applications of the same

    DOEpatents

    Liang, Yu Teng; Vijayan, Baiju K.; Gray, Kimberly A.; Hersam, Mark C.

    2016-07-19

    In one aspect, a method of making non-covalently bonded carbon-titania nanocomposite thin films includes: forming a carbon-based ink; forming a titania (TiO.sub.2) solution; blade-coating a mechanical mixture of the carbon-based ink and the titania solution onto a substrate; and annealing the blade-coated substrate at a first temperature for a first period of time to obtain the carbon-based titania nanocomposite thin films. In certain embodiments, the carbon-based titania nanocomposite thin films may include solvent-exfoliated graphene titania (SEG-TiO.sub.2) nanocomposite thin films, or single walled carbon nanotube titania (SWCNT-TiO.sub.2) nanocomposite thin films.

  20. The interplay of covalency, hydrogen bonding, and dispersion leads to a long range chiral network: The example of 2-butanol

    NASA Astrophysics Data System (ADS)

    Liriano, Melissa L.; Carrasco, Javier; Lewis, Emily A.; Murphy, Colin J.; Lawton, Timothy J.; Marcinkowski, Matthew D.; Therrien, Andrew J.; Michaelides, Angelos; Sykes, E. Charles H.

    2016-03-01

    The assembly of complex structures in nature is driven by an interplay between several intermolecular interactions, from strong covalent bonds to weaker dispersion forces. Understanding and ultimately controlling the self-assembly of materials requires extensive study of how these forces drive local nanoscale interactions and how larger structures evolve. Surface-based self-assembly is particularly amenable to modeling and measuring these interactions in well-defined systems. This study focuses on 2-butanol, the simplest aliphatic chiral alcohol. 2-butanol has recently been shown to have interesting properties as a chiral modifier of surface chemistry; however, its mode of action is not fully understood and a microscopic understanding of the role non-covalent interactions play in its adsorption and assembly on surfaces is lacking. In order to probe its surface properties, we employed high-resolution scanning tunneling microscopy and density functional theory (DFT) simulations. We found a surprisingly rich degree of enantiospecific adsorption, association, chiral cluster growth and ultimately long range, highly ordered chiral templating. Firstly, the chiral molecules acquire a second chiral center when adsorbed to the surface via dative bonding of one of the oxygen atom lone pairs. This interaction is controlled via the molecule's intrinsic chiral center leading to monomers of like chirality, at both chiral centers, adsorbed on the surface. The monomers then associate into tetramers via a cyclical network of hydrogen bonds with an opposite chirality at the oxygen atom. The evolution of these square units is surprising given that the underlying surface has a hexagonal symmetry. Our DFT calculations, however, reveal that the tetramers are stable entities that are able to associate with each other by weaker van der Waals interactions and tessellate in an extended square network. This network of homochiral square pores grows to cover the whole Au(111) surface. Our data

  1. The interplay of covalency, hydrogen bonding, and dispersion leads to a long range chiral network: The example of 2-butanol.

    PubMed

    Liriano, Melissa L; Carrasco, Javier; Lewis, Emily A; Murphy, Colin J; Lawton, Timothy J; Marcinkowski, Matthew D; Therrien, Andrew J; Michaelides, Angelos; Sykes, E Charles H

    2016-03-01

    The assembly of complex structures in nature is driven by an interplay between several intermolecular interactions, from strong covalent bonds to weaker dispersion forces. Understanding and ultimately controlling the self-assembly of materials requires extensive study of how these forces drive local nanoscale interactions and how larger structures evolve. Surface-based self-assembly is particularly amenable to modeling and measuring these interactions in well-defined systems. This study focuses on 2-butanol, the simplest aliphatic chiral alcohol. 2-butanol has recently been shown to have interesting properties as a chiral modifier of surface chemistry; however, its mode of action is not fully understood and a microscopic understanding of the role non-covalent interactions play in its adsorption and assembly on surfaces is lacking. In order to probe its surface properties, we employed high-resolution scanning tunneling microscopy and density functional theory (DFT) simulations. We found a surprisingly rich degree of enantiospecific adsorption, association, chiral cluster growth and ultimately long range, highly ordered chiral templating. Firstly, the chiral molecules acquire a second chiral center when adsorbed to the surface via dative bonding of one of the oxygen atom lone pairs. This interaction is controlled via the molecule's intrinsic chiral center leading to monomers of like chirality, at both chiral centers, adsorbed on the surface. The monomers then associate into tetramers via a cyclical network of hydrogen bonds with an opposite chirality at the oxygen atom. The evolution of these square units is surprising given that the underlying surface has a hexagonal symmetry. Our DFT calculations, however, reveal that the tetramers are stable entities that are able to associate with each other by weaker van der Waals interactions and tessellate in an extended square network. This network of homochiral square pores grows to cover the whole Au(111) surface. Our data

  2. Covalent bonding effect on the mean excitation energy of H2 with the local plasma model

    NASA Technical Reports Server (NTRS)

    Kamaratos, E.

    1984-01-01

    Chemical bonding is taken into account explicitly in the determination of the mean excitation energy (I) for stopping power of H2 with the local plasma approximation by employing molecular electronic wave functions for H2 for the first time. This procedure leads to a new value for IH2 that is higher than all accepted experimental and theoretical values.

  3. Unconventional magnetism on a honeycomb lattice in α -RuCl3 studied by muon spin rotation

    NASA Astrophysics Data System (ADS)

    Lang, F.; Baker, P. J.; Haghighirad, A. A.; Li, Y.; Prabhakaran, D.; Valentí, R.; Blundell, S. J.

    2016-07-01

    Muon spin rotation measurements have been performed on a powder sample of α -RuCl3 , a layered material in which Ru ions are arranged on a honeycomb lattice and which previously has been proposed to be close to a quantum spin liquid ground state. Our data reveal two distinct transitions at 11 and 14 K, which we interpret as originating from the onset of three-dimensional order and in-plane magnetic order, respectively. We identify, with the help of density functional theory calculations, likely muon stopping sites and combine these with dipolar field calculations to show that the two measured muon rotation frequencies are consistent with two inequivalent muon sites within a zigzag antiferromagnetic structure proposed previously.

  4. Magnetic order in α -RuCl3 : A honeycomb-lattice quantum magnet with strong spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Sears, J. A.; Songvilay, M.; Plumb, K. W.; Clancy, J. P.; Qiu, Y.; Zhao, Y.; Parshall, D.; Kim, Young-June

    2015-04-01

    We report magnetic and thermodynamic properties of single crystal α -RuCl3 , in which the Ru3+(4 d5) ion is in its low spin state and forms a honeycomb lattice. Two features are observed in both magnetic susceptibility and specific heat data; a sharp peak at 7 K and a broad hump near 10-15 K. In addition, we observe a metamagnetic transition between 5 and 10 T. Our neutron diffraction study of single crystal samples confirms that the low temperature peak in the specific heat is associated with a magnetic order with unit cell doubling along the honeycomb (100) direction, which is consistent with zigzag order, one of the types of magnetic order predicted within the framework of the Kitaev-Heisenberg model.

  5. Synthesis, characterization and cytotoxic activities of the [RuCl2(NO)(dppp)(L)]PF6 complexes.

    PubMed

    Golfeto, Camilla C; Von Poelhsitz, Gustavo; Selistre-de-Araújo, Heloísa S; de Araujo, Márcio P; Ellena, Javier; Castellano, Eduardo E; Lopes, Luiz G L; Moreira, Icaro S; Batista, Alzir A

    2010-05-01

    The synthesis and characterization of ruthenium compounds of the type [RuCl(2)(NO)(dppp)(L)]PF(6) [dppp=1,3-bis(diphenylphosphino)propane; L=pyridine, 4-methylpyridine, 4-phenylpyridine and dimethyl sulfoxide] are described. The complexes were characterized by elemental analysis, UV/Vis and infrared spectroscopy, cyclic voltammetry, and X-ray crystallography for the complexes with the pyridine and 4-methylpyridine ligands. In vitro evaluation of these nitrosyl complexes revealed cytotoxic activity from 7.1 to 19.0 microM against the MDA-MB-231 breast tumor cells and showed that, in this case, they are more active than the reference metallodrug cisplatin. The 1,3-bis(diphenylphosphino)propane and the N-heterocyclic ligands alone failed to show cytotoxic activities at the concentrations tested (maximum concentration utilized=200 microM). PMID:20117840

  6. C-Au Covalently Bonded Molecular Junctions Using Nonprotected Alkynyl Anchoring Groups.

    PubMed

    Olavarria-Contreras, Ignacio José; Perrin, Mickael L; Chen, Zhi; Klyatskaya, Svetlana; Ruben, Mario; van der Zant, Herre S J

    2016-07-13

    We report on an approach to realize carbon-gold (C-Au) bonded molecular junctions without the need for an additive to deprotect the alkynyl carbon as endstanding anchor group. Using the mechanically controlled break junction (MCBJ) technique, we determine the most probable conductance value of a family of alkynyl terminated oligophenylenes (OPA(n)) connected to gold electrodes through such an akynyl moiety in ambient conditions. The molecules bind to the gold leads through an sp-hybridized carbon atom at each side. Comparing our results with other families of molecules that present organometallic C-Au bonds, we conclude that the conductance of molecules contacted via an sp-hybridized carbon atom is lower than the ones using sp(3) hybridization due to strong differences in the coupling of the conducting orbitals with the gold leads. PMID:27266477

  7. Dynamic Bonds in Covalently Crosslinked Polymer Networks for Photoactivated Strengthening and Healing.

    PubMed

    Gordon, Melissa B; French, Jonathan M; Wagner, Norman J; Kloxin, Christopher J

    2015-12-22

    A photoactivated-strengthening polymer network is reported. This approach incorporates dynamic bonds into the network architecture, which enables a secondary polymerization triggered by UV light. Three attributes of this material are demonstrated, including: i) there is simultaneous photoinduced strengthening and healing after the material is severed, ii) bulk property changes are spatially confined via photopatterning, and iii) there is permanent shape change post-irradiation. PMID:26524195

  8. Covalent Linkage of One-Dimensional DNA Arrays Bonded by Paranemic Cohesion.

    PubMed

    Ohayon, Yoel P; Sha, Ruojie; Flint, Ortho; Liu, Wenyan; Chakraborty, Banani; Subramanian, Hari K K; Zheng, Jianping; Chandrasekaran, Arun Richard; Abdallah, Hatem O; Wang, Xing; Zhang, Xiaoping; Seeman, Nadrian C

    2015-10-27

    The construction of DNA nanostructures from branched DNA motifs, or tiles, typically relies on the use of sticky-ended cohesion, owing to the specificity and programmability of DNA sequences. The stability of such constructs when unligated is restricted to a specific range of temperatures, owing to the disruption of base pairing at elevated temperatures. Paranemic (PX) cohesion was developed as an alternative to sticky ends for the cohesion of large topologically closed species that could be purified reliably on denaturing gels. However, PX cohesion is also of limited stability. In this work, we added sticky-ended interactions to PX-cohesive complexes to create interlocked complexes by functionalizing the sticky ends with psoralen, which can form cross-links between the two strands of a double helix. We were able to reinforce the stability of the constructs by creating covalent linkages between the 3'-ends and 5'-ends of the sticky ends; the sticky ends were added to double crossover domains via 3'-3' and 5'-5' linkages. Catenated arrays were obtained either by enzymatic ligation or by UV cross-linking. We have constructed finite-length one-dimensional arrays linked by interlocking loops and have positioned streptavidin-gold particles on these constructs. PMID:26343906

  9. Polymer GARD: computer simulation of covalent bond formation in reproducing molecular assemblies.

    PubMed

    Shenhav, Barak; Bar-Even, Arren; Kafri, Ran; Lancet, Doron

    2005-04-01

    The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly's composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a 'monomer world' towards polymer-based living entities. We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a 'scaffold' for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer 'take-over' - the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes. PMID:16010993

  10. Polymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies

    NASA Astrophysics Data System (ADS)

    Shenhav, Barak; Bar-Even, Arren; Kafri, Ran; Lancet, Doron

    2005-04-01

    The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly’ s composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a ‘monomer world’ towards polymer-based living entities.We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a ‘scaffold’ for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer ‘take-over’ the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.

  11. Covalent lanthanide(III) macrocyclic complexes: the bonding nature and optical properties of a promising single antenna molecule.

    PubMed

    Rabanal-León, Walter A; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

    2014-12-21

    The present work is focused on the elucidation of the electronic structure, bonding nature and optical properties of a series of low symmetry (C2) coordination compounds of type [Ln(III)HAM](3+), where "Ln(III)" are the trivalent lanthanide ions: La(3+), Ce(3+), Eu(3+) and Lu(3+), while "HAM" is the neutral six-nitrogen donor macrocyclic ligand [C22N6H26]. This systematic study has been performed in the framework of the Relativistic Density Functional Theory (R-DFT) and also using a multi-reference approach via the Complete Active Space (CAS) wavefunction treatment with the aim of analyzing their ground state and excited state electronic structures as well as electronic correlation. Furthermore, the use of the energy decomposition scheme proposed by Morokuma-Ziegler and the electron localization function (ELF) allows us to characterize the bonding between the lanthanide ions and the macrocyclic ligand, obtaining as a result a dative-covalent interaction. Due to a great deal of lanthanide optical properties and their technological applications, the absorption spectra of this set of coordination compounds were calculated using the time-dependent density functional theory (TD-DFT), where the presence of the intense Ligand to Metal Charge Transfer (LMCT) bands in the ultraviolet and visible region and the inherent f-f electronic transitions in the Near-Infra Red (NIR) region for some lanthanide ions allow us to propose these systems as "single antenna molecules" with potential applications in NIR technologies. PMID:25357209

  12. Transesterification of PHA to Oligomers Covalently Bonded with (Bio)Active Compounds Containing Either Carboxyl or Hydroxyl Functionalities

    PubMed Central

    Kwiecień, Iwona; Radecka, Iza; Kowalczuk, Marek; Adamus, Grażyna

    2015-01-01

    This manuscript presents the synthesis and structural characterisation of novel biodegradable polymeric controlled-release systems of pesticides with potentially higher resistance to weather conditions in comparison to conventional forms of pesticides. Two methods for the preparation of pesticide-oligomer conjugates using the transesterification reaction were developed. The first method of obtaining conjugates, which consist of bioactive compounds with the carboxyl group and polyhydroxyalkanoates (PHAs) oligomers, is "one-pot" transesterification. In the second method, conjugates of bioactive compounds with hydroxyl group and polyhydroxyalkanoates oligomers were obtained in two-step method, through cyclic poly(3-hydroxybutyrate) oligomers. The obtained pesticide-PHA conjugates were comprehensively characterised using GPC, 1H NMR and mass spectrometry techniques. The structural characterisation of the obtained products at the molecular level with the aid of mass spectrometry confirmed that both of the synthetic strategies employed led to the formation of conjugates in which selected pesticides were covalently bonded to PHA oligomers via a hydrolysable ester bond. PMID:25781908

  13. Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

    SciTech Connect

    Schmidt, Michael W; Ivanic, Joseph; Ruedenberg, Klaus

    2014-05-28

    An analysis based on the variation principle shows that in the molecules H2 +, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

  14. Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

    PubMed Central

    Schmidt, Michael W.; Ivanic, Joseph; Ruedenberg, Klaus

    2014-01-01

    An analysis based on the variation principle shows that in the molecules H2+, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation. PMID:24880263

  15. Is the decrease of the total electron energy density a covalence indicator in hydrogen and halogen bonds?

    PubMed

    Angelina, Emilio L; Duarte, Darío J R; Peruchena, Nélida M

    2013-05-01

    In this work, halogen bonding (XB) and hydrogen bonding (HB) complexes were studied with the aim of analyzing the variation of the total electronic energy density H(r b ) with the interaction strengthening. The calculations were performed at the MP2/6-311++G(2d,2p) level of approximation. To explain the nature of such interactions, the atoms in molecules theory (AIM) in conjunction with reduced variational space self-consistent field (RVS) energy decomposition analysis were carried out. Based on the local virial theorem, an equation to decompose the total electronic energy density H(r b ) in two energy densities, (-G(r b )) and 1/4∇(2)ρ(r b ), was derived. These energy densities were linked with the RVS interaction energy components. Through the connection between both decomposition schemes, it was possible to conclude that the decrease in H(r b ) with the interaction strengthening observed in the HB as well as the XB complexes, is mainly due to the increase in the attractive electrostatic part of the interaction energy and in lesser extent to the increase in its covalent character, as is commonly considered. PMID:23187685

  16. Driving Forces for Covalent Assembly of Porphyrins by Selective C-H Bond Activation and Intermolecular Coupling on a Copper Surface.

    PubMed

    Floris, Andrea; Haq, Sam; In't Veld, Mendel; Amabilino, David B; Raval, Rasmita; Kantorovich, Lev

    2016-05-11

    Recent synthesis of covalent organic assemblies at surfaces has opened the promise of producing robust nanostructures for functional interfaces. To uncover how this new chemistry works at surfaces and understand the underlying mechanisms that control bond-breaking and bond-making processes at specific positions of the participating molecules, we study here the coupling reaction of tetra(mesityl)porphyrin molecules, which creates covalently connected networks on the Cu(110) surface by utilizing the 4-methyl groups as unique connection points. Using scanning tunneling microscopy (STM), state-of-the-art density functional theory (DFT), and Nudged Elastic Band (NEB) calculations, we show that the unique directionality of the covalent bonding is found to stem from a chain of highly selective C-H activation and dehydrogenation processes, followed by specific intermolecular C-C coupling reactions that are facilitated by the surface, by steric constraints, and by anisotropic molecular diffusion. These insights provide the first steps toward developing synthetic rules for complex two-dimensional covalent organic chemistry that can be enacted directly at a surface to deliver specific macromolecular structures designed for specific functions. PMID:27097295

  17. Interface of covalently bonded phospholipids with a phosphorylcholine head: characterization, protein nonadsorption, and further functionalization.

    PubMed

    Ferez, Lynda; Thami, Thierry; Akpalo, Edefia; Flaud, Valérie; Tauk, Lara; Janot, Jean-Marc; Déjardin, Philippe

    2011-09-20

    Surface anchored poly(methylhydrosiloxane) (PMHS) thin films on oxidized silicon wafers or glass substrates were functionalized via the SiH hydrosilylation reaction with the internal double bonds of 1,2-dilinoleoyl-sn-glycero-3-phosphorylcholine (18:2 Cis). The surface was characterized by X-ray photoelectron spectroscopy, contact angle measurements, atomic force microscopy, and scanning electron microscopy. These studies showed that the PMHS top layer could be efficiently modified resulting in an interfacial high density of phospholipids. Grafted phospholipids made the initially hydrophobic surface (θ = 106°) very hydrophilic and repellent toward avidin, bovine serum albumin, bovine fibrinogen, lysozyme, and α-chymotrypsin adsorption in phosphate saline buffer pH 7.4. The surface may constitute a new background-stable support with increased biocompatibility. Further possibilities of functionalization on the surface remain available owing to the formation of interfacial SiOH groups by Karstedt-catalyzed side reactions of SiH groups with water. The presence of interfacial SiOH groups was shown by zeta potential measurements. The reactivity and surface density of SiOH groups were checked by fluorescence after reaction of a monoethoxy silane coupling agent bearing Alexa as fluorescent probe. PMID:21848263

  18. Do we need covalent bonding of Si nanoparticles on graphene oxide for Li-ion batteries?

    PubMed

    Miroshnikov, Yana; Grinbom, Gal; Gershinsky, Gregory; Nessim, Gilbert D; Zitoun, David

    2014-01-01

    In this manuscript, we report our investigation of anode materials for Li-ion batteries based on silicon-graphene oxide composites. Previous reports in the literature on silicon-graphene oxide (GO) composites as anodes have shown a large discrepancy between the electrochemical properties, mainly capacity and coulombic efficiency. In our research, the surface chemistry of Si nanoparticles has been functionalized to yield a chemical bond between the Si and GO, a further annealing step yields a Si-reduced GO (Si-rGO) composite while controlled experiments have been carried on mechanical mixing of GO and Si. For all samples, including a simple mixing of Si nanoparticles and GO, a high specific capacity of 2000 mA h g(Si)(-1) can be achieved for 50 cycles. The main difference between the samples can be observed in terms of coulombic efficiency, which will determine the future of these composites in full Li-ion cells. The Si-rGO composite shows a very low capacity fading and a coulombic efficiency above 99%. Furthermore, the Si-rGO composite can be cycled at very high rate to 20 C (charge in 3 minutes). PMID:25467631

  19. Antimicrobial activities of amphiphilic peptides covalently bonded to a water-insoluble resin.

    PubMed Central

    Haynie, S L; Crum, G A; Doele, B A

    1995-01-01

    A series of polymer-bound antimicrobial peptides was prepared, and the peptides were tested for their antimicrobial activities. The immobilized peptides were prepared by a strategy that used solid-phase peptide synthesis that linked the carboxy-terminal amino acid with an ethylenediamine-modified polyamide resin (PepsynK). The acid-stable, permanent amide bond between the support and the nascent peptide renders the peptide resistant to cleavage from the support during the final acid-catalyzed deprotection step in the synthesis. Select immobilized peptides containing amino acid sequences that ranged from the naturally occurring magainin to simpler synthetic sequences with idealized secondary structures were excellent antimicrobial agents against several organisms. The immobilized peptides typically reduced the number of viable cells by > or = 5 log units. We show that the reduction in cell numbers cannot be explained by the action of a soluble component. We observed no leached or hydrolyzed peptide from the resin, nor did we observe any antimicrobial activity in soluble extracts from the immobilized peptide. The immobilized peptides were washed and reused for repeated microbial contact and killing. These results suggest that the surface actions by magainins and structurally related antimicrobial peptides are sufficient for their lethal activities. PMID:7726486

  20. Monte Carlo simulation of a film growth with reactive hydrophobic, polar, and aqueous components by a covalent bond fluctuating model

    NASA Astrophysics Data System (ADS)

    Yang, Shihai; Pandey, Ras B.

    2007-04-01

    Using a bond fluctuating model (BFM), Monte Carlo simulations are performed to study the film growth in a mixture of reactive hydrophobic (H) and hydrophilic (P) groups in a simultaneous reactive and evaporating aqueous (A) solution on a simple three dimensional lattice. In addition to the excluded volume, short range phenomenological interactions among each constituents and kinetic functionalities are used to capture their major characteristics. The simulation involves thermodynamic equilibration via stochastic movement of each constituent by Metropolis algorithm as well as cross-linking reaction among constituents with evaporating aqueous component. The film thickness (h) and its interface width (W) are examined with a reactive aqueous solvent for a range of temperatures (T). Results are compared with a previous study [Yang et al. Macromol. Theory Simul. 15, 263 (2006)] with an effective bond fluctuation model (EBFM). Simulation data show a much slower power-law growth for h and W with BFM than that with EBFM. With BFM, growth of the film thickness can be described by h ∝tγ, with a typical value γ1≈0.97 in initial time regime followed by γ2≈0.77 at T =5, for example. Growth of the interface width can also be described by a power law, W ∝tβ, with β1≈0.40 initially and β2≈0.25 in later stage. Corresponding values of the exponents with EBFM are much higher, i.e., γ1≈1.84, γ2≈1.34 and β1≈1.05, β2≈0.60 at T =5. Correct restrictions on the bond length with the excluded volume used with BFM are found to have a greater effect on steady-state film thickness (hs) and the interface width (Ws) at low temperatures than that at high temperatures. The relaxation patterns of the interface width with BFM seem to change noticeably from those with EBFM. A better relaxed film with a smoother surface is thus achieved by the improved cross-linking covalent bond fluctuation model which is more realistic in capturing appropriate details of systems such as

  1. Intermolecular carbon-carbon, nitrogen-nitrogen and oxygen-oxygen non-covalent bonding in dipolar molecules.

    PubMed

    Remya, Karunakaran; Suresh, Cherumuttathu H

    2015-07-28

    Clear evidence for the existence of intermolecular carbon-carbon (C···C), nitrogen-nitrogen (N···N) and oxygen-oxygen (O···O) interactions between atoms in similar chemical environments in homogeneous dimers of organic dipolar molecules has been obtained from molecular orbital (MO), natural bond orbital (NBO) and atoms-in-molecule (AIM) electron density analyses at the M06L/6-311++G(d,p) level of density functional theory (DFT). These X···X type interactions are mainly the result of local polarization effects, causing segregation of electron-rich and electron-deficient regions in the X atoms, leading to complementary electrostatic interactions. NBO analysis provides evidence of charge transfer between the two X atoms. Even in symmetrical molecules such as acetylene, induced dipoles in the dimer create C···C bonding interactions. The strength of this type of interaction increases with increase in the dipole moment of the molecule. Energy decomposition analysis (EDA) shows that the electrostatic component of the interaction energy (Eint) is very high, up to 95.86%. The C···C interactions between similar carbon atoms are located for several crystal structures obtained from the literature. In addition, MO, AIM and electrostatic potential analyses support interactions between similar oxygen (O···O) and nitrogen (N···N) atoms in a variety of molecular dimers. Good prediction of Eint is achieved in terms of the total gain in electron density at non-covalently interacting intermolecular bonds (∑ρ) and the monomer dipole moment (μ). A rigorously tested QSAR equation has been derived to predict Eint for all dimer systems: Eint (kcal mol(-1)) = -138.395∑ρ(au) - 0.551μ (Debye). This equation suggests that the polarization-induced bonding interaction between atoms in a similar chemical environment could well be a general chemical phenomenon. The results have been further validated by different density functional methods and also by G3MP2 method

  2. Mesoporous hybrids containing Eu{sup 3+} complexes covalently bonded to SBA-15 functionalized: Assembly, characterization and photoluminescence

    SciTech Connect

    Kong Lili; Bing Yan; Ying Li

    2009-07-15

    A novel series of luminescent mesoporous organic-inorganic hybrid materials has been prepared by linking Eu{sup 3+} complexes to the functionalized ordered mesoporous SBA-15 which was synthesis by a co-condensation process of 1,3-diphenyl-1,3-propanepione (DBM) modified by the coupling agent 3-(triethoxysilyl)-propyl isocyanate (TEPIC), tetraethoxysilane (TEOS), Pluronic P123 surfactant as a template. It was demonstrated that the efficient intramolecular energy transfer in the mesoporous material Eu(DBMSi-SBA-15){sub 3}phen mainly occurred between the modified DBM (named as DBM-Si) and the central Eu{sup 3+} ion. So the Eu(DBMSi-SBA-15){sub 3}phen showed characteristic emission of Eu{sup 3+} ion under UV irradiation with higher luminescence quantum efficiency. Moreover, the mesoporous hybrid materials exhibited excellent thermal stability as the lanthanide complex was covalently bonded to the mesoporous matrix. - Graphical abstract: A novel organic-inorganic mesoporous luminescent hybrid materials is prepared by linking the binary and ternary Eu{sup 3+} complexes to the functionalized ordered mesoporous SBA-15 with the modified 1,3-diphenyl-1,3-propanepione (DBM) via a co-condensation process of tetraethoxysilane (TEOS) in the presence of Pluronic P123 surfactant as a template.

  3. Analysis of the bond-valence method for calculating (29) Si and (31) P magnetic shielding in covalent network solids.

    PubMed

    Holmes, Sean T; Alkan, Fahri; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

    2016-07-01

    (29) Si and (31) P magnetic-shielding tensors in covalent network solids have been evaluated using periodic and cluster-based calculations. The cluster-based computational methodology employs pseudoatoms to reduce the net charge (resulting from missing co-ordination on the terminal atoms) through valence modification of terminal atoms using bond-valence theory (VMTA/BV). The magnetic-shielding tensors computed with the VMTA/BV method are compared to magnetic-shielding tensors determined with the periodic GIPAW approach. The cluster-based all-electron calculations agree with experiment better than the GIPAW calculations, particularly for predicting absolute magnetic shielding and for predicting chemical shifts. The performance of the DFT functionals CA-PZ, PW91, PBE, rPBE, PBEsol, WC, and PBE0 are assessed for the prediction of (29) Si and (31) P magnetic-shielding constants. Calculations using the hybrid functional PBE0, in combination with the VMTA/BV approach, result in excellent agreement with experiment. © 2016 Wiley Periodicals, Inc. PMID:27117609

  4. Nitric oxide donor trans-[RuCl([15]aneN4)NO]2+ as a possible therapeutic approach for Chagas' disease

    PubMed Central

    Guedes, Paulo MM; Oliveira, Fabiana S; Gutierrez, Fredy RS; da Silva, Grace Kelly; Rodrigues, Gerson Jhonatan; Bendhack, Lusiane Maria; Franco, Douglas W; Do Valle Matta, Maria A; Zamboni, Dario S; da Silva, Roberto Santana; Silva, João Santana

    2010-01-01

    Background and purpose: Benznidazole (Bz) is the therapy currently available for clinical treatment of Chagas' disease. However, many strains of Trypanosoma cruzi parasites are naturally resistant. Nitric oxide (NO) produced by activated macrophages is crucial to the intracellular killing of parasites. Here, we investigate the in vitro and in vivo activities against T. cruzi, of the NO donor, trans-[RuCl([15]aneN4)NO]2+. Experimental approach: Trans-[RuCl([15]aneN4)NO]2+was incubated with a partially drug-resistant T. cruzi Y strain and the anti-proliferative (epimastigote form) and trypanocidal activities (trypomastigote and amastigote) evaluated. Mice were treated during the acute phase of Chagas' disease. The anti-T. cruzi activity was evaluated by parasitaemia, survival rate, cardiac parasitism, myocarditis and the curative rate. Key results: Trans-[RuCl([15]aneN4)NO]2+ was 10- and 100-fold more active than Bz against amastigotes and trypomastigotes respectively. Further, trans-[RuCl([15]aneN4)NO]2+ (0.1 mM) induced 100% of trypanocidal activity (trypomastigotes forms) in vitro. Trans-[RuCl([15]aneN4)NO]2+ induced permanent suppression of parasitaemia and 100% survival in a murine model of acute Chagas' disease. When the drugs were given alone, parasitological cures were confirmed in only 30 and 40% of the animals treated with the NO donor (3.33 µmol·kg−1·day−1) and Bz (385 µmol·kg−1·day−1), respectively, but when given together, 80% of the animals were parasitologically cured. The cured animals showed an absence of myocarditis and a normalisation of cytokine production in the sera. In addition, no in vitro toxicity was observed at the tested doses. Conclusions and implications: These findings indicate that trans-[RuCl([15]aneN4)NO]2+is a promising lead compound for the treatment of human Chagas' disease. This article is commented on by Machado et al., pp. 258–259 of this issue. To view this commentary visit http://dx.doi.org/10.1111/j.1476

  5. New chromogenic and fluorogenic reagents and sensors for neutral and ionic analytes based on covalent bond formation--a review of recent developments.

    PubMed

    Mohr, Gerhard J

    2006-11-01

    To date, hydrogen bonding and Coulomb, van der Waals and hydrophobic interactions are the major contributors to non-covalent analyte recognition using ionophores, ligands, aptamers and chemosensors. However, this article describes recent developments in the use of (reversible) covalent bond formation to detect analyte molecules, with special focus on optical signal transduction. Several new indicator dyes for analytes such as amines and diamines, amino acids, cyanide, formaldehyde, hydrogen peroxide, organophosphates, nitrogen oxide and nitrite, peptides and proteins, as well as saccharides have become available. New means of converting analyte recognition into optical signals have also been introduced, such as colour changes of chiral nematic layers. This article gives an overview of recent developments and discusses response mechanisms, selectivity and sensitivity. PMID:17039383

  6. Connecting a new non-adiabatic vibrational mass to the bonding mechanism of LiH: A quantum superposition of ionic and covalent states

    NASA Astrophysics Data System (ADS)

    Diniz, Leonardo G.; Alijah, Alexander; Adamowicz, Ludwik; Mohallem, José R.

    2015-07-01

    Non-adiabatic vibrational calculations performed with the accuracy of 0.2 cm-1 spanning the whole energy spectrum up to the dissociation limit for 7LiH are reported. A so far unknown v = 23 energy level is predicted. The key feature of the approach used in the calculations is a valence-bond (VB) based procedure for determining the effective masses of the two vibrating atoms, which depend on the internuclear distance, R. It is found that all LiH electrons participate in the vibrational motion. The R-dependent masses are obtained from the analysis of the simple VB two-configuration ionic-covalent representation of the electronic wave function. These findings are consistent with an interpretation of the chemical bond in LiH as a quantum mechanical superposition of one-electron ionic and covalent states.

  7. Isotope effect on the temperature dependence of the 35Cl NQR frequency in (NH4)2RuCl6

    NASA Astrophysics Data System (ADS)

    Kume, Yoshio; Amino, Daiki; Asaji, Tetsuo

    2013-07-01

    The 35Cl nuclear quadrupole resonance frequencies and spin-lattice relaxation times for (NH4)2RuCl6, (ND4)2RuCl6, (NH4)2SnCl6, and (ND4)2SnCl6 were measured in the temperature range 4.2-300 K. In these four compounds, it was confirmed that no phase transition occurs in the observed temperature range. At 4.2 K, discrepancies of the NQR frequency between non-deuterated and deuterated compounds, which are attributed to the difference in the spatial distributions of hydrogen (deuterium) atoms in the ground states of the rotational motion of ammonium ion, reached to 24 kHz and 23 kHz for the ruthenate compounds and the stannate compounds, respectively. The separation between the ground and the first excited states of the rotational motion of the ammonium ion was estimated to be 466 J mol-1 and 840 J mol-1 for (ND4)2RuCl6 and (NH4)2RuCl6, respectively, by least-square fitting calculations of temperature dependence of the NQR frequency. For (ND4)2SnCl6 and (NH4)2SnCl6, these quantities were estimated to be 501 J mol-1 and 1544 J mol-1, respectively. It was clarified that the T1 minimum, which has been observed for the stannate compounds at around 60 K as a feature of the temperature dependence, was dependent on a method of sample preparation. It is concluded that the minimum is not an essential character of the ammonium hexachlorostannate(IV) since the crystals prepared in strong acid condition to prevent a partial substitution of chlorine atoms by hydroxyl groups, did not show such T1 minimum.

  8. UV-Light Exposure of Insulin: Pharmaceutical Implications upon Covalent Insulin Dityrosine Dimerization and Disulphide Bond Photolysis

    PubMed Central

    Correia, Manuel; Neves-Petersen, Maria Teresa; Jeppesen, Per Bendix; Gregersen, Søren; Petersen, Steffen B.

    2012-01-01

    In this work we report the effects of continuous UV-light (276 nm, ∼2.20 W.m−2) excitation of human insulin on its absorption and fluorescence properties, structure and functionality. Continuous UV-excitation of the peptide hormone in solution leads to the progressive formation of tyrosine photo-product dityrosine, formed upon tyrosine radical cross-linkage. Absorbance, fluorescence emission and excitation data confirm dityrosine formation, leading to covalent insulin dimerization. Furthermore, UV-excitation of insulin induces disulphide bridge breakage. Near- and far-UV-CD spectroscopy shows that UV-excitation of insulin induces secondary and tertiary structure losses. In native insulin, the A and B chains are held together by two disulphide bridges. Disruption of either of these bonds is likely to affect insulin’s structure. The UV-light induced structural changes impair its antibody binding capability and in vitro hormonal function. After 1.5 and 3.5 h of 276 nm excitation there is a 33.7% and 62.1% decrease in concentration of insulin recognized by guinea pig anti-insulin antibodies, respectively. Glucose uptake by human skeletal muscle cells decreases 61.7% when the cells are incubated with pre UV-illuminated insulin during 1.5 h. The observations presented in this work highlight the importance of protecting insulin and other drugs from UV-light exposure, which is of outmost relevance to the pharmaceutical industry. Several drug formulations containing insulin in hexameric, dimeric and monomeric forms can be exposed to natural and artificial UV-light during their production, packaging, storage or administration phases. We can estimate that direct long-term exposure of insulin to sunlight and common light sources for indoors lighting and UV-sterilization in industries can be sufficient to induce irreversible changes to human insulin structure. Routine fluorescence and absorption measurements in laboratory experiments may also induce changes in protein

  9. Mass spectrometry and UV-VIS spectrophotometry of ruthenium(II) [RuClCp(mPTA)2](OSO2CF3)2 complex in solution.

    PubMed

    Peña-Méndez, Eladia María; González, Beatriz; Lorenzo, Pablo; Romerosa, Antonio; Havel, Josef

    2009-12-01

    Ruthenium(II) complexes are of great interest as a new class of cancerostatics with advantages over classical platinum compounds including lower toxicity. The stability of the [RuClCp(mPTA)2](OSO2CF3)2 complex (I) (Cp cyclopentadienyl, mPTA N-methyl 1,3,5-triaza-7-phosphaadamantane) in aqueous solution was studied using spectrophotometry, matrix-assisted laser desorption/ionization (MALDI) and laser desorption/ionization (LDI) time-of-flight (TOF) mass spectrometry (MS). Spectrophotometry proves that at least three different reactions take place in water. Dissolution of I leads to fast coordination of water molecules to the Ru(II) cation and then slow hydrolysis and ligand exchange of chloride and mPTA with water, hydroxide or with trifluoromethane sulfonate itself. Via MALDI and LDI of the hydrolyzed solutions the formation of singly positively charged ions of general formula RuCl(p)(Cp)(q)(mPTA)(r)(H2O)(s)(OH)(t) (p = 0-1, q = 0-1, r = 0-2, s = 0-5, t = 0-2) and of some fragment ions was shown. The stoichiometry was determined by analyzing the isotopic envelopes and computer modelling. The [RuClCp(mPTA)2](OSO2CF3)2 complex can be stabilized in dilute hydrochloric acid or in neutral 0.15 M isotonic sodium chloride solution. PMID:19902414

  10. Mass spectrometry analysis of the oxidation states of the pro-oncogenic protein anterior gradient-2 reveals covalent dimerization via an intermolecular disulphide bond.

    PubMed

    Clarke, David J; Murray, Euan; Faktor, Jakub; Mohtar, Aiman; Vojtesek, Borek; MacKay, C Logan; Smith, Pat Langridge; Hupp, Ted R

    2016-05-01

    Anterior Gradient-2 (AGR2) is a component of a pro-oncogenic signalling pathway that can promote p53 inhibition, metastatic cell migration, limb regeneration, and cancer drug-resistance. AGR2 is in the protein-disulphide isomerase superfamily containing a single cysteine (Cys-81) that forms covalent adducts with its client proteins. We have found that mutation of Cysteine-81 attenuates its biochemical activity in its sequence-specific peptide docking function, reduces binding to Reptin, and reduces its stability in cells. As such, we evaluated how chemical oxidation of its cysteine affects its biochemical properties. Recombinant AGR2 spontaneously forms covalent dimers in the absence of reductant whilst DTT promotes dimer to monomer conversion. Mutation of Cysteine-81 to alanine prevents peroxide catalysed dimerization of AGR2 in vitro, suggesting a reactive cysteine is central to covalent dimer formation. Both biochemical assays and ESI mass spectrometry were used to demonstrate that low levels of a chemical oxidant promote an intermolecular disulphide bond through formation of a labile sulfenic acid intermediate. However, higher levels of oxidant promote sulfinic or sulfonic acid formation thus preventing covalent dimerization of AGR2. These data together identify the single cysteine of AGR2 as an oxidant responsive moiety that regulates its propensity for oxidation and its monomeric-dimeric state. This has implications for redox regulation of the pro-oncogenic functions of AGR2 protein in cancer cells. PMID:26876500

  11. Infrared and Raman analyses of the halogen-bonded non-covalent adducts formed by α,ω-diiodoperfluoroalkanes with DABCO and other electron donors

    NASA Astrophysics Data System (ADS)

    Messina, M. T.; Metrangolo, P.; Navarrini, W.; Radice, S.; Resnati, G.; Zerbi, G.

    2000-06-01

    An attractive intermolecular interaction which has been called "halogen bonding" exists between the nitrogen, sulfur, or oxygen atoms present in HC motifs and the iodine atom of PFC residues. The "halogen bonding" is strong enough to overcome the low affinity existing between PFC and HC compounds, driving their self-assembly into supramolecular architectures. The non-covalent co-polymer formed by 1,2-diiodotetrafluoroethane with diazabicyclooctane has been prepared and characterised by FT-IR and -Raman spectroscopies. We propose the changes shown by the vibrational spectra of single PFC and HC components when involved in halogen bonded co-polymers as diagnostic probes of the interaction and as tools to rank the electron-donor ability of differently heteroatom substituted hydrocarbons.

  12. Covalently bonded sulfonic acid magnetic graphene oxide: Fe3O4@GO-Pr-SO3H as a powerful hybrid catalyst for synthesis of indazolophthalazinetriones.

    PubMed

    Doustkhah, Esmail; Rostamnia, Sadegh

    2016-09-15

    Multistep synthesis of covalently sulfonated magnetic graphene oxide was achieved by starting from Hummer's method to produce graphene oxide (GO) from chemical oxidation of graphite. Then, GO nanosheets were applied to support Fe3O4 nanoparticles (Fe3O4@GO) using co-precipitation method in the presence of GO sheets. This strategy led to formation of uniform particles of Fe3O4 on the surface of GO sheets. Then, it was sulfonated (Fe3O4@GO-Pr-SO3H) through modification with 3-mercaptopropyltrimethoxysilane (MPTMS) and subsequent oxidation with hydrogen peroxide (H2O2). In comparison, the covalently bonded propyl sulfonic acid groups were more prevailing rather to sulfonic acids of GO itself. The proposed catalyst was more active and recyclable at least for 11 runs. PMID:27309948

  13. Ligand K-edge x-ray absorption spectroscopy as a probe of ligand-metal bonding: Charge donation and covalency in copper-chloride systems

    SciTech Connect

    Shadle, S.E.; Hedman, B.; Solomon, E.I.; Hodgson, K.O.

    1994-09-14

    X-ray absorption spectra (XAS) have been measured at the chloride K-edge for a series of complexes containing chloride ligands bound to open shell d{sup 9} copper ions in order to probe ligand-metal bonding. The intensity of the pre-edge feature in these spectra reflects the covalency in the half-occupied d{sub x}{sup 2-}{sub y}{sup 2-} derived molecular orbital (HOMO) of the complex. The energy of the pre-edge feature as well as the energy of the rising absorption edge provides quantitative information about the covalency of the ligand-metal interaction, the charge donated by the chloride, and the energy of the copper d-manifold. The results demonstrate that ligand K-edge XAS features can be used to obtain information about ligand-metal bonding. The results also identify the chemical basis for trends in the XAS data for the following complexes: D{sub 4h} CuCl{sub 4}{sup 2-}, D{sub 2d} CuCl{sub 4}{sup 2-}, planar trans-CuCl{sub 2-} (pdmp){sub 2} (pdmp = N-phenyl-3,5-dimethylpyrazole), square pyramidal CuCl{sub 5}{sup 3-}, the planar dimer KCuCl{sub 3}, the distorted tetrahedral dimer (Ph{sub 4}P)CuCl{sub 3}, and two dimers with mixed ligation, one containing a bridging chloride, and the other, containing terminally bound chloride. Several of these results are supported by independent spectral data or by basic ligand field concepts. A geometric distortion from square planar to distorted tetrahedral results in a decrease in the chloride-copper HOMO covalency but an increase in the total charge donation by the chlorides. While the geometry can maximize the overlap for a highly covalent HOMO, this does not necessarily reflect the overall charge donation.

  14. Development and application of a diagnostic instrument to evaluate grade-11 and -12 students' concepts of covalent bonding and structure following a course of instruction

    NASA Astrophysics Data System (ADS)

    Peterson, Raymond F.; Treagust, David F.; Garnett, Patrick

    This article initially outlines a procedure used to develop a written diagnostic instrument to identify grade-11 and -12 students' misconceptions and misunderstandings of the chemistry topic covalent bonding and structure. The content to be taught was carefully defined through a concept map and propositional statements. Following instruction, student understanding of the topic was identified from interviews, student-drawn concept maps, and free-response questions. These data were used to produce 15 two-tier multiple-choice items where the first tier examined content knowledge and the second examined understanding of that knowledge in six conceptual areas, namely, bond polarity, molecular shape, polarity of molecules, lattices, intermolecular forces, and the octet rule. The diagnostic instrument was administered to a total of 243 grade-11 and -12 chemistry students and has a Cronbach alpha reliability of 0.73. Item difficulties ranged from 0.13 to 0.60; discrimination values ranged from 0.32 to 0.65. Each item was analyzed to ascertain student understanding of and identify misconceptions related to the concepts and propositional statements underlying covalent bonding and structure.

  15. Stability of the C-C covalent bonds in fullerenes in the solid body-vapor structure during the thermodynamic action by a quasi-pulsed electron beam

    NASA Astrophysics Data System (ADS)

    Semenov, A. P.; Semenova, I. A.; Churilov, G. N.

    2015-04-01

    The explosive evaporation of a fullerene mixture in a vacuum of ˜10-2 Pa during the contraction of a 1-kW hollow electron beam into a spot on a substrate in a time of 0.1-1 s is considered. A comparative analysis of the Raman spectra and the absorption electron spectra of a starting fullerene mixture powder and the vapor condensates shows that the evaporation of C60 and C70 fullerenes proceeds without breaking C-C covalent bonds.

  16. Selection of two optional covalent bonds by electric stimuli: dual catalytic switching of redox-active copper.

    PubMed

    Kamamoto, Yu; Nitta, Yuya; Kubo, Kazuyuki; Mizuta, Tsutomu; Kume, Shoko

    2016-08-18

    Two types of redox functionality were selected for covalent immobilization on a carbon electrode, using an electric potential as the sole stimulus. A redox-active copper catalyst transformed a terminal alkyne in two ways with and without an oxidation process, to form a triazole or butadiyne. PMID:27435917

  17. Effects of surface residual species in SBA-16 on encapsulated chiral (1S,2S)-DPEN-RuCl2(TPP)2 in asymmetric hydrogenation of acetophenone

    NASA Astrophysics Data System (ADS)

    Shi, Xiufeng; Xing, Bin; Fan, Binbin; Xue, Zhaoteng; Li, Ruifeng

    2016-03-01

    The SBA-16 obtained by different routes of elimination of organic templates were used as the hosts for encapsulation of chiral Ru complex (1S,2S)-DPEN-RuCl2(TPP)2 ( 1) (DPEN = 1,2-diphenylethylene-diamine, TPP = triphenyl phosphine). The methods for removing templates had distinct effects on the amount of residual template in SBA-16, which made the SBA-16 with different surface and structure properties. 1 encapsulated in SBA-16 extracted with the mixture of pyridine and ethanol showed higher activity and enantioselectivity for acetophenone asymmetric hydrogenation.

  18. Evidence of Splitting 1,2,3-Triazole into an Alkyne and Azide by Low Mechanical Force in the Presence of Other Covalent Bonds.

    PubMed

    Khanal, Ashok; Long, Fei; Cao, Bin; Shahbazian-Yassar, Reza; Fang, Shiyue

    2016-07-01

    The cycloaddition reaction of an alkyne and azide to form a 1,2,3-triazole is widely used in many areas. However, the stability of the triazole moiety under mechanical stress is unclear. To see if a triazole could be selectively split into an alkyne and azide in the presence of other typical covalent bonds, a mica surface functionalized with a molecule containing a triazole moiety in the middle and an activated ester at the end was prepared. An atomic force microscope (AFM) tip with amino groups on its surface was ramped over the mica surface at predefined locations, which could temporarily link the tip to the surface through amide bond formation. During retraction, the triazole or another bond in the linkage broke, and a force was recorded. The forces varied widely at different ramps from close to 0 pN to 860 pN due to nonspecific adhesions and to the inherent inconsistency of single bond rupture. If some of the forces were from triazole cycloreversion, there would be alkynes at the predefined ramping locations. The surface was reacted with an azide carboxylic acid followed by labeling with amino Au nanoparticles (AuNPs). AFM imaging revealed AuNPs at the predicted locations, which provided evidence that under certain conditions triazole could be split selectively in the presence of other bonds at forces below 860 pN. PMID:27246264

  19. Boron- and Nitrogen-Doped Phenalenyls: Unexpected 2e/ and 4e/all-sites pi-pi Covalency and Genuine Pancake Double Bonding

    DOE PAGESBeta

    Tian, Yong-Hui; Huang, Jingsong; Sumpter, Bobby G

    2015-01-01

    Phenalenyl is an important neutral pi-radical due to its capability to form unconventional pancake pi-pi bonding interactions, whereas its analogues with graphitic boron (B) or nitrogen (N)-doping have been regarded as closed-shell systems and therefore received much less attention. By using high-level quantum chemistry calculations, we show that the B- and N-doped closed-shell phenalenyls unexpectedly form open-shell singlet pi-dimers with diradicaloid character featuring 2e/all-sites double pi-pi bonding. Moreover, by proper substitutions, the doped phenalenyl derivatives can be made open-shell species that form closed shell singlet pi-dimers bound by stronger 4e/all-sites double pi-pi bonding. The covalent pi-pi bonding overlap is distributedmore » on all of the atomic sites giving robust and genuine pancake-shaped pi-dimers which, depending on the number of electrons available in the bonding interactions, are equally or more stable than the pi-dimers of the pristine phenalenyl.« less

  20. Seven supramolecular frameworks constructed from combination of hydrogen-bonds and other non-covalent associations between organic acids and bis-imidazoles

    NASA Astrophysics Data System (ADS)

    Jin, Shouwen; Zhang, Huan; Zhao, Ying; Jin, Li; Ye, Xianghang; Liu, Hui; Wang, Daqi

    2015-11-01

    Seven crystalline organic acid-base adducts derived from bis(N-imidazolyl) and organic acids (2,4,6-trinitrophenol, p-nitrobenzoic acid, 3,5-dinitrobenzoic acid, oxalic acid, m-phthalic acid, and 1,5-naphthalenedisulfonic acid) were prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. The seven compounds are all organic salts. In salts 1, and 3, the L1 are monoprotonated, while in 4 and 6 the L1 are diprotonated. All supramolecular architectures involve extensive classical hydrogen bonds and C-H⋯O interactions. The role of weak and strong non-covalent interactions in the crystal packing is analyzed. The complexes displayed 2D-3D framework structures for the synergistic effect of the various non-covalent interactions. The results presented herein indicate that the strength and directionality of the N-H⋯N, N-H⋯O, O-H⋯O, O-H⋯N, N-H⋯S, and O-H⋯S hydrogen bonds between the organic acids and the ditopic imidazoles are sufficient to bring about the formation of binary organic salts.

  1. Covalent bonding and J–J mixing effects on the EPR parameters of Er3 + ions in GaN crystal

    NASA Astrophysics Data System (ADS)

    Rui-Peng, Chai; Long, Li; Liang, Liang; Qing, Pang

    2016-07-01

    The EPR parameters of trivalent Er3+ ions doped in hexagonal GaN crystal have been studied by diagonalizing the 364×364 complete energy matrices. The results indicate that the resonance ground states may be derived from the Kramers doublet Γ6. The EPR g-factors may be ascribed to the stronger covalent bonding and nephelauxetic effects compared with other rare-earth doped complexes, as a result of the mismatch of ionic radii of the impurity Er3+ ion and the replaced Ga3+ ion apart from the intrinsic covalency of host GaN. Furthermore, the J–J mixing effects on the EPR parameters from the high-lying manifolds have been evaluated. It is found that the dominant J–J mixing contribution is from the manifold 2K15/2, which accounts for about 2.5%. The next important J–J contribution arises from the crystal–field mixture between the ground state 4I15/2 and the first excited state 4I13/2, and is usually less than 0.2%. The contributions from the rest states may be ignored. Project supported by the Foundation of Education Department of Shaanxi Province, China (Grant No. 16JK1461).

  2. The weak covalent bond in NgAuF (Ng=Ar, Kr, Xe): A challenge for subsystem density functional theory.

    PubMed

    Beyhan, S Maya; Götz, Andreas W; Jacob, Christoph R; Visscher, Lucas

    2010-01-28

    We have assessed the accuracy of a representative set of currently available approximate kinetic-energy functionals used within the frozen-density embedding scheme for the NgAuF (Ng=Ar, Kr, Xe) molecules, which we partitioned into a Ng and a AuF subsystem. Although it is weak, there is a covalent interaction between these subsystems which represents a challenge for this subsystem density functional theory approach. We analyzed the effective-embedding potentials and resulting electron density distributions and provide a quantitative analysis of the latter from dipole moment differences and root-mean-square errors in the density with respect to the supermolecular Kohn-Sham density functional theory reference calculation. Our results lead to the conclusion that none of the tested approximate kinetic-energy functionals performs well enough to describe the bond between the noble gas and gold adequately. This observation contributes to the growing evidence that the current procedure to obtain approximate kinetic-energy functionals by reparametrizing functionals obtained via the "conjointness" hypothesis of Lee, Lee, and Parr [Phys. Rev. A 44, 768 (1991)] is insufficient to treat metal-ligand interactions with covalent character. PMID:20113026

  3. Theoretical study on carbon-carbon short contact of ∼2.3 Å: intermediate state between nonbonding and σ-covalent bonding.

    PubMed

    Hatakeyama, Makoto; Ogata, Koji; Ishida, Toshimasa; Kitamura, Kunihiro; Nakamura, Shinichiro

    2015-01-29

    An unusual intermolecular carbon-carbon short contact, observed previously in the crystal structure of the copper complex of pyridoxal-5-phosphate- pyridoxamine-5-phospate Schiff base, was investigated from a standpoint of quantum chemistry by DFT calculations with plane wave basis sets. The DFT-optimized structure qualitatively reproduced the short contact (2.6-2.8 Å) of the intermolecular carbon-carbon pairs for the dimer of the copper complexes in the unit cell, compared to that (∼2.3 Å) of the X-ray diffraction data. By the occupied and unoccupied orbitals, the dimer showed the in-phase and out-of-phase interactions along the direction of the intermolecular distance. The dimer of the copper complexes was confirmed as the stable intermediate between nonbonding and σ-covalent bonding by the electronic energy curve along the distance of the monomers. PMID:25559884

  4. Can natural fibers be a silver bullet? Antibacterial cellulose fibers through the covalent bonding of silver nanoparticles to electrospun fibers

    NASA Astrophysics Data System (ADS)

    Zheng, Yingying; Cai, Chao; Zhang, Fuming; Monty, Jonathan; Linhardt, Robert J.; Simmons, Trevor J.

    2016-02-01

    Natural cotton was dissolved in a room-temperature ionic liquid 1-ethyl-3-methyl acetate and wet-jet electrospun to obtain nanoscale cotton fibers with a substantially reduced diameter—and therefore an increased surface area—relative to natural cotton fibers. The resulting nano-cotton fibers were esterified with trityl-3-mercaptopropionic acid, which after selective de-tritylation afforded nano-cotton fibers containing reactive thiol functionality. Silver nanoparticles that were covalently attached to these sulfhydryl groups were assembled next. The microstructure of the resulting nanocomposite was characterized, and the antibacterial activity of the resulting nano-cotton Ag-nanoparticle composite was also studied. This nanocomposite showed significant activity against both Gram-negative and Gram-positive bacteria.

  5. Can natural fibers be a silver bullet? Antibacterial cellulose fibers through the covalent bonding of silver nanoparticles to electrospun fibers.

    PubMed

    Zheng, Yingying; Cai, Chao; Zhang, Fuming; Monty, Jonathan; Linhardt, Robert J; Simmons, Trevor J

    2016-02-01

    Natural cotton was dissolved in a room-temperature ionic liquid 1-ethyl-3-methyl acetate and wet-jet electrospun to obtain nanoscale cotton fibers with a substantially reduced diameter-and therefore an increased surface area-relative to natural cotton fibers. The resulting nano-cotton fibers were esterified with trityl-3-mercaptopropionic acid, which after selective de-tritylation afforded nano-cotton fibers containing reactive thiol functionality. Silver nanoparticles that were covalently attached to these sulfhydryl groups were assembled next. The microstructure of the resulting nanocomposite was characterized, and the antibacterial activity of the resulting nano-cotton Ag-nanoparticle composite was also studied. This nanocomposite showed significant activity against both Gram-negative and Gram-positive bacteria. PMID:26751520

  6. Developing Carrier Complexes for “Caged NO”: RuCl3(NO)(H2O)2 Complexes of Dipyridylamine, (dpaH), N,N,N'N'-Tetrakis (2-Pyridyl) Adipamide, (tpada), and (2-Pyridylmethyl) Iminodiacetate, (pida2-)

    PubMed Central

    Slocik, Joseph M.; Kortes, Richard A.

    2000-01-01

    Delivery agents which can carry the {Ru(NO)}6 chromophore (“caged NO”) are desired for vasodilation and for photodynamic therapy of tumors. Toward these goals, complexes derived from [RuCl3(NO)(H2O)2]= (1) have been prepared using dipyridylamine (dpaH) as mono and bis adducts, [Ru(NO)Cl3(dpaH)] = (2) and [Ru(NO)Cl(dpaH)2]Cl2 = (3). The dpaH ligands coordinate cis to the Ru(NO) axis.The mono derivative is a model for a potential DNA groove-spanning binuclear complex {[RuNO)Cl3]2(tpada)} = (4) which has two DNA-coordinating RuII centers, photo-labile {Ru(NO)}6 sites, and a groove-spanning tether moiety.The binuclear assembly is prepared from the tethered dipyridylamine ligand N,N,N',N'-tetrakis(2-pyridylmethyl)adipamide (tpada) which has recently been shown to provide a binuclear carrier complex suited to transporting RuII and PdII agents. A related complex, [Ru(NO)Cl(pida)] = (5) with the {Ru(NO)}6 moiety bound to (2-pyridylmethyl) iminodiacetate (pida2-) is also characterized as a potential “caged NO” carrier. Structural information concerning the placement of the pyridyl donor groups relative to the {Ru(NO)}6 unit has been obtained from 1H and 13C NMR and infrared methods, noting that a pyridyl donor trans to NO+ causes “trans strengthening” of this ligand for [Ru(NO)Cl(pida)], whereas placement of pyridyl groups cis to NO+ causes a weakening of the N-O bond and a lower NO stretching frequency in the dpa-based complexes. PMID:18475928

  7. Interaction between active ruthenium complex [RuCl3(dppb)(VPy)] and phospholipid Langmuir monolayers: Effects on membrane electrical properties

    NASA Astrophysics Data System (ADS)

    Sandrino, B.; Wrobel, E. C.; Nobre, T. M.; Caseli, L.; Lazaro, S. R.; Júnior, A. C.; Garcia, J. R.; Oliveira, O. N.; Wohnrath, K.

    2016-04-01

    We report on the interaction between mer-[RuCl3(dppb)(VPy)] (dppb = 1,4-bis(diphenylphosphine)butane and VPy = 4-vinylpyridine) (RuVPy) and dipalmitoyl phosphatidyl serine (DPPS), in Langmuir and Langmuir-Blodgett (LB) films. Interaction of RuVPy with DPPS, which predominates in cancer cell membranes, should be weaker than for other phospholipids since RuVPy is less toxic to cancer cells than to healthy cells. Incorporation of RuVPy induced smaller changes in electrochemical properties of LB films of DPPS than for other phospholipids, but the same did not apply to surface pressure isotherms. This calls for caution in establishing correlations between effects from a single property and phenomena on cell membranes.

  8. Electrochemical deposition of poly(trans-[RuCl2(4-vinylpyridine)4]) and its reductive desorption: cyclic voltammetry and electrochemical quartz crystal microbalance studies.

    PubMed

    Bandeira, Merlin C E; Crayston, Joe A; Franco, César V; Glidle, Andrew

    2007-02-28

    The electropolymerization of trans-[RuCl(2)(vpy)(4)](vpy = 4-vinylpyridine) on Au or Pt electrodes was studied by cyclic voltammetry and the electrochemical quartz crystal microbalance (EQCM) technique. Cyclic voltammetry of the monomer in DMSO on Au shows reductions at -2.0 and -2.2 V. Potential cycling over the first wave leads to polymer formation; however, scanning over the second wave leads to desorption of the polymer. These observations were confirmed by EQCM measurements which also revealed a high polymerization efficiency. Electrolysis, EQCM and XPS measurements showed that desorption was associated with substitution of chloride ligands by DMSO when the polymer was in a highly reduced state. The film also showed reversible mass changes due to the oxidation and accompanying ingress of charge-balancing anions and solvent into the film. Measurements on the dried films revealed that large quantities of solvent are trapped in the film during the electropolymerization process. PMID:17301891

  9. Covalency in Metal-Oxygen Multiple Bonds Evaluated Using Oxygen K-edge Spectroscopy and Electronic Structure Theory

    SciTech Connect

    Minasian, Stefan G.; Keith, Jason M.; Batista, Enrique R.; Boland, Kevin S.; Bradley, Joseph A.; Daly, Scott R.; Kozimor, Stosh A.; Lukens, Wayne W.; Martin, Richard L.; Nordlund, Dennis; Seidler, Gerald T.; Shuh, David K.; Sokaras, Dimosthenis; Tyliszczak, Tolek; Wagner, Gregory L.; Weng, Tsu-Chein; Yang, Ping

    2014-01-01

    Advancing theories of how metal oxygen bonding influences metal oxo properties can expose new avenues for innovation in materials science, catalysis, and biochemistry. Historically, spectroscopic analyses of the transition metal peroxyanions, MO4x-, have formed the basis for new M O bonding theories. Herein, relative changes in M O orbital mixing in MO42- (M = Cr, Mo, W) and MO41- (M = Mn, Tc, Re) are evaluated for the first time by non-resonant inelastic X-ray scattering, X-ray absorption spectroscopy using fluorescence and transmission (via a scanning transmission X-ray microscope), and linear-response density functional theory. The results suggest that moving from Group 6 to Group 7 or down the triads increases M O e () mixing. Meanwhile, t2 mixing ( + ) remains relatively constant within the same Group. These unexpected changes in frontier orbital energy and composition are evaluated in terms of periodic trends in d orbital energy and radial extension.

  10. Improved anode materials for lithium-ion batteries comprise non-covalently bonded graphene and silicon nanoparticles

    NASA Astrophysics Data System (ADS)

    Ye, Yun-Sheng; Xie, Xiao-Lin; Rick, John; Chang, Feng-Chih; Hwang, Bing-Joe

    2014-02-01

    Si, when compared to conventional graphite, offers an order-of-magnitude improvement as a high capacity anode material for Li-ion batteries. Despite significant advances in nanostructured Si-based anodes, the formation of stable Si anodes remains a challenge, due to the significant volume changes that occur during lithiation and delithiation. Si/graphene composites, with graphene sheets and Si nanoparticles bound in a dispersion obtained by a self-assembly technique using non-covalent electrostatic attraction (following thermal processing to remove residual organic material) are used to prepare Si-based anodes for use in Li-ion batteries. A mesoporous structure, obtained by further thermal processing is able to accommodate large Si nanoparticle volume changes during cycling, thereby facilitating Li-ion diffusion within the electrode. Morphological analysis showed that Si nanoparticles are homogeneously distributed on the graphene sheets, which is thought to account for the excellent electrochemical performance of the resulting Si/graphene composite. A composite containing Si 67.3 wt% exhibits a greatly improved capacity and cycling stability in comparison with bare Si in combination with the thermal reduction of a simple mixture of graphene oxide and Si nanoparticles without electrostatic attraction (Si content = 64.6 wt%; capacity of 512 mAh g-1 in 40th cycle).

  11. Kinetics of rapid covalent bond formation of aniline with humic acid: ESR investigations with nitroxide spin labels

    NASA Astrophysics Data System (ADS)

    Glinka, Kevin; Matthies, Michael; Theiling, Marius; Hideg, Kalman; Steinhoff, Heinz-Jürgen

    2016-04-01

    Sulfonamide antibiotics used in livestock farming are distributed to farmland by application of slurry as fertilizer. Previous work suggests rapid covalent binding of the aniline moiety to humic acids found in soil. In the current work, kinetics of this binding were measured in X-band EPR spectroscopy by incubating Leonardite humic acid (LHA) with a paramagnetic aniline spin label (anilino-NO (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl)). Binding was detected by a pronounced broadening of the spectral lines after incubation of LHA with anilino-NO. The time evolution of the amplitude of this feature was used for determining the reaction kinetics. Single- and double-exponential models were fitted to the data obtained for modelling one or two first-order reactions. Reaction rates of 0.16 min-1 and 0.012 min-1, were found respectively. Addition of laccase peroxidase did not change the kinetics but significantly enhanced the reacting fraction of anilino-NO. This EPR-based method provides a technically simple and effective method for following rapid binding processes of a xenobiotic substance to humic acids.

  12. Synthesis, catalytic properties and biological activity of new water soluble ruthenium cyclopentadienyl PTA complexes [(C5R5)RuCl(PTA)2] (R = H, Me; PTA = 1,3,5-triaza-7-phosphaadamantane).

    PubMed

    Akbayeva, Dina N; Gonsalvi, Luca; Oberhauser, Werner; Peruzzini, Maurizio; Vizza, Francesco; Brüggeller, Peter; Romerosa, Antonio; Sava, Gianni; Bergamo, Alberta

    2003-01-21

    The new water soluble ruthenium complexes [(C5R5)RuCl(PTA)2] (R = H, Me; PTA = 1,3,5-triaza-7-phosphaadamantane) were synthesised and characterised. Their evaluation as regioselective catalysts for hydrogenation of unsaturated ketones in aqueous biphasic conditions and as cytotoxic agents towards the TS/A adenocarcinoma cell line is briefly presented. PMID:12585422

  13. Covalent Chemistry beyond Molecules.

    PubMed

    Jiang, Juncong; Zhao, Yingbo; Yaghi, Omar M

    2016-03-16

    Linking molecular building units by covalent bonds to make crystalline extended structures has given rise to metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), thus bringing the precision and versatility of covalent chemistry beyond discrete molecules to extended structures. The key advance in this regard has been the development of strategies to overcome the "crystallization problem", which is usually encountered when attempting to link molecular building units into covalent solids. Currently, numerous MOFs and COFs are made as crystalline materials in which the large size of the constituent units provides for open frameworks. The molecular units thus reticulated become part of a new environment where they have (a) lower degrees of freedom because they are fixed into position within the framework; (b) well-defined spatial arrangements where their properties are influenced by the intricacies of the pores; and (c) ordered patterns onto which functional groups can be covalently attached to produce chemical complexity. The notion of covalent chemistry beyond molecules is further strengthened by the fact that covalent reactions can be carried out on such frameworks, with full retention of their crystallinity and porosity. MOFs are exemplars of how this chemistry has led to porosity with designed metrics and functionality, chemically-rich sequences of information within their frameworks, and well-defined mesoscopic constructs in which nanoMOFs enclose inorganic nanocrystals and give them new levels of spatial definition, stability, and functionality. PMID:26863450

  14. Thermal, optical and photoinduced properties of a series of homo and co-polyimides with two kinds of covalently bonded azo-dyes and their supramolecular counterparts

    NASA Astrophysics Data System (ADS)

    Konieczkowska, Jolanta; Wojtowicz, Magdalena; Sobolewska, Anna; Noga, Joanna; Jarczyk-Jedryka, Anna; Kozanecka-Szmigiel, Anna; Schab-Balcerzak, Ewa

    2015-10-01

    The paper describes the synthesis and characterization of new aromatic polyimides with one or two different moieties of the azo-dyes covalently attached to the polymer backbone and their supramolecular analogues. Azo-functionalized polyimides were prepared using post-polymerization method including the introduction of Disperse Red 13 and/or 4-[4-(6-hydroxyhexyloxy)phenylazo]pyridine to homo and co-polyimides containing hydroxyl groups via Mitsunobu reaction. The degree of functionalization of polymers with chromophores was estimated by UV-Vis spectroscopy. Polyimides containing hydroxyl groups were applied as matrixes to create supramolecular systems based on hydrogen bonds. Hydrogen-bond interactions in azosystems were studied by FTIR spectroscopy. The polymers were characterized by 1H NMR, FTIR, X-ray, UV-Vis, DSC and TGA methods. The photoisomerization process was investigated in supramolecular systems. The light-induced anisotropy was studied in a holographic gratings recording experiment and by photoinduced birefringence measurements. The polymer films were investigated by atomic force microscopy (AFM) after the diffraction grating recording to confirm formation of surface relief gratings (SRGs). To the best of our knowledge, that the first time photoinduced anisotropy has been studied by birefringence measurements in polyimides containing two different azo-dyes.

  15. Oxidation and aging in U and Pu probed by spin-orbit sum rule analysis: indications for covalent metal-oxide bonds

    SciTech Connect

    Moore, K; der Laan, G v; Haire, R; Wall, M; Schwartz, A

    2005-10-07

    Transmission electron microscopy is used to acquire electron energy-loss spectra from phase-specific regions of Pu and U metal, PuO{sub 2} and UO{sub 2}, and aged, self-irradiated Pu metal. The N{sub 4,5} (4d {yields} 5f) spectra are analyzed using the spin-orbit sum rule. Our results show that the technique is sensitive enough to detect changes in the branching ratio of the white-line peaks between the metal and dioxide of both U and Pu. There is a small change in the branching ratio between different Pu metals, and the data trends as would be expected for varying f electron localization, i.e., {alpha}-Pu, {delta}-Pu, aged {delta}-Pu. Moreover, our results suggest that the metal-oxide bonds in UO{sub 2} and PuO{sub 2} are strongly covalent in nature and do not exhibit an integer valence change as would be expected from purely ionic bonding.

  16. Chloramphenicol Biosynthesis: The Structure of CmlS, a Flavin-Dependent Halogenase Shwing a Covalent Flavin-Aspartate Bond

    SciTech Connect

    Podzelinska, K.; Latimer, R; Bhattacharya, A; Vining, L; Zechel, D; Jia, Z

    2010-01-01

    Chloramphenicol is a halogenated natural product bearing an unusual dichloroacetyl moiety that is critical for its antibiotic activity. The operon for chloramphenicol biosynthesis in Streptomyces venezuelae encodes the chloramphenicol halogenase CmlS, which belongs to the large and diverse family of flavin-dependent halogenases (FDH's). CmlS was previously shown to be essential for the formation of the dichloroacetyl group. Here we report the X-ray crystal structure of CmlS determined at 2.2 {angstrom} resolution, revealing a flavin monooxygenase domain shared by all FDHs, but also a unique 'winged-helix' C-terminal domain that creates a T-shaped tunnel leading to the halogenation active site. Intriguingly, the C-terminal tail of this domain blocks access to the halogenation active site, suggesting a structurally dynamic role during catalysis. The halogenation active site is notably nonpolar and shares nearly identical residues with Chondromyces crocatus tyrosyl halogenase (CndH), including the conserved Lys (K71) that forms the reactive chloramine intermediate. The exception is Y350, which could be used to stabilize enolate formation during substrate halogenation. The strictly conserved residue E44, located near the isoalloxazine ring of the bound flavin adenine dinucleotide (FAD) cofactor, is optimally positioned to function as a remote general acid, through a water-mediated proton relay, which could accelerate the reaction of the chloramine intermediate during substrate halogenation, or the oxidation of chloride by the FAD(C4{alpha})-OOH intermediate. Strikingly, the 8{alpha} carbon of the FAD cofactor is observed to be covalently attached to D277 of CmlS, a residue that is highly conserved in the FDH family. In addition to representing a new type of flavin modification, this has intriguing implications for the mechanism of FDHs. Based on the crystal structure and in analogy to known halogenases, we propose a reaction mechanism for CmlS.

  17. The structure of Na{sub 3}SbTe{sub 3}: How ionic and covalent bonding forces work together

    SciTech Connect

    Lin, Jianhua; Miller, G.J.

    1994-12-01

    The compound Na{sub 3}SbTe{sub 3} has been synthesized from the elements and characterized by single crystal X-ray diffraction. Na{sub 3}SbTe{sub 3} is cubic, crystallizing in the cP28 structure type (isomorphous with Na{sub 3}AsS{sub 3}); space group P2{sub 1}3 (No. 198); a=9.6114(9) {angstrom}; Z = 4; R1 = 0.0324; wR2 = 0.0561 (I {le} 2{sigma}(I)). The structure consists of isolated sodium cations and trigonal pyramidal [SbTe{sub 3}]{sup {minus}3} anions with a Sb-Te bond length of 2.787(1) {angstrom} and a Te-Sb-Te bond angle of 100.0(1){degrees}. The structure is related to both the Li{sub 3}Bi and K{sub 3}AsS{sub 4}-type structures. Both lattice energy and semiempirical electronic structure calculations are utilized to evaluate various local and long-range structural aspects of this Zintl phase.

  18. Direct Covalent Grafting of Phytate to Titanium Surfaces through Ti-O-P Bonding Shows Bone Stimulating Surface Properties and Decreased Bacterial Adhesion.

    PubMed

    Córdoba, Alba; Hierro-Oliva, Margarita; Pacha-Olivenza, Miguel Ángel; Fernández-Calderón, María Coronada; Perelló, Joan; Isern, Bernat; González-Martín, María Luisa; Monjo, Marta; Ramis, Joana M

    2016-05-11

    Myo-inositol hexaphosphate, also called phytic acid or phytate (IP6), is a natural molecule abundant in vegetable seeds and legumes. Among other functions, IP6 inhibits bone resorption. It is adsorbed on the surface of hydroxyapatite, inhibiting its dissolution and decreasing the progressive loss of bone mass. We present here a method to directly functionalize Ti surfaces covalently with IP6, without using a cross-linker molecule, through the reaction of the phosphate groups of IP6 with the TiO2 layer of Ti substrates. The grafting reaction consisted of an immersion in an IP6 solution to allow the physisorption of the molecules onto the substrate, followed by a heating step to obtain its chemisorption, in an adaptation of the T-Bag method. The reaction was highly dependent on the IP6 solution pH, only achieving a covalent Ti-O-P bond at pH 0. We evaluated two acidic pretreatments of the Ti surface, to increase its hydroxylic content, HNO3 30% and HF 0.2%. The structure of the coated surfaces was characterized by X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and ellipsometry. The stability of the IP6 coating after three months of storage and after sterilization with γ-irradiation was also determined. Then, we evaluated the biological effect of Ti-IP6 surfaces in vitro on MC3T3-E1 osteoblastic cells, showing an osteogenic effect. Finally, the effect of the surfaces on the adhesion and biofilm viability of oral microorganisms S. mutans and S. sanguinis was also studied, and we found that Ti-IP6 surfaces decreased the adhesion of S. sanguinis. A surface that actively improves osseointegration while decreasing the bacterial adhesion could be suitable for use in bone implants. PMID:27088315

  19. Simple bond-order-type interatomic potential for an intermixed Fe-Cr-C system of metallic and covalent bondings in heat-resistant ferritic steels

    SciTech Connect

    Kumagai, Tomohisa Nakamura, Kaoru; Yamada, Susumu; Ohnuma, Toshiharu

    2014-12-28

    It is known that M{sub 23}C{sub 6}(M = Cr/Fe) behavior in heat-resistant ferritic steels affects the strength of the material at high temperature. The ability to garner direct information regarding the atomic motion using classical molecular dynamics simulations is useful for investigating the M{sub 23}C{sub 6} behavior in heat-resistant ferritic steels. For such classical molecular dynamics calculations, a suitable interatomic potential is needed. To satisfy this requirement, an empirical bond-order-type interatomic potential for Fe-Cr-C systems was developed because the three main elements to simulate the M{sub 23}C{sub 6} behavior in heat-resistant ferritic steels are Fe, Cr, and C. The angular-dependent term, which applies only in non-metallic systems, was determined based on the similarity between a Finnis-Sinclair-type embedded-atom-method interatomic potential and a Tersoff-type bond-order potential. The potential parameters were determined such that the material properties of Fe-Cr-C systems were reproduced. These properties include the energy and lattice constants of 89 crystal structures; the elastic constants of four realistic precipitates; the bulk moduli of B1, B2, and B3 crystals; the surface energies of B1 and B2 crystals; and the defect-formation energies and atomic configurations of 66 Fe-Cr-C complexes. Most of these material properties were found to be reproduced by our proposed empirical bond-order potentials. The formation energies and lattice constants of randomly mixed Fe-Cr alloys calculated using the interatomic potentials were comparable to those obtained through experiments and first-principles calculations. Furthermore, the energies and structures of interfaces between Cr carbide and α-Fe as predicted through first-principles calculations were well reproduced using these interatomic potentials.

  20. Supramolecular architectures constructed by lanthanum, amino acids and 1,10-phenanthroline via non-covalent bond interactions

    NASA Astrophysics Data System (ADS)

    Zheng, Xiang-Jun; Jin, Lin-Pei

    2003-07-01

    Three supramolecular lanthanum coordination compounds of amino acids, with 1,10-phenanthroline (phen), [La 2(APA) 6(phen) 2(H 2O) 2](ClO 4) 6(phen) 4·2H 2O ( 1), [La 2(ABA) 6(phen) 2(H 2O) 2](ClO 4) 6 (phen) 6·4H 2O ( 2), and [La 2(AHA) 4(phen) 4](ClO 4) 6(phen) 4·2H 2O ( 3) (APA=3-aminopropionic acid; ABA=4-aminobutanoic acid; AHA=6-aminohexanoic acid) were synthesized and characterized by single crystal X-ray diffraction. The results show that the three coordination compounds are all composed of binuclear coordination cations built by metal-ligand coordination. Through hydrogen bonding and π-π stacking interactions, complex 1 forms a two-dimensional supramolecular sheet structure extending in the (001) plane, complex 2 forms a three-dimensional supramolecular network with many cavities occupied by ClO 4- and lattice H 2O molecules, and complex 3 forms a two-dimensional supramolecular lamellar structure in the (100) plane.

  1. Fluorescence and Textural Characterization of Ortho-Amine Tetraphenylporphyrin Covalently Bonded to Organo-Modified Silica Xerogels.

    PubMed

    García-Sánchez, M A; Serratos, I N; Sosa, R; Rojas-González, F; Tello-Solís, S R; Tapia-Esquivel, T; González-García, F; Esparza-Schulz, J M; Huerta-Figueroa, D E

    2016-09-01

    Most of the studies performed with porphyrins involve these species functionalized with peripheral substituents lying on the same macrocyclic molecular plane. The main objective of this work deals with the successful preservation and optimization of the fluorescence of a uncommonly used porphyrin species, i.e. tetrakis-(ortho-amino-phenyl)-porphyrin; a molecule with substituents localized not only at one but at both sides of its molecular plane. In cases like this, it must be stressed that fluorescence can only be partially preserved; nevertheless, intense fluorescence can still be reached by following a twofold functionalization strategy involving: (i) the bonding of substituted macrocycles to the pore walls of (ii) organo-modified silica monoliths synthesized by the sol-gel method. The analysis of both absorption and emission UV spectra evidenced a radiation energy transfer taking place between the porphyrin and the host silica matrix. Our results showed that the adequate displaying of the optical properties of macrocyclic species trapped in SiO2 xerogels depend on the polarity existing inside the pores, a property which can be tuned up through the adequate selection of organic groups used to modify the surface of the pore cavities. Additionally, the pore widths attained in the final xerogels can vary depending on the identity of the organic groups attached to the network. All these facts finally demonstrated that, even if using inefficient surface functionalization species, such as ortho-substituted tetraphenylporphyrins, it is still possible to modulate the pore shape, pore size, and physicochemical environment created around the trapped macrocycles. The most important aspect related to this research deals with the fact that the developed methodology offers a real possibility of controlling both the textural and morphological characteristics of a new kind of hybrid porous materials and to optimize the physicochemical properties of diverse active molecules

  2. Succinimidyl residue formation in hen egg-white lysozyme favors the formation of intermolecular covalent bonds without affecting its tertiary structure.

    PubMed

    Desfougères, Yann; Jardin, Julien; Lechevalier, Valérie; Pezennec, Stéphane; Nau, Françoise

    2011-01-10

    Protein chemical degradations occur naturally into living cells as soon as proteins have been synthesized. Among these modifications, deamidation of asparagine or glutamine residues has been extensively studied, whereas the intermediate state, a succinimide derivative, was poorly investigated because of the difficulty of isolating those transient species. We used an indirect method, a limited thermal treatment in the dry state at acidic pH, to produce stable cyclic imide residues in hen lysozyme molecules, enabling us to examine the structural and functional properties of so modified proteins. Five cyclic imide rings have been located at sites directly accessible to solvent and did not lead to any changes in secondary or tertiary structures. However, they altered the catalytic properties of lysozyme and significantly decreased the intrinsic stability of the molecules. Moreover, dimerization occurred during the treatment, and this phenomenon was proportional to the extent of chemical degradation. We propose that succinimide formation could be responsible for covalent bond formation under specific physicochemical conditions that could be found in vivo. PMID:21166442

  3. Role of composition, bond covalency, and short-range order in the disordering of stannate pyrochlores by swift heavy ion irradiation

    NASA Astrophysics Data System (ADS)

    Tracy, Cameron L.; Shamblin, Jacob; Park, Sulgiye; Zhang, Fuxiang; Trautmann, Christina; Lang, Maik; Ewing, Rodney C.

    2016-08-01

    A2S n2O7 (A =Nd ,Sm,Gd,Er,Yb,and Y) materials with the pyrochlore structure were irradiated with 2.2 GeV Au ions to systematically investigate disordering of this system in response to dense electronic excitation. Structural modifications were characterized, over multiple length scales, by transmission electron microscopy, x-ray diffraction, and Raman spectroscopy. Transformations to amorphous and disordered phases were observed, with disordering dominating the structural response of materials with small A -site cation ionic radii. Both the disordered and amorphous phases were found to possess weberite-type local ordering, differing only in that the disordered phase exhibits a long-range, modulated arrangement of weberite-type structural units into an average defect-fluorite structure, while the amorphous phase remains fully aperiodic. Comparison with the behavior of titanate and zirconate pyrochlores showed minimal influence of the high covalency of the Sn-O bond on this phase behavior. An analytical model of damage accumulation was developed to account for simultaneous amorphization and recrystallization of the disordered phase during irradiation.

  4. Molecular orbitals vs. relativistic orbitals in t2g honeycomb lattices: SrRu2O6 as compared to Na2IrO3, RuCl3, and Li2RuO3

    NASA Astrophysics Data System (ADS)

    Mazin, Igor; Streltsov, Sergey; Foyevtseva, Kateryna

    t2g states on a honeycomb lattice tend to form non-dispersive localized states even if large intersite hopping is present. In the nonrelativistic case, these are molecular orbitals (MO) localized on metal hexagons, if the ligand-assisted nearest and next nearest neighbor hoppings, t1' and t2', dominate, or dimers (DO), if the direct overlap, t1, dominates. In the ultrarelativistic limit t2 g form effective relativistic orbitals (RO), jeff = 3/3 2 2, which are atomically localized if t1'is the dominant hopping. On the first glance, the three regimes are defined by the conditions t1' >>t1 , λ or t1 >>t1' , λ or λ >>t1 ,t1' . In reality, the latter condition is never fulfilled, especially in ruthenates, yet not only Na2IrO3, but also RuCl3 appear to be in a regime dominated by RO, even though the residual effect of MO critically influences magnetic interactions, while Li2RuO3, not far removed from RuCl3 in the parameter space, is firmly in the DO regime. Most surprisingly, SrRu2O6, which is even closer to RuCl3, happens to be fully in the MO regime, with negligible spin-orbit effects. In this talk, we will show that an additional, decisive factor is the doping level per site. The principal difference between Na2IrO3 or RuCl3, Li2RuO3, and SrRu2O6 is that the first two have one t2 ghole per site, the second one two holes, and the last three electrons. In particular, the total dominance of MO in the latter compound fully explains its unique and unexpected magnetic properties. This work was supported by ONR (IIM) and CRDF (IIM and SVS).

  5. A New Crosslinkable Oxygen Sensor Covalently Bonded into Poly(2-hydroxyethyl methacrylate)-CO-Polyacrylamide Thin Film for Dissolved Oxygen Sensing

    PubMed Central

    Tian, Yanqing; Shumway, Bradley R.; Meldrum, Deirdre R.

    2010-01-01

    A new oxygen sensor, compound 2, was synthesized through a chemical modification of a popularly used oxygen sensor of platinum(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorophenyl)-porphyrin (PtTFPP). The new sensor compound 2 possesses four crosslinkable methacrylate functional moieties, enabling it to be polymerized and crosslinked with other monomers for polymer sensing film (also called membrane) preparation. Using this characteristic, compound 2 was covalently bonded to hydrophilic poly(2-hydroxyethyl methacrylate)-co-polyacrylamide (referred to as PHEMA to simplify) and hydrophobic polystyrene (PS) films. To better understand the advantages and disadvantages of chemical crosslinking approaches and the influence of polymer matrices on sensing performance, PtTFPP was physically incorporated into the same PHEMA and PS matrices to compare. Response to dissolved oxygen (DO), leaching of the sensor molecules from their matrices, photostability of the sensors, and response time to DO changes were studied. It was concluded that the chemical crosslinking of the sensor compound 2 in polymer matrices: (i) alleviated the leaching problem of sensor molecules which usually occurred in the physically doped sensing systems and (ii) significantly improved sensors’ photostability. The PHEMA matrix was demonstrated to be more suitable for oxygen sensing than PS, because for the same sensor molecule, the oxygen sensitivity in PHEMA film was higher than that in PS and response time to DO change in the PHEMA film was faster than that in PS. It was the first time oxygen sensing films were successfully prepared using biocompatible hydrophilic PHEMA as a matrix, which does not allow leaching of the sensor molecules from the polymer matrix, has a faster response to DO changes than that of PS, and does not present cytotoxicity to human lung adenocarcinoma epithelial cells (A549). It is expected that the new sensor compound 2 and its similar compounds with chemically crosslinking

  6. Injectable Hydrogel: Amplifying the pH Sensitivity of a Triblock Copolypeptide by Conjugating the N-Termini via Dynamic Covalent Bonding.

    PubMed

    Popescu, Maria-Teodora; Liontos, George; Avgeropoulos, Apostolos; Voulgari, Efstathia; Avgoustakis, Konstantinos; Tsitsilianis, Constantinos

    2016-07-13

    We explore the self-assembly behavior of aqueous solutions of an amphiphilic, pH-sensitive poly(l-alanine)-b-poly(l-glutamic acid)-b-poly(l-alanine), (A5E11A5) triblock copolypeptide, end-capped by benzaldehyde through Schiff base reaction. At elevated concentrations and under physiological pH (7.4) and ionic strength (0.15M), the bare copolypeptide aqueous solutions underwent a sol-gel transition after heating and slow cooling thermal treatment, forming opaque stiff gels due to a hierarchical self-assembly that led to the formation of β-sheet-based twisted super fibers (Popescu et al. Soft Matter 2015, 11, 331-342). The conjugation of the N-termini with benzaldehyde (Bz) through a Schiff base reaction amplifies the copolypeptide pH-sensitivity within a narrow pH window relevant for in vivo applications. Specifically, the dynamic character of the imine bond allowed coupling/decoupling of the Bz upon switching pH. The presence of Bz conjugates to the N-termini of the copolypeptide resulted in enhanced packing of the elementary superfibers into thick and short piles, which inhibited the ability of the system for gelation. However, partial cleavage of Bz upon lowering pH to 6.5 prompted recovery of the hydrogel. The sol-gel transition triggered by pH was reversible, due to the coupling/decoupling of the benzoic-imine dynamic covalent bonding, endowing thus the gelling system with injectability. Undesirably, the gelation temperature window was significantly reduced, which however can be regulated at physiological temperatures by using a suitable mixture of the bare and the Bz-conjugated coplypeptide. This triblock copolypeptide gelator was investigated as a scaffold for the encapsulation of polymersome nanocarriers, loaded with a hydrophilic model drug, calcein. The polymersome/polypeptide complex system showed prolonged probe release in pH 6.5, which is relevant to extracellular tumor environment, rendering the system potentially useful for sustained delivery of

  7. Half-sandwich RuCl2(η(6)-p-cymene) core complexes containing sulfur donor aroylthiourea ligands: DNA and protein binding, DNA cleavage and cytotoxic studies.

    PubMed

    Jeyalakshmi, Kumaramangalam; Haribabu, Jebiti; Bhuvanesh, Nattamai S P; Karvembu, Ramasamy

    2016-08-01

    A series of Ru(ii)(η(6)-p-cymene) complexes (1-4) bearing the general formula [RuCl2(η(6)-p-cymene)L] (L = monodentate aroylthiourea ligand) has been synthesized and characterized by analytical and various spectroscopic techniques. The neutral monodentate coordination of aroylthiourea with Ru via an S atom was confirmed by single crystal X-ray diffraction study. The complexes were tested for their ability to interact with DNA and protein. The complexes bound with calf thymus DNA (CT DNA) with the intrinsic binding constant value in the order of 10(4) M(-1). The intercalative mode of binding was confirmed by the ethidium bromide (EB) displacement study. The interaction of the complexes with CT DNA was further supported by viscosity measurements and circular dichroic (CD) spectra. The Ru(ii) complexes cleaved the supercoiled DNA without the need of any external agent. The spectroscopic evidence showed good binding efficacy of the complexes with BSA (Bovine Serum Albumin). The alterations in the secondary structure of BSA by the Ru(ii) complexes were confirmed by synchronous fluorescence spectra. Cytotoxicity examination by MTT assay was carried out in two cancer cell lines (MCF7 and A549) and one non-cancerous cell line (L929). Complex 4 showed significant activity [IC50 = 52.3 (MCF7) and 54.6 (A549) μM] which was comparable with that of similar known complexes. The morphological changes assessed by Hoechst staining revealed that the cell death occurred by apoptosis. PMID:27435011

  8. Constructing monocrystalline covalent organic networks by polymerization

    NASA Astrophysics Data System (ADS)

    Beaudoin, Daniel; Maris, Thierry; Wuest, James D.

    2013-10-01

    An emerging strategy for making ordered materials is modular construction, which connects preformed molecular subunits to neighbours through interactions of properly selected reactive sites. This strategy has yielded remarkable materials, including metal-organic frameworks joined by coordinative bonds, supramolecular networks linked by strong non-covalent interactions, and covalent organic frameworks in which atoms of carbon and other light elements are bonded covalently. However, the strategy has not yet produced covalently bonded organic materials in the form of large single crystals. Here we show that such materials can result from reversible self-addition polymerizations of suitably designed monomers. In particular, monomers with four tetrahedrally oriented nitroso groups polymerize to form diamondoid azodioxy networks that can be fully characterized by single-crystal X-ray diffraction. This work forges a strong new link between polymer science and supramolecular chemistry by showing how predictably ordered covalent or non-covalent structures can both be built using a single modular strategy.

  9. Multiple light-induced NO linkage isomers in the dinitrosyl complex [RuCl(NO)2(PPh3)2]BF4 unravelled by photocrystallographic and IR analysis

    PubMed Central

    Casaretto, Nicolas; Pillet, Sebastien; Bendeif, El Eulmi; Schaniel, Dominik; Gallien, Anna K. E.; Klüfers, Peter; Woike, Theo

    2015-01-01

    Multiple light-induced reversible metastable NO linkage isomers (PLIs) have been detected in the dinitrosyl compound [RuCl(NO)2(PPh3)2]BF4 by a combination of photocrystallographic and IR analysis. The IR signature of three PLI states has been clearly identified, with estimated populations of 59% (PLI-1), 8% (PLI-2) and 5% (PLI-3) for a total population of the metastable state of 72%. The structural configuration of the major component (PLI-1) has been derived by X-ray photocrystallography. In the ground state, the structure is characterized by a bent and a linear nitrosyl, the bent one being oriented towards the linear equatorial nitrosyl with an Ru—N—O angle of 133.88 (9)°. X-ray Fourier difference maps indicate a selectivity of the photo-isomerization process in PLI-1: only the bent NO ligand changes its position, while the linear NO is unaffected. After irradiation at 405 nm, the orientation is changed by rotation towards the Cl ligand opposite the linear NO, with an Ru—N—O angle in this new position of 109 (1)°. The photocrystallographic analysis provides evidence that, in the photo-induced metastable state, the bent NO group is attached to the Ru atom through the N atom (Ru—N—O), rather than in an isonitrosyl Ru—O—N binding mode. In the IR spectra, the asymmetric NO vibrational band shifts by −33 cm−1 to a lower value, whereas the symmetric band splits and shifts by 5 cm−1 to a higher value and by −8 cm−1 to a lower value. The down shift is a clear indication of the structural change, and the small upward shift in response to the new electronic configuration of the metastable structure. Variable-temperature IR kinetic measurements in the range 80–114 K show that the decay of the PLI-1 state follows an Arrhenius behaviour with an activation energy of 0.22 eV. PMID:25610626

  10. Multiple light-induced NO linkage isomers in the dinitrosyl complex [RuCl(NO)2(PPh3)2]BF4 unravelled by photocrystallographic and IR analysis.

    PubMed

    Casaretto, Nicolas; Pillet, Sebastien; Bendeif, El Eulmi; Schaniel, Dominik; Gallien, Anna K E; Klüfers, Peter; Woike, Theo

    2015-01-01

    Multiple light-induced reversible metastable NO linkage isomers (PLIs) have been detected in the dinitrosyl compound [RuCl(NO)2(PPh3)2]BF4 by a combination of photocrystallographic and IR analysis. The IR signature of three PLI states has been clearly identified, with estimated populations of 59% (PLI-1), 8% (PLI-2) and 5% (PLI-3) for a total population of the metastable state of 72%. The structural configuration of the major component (PLI-1) has been derived by X-ray photocrystallography. In the ground state, the structure is characterized by a bent and a linear nitrosyl, the bent one being oriented towards the linear equatorial nitrosyl with an Ru-N-O angle of 133.88 (9)°. X-ray Fourier difference maps indicate a selectivity of the photo-isomerization process in PLI-1: only the bent NO ligand changes its position, while the linear NO is unaffected. After irradiation at 405 nm, the orientation is changed by rotation towards the Cl ligand opposite the linear NO, with an Ru-N-O angle in this new position of 109 (1)°. The photocrystallographic analysis provides evidence that, in the photo-induced metastable state, the bent NO group is attached to the Ru atom through the N atom (Ru-N-O), rather than in an isonitrosyl Ru-O-N binding mode. In the IR spectra, the asymmetric NO vibrational band shifts by -33 cm(-1) to a lower value, whereas the symmetric band splits and shifts by 5 cm(-1) to a higher value and by -8 cm(-1) to a lower value. The down shift is a clear indication of the structural change, and the small upward shift in response to the new electronic configuration of the metastable structure. Variable-temperature IR kinetic measurements in the range 80-114 K show that the decay of the PLI-1 state follows an Arrhenius behaviour with an activation energy of 0.22 eV. PMID:25610626

  11. Photo-aquation of cis-[RuCl2(mPTA)4](CF3SO3)4 in water (mPTA = N-methyl-1,3,5-triaza-7-phosphaadamantane).

    PubMed

    Girotti, Rugiada; Romerosa, Antonio; Mañas, Sonia; Serrano-Ruiz, Manuel; Perutz, Robin

    2011-01-28

    On irradiating the complex cis-[RuCl(2)(mPTA)(4)](CF(3)SO(3))(4) (2) with near UV light at room temperature, (OC-6-13)-[RuCl(2)(mPTA)(3)(H(2)O)](CF(3)SO(3))(3) (3) was obtained. Complex 3 is the product of the substitution in 2 of one mPTA by a H(2)O molecule and the rearrangement from cis to trans of the two chlorides. The selective photo-reaction of 2 is produced with radiation of 300 < λ < 400 nm or with λ = 367 nm in 50 min (Φ(367 nm) (D(2)O) = 0.18 ± 0.01). The reaction is not reversible with visible light. The transformation of 2 into 3 is not dependent on the pH but only on the radiation used. Reaction of 3 with NaCl leads to (OC-6-21)-[RuCl(3)(mPTA)(3)](CF(3)SO(3))(2) (4) which could be directly obtained by irradiation of 2 with λ = 367 nm in water and 5 eq. of NaCl (Φ(367 nm) (D(2)O) = 0.17 ± 0.01). Complex 4 turns slowly to 2 in water with 1 eq. of mPTA under light of λ > 416 nm. Complete conversion of 4 into 2 was achieved after more than one day. All complexes were characterized by elemental analysis, IR and NMR spectroscopy, and 2, 3 and 4 by single crystal X-ray determination. An easy synthesis for the ligand mPTA(CF(3)SO(3)) is also reported. PMID:21135936

  12. Synthesis and spectral studies of [RuCl(CO)(L)(PPh 3)(B)] (HL = 2'-hydroxychalcones and B = PPh 3, pyridine or piperidine) and their catalytic and biological applications

    NASA Astrophysics Data System (ADS)

    Kaveri, M. V.; Prabhakaran, R.; Karvembu, R.; Natarajan, K.

    2005-10-01

    The reactions of [RuHCl(CO)(PPh 3) 2(B)] (B = PPh 3, pyridine or piperidine) and 2'-hydroxychalcones led to the formation of [RuCl(CO)(PPh 3)(L)(B)] (L = chalconate). The new complexes have been characterized by analytical and spectral (IR, electronic, 1H NMR and 31P NMR) data. They have been assigned an octahedral structure. The complexes have been used as catalysts for the aerial oxidation of cinnamyl alcohol. Some of the complexes have been tested in vitro for growth inhibitory activity against the bacteria E. coli, S. typhi and Pseudomonas sp. and the fungi A. fumigatus.

  13. Stochastic sensing through covalent interactions

    SciTech Connect

    Bayley, Hagan; Shin, Seong-Ho; Luchian, Tudor; Cheley, Stephen

    2013-03-26

    A system and method for stochastic sensing in which the analyte covalently bonds to the sensor element or an adaptor element. If such bonding is irreversible, the bond may be broken by a chemical reagent. The sensor element may be a protein, such as the engineered P.sub.SH type or .alpha.HL protein pore. The analyte may be any reactive analyte, including chemical weapons, environmental toxins and pharmaceuticals. The analyte covalently bonds to the sensor element to produce a detectable signal. Possible signals include change in electrical current, change in force, and change in fluorescence. Detection of the signal allows identification of the analyte and determination of its concentration in a sample solution. Multiple analytes present in the same solution may be detected.

  14. Spontaneous formation of organic helical architectures through dynamic covalent chemistry.

    PubMed

    Li, Wenfang; Dong, Zeyuan; Zhu, Junyan; Luo, Quan; Liu, Junqiu

    2014-12-01

    The spontaneous formation of organic helical structures, accompanied with an amplification of chirality, by dynamic covalent bonds between achiral and chiral building blocks is reported. PMID:25325888

  15. Sulfur K-Edge XAS and DFT Calculations on [Fe4S4]2+Clusters: Effects of H-bonding and Structural Distortion on Covalency and SpinTopology

    SciTech Connect

    Dey, A.; Roche, C.L.; Walters, M.A.; Hodgson, K.O.; B., Hedman; Solomon, E.I.; /Stanford U., Chem. Dept. /SLAC, SSRL

    2006-09-28

    Sulfur K-edge X-ray absorption spectroscopy of a hydrogen-bonded elongated [Fe{sub 4}S{sub 4}]{sup 2+} cube is reported. The data show that this synthetic cube is less covalent than a normal compressed cube with no hydrogen bonding. DFT calculations reveal that the observed difference in electronic structure has significant contributions from both the cluster distortion and from hydrogen bonding. The elongated and compressed Fe{sub 4}S{sub 4} structures are found to have different spin topologies (i.e., orientation of the delocalized Fe{sub 2}S{sub 2} subclusters which are antiferromagnetically coupled to each other). It is suggested that the H-bonding interaction with the counterion does not contribute to the cluster elongation. A magneto-structural correlation is developed for the Fe{sub 4}S{sub 4} cube that is used to identify the redoxactive Fe{sub 2}S{sub 2} subclusters in active sites of HiPIP and ferredoxin proteins involving these clusters.

  16. Solvato-polymorph of [(η6-C6H6)RuCl (L)]PF6 (L = (2,6-dimethyl-phenyl-pyridin-2-yl methylene amine)

    NASA Astrophysics Data System (ADS)

    Gichumbi, Joel M.; Friedrich, Holger B.; Omondi, Bernard

    2016-06-01

    A half-sandwich complex salt of ruthenium containing the Schiff base ligand, 2, 6-dimethyl-N-(pyridin-2-ylmethylene)aniline has been synthesized and structurally characterized. The complex salt 1, [(η6-C6H6)RuCl(C5H4NCHdbnd N(2,6-(CH3)2C6H3)]PF6 was obtained from the reaction of the ruthenium arene precursor, [(η6- C6H6)Ru(μ-Cl)Cl]2 with the Schiff base in a 1:2 ratio followed by treatment with NH4PF6. Its acetone solvate 2, [(η6-C6H6)RuCl(C5H4NCHdbnd N (2, 6- (CH3)2C6H3)]PF6. (CH3)2CO was obtained by recrystallization of 1 from a solution of hexane and acetone. 1 and 2 crystallize in the monoclinic P21/c and P21/n space groups as blocks and as prisms respectively. The ruthenium centers in 1 and 2 are coordinated to the bidentate Schiff base, to a chloride atom, and to the arene ring to give a pseudo-octahedral geometry around them. The whole arrangement is referred to as the familiar three-legged piano stool in which the Schiff base and the Cl atom serve as the base while the arene ring serve as the apex of the stool. Polymorph 2 has an acetone molecule in the asymmetric unit. Of interest is the similar behavior of the solvate on heating which shows the crystals shuttering at about 531.6 and 523.4 K for 1 and 2 respectively.

  17. Synthesis of -C[double bond, length as m-dash]N- linked covalent organic frameworks via the direct condensation of acetals and amines.

    PubMed

    Li, Zhi-Jun; Ding, San-Yuan; Xue, Hua-Dong; Cao, Wei; Wang, Wei

    2016-06-01

    We demonstrate herein a facile approach for constructing -C[double bond, length as m-dash]N- linked COFs from acetals. Three new COFs (imine-linked LZU-20, hydrazone-linked LZU-21, and azine-linked LZU-22) were synthesized by the direct condensation of dimethyl acetals and amines. All the synthesized COFs are highly crystalline and exhibit good thermal stability. PMID:27090755

  18. Hybrid materials of SBA-16 functionalized by rare earth (Eu 3+, Tb 3+) complexes of modified β-diketone (TTA and DBM): Covalently bonding assembly and photophysical properties

    NASA Astrophysics Data System (ADS)

    Li, Yajuan; Yan, Bing; Li, Ying

    2010-04-01

    Novel mesoporous SBA-16 type of hybrids TTA-S16 and DBM-S16 were synthesized by co-condensation of modified β-diketone (TTA-Si and DBM-Si, DBM=1,3-diphenyl-1,3- propanepione, TTA=2-thenoyltrifluoroacetone) and tetraethoxysilane (TEOS) in the presence of Pluronic F127 as template, which were confirmed by FTIR, XRD, 29Si CP-MAS NMR, and N 2 adsorption measurements. Novel organic-inorganic mesoporous luminescent hybrid containing RE3+ (Eu 3+, Tb 3+) complexes covalently attached to the functionalized ordered mesoporous SBA-16 (TTA-S16 and DBM-S16), which were designated as bpy- RE-TTA-S16 and bpy- RE-DBM-S16, were obtained by sol-gel process. The luminescence properties of these resulting materials were characterized in detail, and the results reveal that mesoporous hybrid material bpy-Eu-TTA-S16 present stronger luminescent intensities, longer lifetimes, and higher luminescent quantum efficiencies than the corresponding DBM-containing materials bpy-Eu-DBM-S16, while bpy-Tb-DBM-S16 exhibit the stronger characteristic emission of Tb 3+ and longer lifetime than the corresponding TTA-containing materials bpy-Tb-TTA-S16.

  19. Charge separation and covalent bonding in metal oxide surfaces: A local density functional study on the MgO(001) surface

    SciTech Connect

    Birkenheuer, U. ); Boettger, J.C. ); Roesch, N. )

    1994-05-01

    A first principles local density functional investigation on extended, two-dimensional periodic slab models of the MgO(001) surface is performed, using the linear combination of Gaussian-type orbitals (LCGTO) technique as implemented in the FILMS program package. Stimulated by recent theoretical evidence for a reduced charge separation in MgO(001), a detailed analysis of the charge distribution and its influence on the electrical field above the surface is carried out. Two different methods to quantify the charge separation in the ionic substrate are employed, a local one based on the topological atom approach and a global one derived from the Madelung field of the surface near potential adsorbates. Both procedures lead to a charge separation significantly (10%--20%) below the nominal ionic value of [plus minus]2 a.u. A variational atomic orbital analysis is utilized to discuss the origin of the Mg 3[ital s] and 3[ital p] structures discernible in the crystal orbitals of the MgO slab systems. They are identified as covalent magnesium valence orbital admixtures to the oxygen dominated valence bands in consistence with the reduced charge separation. Their influence on the cohesive energy of crystalline MgO, however, is found to be only 5% ([similar to]0.5 eV).

  20. Structural Analysis of a Viral Ovarian Tumor Domain Protease from the Crimean-Congo Hemorrhagic Fever Virus in Complex with Covalently Bonded Ubiquitin

    SciTech Connect

    Capodagli, Glenn C.; McKercher, Marissa A.; Baker, Erica A.; Masters, Emily M.; Brunzelle, Joseph S.; Pegan, Scott D.

    2014-10-02

    Crimean-Congo hemorrhagic fever (CCHF) virus is a tick-borne, negative-sense, single-stranded RNA [ssRNA(-)] nairovirus that produces fever, prostration, and severe hemorrhages in humans. With fatality rates for CCHF ranging up to 70% based on several factors, CCHF is considered a dangerous emerging disease. Originally identified in the former Soviet Union and the Congo, CCHF has rapidly spread across large sections of Europe, Asia, and Africa. Recent reports have identified a viral homologue of the ovarian tumor protease superfamily (vOTU) within its L protein. This protease has subsequently been implicated in downregulation of the type I interferon immune response through cleavage of posttranslational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15). Additionally, homologues of vOTU have been suggested to perform similar roles in the positive-sense, single-stranded RNA [ssRNA(+)] arteriviruses. By utilizing X-ray crystallographic techniques, the structure of vOTU covalently bound to ubiquitin propylamine, a suicide substrate of the enzyme, was elucidated to 1.7 {angstrom}, revealing unique structural elements that define this new subclass of the OTU superfamily. In addition, kinetic studies were carried out with aminomethylcoumarin (AMC) conjugates of monomeric Ub, ISG15, and NEDD8 (neural precursor cell expressed, developmentally downregulated 8) substrates in order to provide quantitative insights into vOTU's preference for Ub and Ub-like substrates.

  1. Covalent bonding and hybridization effects in the corundum-type transition-metal oxides V2O3 and Ti2O3

    NASA Astrophysics Data System (ADS)

    Eyert, V.; Schwingenschlögl, U.; Eckern, U.

    2005-06-01

    The electronic structure of the corundum-type transition-metal oxides V2O3 and Ti2O3 is studied by means of the augmented spherical wave method, based on density-functional theory and the local density approximation. Comparing the results for the vanadate and the titanate allows us to understand the peculiar shape of the metal 3d a1g density of states, which is present in both compounds. The a1g states are subject to pronounced bonding-antibonding splitting due to metal-metal overlap along the c-axis of the corundum structure. However, the corresponding partial density of states is strongly asymmetric with considerably more weight on the high-energy branch. We argue that this asymmetry is due to an unexpected broadening of the bonding a1g states, which is caused by hybridization with the egπ bands. In contrast, the antibonding a1g states display no such hybridization and form a sharp peak. Our results shed new light on the role of the a1g orbitals for the metal-insulator transitions of V2O3. In particular, due to a1g-egπ hybridization, an interpretation in terms of molecular orbital singlet states on the metal-metal pairs along the c-axis is not an adequate description.

  2. Chemistry of Covalent Organic Frameworks.

    PubMed

    Waller, Peter J; Gándara, Felipe; Yaghi, Omar M

    2015-12-15

    Linking organic molecules by covalent bonds into extended solids typically generates amorphous, disordered materials. The ability to develop strategies for obtaining crystals of such solids is of interest because it opens the way for precise control of the geometry and functionality of the extended structure, and the stereochemical orientation of its constituents. Covalent organic frameworks (COFs) are a new class of porous covalent organic structures whose backbone is composed entirely of light elements (B, C, N, O, Si) that represent a successful demonstration of how crystalline materials of covalent solids can be achieved. COFs are made by combination of organic building units covalently linked into extended structures to make crystalline materials. The attainment of crystals is done by several techniques in which a balance is struck between the thermodynamic reversibility of the linking reactions and their kinetics. This success has led to the expansion of COF materials to include organic units linked by these strong covalent bonds: B-O, C-N, B-N, and B-O-Si. Since the organic constituents of COFs, when linked, do not undergo significant change in their overall geometry, it has been possible to predict the structures of the resulting COFs, and this advantage has facilitated their characterization using powder X-ray diffraction (PXRD) techniques. It has also allowed for the synthesis of COF structures by design and for their formation with the desired composition, pore size, and aperture. In practice, the modeled PXRD pattern for a given expected COF is compared with the experimental one, and depending on the quality of the match, this is used as a starting point for solving and then refining the crystal structure of the target COF. These characteristics make COFs an attractive class of new porous materials. Accordingly, they have been used as gas storage materials for energy applications, solid supports for catalysis, and optoelectronic devices. A large and

  3. Atomic Covalent Functionalization of Graphene

    PubMed Central

    Johns, James E.; Hersam, Mark C.

    2012-01-01

    Conspectus Although graphene’s physical structure is a single atom thick, two-dimensional, hexagonal crystal of sp2 bonded carbon, this simple description belies the myriad interesting and complex physical properties attributed to this fascinating material. Because of its unusual electronic structure and superlative properties, graphene serves as a leading candidate for many next generation technologies including high frequency electronics, broadband photodetectors, biological and gas sensors, and transparent conductive coatings. Despite this promise, researchers could apply graphene more routinely in real-world technologies if they could chemically adjust graphene’s electronic properties. For example, the covalent modification of graphene to create a band gap comparable to silicon (~1 eV) would enable its use in digital electronics, and larger band gaps would provide new opportunities for graphene-based photonics. Towards this end, researchers have focused considerable effort on the chemical functionalization of graphene. Due to its high thermodynamic stability and chemical inertness, new methods and techniques are required to create covalent bonds without promoting undesirable side reactions or irreversible damage to the underlying carbon lattice. In this Account, we review and discuss recent theoretical and experimental work studying covalent modifications to graphene using gas phase atomic radicals. Atomic radicals have sufficient energy to overcome the kinetic and thermodynamic barriers associated with covalent reactions on the basal plane of graphene but lack the energy required to break the C-C sigma bonds that would destroy the carbon lattice. Furthermore, because they are atomic species, radicals substantially reduce the likelihood of unwanted side reactions that confound other covalent chemistries. Overall, these methods based on atomic radicals show promise for the homogeneous functionalization of graphene and the production of new classes of two

  4. Atomic covalent functionalization of graphene.

    PubMed

    Johns, James E; Hersam, Mark C

    2013-01-15

    Although graphene's physical structure is a single atom thick, two-dimensional, hexagonal crystal of sp(2) bonded carbon, this simple description belies the myriad interesting and complex physical properties attributed to this fascinating material. Because of its unusual electronic structure and superlative properties, graphene serves as a leading candidate for many next generation technologies including high frequency electronics, broadband photodetectors, biological and gas sensors, and transparent conductive coatings. Despite this promise, researchers could apply graphene more routinely in real-world technologies if they could chemically adjust graphene's electronic properties. For example, the covalent modification of graphene to create a band gap comparable to silicon (∼1 eV) would enable its use in digital electronics, and larger band gaps would provide new opportunities for graphene-based photonics. Toward this end, researchers have focused considerable effort on the chemical functionalization of graphene. Due to its high thermodynamic stability and chemical inertness, new methods and techniques are required to create covalent bonds without promoting undesirable side reactions or irreversible damage to the underlying carbon lattice. In this Account, we review and discuss recent theoretical and experimental work studying covalent modifications to graphene using gas phase atomic radicals. Atomic radicals have sufficient energy to overcome the kinetic and thermodynamic barriers associated with covalent reactions on the basal plane of graphene but lack the energy required to break the C-C sigma bonds that would destroy the carbon lattice. Furthermore, because they are atomic species, radicals substantially reduce the likelihood of unwanted side reactions that confound other covalent chemistries. Overall, these methods based on atomic radicals show promise for the homogeneous functionalization of graphene and the production of new classes of two

  5. Quantum chemical exploration of the intramolecular hydrogen bond interaction in 2-thiazol-2-yl-phenol and 2-benzothiazol-2-yl-phenol in the context of excited-state intramolecular proton transfer: A focus on the covalency in hydrogen bond

    NASA Astrophysics Data System (ADS)

    Paul, Bijan Kumar; Ganguly, Aniruddha; Guchhait, Nikhil

    2014-10-01

    The present work demonstrates a computational exploration of the intramolecular H-bond (IMHB) interaction in two model heterocyclic compounds - 2-thiazol-2-yl-phenol (2T2YP) and 2-benzothiazol-2-yl-phenol (2B2YP) by meticulous application of various quantum chemical tools. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point using the Atoms-In-Molecule methodology. Topological features based on ρ(r) suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of a covalent interaction. The interplay between aromaticity and Resonance-Assisted H-Bond (RAHB) has also been discussed using both geometrical and magnetic criteria. The occurrence of IMHB interaction in 2T2YP and 2B2YP has also been criticized under the provision of the Natural Bond Orbital (NBO) analysis. The ESIPT phenomenon in the molecular systems is also critically addressed on the lexicon of potential energy surface (PES) analysis.

  6. Highly Emissive Covalent Organic Frameworks.

    PubMed

    Dalapati, Sasanka; Jin, Enquan; Addicoat, Matthew; Heine, Thomas; Jiang, Donglin

    2016-05-11

    Highly luminescent covalent organic frameworks (COFs) are rarely achieved because of the aggregation-caused quenching (ACQ) of π-π stacked layers. Here, we report a general strategy to design highly emissive COFs by introducing an aggregation-induced emission (AIE) mechanism. The integration of AIE-active units into the polygon vertices yields crystalline porous COFs with periodic π-stacked columnar AIE arrays. These columnar AIE π-arrays dominate the luminescence of the COFs, achieve exceptional quantum yield via a synergistic structural locking effect of intralayer covalent bonding and interlayer noncovalent π-π interactions and serve as a highly sensitive sensor to report ammonia down to sub ppm level. Our strategy breaks through the ACQ-based mechanistic limitations of COFs and opens a way to explore highly emissive COF materials. PMID:27108740

  7. Covalent Bonding of Metal-Organic Framework-5/Graphene Oxide Hybrid Composite to Stainless Steel Fiber for Solid-Phase Microextraction of Triazole Fungicides from Fruit and Vegetable Samples.

    PubMed

    Zhang, Shuaihua; Yang, Qian; Wang, Wenchang; Wang, Chun; Wang, Zhi

    2016-04-01

    A hybrid material of the zinc-based metal-organic framework-5 and graphene oxide (metal-organic framework-5/graphene oxide) was prepared as a novel fiber coating material for solid-phase microextraction (SPME). The SPME fibers were fabricated by covalent bonding via chemical cross-linking between the coating material metal-organic framework-5/graphene oxide and stainless steel wire. The prepared fiber was used for the extraction of five triazole fungicides from fruit and vegetable samples. Gas chromatography coupled with microelectron capture detector (GC-μECD) was used for quantification. The developed method gave a low limit of detection (0.05-1.58 ng g(-1)) and good linearity (0.17-100 ng g(-1)) for the determination of the triazole fungicides in fruit and vegetable samples. The relative standard deviations (RSDs) for five replicate extractions of the triazole fungicides ranged from 3.7 to 8.9%. The method recoveries for spiked fungicides (5, 20, and 50 ng g(-1)) in grape, apple, cucumber, celery cabbage, pear, cabbage, and tomato samples were in the range of 85.6-105.8% with the RSDs ranging from 3.6 to 11.4%, respectively, depending on both the analytes and samples. The metal-organic framework-5/graphene oxide coated fiber was stable enough for 120 extraction cycles without a significant loss of extraction efficiency. The method was suitable for the determination of triazole fungicides in fruit and vegetable samples. PMID:26998567

  8. Isomeric [RuCl2(dmso)2(indazole)2] complexes: ruthenium(II)-mediated coupling reaction of acetonitrile with 1H-indazole.

    PubMed

    Reisner, Erwin; Arion, Vladimir B; Rufińska, Anna; Chiorescu, Ion; Schmid, Wolfgang F; Keppler, Bernhard K

    2005-07-21

    Reaction of the antitumor complex trans-[Ru(III)Cl4(Hind)2]- (Hind = indazole) with an excess of dimethyl sulfoxide (dmso) in acetone afforded the complex trans,trans,trans-[Ru(II)Cl2(dmso)2(Hind)2] (1). Two other isomeric compounds trans,cis,cis-[Ru(II)Cl2(dmso)2(Hind)2] (2) and cis,cis,cis-[Ru(II)Cl2(dmso)2(Hind)2] (3) have been obtained on refluxing cis-[Ru(II)Cl(2)(dmso)(4)] with 2 equiv. of indazole in ethanol and methanol, respectively. Isomers 1 and 2 react with acetonitrile yielding the complexes trans-[Ru(II)Cl2(dmso)(Hind){HN=C(Me)ind}].CH3CN (4.CH3CN) and trans,cis-[Ru(II)Cl2(dmso)2{HN=C(Me)ind}].H2O (5.H2O), respectively, containing a cyclic amidine ligand resulting from insertion of the acetonitrile C triple bond N group in the N1-H bond of the N2-coordinated indazole ligand in the nomenclature used for 1H-indazole. These are the first examples of the metal-assisted iminoacylation of indazole. The products isolated have been characterized by elemental analysis, IR spectroscopy, UV-vis spectroscopy, electrospray mass-spectrometry, thermogravimetry, differential scanning calorimetry, 1H NMR spectroscopy, and solid-state 13C CP MAS NMR spectroscopy. The isomeric structures of 1-3 and the presence of a chelating amidine ligand in 4 and 5 have been confirmed by X-ray crystallography. The electrochemical behavior of 1-5 and the formation of 5 have been studied by cyclic voltammetry. PMID:15995743

  9. Photoinduced electron transfer between the cationic complexes Ru(NH3)5pz2+ and trans-RuCl([15]aneN4)NO2+ mediated by phosphate ion: visible light generation of nitric oxide for biological targets.

    PubMed

    da Silva, Roberto S; Marchesi, Mario S P; Khin, Chosu; Lunardi, Claure N; Bendhack, Lusiane M; Ford, Peter C

    2007-06-21

    The photochemical behavior of the tetraazamacrocyclic complex trans-RuCl([15]ane)(NO)2+ (RuNO2+) in a 10 mM phosphate buffer solution, pH 7.4, and in the presence of Ru(NH3)5pz2+ (Rupz2+) is reported. Irradiation (436 nm) of an aqueous solution containing both cationic complexes as PF6- salts labilizes NO from RuNO2+ with a quantum yield (phiNO) dependent on the concentration of Rupz2+ with a maximum value of phiNO (1.03(11)x10(-3) einstein mol-1) found for a solution with equimolar concentrations (5x10(-5) M) of the two complexes in phosphate buffer solution. The quantitative behavior of this system suggests that the two cations undergo preassociation such that photoexcitation of the visible absorbing Rupz2+ is followed by electron or energy transfer to RuNO2+, which does not absorb appreciably at the excitation wavelength, and this leads to NO release from the reduced nitrosyl complex. Notably, the NO release was not seen in the absence of phosphate buffer; thus, it appears that phosphate ions mediate NO generation, perhaps by facilitating formation of a supramolecular complex between the two ruthenium cations. Reexamination of the cyclic voltammetry of Rupz2+ showed that the electrochemical behavior of this species is also affected by the presence of the phosphate buffer. PMID:17439277

  10. Dynamic covalent assembly and disassembly of nanoparticle aggregates.

    PubMed

    Borsley, Stefan; Kay, Euan R

    2016-07-12

    The quantitative assembly and disassembly of a new type of dynamic covalent nanoparticle (NP) building block is reported. In situ spectroscopic characterization reveals constitutionally adaptive NP-bound monolayers of boronate esters. Ditopic linker molecules are used to produce covalently connected AuNP assemblies, displaying open dendritic morphologies, and which, despite being linked by covalent bonds, can be fully disassembled on application of an appropriate chemical stimulus. PMID:27001937

  11. Covalency in oxidized uranium

    NASA Astrophysics Data System (ADS)

    Tobin, J. G.; Yu, S.-W.; Qiao, R.; Yang, W. L.; Booth, C. H.; Shuh, D. K.; Duffin, A. M.; Sokaras, D.; Nordlund, D.; Weng, T.-C.

    2015-07-01

    Using x-ray emission spectroscopy and absorption spectroscopy, it has been possible to directly access the states in the unoccupied conduction bands that are involved with 5 f and 6 d covalency in oxidized uranium. By varying the oxidizing agent, the degree of 5 f covalency can be manipulated and monitored, clearly and irrevocably establishing the importance of 5 f covalency in the electronic structure of the key nuclear fuel, uranium dioxide.

  12. Distinguishing Bonds.

    PubMed

    Rahm, Martin; Hoffmann, Roald

    2016-03-23

    The energy change per electron in a chemical or physical transformation, ΔE/n, may be expressed as Δχ̅ + Δ(VNN + ω)/n, where Δχ̅ is the average electron binding energy, a generalized electronegativity, ΔVNN is the change in nuclear repulsions, and Δω is the change in multielectron interactions in the process considered. The last term can be obtained by the difference from experimental or theoretical estimates of the first terms. Previously obtained consequences of this energy partitioning are extended here to a different analysis of bonding in a great variety of diatomics, including more or less polar ones. Arguments are presented for associating the average change in electron binding energy with covalence, and the change in multielectron interactions with electron transfer, either to, out, or within a molecule. A new descriptor Q, essentially the scaled difference between the Δχ̅ and Δ(VNN + ω)/n terms, when plotted versus the bond energy, separates nicely a wide variety of bonding types, covalent, covalent but more correlated, polar and increasingly ionic, metallogenic, electrostatic, charge-shift bonds, and dispersion interactions. Also, Q itself shows a set of interesting relations with the correlation energy of a bond. PMID:26910496

  13. Exploring Tertiary Students' Understanding of Covalent Bonding.

    ERIC Educational Resources Information Center

    Coll, Richard K.; Treagust, David F.

    2002-01-01

    Explores whether exposure to increasingly sophisticated mental models at different points in a chemistry education class showed up in patterns of preference and use of models in interpreting physical properties and phenomena. (Contains 92 references.) (DDR)

  14. Sulfided heterogeneous, bimetallic RuMo catalysts derived from mixtures of Ru{sub 3}(CO){sub 12} (or RuCl{sub 3}) and a molybdenum heteropolyanion. The reactions of ethanol with tetrahydroquinoline

    SciTech Connect

    Koo, Sang-Man; Ryan, D.; Laine, R.M.

    1992-09-01

    Efforts have been made to develop Ru/Mo bimetallic catalyst systems for hydrodenitrogenation (HDN) of tetrahydroquinoline (THQ)- In the course of these studies, it was discovered that in ethanol, under H{sub 2} and in the presence Of CS2, Precatalyst solutions containing Ru [as Ru{sub 3} (CO){sub 12} or RuCl{sub 3}] and Mo [as the H{sub 3}PMO{sub 12}0{sub 40} heteropolyanion (HPA)] decompose to form bimetallic, sulfided particles. Particle diameters run from 0.1 to 5 {mu}m depending on the rate of stirring. Catalyst particles with sizes ranging from 0.1--1 {mu}m can be prepared reproducibly. BET measured surface areas for these size particles ranged from 2 to 20 m2/g. These sulfided particles were found to catalyze, at temperatures of 200--250{degrees}C and hydrogen pressures of 200--1000 psig H{sub 2}, the N-ethylation of THQ to form NEt-THQ; rather than the formation of propylcyclohexane or propylbenzene, reaction products expected for HDN of THQ. Monometallic heterogeneous catalysts prepared from the individual precatalyst complexes, under identical conditions, show minimal activity for N-ethylation by comparison with the bimetallic catalyst. In the absence of H{sub 2}, the reaction proceeds such that THQ is converted to Q, N-EtTHQ, N-C{sub 6}H{sub 9}-THQ, and N-C{sub 6}H{sub 13}-THQ. The latter products appear to arise via acetaldehyde, formed as an intermediate by dehydrogenation of ethanol. Acetaldehyde either condenses with THQ to form N-Et-THQ, or self condenses (aldol condensation) prior to reaction with THQ thereby giving higher homolog alkylation products.

  15. Sulfided heterogeneous, bimetallic RuMo catalysts derived from mixtures of Ru sub 3 (CO) sub 12 (or RuCl sub 3 ) and a molybdenum heteropolyanion. The reactions of ethanol with tetrahydroquinoline

    SciTech Connect

    Koo, Sang-Man; Ryan, D.; Laine, R.M.

    1992-01-01

    Efforts have been made to develop Ru/Mo bimetallic catalyst systems for hydrodenitrogenation (HDN) of tetrahydroquinoline (THQ)- In the course of these studies, it was discovered that in ethanol, under H{sub 2} and in the presence Of CS2, Precatalyst solutions containing Ru (as Ru{sub 3} (CO){sub 12} or RuCl{sub 3}) and Mo (as the H{sub 3}PMO{sub 12}0{sub 40} heteropolyanion (HPA)) decompose to form bimetallic, sulfided particles. Particle diameters run from 0.1 to 5 {mu}m depending on the rate of stirring. Catalyst particles with sizes ranging from 0.1--1 {mu}m can be prepared reproducibly. BET measured surface areas for these size particles ranged from 2 to 20 m2/g. These sulfided particles were found to catalyze, at temperatures of 200--250{degrees}C and hydrogen pressures of 200--1000 psig H{sub 2}, the N-ethylation of THQ to form NEt-THQ; rather than the formation of propylcyclohexane or propylbenzene, reaction products expected for HDN of THQ. Monometallic heterogeneous catalysts prepared from the individual precatalyst complexes, under identical conditions, show minimal activity for N-ethylation by comparison with the bimetallic catalyst. In the absence of H{sub 2}, the reaction proceeds such that THQ is converted to Q, N-EtTHQ, N-C{sub 6}H{sub 9}-THQ, and N-C{sub 6}H{sub 13}-THQ. The latter products appear to arise via acetaldehyde, formed as an intermediate by dehydrogenation of ethanol. Acetaldehyde either condenses with THQ to form N-Et-THQ, or self condenses (aldol condensation) prior to reaction with THQ thereby giving higher homolog alkylation products.

  16. Interfacial welding of dynamic covalent network polymers

    NASA Astrophysics Data System (ADS)

    Yu, Kai; Shi, Qian; Li, Hao; Jabour, John; Yang, Hua; Dunn, Martin L.; Wang, Tiejun; Qi, H. Jerry

    2016-09-01

    Dynamic covalent network (or covalent adaptable network) polymers can rearrange their macromolecular chain network by bond exchange reactions (BERs) where an active unit replaces a unit in an existing bond to form a new bond. Such macromolecular events, when they occur in large amounts, can attribute to unusual properties that are not seen in conventional covalent network polymers, such as shape reforming and surface welding; the latter further enables the important attributes of material malleability and powder-based reprocessing. In this paper, a multiscale modeling framework is developed to study the surface welding of thermally induced dynamic covalent network polymers. At the macromolecular network level, a lattice model is developed to describe the chain density evolution across the interface and its connection to bulk stress relaxation due to BERs. The chain density evolution rule is then fed into a continuum level interfacial model that takes into account surface roughness and applied pressure to predict the effective elastic modulus and interfacial fracture energy of welded polymers. The model yields particularly accessible results where the moduli and interfacial strength of the welded samples as a function of temperature and pressure can be predicted with four parameters, three of which can be measured directly. The model identifies the dependency of surface welding efficiency on the applied thermal and mechanical fields: the pressure will affect the real contact area under the consideration of surface roughness of dynamic covalent network polymers; the chain density increment on the real contact area of interface is only dependent on the welding time and temperature. The modeling approach shows good agreement with experiments and can be extended to other types of dynamic covalent network polymers using different stimuli for BERs, such as light and moisture etc.

  17. Bulk modulus for polar covalent crystals

    PubMed Central

    Xu, Bo; Wang, Qianqian; Tian, Yongjun

    2013-01-01

    A microscopic empirical model of bulk modulus based on atomic-scale parameters is proposed. These parameters include the bond length, the effective bonded valence electron (EBVE) number, and the coordination number product of two bonded atoms, etc. The estimated bulk moduli from our model are in good agreement with experimental values for various polar covalent crystals including ionic crystals. Our current work sheds lights on the nature of bulk modulus, provides useful clues for design of crystals with low compressibility, and is applicable to complex crystals such as minerals of geophysical importance. PMID:24166098

  18. Self-templated chemically stable hollow spherical covalent organic framework.

    PubMed

    Kandambeth, Sharath; Venkatesh, V; Shinde, Digambar B; Kumari, Sushma; Halder, Arjun; Verma, Sandeep; Banerjee, Rahul

    2015-01-01

    Covalent organic frameworks are a family of crystalline porous materials with promising applications. Although active research on the design and synthesis of covalent organic frameworks has been ongoing for almost a decade, the mechanisms of formation of covalent organic frameworks crystallites remain poorly understood. Here we report the synthesis of a hollow spherical covalent organic framework with mesoporous walls in a single-step template-free method. A detailed time-dependent study of hollow sphere formation reveals that an inside-out Ostwald ripening process is responsible for the hollow sphere formation. The synthesized covalent organic framework hollow spheres are highly porous (surface area ∼1,500 m(2 )g(-1)), crystalline and chemically stable, due to the presence of strong intramolecular hydrogen bonding. These mesoporous hollow sphere covalent organic frameworks are used for a trypsin immobilization study, which shows an uptake of 15.5 μmol g(-1) of trypsin. PMID:25858416

  19. Self-templated chemically stable hollow spherical covalent organic framework

    NASA Astrophysics Data System (ADS)

    Kandambeth, Sharath; Venkatesh, V.; Shinde, Digambar B.; Kumari, Sushma; Halder, Arjun; Verma, Sandeep; Banerjee, Rahul

    2015-04-01

    Covalent organic frameworks are a family of crystalline porous materials with promising applications. Although active research on the design and synthesis of covalent organic frameworks has been ongoing for almost a decade, the mechanisms of formation of covalent organic frameworks crystallites remain poorly understood. Here we report the synthesis of a hollow spherical covalent organic framework with mesoporous walls in a single-step template-free method. A detailed time-dependent study of hollow sphere formation reveals that an inside-out Ostwald ripening process is responsible for the hollow sphere formation. The synthesized covalent organic framework hollow spheres are highly porous (surface area ~1,500 m2 g-1), crystalline and chemically stable, due to the presence of strong intramolecular hydrogen bonding. These mesoporous hollow sphere covalent organic frameworks are used for a trypsin immobilization study, which shows an uptake of 15.5 μmol g-1 of trypsin.

  20. Teaching Chemical Bonding: A Resource Book for Senior Chemistry.

    ERIC Educational Resources Information Center

    Lindsay, Margaret

    This document presents an instructional strategy for teaching chemical bonding using parables and music. Games, student interactions, and worksheets are included in the lesson plans. Topics include metallic bonding, covalent bonding including molecular and network structure, and ionic bonding. (JRH)

  1. Protocol for rational design of covalently interacting inhibitors.

    PubMed

    Schmidt, Thomas C; Welker, Armin; Rieger, Max; Sahu, Prabhat K; Sotriffer, Christoph A; Schirmeister, Tanja; Engels, Bernd

    2014-10-20

    The inhibition potencies of covalent inhibitors mainly result from the formation of a covalent bond to the enzyme during the inhibition mechanism. This class of inhibitors has essentially been ignored in previous target-directed drug discovery projects because of concerns about possible side effects. However, their advantages, such as higher binding energies and longer drug-target residence times moved them into the focus of recent investigations. While the rational design of non-covalent inhibitors became standard the corresponding design of covalent inhibitors is still in its early stages. Potent covalent inhibitors can be retrieved from large compound libraries by covalent docking approaches but protocols are missing that can reliably predict the influence of variations in the substitution pattern on the affinity and/or reactivity of a given covalent inhibitor. Hence, the wanted property profile can only be obtained from trial-and-error proceedings. This paper presents an appropriate protocol which is able to predict improved covalent inhibitors. It uses hybrid approaches, which mix quantum mechanical (QM) and molecular mechanical (MM) methods to predict variations in the reactivity of the inhibitor. They are also used to compute the required information about the non-covalent enzyme-inhibitor complex. Docking tools are employed to improve the inhibitor with respect to the non-covalent interactions formed in the binding site. PMID:25251382

  2. Valence, Covalence, Hypervalence, Oxidation State, and Coordination Number

    ERIC Educational Resources Information Center

    Smith, Derek W.

    2005-01-01

    Valence as a numerical measure of an atom's combining power, expressed by the number of bonds it forms in a molecular formulation of the compound in question, was unable to cope with coordination compounds. The covalence of an atom is the nearest model equivalent, but is subject to ambiguity since it often depends on which bonding model is being…

  3. Covalently linked organic networks

    NASA Astrophysics Data System (ADS)

    Tsotsalas, Manuel; Addicoat, Matthew

    2015-02-01

    In this review, we intend to give an overview of the synthesis of well-defined covalently-bound organic network materials such as covalent organic frameworks (COFs), conjugated microporous frameworks (CMPs) and other “ideal polymer networks” and discuss the different approaches in their synthesis and their potential applications. In addition we will describe the common computational approaches and highlight recent achievements in the computational study of their structure and properties. For further information the interested reader is referred to several excellent and more detailed reviews dealing with the synthesis [Dawson 2012; Ding 2013; Feng 2012] and computational aspects [Han 2009; Colón 2014] of the materials presented here.

  4. Covalent organic frameworks.

    PubMed

    Feng, Xiao; Ding, Xuesong; Jiang, Donglin

    2012-09-21

    Covalent organic frameworks (COFs) are a class of crystalline porous polymers that allow the atomically precise integration of organic units to create predesigned skeletons and nanopores. They have recently emerged as a new molecular platform for designing promising organic materials for gas storage, catalysis, and optoelectronic applications. The reversibility of dynamic covalent reactions, diversity of building blocks, and geometry retention are three key factors involved in the reticular design and synthesis of COFs. This tutorial review describes the basic design concepts, the recent synthetic advancements and structural studies, and the frontiers of functional exploration. PMID:22821129

  5. Bonded semiconductor substrate

    DOEpatents

    Atwater, Jr.; Harry A. , Zahler; James M.

    2010-07-13

    Ge/Si and other nonsilicon film heterostructures are formed by hydrogen-induced exfoliation of the Ge film which is wafer bonded to a cheaper substrate, such as Si. A thin, single-crystal layer of Ge is transferred to Si substrate. The bond at the interface of the Ge/Si heterostructures is covalent to ensure good thermal contact, mechanical strength, and to enable the formation of an ohmic contact between the Si substrate and Ge layers. To accomplish this type of bond, hydrophobic wafer bonding is used, because as the invention demonstrates the hydrogen-surface-terminating species that facilitate van der Waals bonding evolves at temperatures above 600.degree. C. into covalent bonding in hydrophobically bound Ge/Si layer transferred systems.

  6. Coulombic Models in Chemical Bonding.

    ERIC Educational Resources Information Center

    Sacks, Lawrence J.

    1986-01-01

    Compares the coulumbic point charge model for hydrogen chloride with the valence bond model. It is not possible to assign either a nonpolar or ionic canonical form of the valence bond model, while the covalent-ionic bond distribution does conform to the point charge model. (JM)

  7. Quantitative study of non-covalent interactions at the electrode-electrolyte interface using cyanide-modified Pt(111) electrodes.

    SciTech Connect

    Escudero-Escribano, M.; Michoff, M. E. Z.; Leiva, E. P. M.; Markovic, N. M.; Gutierrez, C.; Cuesta, A.

    2011-08-22

    Cations at the outer Helmholtz plane (OHP) can interact through non-covalent interactions with species at the inner Helmholtz plane (IHP), which are covalently bonded to the electrode surface, thereby affecting the structure and the properties of the electrochemical double layer. These non-covalent interactions can be studied quantitatively using cyanide-modified Pt(111) electrodes.

  8. Halogen bonding anion recognition.

    PubMed

    Brown, Asha; Beer, Paul D

    2016-07-01

    A halogen bond is an attractive non-covalent interaction between an electrophilic region in a covalently bonded halogen atom and a Lewis base. While these interactions have long been exploited as a tool in crystal engineering their powerful ability to direct supramolecular self-assembly and molecular recognition processes in solution has, until recently, been overlooked. During the last decade however an ever-increasing number of studies on solution-phase halogen-bond-mediated anion recognition processes has emerged. This Feature Article summarises advancements which have been made thus far in this rapidly developing research area. We survey the use of iodoperfluoroarene, haloimidazolium and halotriazole/triazolium halogen-bond-donor motifs in anion receptor design, before providing an account of our research into the application of mechanically interlocked rotaxane and catenane frameworks as halogen bonding anion host systems. PMID:27273600

  9. Use of (77)Se and (125)Te NMR Spectroscopy to Probe Covalency of the Actinide-Chalcogen Bonding in [Th(En){N(SiMe3)2}3](-) (E = Se, Te; n = 1, 2) and Their Oxo-Uranium(VI) Congeners.

    PubMed

    Smiles, Danil E; Wu, Guang; Hrobárik, Peter; Hayton, Trevor W

    2016-01-27

    Reaction of [Th(I)(NR2)3] (R = SiMe3) (1) with 1 equiv of either [K(18-crown-6)]2[Se4] or [K(18-crown-6)]2[Te2] affords the thorium dichalcogenides, [K(18-crown-6)][Th(η(2)-E2)(NR2)3] (E = Se, 2; E = Te, 3), respectively. Removal of one chalcogen atom via reaction with Et3P, or Et3P and Hg, affords the monoselenide and monotelluride complexes of thorium, [K(18-crown-6)][Th(E)(NR2)3] (E = Se, 4; E = Te, 5), respectively. Both 4 and 5 were characterized by X-ray crystallography and were found to feature the shortest known Th-Se and Th-Te bond distances. The electronic structure and nature of the actinide-chalcogen bonds were investigated with (77)Se and (125)Te NMR spectroscopy accompanied by detailed quantum-chemical analysis. We also recorded the (77)Se NMR shift for a U(VI) oxo-selenido complex, [U(O)(Se)(NR2)3](-) (δ((77)Se) = 4905 ppm), which features the highest frequency (77)Se NMR shift yet reported, and expands the known (77)Se chemical shift range for diamagnetic substances from ∼3300 ppm to almost 6000 ppm. Both (77)Se and (125)Te NMR chemical shifts of given chalcogenide ligands were identified as quantitative measures of the An-E bond covalency within an isoelectronic series and supported significant 5f-orbital participation in actinide-ligand bonding for uranium(VI) complexes in contrast to those involving thorium(IV). Moreover, X-ray diffraction studies together with NMR spectroscopic data and density functional theory (DFT) calculations provide convincing evidence for the actinide-chalcogen multiple bonding in the title complexes. Larger An-E covalency is observed in the [U(O)(E)(NR2)3](-) series, which decreases as the chalcogen atom becomes heavier. PMID:26667146

  10. Supramolecular motifs in dynamic covalent PEG-hemiaminal organogels

    PubMed Central

    Fox, Courtney H.; ter Hurrne, Gijs M.; Wojtecki, Rudy J.; Jones, Gavin O.; Horn, Hans W.; Meijer, E. W.; Frank, Curtis W.; Hedrick, James L.; García, Jeannette M.

    2015-01-01

    Dynamic covalent materials are stable materials that possess reversible behaviour triggered by stimuli such as light, redox conditions or temperature; whereas supramolecular crosslinks depend on the equilibrium constant and relative concentrations of crosslinks as a function of temperature. The combination of these two reversible chemistries can allow access to materials with unique properties. Here, we show that this combination of dynamic covalent and supramolecular chemistry can be used to prepare organogels comprising distinct networks. Two materials containing hemiaminal crosslink junctions were synthesized; one material is comprised of dynamic covalent junctions and the other contains hydrogen-bonding bis-hemiaminal moieties. Under specific network synthesis conditions, these materials exhibited self-healing behaviour. This work reports on both the molecular-level detail of hemiaminal crosslink junction formation as well as the macroscopic behaviour of hemiaminal dynamic covalent network (HDCN) elastomeric organogels. These materials have potential applications as elastomeric components in printable materials, cargo carriers and adhesives. PMID:26174864

  11. Hybrid materials of SBA-16 functionalized by rare earth (Eu{sup 3+}, Tb{sup 3+}) complexes of modified beta-diketone (TTA and DBM): Covalently bonding assembly and photophysical properties

    SciTech Connect

    Li Yajuan; Yan Bing; Li Ying

    2010-04-15

    Novel mesoporous SBA-16 type of hybrids TTA-S16 and DBM-S16 were synthesized by co-condensation of modified beta-diketone (TTA-Si and DBM-Si, DBM=1,3-diphenyl-1,3- propanepione, TTA=2-thenoyltrifluoroacetone) and tetraethoxysilane (TEOS) in the presence of Pluronic F127 as template, which were confirmed by FTIR, XRD, {sup 29}Si CP-MAS NMR, and N{sub 2} adsorption measurements. Novel organic-inorganic mesoporous luminescent hybrid containing RE{sup 3+} (Eu{sup 3+}, Tb{sup 3+}) complexes covalently attached to the functionalized ordered mesoporous SBA-16 (TTA-S16 and DBM-S16), which were designated as bpy-RE-TTA-S16 and bpy-RE-DBM-S16, were obtained by sol-gel process. The luminescence properties of these resulting materials were characterized in detail, and the results reveal that mesoporous hybrid material bpy-Eu-TTA-S16 present stronger luminescent intensities, longer lifetimes, and higher luminescent quantum efficiencies than the corresponding DBM-containing materials bpy-Eu-DBM-S16, while bpy-Tb-DBM-S16 exhibit the stronger characteristic emission of Tb{sup 3+} and longer lifetime than the corresponding TTA-containing materials bpy-Tb-TTA-S16. - Graphical abstract: Novel organic-inorganic mesoporous luminescent hybrids containing RE{sup 3+} complex covalently attached to the beta-diketone-functionalized ordered mesoporous SBA-16, which were designated as bpy-RE-TTA-S16 and bpy-RE-DBM-S16, were obtained by sol-gel process.

  12. Electron tunneling through covalent and noncovalent pathways in proteins

    NASA Technical Reports Server (NTRS)

    Beratan, David N.; Onuchic, Jose Nelson; Hopfield, J. J.

    1987-01-01

    A model is presented for electron tunneling in proteins which allows the donor-acceptor interaction to be mediated by the covalent bonds between amino acids and noncovalent contacts between amino acid chains. The important tunneling pathways are predicted to include mostly bonded groups with less favorable nonbonded interactions being important when the through bond pathway is prohibitively long. In some cases, vibrational motion of nonbonded groups along the tunneling pathway strongly influences the temperature dependence of the rate. Quantitative estimates for the sizes of these noncovalent interactions are made and their role in protein mediated electron transport is discussed.

  13. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  14. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  15. Nucleic acid duplexes incorporating a dissociable covalent base pair.

    PubMed

    Gao, K; Orgel, L E

    1999-12-21

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

  16. Non-bonding interactions and non-covalent delocalization effects play a critical role in the relative stability of group 12 complexes arising from interaction of diethanoldithiocarbamate with the cations of transition metals Zn(II), Cd(II), and Hg(II): a theoretical study.

    PubMed

    Bahrami, Homayoon; Farhadi, Saeed; Siadatnasab, Firouzeh

    2016-07-01

    The chelating properties of diethanoldithiocarbamate (DEDC) and π-electron flow from the nitrogen atom to the sulfur atom via a plane-delocalized π-orbital system (quasi ring) was studied using a density functional theory method. The molecular structure of DEDC and its complexes with Zn(II), Cd(II), and Hg(II) were also considered. First, the geometries of this ligand and DEDC-Zn(II), DEDC-Cd(II), and DEDC-Hg(II) were optimized, and the formation energies of these complexes were then calculated based on the electronic energy, or sum of electronic energies, with the zero point energy of each species. Formation energies indicated the DEDC-Zn(II) complex as the most stable complex, and DEDC-Cd(II) as the least stable. Structural data showed that the N1-C2 π-bond was localized in the complexes rather than the ligand, and a delocalized π-bond over S7-C2-S8 was also present. The stability of DEDC-Zn(II), DEDC-Cd(II), and DEDC-Hg(II) complexes increased in the presence of the non-specific effects of the solvent (PCM model), and their relative stability did not change. There was π-electron flow or resonance along N1-C2-S7 and along S7-C2-S8 in the ligand. The π-electron flow or resonance along N1-C2-S7 was abolished when the metal interacted with sulfur atoms. Energy belonging to van der Waals interactions and non-covalent delocalization effects between the metal and sulfur atoms of the ligand was calculated for each complex. The results of nucleus-independent chemical shift (NICS) indicated a decreasing trend as Zn(II) < Cd(II) < Hg(II) for the aromaticity of the quasi-rings. Finally, by ignoring van der Waals interactions and non-covalent delocalization effects between the metal and sulfur atoms of the ligand, the relative stability of the complexes was changed as follows:[Formula: see text] Graphical Abstract Huge electronic cloud localized on Hg(II) in the Hg(II)-DEDC complex. PMID:27299888

  17. Formation of microcapsules from polyelectrolyte and covalent interactions.

    PubMed

    Breguet, Véronique; Gugerli, Raphaël; Pernetti, Mimma; von Stockar, Urs; Marison, Ian W

    2005-10-11

    A new approach combining electrostatic and covalent bonds was established for the formation of resistant capsules with long-term stability under physiological conditions. Three kinds of interactions were generated in the same membrane: (1) electrostatic bonds between alginate and poly-L-lysine (PLL), (2) covalent bonds (amides) between propylene-glycol-alginate (PGA) and PLL, and (3) covalent bonds (amides) between BSA and PGA. Down-scaling of the capsules size (< or =1 mm diameter) with a jet break-up technology was achieved by modifying the rheological properties of the polymer solution. Viscosity of the PGA solution was reduced by 95% with four successive pH stabilizations (pH 7), while filtration (0.2 microm) and sterilization was possible. Covalent bond formation was initiated by addition of NaOH (pH 11) using a transacylation reaction. Kinetics of the chemical reaction (pH 11) were simulated by two mathematical models and adapted in order to preserve immobilization of animal cells. It was demonstrated that diffusion of NaOH in the absence of BSA resulted in gelation of 94% of the bead and death of 94% of the cells after 10 s reaction. By addition of BSA only 46% of the cells were killed within the same reaction time (10 s). Mechanical resistance of this new type of capsule could be increased 5-fold over the standard polyelectrolytic system (PLL-alginate). Encapsulated CHO cells were successfully cultivated for 1 month in a repetitive batch mode, with the mechanical resistance of the capsules decreasing by only 10% during this period. The combination of a synthetic and natural protein resulted in enhanced stability toward culture medium and proteolytic enzymes (250%). PMID:16207064

  18. Covalent Organic Frameworks for CO2 Capture.

    PubMed

    Zeng, Yongfei; Zou, Ruqiang; Zhao, Yanli

    2016-04-01

    As an emerging class of porous crystalline materials, covalent organic frameworks (COFs) are excellent candidates for various applications. In particular, they can serve as ideal platforms for capturing CO2 to mitigate the dilemma caused by the greenhouse effect. Recent research achievements using COFs for CO2 capture are highlighted. A background overview is provided, consisting of a brief statement on the current CO2 issue, a summary of representative materials utilized for CO2 capture, and an introduction to COFs. Research progresses on: i) experimental CO2 capture using different COFs synthesized based on different covalent bond formations, and ii) computational simulation results of such porous materials on CO2 capture are summarized. Based on these experimental and theoretical studies, careful analyses and discussions in terms of the COF stability, low- and high-pressure CO2 uptake, CO2 selectivity, breakthrough performance, and CO2 capture conditions are provided. Finally, a perspective and conclusion section of COFs for CO2 capture is presented. Recent advancements in the field are highlighted and the strategies and principals involved are discussed. PMID:26924720

  19. Covalent Polymers Containing Discrete Heterocyclic Anion Receptors

    PubMed Central

    Rambo, Brett M.; Silver, Eric S.; Bielawski, Christopher W.; Sessler, Jonathan L.

    2010-01-01

    This chapter covers recent advances in the development of polymeric materials containing discrete heterocyclic anion receptors, and focuses on advances in anion binding and chemosensor chemistry. The development of polymers specific for anionic species is a relatively new and flourishing area of materials chemistry. The incorporation of heterocyclic receptors capable of complexing anions through non-covalent interactions (e.g., hydrogen bonding and electrostatic interactions) provides a route to not only sensitive but also selective polymer materials. Furthermore, these systems have been utilized in the development of polymers capable of extracting anionic species from aqueous environments. These latter materials may lead to advances in water purification and treatment of diseases resulting from surplus ions. PMID:20871791

  20. Dynamic Covalent Nanoparticle Building Blocks.

    PubMed

    Kay, Euan R

    2016-07-25

    Rational and generalisable methods for engineering surface functionality will be crucial to realising the technological potential of nanomaterials. Nanoparticle-bound dynamic covalent exchange combines the error-correcting and environment-responsive features of equilibrium processes with the stability, structural precision, and vast diversity of covalent chemistry, defining a new and powerful approach for manipulating structure, function and properties at nanomaterial surfaces. Dynamic covalent nanoparticle (DCNP) building blocks thus present a whole host of possibilities for constructing adaptive systems, devices and materials that incorporate both nanoscale and molecular functional components. At the same time, DCNPs have the potential to reveal fundamental insights regarding dynamic and complex chemical systems confined to nanoscale interfaces. PMID:27312526

  1. Concurrent Covalent and Supramolecular Polymerization.

    PubMed

    Hou, Xisen; Ke, Chenfeng; Zhou, Yu; Xie, Zhuang; Alngadh, Ahmed; Keane, Denis T; Nassar, Majed S; Botros, Youssry Y; Mirkin, Chad A; Stoddart, J Fraser

    2016-08-22

    Covalent and supramolecular polymerizations, both of which offer their own unique advantages, have emerged as popular strategies for making artificial materials. Herein, we describe a concurrent covalent and supramolecular polymerization strategy-namely, one which utilizes 1) a bis-azide-functionalized diazaperopyrenium dication that undergoes polymeriation covalently with a bis-alkyne-functionalized biphenyl derivative in one dimension as a result of a rapid and efficient β-cyclodextrin(CD)-accelerated, cucurbit[6]uril(CB)-templated azide-alkyne cycloaddition, while 2) the aromatic core of the dication is able to dimerize in a criss-cross fashion by dint of π-π interactions, enabling simultaneous supramolecular assembly, resulting in an extended polymer network in an orthogonal dimension. PMID:27338246

  2. Trans/cis isomerization of [RuCl2{H2Cdbnd C(CH2PPh2)2)}(diamine)] complexes: Synthesis, spectral, crystal structure and DFT calculations and catalytic activity in the hydrogenation of α,β-unsaturated ketones

    NASA Astrophysics Data System (ADS)

    Warad, Ismail; Al-Noaimi, Mousa; Abdel-Rahman, Obadah S.; Awwadi, Firas F.; Hammouti, Belkheir; Hadda, Taibi B.

    2014-01-01

    Three complexes of the general formula trans/cis-[Ru(II)(dppme)(Nsbnd N)Cl2] {dppme is H2Cdbnd C(CH2PPh2)2 and Nsbnd N is 1,2-diaminocyclohexane (trans/cis-(1)) and 1-methyl-1,2-diaminopropane (trans-(2)} were obtained by reacting trans-[RuCl2(dppme)2] with an excess amount of corresponding diamine in CH2Cl2 as a solvent. The complexes were characterized by an elemental analysis, IR, 1H, 13C and 31P{1H} NMR, FAB-MS and UV-visible. The trans-(1) (kinetic product) readily isomerizes to the cis-(1) (thermodynamic product) and this process was followed by using 31P{1H} NMR, cyclic voltammetry and UV-vis spectroscopy. The electrochemical studies on complex (1) reveal that the Ru(III)/Ru(II) couples are sensitive to the isomer (trans/cis) formed. The cis-(1) was confirmed by X-ray structure and 31P{1H} NMR. Transfer-hydrogenation reactions for reduction of trans-4-phenyl-3-butene-2-one were conducted using complexes trans/cis-(1) and trans-(2). The electronic spectra of cis/trans-(1) in dichloromethane were calculated with the use of time-dependent DFT methods.

  3. Constructing Models in Teaching of Chemical Bonds: Ionic Bond, Covalent Bond, Double and Triple Bonds, Hydrogen Bond and Molecular Geometry

    ERIC Educational Resources Information Center

    Uce, Musa

    2015-01-01

    Studies in chemistry education show that chemistry topics are considered as abstract, complicated and hard to understand by students. For this reason, it is important to develop new materials and use them in classes for better understanding of abstract concepts. Moving from this point, a student-centered research guided by a teacher was conducted…

  4. Valence-Bond Concepts in Coordination Chemistry and the Nature of Metal-Metal Bonds.

    ERIC Educational Resources Information Center

    Pauling, Linus; Herman, Zelek S.

    1984-01-01

    Discusses the valence-bond method, applying it to some coordination compounds of metals, especially those involving metal-metal bonds. Suggests that transition metals can form as many as nine covalent bonds, permitting valence-theory to be extended to transition metal compounds in a more effective way than has been possible before. (JN)

  5. Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies.

    PubMed

    Bauer, Renato A

    2015-09-01

    Drugs that covalently bond to their biological targets have a long history in drug discovery. A look at drug approvals in recent years suggests that covalent drugs will continue to make impacts on human health for years to come. Although fraught with concerns about toxicity, the high potencies and prolonged effects achievable with covalent drugs may result in less-frequent drug dosing and in wide therapeutic margins for patients. Covalent inhibition can also dissociate drug pharmacodynamics (PD) from pharmacokinetics (PK), which can result in desired drug efficacy for inhibitors that have short systemic exposure. Evidence suggests that there is a reduced risk for the development of resistance against covalent drugs, which is a major challenge in areas such as oncology and infectious disease. PMID:26002380

  6. NCIPLOT: a program for plotting non-covalent interaction regions.

    PubMed

    Contreras-García, Julia; Johnson, Erin R; Keinan, Shahar; Chaudret, Robin; Piquemal, Jean-Philip; Beratan, David N; Yang, Weitao

    2011-03-01

    Non-covalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these non-covalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define non-covalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their van der Waals radii. We recently developed an alternative perspective, derived from the electronic density: the Non-Covalent Interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of non-covalent interactions is of great potential value. Here, we describe the NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities. A wide range of options for tuning the range of interactions to be plotted is also presented. To demonstrate the capabilities of our approach, several examples are given from organic, inorganic, solid state, and macromolecular chemistry, including cases where NCI analysis gives insight into unconventional chemical bonding. The NCI code and its manual are available for download at http://www.chem.duke.edu/~yang/software.htm. PMID:21516178

  7. Non-covalent and covalent functionalization of graphene for device applications

    NASA Astrophysics Data System (ADS)

    Jandhyala, Srikar

    In order to continue improving the performance of electronic devices and also to increase functionality, incorporation of alternative channel materials into the current silicon based technology is inevitable. Graphene is one such material which is being heavily investigated owing to its high carrier mobility, one atom thickness, and other electronic as well as physical attributes. There are various architectures proposed for graphene based devices. This dissertation focuses on one of the challenges in integrating graphene based devices, i.e. gate dielectrics. For the more common device architectures utilizing electric field-effect in graphene, a thin and high dielectric constant (high-kappa) material is desired for gate dielectric applications. Although, atomic layer deposition (ALD) is the most suitable technique for depositing such dielectrics on various substrates, it is difficult to initiate dielectric growth using ALD on graphene because it lacks out-of-plane bonds owing to the sp2 hybridization of carbon atoms. An approach involving non-covalent functionalization of graphene surface with ozone (O3) at room temperature is studied for depositing high-kappa oxides with ALD. A scheme was developed for in-situ electrical monitoring of transport properties of back-gate graphene field-effect transistors (GFETs) during the ALD process. It was established that O 3 is mostly physisorbed on (high-quality) graphene at room temperature and its effects on graphene properties are reversed upon introduction of metal precursor which reacts with the adsorbed O3 molecules resulting in oxide deposition. Utilizing this knowledge, a high-pressure O3 functionalization approach was developed for depositing oxide gate dielectrics on graphene using ALD and top-gate GFETs with dielectric thickness below 5 nm were demonstrated. A low-kappa tunnel dielectric is the proposed requirement for certain graphene based devices. Covalent functionalization of graphene with fluorine through plasma

  8. Nucleophile-catalyzed additions to activated triple bonds. Protection of lactams, imides, and nucleosides with MocVinyl and related groups.

    PubMed

    Mola, Laura; Font, Joan; Bosch, Lluís; Caner, Joaquim; Costa, Anna M; Etxebarría-Jardí, Gorka; Pineda, Oriol; de Vicente, David; Vilarrasa, Jaume

    2013-06-21

    Additions of lactams, imides, (S)-4-benzyl-1,3-oxazolidin-2-one, 2-pyridone, pyrimidine-2,4-diones (AZT derivatives), or inosines to the electron-deficient triple bonds of methyl propynoate, tert-butyl propynoate, 3-butyn-2-one, N-propynoylmorpholine, or N-methoxy-N-methylpropynamide in the presence of many potential catalysts were examined. DABCO and, second, DMAP appeared to be the best (highest reaction rates and E/Z ratios), while RuCl3, RuClCp*(PPh3)2, AuCl, AuCl(PPh3), CuI, and Cu2(OTf)2 were incapable of catalyzing such additions. The groups incorporated (for example, the 2-(methoxycarbonyl)ethenyl group that we name MocVinyl) serve as protecting groups for the above-mentioned heterocyclic CONH or CONHCO moieties. Deprotections were accomplished via exchange with good nucleophiles: the 1-dodecanethiolate anion turned out to be the most general and efficient reagent, but in some particular cases other nucleophiles also worked (e.g., MocVinyl-inosines can be cleaved with succinimide anion). Some structural and mechanistic details have been accounted for with the help of DFT and MP2 calculations. PMID:23713491

  9. Metallic Adhesion and Bonding

    NASA Technical Reports Server (NTRS)

    Ferrante, J.; Smith, J. R.; Rose, J. H.

    1984-01-01

    Although metallic adhesion has played a central part in much tribological speculation, few quantitative theoretical calculations are available. This is in part because of the difficulties involved in such calculations and in part because the theoretical physics community is not particularly involved with tribology. The calculations currently involved in metallic adhesion are summarized and shown that these can be generalized into a scaled universal relationship. Relationships exist to other types of covalent bonding, such as cohesive, chemisorptive, and molecular bonding. A simple relationship between surface energy and cohesive energy is offered.

  10. Electronegativity and the Bond Triangle

    ERIC Educational Resources Information Center

    Meek, Terry L.; Garner, Leah D.

    2005-01-01

    The usefulness of the bond triangle for categorizing compounds of the main-group elements may be extended by the use of weighted average electronegativities to allow distinction between compounds of the same elements with different stoichiometries. In such cases a higher valency for the central atom leads to greater covalent character and the…

  11. Reactions of Cp{sub *}Ir(2,5-dimethylthiophene) with Ru{sub 3}(CO){sub 12}, Re{sub 2}(CO){sub 10}, Mn{sub 2}(CO){sub 10}, and [({eta}{sub 6}-C{sub 6}H{sub 6})RuCl{sub 2}]{sub 2}

    SciTech Connect

    Chen, J.; Young, V.G. Jr.; Angelici, R.J. |

    1996-06-11

    Reactions of the isomers Cp{sub *}Ir({eta}{sub 4}-2,5-Me{sub 2}T) (1) and Cp{sub *}Ir(C,S-2,5-Me{sub 2}T) (2), where 2,5-Me{sub 2}T is 2.5-dimethylthiophene, with Ru{sub 3}(CO){sub 12}, Re{sub 2}(CO){sub 10}, Mn{sub 2}(CO){sub 10}, and [{eta}{sub 6}-C{sub 6}H{sub 6})RuCl{sub 2}]{sub 2} yield a remarkable diversity of products. With Ru{sub 3}(CO){sub 12}, both 1 and 2 give the CO-substituted product Cp{sub *}Ir{eta}{sub 4}-2,5-Me{sub 2}T.Ru{sub 3}(CO){sub 11} (4), in which the 2,5-Me{sub 2}T group is {eta}{sub 4}-coordinated to the Ir and S-coordinated to a Ru in the plane of the triangular Ru{sub 3}(CO){sub 11} cluster. With Re{sub 2}(CO){sub 10}, 1 reacts to give the CO-substituted product Cp{sub *}Ir({eta}{sub 4}-2,5-Me{sub 2}T.Re{sub 2}(CO){sub 9}) (6), in which 1 is S-coordinated in an equatorial position of the metal-metal dimer Re{sub 2}(CO){sub 9}. However, another product of this reaction is Cp{sub *}Ir({eta}{sub 4}-SC{sub 3}H{sub 2}MeC(=O)Me)[Re{sub 2}-(CO){sub 9}] (7), in which the 2,5-Me{sub 2}T ligand has been converted to a ring-opened acyl-thiolate unit that is S-coordinated to Re{sub 2}(CO){sub 9}. Compound 7 is the major product of the reaction of 2 with Re{sub 2}(CO){sub 10}. The reaction of 2 with Mn{sub 2}(CO){sub 10} gives Cp{sub *}Ir({eta}{sub 4}SC{sub 3}H{sub 2}MeC(=O)Me)[Mn{sub 2}(CO){sub 9}] (9), the Mn analog of 7. The reaction of [({eta}{sub 6}-C{sub 6}H{sub 6})RuCl{sub 2}]{sub 2} with 1 gives the product Cp{sub *}Ir({eta}{sub 4}-2,5-Me{sub 2}T.Ru({eta}{sub 6}-C{sub 6}H{sub 6})Cl{sub 2} (10), which illustrates again the strong S-donor ability of the Cp{sub *}Ir({eta}{sub 4}-2,5-Me{sub 2}T) (1), group. 39 refs., 3 figs., 4 tabs.

  12. Mouldable liquid-crystalline elastomer actuators with exchangeable covalent bonds.

    PubMed

    Pei, Zhiqiang; Yang, Yang; Chen, Qiaomei; Terentjev, Eugene M; Wei, Yen; Ji, Yan

    2014-01-01

    Liquid-crystal elastomers (LCEs) are a class of actively moving polymers with remarkable practical potential for converting external stimuli into mechanical actuation. However, real-world applications of LCEs are lacking because macroscopic orientation of liquid-crystal order, which is required for reversible actuations, is hard to achieve in practice. Here we show that the processing bottleneck of LCEs can be overcome by introducing exchangeable links in place of permanent network crosslinks, a concept previously demonstrated for vitrimers. Liquid-crystal elastomers with exchangeable links (xLCEs) are mouldable, allow for easy processing and alignment, and can be subsequently altered through remoulding with different stress patterns, thus opening the way to practical xLCE actuators and artificial muscles. Surprisingly, instead of external-stress relaxation through the creep of non-liquid-crystal transient networks with exchangeable links, xLCEs develop strong liquid-crystal alignment as an alternative mechanism of mechanical relaxation. PMID:24292422

  13. Covalent bonding of polycations to small polymeric particles

    NASA Technical Reports Server (NTRS)

    Rembaum, A.

    1975-01-01

    Process produces small spherical polymeric particles which have polycations bound to them. In emulsion form, particles present large positively charged surface which is available to absorb polyanions. This properly can be used in removing heparin from blood or bile acids from the digestive tract. Other anions, such as DNA and RNA, can also be removed from aqueous solutions.

  14. Covalent bonding of antibodies of polystyrene latex beads: A concept

    NASA Technical Reports Server (NTRS)

    Tenoso, H. J.; Smith, D. G.

    1972-01-01

    Technique facilitates purification of vaccines and production of immunoadsorption columns exhibiting relatively long stability. Information interests biochemists, medical researchers, and pharmaceutical manufacturers.

  15. Specific covalent immobilization of proteins through dityrosine cross-links.

    PubMed

    Endrizzi, Betsy J; Huang, Gang; Kiser, Patrick F; Stewart, Russell J

    2006-12-19

    Dityrosine cross-links are widely observed in nature in structural proteins such as elastin and silk. Natural oxidative cross-linking between tyrosine residues is catalyzed by a diverse group of metalloenzymes. Dityrosine formation is also catalyzed in vitro by metal-peptide complexes such as Gly-Gly-His-Ni(II). On the basis of these observations, a system was developed to specifically and covalently surface immobilize proteins through dityrosine cross-links. Methacrylate monomers of the catalytic peptide Gly-Gly-His-Tyr-OH (GGHY) and the Ni(II)-chelating group nitrilotriacetic acid (NTA) were copolymerized with acrylamide into microbeads. Green fluorescent protein (GFP), as a model protein, was genetically tagged with a tyrosine-modified His6 peptide on its carboxy terminus. GFP-YGH6, specifically associated with the NTA-Ni(II) groups, was covalently coupled to the bead surface through dityrosine bond formation catalyzed by the colocalized GGHY-Ni(II) complex. After extensive washing with EDTA to disrupt metal coordination bonds, we observed that up to 75% of the initially bound GFP-YGH6 remained covalently bound to the bead while retaining its structure and activity. Dityrosine cross-linking was confirmed by quenching the reaction with free tyrosine. The method may find particular utility in the construction and optimization of protein microarrays. PMID:17154619

  16. A Structure-guided Approach to Creating Covalent FGFR Inhibitors

    PubMed Central

    Zhou, Wenjun; Hur, Wooyoung; McDermott, Ultan; Dutt, Amit; Xian, Wa; Picarro, Scott B.; Zhang, Jianming; Sharma, Sreenath V.; Brugge, Joan; Meyerson, Matthew; Settleman, Jeffrey; Gray, Nathanael S.

    2010-01-01

    Summary The fibroblast growth factor receptor tyrosine kinases (FGFR1, 2, 3, and 4) represent promising therapeutic targets in a number of cancers. We have developed the first potent and selective irreversible inhibitor of FGFR1, 2, 3, and 4 which we named FIIN-1 that forms a covalent bond with cysteine 486 located in the P-loop of the FGFR1 ATP-binding site. We demonstrate that the inhibitor potently inhibits Tel-FGFR1 transformed Ba/F3 cells (EC50 = 14 nM) as well as numerous FGFR-dependent cancer cell lines. A biotin-derivatized version of the inhibitor, FIIN-1-biotin, was shown to covalently label FGFR1 at Cys486. FIIN-1 is a useful probe of FGFR-dependent cellular phenomena and may provide a starting point of the development of therapeutically relevant irreversible inhibitors of wild-type and drug-resistant forms of FGFR kinases. PMID:20338520

  17. Theoretical insights into covalency driven f element separations.

    PubMed

    Roy, Lindsay E; Bridges, Nicholas J; Martin, Leigh R

    2013-02-21

    Through Density Function Theory (DFT) calculations, we set out to understand the structures and stabilities of the aqueous phase complexes [M(III)(DTPA)-H(2)O](2-) (M = Nd, Am) as well as the changes in Gibbs free energy for complexation in the gas phase and aqueous solution. All bonding analyses suggest that the preference of the DTPA(5-) ligand for Am over Nd is mainly due to electrostatic and covalent interactions from the oxygen atoms with the nitrogen chelates providing an additional, yet small, covalent interaction. These results question the exclusive use of hard and soft acids and bases (HSAB) concepts for the design of extracting reagents and suggest that hard-soft interactions may play more of a role in the separations process than previously thought. PMID:23223573

  18. Covalent organic frameworks (COFs): from design to applications.

    PubMed

    Ding, San-Yuan; Wang, Wei

    2013-01-21

    Covalent organic frameworks (COFs) represent an exciting new type of porous organic materials, which are ingeniously constructed with organic building units via strong covalent bonds. The well-defined crystalline porous structures together with tailored functionalities have offered the COF materials superior potential in diverse applications, such as gas storage, adsorption, optoelectricity, and catalysis. Since the seminal work of Yaghi and co-workers in 2005, the rapid development in this research area has attracted intensive interest from researchers with diverse expertise. This critical review describes the state-of-the-art development in the design, synthesis, characterisation, and application of the crystalline porous COF materials. Our own opinions on further development of the COF materials are also presented for discussion (155 references). PMID:23060270

  19. Reconstruction of Covalent Organic Frameworks by Dynamic Equilibrium.

    PubMed

    Gao, Qiang; Bai, Linyi; Zeng, Yongfei; Wang, Peng; Zhang, Xiaojing; Zou, Ruqiang; Zhao, Yanli

    2015-11-16

    Covalent organic frameworks (COFs) are periodic two- or three-dimensional polymeric networks with high surface areas, low density, and designed structures. Because COFs are normally prepared based on reversible formation of covalent bonds with relatively weak stability, their structures can be easily broken or damaged due to changes in the surrounding environment. Thus, developing strategies to realize the reconstruction of COFs in order to extend their usage lifetime is crucial for practical applications. In addition, exploring the kinetics of COF growth under varied reaction conditions is important for better understanding the nucleation and growth processes of COFs. In this work, the reformation mechanism of an imine-based COF using an ex situ characterization method was investigated, disclosing an interesting COF reconstruction progress from disorder to order. The present study shows the regeneration ability of COFs, and the developed method could be generalized for broader use in the field. PMID:26450522

  20. Non-covalent intermolecular carbon-carbon interactions in polyynes.

    PubMed

    Remya, Karunakaran; Suresh, Cherumuttathu H

    2015-10-28

    Polyynes, the smaller analogues of one dimensional infinite chain carbon allotrope carbyne, have been studied for the type and strength of the intermolecular interactions in their dimer and tetramer complexes using density functional theory. The nature of end group functionalities and the chain length of the polyynes are varied to assess their role in modulating the non-covalent interaction energy. As seen in molecular electrostatic potential analysis, all the polyyne complexes showed a multitude of non-covalent CC interactions, resulting from complementary electrostatic interactions between relatively electron rich formal triple bond region of one monomer and the electron deficient formal single bond region of the other monomer. This type of paired (C[triple bond, length as m-dash]C)(C-C) bonding interaction, also characterized using quantum theory of atoms-in-molecules, increases with increase in the monomer chain length leading to substantial increase in interaction energy (Eint); -1.07 kcal mol(-1) for the acetylene dimer to -45.83 kcal mol(-1) for the 50yne dimer. The magnitude of Eint increases with substitutions at end positions of the polyyne and this effect persists even up to 50 triple bonds, the largest chain length analyzed in this paper. The role of CC interactions in stabilizing the polyyne dimers is also shown by sliding one monomer in a dimer over the other, which resulted in multiple minima with a reduced number of CC interactions and lower values of Eint. Furthermore, strong cooperativity in the CC bond strength in tetramers is observed as the interaction energy per monomer (Em) of the polyyne is 2.5-2.8 times higher compared to that of the dimer in a test set of four tetramers. The huge gain in energy observed in large polyyene dimers and tetramers predicts the formation of polyyne bundles which may find use in the design of new functional molecular materials. PMID:26412713

  1. Covalency-reinforced oxygen evolution reaction catalyst

    PubMed Central

    Yagi, Shunsuke; Yamada, Ikuya; Tsukasaki, Hirofumi; Seno, Akihiro; Murakami, Makoto; Fujii, Hiroshi; Chen, Hungru; Umezawa, Naoto; Abe, Hideki; Nishiyama, Norimasa; Mori, Shigeo

    2015-01-01

    The oxygen evolution reaction that occurs during water oxidation is of considerable importance as an essential energy conversion reaction for rechargeable metal–air batteries and direct solar water splitting. Cost-efficient ABO3 perovskites have been studied extensively because of their high activity for the oxygen evolution reaction; however, they lack stability, and an effective solution to this problem has not yet been demonstrated. Here we report that the Fe4+-based quadruple perovskite CaCu3Fe4O12 has high activity, which is comparable to or exceeding those of state-of-the-art catalysts such as Ba0.5Sr0.5Co0.8Fe0.2O3−δ and the gold standard RuO2. The covalent bonding network incorporating multiple Cu2+ and Fe4+ transition metal ions significantly enhances the structural stability of CaCu3Fe4O12, which is key to achieving highly active long-life catalysts. PMID:26354832

  2. Covalency-reinforced oxygen evolution reaction catalyst.

    PubMed

    Yagi, Shunsuke; Yamada, Ikuya; Tsukasaki, Hirofumi; Seno, Akihiro; Murakami, Makoto; Fujii, Hiroshi; Chen, Hungru; Umezawa, Naoto; Abe, Hideki; Nishiyama, Norimasa; Mori, Shigeo

    2015-01-01

    The oxygen evolution reaction that occurs during water oxidation is of considerable importance as an essential energy conversion reaction for rechargeable metal-air batteries and direct solar water splitting. Cost-efficient ABO3 perovskites have been studied extensively because of their high activity for the oxygen evolution reaction; however, they lack stability, and an effective solution to this problem has not yet been demonstrated. Here we report that the Fe(4+)-based quadruple perovskite CaCu3Fe4O12 has high activity, which is comparable to or exceeding those of state-of-the-art catalysts such as Ba(0.5)Sr(0.5)Co(0.8)Fe(0.2)O(3-δ) and the gold standard RuO2. The covalent bonding network incorporating multiple Cu(2+) and Fe(4+) transition metal ions significantly enhances the structural stability of CaCu3Fe4O12, which is key to achieving highly active long-life catalysts. PMID:26354832

  3. Covalency-reinforced oxygen evolution reaction catalyst

    NASA Astrophysics Data System (ADS)

    Yagi, Shunsuke; Yamada, Ikuya; Tsukasaki, Hirofumi; Seno, Akihiro; Murakami, Makoto; Fujii, Hiroshi; Chen, Hungru; Umezawa, Naoto; Abe, Hideki; Nishiyama, Norimasa; Mori, Shigeo

    2015-09-01

    The oxygen evolution reaction that occurs during water oxidation is of considerable importance as an essential energy conversion reaction for rechargeable metal-air batteries and direct solar water splitting. Cost-efficient ABO3 perovskites have been studied extensively because of their high activity for the oxygen evolution reaction; however, they lack stability, and an effective solution to this problem has not yet been demonstrated. Here we report that the Fe4+-based quadruple perovskite CaCu3Fe4O12 has high activity, which is comparable to or exceeding those of state-of-the-art catalysts such as Ba0.5Sr0.5Co0.8Fe0.2O3-δ and the gold standard RuO2. The covalent bonding network incorporating multiple Cu2+ and Fe4+ transition metal ions significantly enhances the structural stability of CaCu3Fe4O12, which is key to achieving highly active long-life catalysts.

  4. Supramolecular reactivity in the gas phase: investigating the intrinsic properties of non-covalent complexes.

    PubMed

    Cera, Luca; Schalley, Christoph A

    2014-03-21

    The high vacuum inside a mass spectrometer offers unique conditions to broaden our view on the reactivity of supramolecules. Because dynamic exchange processes between complexes are efficiently suppressed, the intrinsic and intramolecular reactivity of the complexes of interest is observed. Besides this, the significantly higher strength of non-covalent interactions in the absence of competing solvent allows processes to occur that are unable to compete in solution. The present review highlights a series of examples illustrating different aspects of supramolecular gas-phase reactivity ranging from the dissociation and formation of covalent bonds in non-covalent complexes through the reactivity in the restricted inner phase of container molecules and step-by-step mechanistic studies of organocatalytic reaction cycles to cage contraction reactions, processes induced by electron capture, and finally dynamic molecular motion within non-covalent complexes as unravelled by hydrogen-deuterium exchange processes performed in the gas phase. PMID:24435245

  5. Genetically Encoding an Electrophilic Amino Acid for Protein Stapling and Covalent Binding to Native Receptors

    PubMed Central

    2015-01-01

    Covalent bonds can be generated within and between proteins by an unnatural amino acid (Uaa) reacting with a natural residue through proximity-enabled bioreactivity. Until now, Uaas have been developed to react mainly with cysteine in proteins. Here we genetically encoded an electrophilic Uaa capable of reacting with histidine and lysine, thereby expanding the diversity of target proteins and the scope of the proximity-enabled protein cross-linking technology. In addition to efficient cross-linking of proteins inter- and intramolecularly, this Uaa permits direct stapling of a protein α-helix in a recombinant manner and covalent binding of native membrane receptors in live cells. The target diversity, recombinant stapling, and covalent targeting of endogenous proteins enabled by this versatile Uaa should prove valuable in developing novel research tools, biological diagnostics, and therapeutics by exploiting covalent protein linkages for specificity, irreversibility, and stability. PMID:25010185

  6. An optimal hydrogen-bond surrogate for α-helices.

    PubMed

    Joy, Stephen T; Arora, Paramjit S

    2016-04-14

    Substitution of a main chain i → i + 4 hydrogen bond with a covalent bond can nucleate and stabilize the α-helical conformation in peptides. Herein we describe the potential of different alkene isosteres to mimic intramolecular hydrogen bonds and stabilize α-helices in diverse peptide sequences. PMID:27046675

  7. Covalent bulk functionalization of graphene.

    PubMed

    Englert, Jan M; Dotzer, Christoph; Yang, Guang; Schmid, Martin; Papp, Christian; Gottfried, J Michael; Steinrück, Hans-Peter; Spiecker, Erdmann; Hauke, Frank; Hirsch, Andreas

    2011-04-01

    Graphene, a truly two-dimensional and fully π-conjugated honeycomb carbon network, is currently evolving into the most promising successor to silicon in micro- and nanoelectronic applications. However, its wider application is impeded by the difficulties in opening a bandgap in its gapless band-structure, as well as the lack of processability in the resultant intrinscially insoluble material. Covalent chemical modification of the π-electron system is capable of addressing both of these issues through the introduction of variable chemical decoration. Although there has been significant research activity in the field of functionalized graphene, most work to date has focused on the use of graphene oxide. In this Article, we report on the first wet chemical bulk functionalization route beginning with pristine graphite that does not require initial oxidative damage of the graphene basal planes. Through effective reductive activation, covalent functionalization of the charged graphene is achieved by organic diazonium salts. Functionalization was observed spectroscopically, and successfully prevents reaggregation while providing solubility in common organic media. PMID:21430685

  8. Simultaneous covalent and noncovalent hybrid polymerizations

    NASA Astrophysics Data System (ADS)

    Yu, Zhilin; Tantakitti, Faifan; Yu, Tao; Palmer, Liam C.; Schatz, George C.; Stupp, Samuel I.

    2016-01-01

    Covalent and supramolecular polymers are two distinct forms of soft matter, composed of long chains of covalently and noncovalently linked structural units, respectively. We report a hybrid system formed by simultaneous covalent and supramolecular polymerizations of monomers. The process yields cylindrical fibers of uniform diameter that contain covalent and supramolecular compartments, a morphology not observed when the two polymers are formed independently. The covalent polymer has a rigid aromatic imine backbone with helicoidal conformation, and its alkylated peptide side chains are structurally identical to the monomer molecules of supramolecular polymers. In the hybrid system, covalent chains grow to higher average molar mass relative to chains formed via the same polymerization in the absence of a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure, suggesting soft materials with novel delivery or repair functions.

  9. Simultaneous covalent and noncovalent hybrid polymerizations.

    PubMed

    Yu, Zhilin; Tantakitti, Faifan; Yu, Tao; Palmer, Liam C; Schatz, George C; Stupp, Samuel I

    2016-01-29

    Covalent and supramolecular polymers are two distinct forms of soft matter, composed of long chains of covalently and noncovalently linked structural units, respectively. We report a hybrid system formed by simultaneous covalent and supramolecular polymerizations of monomers. The process yields cylindrical fibers of uniform diameter that contain covalent and supramolecular compartments, a morphology not observed when the two polymers are formed independently. The covalent polymer has a rigid aromatic imine backbone with helicoidal conformation, and its alkylated peptide side chains are structurally identical to the monomer molecules of supramolecular polymers. In the hybrid system, covalent chains grow to higher average molar mass relative to chains formed via the same polymerization in the absence of a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure, suggesting soft materials with novel delivery or repair functions. PMID:26823427

  10. Covalent Functionalization of Boron Nitride Nanotubes via Reduction Chemistry.

    PubMed

    Shin, Homin; Guan, Jingwen; Zgierski, Marek Z; Kim, Keun Su; Kingston, Christopher T; Simard, Benoit

    2015-12-22

    Boron nitride nanotubes (BNNTs) exhibit a range of properties that hold great potential for many fields of science and technology; however, they have inherently low chemical reactivity, making functionalization for specific applications difficult. Here we propose that covalent functionalization of BNNTs via reduction chemistry could be a highly promising and viable strategy. Through density functional theory calculations of the electron affinity of BNNTs and their binding energies with various radicals, we reveal that their chemical reactivity can be significantly enhanced via reducing the nanotubes (i.e., negatively charging). For example, a 5.5-fold enhancement in reactivity of reduced BNNTs toward NH2 radicals was predicted relative to their neutral counterparts. The localization characteristics of the BNNT π electron system lead the excess electrons to fill the empty p orbitals of boron sites, which promote covalent bond formation with an unpaired electron from a radical molecule. In support of our theoretical findings, we also experimentally investigated the covalent alkylation of BNNTs via reduction chemistry using 1-bromohexane. The thermogravimetric measurements showed a considerable weight loss (12-14%) only for samples alkylated using reduced BNNTs, suggesting their significantly improved reactivity over neutral BNNTs. This finding will provide an insight in developing an effective route to chemical functionalization of BNNTs. PMID:26580970

  11. Exceptional ammonia uptake by a covalent organic framework

    NASA Astrophysics Data System (ADS)

    Doonan, Christian J.; Tranchemontagne, David J.; Glover, T. Grant; Hunt, Joseph R.; Yaghi, Omar M.

    2010-03-01

    Covalent organic frameworks (COFs) are porous crystalline materials composed of light elements linked by strong covalent bonds. A number of these materials contain a high density of Lewis acid boron sites that can strongly interact with Lewis basic guests, which makes them ideal for the storage of corrosive chemicals such as ammonia. We found that a member of the covalent organic framework family, COF-10, shows the highest uptake capacity (15 mol kg-1, 298 K, 1 bar) of any porous material, including microporous 13X zeolite (9 mol kg-1), Amberlyst 15 (11 mol kg-1) and mesoporous silica, MCM-41 (7.9 mol kg-1). Notably, ammonia can be removed from the pores of COF-10 by heating samples at 200 °C under vacuum. In addition, repeated adsorption of ammonia into COF-10 causes a shift in the interlayer packing, which reduces its apparent surface area to nitrogen. However, owing to the strong Lewis acid-base interactions, the total uptake capacity of ammonia and the structural integrity of the COF are maintained after several cycles of adsorption/desorption.

  12. Bent Bonds and Multiple Bonds.

    ERIC Educational Resources Information Center

    Robinson, Edward A.; Gillespie, Ronald J.

    1980-01-01

    Considers carbon-carbon multiple bonds in terms of Pauling's bent bond model, which allows direct calculation of double and triple bonds from the length of a CC single bond. Lengths of these multiple bonds are estimated from direct measurements on "bent-bond" models constructed of plastic tubing and standard kits. (CS)

  13. Hydrogels with covalent and noncovalent crosslinks

    NASA Technical Reports Server (NTRS)

    Kilck, Kristi L. (Inventor); Yamaguchi, Nori (Inventor)

    2013-01-01

    A method for targeted delivery of therapeutic compounds from hydrogels is presented. The method involves administering to a cell a hydrogel in which a therapeutic compound is noncovalently bound to heparin. The hydrogel may contain covalent and non-covalent crosslinks.

  14. Theoretical Insights into Covalency Driven f Element Separations

    SciTech Connect

    Lindsay E. Roy; Nicholas J. Bridges; Leigh R. Martin

    2013-02-01

    The lanthanide series, Am, and Cm are predominantly found in the trivalent oxidation state in aqueous solutions making their separation very difficult to achieve. To date, one of the mostly promising separation processes for transplutonium elements from the lanthanides is the TALSPEAK process. Though the mechanism of the TALSPEAK process is not fully understood, it has been demonstrated to provide excellent separation factors between the lanthanides and the trivalent lanthanides. Through Density Function Theory (DFT) calculations of di 2-ethylenetriamine-N,N,N',N”,N”-pentaacetic acid (DTPA), we set out to understand the structures and stabilities of the aqueous phase complexes [MIII(DTPA)-H2O]2- (M = Nd, Am) as well as the changes in Gibbs free energy for complexation in the gas phase and aqueous solution. Mulliken population analysis, Bader’s Atoms-in-Molecules (AIM) approach, and Natural Bond Orbital (NBO) analysis were then used to analyze the bonding in both molecules. The results discussed below suggest that the preference of the DTPA5- ligand for Am over Nd is mainly due to electrostatic and covalent interactions from the oxygen atoms with the nitrogen chelates provide an additional, yet small, covalent interaction. These results question the exclusive use of hard and soft acids and bases (HSAB) concepts for the design of extracting reagents and suggest that hard-soft interactions play more of a role in the separations process than previously thought.

  15. Formulation and Characterization of a Covalently Coated Magnetic Nanogel

    PubMed Central

    Rahimi, Maham; Yousef, Monet; Cheng, Yuhang; Meletis, Efstathios I.; Eberhart, Robert C.; Nguyen, Kytai

    2010-01-01

    The aim of this study was to develop a novel method to encapsulate magnetic nanoparticles (MNPs) with polymer via covalent bonding, in order to increase the magnetic nanoparticle stability and ease the synthesis process. In this technique, silane coated MNPs act as a template for polymerization of the monomer N-isopropylacrylamide, (NIPA) via radical polymerization. Transmission and scanning electron microscopy indicated the size of the original MNP was approximately 10 nm, the silane-coated MNP was 40 nm and the NIPA silane-coated MNP was 100 ± 10 nm. Chemical composition and chemical state analysis of NIPA MNPs by FTIR and XPS showed that the MNPs were actually encapsulated by silane and NIPA. Furthermore, the magnetic properties of different layers on the MNP, analyzed by SQUID, indicated a decrease in saturation magnetization for each layer. The results demonstrate the feasibility of encapsulation of the MNP with NIPA by means of silane covalent bonding. Future work will investigate the phase transition and biocompatibility properties of the NIPA-coated MNP for drug delivery and tissue engineering applications. PMID:19916419

  16. Lipid Bilayers Covalently Anchored to Carbon Nanotubes

    PubMed Central

    Dayani, Yasaman; Malmstadt, Noah

    2012-01-01

    The unique physical and electrical properties of carbon nanotubes make them an exciting material for applications in various fields such as bioelectronics and biosensing. Due to the poor water solubility of carbon nanotubes, functionalization for such applications has been a challenge. Of particular need are functionalization methods for integrating carbon nanotubes with biomolecules and constructing novel hybrid nanostructures for bionanoelectronic applications. We present a novel method for the fabrication of dispersible, biocompatible carbon nanotube-based materials. Multi-walled carbon nanotubes (MWCNTs) are covalently modified with primary amine-bearing phospholipids in a carbodiimide-activated reaction. These modified carbon nanotubes have good dispersibility in nonpolar solvents. Fourier transform infrared (FTIR) spectroscopy shows peaks attributable to the formation of amide bonds between lipids and the nanotube surface. Simple sonication of lipid-modified nanotubes with other lipid molecules leads to the formation of a uniform lipid bilayer coating the nanotubes. These bilayer-coated nanotubes are highly dispersible and stable in aqueous solution. Confocal fluorescence microscopy shows labeled lipids on the surface of bilayer-modified nanotubes. Transmission electron microscopy (TEM) shows the morphology of dispersed bilayer-coated MWCNTs. Fluorescence quenching of lipid-coated MWCNTs confirms the bilayer configuration of the lipids on the nanotube surface and fluorescence anisotropy measurements show that the bilayer is fluid above the gel-to-liquid transition temperature. The membrane protein α-hemolysin spontaneously inserts into the MWCNT-supported bilayer, confirming the biomimetic membrane structure. These biomimetic nanostructures are a promising platform for the integration of carbon nanotube-based materials with biomolecules. PMID:22568448

  17. Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy

    NASA Astrophysics Data System (ADS)

    Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

    2014-11-01

    Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

  18. Functional Importance of Covalent Homodimer of Reelin Protein Linked via Its Central Region*

    PubMed Central

    Yasui, Norihisa; Kitago, Yu; Beppu, Ayako; Kohno, Takao; Morishita, Shunsuke; Gomi, Hiroki; Nagae, Masamichi; Hattori, Mitsuharu; Takagi, Junichi

    2011-01-01

    Reelin is a 3461-residue secreted glycoprotein that plays a critical role in brain development through its action on target neurons. Although it is known that functional reelin protein exists as multimer formed by interchain disulfide bond(s) as well as through non-covalent interactions, the chemical nature of the multimer assembly has been elusive. In the present study, we identified, among 122 cysteines present in full-length reelin, the single critical cysteine residue (Cys2101) responsible for the covalent multimerization. C2101A mutant reelin failed to assemble into disulfide-bonded multimers, whereas it still exhibited non-covalently associated high molecular weight oligomeric states in solution. Detailed analysis of tryptic fragments produced from the purified reelin proteins revealed that the minimum unit of the multimer is a homodimeric reelin linked via Cys2101 present in the central region and that this cysteine does not connect to the N-terminal region of reelin, which had been postulated as the primary oligomerization domain. A surface plasmon resonance binding assay confirmed that C2101A mutant reelin retained binding capability toward two neuronal receptors apolipoprotein E receptor 2 and very low density lipoprotein receptor. However, it failed to show signaling activity in the assay using the cultured neurons. These results indicate that an intact higher order architecture of reelin multimer maintained by both Cys2101-mediated homodimerization and other non-covalent association present elsewhere in the reelin primary structure are essential for exerting its full biological activity. PMID:21844191

  19. Covalent modification of proteins by cocaine

    NASA Astrophysics Data System (ADS)

    Deng, Shi-Xian; Bharat, Narine; Fischman, Marian C.; Landry, Donald W.

    2002-03-01

    Cocaine covalently modifies proteins through a reaction in which the methyl ester of cocaine acylates the -amino group of lysine residues. This reaction is highly specific in vitro, because no other amino acid reacts with cocaine, and only cocaine's methyl ester reacts with the lysine side chain. Covalently modified proteins were present in the plasma of rats and human subjects chronically exposed to cocaine. Modified endogenous proteins are immunogenic, and specific antibodies were elicited in mouse and detected in the plasma of human subjects. Covalent modification of proteins could explain cocaine's autoimmune effects and provide a new biochemical approach to cocaine's long-term actions.

  20. Synergistic Assembly of Covalent and Supramolecular Polymers.

    PubMed

    Bai, Linyi; Zhao, Yanli

    2016-06-01

    Integrating irreplaceable features of both covalent chemistry and noncovalent interactions into a single entity to maximize the applicability is highly desired. Here, a discovery of this type of hybrid, developed by Stupp and co-workers, is developed, where a synergistic combination of covalent and noncovalent compartments enables them to assemble by each other perfectively. The covalent compartments can grow into polymer chains assisted by a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure. The obtained soft materials can serve as functional platforms for molecular delivery or self-repairing materials. PMID:27076255

  1. σ-Hole Bond vs π-Hole Bond: A Comparison Based on Halogen Bond.

    PubMed

    Wang, Hui; Wang, Weizhou; Jin, Wei Jun

    2016-05-11

    The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future. PMID:26886515

  2. An internal thioester in a pathogen surface protein mediates covalent host binding.

    PubMed

    Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

    2015-01-01

    To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a 'chemical harpoon'. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. PMID:26032562

  3. Short peptide tag for covalent protein labeling based on coiled coils.

    PubMed

    Wang, Jianpeng; Yu, Yongsheng; Xia, Jiang

    2014-01-15

    To label proteins covalently, one faces a trade-off between labeling a protein specifically and using a small tag. Often one must compromise one parameter for the other or use additional components, such as an enzyme, to satisfy both requirements. Here, we report a new reaction that covalently labels proteins by using engineered coiled-coil peptides. Harnessing the concept of "proximity-induced reactivity", the 21-amino-acid three-heptad peptides CCE/CCK were modified with a nucleophilic cysteine and an α-chloroacetyl group at selected positions. When pairs of coiled coils associated, an irreversible covalent bond spontaneously formed between the peptides. The specificity of the cross-linking reaction was characterized, the probes were improved by making them bivalent, and the system was used to label a protein in vitro and receptors on the surface of mammalian cells. PMID:24341800

  4. Ionic-covalent character of metal and nonmetal oxides.

    PubMed

    Duffy, J A

    2006-12-14

    The acid-base properties of oxidic media are quantified in terms of the optical basicity concept, which serves to correlate many properties with chemical constitution. Optical basicity values, Lambda, have been assigned to 25 oxides such that they relate to Lambda for crystalline CaO being taken as unity. Since Lambda for an oxide is proportional to the degree of negative charge borne by the oxide-(-II) atom or ion, it follows that optical basicity should go hand-in-hand with the ionic/covalent nature of the cation-oxide-(-II) bonding. Unfortunately, this assumption produces many anomalies and trends that do not fit normal inorganic trends. The problem is resolved by adjusting the influence of ionic forms to the bonding by taking into account the heats of formation. In contrast to the (Pauling) electronegativity treatment of oxides, this procedure allows assignment of percentage ionicity to the bonding, and the trends in these in the Periodic Table are as expected for inorganic oxides. PMID:17149841

  5. Prevention of sulfide mineral leaching through covalent coating

    SciTech Connect

    K.M. Zaman; C. Chusuei; L.Y. Blue; D.A. Atwood

    2007-09-15

    The use of benzene-1,3-diamidoethanethiol as a covalent surface coating for the prevention of metal leaching was demonstrated with several sulfide minerals including cinnabar (HgS), pyrite (FeS{sub 2}), chalcopyrite (CuFeS{sub 2}), covellite (CuS), galena (PbS), realgar (As{sub 4}S{sub 4}) and sphalerite (ZnS). The minerals were coated with sufficient H2BDT to bind the surface metals in a 1:1 ratio. Leaching at pH 1, 3 and 7 was then conducted on both treated and untreated minerals. ICP and CVAFS (for mercury) analyses revealed that the coated minerals showed a dramatic reduction in metal leaching as compared to uncoated control samples. X-ray photoelectron spectroscopy indicated the formation of covalent bonds between the sulphur of the ligand and the metals from the minerals. Results indicate that it would be possible to prevent acid mine drainage through the binding of the metals in coal. 51 refs., 4 figs., 8 tabs.

  6. Covalent immobilization of liposomes on plasma functionalized metallic surfaces.

    PubMed

    Mourtas, S; Kastellorizios, M; Klepetsanis, P; Farsari, E; Amanatides, E; Mataras, D; Pistillo, B R; Favia, P; Sardella, E; d'Agostino, R; Antimisiaris, S G

    2011-05-01

    A method was developed to functionalize biomedical metals with liposomes. The novelty of the method includes the plasma-functionalization of the metal surface with proper chemical groups to be used as anchor sites for the covalent immobilization of the liposomes. Stainless steel (SS-316) disks were processed in radiofrequency glow discharges fed with vapors of acrylic acid to coat them with thin adherent films characterized by surface carboxylic groups, where liposomes were covalently bound through the formation of amide bonds. For this, liposomes decorated with polyethylene glycol molecules bearing terminal amine-groups were prepared. After ensuring that the liposomes remain intact, under the conditions applying for immobilization; different attachment conditions were evaluated (incubation time, concentration of liposome dispersion) for optimization of the technique. Immobilization of calcein-entrapping liposomes was evaluated by monitoring the percent of calcein attached on the surfaces. Best results were obtained when liposome dispersions with 5mg/ml (liposomal lipid) concentration were incubated on each disk for 24h at 37°C. The method is proposed for developing drug-eluting biomedical materials or devices by using liposomes that have appropriate membrane compositions and are loaded with drugs or other bioactive agents. PMID:21273051

  7. Oxidized Porous Silicon Particles Covalently Grafted with Daunorubicin as a Sustained Intraocular Drug Delivery System

    PubMed Central

    Chhablani, Jay; Nieto, Alejandra; Hou, Huiyuan; Wu, Elizabeth C.; Freeman, William R.; Sailor, Michael J.; Cheng, Lingyun

    2013-01-01

    Purpose. To test the feasibility of covalent loading of daunorubicin into oxidized porous silicon (OPS) and to evaluate the ocular properties of sustained delivery of daunorubicin in this system. Methods. Porous silicon was heat oxidized and chemically functionalized so that the functional linker on the surface was covalently bonded with daunorubicin. The drug loading rate was determined by thermogravimetric analysis. Release of daunorubicin was confirmed in PBS and excised rabbit vitreous by mass spectrometry. Daunorubicin-loaded OPS particles (3 mg) were intravitreally injected into six rabbits, and ocular properties were evaluated through ophthalmic examinations and histology during a 3-month study. The same OPS was loaded with daunorubicin using physical adsorption and was evaluated similarly as a control for the covalent loading. Results. In the case of covalent loading, 67 ± 10 μg daunorubicin was loaded into each milligram of the particles while 27 ± 10 μg/mg particles were loaded by physical adsorption. Rapid release of daunorubicin was observed in both PBS and excised vitreous (∼75% and ∼18%) from the physical adsorption loading, while less than 1% was released from the covalently loaded particles. Following intravitreal injection, the covalently loaded particles demonstrated a sustained degradation of OPS with drug release for 3 months without evidence of toxicity; physical adsorption loading revealed a complete release within 2 weeks and localized retinal toxicity due to high daunorubicin concentration. Conclusions. OPS with covalently loaded daunorubicin demonstrated sustained intravitreal drug release without ocular toxicity, which may be useful to inhibit unwanted intraocular proliferation. PMID:23322571

  8. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    PubMed

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-01

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes. PMID:27074500

  9. Covalent Docking of Large Libraries for the Discovery of Chemical Probes

    PubMed Central

    London, Nir; Miller, Rand M.; Krishnan, Shyam; Uchida, Kenji; Irwin, John J.; Eidam, Oliv; Gibold, Lucie; Cimermančič, Peter; Bonnet, Richard; Shoichet, Brian K.; Taunton, Jack

    2014-01-01

    Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency, and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC β-lactamase and noncatalytic cysteines in RSK2, MSK1, and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org). PMID:25344815

  10. Covalent interaction of ascorbic acid with natural products

    PubMed Central

    Kesinger, Nicholas G.; Stevens, Jan F.

    2009-01-01

    While ascorbic acid (Vitamin C) is mostly known as a cofactor for proline hydroxylase and as a biological antioxidant, it also forms covalent bonds with natural products which we here refer to as ‘ascorbylation’. A number of natural products containing an ascorbate moiety has been isolated and characterized from a variety of biological sources, ranging from marine algae to flowering plants. Most of these compounds are formed as a result of nucleophilic substitution or addition by ascorbate, e.g. the ascorbigens from Brassica species are ascorbylated indole derivatives. Some ascorbylated tannins appear to be formed from electrophilic addition to dehydroascorbic acid. There are also examples of annulations of ascorbate with dietary polyphenols, e.g., epigallocatechin gallate (EGCG) and resveratrol derivatives. Herein is a survey of thirty-three ascorbylated natural products and their reported biological activities. PMID:19875138

  11. Covalent Metal-Nanotube Heterojunctions as Ultimate Nano-Contacts

    SciTech Connect

    Rodriguez-Manzo, Jose; Banhart, Florian; Terrones Maldonado, Mauricio; Terrones Maldonado, Humberto; Grobert, Nicole; Ajayan, Pullikel M; Sumpter, Bobby G; Meunier, Vincent

    2009-01-01

    We report the controlled formation and characterization of heterojunctions between carbon nanotubes and different metal nanocrystals (Fe, Co, Ni, and FeCo). The heterojunctions are formed from metal-filled multiwall carbon nanotubes (MWNTs) via intense electron beam irradiation at temperatures in the range of 450-700 C and observed in situ in a transmission electron microscope. Under irradiation, the segregation of metal and carbon atoms occurs, leading to the formation of heterojunctions between metal and graphite. Metallic conductivity of the metal-nanotube junctions was found by using in situ transport measurements in an electron microscope. Density functional calculations show that these structures are mechanically strong, the bonding at the interface is covalent, and the electronic states at and around the Fermi level are delocalized across the entire system. These properties are essential for the application of such heterojunctions as contacts in electronic devices and vital for the fabrication of robust nanotube-metal composite materials.

  12. Covalent organic frameworks: Potential adsorbent for carbon dioxide adsorption

    NASA Astrophysics Data System (ADS)

    Xie, Yinhuan

    A series of covalent organic frameworks (COFs) based on propeller shaped hexaphenylbenzene derivatives were obtained under solvothermal conditions via Schiff base reaction. The relationship between the geometry parameters of monomers and gas absorption behaviors of planar COFs was investigated. The FT-IR spectroscopy confirms the formation of imine double bond in the obtained COFs by showing a peak around 1620 cm-1. The resulting frameworks have high BET surface areas approaching 700 m2/g and CO2 uptake up to 14% at 273 K and 1 bar, which are better than most of the 2-D porous aromatic frameworks. The thermogravimetric analysis shows those frameworks are stable until 773 K, allowing for the practical application of the post-combustion CO2 technology. Moreover, a novel synthetic strategy for the trigonal pyramidal hydrozide monomers was established. It provides an efficient way to synthesize the hydrozide monomers at multi-gram scale, promising for the synthesis of hydrozane porous organic cages.

  13. Benchmarking in vitro covalent binding burden as a tool to assess potential toxicity caused by nonspecific covalent binding of covalent drugs.

    PubMed

    Dahal, Upendra P; Obach, R Scott; Gilbert, Adam M

    2013-11-18

    Despite several advantages of covalent inhibitors (such as increased biochemical efficiency, longer duration of action on the target, and lower efficacious doses) over their reversible binding counterparts, there is a reluctance to use covalent inhibitors as a drug design strategy in pharmaceutical research. This reluctance is due to their anticipated reactions with nontargeted macromolecules. We hypothesized that there may be a threshold limit for nonspecific covalent binding, below which a covalent binding drug may be less likely to cause toxicity due to irreversible binding to off-target macromolecules. Estimation of in vivo covalent binding burden from in vitro data has previously been used as an approach to distinguish those agents more likely to cause toxicity (e.g., hepatotoxicity) via metabolic activation to reactive metabolites. We have extended this approach to nine covalent binding drugs to determine in vitro covalent binding burden. In vitro covalent binding burden was determined by incubating radiolabeled drugs with pooled human hepatocytes. These data were scaled to an estimate of in vivo covalent binding burden by combining the in vitro data with daily dose. Scaled in vivo daily covalent binding burden of marketed covalent drugs was found to be under 10 mg/day, which is in agreement with previously reported threshold value for metabolically activated reversible drugs. Covalent binding was also compared to the intrinsic reactivities of the covalent inhibitors assessed using nucleophiles glutathione and N-α-acetyl lysine. The intrinsic reactivity did not correlate with observed in vitro covalent binding, which demonstrated that the intrinsic reactivity of the electrophilic groups of covalent drugs does not exclusively account for the extent of covalent binding. The ramifications of these findings for consideration of using a covalent strategy in drug design are discussed. PMID:24164572

  14. CovalentDock Cloud: a web server for automated covalent docking.

    PubMed

    Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

    2013-07-01

    Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

  15. Bond Issues.

    ERIC Educational Resources Information Center

    Pollack, Rachel H.

    2000-01-01

    Notes trends toward increased borrowing by colleges and universities and offers guidelines for institutions that are considering issuing bonds to raise money for capital projects. Discussion covers advantages of using bond financing, how use of bonds impacts on traditional fund raising, other cautions and concerns, and some troubling aspects of…

  16. Multiple-component covalent organic frameworks

    NASA Astrophysics Data System (ADS)

    Huang, Ning; Zhai, Lipeng; Coupry, Damien E.; Addicoat, Matthew A.; Okushita, Keiko; Nishimura, Katsuyuki; Heine, Thomas; Jiang, Donglin

    2016-07-01

    Covalent organic frameworks are a class of crystalline porous polymers that integrate molecular building blocks into periodic structures and are usually synthesized using two-component [1+1] condensation systems comprised of one knot and one linker. Here we report a general strategy based on multiple-component [1+2] and [1+3] condensation systems that enable the use of one knot and two or three linker units for the synthesis of hexagonal and tetragonal multiple-component covalent organic frameworks. Unlike two-component systems, multiple-component covalent organic frameworks feature asymmetric tiling of organic units into anisotropic skeletons and unusually shaped pores. This strategy not only expands the structural complexity of skeletons and pores but also greatly enhances their structural diversity. This synthetic platform is also widely applicable to multiple-component electron donor-acceptor systems, which lead to electronic properties that are not simply linear summations of those of the conventional [1+1] counterparts.

  17. Locking GTPases covalently in their functional states

    NASA Astrophysics Data System (ADS)

    Wiegandt, David; Vieweg, Sophie; Hofmann, Frank; Koch, Daniel; Li, Fu; Wu, Yao-Wen; Itzen, Aymelt; Müller, Matthias P.; Goody, Roger S.

    2015-07-01

    GTPases act as key regulators of many cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states. In many cases, understanding their mode of action has been aided by artificially stabilizing one of these states either by designing mutant proteins or by complexation with non-hydrolysable GTP analogues. Because of inherent disadvantages in these approaches, we have developed acryl-bearing GTP and GDP derivatives that can be covalently linked with strategically placed cysteines within the GTPase of interest. Binding studies with GTPase-interacting proteins and X-ray crystallography analysis demonstrate that the molecular properties of the covalent GTPase-acryl-nucleotide adducts are a faithful reflection of those of the corresponding native states and are advantageously permanently locked in a defined nucleotide (that is active or inactive) state. In a first application, in vivo experiments using covalently locked Rab5 variants provide new insights into the mechanism of correct intracellular localization of Rab proteins.

  18. Managing bond tension in spreading macromolecules.

    NASA Astrophysics Data System (ADS)

    Sheyko, Sergey; Park, Insun; Nese, Alper; Matyjaszewski, Krzysztof; Shirvaniants, David; Rubinstein, Michael

    2009-03-01

    Mechanical activation of chemical bonds plays a vital role in biology, chemistry, and engineering. Unlike other activation stimuli, such as light and temperature, mechanical activation is site and direction specific. However, in a typical experiment, macroscopic stress is distributed over myriads of different molecules. This results in significant and ill-defined variation of both the magnitude and direction of forces at individual chemical bonds. Here, we show how to achieve a great degree of control over bond tension in flowing polymer films. The distinctive feature of this finding is that the mechanical tension is controlled on three different length scales. First, chemical bonds are activated within a narrowly defined area of a macroscopic film. Second, only certain molecules are activated within a mixture of molecules. Third, the tension can be focused to a specific bond within a flowing macromolecule. It is demonstrated that the focused tension breaks covalent bonds with a molecular-scale precision.

  19. Halogen Bonding in Hypervalent Iodine Compounds.

    PubMed

    Catalano, Luca; Cavallo, Gabriella; Metrangolo, Pierangelo; Resnati, Giuseppe; Terraneo, Giancarlo

    2016-01-01

    Halogen bonds occur when electrophilic halogens (Lewis acids) attractively interact with donors of electron density (Lewis bases). This term is commonly used for interactions undertaken by monovalent halogen derivatives. The aim of this chapter is to show that the geometric features of the bonding pattern around iodine in its hypervalent derivatives justify the understanding of some of the longer bonds as halogen bonds. We suggest that interactions directionality in ionic and neutral λ(3)-iodane derivatives is evidence that the electron density distribution around iodine atoms is anisotropic, a region of most positive electrostatic potential exists on the extensions of the covalent bonds formed by iodine, and these positive caps affect, or even determine, the crystal packing of these derivatives. For instance, the short cation-anion contacts in ionic λ(3)-iodane and λ(5)-iodane derivatives fully match the halogen bond definition and geometrical prerequisites. The same holds for the short contacts the cation of ionic λ(3)-iodanes forms with lone-pair donors or the short contacts given by neutral λ(3)-iodanes with incoming nucleophiles. The longer and weaker bonds formed by iodine in hypervalent compounds are usually called secondary bondings and we propose that the term halogen bond can also be used. Compared to the term secondary bond, halogen bond may possibly be more descriptive of some bonding features, e.g., its directionality and the relationships between structure of interacting groups and interaction strength. PMID:26809623

  20. Self-assembly of bridged silsesquioxanes: modulating structural evolution via cooperative covalent and noncovalent interactions.

    PubMed

    Creff, Gaelle; Pichon, Benoît P; Blanc, Christophe; Maurin, David; Sauvajol, Jean-Louis; Carcel, Carole; Moreau, Joël J E; Roy, Pascale; Bartlett, John R; Man, Michel Wong Chi; Bantignies, Jean-Louis

    2013-05-01

    The self-assembly of a bis-urea phenylene-bridged silsesquioxane precursor during sol-gel synthesis has been investigated by in situ infrared spectroscopy, optical microscopy, and light scattering. In particular, the evolution of the system as a function of processing time was correlated with covalent interactions associated with increasing polycondensation and noncovalent interactions such as hydrogen bonding. A comprehensive mechanism based on the hydrolysis of the phenylene-bridged organosilane precursor prior to the crystallization of the corresponding bridged silsesquioxane via H-bonding and subsequent irreversible polycondensation is proposed. PMID:23574041

  1. Mechanical Property and Structure of Covalent Functionalised Graphene/Epoxy Nanocomposites

    PubMed Central

    Naebe, Minoo; Wang, Jing; Amini, Abbas; Khayyam, Hamid; Hameed, Nishar; Li, Lu Hua; Chen, Ying; Fox, Bronwyn

    2014-01-01

    Thermally reduced graphene nanoplatelets were covalently functionalised via Bingel reaction to improve their dispersion and interfacial bonding with an epoxy resin. Functionalised graphene were characterized by microscopic, thermal and spectroscopic techniques. Thermal analysis of functionalised graphene revealed a significantly higher thermal stability compared to graphene oxide. Inclusion of only 0.1 wt% of functionalised graphene in an epoxy resin showed 22% increase in flexural strength and 18% improvement in storage modulus. The improved mechanical properties of nanocomposites is due to the uniform dispersion of functionalised graphene and strong interfacial bonding between modified graphene and epoxy resin as confirmed by microscopy observations. PMID:24625497

  2. Bonding and Structure. Independent Learning Project for Advanced Chemistry (ILPAC). Unit S4.

    ERIC Educational Resources Information Center

    Inner London Education Authority (England).

    This unit on chemical bonding is one of 10 first year units produced by the Independent Learning Project for Advanced Chemistry (ILPAC). The unit, which consists of two levels, provides an introduction to the main types of chemical bonding and important aspects of structure. The main emphasis is placed on such topics as ionic and covalent bonding,…

  3. Modern ab initio valence bond theory calculations reveal charge shift bonding in protic ionic liquids.

    PubMed

    Patil, Amol Baliram; Bhanage, Bhalchandra Mahadeo

    2016-06-21

    The nature of bonding interactions between the cation and the anion of an ionic liquid is at the heart of understanding ionic liquid properties. A particularly interesting case is a special class of ionic liquids known as protic ionic liquids. The extent of proton transfer in protic ionic liquids has been observed to vary according to the interacting species. Back proton transfer renders protic ionic liquids volatile and to be considered as inferior ionic liquids. We try to address this issue by employing modern ab initio valence bond theory calculations. The results indicate that the bonding in the cation and the anion of a prototypical ionic liquid, ethylammonium nitrate, is fundamentally different. It is neither characteristic of covalent/polar covalent bonding nor ionic bonding but rather charge shift bonding as a resonance hybrid of two competing ionic molecular electronic structure configurations. An investigation of other analogous protic ionic liquids reveals that this charge shift bonding seems to be a typical characteristic of protic ionic liquids while the ionic solid analogue compound ammonium nitrate has less charge shift bonding character as compared to protic ionic liquids. Further the extent of charge shift bonding character has been found to be congruent with the trends in many physicochemical properties such as melting point, conductivity, viscosity, and ionicity of the studied ionic liquids indicating that percentage charge shift character may serve as a key descriptor for large scale computational screening of ionic liquids with desired properties. PMID:27229870

  4. In-silico bonding schemes to encode chemical bonds involving sharing of electrons in molecular structures.

    PubMed

    Punnaivanam, Sankar; Sathiadhas, Jerome Pastal Raj; Panneerselvam, Vinoth

    2016-05-01

    Encoding of covalent and coordinate covalent bonds in molecular structures using ground state valence electronic configuration is achieved. The bonding due to electron sharing in the molecular structures is described with five fundamental bonding categories viz. uPair-uPair, lPair-uPair, uPair-lPair, vPair-lPair, and lPair-lPair. The involvement of lone pair electrons and the vacant electron orbitals in chemical bonding are explained with bonding schemes namely "target vacant promotion", "source vacant promotion", "target pairing promotion", "source pairing promotion", "source cation promotion", "source pairing double bond", "target vacant occupation", and "double pairing promotion" schemes. The bonding schemes are verified with a chemical structure editor. The bonding in the structures like ylides, PCl5, SF6, IF7, N-Oxides, BF4(-), AlCl4(-) etc. are explained and encoded unambiguously. The encoding of bonding in the structures of various organic compounds, transition metals compounds, coordination complexes and metal carbonyls is accomplished. PMID:27041446

  5. Covalent organic frameworks: Crossing the channel

    NASA Astrophysics Data System (ADS)

    Xu, Hong; Jiang, Donglin

    2014-07-01

    The ordered one-dimensional nanochannels found in covalent organic frameworks (COFs) could render them able to conduct protons. However, the frameworks' instability in acid has thus far precluded any practical implementations. Now, a strategy to overcome this instability has enabled proton conduction using a COF for the first time.

  6. Covalent and non-covalent binding in the ion/ion charge inversion of peptide cations with benzene-disulfonic acid anions.

    PubMed

    Stutzman, John R; Luongo, Carl A; McLuckey, Scott A

    2012-06-01

    Protonated angiotensin II and protonated leucine enkephalin-based peptides, which included YGGFL, YGGFLF, YGGFLH, YGGFLK and YGGFLR, were subjected to ion/ion reactions with the doubly deprotonated reagents 4-formyl-1,3-benzenedisulfonic acid (FBDSA) and 1,3-benzenedisulfonic acid (BDSA). The major product of the ion/ion reaction is a negatively charged complex of the peptide and reagent. Following dehydration of [M + FBDSA-H](-) via collisional-induced dissociation (CID), angiotensin II (DRVYIHPF) showed evidence for two product populations, one in which a covalent modification has taken place and one in which an electrostatic modification has occurred (i.e. no covalent bond formation). A series of studies with model systems confirmed that strong non-covalent binding of the FBDSA reagent can occur with subsequent ion trap CID resulting in dehydration unrelated to the adduct. Ion trap CID of the dehydration product can result in cleavage of amide bonds in competition with loss of the FBDSA adduct. This scenario is most likely for electrostatically bound complexes in which the peptide contains both an arginine residue and one or more carboxyl groups. Otherwise, loss of the reagent species from the complex, either as an anion or as a neutral species, is the dominant process for electrostatically bound complexes. The results reported here shed new light on the nature of non-covalent interactions in gas phase complexes of peptide ions that can be used in the rationale design of reagent ions for specific ion/ion reaction applications. PMID:22707160

  7. The hierarchical construction of cross-junctions of molecular wires with covalent and noncovalent interactions at the liquid/solid interface.

    PubMed

    Yu, Yanxia; Yang, Ling; Liu, Chunhua; Tian, Wei Quan; Wang, Yan; Lei, Shengbin

    2016-07-01

    Hierarchical networks, constructed by non-covalent bond stabilized cross-junctions of covalent one-dimensional molecular wires, are synergistically formed at the liquid/solid interface through in situ on-surface condensation of aromatic amines and aldehydes. Our investigation demonstrates the significant impact of the concentration and structure of monomers on the hierarchical construction of these nanoarchitectures at the interface. PMID:27296368

  8. Covalent EGFR inhibitor analysis reveals importance of reversible interactions to potency and mechanisms of drug resistance.

    PubMed

    Schwartz, Phillip A; Kuzmic, Petr; Solowiej, James; Bergqvist, Simon; Bolanos, Ben; Almaden, Chau; Nagata, Asako; Ryan, Kevin; Feng, Junli; Dalvie, Deepak; Kath, John C; Xu, Meirong; Wani, Revati; Murray, Brion William

    2014-01-01

    Covalent inhibition is a reemerging paradigm in kinase drug design, but the roles of inhibitor binding affinity and chemical reactivity in overall potency are not well-understood. To characterize the underlying molecular processes at a microscopic level and determine the appropriate kinetic constants, specialized experimental design and advanced numerical integration of differential equations are developed. Previously uncharacterized investigational covalent drugs reported here are shown to be extremely effective epidermal growth factor receptor (EGFR) inhibitors (kinact/Ki in the range 10(5)-10(7) M(-1)s(-1)), despite their low specific reactivity (kinact ≤ 2.1 × 10(-3) s(-1)), which is compensated for by high binding affinities (Ki < 1 nM). For inhibitors relying on reactivity to achieve potency, noncovalent enzyme-inhibitor complex partitioning between inhibitor dissociation and bond formation is central. Interestingly, reversible binding affinity of EGFR covalent inhibitors is highly correlated with antitumor cell potency. Furthermore, cellular potency for a subset of covalent inhibitors can be accounted for solely through reversible interactions. One reversible interaction is between EGFR-Cys797 nucleophile and the inhibitor's reactive group, which may also contribute to drug resistance. Because covalent inhibitors target a cysteine residue, the effects of its oxidation on enzyme catalysis and inhibitor pharmacology are characterized. Oxidation of the EGFR cysteine nucleophile does not alter catalysis but has widely varied effects on inhibitor potency depending on the EGFR context (e.g., oncogenic mutations), type of oxidation (sulfinylation or glutathiolation), and inhibitor architecture. These methods, parameters, and insights provide a rational framework for assessing and designing effective covalent inhibitors. PMID:24347635

  9. Covalence and ionicity in MgAgAs-type compounds.

    PubMed

    Bende, David; Grin, Yuri; Wagner, Frank R

    2014-07-28

    MgAgAs-type "half-Heusler" compounds are known to realize two out of three possible atomic arrangements of this structure type. The number of transition metal components typically determines which of the alternatives is favored. On the basis of DFT calculations for all three variants of 20 eight- and eighteen-valence-electron compounds, the experimentally observed structural variant was found to be determined by basically two different bonding patterns. They are quantified by employing two complementary position-space bonding measures. The Madelung energy E((M)(QTAIM)) calculated with the QTAIM effective charges reflects contributions of the ionic interactions to the total energy. The sum of nearest-neighbor delocalization indices ςnn characterizes the covalent interactions through electron sharing. With the aid of these quantities, the energetic sequence of the three atomic arrangements for each compound is rationalized. The resulting systematic is used to predict a scenario in which an untypical atomic arrangement becomes most favorable. PMID:24990108

  10. Improving the Thermostability and Optimal Temperature of a Lipase from the Hyperthermophilic Archaeon Pyrococcus furiosus by Covalent Immobilization

    PubMed Central

    Branco, Roberta V.; Gutarra, Melissa L. E.; Freire, Denise M. G.; Almeida, Rodrigo V.; Palomo, Jose M.

    2015-01-01

    A recombinant thermostable lipase (Pf2001Δ60) from the hyperthermophilic Archaeon Pyrococcus furiosus (PFUL) was immobilized by hydrophobic interaction on octyl-agarose (octyl PFUL) and by covalent bond on aldehyde activated-agarose in the presence of DTT at pH = 7.0 (one-point covalent attachment) (glyoxyl-DTT PFUL) and on glyoxyl-agarose at pH 10.2 (multipoint covalent attachment) (glyoxyl PFUL). The enzyme's properties, such as optimal temperature and pH, thermostability, and selectivity, were improved by covalent immobilization. The highest enzyme stability at 70°C for 48 h incubation was achieved for glyoxyl PFUL (around 82% of residual activity), whereas glyoxyl-DTT PFUL maintained around 69% activity, followed by octyl PFUL (27% remaining activity). Immobilization on glyoxyl-agarose improved the optimal temperature to 90°C, while the optimal temperature of octyl PFUL was 70°C. Also, very significant changes in activity with different substrates were found. In general, the covalent bond derivatives were more active than octyl PFUL. The E value also depended substantially on the derivative and the conditions used. It was observed that the reaction of glyoxyl-DTT PFUL using methyl mandelate as a substrate at pH 7 presented the best results for enantioselectivity (E = 22) and enantiomeric excess (ee (%) = 91). PMID:25839031

  11. Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

    PubMed Central

    2015-01-01

    Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

  12. Influence of the chemical bond on the K emission spectrum of oxygen and fluorine.

    NASA Technical Reports Server (NTRS)

    Koster, A. S.

    1971-01-01

    The K emission spectrum of oxygen and fluorine from a number of simple oxides and fluorides is divided into three to six sub-peaks. The spectra of many of these oxides and fluorides resemble one another owing to their basically ionic bonding. Certain sub-peaks, however, are ascribed to cross-over transitions and partially covalent energy levels. The different fluorine spectrum of Teflon is due to the hybrid nature of its covalent bonds.

  13. Institutional Bonding.

    ERIC Educational Resources Information Center

    Allard, M. June

    Institutional bonding was examined at a public, urban commuter college with exceptionally high attrition and visibly low morale. Changes in bonding and attrition were measured 6 years after a 2-year effort to develop school identity and student feelings of membership. It was found that a simple index of campus morale is provided by level of…

  14. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II.

    PubMed

    Maklashina, Elena; Rajagukguk, Sany; Starbird, Chrystal A; McDonald, W Hayes; Koganitsky, Anna; Eisenbach, Michael; Iverson, Tina M; Cecchini, Gary

    2016-02-01

    Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation. PMID:26644464

  15. Mechanisms for Covalent Immobilization of Horseradish Peroxidase on Ion-Beam-Treated Polyethylene

    PubMed Central

    Kondyurin, Alexey V.; Naseri, Pourandokht; Tilley, Jennifer M. R.; Nosworthy, Neil J.; Bilek, Marcela M. M.; McKenzie, David R.

    2012-01-01

    The surface of polyethylene was modified by plasma immersion ion implantation. Structure changes including carbonization and oxidation were observed. High surface energy of the modified polyethylene was attributed to the presence of free radicals on the surface. The surface energy decay with storage time after treatment was explained by a decay of the free radical concentration while the concentration of oxygen-containing groups increased with storage time. Horseradish peroxidase was covalently attached onto the modified surface by the reaction with free radicals. Appropriate blocking agents can block this reaction. All aminoacid residues can take part in the covalent attachment process, providing a universal mechanism of attachment for all proteins. The native conformation of attached protein is retained due to hydrophilic interactions in the interface region. The enzymatic activity of covalently attached protein remained high. The long-term activity of the modified layer to attach protein is explained by stabilisation of unpaired electrons in sp2 carbon structures. A high concentration of free radicals can give multiple covalent bonds to the protein molecule and destroy the native conformation and with it the catalytic activity. The universal mechanism of protein attachment to free radicals could be extended to various methods of radiation damage of polymers. PMID:24278665

  16. Quantitative Reactivity Scales for Dynamic Covalent and Systems Chemistry.

    PubMed

    Zhou, Yuntao; Li, Lijie; Ye, Hebo; Zhang, Ling; You, Lei

    2016-01-13

    Dynamic covalent chemistry (DCC) has become a powerful tool for the creation of molecular assemblies and complex systems in chemistry and materials science. Herein we developed for the first time quantitative reactivity scales capable of correlation and prediction of the equilibrium of dynamic covalent reactions (DCRs). The reference reactions are based upon universal DCRs between imines, one of the most utilized structural motifs in DCC, and a series of O-, N-, and S- mononucleophiles. Aromatic imines derived from pyridine-2-carboxyaldehyde exhibit capability for controlling the equilibrium through distinct substituent effects. Electron-donating groups (EDGs) stabilize the imine through quinoidal resonance, while electron-withdrawing groups (EWGs) stabilize the adduct by enhancing intramolecular hydrogen bonding, resulting in curvature in Hammett analysis. Notably, unique nonlinearity induced by both EDGs and EWGs emerged in Hammett plot when cyclic secondary amines were used. This is the first time such a behavior is observed in a thermodynamically controlled system, to the best of our knowledge. Unified quantitative reactivity scales were proposed for DCC and defined by the correlation log K = S(N) (R(N) + R(E)). Nucleophilicity parameters (R(N) and S(N)) and electrophilicity parameters (R(E)) were then developed from DCRs discovered. Furthermore, the predictive power of those parameters was verified by successful correlation of other DCRs, validating our reactivity scales as a general and useful tool for the evaluation and modeling of DCRs. The reactivity parameters proposed here should be complementary to well-established kinetics based parameters and find applications in many aspects, such as DCR discovery, bioconjugation, and catalysis. PMID:26652793

  17. Surface-confined single-layer covalent organic framework on single-layer graphene grown on copper foil.

    PubMed

    Xu, Lirong; Zhou, Xin; Tian, Wei Quan; Gao, Teng; Zhang, Yan Feng; Lei, Shengbin; Liu, Zhong Fan

    2014-09-01

    The integration of 2D covalent organic frameworks (COFs) with atomic thickness with graphene will lead to intriguing two-dimensional materials. A surface-confined covalently bonded Schiff base network was prepared on single-layer graphene grown on copper foil and the dynamic reaction process was investigated with scanning tunneling microscopy. DFT simulations provide an understanding of the electronic structures and the interactions between the surface COF and graphene. Strong coupling between the surface COF and graphene was confirmed by the dispersive bands of the surface COF after interaction with graphene, and also by the experimental observation of tunneling condition dependent contrast of the surface COF. PMID:25145927

  18. Structural and in vitro adhesion analysis of a novel covalently coupled bioactive composite.

    PubMed

    Khan, Abdul S; Hassan, Khawaja R; Bukhari, Syeda F; Wong, Ferranti S L; Rehman, Ihtesham U

    2012-01-01

    The interfacial adhesion between a restorative composite and tooth is one of the major factors that determine the ultimate performance of composite restoration. A novel polyurethane (PU) composite material was prepared by chemically binding the nano-hydroxyapatite (nHA) to the diisocyanate component in the PU backbone by utilizing solvent polymerization. The procedure involved stepwise addition of monomeric units of the PU and optimizing the reagent concentrations. The resultant materials were characterized structurally (Raman Spectroscopy) and in vitro bioactive analysis was conducted in modified-simulated body fluid for periodical time intervals. The in vitro study evaluated the push-out bond strength of existing obturating material and novel covalently linked PU/nHA composites to dentin after long-term storage in deionized water and artificial saliva. Human extracted molar roots were filled with experimental samples and analyzed at predetermined time intervals. The shear bond strength of samples was measured and surface morphologies were evaluated. Covalent bond formation was achieved between PU and nHA without intermediate coupling agent. With the increase in concentration of nHA, the composite showed more bioactivity and adhesion toward tooth structure. Bond strength of this new composite were in accordance with obutrating material, therefore, the material can be used as an obturating material because of its direct adhesion with tooth structure. PMID:22102537

  19. In situ Formation of Highly Conducting Covalent Au-C Contacts for Single-Molecule Junctions

    SciTech Connect

    Cheng, Z.L.; Hybertsen, M.; Skouta, R.; Vazquez, H.; Widawsky, J.R.; Schneebeli, S.; Chen, W.; Breslow, R.; Venkataraman, L.

    2011-06-01

    Charge transport across metal-molecule interfaces has an important role in organic electronics. Typically, chemical link groups such as thiols or amines are used to bind organic molecules to metal electrodes in single-molecule circuits, with these groups controlling both the physical structure and the electronic coupling at the interface. Direct metal-carbon coupling has been shown through C60, benzene and {pi}-stacked benzene but ideally the carbon backbone of the molecule should be covalently bonded to the electrode without intervening link groups. Here, we demonstrate a method to create junctions with such contacts. Trimethyl tin (SnMe{sub 3})-terminated polymethylene chains are used to form single-molecule junctions with a break-junction technique. Gold atoms at the electrode displace the SnMe{sub 3} linkers, leading to the formation of direct Au-C bonded single-molecule junctions with a conductance that is {approx}100 times larger than analogous alkanes with most other terminations. The conductance of these Au-C bonded alkanes decreases exponentially with molecular length, with a decay constant of 0.97 per methylene, consistent with a non-resonant transport mechanism. Control experiments and ab initio calculations show that high conductances are achieved because a covalent Au-C sigma ({sigma}) bond is formed. This offers a new method for making reproducible and highly conducting metal-organic contacts.

  20. Electron beam controlled covalent attachment of small organic molecules to graphene

    NASA Astrophysics Data System (ADS)

    Markevich, Alexander; Kurasch, Simon; Lehtinen, Ossi; Reimer, Oliver; Feng, Xinliang; Müllen, Klaus; Turchanin, Andrey; Khlobystov, Andrei N.; Kaiser, Ute; Besley, Elena

    2016-01-01

    The electron beam induced functionalization of graphene through the formation of covalent bonds between free radicals of polyaromatic molecules and C&z.dbd;C bonds of pristine graphene surface has been explored using first principles calculations and high-resolution transmission electron microscopy. We show that the energetically strongest attachment of the radicals occurs along the armchair direction in graphene to carbon atoms residing in different graphene sub-lattices. The radicals tend to assume vertical position on graphene substrate irrespective of direction of the bonding and the initial configuration. The ``standing up'' molecules, covalently anchored to graphene, exhibit two types of oscillatory motion - bending and twisting - caused by the presence of acoustic phonons in graphene and dispersion attraction to the substrate. The theoretically derived mechanisms are confirmed by near atomic resolution imaging of individual perchlorocoronene (C24Cl12) molecules on graphene. Our results facilitate the understanding of controlled functionalization of graphene employing electron irradiation as well as mechanisms of attachment of impurities via the processing of graphene nanoelectronic devices by electron beam lithography.The electron beam induced functionalization of graphene through the formation of covalent bonds between free radicals of polyaromatic molecules and C&z.dbd;C bonds of pristine graphene surface has been explored using first principles calculations and high-resolution transmission electron microscopy. We show that the energetically strongest attachment of the radicals occurs along the armchair direction in graphene to carbon atoms residing in different graphene sub-lattices. The radicals tend to assume vertical position on graphene substrate irrespective of direction of the bonding and the initial configuration. The ``standing up'' molecules, covalently anchored to graphene, exhibit two types of oscillatory motion - bending and twisting - caused

  1. Nanoparticle mediated non-covalent drug delivery☆

    PubMed Central

    Doane, Tennyson; Burda, Clemens

    2013-01-01

    The use of nanoparticles (NPs) for enhanced drug delivery has been heavily explored during the last decade. Within the field, it is has become increasingly apparent that the physical properties of the particles themselves dictate their efficacy, and the relevant non-covalent chemistry at the NP interface also influences how drugs are immobilized and delivered. In this review, we reflect on the physical chemistry of NP mediated drug delivery (and more specifically, non-covalent drug delivery) at the three main experimental stages of drug loading, NP–drug conjugate transport, and the resulting cellular drug delivery. Through a critical evaluation of advances in drug delivery within the last decade, an outlook for biomedical applications of nanoscale transport vectors will be presented. PMID:22664231

  2. Covalent Sidewall Functionalization of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Chiang, I.W.; Saini, R. K.; Mickelson, E. T.; Billups, W. E.; Hauge, R. H.; Margrave, J. L.

    2001-01-01

    Progress of fluorination of single-wall carbon nanotubes is being reported. Covalent attachment of alkyl groups including methyl, n-butyl and n-hexyl groups to the sidewalls of single wall carbon nanotubes (SWNTs) has been achieved. Quantitative measurement of the alkylation was done by thermal gravimetric analysis. FTIR, Raman and UV-Vis-NIR were used to characterize these alkylated SWNTs. Application of these nanotubes are being investigated-fibers, composites, batteries, lubricants, etc.

  3. Locking GTPases covalently in their functional states

    PubMed Central

    Wiegandt, David; Vieweg, Sophie; Hofmann, Frank; Koch, Daniel; Li, Fu; Wu, Yao-Wen; Itzen, Aymelt; Müller, Matthias P.; Goody, Roger S.

    2015-01-01

    GTPases act as key regulators of many cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states. In many cases, understanding their mode of action has been aided by artificially stabilizing one of these states either by designing mutant proteins or by complexation with non-hydrolysable GTP analogues. Because of inherent disadvantages in these approaches, we have developed acryl-bearing GTP and GDP derivatives that can be covalently linked with strategically placed cysteines within the GTPase of interest. Binding studies with GTPase-interacting proteins and X-ray crystallography analysis demonstrate that the molecular properties of the covalent GTPase–acryl–nucleotide adducts are a faithful reflection of those of the corresponding native states and are advantageously permanently locked in a defined nucleotide (that is active or inactive) state. In a first application, in vivo experiments using covalently locked Rab5 variants provide new insights into the mechanism of correct intracellular localization of Rab proteins. PMID:26178622

  4. Multiple-component covalent organic frameworks

    PubMed Central

    Huang, Ning; Zhai, Lipeng; Coupry, Damien E.; Addicoat, Matthew A.; Okushita, Keiko; Nishimura, Katsuyuki; Heine, Thomas; Jiang, Donglin

    2016-01-01

    Covalent organic frameworks are a class of crystalline porous polymers that integrate molecular building blocks into periodic structures and are usually synthesized using two-component [1+1] condensation systems comprised of one knot and one linker. Here we report a general strategy based on multiple-component [1+2] and [1+3] condensation systems that enable the use of one knot and two or three linker units for the synthesis of hexagonal and tetragonal multiple-component covalent organic frameworks. Unlike two-component systems, multiple-component covalent organic frameworks feature asymmetric tiling of organic units into anisotropic skeletons and unusually shaped pores. This strategy not only expands the structural complexity of skeletons and pores but also greatly enhances their structural diversity. This synthetic platform is also widely applicable to multiple-component electron donor–acceptor systems, which lead to electronic properties that are not simply linear summations of those of the conventional [1+1] counterparts. PMID:27460607

  5. Multiple-component covalent organic frameworks.

    PubMed

    Huang, Ning; Zhai, Lipeng; Coupry, Damien E; Addicoat, Matthew A; Okushita, Keiko; Nishimura, Katsuyuki; Heine, Thomas; Jiang, Donglin

    2016-01-01

    Covalent organic frameworks are a class of crystalline porous polymers that integrate molecular building blocks into periodic structures and are usually synthesized using two-component [1+1] condensation systems comprised of one knot and one linker. Here we report a general strategy based on multiple-component [1+2] and [1+3] condensation systems that enable the use of one knot and two or three linker units for the synthesis of hexagonal and tetragonal multiple-component covalent organic frameworks. Unlike two-component systems, multiple-component covalent organic frameworks feature asymmetric tiling of organic units into anisotropic skeletons and unusually shaped pores. This strategy not only expands the structural complexity of skeletons and pores but also greatly enhances their structural diversity. This synthetic platform is also widely applicable to multiple-component electron donor-acceptor systems, which lead to electronic properties that are not simply linear summations of those of the conventional [1+1] counterparts. PMID:27460607

  6. Bonding in the Superionic Phase of Water

    SciTech Connect

    Goldman, N; Fried, L E; Kuo, I W; Mundy, C J

    2005-02-07

    The predicted superionic phase of water is investigated via ab initio molecular dynamics at densities of 2.0-3.0 g/cc (34-115 GPa) along the 2000K isotherm. They find that extremely rapid (superionic) diffusion of protons occurs in a fluid phase at pressures between 34 and 58 GPa. A transition to a stable body-centered cubic (bcc) O lattice with superionic proton conductivity is observed between 70 and 75 GPa, a much higher pressure than suggested in prior work. They find that all molecular species at pressures greater than 75 GPa are too short lived to be classified as bound states. Up to 95 GPa, they find a solid superionic phase characterization by covalent O-H bonding. Above 95 GPa, a transient network phase is found characterized by symmetric O-H hydrogen bonding with nearly 50% covalent character. In addition, they describe a new metastable superionic phase with quenched O disorder.

  7. A revised set of values of single-bond radii derived from the observed interatomic distances in metals by correction for bond number and resonance energy

    PubMed Central

    Pauling, Linus; Kamb, Barclay

    1986-01-01

    An earlier discussion [Pauling, L. (1947) J. Am. Chem. Soc. 69, 542] of observed bond lengths in elemental metals with correction for bond number and resonance energy led to a set of single-bond metallic radii with values usually somewhat less than the corresponding values obtained from molecules and complex ions. A theory of resonating covalent bonds has now been developed that permits calculation of the number of resonance structures per atom and of the effective resonance energy per bond. With this refined method of correcting the observed bond lengths for the effect of resonance energy, a new set of single-bond covalent radii, in better agreement with values from molecules and complex ions, has been constructed. PMID:16593698

  8. Covalent Immobilization of Oriented Photosystem II on a Nanostructured Electrode for Solar Water Oxidation

    PubMed Central

    2013-01-01

    Photosystem II (PSII) offers a biological and sustainable route of photochemical water oxidation to O2 and can provide protons and electrons for the generation of solar fuels, such as H2. We present a rational strategy to electrostatically improve the orientation of PSII from a thermophilic cyanobacterium, Thermosynechococcus elongatus, on a nanostructured indium tin oxide (ITO) electrode and to covalently immobilize PSII on the electrode. The ITO electrode was modified with a self-assembled monolayer (SAM) of phosphonic acid ITO linkers with a dangling carboxylate moiety. The negatively charged carboxylate attracts the positive dipole on the electron acceptor side of PSII via Coulomb interactions. Covalent attachment of PSII in its electrostatically improved orientation to the SAM-modified ITO electrode was accomplished via an amide bond to further enhance red-light-driven, direct electron transfer and stability of the PSII hybrid photoelectrode. PMID:23829513

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

    PubMed

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

    2013-07-24

    Photosystem II (PSII) offers a biological and sustainable route of photochemical water oxidation to O2 and can provide protons and electrons for the generation of solar fuels, such as H2. We present a rational strategy to electrostatically improve the orientation of PSII from a thermophilic cyanobacterium, Thermosynechococcus elongatus , on a nanostructured indium tin oxide (ITO) electrode and to covalently immobilize PSII on the electrode. The ITO electrode was modified with a self-assembled monolayer (SAM) of phosphonic acid ITO linkers with a dangling carboxylate moiety. The negatively charged carboxylate attracts the positive dipole on the electron acceptor side of PSII via Coulomb interactions. Covalent attachment of PSII in its electrostatically improved orientation to the SAM-modified ITO electrode was accomplished via an amide bond to further enhance red-light-driven, direct electron transfer and stability of the PSII hybrid photoelectrode. PMID:23829513

  10. Breaking the Covalent Bond—A Pigment Property that Contributes to Desensitization in Cones

    PubMed Central

    Kefalov, Vladimir J.; Estevez, Maureen E.; Kono, Massahiro; Goletz, Patrice W.; Crouch, Rosalie K.; Cornwall, M. Carter; Yau, King-Wai

    2010-01-01

    Summary Retinal rod and cone pigments consist of an apoprotein, opsin, covalently linked to a chromophore, 11-cis retinal. Here we demonstrate that the formation of the covalent bond between opsin and 11-cis retinal is reversible in darkness in amphibian red cones, but essentially irreversible in red rods. This dissociation, apparently a general property of cone pigments, results in a surprisingly large amount of free opsin—about 10% of total opsin—in dark-adapted red cones. We attribute this significant level of free opsin to the low concentration of intracellular free 11-cis retinal, estimated to be only a tiny fraction (~0.1 %) of the pigment content in red cones. With its constitutive transducin-stimulating activity, the free cone opsin produces an ~2-fold desensitization in red cones, equivalent to that produced by a steady light causing 500 photoisomerizations s−1. Cone pigment dissociation therefore contributes to the sensitivity difference between rods and cones. PMID:15953417

  11. Dynamic Multi-Component Covalent Assembly for the Reversible Binding of Secondary Alcohols and Chirality Sensing

    PubMed Central

    You, Lei; Berman, Jeffrey S.; Anslyn, Eric V.

    2011-01-01

    Reversible covalent bonding is often employed for the creation of novel supramolecular structures, multi-component assemblies, and sensing ensembles. In spite of remarkable success of dynamic covalent systems, the reversible binding of a mono-alcohol with high strength is challenging. Here we show that a strategy of carbonyl activation and hemiaminal ether stabilization can be embodied in a four-component reversible assembly that creates a tetradentate ligand and incorporates secondary alcohols with exceptionally high affinity. Evidence is presented that the intermediate leading to binding and exchange of alcohols is an iminium ion. Further, to demonstrate the use of this assembly process we explored chirality sensing and enantiomeric excess determinations. An induced twist in the ligand by a chiral mono-ol results in large Cotton effects in the circular dichroism spectra indicative of the alcohol’s handedness. The strategy revealed in this study should prove broadly applicable for the incorporation of alcohols into supramolecular architecture construction. PMID:22109274

  12. Precursor of ether phospholipids is synthesized by a flavoenzyme through covalent catalysis

    PubMed Central

    Nenci, Simone; Piano, Valentina; Rosati, Sara; Aliverti, Alessandro; Pandini, Vittorio; Fraaije, Marco W.; Heck, Albert J. R.; Edmondson, Dale E.; Mattevi, Andrea

    2012-01-01

    The precursor of the essential ether phospholipids is synthesized by a peroxisomal enzyme that uses a flavin cofactor to catalyze a reaction that does not alter the redox state of the substrates. The enzyme crystal structure reveals a V-shaped active site with a narrow constriction in front of the prosthetic group. Mutations causing inborn ether phospholipid deficiency, a very severe genetic disease, target residues that are part of the catalytic center. Biochemical analysis using substrate and flavin analogs, absorbance spectroscopy, mutagenesis, and mass spectrometry provide compelling evidence supporting an unusual mechanism of covalent catalysis. The flavin functions as a chemical trap that promotes exchange of an acyl with an alkyl group, generating the characteristic ether bond. Structural comparisons show that the covalent versus noncovalent mechanistic distinction in flavoenzyme catalysis and evolution relies on subtle factors rather than on gross modifications of the cofactor environment. PMID:23112191

  13. Molecular docking sites designed for the generation of highly crystalline covalent organic frameworks

    NASA Astrophysics Data System (ADS)

    Ascherl, Laura; Sick, Torben; Margraf, Johannes T.; Lapidus, Saul H.; Calik, Mona; Hettstedt, Christina; Karaghiosoff, Konstantin; Döblinger, Markus; Clark, Timothy; Chapman, Karena W.; Auras, Florian; Bein, Thomas

    2016-04-01

    Covalent organic frameworks (COFs) formed by connecting multidentate organic building blocks through covalent bonds provide a platform for designing multifunctional porous materials with atomic precision. As they are promising materials for applications in optoelectronics, they would benefit from a maximum degree of long-range order within the framework, which has remained a major challenge. We have developed a synthetic concept to allow consecutive COF sheets to lock in position during crystal growth, and thus minimize the occurrence of stacking faults and dislocations. Hereby, the three-dimensional conformation of propeller-shaped molecular building units was used to generate well-defined periodic docking sites, which guided the attachment of successive building blocks that, in turn, promoted long-range order during COF formation. This approach enables us to achieve a very high crystallinity for a series of COFs that comprise tri- and tetradentate central building blocks. We expect this strategy to be transferable to a broad range of customized COFs.

  14. Dynamic urea bond for the design of reversible and self-healing polymers

    PubMed Central

    Ying, Hanze; Zhang, Yanfeng; Cheng, Jianjun

    2014-01-01

    Polymers bearing dynamic covalent bonds may exhibit dynamic properties, such as self-healing, shape memory and environmental adaptation. However, most dynamic covalent chemistries developed so far require either catalyst or change of environmental conditions to facilitate bond reversion and dynamic property change in bulk materials. Here we report the rational design of hindered urea bonds (urea with bulky substituent attached to its nitrogen) and the use of them to make polyureas and poly(urethane-ureas) capable of catalyst-free dynamic property change and autonomous repairing at low temperature. Given the simplicity of the hindered urea bond chemistry (reaction of a bulky amine with an isocyanate), incorporation of the catalyst-free dynamic covalent urea bonds to conventional polyurea or urea-containing polymers that typically have stable bulk properties may further broaden the scope of applications of these widely used materials. PMID:24492620

  15. Agaricus meleagris pyranose dehydrogenase: Influence of covalent FAD linkage on catalysis and stability

    PubMed Central

    Krondorfer, Iris; Brugger, Dagmar; Paukner, Regina; Scheiblbrandner, Stefan; Pirker, Katharina F.; Hofbauer, Stefan; Furtmüller, Paul G.; Obinger, Christian; Haltrich, Dietmar; Peterbauer, Clemens K.

    2014-01-01

    Pyranose dehydrogenase (PDH) is a monomeric flavoprotein belonging to the glucose–methanol–choline (GMC) family of oxidoreductases. It catalyzes the oxidation of free, non-phosphorylated sugars to the corresponding keto sugars. The enzyme harbors an FAD cofactor that is covalently attached to histidine 103 via an 8α-N(3) histidyl linkage. Our previous work showed that variant H103Y was still able to bind FAD (non-covalently) and perform catalysis but steady-state kinetic parameters for several substrates were negatively affected. In order to investigate the impact of the covalent FAD attachment in Agaricus meleagris PDH in more detail, pre-steady-state kinetics, reduction potential and stability of the variant H103Y in comparison to the wild-type enzyme were probed. Stopped-flow analysis revealed that the mutation slowed down the reductive half-reaction by around three orders of magnitude whereas the oxidative half-reaction was affected only to a minor degree. This was reflected by a decrease in the standard reduction potential of variant H103Y compared to the wild-type protein. The existence of an anionic semiquinone radical in the resting state of both the wild-type and variant H103Y was demonstrated using electron paramagnetic resonance (EPR) spectroscopy and suggested a higher mobility of the cofactor in the variant H103Y. Unfolding studies showed significant negative effects of the disruption of the covalent bond on thermal and conformational stability. The results are discussed with respect to the role of covalently bound FAD in catalysis and stability. PMID:25043975

  16. The nature of chemical bonds from PNOF5 calculations.

    PubMed

    Matxain, Jon M; Piris, Mario; Uranga, Jon; Lopez, Xabier; Merino, Gabriel; Ugalde, Jesus M

    2012-06-18

    Natural orbital functional theory (NOFT) is used for the first time in the analysis of different types of chemical bonds. Concretely, the Piris natural orbital functional PNOF5 is used. It provides a localization scheme that yields an orbital picture which agrees very well with the empirical valence shell electron pair repulsion theory (VSEPR) and Bent's rule, as well as with other theoretical pictures provided by valence bond (VB) or linear combination of atomic orbitals-molecular orbital (LCAO-MO) methods. In this context, PNOF5 provides a novel tool for chemical bond analysis. In this work, PNOF5 is applied to selected molecules that have ionic, polar covalent, covalent, multiple (σ and π), 3c-2e, and 3c-4e bonds. PMID:22615195

  17. Non Covalent Interactions and Internal Dynamics in Adducts of Freons

    NASA Astrophysics Data System (ADS)

    Caminati, Walther; Gou, Qian; Evangelisti, Luca; Feng, Gang; Spada, Lorenzo; Vallejo-López, Montserrat; Lesarri, Alberto; Cocinero, Emilio J.

    2014-06-01

    The complexation of chlorofluorocarbons (CFCs) with atmospheric water and pollutants of the atmosphere affects their reactivity and it seems to accelerate, for example, the decomposition rate of freons in the atmosphere [1]. For this reason we characterized shapes, stabilities, nature of the non-covalent interactions, structures and internal dynamics of a number of complexes of CFCs with water and of their dimers or oligomers by rotational spectroscopy. It has been found that hydrogenated CFCs form adducts with other molecules through weak hydrogen bonds (WHBs). Their C-H groups can act as proton donors, enhanced by the electron withdrawing of the halogen atoms, interacting with the electron rich regions of the partner molecules [2]. Also in adducts or oligomers of hydrogenated CFCs the monomer units are held together by nets of WHBs [3]. When CFCs are perhalogenated, the positive electrostatic region ("σ-hole") can interact electrostatically with negative sites of another, or of the same molecular entity, giving rise, according to IUPAC, to the so called halogen bond (HaB). However, it has been observed that when the perhalogenated CFCs has a Π electron system, a lone pair•••Π interaction (Bürgi-Dunitz) is favoured [4]. We describe here the HaBs that CF4 and CF3Cl form with a variety of partner molecules such as water, ammonia, dimethyl ether, etc. Important spectroscopic features outline strong dynamics effects taking place in this kind of complex. References [1] V. Vaida, H. G. Kjaergaard, K. J. Feierabend, Int. Rev. Phys. Chem. 22 (2003) 203. [2] See, for example: W. Caminati, S. Melandri, A. Maris, P. Ottaviani, Angew. Chem. Int. Ed. 45 (2006) 2438. [3] G. Feng, L. Evangelisti, I. Cacelli, L. Carbonaro, G. Prampolini, W. Caminati, Chem. Commun. 50 (2014) 171. [4] Q. Gou, G. Feng, L. Evangelisti, W. Caminati, Angew. Chem. Int. Ed. 52 (2013) 52 11888.

  18. Thiophene-based covalent organic frameworks

    PubMed Central

    Bertrand, Guillaume H. V.; Michaelis, Vladimir K.; Ong, Ta-Chung; Griffin, Robert G.; Dincă, Mircea

    2013-01-01

    We report the synthesis and characterization of covalent organic frameworks (COFs) incorporating thiophene-based building blocks. We show that these are amenable to reticular synthesis, and that bent ditopic monomers, such as 2,5-thiophenediboronic acid, are defect-prone building blocks that are susceptible to synthetic variations during COF synthesis. The synthesis and characterization of an unusual charge transfer complex between thieno[3,2-b]thiophene-2,5-diboronic acid and tetracyanoquinodimethane enabled by the unique COF architecture is also presented. Together, these results delineate important synthetic advances toward the implementation of COFs in electronic devices. PMID:23479656

  19. Floating electron states in covalent semiconductors.

    PubMed

    Matsushita, Yu-ichiro; Furuya, Shinnosuke; Oshiyama, Atsushi

    2012-06-15

    We report first-principles electronic-structure calculations that clarify the floating nature of electron states in covalent semiconductors. It is found that wave functions of several conduction- and valence-band states, including the conduction-band minima, do not distribute near atomic sites, as was taken for granted, but float in interstitial channels in most semiconductors. The directions and shapes of the interstitial channels depend on the crystal symmetry so that mysterious variation of the energy gaps in SiC polymorphs is naturally explained by considering the floating nature. PMID:23004300

  20. Thiophene-based covalent organic frameworks.

    PubMed

    Bertrand, Guillaume H V; Michaelis, Vladimir K; Ong, Ta-Chung; Griffin, Robert G; Dincă, Mircea

    2013-03-26

    We report the synthesis and characterization of covalent organic frameworks (COFs) incorporating thiophene-based building blocks. We show that these are amenable to reticular synthesis, and that bent ditopic monomers, such as 2,5-thiophenediboronic acid, are defect-prone building blocks that are susceptible to synthetic variations during COF synthesis. The synthesis and characterization of an unusual charge transfer complex between thieno[3,2-b]thiophene-2,5-diboronic acid and tetracyanoquinodimethane enabled by the unique COF architecture is also presented. Together, these results delineate important synthetic advances toward the implementation of COFs in electronic devices. PMID:23479656

  1. Reversible and formaldehyde-mediated covalent binding of a bis-amino mitoxantrone analogue to DNA.

    PubMed

    Konda, Shyam K; Kelso, Celine; Pumuye, Paul P; Medan, Jelena; Sleebs, Brad E; Cutts, Suzanne M; Phillips, Don R; Collins, J Grant

    2016-05-18

    The ability of a bis-amino mitoxantrone anticancer drug (named WEHI-150) to form covalent adducts with DNA, after activation by formaldehyde, has been studied by electrospray ionisation mass spectrometry and HPLC. Mass spectrometry results showed that WEHI-150 could form covalent adducts with d(ACGCGCGT)2 that contained one, two or three covalent links to the octanucleotide, whereas the control drugs (daunorubicin and the anthracenediones mitoxantrone and pixantrone) only formed adducts with one covalent link to the octanucleotide. HPLC was used to examine the extent of covalent bond formation of WEHI-150 with d(CGCGCG)2 and d(CG(5Me)CGCG)2. Incubation of WEHI-150 with d(CG(5Me)CGCG)2 in the presence of formaldehyde resulted in the formation of significantly greater amounts of covalent adducts than was observed with d(CGCGCG)2. In order to understand the observed increase of covalent adducts with d(CG(5Me)CGCG)2, an NMR study of the reversible interaction of WEHI-150 at both CpG and (5Me)CpG sites was undertaken. Intermolecular NOEs were observed in the NOESY spectra of d(ACGGCCGT)2 with added WEHI-150 that indicated that the drug selectively intercalated at the CpG sites and from the major groove. In particular, NOEs were observed from the WEHI-150 H2,3 protons to the H1' protons of G3 and G7 and from the H6,7 protons to the H5 protons of C2 and C6. By contrast, intermolecular NOEs were observed between the WEHI-150 H2,3 protons to the H2'' proton of the (5Me)C3 in d(CG(5Me)CGCG)2, and between the drug aliphatic protons and the H1' proton of G4. This demonstrated that WEHI-150 preferentially intercalates at (5Me)CpG sites, compared to CpG sequences, and predominantly via the minor groove at the (5Me)CpG site. The results of this study demonstrate that WEHI-150 is likely to form interstrand DNA cross-links, upon activation by formaldehyde, and consequently exhibit greater cytotoxicity than other current anthracenedione drugs. PMID:27142235

  2. Electron beam controlled covalent attachment of small organic molecules to graphene.

    PubMed

    Markevich, Alexander; Kurasch, Simon; Lehtinen, Ossi; Reimer, Oliver; Feng, Xinliang; Müllen, Klaus; Turchanin, Andrey; Khlobystov, Andrei N; Kaiser, Ute; Besley, Elena

    2016-02-01

    The electron beam induced functionalization of graphene through the formation of covalent bonds between free radicals of polyaromatic molecules and C=C bonds of pristine graphene surface has been explored using first principles calculations and high-resolution transmission electron microscopy. We show that the energetically strongest attachment of the radicals occurs along the armchair direction in graphene to carbon atoms residing in different graphene sub-lattices. The radicals tend to assume vertical position on graphene substrate irrespective of direction of the bonding and the initial configuration. The "standing up" molecules, covalently anchored to graphene, exhibit two types of oscillatory motion--bending and twisting--caused by the presence of acoustic phonons in graphene and dispersion attraction to the substrate. The theoretically derived mechanisms are confirmed by near atomic resolution imaging of individual perchlorocoronene (C24Cl12) molecules on graphene. Our results facilitate the understanding of controlled functionalization of graphene employing electron irradiation as well as mechanisms of attachment of impurities via the processing of graphene nanoelectronic devices by electron beam lithography. PMID:26757842

  3. Thermochemistry of Non-Covalent Ion–Molecule Interactions

    PubMed Central

    Armentrout, P. B.; Rodgers, M. T.

    2013-01-01

    The thermochemistry of non-covalent ion–molecule complexes has been examined by measuring quantitative bond dissociation energies using threshold collision-induced dissociation in guided ion beam tandem mass spectrometers (GIBMS). The methods used are briefly reviewed and several examples of the types of information and insight that can be obtained from such thermodynamic information are discussed. The hydration of metal cations, both singly and doubly charged, is reviewed and the trends elucidated, mainly on the basis of electrostatic contributions. The binding of alkali metal cations to amino acids has been examined for a range of systems, with both the overall polarizability of the amino acid and the local dipole moment of heteroatomic side-chains shown to be important contributors. The gas-phase interactions of the 12-crown-4 (12C4) polyether with alkali metal cations, classic molecular recognition systems in solution, have been newly compared to previous GIBMS work. These results validate the previous hypothesis that excited conformers were present for Rb+(12C4) and Cs+(12C4) and offer clues as to how and why they are formed. PMID:24349924

  4. Photofunctional hybrid silica microspheres covalently functionalized with metalloporphyrins

    SciTech Connect

    Guo, Lei; Fu, Lianshe; Ferreira, Rute A.S.; Carlos, Luis D.; Yan, Bing

    2012-10-15

    The entrapment of metalloporphyrins (with Zn{sup 2+} and Yb{sup 3+}) in silica microspheres is achieved by modification of protoporphyrin IX (Pp-IX) molecules with three different organosilane precursors via the sol-gel method. The obtained hybrid materials are characterized by electronic absorption spectra, Fourier-transform infrared (FT-IR), X-ray diffraction (XRD), {sup 29}Si MAS NMR spectrum, scanning electron microscopy (SEM), nitrogen adsorption/desorption isotherms and thermogravimetric analysis (TGA), and their luminescence properties have also been determined. The results reveal that the obtained porphyrins networks are covalently bonded to the inorganic matrix through the bridging action of the functionalized silica microspheres. Furthermore, it has also been observed that porphyrins molecules located in different environments exhibit different photophysical properties in the visible and near-infrared regions. - Graphical abstract: The entrapment of metalloporphyrins (with Zn{sup 2+} and Yb{sup 3+}) in silica microspheres is achieved by modification of protoporphyrin IX (Pp-IX) molecules with three different organosilane precursors via the sol-gel method. Highlights: Black-Right-Pointing-Pointer Novel functionalized silica microsphere is assembled. Black-Right-Pointing-Pointer Metal phorphyrin derivatives are used as a chemical linkage. Black-Right-Pointing-Pointer Luminescence is obtained in the visible and near infrared regions.

  5. Discovery of a novel covalent non-β-lactam inhibitor of the metallo-β-lactamase NDM-1.

    PubMed

    Christopeit, Tony; Albert, Anastasia; Leiros, Hanna-Kirsti S

    2016-07-01

    The inhibition of metallo-β-lactamases (MBL) can prevent the hydrolysis of β-lactam antibiotics and hence is a promising strategy for the treatment of antibiotic resistant infections. In this study, we present a novel reversible covalent inhibitor of the clinically relevant MBL New Delhi metallo-β-lactamase 1 (NDM-1). Electrospray ionization-mass spectrometry (ESI-MS) and single site directed mutagenesis were used to show that the inhibitor forms a covalent bond with Lys224 in the active site of NDM-1. The inhibitor was further characterized using an enzyme inhibition assay, a surface plasmon resonance (SPR) based biosensor assay and covalent docking. The determined inhibition constant (KI(∗)) was 580nM and the inhibition constant for the initial complex (KI) was 76μM. To our knowledge, this inhibitor is the first example for a reversible covalent non-β-lactam inhibitor targeting NDM-1 and a promising starting point for the design of potent covalent inhibitors. PMID:27184103

  6. DNA binding properties, histidine interaction and cytotoxicity studies of water soluble ruthenium(ii) terpyridine complexes.

    PubMed

    Lazić, Dejan; Arsenijević, Aleksandar; Puchta, Ralph; Bugarčić, Živadin D; Rilak, Ana

    2016-03-21

    In this study, two representatives of previously synthesized ruthenium(ii) terpyridine complexes, i.e., [Ru(Cl-tpy)(en)Cl][Cl] (1) and [Ru(Cl-tpy)(dach)Cl][Cl] (2), were chosen and a detailed study of the kinetic parameters of their reactivity toward l-histidine (l-His), using the UV-Vis and (1)H NMR techniques, was developed. The inner molecular rearrangement from N3-coordinated l-His to the N1 bound isomer, observable in the NMR data, was corroborated by DFT calculations favoring N1 coordination by nearly 4 kcal mol(-1). These two ruthenium(ii) terpyridine complexes were investigated for their interactions with DNA employing UV-Vis spectroscopy, DNA viscosity measurements and fluorescence quenching measurements. The high binding constants obtained in the DNA binding studies (Kb = 10(4)-10(5) M(-1)) suggest a strong binding of the complexes to calf thymus (CT) DNA. Competitive studies with ethidium bromide (EB) showed that the complexes can displace DNA-bound EB, suggesting strong competition with EB (Ksv = 1.5-2.5 × 10(4) M(-1)). In fact, the results indicate that these complexes can bind to DNA covalently and non-covalently. In order to gain insight of the behavior of a neutral compound, besides the four previously synthesized cationic complexes [Ru(Cl-tpy)(en)Cl][Cl] (1), [Ru(Cl-tpy)(dach)Cl][Cl] (2), [Ru(Cl-tpy)(bpy)Cl][Cl] (3) and [Ru(tpy)Cl3] (P2), a new complex, [Ru(Cl-tpy)(pic)Cl] (4), was used in the biological studies. Their cytotoxicity was investigated against three different tumor cell lines, i.e., A549 (human lung carcinoma cell line), HCT116 (human colon carcinoma cell line), and CT26 (mouse colon carcinoma cell line), by the MTT assay. Complexes 1 and 2 showed higher activity than complexes 3, 4 and P2 against all the selected cell lines. The results on in vitro anticancer activity confirmed that only compounds that hydrolyze the monodentate ligand at a reasonable rate show moderate activity, provided that the chelate ligand is a hydrogen bond

  7. Hydrogen Bond Nanoscale Networks Showing Switchable Transport Performance

    NASA Astrophysics Data System (ADS)

    Long, Yong; Hui, Jun-Feng; Wang, Peng-Peng; Xiang, Guo-Lei; Xu, Biao; Hu, Shi; Zhu, Wan-Cheng; Lü, Xing-Qiang; Zhuang, Jing; Wang, Xun

    2012-08-01

    Hydrogen bond is a typical noncovalent bond with its strength only one-tenth of a general covalent bond. Because of its easiness to fracture and re-formation, materials based on hydrogen bonds can enable a reversible behavior in their assembly and other properties, which supplies advantages in fabrication and recyclability. In this paper, hydrogen bond nanoscale networks have been utilized to separate water and oil in macroscale. This is realized upon using nanowire macro-membranes with pore sizes ~tens of nanometers, which can form hydrogen bonds with the water molecules on the surfaces. It is also found that the gradual replacement of the water by ethanol molecules can endow this film tunable transport properties. It is proposed that a hydrogen bond network in the membrane is responsible for this switching effect. Significant application potential is demonstrated by the successful separation of oil and water, especially in the emulsion forms.

  8. Non-covalent and covalent modifications modulate the reactivity of monomeric mammalian globins.

    PubMed

    Ascenzi, Paolo; Marino, Maria; Polticelli, Fabio; Coletta, Massimo; Gioia, Magda; Marini, Stefano; Pesce, Alessandra; Nardini, Marco; Bolognesi, Martino; Reeder, Brandon J; Wilson, Michael T

    2013-09-01

    Multimeric globins (e.g., hemoglobin) are considered to be the prototypes of allosteric enzymes, whereas monomeric globins (e.g., myoglobin; Mb) usually are assumed to be non-allosteric. However, the modulation of the functional properties of monomeric globins by non-covalent (or allosteric) and covalent modifications casts doubts on this general assumption. Here, we report examples referable to these two extreme mechanisms modulating the reactivity of three mammalian monomeric globins. Sperm whale Mb, which acts as a reserve supply of O2 and facilitates the O2 flux within a myocyte, displays the allosteric modulation of the O2 affinity on lactate, an obligatory product of glycolysis under anaerobic conditions, thus facilitating O2 diffusion to the mitochondria in supporting oxidative phosphorylation. Human neuroglobin (NGB), which appears to protect neurons from hypoxia in vitro and in vivo, undergoes hypoxia-dependent phosphorylation (i.e., covalent modulation) affecting the coordination equilibrium of the heme-Fe atom and, in turn, the heme-protein reactivity. This facilitates heme-Fe-ligand binding and enhances the rate of anaerobic nitrite reduction to form NO, thus contributing to cellular adaptation to hypoxia. The reactivity of human cytoglobin (CYGB), which has been postulated to protect cells against oxidative stress, depends on both non-covalent and covalent mechanisms. In fact, the heme reactivity of CYGB depends on the lipid, such as oleate, binding which stabilizes the penta-coordination geometry of the heme-Fe atom. Lastly, the reactivity of NGB and CYGB is modulated by the redox state of the intramolecular CysCD7/CysD5 and CysB2/CysE9 residue pairs, respectively, affecting the heme-Fe atom coordination state. In conclusion, the modulation of monomeric globins reactivity by non-covalent and covalent modifications appears a very widespread phenomenon, opening new perspectives in cell survival and protection. This article is part of a Special Issue

  9. Electrochemical controlling and monitoring of halogen bond formation in solution.

    PubMed

    Groni, Sihem; Maby-Raud, Tanguy; Fave, Claire; Branca, Mathieu; Schöllhorn, Bernd

    2014-12-01

    Cyclic voltammetry has been used for the first time to probe and to control the formation of non-covalent halogen bonding (XB) via redox switching. These results strongly encourage the use of electrochemistry as an economical and precisely controllable tool for the investigation of XB in solution. PMID:25313384

  10. The non-covalent nature of the molecular structure of the benzene molecule.

    PubMed

    Cardozo, Thiago Messias; Fantuzzi, Felipe; Nascimento, Marco Antonio Chaer

    2014-06-14

    The benzene molecule is one of the most emblematic systems in chemistry, with its structural features being present in numerous different compounds. We have carried out an analysis of the influence of quantum mechanical interference on the geometric features of the benzene molecule, showing that many of the characteristics of its equilibrium geometry are a consequence of non-covalent contributions to the energy. This result implies that quasi-classical reasoning should be sufficient to predict the defining aspects of the benzene structure such as its planarity and equivalence of its bond lengths. PMID:24779029

  11. Is There a Quadruple Bond in C2?

    PubMed

    de Sousa, David Wilian Oliveira; Nascimento, Marco Antonio Chaer

    2016-05-10

    The chemical structure of the ground state of C2 has been the subject of intense debate after the suggestion that the molecule could exhibit a "fourth" covalent bond. In this paper, we investigate this problem explicitly avoiding all the points of conflict from the previous papers to show that there is no quadruple bond in C2. The generalized product function energy partitioning (GPF-EP) method has been applied to calculate the interference energy (IE) that accounts for the formation of covalent bonds for each bond of the molecule. The IE analysis shows that for the standard σ and π bonds interference exhibits the expected behavior, while for the "fourth" bond interference is a destabilizing factor. To make sure this could not be attributed to a new kind of bond, we performed an equivalent analysis for the (3)Σ(-) excited state of C3 molecule in which similar "bonding" occurs between the two ending carbon atoms. We also show that the difference in force constants of C2 and acetylene can be rationalized in terms of the amount of charge density in the internuclear region by looking at the changes in the overlaps between orbitals along the bond axis. PMID:27045682

  12. Yankee bonds

    SciTech Connect

    Delaney, P. )

    1993-10-01

    Yankee and Euromarket bonds may soon find their way into the financing of power projects in Latin America. For developers seeking long-term commitments under build, own, operate, and transfer (BOOT) power projects in Latin America, the benefits are substantial.

  13. Covalently functionalized carbon nanostructures and methods for their separation

    DOEpatents

    Wang, YuHuang; Brozena, Alexandra H; Deng, Shunliu; Zhang, Yin

    2015-03-17

    The present invention is directed to carbon nanostructures, e.g., carbon nanotubes, methods of covalently functionalizing carbon nanostructures, and methods of separating and isolating covalently functionalized carbon. In some embodiments, carbon nanotubes are reacted with alkylating agents to provide water soluble covalently functionalized carbon nanotubes. In other embodiments, carbon nanotubes are reacted with a thermally-responsive agent and exposed to light in order to separate carbon nanotubes of a specific chirality from a mixture of carbon nanotubes.

  14. Towards an understanding of the bonding in polyoxometalates through bond order and bond energy analysis.

    PubMed

    Bridgeman, Adam J; Cavigliasso, Germán

    2003-01-01

    The molecular and electronic structures of transition metal complexes, [MOCl5]n- (n = 2 for M = V,Nb,Ta and n = 1 for Mo,W) and mixed-metal polyoxometalates, [M'M5O19]3-V,Nb,Ta, M = Mo,W) containing a single terminal oxo group on each metal, and of complexes of the uranyl ion [UO2]2+, [UO2(H2O)5]2+ and [UO2Cl4]2-, have been calculated using density functional methods. The calculated structures of the complexes are in good agreement with available experimental parameters. For the mixed-metal hexametalates, for which no crystallographic data is available, the calculations predict a small tetragonal compression of the clusters with only minor structural changes compared to the parent molybdate and tungstate. The metal oxygen bonding in these anions has been probed using Mayer-Mulliken, bond energy and atoms in molecule analyses (AIM). These methods provide a consistent description of the bonding in polyoxometalates. The terminal bonds between transition metal or uranium and oxygen atoms have large sigma and pi components with the pi contributions exceeding the sigma bonding. The transition metals utilize their d orbitals almost exclusively to bond to oxygen whilst uranium uses both its 5f and 6d orbitals. Oxygen atom charges increase and covalency indexes decrease with coordination number, with a marked separation of these terms according to the oxygen atom type. The total valency and AIM energies of the oxygen atoms are predicted to be almost constant for all types of oxygen site. The constancy of the bonding power of the oxygen atoms appears to be an important factor in determining the gross structures and details of the bonding in polyoxometalates. The Mayer Mulliken approach provides direct characterization of the bonding power of atoms and the extent of the interaction between pairs of atoms that is consistent with the results of the considerably more computationally demanding bond energy and AIM approaches. PMID:14527219

  15. A robust and luminescent covalent organic framework as a highly sensitive and selective sensor for the detection of Cu(2+) ions.

    PubMed

    Li, Zhongping; Zhang, Yuwei; Xia, Hong; Mu, Ying; Liu, Xiaoming

    2016-05-01

    A hydrogen bond assisted azine-linked covalent organic framework, COF-JLU3, was synthesized under solvothermal conditions. Combining excellent crystallinity, porosity, stability and luminescence, it can be the first COF as a fluorescent sensor for toxic metal ions, exhibiting high sensitivity and selectivity to Cu(2+). PMID:27114234

  16. An internal thioester in a pathogen surface protein mediates covalent host binding

    PubMed Central

    Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

    2015-01-01

    To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI: http://dx.doi.org/10.7554/eLife.06638.001 PMID:26032562

  17. Inactivation of the Mycobacterium tuberculosis antigen 85 complex by covalent, allosteric inhibitors.

    PubMed

    Favrot, Lorenza; Lajiness, Daniel H; Ronning, Donald R

    2014-09-01

    The rise of multidrug-resistant and totally drug-resistant tuberculosis and the association with an increasing number of HIV-positive patients developing tuberculosis emphasize the necessity to find new antitubercular targets and drugs. The antigen 85 (Ag85) complex from Mycobacterium tuberculosis plays important roles in the biosynthesis of major components of the mycobacterial cell envelope. For this reason, Ag85 has emerged as an attractive drug target. Recently, ebselen was identified as an effective inhibitor of the Ag85 complex through covalent modification of a cysteine residue proximal to the Ag85 active site and is therefore a covalent, allosteric inhibitor. To expand the understanding of this process, we have solved the x-ray crystal structures of Ag85C covalently modified with ebselen and other thiol-reactive compounds, p-chloromercuribenzoic acid and iodoacetamide, as well as the structure of a cysteine to glycine mutant. All four structures confirm that chemical modification or mutation at this particular cysteine residue leads to the disruption of the active site hydrogen-bonded network essential for Ag85 catalysis. We also describe x-ray crystal structures of Ag85C single mutants within the catalytic triad and show that a mutation of any one of these three residues promotes the same conformational change observed in the cysteine-modified forms. These results provide evidence for active site dynamics that may afford new strategies for the development of selective and potent Ag85 inhibitors. PMID:25028518

  18. Inactivation of the Mycobacterium tuberculosis Antigen 85 Complex by Covalent, Allosteric Inhibitors*

    PubMed Central

    Favrot, Lorenza; Lajiness, Daniel H.; Ronning, Donald R.

    2014-01-01

    The rise of multidrug-resistant and totally drug-resistant tuberculosis and the association with an increasing number of HIV-positive patients developing tuberculosis emphasize the necessity to find new antitubercular targets and drugs. The antigen 85 (Ag85) complex from Mycobacterium tuberculosis plays important roles in the biosynthesis of major components of the mycobacterial cell envelope. For this reason, Ag85 has emerged as an attractive drug target. Recently, ebselen was identified as an effective inhibitor of the Ag85 complex through covalent modification of a cysteine residue proximal to the Ag85 active site and is therefore a covalent, allosteric inhibitor. To expand the understanding of this process, we have solved the x-ray crystal structures of Ag85C covalently modified with ebselen and other thiol-reactive compounds, p-chloromercuribenzoic acid and iodoacetamide, as well as the structure of a cysteine to glycine mutant. All four structures confirm that chemical modification or mutation at this particular cysteine residue leads to the disruption of the active site hydrogen-bonded network essential for Ag85 catalysis. We also describe x-ray crystal structures of Ag85C single mutants within the catalytic triad and show that a mutation of any one of these three residues promotes the same conformational change observed in the cysteine-modified forms. These results provide evidence for active site dynamics that may afford new strategies for the development of selective and potent Ag85 inhibitors. PMID:25028518

  19. Surface functionalization by covalent immobilization of an innovative carvacrol derivative to avoid fungal biofilm formation.

    PubMed

    Gharbi, Aïcha; Legigan, Thibaut; Humblot, Vincent; Papot, Sébastien; Berjeaud, Jean-Marc

    2015-01-01

    Carvacrol, an aromatic terpenic compound, known to be antimicrobial was grafted onto gold surfaces via two strategies based on newly-synthesized cross-linkers involving either an ester bond which can be cleaved by microbial esterases, or a covalent ether link. Surface functionalizations were characterized at each step by reflection absorption infrared spectroscopy (RAIRS). The two functionalized gold samples both led to a loss of culturability of the yeast Candida albicans, higher than 65%, indicating that the activity of the freshly-designed surfaces was probably due to still covalently immobilized carvacrol. On the contrary, when a phenyl group replaced the terpenic moiety, the yeast culturability increased by about 30%, highlighting the specific activity of carvacrol grafted on the surfaces. Confocal microscopy analyses showed that the mode of action of the functionalized surfaces with the ester or the ether of carvacrol was, in both cases, fungicidal and not anti-adhesive. Finally, this study shows that covalently immobilization of terpenic compounds can be used to design promising antimicrobial surfaces. PMID:25852986

  20. Cell Signalling Through Covalent Modification and Allostery

    NASA Astrophysics Data System (ADS)

    Johnson, Louise N.

    Phosphorylation plays essential roles in nearly every aspect of cell life. Protein kinases catalyze the transfer of the γ-phosphate of ATP to a serine, threonine or tyrosine residue in protein substrates. This covalent modification allows activation or inhibition of enzyme activity, creates recognition sites for other proteins and promotes order/disorder or disorder/order transitions. These properties regulate ­signalling pathways and cellular processes that mediate metabolism, transcription, cell cycle progression, differentiation, cytoskeleton arrangement and cell movement, apoptosis, intercellular communication, and neuronal and immunological functions. In this lecture I shall review the structural consequences of protein phosphorylation using our work on glycogen phosphorylase and the cell cycle cyclin dependent protein kinases as illustrations. Regulation of protein phosphorylation may be disrupted in the diseased state and protein kinases have become high profile targets for drug development. To date there are 11 compounds that have been approved for clinical use in the treatment of cancer.

  1. A Photoresponsive Smart Covalent Organic Framework.

    PubMed

    Huang, Ning; Ding, Xuesong; Kim, Jangbae; Ihee, Hyotcherl; Jiang, Donglin

    2015-07-20

    Ordered π-columnar structures found in covalent organic frameworks (COFs) render them attractive as smart materials. However, external-stimuli-responsive COFs have not been explored. Here we report the design and synthesis of a photoresponsive COF with anthracene units as the photoresponsive π-building blocks. The COF is switchable upon photoirradiation to yield a concavo-convex polygon skeleton through the interlayer [4π+4π] cycloaddition of anthracene units stacked in the π-columns. This cycloaddition reaction is thermally reversible; heating resets the anthracene layers and regenerates the COF. These external-stimuli-induced structural transformations are accompanied by profound changes in properties, including gas adsorption, π-electronic function, and luminescence. The results suggest that COFs are useful for designing smart porous materials with properties that are controllable by external stimuli. PMID:26095503

  2. A Photoresponsive Smart Covalent Organic Framework**

    PubMed Central

    Huang, Ning; Ding, Xuesong; Kim, Jangbae; Ihee, Hyotcherl; Jiang, Donglin

    2015-01-01

    Ordered π-columnar structures found in covalent organic frameworks (COFs) render them attractive as smart materials. However, external-stimuli-responsive COFs have not been explored. Here we report the design and synthesis of a photoresponsive COF with anthracene units as the photoresponsive π-building blocks. The COF is switchable upon photoirradiation to yield a concavo-convex polygon skeleton through the interlayer [4π+4π] cycloaddition of anthracene units stacked in the π-columns. This cycloaddition reaction is thermally reversible; heating resets the anthracene layers and regenerates the COF. These external-stimuli-induced structural transformations are accompanied by profound changes in properties, including gas adsorption, π-electronic function, and luminescence. The results suggest that COFs are useful for designing smart porous materials with properties that are controllable by external stimuli. PMID:26095503

  3. Hardness of covalent compounds: Roles of metallic component and d valence electrons

    NASA Astrophysics Data System (ADS)

    Guo, Xiaoju; Li, Lei; Liu, Zhongyuan; Yu, Dongli; He, Julong; Liu, Riping; Xu, Bo; Tian, Yongjun; Wang, Hui-Tian

    2008-07-01

    Based on the detailed analysis of chemical bonds, we present a Vickers hardness expression for the covalency-dominant crystals such as transition-metal carbides and nitrides. Hardness is dependent not only on bond length, bond density, and ionicity of bond [F. M. Gao et al., Phys. Rev. Lett. 91, 015502 (2003)] but also on the metallicity of bond and orbital form in the crystal structure of a compound, and all of these parameters can be determined by first-principles calculations. The calculated hardness using our expression has a good agreement with the experimental values for known monocarbides, mononitrides of transition metals, and cubic Zr3N4 with Th3P4 structure. In addition, we have predicted the Vickers hardness of the recently predicted tetragonal BC3 and tetragonal B2CN, and the recently synthesized pyrite PtN2 and marcasite OsN2. Our method offers one useful technique to search for superhard materials in transition-metal carbides and nitrides.

  4. Diffusion bonding

    DOEpatents

    Anderson, Robert C.

    1976-06-22

    1. A method for joining beryllium to beryllium by diffusion bonding, comprising the steps of coating at least one surface portion of at least two beryllium pieces with nickel, positioning a coated surface portion in a contiguous relationship with an other surface portion, subjecting the contiguously disposed surface portions to an environment having an atmosphere at a pressure lower than ambient pressure, applying a force upon the beryllium pieces for causing the contiguous surface portions to abut against each other, heating the contiguous surface portions to a maximum temperature less than the melting temperature of the beryllium, substantially uniformly decreasing the applied force while increasing the temperature after attaining a temperature substantially above room temperature, and maintaining a portion of the applied force at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions.

  5. Polymers incorporating covalently attached organoimido polyoxometalates

    DOEpatents

    Maatta, Eric A.; Moore, Aaron R.

    2004-03-16

    New polyoxometalate compounds and polymers comprising recurring monomers of those compounds are provided. The compounds are formed by replacing at least one oxide of the starting polyoxometalate with an organoimido (NR) group bonded to the polyoxometalate via a triple bond to the nitrogen atom. The R of the (NR) group comprises a reactive functional group which renders the compound readily polymerizable, alone or with other monomers (e.g., divinylbenzene), to form the inventive polymers. Additionally, a countercation (e.g., bis(tetra-n-butylammonium)) can be mixed with the polyoxometalate compounds in order to neutralize the negative charge thereof as well as to make those compounds more soluble in organic solvents.

  6. DNA Linked To Single Wall Carbon Nanotubes: Covalent Versus Non-Covalent Approach

    NASA Astrophysics Data System (ADS)

    Chung, C.-L.; Nguyen, K.; Lyonnais, S.; Streiff, S.; Campidelli, S.; Goux-Capes, L.; Bourgoin, J.-P.; Filoramo, A.

    2008-10-01

    Nanometer-scale structures represent a novel and intriguing field, where scientists and engineers manipulate materials at the atomic and molecular scale levels to produce innovative materials. Carbon nanotubes constitute a relatively new class of materials exhibiting exceptional mechanical and electronic properties and were found to be promising candidates for molecular electronics, sensing or biomedical applications. Considering the bottom-up strategy in nanotechnology, the combination of the recognition properties of DNA with the electronic properties of single walled carbon nanotubes (SWNTs) seems to be a promising approach for the future of electronics. With the aim to assemble DNA with SWNTs, two complementary strategies have been envisioned: the covalent linkage of DNA on carboxylic groups of SWNTs under classical coupling condition and the non-covalent approach based on biotin-streptavidin molecular recognition properties. Here, we present and compare the results that we obtained with these two different methods; we want to objectively show the advantages and disadvantages of each approach.

  7. How resonance assists hydrogen bonding interactions: an energy decomposition analysis.

    PubMed

    Beck, John Frederick; Mo, Yirong

    2007-01-15

    Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. PMID:17143867

  8. Covalent Docking Predicts Substrates for Haloalkanoate Dehalogenase Superfamily Phosphatases

    PubMed Central

    2015-01-01

    Enzyme function prediction remains an important open problem. Though structure-based modeling, such as metabolite docking, can identify substrates of some enzymes, it is ill-suited to reactions that progress through a covalent intermediate. Here we investigated the ability of covalent docking to identify substrates that pass through such a covalent intermediate, focusing particularly on the haloalkanoate dehalogenase superfamily. In retrospective assessments, covalent docking recapitulated substrate binding modes of known cocrystal structures and identified experimental substrates from a set of putative phosphorylated metabolites. In comparison, noncovalent docking of high-energy intermediates yielded nonproductive poses. In prospective predictions against seven enzymes, a substrate was identified for five. For one of those cases, a covalent docking prediction, confirmed by empirical screening, and combined with genomic context analysis, suggested the identity of the enzyme that catalyzes the orphan phosphatase reaction in the riboflavin biosynthetic pathway of Bacteroides. PMID:25513739

  9. Luminescent homo- and hetero-metallic hybrid molecular materials constructed by covalent grafting

    NASA Astrophysics Data System (ADS)

    Wang, F. F.; Yan, B.

    2013-01-01

    In this paper, 3-(triethoxysilyl)-propyl isocyanate (abbreviated as TESPIC) was modified by ethylparaben (EPB) to produce corresponding organic-inorganic monomers (EPB-TESPIC) with two components equipped with covalent bonds, which not only can coordinate to RE ions (Tb3+ and Eu3+) but also act as a sol-gel precursor. Luminescent hybrid materials consisting of terbium-europium complex, covalently bonded to silica-based network, have been obtained in situ via a sol-gel approach. Proton nuclear magnetic resonance spectroscopy (1HNMR) and Fourier transform infrared spectroscopy (FT-IR) were applied to characterize the structure of EPB-TESPIC. UV-visible, phosphorescence, and luminescence spectra were obtained to characterize the photophysical properties of the obtained hybrid material. Through co-hydrolysis and polycondensation, Tb3+ and Eu3+ can be introduced into the same organic-inorganic hybrid monomer, forming Si-O backbones. The experimental results show that the strong luminescence of rare-earth ions substantiates the optimum energy match and effective intramolecular energy transfer between the triplet state energy of coordination complex and the emissive energy level of the rare-earth ions. The hybrid material systems are expected to have potential applications in photophysical sensors.

  10. Superior H2 production by hydrophilic ultrafine Ta2O5 engineered covalently on graphene.

    PubMed

    Mao, Lin; Zhu, Shenmin; Ma, Jun; Shi, Dian; Chen, Yixin; Chen, Zhixin; Yin, Chao; Li, Yao; Zhang, Di

    2014-05-30

    A H2O2-mediated hydrothermal method was developed for the fabrication of hydrophilic Ta2O5/graphene composite. The composite shows a superior H2 productivity, up to 30 mmol g(-1) h(-1) when used as a photocatalyst for water splitting, corresponding to an apparent quantum efficiency of 33.8% at 254 nm. This superior performance is due to the hydrophilic nature of the composite and more importantly due to the ultrafine Ta2O5 nanoparticles (about 4.0 ± 1.5 nm) which are covalently bonded with the conductive graphene. The hydrophilic property of the composite is attributed to the use of H2O2 in the hydrothermal process. The ultrafine size of the Ta2O5 particles which are covalently bonded with the graphene sheets is attributed to the use of sonication in the synthesis process. Furthermore, the hydrophilic Ta2O5/Gr composite is durable, which is beneficial to long term photocatalysis. The strategy reported here provides a new approach to designing photocatalysts with superior performance for H2 production. PMID:24787652

  11. Chemical Bonding: The Orthogonal Valence-Bond View

    PubMed Central

    Sax, Alexander F.

    2015-01-01

    Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can be calculated, but the local information is hidden by the delocalized molecular orbitals (MO) used to construct the wave functions. The transformation of such wave functions into valence bond (VB) wave functions, which are based on localized orbitals, reveals the hidden information; this transformation is called a VB reading of MCSCF wave functions. The two-electron VB wave functions describing the Lewis electron pair that connects two atoms are frequently called covalent or neutral, suggesting that these wave functions describe an electronic situation where two electrons are never located at the same atom; such electronic situations and the wave functions describing them are called ionic. When the distance between two atoms decreases, however, every covalent VB wave function composed of non-orthogonal atomic orbitals changes its character from neutral to ionic. However, this change in the character of conventional VB wave functions is hidden by its mathematical form. Orthogonal VB wave functions composed of orthonormalized orbitals never change their character. When localized fragment orbitals are used instead of atomic orbitals, one can decide which local information is revealed and which remains hidden. In this paper, we analyze four chemical reactions by transforming the MCSCF wave functions into orthogonal VB wave functions; we show how the reactions are influenced by changing the atoms involved or by changing their local symmetry. Using orthogonal instead of non-orthogonal orbitals is not just a technical issue; it also changes the interpretation, revealing the properties of wave functions that remain otherwise undetected. PMID:25906476

  12. Pi Bond Orders and Bond Lengths

    ERIC Educational Resources Information Center

    Herndon, William C.; Parkanyi, Cyril

    1976-01-01

    Discusses three methods of correlating bond orders and bond lengths in unsaturated hydrocarbons: the Pauling theory, the Huckel molecular orbital technique, and self-consistent-field techniques. (MLH)

  13. Self-assembled and covalently linked capillary coating of diazoresin and cyclodextrin-derived dendrimer for analysis of proteins by capillary electrophoresis.

    PubMed

    Yu, Bing; Chi, Ming; Han, Yuxing; Cong, Hailin; Tang, Jianbin; Peng, Qiaohong

    2016-05-15

    Self-assembled and covalently linked capillary coatings of cyclodextrin-derived (CD) dendrimer were prepared using photosensitive diazoresin (DR) as a coupling agent. Layer by layer (LBL) self-assembled DR/CD-dendrimer coatings based on ionic bonding was fabricated first on the inner surface of capillary, and subsequently converted into covalent bonding after treatment with UV light through a unique photochemistry reaction of DR. Protein adsorption on the inner surface of capillary was suppressed by the DR/CD-dendrimer coating, and thus a baseline separation of lysozyme (Lys), myoglobin (Mb), bovine serum albumin (BSA) and ribonuclease A (RNase A) was achieved using capillary electrophoresis (CE). Compared with the bare capillary, the DR/CD-dendrimer covalently linked capillary coatings showed excellent protein separation performance with good stability and repeatability. Because of the replacement of highly toxic and moisture sensitive silane coupling agent by DR in the covalent coating preparation, this method may provide an environmentally friendly and simple way to prepare the covalently coated capillaries for CE. PMID:26992496

  14. Free radicals created by plasmas cause autohesive bonding in polymers

    SciTech Connect

    Awaja, Firas; McKenzie, David R.; Zhang Shengnan; James, Natalie

    2011-05-23

    We find that plasma immersion ion implantation of polymer surfaces enhances their autohesive bond strength when pressed together by more than a factor of five. Both polymerising (CH{sub 4}/O{sub 2}) and nonpolymerising (Ar) plasmas are effective. There is currently no satisfactory theory for predicting this remarkable phenomenon. We propose that free radicals created by the plasma treatment process diffuse to the interface and cause covalent bonds to form. This theory predicts the dependence of bond strength on plasma bias voltage, treatment time, and autohesive process conditions.

  15. The Calculation of Accurate Metal-Ligand Bond Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)

    1997-01-01

    The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.

  16. OH-transition metal bonding

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.

    1986-01-01

    The bonding in both CuOH and AgOH has a covalent component that leads to a bent structure. The larger electrostatic stabilization in CuOH leads to a larger D(e) (2.83 eV) compared with AgOH (2.20 eV). Using Ni5OH to model chemisorption of OH on a Ni surface, it is found that OH adsorption in the fourfold hollow of Ni(100) leads to an OH normal to the surface, while adsorption directly above a Ni atom leads to a tilted OH. These qualitative Ni5OH calculations allow for speculation on the observed variation of OH on metal surfaces.

  17. Complexes between hypohalous acids and phosphine derivatives. Pnicogen bond versus halogen bond versus hydrogen bond

    NASA Astrophysics Data System (ADS)

    Li, Qingzhong; Zhu, Hongjie; Zhuo, Hongying; Yang, Xin; Li, Wenzuo; Cheng, Jianbo

    2014-11-01

    The complexes of HOBr:PH2Y (Y = H, F, Cl, Br, CH3, NH2, OH, and NO2), HOCl:PH2F, and HOI:PH2F have been investigated with ab initio calculations at the MP2/aug-cc-pVTZ level. Four types of structures (1, 2, 3a, and 3b) were observed for these complexes. 1 is stabilized by an O⋯P pnicogen bond, 2 by a P⋯X halogen bond, 3a by a H⋯P hydrogen bond and a P⋯X pnicogen bond, and 3b by H⋯P and H⋯Br hydrogen bonds. Their relative stability is related to the halogen X of HOX and the substituent Y of PH2Y. These structures can compete with interaction energy of -10.22 ∼ -29.40 kJ/mol. The Hsbnd O stretch vibration shows a small red shift in 1, a small irregular shift in 2, but a prominent red shift in 3a and 3b. The Xsbnd O stretch vibration exhibits a smaller red shift in 1, a larger red shift in 2, but an insignificant blue shift in 3a and 3b. The Psbnd Y stretch vibration displays a red shift in 1 but a blue shift in 2, 3a, and 3b. The formation mechanism, stability, and properties of these structures have been analyzed with molecular electrostatic potentials, orbital interactions, and non-covalent interaction index.

  18. Nucleation and growth studies of polycrystalline covalent materials

    NASA Astrophysics Data System (ADS)

    Yun, Jungheum

    The chemical vapor deposition of different covalent polycrystalline materials---including diamond, silicon carbide, and carbon nitride---in stagnation flow reactors was rigorously simulated to determine the nucleation and growth mechanisms of these materials. Kinetic models were used to predict the rates of gas-phase and surface chemistry, the temperature and velocity profiles, potential gaseous film growth precursors, the time evolution of nucleation and intermediate layer formation, and the morphological evolution of continuous polycrystalline films. Numerical studies were also carried out to determine the dependence of the kinetics of nucleation and subsequent polycrystalline film growth on operating conditions. The calculated results for carbon nitride deposition indicate that the experimentally measured bond types in the carbon nitride films must result from chemical bond rearrangement occurring on the deposition surface or in the bulk phase once gaseous film growth precursors, including C, CH2 , CH3, C2H2, N, NH, NH2, HCN, and H2CN, are adsorbed. Of these precursors, C and CH 3 dominate the carbon contribution to carbon nitride film growth, and atomic nitrogen is the principal nitrogen bearing species. When the evolution rates of a silicon carbide intermediate layer and diamond clusters are calculated by accounting for gas-phase and surface reactions, surface and bulk diffusion, the mechanism for intermediate layer formation, and heterogeneous diamond nucleation kinetics, it is predicted that higher adsorption energies, in the range of 3.7 to 4.5 eV, lead to larger surface adatom densities, lower saturated nucleation densities, and larger silicon carbide intermediate layer thicknesses. The intermediate layer thickness becomes saturated while the growing diamond nuclei still cover a very small fraction of the silicon carbide. Reports of heteroepitaxial diamond nucleation without silicon carbide intermediate layer formation may be readily explained by a

  19. 6-Ethynylthieno[3,2-d]- and 6-ethynylthieno[2,3-d]pyrimidin-4-anilines as tunable covalent modifiers of ErbB kinases

    SciTech Connect

    Wood, Edgar R.; Shewchuk, Lisa M.; Ellis, Byron; Brignola, Perry; Brashear, Ronald L.; Caferro, Thomas R.; Dickerson, Scott H.; Dickson, Hamilton D.; Donaldson, Kelly H.; Gaul, Michael; Griffin, Robert J.; Hassell, Anne M.; Keith, Barry; Mullin, Robert; Petrov, Kimberly G.; Reno, Michael J.; Rusnak, David W.; Tadepalli, Sarva M.; Ulrich, John C.; Wagner, Craig D.; Vanderwall, Dana E.; Waterson, Alex G.; Williams, Jon D.; White, Wendy L.; Uehlinge, David E.

    2008-06-30

    Analysis of the x-ray crystal structure of mono-substituted acetylenic thienopyrimidine 6 complexed with the ErbB family enzyme ErbB-4 revealed a covalent bond between the terminal carbon of the acetylene moiety and the sulfhydryl group of Cys-803 at the solvent interface. The identification of this covalent adduct suggested that acetylenic thienopyrimidine 6 and related analogs might also be capable of forming an analogous covalent adduct with EGFR, which has a conserved cysteine (797) near the ATP binding pocket. To test this hypothesis, we treated a truncated, catalytically competent form of EGFR (678-1020) with a structurally related propargylic amine (8). An investigation of the resulting complex by mass spectrometry revealed the formation of a covalent complex of thienopyrimidine 8 with Cys-797 of EGFR. This finding enabled us to readily assess the irreversibility of various inhibitors and also facilitated a structure-activity relationship understanding of the covalent modifying potential and biological activity of a series of acetylenic thienopyrimidine compounds with potent antitumor activity. Several ErbB family enzyme and cell potent 6-ethynyl thienopyrimidine kinase inhibitors were found to form covalent adducts with EGFR.

  20. Determination of the amino acid residue involved in [3H]beta-funaltrexamine covalent binding in the cloned rat mu-opioid receptor.

    PubMed

    Chen, C; Yin, J; Riel, J K; DesJarlais, R L; Raveglia, L F; Zhu, J; Liu-Chen, L Y

    1996-08-30

    We previously demonstrated that [3H]beta-funaltrexamine ([3H]beta-FNA) labeled the rat mu opioid receptor expressed in Chinese hamster ovary cells with high specificity, and [3H]beta-FNA-labeled receptors migrated as one broad band with a mass of 80 kDa. In this study, we determined the region and then the amino acid residue of the mu receptor involved in the covalent binding of [3H]beta-FNA. [3H]beta-FNA-labeled receptors were solubilized and purified to approximately 10% purity by immunoaffinity chromatography with antibodies against a C-terminal domain peptide. The site of covalent bond formation was determined to be within Ala206-Met243 by CNBr cleavage of partially purified labeled mu receptors and determinations of sizes of labeled receptor fragments. The amino acid residue of beta-FNA covalent incorporation was then determined by site-directed mutagenesis studies within this region. Mutation of Lys233 to Ala, Arg, His, and Leu completely eliminated covalent binding of [3H]beta-FNA, although these mutants bound beta-FNA with high affinity. Mutations of other amino acid residues did not affect covalent binding of [3H]beta-FNA. These results indicate that [3H]beta-FNA binds covalently to Lys233. Since [3H]beta-FNA is a rigid molecule, the information will be very useful for molecular modeling of interaction between morphinans and the mu receptor. PMID:8702924

  1. Self-assembled covalent capillary coating of diazoresin/carboxyl fullerene for analysis of proteins by capillary electrophoresis and a comparison with diazoresin/graphene oxide coating.

    PubMed

    Yu, Bing; Shu, Xi; Cong, Hailin; Chen, Xin; Liu, Huwei; Yuan, Hua; Chi, Ming

    2016-03-11

    Self-assembled and covalently linked capillary coatings of carboxyl fullerenes (C60-COOH) were prepared using photosensitive diazoresin (DR) as a coupling agent. Layer by layer (LBL) self-assembled DR/C60-COOH coatings based on ionic bonding was fabricated first on the inner surface of silica capillary, and subsequently converted into covalent bonding after treatment with UV light through a unique photochemistry reaction of DR. The covalently bonded coatings had the ability of suppressing protein adsorption on the inner surface of silica capillary, and thus the baseline separation of lysozyme (Lys), cytochrome c (Cyt-c), bovine serum albumin (BSA) and myoglobin (Mb) was achieved within 13min by using capillary electrophoresis (CE). The covalently linked DR/C60-COOH capillary coatings presented good chemical stability and repeatability. The reproducibility of the separation of proteins was less than 1%, 2.5%, and 3.5%, respectively, for run-to-run, day-to-day, capillary-to-capillary, respectively; and the RSD of migration time for the proteins are all less than 2.5% after a continuous 100 times running in a coating column. Compared with DR/graphene oxide (GO) coatings prepared by the same method, the DR/C60-COOH capillary coatings showed excellent protein separation performance due to a self-lubrication based anti-fouling mechanism. Because of the replacement of highly toxic and moisture sensitive silane coupling agent by DR in the covalent coating preparation, this method may provide an environmentally friendly and simple way to prepare the covalently coated capillaries for CE. PMID:26875118

  2. Bonded Lubricants

    NASA Technical Reports Server (NTRS)

    1977-01-01

    Another spinoff to the food processing industry involves a dry lubricant developed by General Magnaplate Corp. of Linden, N.J. Used in such spacecraft as Apollo, Skylab and Viking, the lubricant is a coating bonded to metal surfaces providing permanent lubrication and corrosion resistance. The coating lengthens equipment life and permits machinery to be operated at greater speed, thus increasing productivity and reducing costs. Bonded lubricants are used in scores of commercia1 applications. They have proved particularly valuable to food processing firms because, while increasing production efficiency, they also help meet the stringent USDA sanitation codes for food-handling equipment. For example, a cookie manufacturer plagued production interruptions because sticky batter was clogging the cookie molds had the brass molds coated to solve the problem. Similarly, a pasta producer faced USDA action on a sanitation violation because dough was clinging to an automatic ravioli-forming machine; use of the anti-stick coating on the steel forming plates solved the dual problem of sanitation deficiency and production line downtime.

  3. Si-O Bonded Interactions in Silicate Crystals and Molecules: A Comparison

    SciTech Connect

    Gibbs, Gerald V.; Jayatilaka, Dylan; Spackman, M. A.; Cox, David F.; Rosso, Kevin M.

    2006-11-16

    Bond critical point, local kinetic energy density, G(rc), and local potential energy density, V(rc), properties of the electron density distributions, ρ(r), calculated for silicates like quartz and molecules like disiloxane are similar, indicating that the forces that govern the Si-O bonded interactions in crystals are short-ranged and molecular-like. Using the G(rc)/ρ(rc) ratio as a measure of bond character, the ratio increases as the Si-O bond length, the local electronic energy density, H(rc) = G(rc) + V(rc), and the oordination number of the Si atom decrease, and as the value of the electron density at the bond critical point, ρ(rc) and the Laplacian, ∇2ρ(rc), increase. The G(rc)/ρ(rc) and H(rc)/ρ(rc) ratios categorize the bond as observed for other second row atom M-O bonds into nonequivalent classes with the covalent character of each of the M-O bonds increasing with the H(rc)/ρ(rc) ratio. Some workers consider the Si-O bond to be highly ionic and others considered it to be either intermediate or substantially covalent. The character of the bond is examined in terms of the large net atomic basin charges conferred on the Si atoms comprising disiloxane, stishovite, quartz and forsterite, the domains of localized electron density along the Si-O bond vectors and on the reflex side of the Si-O-Si angle together with the close similarity of the Si-O bonded interactions observed for a variety of hydroxyacid silicate molecules and a large number of silicate crystals. The bond critical point and local energy density properties of the electron density distribution indicate that the bond is intermediate in character between Al-O and P-O bonded interations rather than being ionic or covalent.

  4. Bonding and Geometry of OCF(3)(-), ONF(3), and Related Molecules in Terms of the Ligand Close Packing Model.

    PubMed

    Gillespie, Ronald J.; Robinson, Edward A.; Heard, George L.

    1998-12-28

    The nature of the bonding in OCF(3)(-) and the isoelectronic molecule ONF(3) has been the subject of much discussion for many years, because these species appear to have unusual bond lengths and angles. We have reinvestigated the nature of the bonding in these and some related molecules by analyzing their calculated electron density distributions. The results show that the bonding in the series OBF(3)(2)(-), OCF(3)(-), ONF(3) ranges from predominately ionic in OBF(3)(2)(-) to predominately covalent in ONF(3) and that the interligand distances are consistent with the close packing of the ligands around the central atom. The AO bonds (A = B, C, N) are double bonds ranging in nature from a very ionic B=O bond to a predominately covalent N=O double bond, but all three are strong and short so that, in accordance with the ligand close packing (LCP) model, the AF bonds are correspondingly long. Also consistent with this model the bonds in a three-coordinated AOF(2) molecule are shorter than those in the corresponding AOF(3) molecule. Protonation of the doubly bonded oxygen, which converts the A=O bond to a single A-OH bond in each case, considerably lengthens the A-O bond, and the bond angles accordingly adopt values much closer to the tetrahedral angle. The difficulties of trying to describe the bonding in these molecules in terms of Lewis structures are discussed. PMID:11670825

  5. Covalently crosslinked diels-alder polymer networks.

    SciTech Connect

    Bowman, Christopher; Adzima, Brian J.; Anderson, Benjamin John

    2011-09-01

    This project examines the utility of cycloaddition reactions for the synthesis of polymer networks. Cycloaddition reactions are desirable because they produce no unwanted side reactions or small molecules, allowing for the formation of high molecular weight species and glassy crosslinked networks. Both the Diels-Alder reaction and the copper-catalyzed azide-alkyne cycloaddition (CuAAC) were studied. Accomplishments include externally triggered healing of a thermoreversible covalent network via self-limited hysteresis heating, the creation of Diels-Alder based photoresists, and the successful photochemical catalysis of CuAAC as an alternative to the use of ascorbic acid for the generation of Cu(I) in click reactions. An analysis of the results reveals that these new methods offer the promise of efficiently creating robust, high molecular weight species and delicate three dimensional structures that incorporate chemical functionality in the patterned material. This work was performed under a Strategic Partnerships LDRD during FY10 and FY11 as part of a Sandia National Laboratories/University of Colorado-Boulder Excellence in Science and Engineering Fellowship awarded to Brian J. Adzima, a graduate student at UC-Boulder. Benjamin J. Anderson (Org. 1833) was the Sandia National Laboratories point-of-contact for this fellowship.

  6. Repeating covalent structure of streptococcal M protein.

    PubMed Central

    Beachey, E H; Seyer, J M; Kang, A H

    1978-01-01

    We have attempted to identify the covalent structure of the M protein molecule of group A streptococci that is responsible for inducing type-specific, protective immunity. M protein was extracted from type 24 streptococci, purified, and cleaved with cyanogen bromide. Seven cyanogen bromide peptides were purified and further characterized. Together, the peptides account for the entire amino acid content of the M protein molecule. Each of the purified peptides possessed the type-specific determinant that inhibits opsonic antibodies for group A streptococci. The primary structures of the amino-terminal regions of each of the purified peptides was studied by automated Edman degradation. The partial sequences of two of the peptides were found to be identical to each other and to that of the uncleaved M protein molecule through at least the first 27 residues. The amino-terminal sequences of the remaining five peptides were identical to each other through the twentieth residue but completely different from the amino-terminal region of the other two peptides. However, the type-specific immunoreactivity and the incomplete analysis of the primary structure of the seven peptides suggest that the antiphagocytic determinant resides in a repeating amino acid sequence in the M protein molecule. PMID:80011

  7. Ionic Covalent Organic Frameworks with Spiroborate Linkage.

    PubMed

    Du, Ya; Yang, Haishen; Whiteley, Justin Michael; Wan, Shun; Jin, Yinghua; Lee, Se-Hee; Zhang, Wei

    2016-01-26

    A novel type of ionic covalent organic framework (ICOF), which contains sp(3)  hybridized boron anionic centers and tunable countercations, was constructed by formation of spiroborate linkages. These ICOFs exhibit high BET surface areas up to 1259 m(2)  g(-1) and adsorb a significant amount of H2 (up to 3.11 wt %, 77 K, 1 bar) and CH4 (up to 4.62 wt %, 273 K, 1 bar). Importantly, the materials show good thermal stabilities and excellent resistance to hydrolysis, remaining nearly intact when immersed in water or basic solution for two days. The presence of permanently immobilized ion centers in ICOFs enables the transportation of lithium ions with room-temperature lithium-ion conductivity of 3.05×10(-5)  S cm(-1) and an average Li(+) transference number value of 0.80±0.02. Our approach thus provides a convenient route to highly stable COFs with ionic linkages, which can potentially serve as absorbents for alternative energy sources such as H2, CH4, and also as solid lithium electrolytes/separators for the next-generation lithium batteries. PMID:26696304

  8. Basics of Fidelity Bonding.

    ERIC Educational Resources Information Center

    Kahn, Steven P.

    Fidelity bonds are important for an agency to hold to protect itself against any financial loss that can result from dishonest acts by its employees. Three types of fidelity bonds are available to an agency: (1) public official bonds; (2) dishonesty bonds; and (3) faithful performance bonds. Public official bonds are required by state law to be…

  9. Selective Covalent Chemistry via Gas-Phase Ion/ion Reactions: An Exploration of the Energy Surfaces Associated with N-Hydroxysuccinimide Ester Reagents and Primary Amines and Guanidine Groups

    NASA Astrophysics Data System (ADS)

    Bu, Jiexun; Fisher, Christine M.; Gilbert, Joshua D.; Prentice, Boone M.; McLuckey, Scott A.

    2016-03-01

    Selective covalent bond forming reactions (referred to as covalent reactions) can occur in gas-phase ion/ion reactions and take place via the formation of a long-lived chemical complex. The gas-phase ion/ion reactivity between sulfo-N-hydroxysuccinimide (sulfo-NHS) ester reagent anions and peptide cations containing a primary amine or guanidine group has been examined via DFT calculations and complex dissociation rate measurements. The results reveal insights regarding the roles of the barriers of competing processes within the complex. When the covalent reaction is exothermic, two prototypical cases, determined by the nature of the energy surface, are apparent. The product partitioning between covalent reaction and simple proton transfer upon dissociation of the long-lived complex is sensitive to activation conditions when the transition state barrier for covalent reaction is relatively high (case 1) but is insensitive to activation conditions when the transition state barrier is relatively low (case 2). Covalent reaction efficiencies are very high in case 2 scenarios, such as when the reactive site is a guanidine and the anion attachment site is a guanidinium ion. Covalent reaction efficiencies are variable, and generally low, in case 1 scenarios, such as when an amine is the reactive site and an ammonium ion is the site of anion attachment. A relatively long slow-heating step prior to the complex dissociation step, however, can dramatically increase covalent reaction yield in case 1 scenarios.

  10. Selective Covalent Chemistry via Gas-Phase Ion/ion Reactions: An Exploration of the Energy Surfaces Associated with N-Hydroxysuccinimide Ester Reagents and Primary Amines and Guanidine Groups

    NASA Astrophysics Data System (ADS)

    Bu, Jiexun; Fisher, Christine M.; Gilbert, Joshua D.; Prentice, Boone M.; McLuckey, Scott A.

    2016-06-01

    Selective covalent bond forming reactions (referred to as covalent reactions) can occur in gas-phase ion/ion reactions and take place via the formation of a long-lived chemical complex. The gas-phase ion/ion reactivity between sulfo- N-hydroxysuccinimide (sulfo-NHS) ester reagent anions and peptide cations containing a primary amine or guanidine group has been examined via DFT calculations and complex dissociation rate measurements. The results reveal insights regarding the roles of the barriers of competing processes within the complex. When the covalent reaction is exothermic, two prototypical cases, determined by the nature of the energy surface, are apparent. The product partitioning between covalent reaction and simple proton transfer upon dissociation of the long-lived complex is sensitive to activation conditions when the transition state barrier for covalent reaction is relatively high ( case 1) but is insensitive to activation conditions when the transition state barrier is relatively low ( case 2). Covalent reaction efficiencies are very high in case 2 scenarios, such as when the reactive site is a guanidine and the anion attachment site is a guanidinium ion. Covalent reaction efficiencies are variable, and generally low, in case 1 scenarios, such as when an amine is the reactive site and an ammonium ion is the site of anion attachment. A relatively long slow-heating step prior to the complex dissociation step, however, can dramatically increase covalent reaction yield in case 1 scenarios.

  11. Selective Covalent Chemistry via Gas-Phase Ion/ion Reactions: An Exploration of the Energy Surfaces Associated with N-Hydroxysuccinimide Ester Reagents and Primary Amines and Guanidine Groups.

    PubMed

    Bu, Jiexun; Fisher, Christine M; Gilbert, Joshua D; Prentice, Boone M; McLuckey, Scott A

    2016-06-01

    Selective covalent bond forming reactions (referred to as covalent reactions) can occur in gas-phase ion/ion reactions and take place via the formation of a long-lived chemical complex. The gas-phase ion/ion reactivity between sulfo-N-hydroxysuccinimide (sulfo-NHS) ester reagent anions and peptide cations containing a primary amine or guanidine group has been examined via DFT calculations and complex dissociation rate measurements. The results reveal insights regarding the roles of the barriers of competing processes within the complex. When the covalent reaction is exothermic, two prototypical cases, determined by the nature of the energy surface, are apparent. The product partitioning between covalent reaction and simple proton transfer upon dissociation of the long-lived complex is sensitive to activation conditions when the transition state barrier for covalent reaction is relatively high (case 1) but is insensitive to activation conditions when the transition state barrier is relatively low (case 2). Covalent reaction efficiencies are very high in case 2 scenarios, such as when the reactive site is a guanidine and the anion attachment site is a guanidinium ion. Covalent reaction efficiencies are variable, and generally low, in case 1 scenarios, such as when an amine is the reactive site and an ammonium ion is the site of anion attachment. A relatively long slow-heating step prior to the complex dissociation step, however, can dramatically increase covalent reaction yield in case 1 scenarios. Graphical Abstract ᅟ. PMID:27020926

  12. Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate

    NASA Astrophysics Data System (ADS)

    Weber, Arthur L.

    1989-03-01

    Glyceraldehyde-3-phosphate acts as the substrate in a model of early self-replication of a phosphodiester copolymer of glycerate-3-phosphate and glycerol-3-phosphate. This model of self-replication is based on covalent complementarity in which information transfer is mediated by a single covalent bond, in contrast to multiple weak interactions that establish complementarity in nucleic acid replication. This replication model is connected to contemporary biochemistry through its use of glyceraldehyde-3-phosphate, a central metabolite of glycolysis and photosynthesis.

  13. A novel tyrosine-heme C−O covalent linkage in F43Y myoglobin: a new post-translational modification of heme proteins.

    PubMed

    Yan, Dao-Jing; Li, Wei; Xiang, Yu; Wen, Ge-Bo; Lin, Ying-Wu; Tan, Xiangshi

    2015-01-01

    Heme post-translational modification plays a key role in tuning the structure and function of heme proteins. We herein report a novel tyrosine-heme covalent C−O bond in an artificially produced sperm whale myoglobin (Mb) mutant, F43Y Mb, which formed spontaneously in vivo between the Tyr43 hydroxy group and the heme 4-vinyl group. This highlights the diverse chemistry of heme post-translational modifications, and lays groundwork for further investigation of the structural and functional diversity of covalently-bound heme proteins. PMID:25392956

  14. Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.

    1989-01-01

    Glyceraldehyde-3-phosphate acts as the substrate in a model of early self-replication of a phosphodiester copolymer of glycerate-3-phosphate and glycerol-3-phosphate. This model of self-replication is based on covalent complementarity in which information transfer is mediated by a single covalent bond, in contrast to multiple weak interactions that establish complementarity in nucleic acid replication. This replication model is connected to contemporary biochemistry through its use of glyceraldehyde-3-phosphate, a central metabolite of glycolysis and photosynthesis.

  15. Intramolecular Hydrogen Bonding in Substituted Aminoalcohols.

    PubMed

    Lane, Joseph R; Schrøder, Sidsel D; Saunders, Graham C; Kjaergaard, Henrik G

    2016-08-18

    The qualifying features of a hydrogen bond can be contentious, particularly where the hydrogen bond is due to a constrained intramolecular interaction. Indeed there is disagreement within the literature whether it is even possible for an intramolecular hydrogen bond to form between functional groups on adjacent carbon atoms. This work considers the nature of the intramolecular interaction between the OH (donor) and NH2 (acceptor) groups of 2-aminoethanol, with varying substitution at the OH carbon. Gas-phase vibrational spectra of 1-amino-2-methyl-2-propanol (BMAE) and 1-amino-2,2-bis(trifluoromethyl)-2-ethanol (BFMAE) were recorded using Fourier transform infrared spectroscopy and compared to literature spectra of 2-aminoethanol (AE). Based on the experimental OH-stretching frequencies, the strength of the intramolecular hydrogen bond appears to increase from AE < BMAE ≪ BFMAE. Non-covalent interaction analysis shows evidence of an intramolecular hydrogen bond in all three molecules, with the order of the strength of interaction matching that of experiment. The experimental OH-stretching vibrational frequencies were found to correlate well with the calculated kinetic energy density, suggesting that this approach can be used to estimate the strength of an intramolecular hydrogen bond. PMID:27447952

  16. Dynamic Ordering and Phase Segregation in Hydrogen-Bonded Polymers.

    PubMed

    Chen, Senbin; Binder, Wolfgang H

    2016-07-19

    Hydrogen bonds (H-bonds) constitute highly relevant structural units of molecular self-assembly. They bridge biological and synthetic sciences, implementing dynamic properties into materials and molecules, not achieved via purely covalent bonds. Phase segregation on the other hand represents another important assembly principle, responsible for, e.g., cell compartimentation, membrane-formation, and microphase segregation in polymers. Yet, despite the expanding elegant synthetic strategies of supramolecular polymers, the investigation of phase behavior of macromolecules driven by H-bonding forces still remains in its infancy. Compared to phase segregation arising from covalently linked block copolymers, the generation of phase segregated nanostructures via supramolecular polymers facilitates the design of novel functional materials, such as those with stimuli-responsive, self-healing, and erasable-material properties. We here discuss the phase segregation of H-bonding polymers in both the solution and solid state, wherein the molecular recognition elements are based on multiple H-bonding moieties, such as thymine/2,6-diamino-pyridine (THY/DAP), thymine/diamino triazine (THY/DAT), and barbiturate/Hamilton wedge (Ba/HW) elements. The specific aggregation of a series of different H-bonding polymers in solution, both linear and dendritic polymers, bearing heterocomplementary H-bonding moieties are described, in particular focusing on the issue of phase segregation. The exploitation of H-bonded supramolecular dendrons with segregating polymer chains leads to the formation of three-phase segregated hierarchical micelles in solution, purely linking the components via H-bonds, in turn displaying a versatile spectrum of segregated morphologies. We also focus on segregation effects of H-bonded amorphous and crystalline polymers: thus the formation of nanostructures, such as disordered micelles and well-ordered body centered cubic (BCC) packed spheres from telechelic polymers

  17. Capillary electrophoretic focusing of covalently derivatized protein induced by surfactant.

    PubMed

    Oukacine, Farid; Quirino, Joselito P; Mesbah, Kiarach; Taverna, Myriam

    2016-05-01

    In this communication, we present a very simple strategy to focus covalently derivatized proteins for high sensitivity CE analysis by LIF detection. We demonstrated that the covalently tagged protein can be focused just by adding SDS at a concentration above the CMC in the derivatized sample. Under specific injection conditions, SDS concentration below the CMC is also sufficient to induce the focusing of the tagged protein. This method allows the quantification and detection of the covalently tagged protein in a narrow zone with an efficiency approaching 220 000 plates/m. Very good linearity was obtained for the ubiquitin in a concentration range of 2-25 μM. PMID:26940436

  18. Theoretical investigation of non-covalent interactions and spectroscopic properties of a new mixed-ligand Co(II) complex

    NASA Astrophysics Data System (ADS)

    Chahkandi, Mohammad

    2016-05-01

    A new mixed ligand complex formulated as [Co(pydc)(2-apym)(H2O)2]·H2O (1) (pydcH2 = pyridine-2,6-dicarboxylic acid, 2-apym = 2-aminopyrimidine) has been used for density functional theory (DFT) calculations. The neutral monomeric complex participates in a variety of non-covalent interactions including H-bonding and π-stacking to create a 1-D coordination chain. In order to determine the binding energy of the non-covalent interactions responsible for the crystalline network formation of 1 they have been studied by dispersion corrected density functional theory (DFT-D) calculations. For this purpose, the independent smallest fragment (monomer) and subsequently the related network including seven monomers bearing all non-covalent interactions have been optimized. The results demonstrate that hydrogen bonds, especially N-H···O interactions, govern the network formation. The calculated electronic absorption spectrum agrees with experiment in which three major electron-transition bands derived from (σ, p) → π∗ and π → π∗ ligand to ligand charge transfer (LLCT), and π → n and π → π∗ pydc intra-ligand charge transfer (ILCT) transitions are seen.

  19. Production of a covalent flavin linkage in lipoamide dehydrogenase. Reaction with 8-Cl-FAD.

    PubMed

    Moore, E G; Cardemil, E; Massey, V

    1978-09-25

    dehydrogenase. The maximum turnover rates differ dramatically. Enzyme fractionating between 55% and 75% ammonium sulfate has a Vmax which is 61 times slower than native enzyme. Enzyme fractionating between 20% and 45% ammonium sulfate has a Vmax which is 7400 times slower than native enzyme. These slower rates are partially explainable by the oxidation-reduction potentials of the modified enzymes. Both covalently bound FAD and noncovalently bound FAD appear to reside in the native flavin binding site of the enzyme. However, once dimerization of the protien has taken place, the noncovalently bound 8-Cl-FAD cannot be induced to form a covalent bond with the protein except under protein denaturing conditions. The implications of these findings are discussed. PMID:681358

  20. Bonding nature of the actinide tetrafluorides AnF4 (An = Th-Cm)

    NASA Astrophysics Data System (ADS)

    Wang, Chang-Ying; Cheng, Cheng; Su, Jing; Huai, Ping

    2015-11-01

    The knowledge of chemical bonding for actinide fluoride compounds is essential to understand and predict the physical and chemical behaviour of actinide elements in fluoride molten salt. In this work, the bonding nature of actinide tetrafluorides AnF4 (An = Th-Cm) is investigated by using scalar relativistic density functional theory. Bond order analyses show relatively stronger An-F bonds for An = U-Np and weaker ones for An = Th, Am, and Cm. Despite the dominant ionic character of An-F bonds, a considerable covalent interaction is indicated by the overlap integral value of F 2p and actinide 5f, 6d orbitals. Both natural population analyses and electron density analyses show that An-F covalency rises initially before reducing in the latter systems with the maximum at Np and Pu and the obviously strong ionic bonding character in An = Th, Am, and Cm. Compared to AnCp4 (Cp = η5-C5H5) reported in the literature, our study on AnF4 suggests a much more prominent actinide-ligand covalent interaction. And the roles of orbital overlap and near-degeneracy in driving covalency are discussed.

  1. Non-covalent interactions in ionic liquid ion pairs and ion pair dimers: a quantum chemical calculation analysis.

    PubMed

    Marekha, Bogdan A; Kalugin, Oleg N; Idrissi, Abdenacer

    2015-07-14

    Ionic liquids (ILs) being composed of bulky multiatomic ions reveal a plethora of non-covalent interactions which determine their microscopic structure. In order to establish the main peculiarities of these interactions in an IL-environment, we have performed quantum chemical calculations for a set of representative model molecular clusters. These calculations were coupled with advanced methods of analysis of the electron density distribution, namely, the quantum theory of atoms in molecules (QTAIM) and the non-covalent interaction (NCI; J. Am. Chem. Soc., 2010, 132, 6499) approaches. The former allows for profound quantitative characterization of non-covalent interactions between atoms while the latter gives an overview of spatial extent, delocalization, and relative strength of such interactions. The studied systems consist of 1-butyl-3-methylimidazolium (Bmim(+)) cations and different perfluorinated anions: tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), and bis(trifluoromethanesulfonyl)imide (TFSI(-)). IL ion pairs and ion pair dimers were considered as model structures for the neat ILs and large aggregates. Weak electrostatic hydrogen bonding was found between the anions and the imidazolium ring hydrogen atoms of cations. Weaker but still appreciable hydrogen bonding was also noted for hydrogen atoms adjacent to the imidazolium ring alkyl groups of Bmim(+). The relative strength of the hydrogen bonding is higher in BmimTfO and BmimBF4 ILs than in BmimPF6 and BmimTFSI, whereas BmimTfO and BmimTFSI reveal higher sensitivity of hydrogen bonding at the different hydrogen atoms of the imidazolium ring. PMID:26059822

  2. Adsorption-induced scission of carbon carbon bonds

    NASA Astrophysics Data System (ADS)

    Sheiko, Sergei S.; Sun, Frank C.; Randall, Adrian; Shirvanyants, David; Rubinstein, Michael; Lee, Hyung-Il; Matyjaszewski, Krzysztof

    2006-03-01

    Covalent carbon-carbon bonds are hard to break. Their strength is evident in the hardness of diamonds and tensile strength of polymeric fibres; on the single-molecule level, it manifests itself in the need for forces of several nanonewtons to extend and mechanically rupture one bond. Such forces have been generated using extensional flow, ultrasonic irradiation, receding meniscus and by directly stretching a single molecule with nanoprobes. Here we show that simple adsorption of brush-like macromolecules with long side chains on a substrate can induce not only conformational deformations, but also spontaneous rupture of covalent bonds in the macromolecular backbone. We attribute this behaviour to the fact that the attractive interaction between the side chains and the substrate is maximized by the spreading of the side chains, which in turn induces tension along the polymer backbone. Provided the side-chain densities and substrate interaction are sufficiently high, the tension generated will be strong enough to rupture covalent carbon-carbon bonds. We expect similar adsorption-induced backbone scission to occur for all macromolecules with highly branched architectures, such as brushes and dendrimers. This behaviour needs to be considered when designing surface-targeted macromolecules of this type-either to avoid undesired degradation, or to ensure rupture at predetermined macromolecular sites.

  3. Chemically stable multilayered covalent organic nanosheets from covalent organic frameworks via mechanical delamination.

    PubMed

    Chandra, Suman; Kandambeth, Sharath; Biswal, Bishnu P; Lukose, Binit; Kunjir, Shrikant M; Chaudhary, Minakshi; Babarao, Ravichandar; Heine, Thomas; Banerjee, Rahul

    2013-11-27

    A series of five thermally and chemically stable functionalized covalent organic frameworks (COFs), namely, TpPa-NO2, TpPa-F4, TpBD-(NO2)2, TpBD-Me2, and TpBD-(OMe)2 were synthesized by employing the solvothermal aldehyde-amine Schiff base condensation reaction. In order to complete the series, previously reported TpPa-1, TpPa-2, and TpBD have also been synthesized, and altogether, eight COFs were fully characterized through powder X-ray diffraction (PXRD), Fourier transform IR (FT-IR) spectroscopy, (13)C solid-state NMR spectroscopy, and thermogravimetric analysis. These COFs are crystalline, permanently porous, and stable in boiling water, acid (9 N HCl), and base (3 N NaOH). The synthesized COFs (all eight) were successfully delaminated using a simple, safe, and environmentally friendly mechanical grinding route to transform into covalent organic nanosheets (CONs) and were well characterized via transmission electron microscopy and atomic force microscopy. Further PXRD and FT-IR analyses confirm that these CONs retain their structural integrity throughout the delamination process and also remain stable in aqueous, acidic, and basic media like the parent COFs. These exfoliated CONs have graphene-like layered morphology (delaminated layers), unlike the COFs from which they were synthesized. PMID:24168521

  4. Intramolecular amide bonds stabilize pili on the surface of bacilli

    SciTech Connect

    Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.; Whitelegge, Julian P.; He, Chuan; Schneewind, Olaf

    2010-01-12

    Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili. We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.

  5. New Phases of Hydrogen-Bonded Systems at Extreme Conditions

    SciTech Connect

    Manaa, M R; Goldman, N; Fried, L E

    2006-10-23

    We study the behavior of hydrogen-bonded systems under high-pressure and temperature. First principle calculations of formic acid under isotropic pressure up to 70 GPa reveal the existence of a polymerization phase at around 20 GPa, in support of recent IR, Raman, and XRD experiments. In this phase, covalent bonding develops between molecules of the same chain through symmetrization of hydrogen bonds. We also performed molecular dynamics simulations of water at pressures up to 115 GPa and 2000 K. Along this isotherm, we are able to define three different phases. We observe a molecular fluid phase with superionic diffusion of the hydrogens for pressure 34 GPa to 58 GPa. We report a transformation to a phase dominated by transient networks of symmetric O-H hydrogen bonds at 95-115 GPa. As in formic acid, the network can be attributed to the symmetrization of the hydrogen bond, similar to the ice VII to ice X transition.

  6. Photogeneration of singlet oxygen by the phenothiazine derivatives covalently bound to the surface-modified glassy carbon

    NASA Astrophysics Data System (ADS)

    Blacha-Grzechnik, Agata; Piwowar, Katarzyna; Krukiewicz, Katarzyna; Koscielniak, Piotr; Szuber, Jacek; Zak, Jerzy K.

    2016-05-01

    The selected group of four amine-derivatives of phenothiazine was covalently grafted to the glassy carbon surface in the four-step procedure consisting of the electrochemical reduction of the diazonium salt followed by the electrochemical and chemical post-modification steps. The proposed strategy involves the bonding of linker molecule to which the photosensitizer is attached. The synthesized organic layers were characterized by means of cyclic voltammetry, XPS and Raman Spectroscopy. It was shown that the phenothiazines immobilized via proposed strategy retain their photochemical properties and are able to generate 1O2 when activated by the laser radiation. The effectiveness of in situ singlet oxygen generation by those new solid photoactive materials was determined by means of UVVis spectroscopy. The reported, covalently modified solid surfaces may find their application as the singlet oxygen photogenerators in the fine chemicals' synthesis or in the wastewater treatment.

  7. Strategies for discovering and derisking covalent, irreversible enzyme inhibitors

    PubMed Central

    Johnson, Douglas S; Weerapana, Eranthie; Cravatt, Benjamin F

    2010-01-01

    This article presents several covalent inhibitors, including examples of successful drugs, as well as highly selective, irreversible inhibitors of emerging therapeutic targets, such as fatty acid amide hydolase. Covalent inhibitors have many desirable features, including increased biochemical efficiency of target disruption, less sensitivity toward pharmacokinetic parameters and increased duration of action that outlasts the pharmacokinetics of the compound. Safety concerns that must be mitigated include lack of specificity and the potential immunogenicity of protein–inhibitor adduct(s). Particular attention will be given to recent technologies, such as activity-based protein profiling, which allow one to define the proteome-wide selectivity patterns for covalent inhibitors in vitro and in vivo. For instance, any covalent inhibitor can, in principle, be modified with a ‘clickable’ tag to generate an activity probe that is almost indistinguishable from the original agent. These probes can be applied to any living system across a broad dose range to fully inventory their on and off targets. The substantial number of drugs on the market today that act by a covalent mechanism belies historical prejudices against the development of irreversibly acting therapeutic small molecules. Emerging proteomic technologies offer a means to systematically discriminate safe (selective) versus deleterious (nonselective) covalent inhibitors and thus should inspire their future design and development. PMID:20640225

  8. Non-covalent interactions between carbon nanotubes and conjugated polymers

    NASA Astrophysics Data System (ADS)

    Tuncel, Dönüs

    2011-09-01

    Carbon nanotubes (CNTs) are interest to many different disciplines including chemistry, physics, biology, material science and engineering because of their unique properties and potential applications in various areas spanning from optoelectronics to biotechnology. However, one of the drawbacks associated with these materials is their insolubility which limits their wide accessibility for many applications. Various approaches have been adopted to circumvent this problem including modification of carbon nanotube surfaces by non-covalent and covalent attachments of solubilizing groups. Covalent approach modification may alter the intrinsic properties of carbon nanotubes and, in turn make them undesirable for many applications. On the other hand, a non-covalent approach helps to improve the solubility of CNTs while preserving their intrinsic properties. Among many non-covalent modifiers of CNTs, conjugated polymers are receiving increasing attention and highly appealing because of a number of reasons. To this end, the aim of this feature article is to review the recent results on the conjugated polymer-based non-covalent functionalization of CNTs with an emphasis on the effect of conjugated polymers in the dispersibility/solubility, optical, thermal and mechanical properties of carbon nanotubes as well as their usage in the purification and isolation of a specific single-walled nanotube from the mixture of the various tubes.

  9. Immunodetection of human topoisomerase I-DNA covalent complexes

    PubMed Central

    Patel, Anand G.; Flatten, Karen S.; Peterson, Kevin L.; Beito, Thomas G.; Schneider, Paula A.; Perkins, Angela L.; Harki, Daniel A.; Kaufmann, Scott H.

    2016-01-01

    A number of established and investigational anticancer drugs slow the religation step of DNA topoisomerase I (topo I). These agents induce cytotoxicity by stabilizing topo I-DNA covalent complexes, which in turn interact with advancing replication forks or transcription complexes to generate lethal lesions. Despite the importance of topo I-DNA covalent complexes, it has been difficult to detect these lesions within intact cells and tumors. Here, we report development of a monoclonal antibody that specifically recognizes covalent topo I-DNA complexes, but not free topo I or DNA, by immunoblotting, immunofluorescence or flow cytometry. Utilizing this antibody, we demonstrate readily detectable topo I-DNA covalent complexes after treatment with camptothecins, indenoisoquinolines and cisplatin but not nucleoside analogues. Topotecan-induced topo I-DNA complexes peak at 15–30 min after drug addition and then decrease, whereas indotecan-induced complexes persist for at least 4 h. Interestingly, simultaneous staining for covalent topo I-DNA complexes, phospho-H2AX and Rad51 suggests that topotecan-induced DNA double-strand breaks occur at sites distinct from stabilized topo I-DNA covalent complexes. These studies not only provide new insight into the action of topo I-directed agents, but also illustrate a strategy that can be applied to study additional topoisomerases and their inhibitors in vitro and in vivo. PMID:26917015

  10. Immunodetection of human topoisomerase I-DNA covalent complexes.

    PubMed

    Patel, Anand G; Flatten, Karen S; Peterson, Kevin L; Beito, Thomas G; Schneider, Paula A; Perkins, Angela L; Harki, Daniel A; Kaufmann, Scott H

    2016-04-01

    A number of established and investigational anticancer drugs slow the religation step of DNA topoisomerase I (topo I). These agents induce cytotoxicity by stabilizing topo I-DNA covalent complexes, which in turn interact with advancing replication forks or transcription complexes to generate lethal lesions. Despite the importance of topo I-DNA covalent complexes, it has been difficult to detect these lesions within intact cells and tumors. Here, we report development of a monoclonal antibody that specifically recognizes covalent topo I-DNA complexes, but not free topo I or DNA, by immunoblotting, immunofluorescence or flow cytometry. Utilizing this antibody, we demonstrate readily detectable topo I-DNA covalent complexes after treatment with camptothecins, indenoisoquinolines and cisplatin but not nucleoside analogues. Topotecan-induced topo I-DNA complexes peak at 15-30 min after drug addition and then decrease, whereas indotecan-induced complexes persist for at least 4 h. Interestingly, simultaneous staining for covalent topo I-DNA complexes, phospho-H2AX and Rad51 suggests that topotecan-induced DNA double-strand breaks occur at sites distinct from stabilized topo I-DNA covalent complexes. These studies not only provide new insight into the action of topo I-directed agents, but also illustrate a strategy that can be applied to study additional topoisomerases and their inhibitorsin vitroandin vivo. PMID:26917015

  11. New Developments in Orbital-Free Density Functional Theory Enabling Simulations of Covalent Materials

    NASA Astrophysics Data System (ADS)

    Xia, Junchao

    Orbital-free (OF) density functional theory (DFT) is a powerful and numerically efficient first principles quantum mechanics method. Its application has contributed to understanding a diverse set of materials properties in recent decades. However, most previous studies were confined to simple metals. In this thesis, we focus on extending OFDFT to describe covalently-bonded materials and aiming for a balance between accuracy and efficiency. We first apply OFDFT to study diatomic molecules, with the Huang-Carter (HC) kinetic energy density functional (KEDF). OFDFT predicts reasonable equilibrium bond lengths, bond dissociation energies, and vibrational frequencies compared to Kohn-Sham (KS) DFT benchmarks. This work indicates significant progress of OFDFT in describing molecules. However, we find that the HC KEDF is computationally expensive and thus inapplicable for large-scale simulations. Consequently, we propose an electron density decomposition formalism for covalent materials. Based on local density information, the total density is decomposed into localized and delocalized electron densities, which are then described by different KEDF models separately. The resulting Wang--Govind--Carter-decomposition (WGCD) KEDF gives accurate properties for bulk semiconductors and isolated molecules. Furthermore, it offers far superior numerical efficiency compared to the previous HC KEDF. We then test the HC and WGCD KEDFs on Li-Si alloys and obtain accurate structures and bulk properties. The OFDFT Li adsorption energies on the Si(100) surface are also close to KSDFT values. OFDFT is thus promising to study mechanical properties of Li-Si alloys and the mixing mechanism during lithiation and delithiation processes. We next focus on single-point KEDFs for localized densities and pointwise quantities including the local kinetic energy density (KED) and the electron localization function (ELF). Based on a transferable correlation between the reduced density and the KED

  12. Electronic Coupling between Two Covalently Bonded Dimolybdenum Units Bridged by a Naphthalene Group.

    PubMed

    Zhu, Guang Yuan; Meng, Miao; Tan, Ying Ning; Xiao, Xuan; Liu, Chun Y

    2016-06-20

    Using 2,6-naphthalenedicarboxylate and its thiolated derivatives as bridging ligands, three Mo2 dimers of the type [Mo2(DAniF)3](E2CC10H6CE2)[Mo2(DAniF)3] (DAniF = N,N'-di-p-anisylformamidinate; E = O, S) have been synthesized and characterized by X-ray diffraction. These compounds can be generally formulated as [Mo2]-naph-[Mo2], where the complex unit [Mo2] ([Mo2(DAniF)3(μ-E2C)]) functions as an electron donor (acceptor) and the naphthalene (naph) group is the bridge. The mixed-valence (MV) complexes, generated by one-electron oxidation of the neutral precursors, display weak, very broad intervalence charge-transfer absorption bands in the near-to-mid-IR regions. The electronic coupling matrix elements for the MV complexes, Hab = 390-570 cm(-1), are calculated from the Mulliken-Hush equation, which fall between those for the phenyl (ph) and biphenyl (biph) analogues reported previously. The three series consisting of three complexes with the same [Mo2] units exhibit exponential decay of Hab as the bridge changes from ph to biph via naph, with decay factors of 0.21-0.17 Å(-1). Therefore, it is evidenced that while the extent of the bridge conjugacy varies, the electronic coupling between the two [Mo2] units is dominated by the Mo2···Mo2 separation. The absorption band energies for metal-to-ligand charge transfer are in the middle of those for the ph and biph analogues, which is consistent with variation of the HOMO-LUMO energy gaps for the complex series. These results indicate that the interplay of the bridge length and conjugacy is to affect the enegy for charge transfer crossing the intervening moiety, in accordance with a superechange mechanism. PMID:27243960

  13. Local structure of Iridium organometallic catalysts covalently bonded to carbon nanotubes.

    NASA Astrophysics Data System (ADS)

    Blasco, J.; Cuartero, V.; Subías, G.; Jiménez, M. V.; Pérez-Torrente, J. J.; Oro, L. A.; Blanco, M.; Álvarez, P.; Blanco, C.; Menéndez, R.

    2016-05-01

    Hybrid catalysts based on Iridium N-heterocyclic carbenes anchored to carbon nanotubes (CNT) have been studied by XAFS spectroscopy. Oxidation of CNT yields a large amount of functional groups, mainly hydroxyl groups at the walls and carboxylic groups at the tips, defects and edges. Different kinds of esterification reactions were performed to functionalize oxidized CNT with imidazolium salts. Then, the resulting products were reacted with an Ir organometallic compound to form hybrid catalysts efficient in hydrogen transfer processes. XANES spectroscopy agree with the presence of Ir(I) in these catalysts and the EXAFS spectra detected differences in the local structure of Ir atoms between the initial Ir organometallic compound and the Ir complexes anchored to the CNT. Our results confirm that the halide atom, present in the Ir precursor, was replaced by oxygen from -OH groups at the CNT wall in the first coordination shell of Ir. The lability of this group accounts for the good recyclability and the good efficiency shown by these hybrid catalysts.

  14. From covalent bonds to eco-physiological pharmacology of secondary plant metabolites.

    PubMed

    Chatterjee, Shyam Sunder

    2015-11-15

    Despite the availability of numerous drugs and other therapeutic modalities, the prevention and cure of over- and under-nutrition triggered metabolic and other disease states continues as a major challenge for modern medicine. Such silently progressing and eventually life-threatening diseases often accompany diverse spectrum of comorbid psychiatric disorders. Majority of the global population suffering from metabolic diseases live in economically developing or underdeveloped countries, where due to socioeconomic, cultural, and other reasons, therapies may be unavailable. Evidence from preclinical, clinical, and epidemiological studies of numerous structurally and functionally diverse secondary metabolites of plants suggest that many of these could be promising therapeutic leads for the treatment and prevention of malnutrition-associated diseases and mental health problems. The review discusses the potential therapeutic uses of secondary plant metabolites and their bacterial and mammalian catabolites based on their bioactivity profiles, with special emphasis on their modulating effects on gut microbial ecology and physiological stress responses. Based on concepts in medicinal chemistry and pharmacology considerations that evolved during the author's interactions with David Triggle, secondary plant metabolites may represent an alternative and economically feasible approach to new drugs. PMID:26253688

  15. Electron transport in DNA initiated by diaminonaphthalene donors alternatively bound by non-covalent and covalent association.

    PubMed

    Campbell, Neil P; Rokita, Steven E

    2014-02-21

    Covalent conjugation is typically used to fix a potential charge donor to a chosen site for studying either hole or excess electron transport in duplex DNA. A model system based on oligonucleotides containing an abasic site and (Br)dU was previously developed to provide a rapid method of screening new donors without the need of synthetic chemistry. While this strategy is effective for discovering important lead compounds, it is not appropriate for establishing extensive correlations between molecular structure and donor efficiency as demonstrated with a series of closely related electron donors based on diaminonaphthalene. The non-covalent system accurately identified the ability of the donors to reduce a distal (Br)dU in DNA, but their varying efficiencies were not recapitulated when attached covalently to an equivalent sequence of DNA. Reduction within the covalent system was not sensitive to the strong donor potentials as consistent with charge recombination dominating the net migration of charge. PMID:24398596

  16. A photoviscoplastic model for photoactivated covalent adaptive networks

    NASA Astrophysics Data System (ADS)

    Ma, Jing; Mu, Xiaoming; Bowman, Christopher N.; Sun, Youyi; Dunn, Martin L.; Qi, H. Jerry; Fang, Daining

    2014-10-01

    Light activated polymers (LAPs) are a class of contemporary materials that when irradiated with light respond with mechanical deformation. Among the different molecular mechanisms of photoactuation, here we study radical induced bond exchange reactions (BERs) that alter macromolecular chains through an addition-fragmentation process where a free chain whose active end group attaches then breaks a network chain. Thus the BER yields a polymer with a covalently adaptable network. When a LAP sample is loaded, the macroscopic consequence of BERs is stress relaxation and plastic deformation. Furthermore, if light penetration through the sample is nonuniform, resulting in nonuniform stress relaxation, the sample will deform after unloading in order to achieve equilibrium. In the past, this light activation mechanism was modeled as a phase evolution process where chain addition-fragmentation process was considered as a phase transformation between stressed phases and newly-born phases that are undeformed and stress free at birth. Such a modeling scheme describes the underlying physics with reasonable fidelity but is computationally expensive. In this paper, we propose a new approach where the BER induced macromolecular network alteration is modeled as a viscoplastic deformation process, based on the observation that stress relaxation due to light irradiation is a time-dependent process similar to that in viscoelastic solids with an irrecoverable deformation after light irradiation. This modeling concept is further translated into a finite deformation photomechanical constitutive model. The rheological representation of this model is a photoviscoplastic element placed in series with a standard linear solid model in viscoelasticity. A two-step iterative implicit scheme is developed for time integration of the two time-dependent elements. We carry out a series of experiments to determine material parameters in our model as well as to validate the performance of the model in

  17. Mechanochemical Reactions Reporting and Repairing Bond Scission in Polymers.

    PubMed

    Clough, Jess M; Balan, Abidin; Sijbesma, Rint P

    2015-01-01

    The past 10 years have seen a resurgence of interest in the field of polymer mechanochemistry. Whilst the destructive effects of mechanical force on polymer chains have been known for decades, it was only recently that researchers tapped into these forces to realize more useful chemical transformations. The current review discusses the strategic incorporation of weak covalent bonds in polymers to create materials with stress-sensing and damage-repairing properties. Firstly, the development of mechanochromism and mechanoluminescence as stress reporters is considered. The second half focuses on the net formation of covalent bonds as a response to mechanical force, via mechanocatalysis and mechanically unmasked chemical reactivity, and concludes with perspectives for the field. PMID:26104999

  18. Chemical Bonds II

    ERIC Educational Resources Information Center

    Sanderson, R. T.

    1972-01-01

    The continuation of a paper discussing chemical bonding from a bond energy viewpoint, with a number of examples of single and multiple bonds. (Part I appeared in volume 1 number 3, pages 16-23, February 1972.) (AL)

  19. What Determines Bond Costs. Municipal Bonds Series.

    ERIC Educational Resources Information Center

    Young, Douglas; And Others

    Public officials in small towns who participate infrequently in the bond market need information about bond financing. This publication, one in a series of booklets published by the Western Rural Development Center using research gathered between 1967-77, discusses factors influencing the marketability and cost of bond financing for towns and…

  20. Theoretical rovibrational analysis of the covalent noble gas compound ArNH+

    NASA Astrophysics Data System (ADS)

    Novak, Carlie M.; Fortenberry, Ryan C.

    2016-04-01

    Noble gasses can make covalent bonds. This has been clearly shown for ArH+ as is evidenced by the observation of this molecule ubiquitously in the interstellar medium. In order to augment the list of potential noble gas molecules, highly-accurate quartic field methods are employed here to analyze the ArNH+ radical cation for the first time. This study is in line with previous examinations of ArOH+, ArH2+, and ArH3+. It is shown here that the Arsbnd N bond strength falls below the Arsbnd O bond energy in ArOH+ but in line with that from ArH2+ indicating that ArNH+ could certainly be synthesized in the lab or, potentially, in nature. In order to aid in the search for this noble gas molecular cation, spectroscopic constants, fundamental vibrational frequencies, absorption intensities, and the center-of-mass dipole moment are provided at high-level in order to augment our understanding of noble gas chemistry.

  1. Role of interatomic bonding in the mechanical anisotropy and interlayer cohesion of CSH crystals

    SciTech Connect

    Dharmawardhana, C.C.; Misra, A.; Aryal, S.; Rulis, P.; Ching, W.Y.

    2013-10-15

    Atomic scale properties of calcium silicate hydrate (CSH), the main binding phase of hardened Portland cement, are not well understood. Over a century of intense research has identified almost 50 different crystalline CSH minerals which are mainly categorized by their Ca/Si ratio. The electronic structure and interatomic bonding in four major CSH crystalline phases with structures close to those found in hardened cement are investigated via ab initio methods. Our result reveals the critical role of hydrogen bonding and importance of specifying precise locations for water molecules. Quantitative analysis of contributions from different bond types to the overall cohesion shows that while the Si-O covalent bonds dominate, the hydrogen bonding and Ca-O bonding are also very significant. Calculated results reveal the correlation between bond topology and interlayer cohesion. The overall bond order density (BOD) is found to be a more critical measure than the Ca/Si ratio in classifying different CSH crystals.

  2. Relevant insight of surface characterization techniques to study covalent grafting of a biopolymer to titanium implant and its acidic resistance

    NASA Astrophysics Data System (ADS)

    D'Almeida, Mélanie; Amalric, Julien; Brunon, Céline; Grosgogeat, Brigitte; Toury, Bérangère

    2015-02-01

    Peri-implant bacterial infections are the main cause of complications in dentistry. Our group has previously proposed the attachment of chitosan on titanium implants via a covalent bond to improve its antibacterial properties while maintaining its biocompatibility. A better knowledge of the coating preparation process allows a better understanding of the bioactive coating in biological conditions. In this work, several relevant characterization techniques were used to assess an implant device during its production phase and its resistance in natural media at different pH. The titanium surface was functionalized with 3-aminopropyltriethoxysilane (APTES) followed by grafting of an organic coupling agent; succinic anhydride, able to form two covalent links, with the substrate through a Ti-O-Si bond and the biopolymer through a peptide bond. Each step of the coating synthesis as well as the presence confirmation of the biopolymer on titanium after saliva immersion was followed by FTIR-ATR, SEM, EDS, 3D profilometry, XPS and ToF-SIMS analyses. Results allowed to highlight the efficiency of each step of the process, and to propose a mechanism occurring during the chitosan coating degradation in saliva media at pH 5 and at pH 3.

  3. The role of the substrate structure in the on-surface synthesis of organometallic and covalent oligophenylene chains.

    PubMed

    Dai, Jingya; Fan, Qitang; Wang, Tao; Kuttner, Julian; Hilt, Gerhard; Gottfried, J Michael; Zhu, Junfa

    2016-07-27

    The influences of the substrate structure on the formation of one-dimensional organometallic and covalent oligomers on a Cu(110) surface were studied using scanning tunneling microscopy (STM), X-ray photoemission spectroscopy (XPS), and low energy electron diffraction (LEED) in ultrahigh vacuum (UHV). Vapor deposition of submonolayer 4,4''-dibromo-meta-terphenyl (DMTP) onto a Cu(110) surface at 300 K leads to scission of C-Br bonds and the formation of organometallic chains (cis/trans and all-trans) connected by C-Cu-C bonds. Larger islands (120 × 120 nm(2)) of all-trans zigzag organometallic chains as sole products were obtained by the deposition of DMTP onto Cu(110) held at 383 K. The domains are oriented along two directions with an angle of ±13° relative to the [0 0 1] direction due to the two-fold symmetry of the Cu(110) surface lattice. This study reveals at a sub-molecular level that the organometallic chains firstly lose copper atoms and then undergo C-C coupling into oligophenylene chains at a substrate temperature around 417 K. Annealing the large islands of organometallic chains at 458 K results in the formation of completely C-C covalently bonded zigzag oligophenylene chains. The zigzag angle of 125° slightly deviates from the ideal value of 120°. This is attributed to a stretching of the zigzag oligophenylene chains due to substrate template effects. PMID:27411742

  4. Targeted Drug Delivery with Polymers and Magnetic Nanoparticles: Covalent and Noncovalent Approaches, Release Control, and Clinical Studies.

    PubMed

    Ulbrich, Karel; Holá, Kateřina; Šubr, Vladimir; Bakandritsos, Aristides; Tuček, Jiří; Zbořil, Radek

    2016-05-11

    Targeted delivery combined with controlled drug release has a pivotal role in the future of personalized medicine. This review covers the principles, advantages, and drawbacks of passive and active targeting based on various polymer and magnetic iron oxide nanoparticle carriers with drug attached by both covalent and noncovalent pathways. Attention is devoted to the tailored conjugation of targeting ligands (e.g., enzymes, antibodies, peptides) to drug carrier systems. Similarly, the approaches toward controlled drug release are discussed. Various polymer-drug conjugates based, for example, on polyethylene glycol (PEG), N-(2-hydroxypropyl)methacrylamide (HPMA), polymeric micelles, and nanoparticle carriers are explored with respect to absorption, distribution, metabolism, and excretion (ADME scheme) of administrated drug. Design and structure of superparamagnetic iron oxide nanoparticles (SPION) and condensed magnetic clusters are classified according to the mechanism of noncovalent drug loading involving hydrophobic and electrostatic interactions, coordination chemistry, and encapsulation in porous materials. Principles of covalent conjugation of drugs with SPIONs including thermo- and pH-degradable bonds, amide linkage, redox-cleavable bonds, and enzymatically-cleavable bonds are also thoroughly described. Finally, results of clinical trials obtained with polymeric and magnetic carriers are analyzed highlighting the potential advantages and future directions in targeted anticancer therapy. PMID:27109701

  5. Design-atom approach for the QM/MM covalent boundary: A design-carbon atom with five valence electrons

    PubMed Central

    Xiao, Chuanyun; Zhang, Yingkai

    2009-01-01

    A critical issue underlying the accuracy and applicability of the combined quantum mechanical/molecular mechanical (QM/MM) methods is how to describe the QM/MM boundary across covalent bonds. Inspired by the ab initio pseudo-potential theory, here we introduce a novel design-atom approach for a more fundamental and transparent treatment of this QM/MM covalent boundary problem. The main idea is to replace the boundary atom of the active part with a design-atom, which has a different number of valence electrons but very similar atomic properties. By modifying the Troullier-Martins scheme, which has been widely employed to construct norm-conserving pseudo-potentials for density functional calculations, we have successfully developed a design-carbon atom with five valence electrons. Tests on a series of molecules yield very good structural and energetic results, and indicate its transferability in describing a variety of chemical bonds, including double and triple bonds. PMID:17902888

  6. Graphene Oxide Quantum Dots Covalently Functionalized PVDF Membrane with Significantly-Enhanced Bactericidal and Antibiofouling Performances.

    PubMed

    Zeng, Zhiping; Yu, Dingshan; He, Ziming; Liu, Jing; Xiao, Fang-Xing; Zhang, Yan; Wang, Rong; Bhattacharyya, Dibakar; Tan, Timothy Thatt Yang

    2016-01-01

    Covalent bonding of graphene oxide quantum dots (GOQDs) onto amino modified polyvinylidene fluoride (PVDF) membrane has generated a new type of nano-carbon functionalized membrane with significantly enhanced antibacterial and antibiofouling properties. A continuous filtration test using E. coli containing feedwater shows that the relative flux drop over GOQDs modified PVDF is 23%, which is significantly lower than those over pristine PVDF (86%) and GO-sheet modified PVDF (62%) after 10 h of filtration. The presence of GOQD coating layer effectively inactivates E. coli and S. aureus cells, and prevents the biofilm formation on the membrane surface, producing excellent antimicrobial activity and potentially antibiofouling capability, more superior than those of previously reported two-dimensional GO sheets and one-dimensional CNTs modified membranes. The distinctive antimicrobial and antibiofouling performances could be attributed to the unique structure and uniform dispersion of GOQDs, enabling the exposure of a larger fraction of active edges and facilitating the formation of oxidation stress. Furthermore, GOQDs modified membrane possesses satisfying long-term stability and durability due to the strong covalent interaction between PVDF and GOQDs. This study opens up a new synthetic avenue in the fabrication of efficient surface-functionalized polymer membranes for potential waste water treatment and biomolecules separation. PMID:26832603

  7. Mechanistic studies of two-dimensional covalent organic frameworks rapidly polymerized from initially homogenous conditions.

    PubMed

    Smith, Brian J; Dichtel, William R

    2014-06-18

    Covalent organic frameworks (COFs) are periodic two- and three-dimensional (2D and 3D) polymer networks with high surface areas, low densities, and designed structures. Despite intense interest in framework materials, the nucleation and growth processes of COFs, and even of more established metal-organic frameworks (MOFs), are poorly understood. The kinetics of COF growth under varied reaction conditions provides mechanistic insight needed to improve their crystallinity and rationally synthesize new materials. Such kinetic measurements are unprecedented and difficult to perform on typical heterogeneous COF reaction mixtures. Here we synthesize 2D boronate ester-linked COF-5 under conditions in which the monomers are fully soluble. These homogeneous growth conditions provide equal or better material quality compared to any previous report and enable the first rigorous studies of the early stages of COF growth. COF-5 forms within minutes, and the precipitation rate is readily quantified from optical turbidity measurements. COF-5 formation follows an Arrhenius temperature dependence between 60-90 °C with an activation energy of 22-27 kcal/mol. The measured rate law includes a second order in both boronic acid and catechol moieties, and inverse second order in MeOH concentration. A competitive monofunctional catechol slows COF-5 formation but does not redissolve already precipitated COF, indicating both dynamic covalent bond formation and irreversible precipitation. Finally, stoichiometric H2O provides a 4-fold increase in crystallite domain areas, representing the first rational link between reaction conditions and material quality. PMID:24892961

  8. Ab initio theoretical study of non-covalent adsorption of aromatic molecules on boron nitride nanotubes.

    PubMed

    Zhao, Yu; Wu, Xiaojun; Yang, Jinlong; Zeng, Xiao Cheng

    2011-06-28

    We have studied non-covalent functionalization of boron nitride nanotubes (BNNTs) with benzene molecule and with seven other different heterocyclic aromatic rings (furan, thiophene, pyrrole, pyridine, pyrazine, pyrimidine, and pyridazine, respectively). A hybrid density functional theory (DFT) method with the inclusion of dispersion correction is employed. The structural and electronic properties of the functionalized BNNTs are obtained. The DFT calculation shows that upon adsorption to the BNNT, the center of aromatic rings tend to locate on top of the nitrogen site. The trend of adsorption energy for the aromatic rings on the BNNTs shows marked dependence on different intermolecular interactions, including the dispersion interaction (area of the delocalized π bond), the dipole-dipole interaction (polarization), and the electrostatic repulsion (lone pair electrons). The DFT calculation also shows that non-covalent functionalization of BNNTs with aromatic rings can give rise to new impurity states within the band gap of pristine BNNTs, suggesting possible carrier doping of BNNTs via selective adsorption of aromatic rings. PMID:21603684

  9. A novel methotrexate delivery system based on chitosan-methotrexate covalently conjugated nanoparticles.

    PubMed

    Wu, Ping; He, Xiaoxiao; Wang, Kemin; Tan, Weihong; He, Chunmei; Zheng, Mingbin

    2009-10-01

    In this paper, a chitosan-methotrexate covalently conjugated nanoparticles (CS-MTX-TPP NPs) has been developed as a potential delivery system for methotrexate (MTX). MTX was first conjugated to CS by using glutaraldehyde as cross-linked agent, and followed by the process of ionic gelation between MTX-conjugated CS and sodium tripolyphosphate (TPP) to form CS-MTX-TPP NPs at mild reaction conditions. The hydrodynamic diameter of CS-MTX-TPP NPs and the encapsulation efficiency of MTX were affected by the weight ratio of MTX/CS. At the ratio of 1/11, the mean hydrodynamic diameter of CS-MTX-TPP NPs was the lowest (187.9 +/- 9.0 nm) and the nanoparticles presented the encapsulation efficiency of MTX with 53.0 +/- 3.2%. The characterizations by atomic force microscopy (AFM) and photon correlation spectroscopy (PCS) showed the CS-MTX-TPP NPs had a spherical shape and good dispersion with diameter of sub-200-nm and zeta potential of 30 mV. Additionally, in vitro release test revealed that the stable covalent bonding of CS and MTX was beneficial for providing slow release for MTX. Especially, cellular toxicity study in MCF-7 cancer cells further demonstrated the effective anticancer efficacy of this new type of delivery for MTX. PMID:20201432

  10. Surface functionalization of silica-coated magnetic nanoparticles for covalent attachment of cholesterol oxidase

    NASA Astrophysics Data System (ADS)

    Šulek, Franja; Drofenik, Miha; Habulin, Maja; Knez, Željko

    2010-01-01

    A systematic approach towards the fabrication of highly functionalized silica shell magnetic nanoparticles, presently used for enzyme immobilization, is herein fully presented. The synthesis of bare maghemite (γ-Fe 2O 3) nanoparticles was accomplished by thermal co-precipitation of iron ions in ammonia alkaline solution at harsh reaction conditions, respectively. Primary surface engineering of maghemite nanoparticles was successfully performed by the proper deposition of silica onto nanoparticles surface under strictly regulated reaction conditions. Next, the secondary surface functionalization of the particles was achieved by coating the particles with organosilane followed by glutaraldehyde activation in order to enhance protein immobilization. Covalent immobilization of cholesterol oxidase was attempted afterwards. The structural and magnetic properties of magnetic silica nanocomposites were characterized by TEM and vibrating sample magnetometer (VSM) instruments. X-ray diffraction measurements confirmed the spinel structure and average size of uncoated maghemite nanoparticles to be around 20 nm in diameter. SEM-EDS spectra indicated a strong signal for Si, implying the coating procedure of silica onto the particles surface to be successfully accomplished. Fourier transform infrared (FT-IR) spectra analysis confirmed the binding of amino silane molecules onto the surface of the maghemite nanoparticles mediated Si-O-Si chemical bonds. Compared to the free enzyme, the covalently bound cholesterol oxidase retained 50% of its activity. Binding of enzyme onto chemically modified magnetic nanoparticles via glutaraldehyde activation is a promising method for developing biosensing components in biomedicine.

  11. A rapid and sensitive assay for DNA-protein covalent complexes in living cells.

    PubMed

    Kiianitsa, Kostantin; Maizels, Nancy

    2013-05-01

    A number of proteins form covalent bonds with DNA as obligatory transient intermediates in normal nuclear transactions. Drugs that trap these complexes have proven to be potent therapeutics in both cancer and infectious disease. Nonetheless, current assays for DNA-protein adducts are cumbersome, limiting both mechanistic studies and translational applications. We have developed a rapid and sensitive assay that enables quantitative immunodetection of protein-DNA adducts. This new 'RADAR' (rapid approach to DNA adduct recovery) assay accelerates processing time 4-fold, increases sample throughput 20-fold and requires 50-fold less starting material than the current standard. It can be used to detect topoisomerase 1-DNA adducts in as little as 60 ng of DNA, corresponding to 10 000 human cells. We apply the RADAR assay to demonstrate that expression of SLFN11 does not increase camptothecin sensitivity by promoting accumulation of topoisomerase 1-DNA adducts. The RADAR assay will be useful for analysis of the mechanisms of formation and resolution of DNA-protein adducts in living cells, and identification and characterization of reactions in which covalent DNA adducts are transient intermediates. The assay also has potential application to drug discovery and individualized medicine. PMID:23519618

  12. Crystal-Field and Covalency Effects in Uranates: An X-ray Spectroscopic Study.

    PubMed

    Butorin, Sergei M; Kvashnina, Kristina O; Smith, Anna L; Popa, Karin; Martin, Philippe M

    2016-07-01

    The electronic structure of U(V) - and U(VI) -containing uranates NaUO3 and Pb3 UO6 was studied by using an advanced technique, namely X-ray absorption spectroscopy (XAS) in high-energy-resolution fluorescence-detection (HERFD) mode. Due to a significant reduction in core-hole lifetime broadening, the crystal-field splittings of the 5f shell were probed directly in HERFD-XAS spectra collected at the U 3d edge, which is not possible by using conventional XAS. In addition, the charge-transfer satellites that result from U 5f-O 2p hybridization were clearly resolved. The crystal-field parameters, 5f occupancy, and degree of covalency of the chemical bonding in these uranates were estimated by using the Anderson impurity model by calculating the U 3d HERFD-XAS, conventional XAS, core-to-core (U 4f-3d transitions) resonant inelastic X-ray scattering (RIXS), and U 4f X-ray photoelectron spectra. The crystal field was found to be strong in these systems and the 5f occupancy was determined to be 1.32 and 0.84 electrons in the ground state for NaUO3 and Pb3 UO6 , respectively, which indicates a significant covalent character for these compounds. PMID:27257782

  13. Graphene Oxide Quantum Dots Covalently Functionalized PVDF Membrane with Significantly-Enhanced Bactericidal and Antibiofouling Performances

    NASA Astrophysics Data System (ADS)

    Zeng, Zhiping; Yu, Dingshan; He, Ziming; Liu, Jing; Xiao, Fang-Xing; Zhang, Yan; Wang, Rong; Bhattacharyya, Dibakar; Tan, Timothy Thatt Yang

    2016-02-01

    Covalent bonding of graphene oxide quantum dots (GOQDs) onto amino modified polyvinylidene fluoride (PVDF) membrane has generated a new type of nano-carbon functionalized membrane with significantly enhanced antibacterial and antibiofouling properties. A continuous filtration test using E. coli containing feedwater shows that the relative flux drop over GOQDs modified PVDF is 23%, which is significantly lower than those over pristine PVDF (86%) and GO-sheet modified PVDF (62%) after 10 h of filtration. The presence of GOQD coating layer effectively inactivates E. coli and S. aureus cells, and prevents the biofilm formation on the membrane surface, producing excellent antimicrobial activity and potentially antibiofouling capability, more superior than those of previously reported two-dimensional GO sheets and one-dimensional CNTs modified membranes. The distinctive antimicrobial and antibiofouling performances could be attributed to the unique structure and uniform dispersion of GOQDs, enabling the exposure of a larger fraction of active edges and facilitating the formation of oxidation stress. Furthermore, GOQDs modified membrane possesses satisfying long-term stability and durability due to the strong covalent interaction between PVDF and GOQDs. This study opens up a new synthetic avenue in the fabrication of efficient surface-functionalized polymer membranes for potential waste water treatment and biomolecules separation.

  14. Graphene Oxide Quantum Dots Covalently Functionalized PVDF Membrane with Significantly-Enhanced Bactericidal and Antibiofouling Performances

    PubMed Central

    Zeng, Zhiping; Yu, Dingshan; He, Ziming; Liu, Jing; Xiao, Fang-Xing; Zhang, Yan; Wang, Rong; Bhattacharyya, Dibakar; Tan, Timothy Thatt Yang

    2016-01-01

    Covalent bonding of graphene oxide quantum dots (GOQDs) onto amino modified polyvinylidene fluoride (PVDF) membrane has generated a new type of nano-carbon functionalized membrane with significantly enhanced antibacterial and antibiofouling properties. A continuous filtration test using E. coli containing feedwater shows that the relative flux drop over GOQDs modified PVDF is 23%, which is significantly lower than those over pristine PVDF (86%) and GO-sheet modified PVDF (62%) after 10 h of filtration. The presence of GOQD coating layer effectively inactivates E. coli and S. aureus cells, and prevents the biofilm formation on the membrane surface, producing excellent antimicrobial activity and potentially antibiofouling capability, more superior than those of previously reported two-dimensional GO sheets and one-dimensional CNTs modified membranes. The distinctive antimicrobial and antibiofouling performances could be attributed to the unique structure and uniform dispersion of GOQDs, enabling the exposure of a larger fraction of active edges and facilitating the formation of oxidation stress. Furthermore, GOQDs modified membrane possesses satisfying long-term stability and durability due to the strong covalent interaction between PVDF and GOQDs. This study opens up a new synthetic avenue in the fabrication of efficient surface-functionalized polymer membranes for potential waste water treatment and biomolecules separation. PMID:26832603

  15. Covalent albumin microparticles as an adjuvant for production of mucosal vaccines against hepatitis B.

    PubMed

    Sitta, Danielly L A; Guilherme, Marcos R; Garcia, Francielle P; Cellet, Thelma S P; Nakamura, Celso V; Muniz, Edvani C; Rubira, Adley F

    2013-09-01

    Covalently modified albumin (BSA) microparticles were developed for potential use as an adjuvant in mucosal vaccines against hepatitis B. To synthesize consistent protein particles, a covalent approach was proposed to modify BSA. Our strategy was to bond maleic anhydride (MA) molecules to BSA structure by nucleophilic reaction for further radical cross-linking/polymerization reaction with N',N'-dimethylacrylamide (DMAAm). The presence of poly(N',N'-dimethylacrylamide) in the protein network enables the microparticles to show well-defined, homogeneous forms. Cytotoxicity tests showed that the cytotoxic concentration for 50% of VERO cells (CC50) was 216.25 ± 5.30 μg mL(-1) in 72 h of incubation. The obtained CC50 value is relatively low for an incubation time of 72 h, suggesting an acceptable biocompatibility. Assay of total protein showed that the encapsulation efficiency of the microparticles with hepatitis B surface antigen (HBsAg) was 77.7 ± 0.2%. For the reference sample, which was incubated without HBsAg, the quantity of protein was below the limit of detection. PMID:23863080

  16. Rattler Site Selectivity and Covalency Effects in Type-I Clathrates

    NASA Astrophysics Data System (ADS)

    Arčon, Denis; Zorko, Andrej; Jeglič, Peter; Xu, Jingtao; Tang, Jun; Tanabe, Yoichi; Heguri, Satoshi; Tanigaki, Katsumi

    2013-01-01

    Type-I germanium clathrates comprised of Ga/Ge tetrakaidecahedra and dodecahedra cages that host alkaline earth atoms exemplify the properties of good thermoelectrics where the guest-atom anharmonic vibrations play a major role. However, while the host lattice--guest atom interaction is essential for this class of materials it is at the same time difficult to investigate due to the random Ga/Ge site occupation in the host lattice. In the present 71Ga NMR study of Sr8Ga16Ge30 and Ba8Ga16Ge30 samples we extract different Ga crystallographic site contributions from otherwise complex NMR spectra by exploring differences in their spin--lattice relaxation rates. Such approach opens a unique possibility for a site-selective study that directly proves non-negligible interaction of the anisotropic rattling motions of endohedral Sr with Ga atoms occupying the specific 24k sites of larger tetrakaidecahedral cages. This interaction affects electron--phonon coupling and modifies the local chemical environment --- possibly even through weak covalent bonding of Sr to the cage. Our results are thus in agreement with claims that the conventional picture of purely ionic interactions between the rattling guest atoms and the cage is only approximate and that covalent effects should be taken into account in clathrates or similar thermoelectric cage materials.

  17. Chemoselective small molecules that covalently modify one lysine in a non-enzyme protein in plasma

    SciTech Connect

    Choi, Sungwook; Connelly, Stephen; Reixach, Natàlia; Wilson, Ian A.; Kelly, Jeffery W.

    2010-02-19

    A small molecule that could bind selectively to and then react chemoselectively with a non-enzyme protein in a complex biological fluid, such as blood, could have numerous practical applications. Herein, we report a family of designed stilbenes that selectively and covalently modify the prominent plasma protein transthyretin in preference to more than 4,000 other human plasma proteins. They react chemoselectively with only one of eight lysine {epsilon}-amino groups within transthyretin. The crystal structure confirms the expected binding orientation of the stilbene substructure and the anticipated conjugating amide bond. These covalent transthyretin kinetic stabilizers exhibit superior amyloid inhibition potency compared to their noncovalent counterparts, and they prevent cytotoxicity associated with amyloidogenesis. Though there are a few prodrugs that, upon metabolic activation, react with a cysteine residue inactivating a specific non-enzyme, we are unaware of designed small molecules that react with one lysine {epsilon}-amine within a specific non-enzyme protein in a complex biological fluid.

  18. K3036.58 in the μ opioid (MOP) receptor is important in conferring selectivity for covalent binding of β-funaltrexamine (β-FNA)

    PubMed Central

    DiMattio, Kelly M.; Chen, Chongguang; Shi, Lei; Liu-Chen, Lee-Yuan

    2014-01-01

    β-funaltrexamine (β-FNA) is an irreversible μ opioid (MOP) receptor antagonist and a reversible agonist of κ opioid (KOP) receptor. β-FNA binds covalently to the MOP receptor at Lys2335.39, which is conserved among opioid receptors. Molecular docking of β-FNA showed that K3036.58 in the MOP receptor and E2976.58 in the KOP receptor played distinct roles in positioning β-FNA. K3036.58E MOP receptor and E2976.58K KOP receptor mutants were generated. The mutations did not affect β-FNA affinity or efficacy. K3036.58E mutation in the MOP receptor greatly reduced covalent binding of [3H]β-FNA; however, E2976.58K did not enable the KOP receptor to bind irreversibly to β-FNA. Molecular modeling demonstrated that the ε-amino group of K3036.58 in the MOP receptor interacted with C=O of the acetate group of β-FNA to facilitate covalent bond formation with Lys2335.39. Replacement of K3036.58 with Glu in the MOP receptor resulted in repulsion between the COOH of Glu and the C=O of β-FNA and increased the distance between K2335.39 and the fumarate group, making it impossible for covalent bond formation. These findings will be helpful for design of selective non-peptide MOP receptor antagonists. PMID:25481857

  19. Real-space identification of intermolecular bonding with atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Qiu, Xiaohui

    2014-03-01

    A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms, whose formation and breaking result in chemical reactions and the production of new substances. Distinct from the covalent bond, the intermolecular interactions are often a vague concept elusive in experimental observations. Nevertheless, intermolecular interactions virtually affect all physical and chemical properties of substances in the condensed phases. The interactions between molecules, particularly the hydrogen bond, are responsible for the structural transformations and functions of biological molecules. Because most of the molecular characterization techniques are more sensitive to the covalent structures of the molecules, it remains a challenge to quantitatively study the weak interactions between molecules despite the tremendous efforts toward this goal. Here we report a real-space identification of the formation of hydrogen bonding between molecules adsorbed on metal substrate using a non-contact atomic force microscope (nc-AFM). The atomically resolved molecular structures with unprecedented details enable a precise determination of the characteristics of the hydrogen bond network, including bonding sites, orientations and lengths. The observed bond contrast was interpreted by ab initio density functional calculations that indicate the electron density contribution from the hybridized electronic state of hydrogen bond. Given the extensively discussion on the nature of hydrogen bonding and the recent redefinition by IUPAC, the observation of hydrogen bonding in real-space may be a stimulating evidence for theoretical chemistry. Meanwhile, the direct identification of local bonding configurations by nc-AFM would advance the understanding of intermolecular interactions in complex molecules with multiple active sites, offering complementary structural information essential for various applications in materials and biological sciences.

  20. Covalent functionalization and passivation of exfoliated black phosphorus via aryl diazonium chemistry.

    PubMed

    Ryder, Christopher R; Wood, Joshua D; Wells, Spencer A; Yang, Yang; Jariwala, Deep; Marks, Tobin J; Schatz, George C; Hersam, Mark C

    2016-06-01

    Functionalization of atomically thin nanomaterials enables the tailoring of their chemical, optical and electronic properties. Exfoliated black phosphorus (BP)-a layered two-dimensional semiconductor-exhibits favourable charge-carrier mobility, tunable bandgap and highly anisotropic properties, but it is chemically reactive and degrades rapidly in ambient conditions. Here we show that covalent aryl diazonium functionalization suppresses the chemical degradation of exfoliated BP even after three weeks of ambient exposure. This chemical modification scheme spontaneously forms phosphorus-carbon bonds, has a reaction rate sensitive to the aryl diazonium substituent and alters the electronic properties of exfoliated BP, ultimately yielding a strong, tunable p-type doping that simultaneously improves the field-effect transistor mobility and on/off current ratio. This chemical functionalization pathway controllably modifies the properties of exfoliated BP, and thus improves its prospects for nanoelectronic applications. PMID:27219705

  1. Covalent functionalization and passivation of exfoliated black phosphorus via aryl diazonium chemistry

    NASA Astrophysics Data System (ADS)

    Ryder, Christopher R.; Wood, Joshua D.; Wells, Spencer A.; Yang, Yang; Jariwala, Deep; Marks, Tobin J.; Schatz, George C.; Hersam, Mark C.

    2016-06-01

    Functionalization of atomically thin nanomaterials enables the tailoring of their chemical, optical and electronic properties. Exfoliated black phosphorus (BP)—a layered two-dimensional semiconductor—exhibits favourable charge-carrier mobility, tunable bandgap and highly anisotropic properties, but it is chemically reactive and degrades rapidly in ambient conditions. Here we show that covalent aryl diazonium functionalization suppresses the chemical degradation of exfoliated BP even after three weeks of ambient exposure. This chemical modification scheme spontaneously forms phosphorus–carbon bonds, has a reaction rate sensitive to the aryl diazonium substituent and alters the electronic properties of exfoliated BP, ultimately yielding a strong, tunable p-type doping that simultaneously improves the field-effect transistor mobility and on/off current ratio. This chemical functionalization pathway controllably modifies the properties of exfoliated BP, and thus improves its prospects for nanoelectronic applications.

  2. Lattice-Directed Formation of Covalent and Organometallic Molecular Wires by Terminal Alkynes on Ag Surfaces.

    PubMed

    Liu, Jing; Chen, Qiwei; Xiao, Lianghong; Shang, Jian; Zhou, Xiong; Zhang, Yajie; Wang, Yongfeng; Shao, Xiang; Li, Jianlong; Chen, Wei; Xu, Guo Qin; Tang, Hao; Zhao, Dahui; Wu, Kai

    2015-06-23

    Surface reactions of 2,5-diethynyl-1,4-bis(phenylethynyl)benzene on Ag(111), Ag(110), and Ag(100) were systematically explored and scrutinized by scanning tunneling microscopy, molecular mechanics simulations, and density functional theory calculations. On Ag(111), Glaser coupling reaction became dominant, yielding one-dimensional molecular wires formed by covalent bonds. On Ag(110) and Ag(100), however, the terminal alkynes reacted with surface metal atoms, leading to one-dimensional organometallic nanostructures. Detailed experimental and theoretical analyses revealed that such a lattice dependence of the terminal alkyne reaction at surfaces originated from the matching degree between the periodicities of the produced molecular wires and the substrate lattice structures. PMID:25990647

  3. Pironetin reacts covalently with cysteine-316 of α-tubulin to destabilize microtubule

    NASA Astrophysics Data System (ADS)

    Yang, Jianhong; Wang, Yuxi; Wang, Taijing; Jiang, Jian; Botting, Catherine H.; Liu, Huanting; Chen, Qiang; Yang, Jinliang; Naismith, James H.; Zhu, Xiaofeng; Chen, Lijuan

    2016-06-01

    Molecules that alter the normal dynamics of microtubule assembly and disassembly include many anticancer drugs in clinical use. So far all such therapeutics target β-tubulin, and structural biology has explained the basis of their action and permitted design of new drugs. However, by shifting the profile of β-tubulin isoforms, cancer cells become resistant to treatment. Compounds that bind to α-tubulin are less well characterized and unexploited. The natural product pironetin is known to bind to α-tubulin and is a potent inhibitor of microtubule polymerization. Previous reports had identified that pironetin reacts with lysine-352 residue however analogues designed on this model had much lower potency, which was difficult to explain, hindering further development. We report crystallographic and mass spectrometric data that reveal that pironetin forms a covalent bond to cysteine-316 in α-tubulin via a Michael addition reaction. These data provide a basis for the rational design of α-tubulin targeting chemotherapeutics.

  4. Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher.

    PubMed

    Reddington, Samuel C; Howarth, Mark

    2015-12-01

    SpyTag is a short peptide that forms an isopeptide bond upon encountering its protein partner SpyCatcher. This covalent peptide interaction is a simple and powerful tool for bioconjugation and extending what protein architectures are accessible. Here we review the origin and mechanism of SpyTag/SpyCatcher, focusing on recent innovative applications. Ligation of targeting-antibody with antigen provided a simple route to vaccine generation. SpyRings, from head-to-tail cyclisation, gave major enhancements in enzyme resilience. Linking multiple SpyCatchers gave dendrimers for T-cell activation or Spy networks forming hydrogels for stem cell culture. Synthetic biology applications include integrating amyloid biomaterials with living bacteria, for irreversible derivatisation of biofilms with enzymes or nanoparticles. We also discuss further opportunities to apply and enhance SpyTag/SpyCatcher technology. PMID:26517567

  5. Covalent hybridization of thiolated graphene sheet and platinum nanoparticles for electrocatalytic oxygen reduction reaction.

    PubMed

    Ahmed, Mohammad Shamsuddin; Kim, Daekun; Han, Hyoung Soon; Jeong, Haesang; Jeon, Seungwon

    2012-11-01

    A covalently bonded thiolated graphene sheet-supported platinum electrocatalyst (GOS-Pt) has synthesized for electrochemical oxygen reduction reaction (ORR) in neutral media. The catalyst's structural features are characterized by transmission electron microscopy (TEM), energy dispersive X-ray (EDX), and X-ray photoelectron spectroscopy (XPS). Its activity towards the ORR has investigated by using cyclic voltammetry (CV), rotating disk electrode (RDE), and rotating ring disk electrode (RRDE) in 0.1 mol l(-1) phosphate buffer solution (PBS) at pH 7, which is also used to assess the catalyst's kinetic parameters. On a glassy carbon electrode (GCE), the catalyst shows a significant catalytic activity, with its electrocatalysis of O2 reduction occurring via four-electron transfer reduction to H2O with minimal generation of H2O2. PMID:23421215

  6. Synthesis of Photoactivatable Analogues of Lysophosphatidic Acid and Covalent Labeling of Plasma Proteins

    PubMed Central

    Li, Zaiguo; Baker, Daniel L.; Tigyi, Gabor; Bittman, Robert

    2008-01-01

    Lysophosphatidic acid bearing a benzophenone group in either the sn-1 or sn-2 chain of an oleoyl-type ester or oleyl-type ether chain and 32P in the phosphate group were synthesized. The benzophenone moiety was introduced by selective hydroboration of the double bond of enyne 11 at low temperature, followed by Suzuki reaction with 4-bromobenzophenone. The key intermediates for the preparation of ester-linked LPA 1 and 3 were obtained in one pot by a modified DIBAL-H reduction of orthoformate intermediate 22. These probes were shown to covalently modify a single protein target in rat plasma containing albumin and several protein targets in rat plasma containing a low level of albumin. PMID:16408973

  7. Nonlinear behavior of ionically and covalently cross-linked alginate hydrogels

    NASA Astrophysics Data System (ADS)

    Hashemnejad, Seyedmeysam; Zabet, Mahla; Kundu, Santanu

    2015-03-01

    Gels deform differently under applied load and the deformation behavior is related to their network structures and environmental conditions, specifically, strength and density of crosslinking, polymer concentration, applied load, and temperature. Here, we investigate the mechanical behavior of both ionically and covalent cross-linked alginate hydrogel using large amplitude oscillatory shear (LAOS) and cavitation experiments. Ionically-bonded alginate gels were obtained by using divalent calcium. Alginate volume fraction and alginate to calcium ratio were varied to obtain gels with different mechanical properties. Chemical gels were synthesized using adipic acid dihdrazide (AAD) as a cross-linker. The non-linear rheological parameters are estimated from the stress responses to elucidate the strain softening behavior of these gels. Fracture initiation and propagation mechanism during shear rheology and cavitation experiments will be presented. Our results provide a better understanding on the deformation mechanism of alginate gel under large-deformation.

  8. Covalent organic frameworks comprising cobalt porphyrins for catalytic CO₂ reduction in water.

    PubMed

    Lin, Song; Diercks, Christian S; Zhang, Yue-Biao; Kornienko, Nikolay; Nichols, Eva M; Zhao, Yingbo; Paris, Aubrey R; Kim, Dohyung; Yang, Peidong; Yaghi, Omar M; Chang, Christopher J

    2015-09-11

    Conversion of carbon dioxide (CO2) to carbon monoxide (CO) and other value-added carbon products is an important challenge for clean energy research. Here we report modular optimization of covalent organic frameworks (COFs), in which the building units are cobalt porphyrin catalysts linked by organic struts through imine bonds, to prepare a catalytic material for aqueous electrochemical reduction of CO2 to CO. The catalysts exhibit high Faradaic efficiency (90%) and turnover numbers (up to 290,000, with initial turnover frequency of 9400 hour(-1)) at pH 7 with an overpotential of -0.55 volts, equivalent to a 26-fold improvement in activity compared with the molecular cobalt complex, with no degradation over 24 hours. X-ray absorption data reveal the influence of the COF environment on the electronic structure of the catalytic cobalt centers. PMID:26292706

  9. Stable, crystalline, porous, covalent organic frameworks as a platform for chiral organocatalysts.

    PubMed

    Xu, Hong; Gao, Jia; Jiang, Donglin

    2015-11-01

    The periodic layers and ordered nanochannels of covalent organic frameworks (COFs) make these materials viable open catalytic nanoreactors, but their low stability has precluded their practical implementation. Here we report the synthesis of a crystalline porous COF that is stable against water, strong acids and strong bases, and we demonstrate its utility as a material platform for structural design and functional development. We endowed a crystalline and porous imine-based COF with stability by incorporating methoxy groups into its pore walls to reinforce interlayer interactions. We subsequently converted the resulting achiral material into two distinct chiral organocatalysts, with the high crystallinity and porosity retained, by appending chiral centres and catalytically active sites on its channel walls. The COFs thus prepared combine catalytic activity, enantioselectivity and recyclability, which are attractive in heterogeneous organocatalysis, and were shown to promote asymmetric C-C bond formation in water under ambient conditions. PMID:26492011

  10. Stable, crystalline, porous, covalent organic frameworks as a platform for chiral organocatalysts

    NASA Astrophysics Data System (ADS)

    Xu, Hong; Gao, Jia; Jiang, Donglin

    2015-11-01

    The periodic layers and ordered nanochannels of covalent organic frameworks (COFs) make these materials viable open catalytic nanoreactors, but their low stability has precluded their practical implementation. Here we report the synthesis of a crystalline porous COF that is stable against water, strong acids and strong bases, and we demonstrate its utility as a material platform for structural design and functional development. We endowed a crystalline and porous imine-based COF with stability by incorporating methoxy groups into its pore walls to reinforce interlayer interactions. We subsequently converted the resulting achiral material into two distinct chiral organocatalysts, with the high crystallinity and porosity retained, by appending chiral centres and catalytically active sites on its channel walls. The COFs thus prepared combine catalytic activity, enantioselectivity and recyclability, which are attractive in heterogeneous organocatalysis, and were shown to promote asymmetric C-C bond formation in water under ambient conditions.

  11. Cooperative effects between tetrel bond and other σ-hole bond interactions: a comparative investigation

    NASA Astrophysics Data System (ADS)

    Esrafili, Mehdi D.; Nurazar, Roghaye; Mohammadian-Sabet, Fariba

    2015-12-01

    Covalently bonded atoms of Groups IV-VII tend to have anisotropic charge distributions, the electronic densities being less on the extensions of the bonds (σ-holes) than in the intervening regions. These σ-holes often give rise to positive electrostatic potentials through which the atom can interact attractively and highly directionally with negative sites. In this work, cooperative effects between tetrel bond and halogen/chalcogen/pnicogen bond interactions are studied in multi-component YH3M...NCX...NH3 complexes, where Y = F, CN; M = C, Si and X = Cl, SH and PH2. These effects are analysed in detail in terms of the structural, energetic, charge-transfer and electron density properties of the complexes. The nature of the σ-hole bonds is unveiled by quantum theory of atoms in molecules and natural bond orbital theory. A favourable cooperativity is found with values that range between -0.34 and -1.15 kcal/mol. Many-body decomposition of interaction energies indicate that two-body energy term is the most important source of the attraction, which its contribution accounts for 87%-96% of the total interaction energy.

  12. Covalent agonists for studying G protein-coupled receptor activation

    PubMed Central

    Weichert, Dietmar; Kruse, Andrew C.; Manglik, Aashish; Hiller, Christine; Zhang, Cheng; Hübner, Harald; Kobilka, Brian K.; Gmeiner, Peter

    2014-01-01

    Structural studies on G protein-coupled receptors (GPCRs) provide important insights into the architecture and function of these important drug targets. However, the crystallization of GPCRs in active states is particularly challenging, requiring the formation of stable and conformationally homogeneous ligand-receptor complexes. Native hormones, neurotransmitters, and synthetic agonists that bind with low affinity are ineffective at stabilizing an active state for crystallogenesis. To promote structural studies on the pharmacologically highly relevant class of aminergic GPCRs, we here present the development of covalently binding molecular tools activating Gs-, Gi-, and Gq-coupled receptors. The covalent agonists are derived from the monoamine neurotransmitters noradrenaline, dopamine, serotonin, and histamine, and they were accessed using a general and versatile synthetic strategy. We demonstrate that the tool compounds presented herein display an efficient covalent binding mode and that the respective covalent ligand-receptor complexes activate G proteins comparable to the natural neurotransmitters. A crystal structure of the β2-adrenoreceptor in complex with a covalent noradrenaline analog and a conformationally selective antibody (nanobody) verified that these agonists can be used to facilitate crystallogenesis. PMID:25006259

  13. Visualizing the mixed bonding properties of liquid boron with high-resolution x-ray Compton scattering.

    PubMed

    Okada, J T; Sit, P H-L; Watanabe, Y; Barbiellini, B; Ishikawa, T; Wang, Y J; Itou, M; Sakurai, Y; Bansil, A; Ishikawa, R; Hamaishi, M; Paradis, P-F; Kimura, K; Ishikawa, T; Nanao, S

    2015-05-01

    Bonding characteristics of liquid boron at 2500 K are studied by using high-resolution Compton scattering. An excellent agreement is found between the measurements and the corresponding Car-Parrinello molecular dynamics simulations. Covalent bond pairs are clearly shown to dominate in liquid boron along with the coexistence of diffuse pairs. Our study reveals the complex bonding pattern of liquid boron and gives insight into the unusual properties of this high-temperature liquid. PMID:25978262

  14. Robustly Engineering Thermal Conductivity of Bilayer Graphene by Interlayer Bonding

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoliang; Gao, Yufei; Chen, Yuli; Hu, Ming

    2016-02-01

    Graphene and its bilayer structure are the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. Their realistic applications in emerging nanoelectronics usually call for thermal transport manipulation in a controllable and precise manner. In this paper we systematically studied the effect of interlayer covalent bonding, in particular different interlay bonding arrangement, on the thermal conductivity of bilayer graphene using equilibrium molecular dynamics simulations. It is revealed that, the thermal conductivity of randomly bonded bilayer graphene decreases monotonically with the increase of interlayer bonding density, however, for the regularly bonded bilayer graphene structure the thermal conductivity possesses unexpectedly non-monotonic dependence on the interlayer bonding density. The results suggest that the thermal conductivity of bilayer graphene depends not only on the interlayer bonding density, but also on the detailed topological configuration of the interlayer bonding. The underlying mechanism for this abnormal phenomenon is identified by means of phonon spectral energy density, participation ratio and mode weight factor analysis. The large tunability of thermal conductivity of bilayer graphene through rational interlayer bonding arrangement paves the way to achieve other desired properties for potential nanoelectronics applications involving graphene layers.

  15. Robustly Engineering Thermal Conductivity of Bilayer Graphene by Interlayer Bonding

    PubMed Central

    Zhang, Xiaoliang; Gao, Yufei; Chen, Yuli; Hu, Ming

    2016-01-01

    Graphene and its bilayer structure are the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. Their realistic applications in emerging nanoelectronics usually call for thermal transport manipulation in a controllable and precise manner. In this paper we systematically studied the effect of interlayer covalent bonding, in particular different interlay bonding arrangement, on the thermal conductivity of bilayer graphene using equilibrium molecular dynamics simulations. It is revealed that, the thermal conductivity of randomly bonded bilayer graphene decreases monotonically with the increase of interlayer bonding density, however, for the regularly bonded bilayer graphene structure the thermal conductivity possesses unexpectedly non-monotonic dependence on the interlayer bonding density. The results suggest that the thermal conductivity of bilayer graphene depends not only on the interlayer bonding density, but also on the detailed topological configuration of the interlayer bonding. The underlying mechanism for this abnormal phenomenon is identified by means of phonon spectral energy density, participation ratio and mode weight factor analysis. The large tunability of thermal conductivity of bilayer graphene through rational interlayer bonding arrangement paves the way to achieve other desired properties for potential nanoelectronics applications involving graphene layers. PMID:26911859

  16. The varying nature of fluorine oxygen bonds

    NASA Astrophysics Data System (ADS)

    Julia, Timothy J. Lee; Rice Christopher, E.; Dateo, E.

    The singles and doubles coupled cluster method that includes a per turbational estimate of the effects of connected triple excitations CCSD T together with a triple zeta double polarized TZ2P one particle basis set is used to determine the geometries harmonic frequencies infrared intensities and dipole moments of HOF F O HOOF FOOF ClOOF Agreement with experiment is very good with the exception that the currently accepted experimental assignment of the symmetric and antisymmetric O F stretches in FOOF is shown to be reversed and to be consistent with an earlier experimental study Very accurate heats of formation of HOOF FOOF and ClOOF are also computed using the CCSD T method in conjunction with large atomic natural orbital basis sets The F O bond distances quadratic force constants bond energies and fluorine and oxygen atomic charges from the above five molecules and six previously studied molecules FONO trans FONO cis FONO FOCl FOBr and FON are compared and used to deduce a simple model of F O bonding The unusual relationship between the F O bond distance and quadratic force constant shows that F O bonding is a function of at least three effects which are degree of covalent character degree of ionic character and extent of lone electron pair repulsions All of the data are qualitatively consistent with this simple model The bonding in cis FONO is even more complicated involving also dispersion interactions between fluorine and the terminal oxygen It is suggested that the general importance of lone pair repulsions in F O bonding and the additional importance of intra molecular dispersion interactions explains why many density functionals have difficulty in describing the geometry of cis FONO

  17. Hydrogen bonding mediated orthogonal and reversible self-assembly of porphyrin sensitizers onto TiO2 nanoparticles.

    PubMed

    Zeininger, Lukas; Lodermeyer, Fabian; Costa, Ruben D; Guldi, Dirk M; Hirsch, Andreas

    2016-07-01

    We report on the orthogonal, highly directional and reversible self-assembly of porphyrins onto TiO2 nanoparticles by means of hydrogen bonding interactions. Unifying the stable covalent surface attachment of tailored, synthesized Hamilton receptors with the advantages of a non-covalent supramolecular immobilization of porphyrin cyanurates resulted in a redox- and photo-active nanohybrid. The latter was successfully implemented into a new type of supramolecular dye-sensitized solar cells. PMID:27346702

  18. On the similarity of the bonding in NiS and NiO

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.

    1985-01-01

    The bonding in NiS is found to be quite similar to that in NiO, having an ionic contribution arising from the donation of the Ni 4s electron to the S atom and a covalent component arising from bonds between the Ni 3d and the S 3p. The one-electron d bonds are found to be of equal strength for NiO and NiS, but the two-electron d bonds are weaker for NiS.

  19. Mass Spectrometric Studies of Non-Covalent Binding Interactions Between Metallointercalators and DNA

    NASA Astrophysics Data System (ADS)

    Urathamakul, Thitima; Talib, Jihan; Beck, Jennifer L.; Ralph, Stephen F.

    Over the past 2 decades there has been increasing interest in metal complexes that bind non-covalently to DNA, driven in part by a host of potential applications for molecules that can accomplish this task with high affinity and selectivity. As a result many workers have used a wide variety of experimental techniques, several of which are discussed in other chapters of this book, to unravel the details of the precise intermolecular interactions involved. Here we discuss one of the most recent additions to the armory of techniques used by chemists to interrogate metal complex/DNA interactions. For the majority of its existence mass spectrometry (MS) has proven to be of enormous advantage to chemists by virtue of its ability to provide the molecular weights of compounds as well as structural information via fragmentation patterns. However, the high energies associated with many earlier MS techniques which result in fragmentation of covalent bonds, prevent its application for studying weaker intermolecular interactions. The advent of soft ionisation methods such as matrix assisted laser desorption ionisation (MALDI) and electrospray ionisation (ESI) has revolutionised mass spectrometric analysis of biomolecules, by allowing these normally fragile molecules to be introduced into the gas phase for analysis with minimal, if any, fragmentation. It was then recognised that ESI-MS, in particular, might be suitable for investigating non-covalent interactions between small molecules and either proteins or nucleic acids. This was confirmed by a number of early studies involving organic intercalators and minor groove binding ligands, prompting our interest in evaluating ESI-MS as a tool for studying non-covalent interactions between metal complexes and DNA. This chapter contains a discussion of the basic principles behind ESI-MS that enable it to introduce representative samples of solutions containing metal complexes and DNA into the gas phase for analysis. This will be

  20. Chemical bonding in view of electron charge density and kinetic energy density descriptors.

    PubMed

    Jacobsen, Heiko

    2009-05-01

    Stalke's dilemma, stating that different chemical interpretations are obtained when one and the same density is interpreted either by means of natural bond orbital (NBO) and subsequent natural resonance theory (NRT) application or by the quantum theory of atoms in molecules (QTAIM), is reinvestigated. It is shown that within the framework of QTAIM, the question as to whether for a given molecule two atoms are bonded or not is only meaningful in the context of a well-defined reference geometry. The localized-orbital-locator (LOL) is applied to map out patterns in covalent bonding interaction, and produces results that are consistent for a variety of reference geometries. Furthermore, LOL interpretations are in accord with NBO/NRT, and assist in an interpretation in terms of covalent bonding. PMID:19090572

  1. Covalent functionalization of monolayered transition metal dichalcogenides by phase engineering.

    PubMed

    Voiry, Damien; Goswami, Anandarup; Kappera, Rajesh; e Silva, Cecilia de Carvalho Castro; Kaplan, Daniel; Fujita, Takeshi; Chen, Mingwei; Asefa, Tewodros; Chhowalla, Manish

    2015-01-01

    Chemical functionalization of low-dimensional materials such as nanotubes, nanowires and graphene leads to profound changes in their properties and is essential for solubilizing them in common solvents. Covalent attachment of functional groups is generally achieved at defect sites, which facilitate electron transfer. Here, we describe a simple and general method for covalent functionalization of two-dimensional transition metal dichalcogenide nanosheets (MoS₂, WS₂ and MoSe₂), which does not rely on defect engineering. The functionalization reaction is instead facilitated by electron transfer between the electron-rich metallic 1T phase and an organohalide reactant, resulting in functional groups that are covalently attached to the chalcogen atoms of the transition metal dichalcogenide. The attachment of functional groups leads to dramatic changes in the optoelectronic properties of the material. For example, we show that it renders the metallic 1T phase semiconducting, and gives it strong and tunable photoluminescence and gate modulation in field-effect transistors. PMID:25515889

  2. Fluorescence anisotropy metrology of electrostatically and covalently labelled silica nanoparticles

    NASA Astrophysics Data System (ADS)

    Yip, Philip; Karolin, Jan; Birch, David J. S.

    2012-08-01

    We compare determining the size of silica nanoparticles using the time-resolved fluorescence anisotropy decay of dye molecules when electrostatically and covalently bound to stable silica nanoparticles. Covalent labelling is shown to offer advantages by simplifying the dye rotational kinetics and the appropriateness of various kinetic models is discussed. Silica nanoparticles produced using Stöber synthesis of tetraethylorthosilicate (TEOS) are found to be controllable between ˜3.1 and 3.8 nm radius by adjusting the relative water:TEOS concentration. Covalent labelling with fluorescein 5(6)-isothiocyanate (FITC) bound to (3-aminopropyl) trimethoxysilane (FITC-APS) predicts a larger particle than electrostatically labelling with rhodamine 6G. The difference is attributed to the presence of an additional depolarization mechanism to Brownian rotation of the nanoparticle and dye wobbling with electrostatic labelling in the form of dye diffusion on the surface of the nanoparticle.

  3. Electronic properties of two-dimensional covalent organic frameworks.

    PubMed

    Zhu, P; Meunier, V

    2012-12-28

    The electronic properties of a number of two-dimensional covalent organic frameworks are studied using a combination of density functional theory and quasiparticle theory calculations. The effect of composition and system size on the electronic band gap is systematically considered for a series of systems, using van der Waals corrected density functional theory calculations to determine the effect of a graphene substrate on deposited covalent frameworks. We predict that covalent organic frameworks' (COFs') electronic properties, such as their band gap can be fine tuned by appropriate modifications of their structures, specifically by increasing organic chain-links in the framework. The effect of strain on the electronic properties is also studied. The graphene substrate is shown to not significantly alter the properties of COFs, thereby indicating the robustness of COFs' intrinsic properties for practical applications. PMID:23277948

  4. Electronic properties of two-dimensional covalent organic frameworks

    NASA Astrophysics Data System (ADS)

    Zhu, P.; Meunier, V.

    2012-12-01

    The electronic properties of a number of two-dimensional covalent organic frameworks are studied using a combination of density functional theory and quasiparticle theory calculations. The effect of composition and system size on the electronic band gap is systematically considered for a series of systems, using van der Waals corrected density functional theory calculations to determine the effect of a graphene substrate on deposited covalent frameworks. We predict that covalent organic frameworks' (COFs') electronic properties, such as their band gap can be fine tuned by appropriate modifications of their structures, specifically by increasing organic chain-links in the framework. The effect of strain on the electronic properties is also studied. The graphene substrate is shown to not significantly alter the properties of COFs, thereby indicating the robustness of COFs' intrinsic properties for practical applications.

  5. Materials Data on K2RuCl6 (SG:225) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-02-09

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  6. Materials Data on RuCl3 (SG:193) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-02-09

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  7. The unexpected non-monotonic inter-layer bonding dependence of the thermal conductivity of bilayered boron nitride

    NASA Astrophysics Data System (ADS)

    Gao, Yufei; Zhang, Xiaoliang; Jing, Yuhang; Hu, Ming

    2015-04-01

    Hexagonal boron nitride (BN) and its bilayer form are very fascinating two-dimensional materials that have attracted tremendous interest recently. Their realistic applications in emerging nanoelectronics usually quest for manipulating the thermal transport properties in a precise manner. Using nonequilibrium molecular dynamics simulations, we herein studied the effect of inter-layer covalent bonding on the thermal conductivity of bilayered BN. We found that the in-plane thermal conductivity of bilayered BN, which can be largely tuned by introducing covalent bonding between the two BN layers, depends not only on the inter-layer bonding density, but also on the detailed topological configuration of the inter-layer bonds. For randomly distributed inter-layer bonding the thermal conductivity of bilayered BN decreases monotonically with inter-layer bonding density, the same behavior already found for bilayered graphene. However, for regularly arranged inter-layer bonding the thermal conductivity of bilayered BN surprisingly possesses a non-monotonic dependence on the inter-layer bonding density. This non-intuitive non-monotonic dependence is further explained by performing spectral energy density analysis, where the peak and valley values of the thermal conductivity are governed by different mechanisms. These results suggest the application of inter-layer covalent bonding in designing nanoscale devices with precisely tunable thermal conductivities.

  8. Covalent and non-covalent curcumin loading in acid-responsive polymeric micellar nanocarriers

    NASA Astrophysics Data System (ADS)

    Gao, Min; Chen, Chao; Fan, Aiping; Zhang, Ju; Kong, Deling; Wang, Zheng; Zhao, Yanjun

    2015-07-01

    Poor aqueous solubility, potential degradation, rapid metabolism and elimination lead to low bioavailability of pleiotropic impotent curcumin. Herein, we report two types of acid-responsive polymeric micelles where curcumin was encapsulated via both covalent and non-covalent modes for enhanced loading capacity and on-demand release. Biodegradable methoxy poly(ethylene glycol)-poly(lactic acid) copolymer (mPEG-PLA) was conjugated with curcumin via a hydrazone linker, generating two conjugates differing in architecture (single-tail versus double-tail) and free curcumin was encapsulated therein. The two micelles exhibited similar hydrodynamic size at 95 ± 3 nm (single-tail) and 96 ± 3 nm (double-tail), but their loading capacities differed significantly at 15.0 ± 0.5% (w/w) (single-tail) and 4.8 ± 0.5% (w/w) (double-tail). Under acidic sink conditions (pH 5.0 and 6.0), curcumin displayed a faster release from the single-tail nanocarrier, which was correlated to a low IC50 of 14.7 ± 1.6 (μg mL-1) compared to the value of double-tail micelle (24.9 ± 1.3 μg mL-1) in HeLa cells. The confocal imaging and flow cytometry analysis demonstrated a superior capability of single-tail micelle for intracellular curcumin delivery, which was a consequence of the higher loading capacity and lower degree of mPEG surface coverage. In conclusion, the dual loading mode is an effective means to increase the drug content in the micellar nanocarriers whose delivery efficiency is highly dependent on its polymer-drug conjugate architecture. This strategy offers an alternative nanoplatform for intracellularly delivering impotent hydrophobic agents (i.e. curcumin) in an efficient stimuli-triggered way, which is valuable for the enhancement of curcumin’s efficacy in managing a diverse range of disorders.

  9. Covalency hinders AnO2(H2O)(+)→ AnO(OH)2(+) isomerisation (An = Pa-Pu).

    PubMed

    Kaltsoyannis, Nikolas

    2016-02-21

    The enthalpies of the reactions AnO2(+)→ AnO(+) + O and AnO2(+) + H2O → AnO2(H2O)(+), and those of the isomerisation of the latter to AnO(OH)2(+), have been calculated for An = Pa-Pu. The data match previous experimental and computational values very closely, and the computed enthalpy for the isomerisation of PaO2(H2O)(+) to PaO(OH)2(+), requested by the authors of Inorg. Chem., 2015, 54, 7474, is found to be 0.8 kJ mol(-1). The NPA, NBO and QTAIM approaches are used to probe covalency in the An-Oyl bond of AnO2(H2O)(+), and all metrics agree that these bonds become increasingly covalent as the 5f series is crossed, providing rationalisation for the increasingly endothermic isomerisation reactions. QTAIM analysis indicates that the An=O and An-OH bonds in the oxide hydroxide isomers also become increasingly covalent as the 5f series is crossed. PMID:26781751

  10. Using Multiple Bonding Strategies.

    PubMed

    Larson, Thomas D

    2015-01-01

    There are many ways to bond to tooth structure, some micro-mechanical some chemical, some a combination. Different dentin bonding materials have different bonding strengths to differently prepared surfaces, and because of differences in their nature, different areas of tooth structure present peculiar bonding challenges. This paper will review a variety of material types, elucidating their particular bonding strengths and commenting on improved bonding strategies to increase durability, strength, and favorable pulpal response. In this discussion, resin dentin bonding systems, glass ionomers, Gluma, resin cements, and newer combined products will br reviewed. PMID:26485903

  11. Stability and electronic properties of 3D covalent organic frameworks.

    PubMed

    Lukose, Binit; Kuc, Agnieszka; Heine, Thomas

    2013-05-01

    Covalent organic frameworks (COFs) are a class of covalently linked crystalline nanoporous materials, versatile for nanoelectronic and storage applications. 3D COFs, in particular, have very large pores and low mass densities. Extensive theoretical studies of their energetic and mechanical stability, as well as their electronic properties, have been carried out for all known 3D COFs. COFs are energetically stable and their bulk modulus ranges from 3 to 20 GPa. Electronically, all COFs are semiconductors with band gaps corresponding to the HOMO-LUMO gaps of the building units. PMID:23212235

  12. On the road towards electroactive covalent organic frameworks.

    PubMed

    Dogru, Mirjam; Bein, Thomas

    2014-05-30

    Covalent organic frameworks (COFs) are a novel class of porous crystalline organic materials assembled from molecular building blocks. The construction principles of these materials allow for the design of precisely controllable structures since their chemical and physical properties can be easily tuned through the selection of the building blocks and the linkage motif. Their extraordinary and versatile properties impart functionality that is of great interest in areas such as gas storage, separation, catalysis and optoelectronics. This feature article discusses key aspects of the design of covalent organic frameworks with a focus on electroactive COFs for potential optoelectronic and photovoltaic applications. PMID:24667827

  13. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures.

    PubMed

    Herrmann, Andreas

    2014-03-21

    Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems. PMID:24296754

  14. Construction of Covalent Organic Nanotubes by Light-Induced Cross-Linking of Diacetylene-Based Helical Polymers.

    PubMed

    Maeda, Kaho; Hong, Liu; Nishihara, Taishi; Nakanishi, Yusuke; Miyauchi, Yuhei; Kitaura, Ryo; Ousaka, Naoki; Yashima, Eiji; Ito, Hideto; Itami, Kenichiro

    2016-08-31

    Organic nanotubes (ONTs) are tubular nanostructures composed of small molecules or macromolecules that have found various applications including ion sensor/channels, gas absorption, and photovoltaics. While most ONTs are constructed by self-assembly processes based on weak noncovalent interactions, this unique property gives rise to the inherent instability of their tubular structures. Herein, we report a simple "helix-to-tube" strategy to construct robust, covalent ONTs from easily accessible poly(m-phenylene diethynylene)s (poly-PDEs) possessing chiral amide side chains that can adopt a helical conformation through hydrogen-bonding interactions. The helically folded poly-PDEs subsequently undergo light-induced cross-linking at longitudinally aligned 1,3-butadiyne moieties across the whole helix to form covalent tubes (ONTs) both in solution and solid phases. The structures of poly-PDEs and covalent ONTs were characterized by spectroscopic analyses, diffraction analysis, and microscopic analyses. We envisage that this simple yet powerful "helix-to-tube" strategy will generate a range of ONT-based materials by introducing functional moieties into a monomer. PMID:27486790

  15. Non-covalent interactions between ATP and RecA DNA-repairing proteins: DFT and semiempirical calculations

    NASA Astrophysics Data System (ADS)

    Rodriguez, Jorge

    2015-03-01

    The role of Bacterial RecA in the structural maintenance of genomes and the genetic information they carry has been established. In particular, the RecA DNA-repairing protein from D. Radiodurans, a radiation-resistant bacteria, is crucial for the repair of double strand breaks (DSBs). We have performed semi-empirical free-energy calculations and QM/MM calculations to study their non-covalent interactions with ATP and ADP. Such studies provide insight into the mechanisms of ATP/ADP --> RecA energy transfer and, therefore, about specific functional uses of incoming energy for DNA repairing mechanisms. We present a detailed analysis of the non-covalent interactions which minimize the interaction Gibbs free energies leading to the most stable non-covalent binding sites. Van der Waal, hydrogen bonding and electrostatic interactions has been quantified which provides a detailed insight into the mechanisms of ATP-RecA interaction. Further, possible chemical interactions and functional roles of RecA proteins are explored based on the previously mentioned studies. Acknowledgements: Funded, in part, by DTRA award 106339 (JHR). Dr. Mark C. Palenik and Mrs. Lora Beard are gratefully acknowledged Supported in part by DTRA Award 106339.

  16. Revealing non-covalent interactions in molecular crystals through their experimental electron densities.

    PubMed

    Saleh, Gabriele; Gatti, Carlo; Lo Presti, Leonardo; Contreras-García, Julia

    2012-11-26

    Non-covalent interactions (NCI) define the rules underlying crystallisation, self-assembly and drug-receptor docking processes. A novel NCI descriptor, based on the reduced electron density gradient (RDG), that enables easy visualisation of the zones of the electron density (ED) involved in either the supposedly attractive (dispersive, hydrogen bonding) or allegedly repulsive (steric) intermolecular interactions, was recently developed by Johnson et al. Here, it is applied for the first time to EDs derived from single-crystal X-ray diffraction data. A computer code handling both experimental and ab initio EDs in the RDG-NCI perspective was purposely written. Three cases spanning a wide range of NCI classes were analysed: 1) benzene, as the prototype of stacking and weak CH···π interactions; 2) austdiol, a heavily functionalised fungal metabolite with a complex hydrogen-bonding network; 3) two polymorphs of the heteroatom-rich anti-ulcer drug famotidine, with van der Waals and hydrogen-bond contacts between N- and S-containing groups. Even when applied to experimental EDs, the RDG index is a valuable NCI descriptor that can highlight their different nature and strength and provide results of comparable quality to ab initio approaches. Combining the RDG-NCI study with Bader's ED approach was a key step forward, as the RDG index can depict inherently delocalised interactions in terms of extended and flat RDG isosurfaces, in contrast to the bond path analysis, which is often bounded to a too localised and possibly discontinuous (yes/no) description. Conversely, the topological tool can provide quantitative insight into the simple, qualitative NCI picture offered by the RDG index. Hopefully, this study may pave the way to a deeper analysis of weak interactions in proteins using structural and ED information from experiment. PMID:23038653

  17. Biofriendly bonding processes for nanoporous implantable SU-8 microcapsules for encapsulated cell therapy

    PubMed Central

    Nemani, Krishnamurthy; Kwon, Joonbum; Trivedi, Krutarth; Hu, Walter; Lee, Jeong-Bong; Gimi, Barjor

    2013-01-01

    Mechanically robust, cell encapsulating microdevices fabricated using photolithographic methods can lead to more efficient immunoisolation in comparison to cell encapsulating hydrogels. There is a need to develop adhesive bonding methods which can seal such microdevices under physiologically friendly conditions. We report the bonding of SU-8 based substrates through (i) magnetic self assembly, (ii) using medical grade photocured adhesive and (iii) moisture and photochemical cured polymerization. Magnetic self-assembly, carried out in biofriendly aqueous buffers, provides weak bonding not suitable for long term applications. Moisture cured bonding of covalently modified SU-8 substrates, based on silanol condensation, resulted in weak and inconsistent bonding. Photocured bonding using a medical grade adhesive and of acrylate modified substrates provided stable bonding. Of the methods evaluated, photo-cured adhesion provided the strongest and most stable adhesion. PMID:21970658

  18. Bond energy effects on strength, cooperativity and robustness of molecular structures.

    PubMed

    Chou, Chia-Ching; Buehler, Markus J

    2011-10-01

    A fundamental challenge in engineering biologically inspired materials and systems is the identification of molecular structures that define fundamental building blocks. Here, we report a systematic study of the effect of the energy of chemical bonds on the mechanical properties of molecular structures, specifically, their strength and robustness. By considering a simple model system of an assembly of bonds in a cluster, we demonstrate that weak bonding, as found for example in H-bonds, results in a highly cooperative behaviour where clusters of bonds operate synergistically to form relatively strong molecular clusters. The cooperative effect of bonding results in an enhanced robustness since the drop of strength owing to the loss of a bond in a larger cluster only results in a marginal reduction of the strength. Strong bonding, as found in covalent interactions such as disulphide bonds or in the backbone of proteins, results in a larger mechanical strength. However, the ability for bonds to interact cooperatively is lost, and, as a result, the overall robustness is lower since the mechanical strength hinges on individual bonds rather than a cluster of bonds. The systematic analysis presented here provides general insight into the interplay of bond energy, robustness and other geometric parameters such as bond spacing. We conclude our analysis with a correlation of structural data of natural protein structures, which confirms the conclusions derived from our study. PMID:23050078

  19. Alternative pathways of disulfide bond formation yield secretion-competent, stable and functional immunoglobulins

    PubMed Central

    Elkabetz, Yechiel; Ofir, Ayala; Argon, Yair; Bar-Nun, Shoshana

    2009-01-01

    Disulfide bonds within and between proteins are responsible for stabilizing folding and covalent assembly. They are thought to form by an obligatory pathway that leads to a single native structure compatible with secretion. We have previously demonstrated that the intradomain disulfide in the CH1 domain of the Ig γ2b heavy chains was dispensable for secretion (Elkabetz et al., 2005). Here we show that the heavy chain-light chain interchain disulfide is also dispensable. γ2b with mutated Cys128, which normally disulfide bonds with the light chain, still assembled with λI light chain into a secretion-competent, tetrameric IgG2b. This assembly comprised of a covalent homo-dimer of mutant heavy chains (C128S2) accompanied non-covalently by a covalent homo-dimer of light chains (λ2). The λ2 homo-dimer formed only upon association with C128S2, through disulfide bonding of the two “orphan” heavy chain-interacting Cys214 in λI. The unique Ig tetramer was secreted efficiently as a functional antibody whose antigen binding capacity resembled that of normal IgG2b. Therefore, disulfide bonding of Ig manifests considerable plasticity and can generate more than one functional structure that is considered native by the cellular quality control system. PMID:18692901

  20. The Bondons: The Quantum Particles of the Chemical Bond

    PubMed Central

    Putz, Mihai V.

    2010-01-01

    By employing the combined Bohmian quantum formalism with the U(1) and SU(2) gauge transformations of the non-relativistic wave-function and the relativistic spinor, within the Schrödinger and Dirac quantum pictures of electron motions, the existence of the chemical field is revealed along the associate bondon particle B̶ characterized by its mass (mB̶), velocity (vB̶), charge (eB̶), and life-time (tB̶). This is quantized either in ground or excited states of the chemical bond in terms of reduced Planck constant ħ, the bond energy Ebond and length Xbond, respectively. The mass-velocity-charge-time quaternion properties of bondons’ particles were used in discussing various paradigmatic types of chemical bond towards assessing their covalent, multiple bonding, metallic and ionic features. The bondonic picture was completed by discussing the relativistic charge and life-time (the actual zitterbewegung) problem, i.e., showing that the bondon equals the benchmark electronic charge through moving with almost light velocity. It carries negligible, although non-zero, mass in special bonding conditions and towards observable femtosecond life-time as the bonding length increases in the nanosystems and bonding energy decreases according with the bonding length-energy relationship Ebond[kcal/mol]×Xbond[A0]=182019, providing this way the predictive framework in which the B̶ particle may be observed. Finally, its role in establishing the virtual states in Raman scattering was also established. PMID:21151435