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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. Facile O-H bond activation in alcohols by [Cp*RuCl((I)Pr2PSX)] (X = pyridyl, quinolyl): a route to ruthenium(IV) hydrido(alkoxo) derivatives.

    PubMed

    Jiménez-Tenorio, Manuel; Puerta, M Carmen; Valerga, Pedro

    2011-12-19

    The complexes [Cp*RuCl((i)Pr(2)PSX)] (X = pyridyl, quinolyl) react directly with alcohols ROH (R = Me, Et, (i)Pr, (n)Pr) and NaBPh(4), affording the novel cationic hydrido(alkoxo) derivatives [Cp*RuH(OR)((i)Pr(2)PSX)][BPh(4)]. These ruthenium(IV) compounds result from the formal oxidative addition of the alcohol to the 16-electron fragment {[Cp*Ru((i)Pr(2)PSX)](+)}, generated in situ upon chloride dissociation. The hydrido(alkoxo) complexes are reversibly deprotonated by a strong base such as KOBu(t), yielding the neutral alkoxides [Cp*Ru(OR)((i)Pr(2)PSX)], which are remarkably stable toward β elimination and do not generate the corresponding hydrides. The hydrido(alkoxo) complexes undergo a slow electron-transfer process, releasing H(2) and generating the dinuclear ruthenium(III) complex [{Cp*Ru(κ(2)-N,S-μ S-SC(5)H(4)N)}(2)][BPh(4)](2). In this species, the Ru-Ru separation is very short and consistent with what is expected for a Ru≡Ru triple bond. PMID:22087635

  4. Semiempirical model of covalent bonding in silicon

    NASA Astrophysics Data System (ADS)

    Ackland, Graeme

    1989-11-01

    A simple, analytic model for energetics in silicon is presented. The model incorporates ionic core repulsions written as a pairwise repulsion between ions, and a cohesive energy written as a sum over valence-electron energies. The electrons form covalent bonds represented by pair potentials, and other interactions by a simple repulsive pair potential. The resulting model has a simpler interpretation and fewer parameters than previously published empirical potentials, yet yields structural results in better agreement with density-functional calculations and experimental observations. This shows that by representing cohesion in silicon explicitly in terms of electron bonds, and not by effective interactions between ions as has been done previously, a simple mathematical model can give a better insight into the physics of covalent bonding.

  5. 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.

  6. 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).

  7. 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.

  8. ARPES study of the Kitaev Candidate RuCl3

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaoqing; Li, Haoxiang; Waugh, Justin; Parham, Stephen; Kim, Heung-Sik; Kee, Hae-Young; Sears, Jennifer; Kim, Young-June; Dessau, Daniel

    RuCl3 has been identified as a spin-orbital-assisted Mott insulator with possible Kitaev magnetic orders at low temperature by X-ray absorption, susceptibility, specific heat and Raman scattering. Here we report high resolution ARPES spectroscopy measurements on single crystal RuCl3, and compare it with DFT calculations with and without magnetic order. Furthermore, the possible spin-orbital-assisted Mott transition is investigated through electron doping

  9. Two Dimensional Antiferromagnetic Chern Insulator: NiRuCl6

    NASA Astrophysics Data System (ADS)

    Zhou, P.; Sun, C. Q.; Sun, L. Z.

    2016-10-01

    Based on DFT and Berry curvature calculations, we predict that quantum anomalous hall effect (QAHE) can be realized in two dimensional anti-ferromagnetic (AFM) NiRuCl6 with zero net magnetic moment. By tuning spin-orbits coupling (SOC), we find that the topological properties of NiRuCl6 come from its energy band reversal. The results indicate that NiRuCl6 behaves as AFM Chern insulator and its spin-polarized electronic structure and strong spin-orbits coupling (SOC) are the origin of QAHE. Considering the compatibility between AFM and insulator, AFM Chern insulator is more suitable to realize high temperature QAHE because generally Neel temperature of AFM systems is more easily improved than Curie temperature of ferromagnetic (FM) systems. Due to the different magnetic coupling mechanism between FM and AFM Chern insulator, AFM Chern insulator provides a new way to archive high temperature QAHE in experiments.

  10. Two-center two-electron covalent bonds with deficient bonding densities.

    PubMed

    Yang, Yang

    2012-10-18

    Electron-deficient covalent bonds are a type of covalent bonds without electron accumulation at their bonding regions. Compared with normal covalent bonds, they are quite sensitive to chemical environments. Electron-deficient and normal covalent bonds are not isolated from each other. An electron-deficient bond may change to a normal one upon the change of substituting groups. Neither bond elongation nor atom electronegativity is directly related to the electron deficiency in an electron-deficient bond. Atoms in molecules (AIM) analyses suggest that electron-deficient bonds are characterized by positive Laplacians and small ρ(BCP) values. The positive Laplacian is caused by insignificant electron accumulation perpendicular to the bond path. On the basis of electron localization function (ELF) descriptors, electron-deficient bonds have small basin populations, low η values and high relative fluctuations. There may be one or two bond basins for an electron-deficient bond. In addition, such a bond may correlate with two more valence basins close to the two participating atoms. Electron-deficient bonds are usually weak and long. This is consistent with the low s characters in their natural bond orbitals (NBOs).

  11. 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.

  12. 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

  13. 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

  14. Covalent bonding: the fundamental role of the kinetic energy.

    PubMed

    Bacskay, George B; Nordholm, Sture

    2013-08-22

    This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity. PMID:23859401

  15. How cellulose stretches: synergism between covalent and hydrogen bonding.

    PubMed

    Altaner, Clemens M; Thomas, Lynne H; Fernandes, Anwesha N; Jarvis, Michael C

    2014-03-10

    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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. Orbital reconstruction and covalent bonding at an oxide interface.

    SciTech Connect

    Chakhalian, J.; Freeland, J. W.; Habermeier, H.-U.; Cristiani, G.; Khaliullin, G.; van Veenendaal, M.; Keimer, B.; X-Ray Science Division; Univ. of Arkansas; Max Planck Inst.for Solid State Research; Northern Illinois Univ.

    2007-11-16

    Orbital reconstructions and covalent bonding must be considered as important factors in the rational design of oxide heterostructures with engineered physical properties. We have investigated the interface between high-temperature superconducting (Y,Ca)Ba{sub 2}Cu{sub 3}O{sub 7} and metallic La{sub 0.67}Ca{sub 0.33}MnO{sub 3} by resonant x-ray spectroscopy. A charge of about -0.2 electron is transferred from Mn to Cu ions across the interface and induces a major reconstruction of the orbital occupation and orbital symmetry in the interfacial CuO{sub 2} layers. In particular, the Cu d{sub 3z{sup 2}-r{sup 2}} orbital, which is fully occupied and electronically inactive in the bulk, is partially occupied at the interface. Supported by exact-diagonalization calculations, these data indicate the formation of a strong chemical bond between Cu and Mn atoms across the interface. Orbital reconstructions and associated covalent bonding are thus important factors in determining the physical properties of oxide heterostructures.

  2. 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.

  3. Evidence of Significant Covalent Bonding in Au(CN)2-

    SciTech Connect

    Wang, Xue B.; wang, Yi-Lei; Yang, Jie; Xing, Xiaopeng; Li, Jun; Wang, Lai S.

    2009-11-18

    There have been intense recent interests in the homogeneous catalytic chemistry of Au(I) complexes.1 Among the Au(I) molecules, the Au(CN)2- ion is the most stable and has been widely used in gold extraction back to ancient times. Although AuCN in the condensed phase has been studied, including solution phase vibrational spectroscopy2 and crystal structures,3 the free AuCN molecule has been studied only very recently by microwave spectroscopy.4 The important Au(CN)2- complex has not been observed and studied in the gas phase. Because of the relativistic effects,5 Au-containing molecules exhibit distinctly different properties among the coinage elements. To elucidate the nature of the Au-ligand binding, high-level ab initio calculations are needed due to the complicated electron correlation and relativistic effects.6-8 The structure and bonding of the AuCN molecule were first examined computationally by Frenking and co-workers.7 Recent high-precision calculations by Pyykkö and co-workers suggest multiple-bond characters between Au-C in AuCN because the Au-C bond length is only slightly longer than the sum of the triple bond covalent radii.

  4. 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…

  5. Highly covalent ferric-thiolate bonds exhibit surprisingly low mechanical stability.

    PubMed

    Zheng, Peng; Li, Hongbin

    2011-05-01

    Depending on their nature, different chemical bonds show vastly different stability with covalent bonds being the most stable ones that rupture at forces above nanonewton. Studies have revealed that ferric-thiolate bonds are highly covalent and are conceived to be of high mechanical stability. Here, we used single molecule force spectroscopy techniques to directly determine the mechanical strength of such highly covalent ferric-thiolate bonds in rubredoxin. We observed that the ferric-thiolate bond ruptures at surprisingly low forces of ∼200 pN, significantly lower than that of typical covalent bonds, such as C-Si, S-S, and Au-thiolate bonds, which typically ruptures at >1.5 nN. And the mechanical strength of Fe-thiolate bonds is observed to correlate with the covalency of the bonds. Our results indicated that highly covalent Fe-thiolate bonds are mechanically labile and display features that clearly distinguish themselves from typical covalent bonds. Our study not only opens new avenues to investigating this important class of chemical bonds, but may also shed new lights on our understanding of the chemical nature of these metal thiolate bonds.

  6. Covalent bonds against magnetism in transition metal compounds.

    PubMed

    Streltsov, Sergey V; Khomskii, Daniel I

    2016-09-20

    Magnetism in transition metal compounds is usually considered starting from a description of isolated ions, as exact as possible, and treating their (exchange) interaction at a later stage. We show that this standard approach may break down in many cases, especially in 4d and 5d compounds. We argue that there is an important intersite effect-an orbital-selective formation of covalent metal-metal bonds that leads to an "exclusion" of corresponding electrons from the magnetic subsystem, and thus strongly affects magnetic properties of the system. This effect is especially prominent for noninteger electron number, when it results in suppression of the famous double exchange, the main mechanism of ferromagnetism in transition metal compounds. We study this mechanism analytically and numerically and show that it explains magnetic properties of not only several 4d-5d materials, including Nb2O2F3 and Ba5AlIr2O11, but can also be operative in 3d transition metal oxides, e.g., in CrO2 under pressure. We also discuss the role of spin-orbit coupling on the competition between covalency and magnetism. Our results demonstrate that strong intersite coupling may invalidate the standard single-site starting point for considering magnetism, and can lead to a qualitatively new behavior. PMID:27601669

  7. Covalent bonds against magnetism in transition metal compounds.

    PubMed

    Streltsov, Sergey V; Khomskii, Daniel I

    2016-09-20

    Magnetism in transition metal compounds is usually considered starting from a description of isolated ions, as exact as possible, and treating their (exchange) interaction at a later stage. We show that this standard approach may break down in many cases, especially in 4d and 5d compounds. We argue that there is an important intersite effect-an orbital-selective formation of covalent metal-metal bonds that leads to an "exclusion" of corresponding electrons from the magnetic subsystem, and thus strongly affects magnetic properties of the system. This effect is especially prominent for noninteger electron number, when it results in suppression of the famous double exchange, the main mechanism of ferromagnetism in transition metal compounds. We study this mechanism analytically and numerically and show that it explains magnetic properties of not only several 4d-5d materials, including Nb2O2F3 and Ba5AlIr2O11, but can also be operative in 3d transition metal oxides, e.g., in CrO2 under pressure. We also discuss the role of spin-orbit coupling on the competition between covalency and magnetism. Our results demonstrate that strong intersite coupling may invalidate the standard single-site starting point for considering magnetism, and can lead to a qualitatively new behavior.

  8. 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

  9. 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

    2015-09-15

    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.

  10. 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

  11. Interplay between non-covalent interactions in complexes and crystals with halogen bonds

    NASA Astrophysics Data System (ADS)

    Bartashevich, E. V.; Tsirelson, V. G.

    2014-12-01

    Studies on the structure and properties of complexes and crystals with halogen bonding accompanied by different secondary non-covalent interactions are summarized. The signs of halogen bonding are systematized and modern methods and approaches used to provide clear and reproducible estimates of the strength of halogen bonds are analyzed. The halogen bond strength values are compared with the strength of the other non-covalent interactions. The contradictions in the interpretation of the results from different studies of the strength of halogen bond are discussed. The bibliography includes 249 references.

  12. 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.

  13. 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…

  14. 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.

  15. A Cost-Effective Physical Modeling Exercise to Develop Students' Understanding of Covalent Bonding

    ERIC Educational Resources Information Center

    Turner, Kristy L.

    2016-01-01

    Chemical bonding is one of the basic concepts in chemistry, and the topic of covalent bonding forms an important core of knowledge for the high school chemistry student. For many teachers it is a challenging concept to teach, not least because it relies mainly on traditional instruction and written work. Similarly, many students find the topic…

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. JeffDescription of the Honeycomb Mott Insulatorα‑RuCl3

    NASA Astrophysics Data System (ADS)

    Koitzsch, A.; Habenicht, C.; Müller, E.; Knupfer, M.; Büchner, B.; Kandpal, H. C.; van den Brink, J.; Nowak, D.; Isaeva, A.; Doert, Th.

    2016-09-01

    Novel ground states might be realized in honeycomb lattices with strong spin-orbit coupling. Here we study the electronic structure of {\\alpha}-RuCl_3, in which the Ru ions are in a d5 configuration and form a honeycomb lattice, by angle-resolved photoemission, x-ray photoemission and electron energy loss spectroscopy supported by density functional theory and multiplet calculations. We find that {\\alpha}-RuCl_3 is a Mott insulator with significant spin-orbit coupling, whose low energy electronic structure is naturally mapped onto Jeff states. This makes {\\alpha}-RuCl_3 a promising candidate for the realization of Kitaev physics. Relevant electronic parameters such as the Hubbard energy U, the crystal field splitting 10Dq and the charge transfer energy are evaluated. Furthermore, we observe significant Cl photodesorption with time, which must be taken into account when interpreting photoemission and other surface sensitive experiments.

  1. Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates.

    PubMed

    Ravi, Vijay Kumar; Goel, Mohit; Kotamarthi, Hema Chandra; Ainavarapu, Sri Rama Koti; Swaminathan, Rajaram

    2014-01-01

    Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL) at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control) and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL) on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.

  2. 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.

  3. Complexes trans-[RuCl(2)(nic)(4)] and trans-[RuCl(2)(i-nic)(4)] as free radical scavengers.

    PubMed

    Creczynski-Pasa, T B; Bonetti, V R; Beirith, A; Ckless, K; Konzen, M; Seifriz, I; Paula, M S; Franco, C V; Wilhelm Filho, D; Calixto, J B

    2001-09-01

    This study evaluates the action of the new ruthenium complexes trans-RuCl(2)(nic)(4)] (I) and trans-[RuCl(2)(i-nic)(4)] (II) as free radical scavengers. In our experiments, both compounds acted as scavengers of superoxide anion (O(2)*(-)), hydroxyl radicals (HO*) and nitrogen monoxide (formally known as 'nitric oxide'; NO*). In addition, complexes I and II potentiated the release of NO* from S-nitroso-N-acetyl-DL-penicilamine (SNAP), a NO* donor. Complex II, but not I, also decreased the nitrite levels in culture media of activated macrophages. A hypsochromic shift of lambda(max) and a significant change in half-wave potential (E(1/2)) was observed when NO* was added to the Complex II. Thiobarbituric reactive substance (TBARS) levels were significantly reduced in rats treated for 1 week with Complex II plus tert-butylhydroperoxide, when compared to rats treated only with tert-butylhydroperoxide. None of the complexes showed cytotoxicity. These findings support the suggestion that the new ruthenium complexes, especially trans-[RuCl(2)(i-nic)(4)] or its derivatives, might provide potential therapeutic benefits in disorders where reactive nitrogen (RNS) or oxygen (ROS) species are involved.

  4. 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

  5. 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

  6. Density functionals that recognize covalent, metallic, and weak bonds.

    PubMed

    Sun, Jianwei; Xiao, Bing; Fang, Yuan; Haunschild, Robin; Hao, Pan; Ruzsinszky, Adrienn; Csonka, Gábor I; Scuseria, Gustavo E; Perdew, John P

    2013-09-01

    Computationally efficient semilocal approximations of density functional theory at the level of the local spin density approximation (LSDA) or generalized gradient approximation (GGA) poorly describe weak interactions. We show improved descriptions for weak bonds (without loss of accuracy for strong ones) from a newly developed semilocal meta-GGA (MGGA), by applying it to molecules, surfaces, and solids. We argue that this improvement comes from using the right MGGA dimensionless ingredient to recognize all types of orbital overlap. PMID:25166685

  7. 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

  8. 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

  9. 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

  10. Structural model for covalent adhesion of the Streptococcus pyogenes pilus through a thioester bond.

    PubMed

    Linke-Winnebeck, Christian; Paterson, Neil G; Young, Paul G; Middleditch, Martin J; Greenwood, David R; Witte, Gregor; Baker, Edward N

    2014-01-01

    The human pathogen Streptococcus pyogenes produces pili that are essential for adhesion to host surface receptors. Cpa, the adhesin at the pilus tip, was recently shown to have a thioester-containing domain. The thioester bond is believed to be important in adhesion, implying a mechanism of covalent attachment analogous to that used by human complement factors. Here, we have characterized a second active thioester-containing domain on Cpa, the N-terminal domain of Cpa (CpaN). Expression of CpaN in Escherichia coli gave covalently linked dimers. These were shown by x-ray crystallography and mass spectrometry to comprise two CpaN molecules cross-linked by the polyamine spermidine following reaction with the thioester bonds. This cross-linked CpaN dimer provides a model for the covalent attachment of Cpa to target receptors and thus the streptococcal pilus to host cells. Similar thioester domains were identified in cell wall proteins of other Gram-positive pathogens, suggesting that thioester domains are more widely used and provide a mechanism of adhesion by covalent bonding to target molecules on host cells that mimics that used by the human complement system to eliminate pathogens.

  11. 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

  12. 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.

  13. Sequence-specific association in aqueous media by integrating hydrogen bonding and dynamic covalent interactions.

    PubMed

    Li, Minfeng; Yamato, Kazuhiro; Ferguson, Joseph S; Gong, Bing

    2006-10-01

    Oligoamide strands that associate in a sequence-specific fashion into hydrogen-bonded duplexes in nonpolar solvents were converted into disulfide cross-linked duplexes in aqueous media. Thus, by incorporating trityl-protected thiol groups, which allows the reversible formation of disulfide bonds, into the oligoamide strands, only duplexes consisting of complementary hydrogen-bonding sequences were formed in aqueous solution as well as in methanol. The sequence-specific cross-linking of oligoamide strands was confirmed by MALDI-TOF, reverse-phase HPLC, and by isolating a cross-linked duplex. This study demonstrates that the sequence-specificity characteristic of multiply hydrogen-bonded systems can be extended into competitive media through the interplay of H-bonding and reversible covalent interactions, based on which a new class of molecular associating and ligating units that are compatible with both polar and nonpolar environments can be conveniently obtained.

  14. Competition between covalent and noncovalent bond cleavages in dissociation of phosphopeptide-amine complexes.

    PubMed

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

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature and have been extensively studied phenomenologically. However, little is known about the binding energies in non-covalent complexes containing these functional groups. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A(3)pXA(3)-NH(2) (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. For systems examined in this study, 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.

  15. Correlations of acute toxicity of metal ions and the covalent/ionic character of their bonds

    SciTech Connect

    Turner, J.E.; Williams, M.W.; Jacobson, K.B.; Hingerty, B.E.

    1984-01-01

    We have investigated correlations between physicochemical properties of 24 metal ions and their acute toxicity in mice and Drosophila. A high correlation for a softness parameter suggests that the relative covalent/ionic character of the bonds formed by the metal ions may be important in determining their toxicity. This hypothesis is reinforced by model calculations of metal binding to dinucleotides in water. Since the nature of bonds depends on ligand electronegativity, we searched for correlations involving this parameter. Although electronegativity is useful for interpreting some aspects of metal-ion behavior related to toxicity, it does not yield improved correlations. 8 refs., 3 figs., 1 tab.

  16. 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.

  17. 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.

  18. A molecular dynamics study of bond exchange reactions in covalent adaptable networks.

    PubMed

    Yang, Hua; Yu, Kai; Mu, Xiaoming; Shi, Xinghua; Wei, Yujie; Guo, Yafang; Qi, H Jerry

    2015-08-21

    Covalent adaptable networks are polymers that can alter the arrangement of network connections by bond exchange reactions where an active unit attaches to an existing bond then kicks off its pre-existing peer to form a new bond. When the polymer is stretched, bond exchange reactions lead to stress relaxation and plastic deformation, or the so-called reforming. In addition, two pieces of polymers can be rejoined together without introducing additional monomers or chemicals on the interface, enabling welding and reprocessing. Although covalent adaptable networks have been researched extensively in the past, knowledge about the macromolecular level network alternations is limited. In this study, molecular dynamics simulations are used to investigate the macromolecular details of bond exchange reactions in a recently reported epoxy system. An algorithm for bond exchange reactions is first developed and applied to study a crosslinking network formed by epoxy resin DGEBA with the crosslinking agent tricarballylic acid. The trace of the active units is tracked to show the migration of these units within the network. Network properties, such as the distance between two neighboring crosslink sites, the chain angle, and the initial modulus, are examined after each iteration of the bond exchange reactions to provide detailed information about how material behaviors and macromolecular structure evolve. Stress relaxation simulations are also conducted. It is found that even though bond exchange reactions change the macroscopic shape of the network, microscopic network characteristic features, such as the distance between two neighboring crosslink sites and the chain angle, relax back to the unstretched isotropic state. Comparison with a recent scaling theory also shows good agreement.

  19. Covalent bonds and their crucial effects on pseudogap formation in α-Al(Mn,Re)Si icosahedral quasicrystalline approximant

    NASA Astrophysics Data System (ADS)

    Kirihara, K.; Nagata, T.; Kimura, K.; Kato, K.; Takata, M.; Nishibori, E.; Sakata, M.

    2003-07-01

    X-ray charge densities of Al-based icosahedral quasicrystalline approximant crystals α-AlReSi, α-AlMnSi, and Al12Re were observed by a combination of the maximum entropy method with the Rietveld method. We successfully obtained the clear images of interatomic covalent bonds between Al and transition metals (Mn, Re) and those in the Al (or Si) icosahedron in Mackay icosahedral clusters of both α-AlReSi and α-AlMnSi approximant crystals. The bonding nature of the three kinds of glue atom sites connecting Mackay icosahedral clusters was also clarified. This covalent bonding nature should strongly relate with the enhancement of the electron density-of-states pseudogap near the Fermi level. In addition, the interatomic covalent bonds of α-AlReSi are stronger than those of α-AlMnSi. This fact leads to the low effective carrier density of α-AlReSi in comparison with that of α-AlMnSi. Unlike the covalent bonding nature of an icosahedron in α-AlReSi and α-AlMnSi crystals, the Al icosahedron with an Re center atom exhibits no Al-Al interatomic covalent bonds in the Al12Re crystal. The tendency for metallic-covalent bonding conversion in the Al icosahedron, which is related to the atom site occupancy of the icosahedral cluster center, is also strongly supported.

  20. 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.

  1. Molecular functionalization of silicene/Ag(111) by covalent bonds: a DFT study.

    PubMed

    Stephan, Régis; Hanf, Marie-Christine; Sonnet, Philippe

    2015-06-14

    Among the 2D crystals, silicene, which forms sp(2)-sp(3) bonds, is expected to present a higher reactivity than graphene, characterized by sp(2) bonds only. However, silicene functionalization, in particular with organic molecules, remains an open question. By means of density functional theory, we study the adsorption of benzene, a model organic molecule, on (3 × 3) silicene on the (4 × 4) Ag(111) surface. Our calculations show that the dispersion interactions must be taken into account in order to describe this system properly. The adsorption energy is calculated by means of the semi-empirical dispersion-corrected density functional theory (DFT-D2) and the optB86b-vdW density functional. The charge density and electron localization function maps indicate that the molecule is chemisorbed on the silicene surface by means of two Si-C covalent bonds. In agreement with charge density difference calculations, two C-C double bonds are formed in the benzene molecule, which adopts a butterfly configuration. The silicene lattice is slightly deformed upon benzene adsorption, but the Si-Si distance remains the same as in bare silicene/Ag(111). Bader analysis shows a charge transfer from top Si atoms to both molecules and Ag substrates. Finally, we show that the covalent functionalization of silicene is possible.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Lee, Sang-Hoon; Jhi, Seung-Hoon

    2015-02-01

    We studied three-dimensional honeycomb-structure boron nitride (BN) allotrope using first-principles calculations and the tight-binding method. Interconnected by sp3-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 sp2- and sp3-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 sp2-bonded atoms in adjacent nanoribbons.

  12. 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…

  13. 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.

  14. 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.

  15. 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.

  16. Multi-walled carbon nanotubes covalently bonded cellulose composite for chemical vapor sensor

    NASA Astrophysics Data System (ADS)

    Yun, Sungryul; Yang, Sang Yeol; Kim, Jaehwan

    2010-04-01

    A cellulose solution was prepared by dissolving cotton pulp in LiCl/ N,N-Dimethylacetamide (DMAc) solution, and functionalized multi-walled carbon nanotubes (MWCNTs) were reacted with N, N-Carbonyldiimidazoles to obtain MWCNTs-imidazolides. By acylation of cellulose with MWCNTs-imidazolides, MWCNTs were covalently bonded with cellulose chains. Using the product, MWCNTs covalently bonded cellulose composite (M/C) composite was fabricated with mechanical stretching to align MWCNTs with cellulose. Finally, inter-digital comb electrode was formed on the composite via lift-off process. Chemo-electrical properties of the M/C composite in response of absorption of the volatile vapors corresponding to 1-propanol, 1-butanol, methanol and ethanol were investigated. Due to sensitive and reversible expansion/contraction of the M/C composite matrix in response to absorption of each analyte, the M/C composite showed fast and reversible change in chemo-electrical property. The ranking of relative resistance response of the composite was methanol < ethanol < 1-propanol < 1-butanol.

  17. 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

  18. Nitrogen Doping Enables Covalent-Like π-π Bonding between Graphenes.

    PubMed

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

    2015-08-12

    The neighboring layers in bilayer (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) π-π 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 π-π overlap across the vdW gap while the individual layers maintain their in-plane π-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. PMID:26151153

  19. Nitrogen Doping Enables Covalent-Like π-π Bonding between Graphenes.

    PubMed

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

    2015-08-12

    The neighboring layers in bilayer (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) π-π 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 π-π overlap across the vdW gap while the individual layers maintain their in-plane π-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.

  20. 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.

  1. 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.

  2. Angle-resolved photoemission study of the Kitaev candidate α -RuCl3

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaoqing; Li, Haoxiang; Waugh, J. A.; Parham, S.; Kim, Heung-Sik; Sears, J. A.; Gomes, A.; Kee, Hae-Young; Kim, Young-June; Dessau, D. S.

    2016-10-01

    α -RuCl3 has been hinted to be a spin-orbital-assisted Mott insulator in proximity to a Kitaev spin liquid state. Here we present angle-resolved photoemission measurements on single-crystal α -RuCl3 in both the pristine and electron-doped states, and combine them with Local Density Approximation (LDA)+Spin Orbital Coupling (SOC)+U calculations performed for several low-energy competing magnetically ordered states as well as the paramagnetic state. A large Mott gap is found in the measured band structure of the pristine compound that persists to more than 30 times beyond the magnetic ordering temperature, though the paramagnetic calculation shows almost no gap. Upon electron doping, spectral weight is transferred into the gap but the new states still maintain a sizable gap from the Fermi edge. These findings are most consistent with a Mott insulator with a somewhat exotic evolution out of the Mott state with both temperature and doping, likely related to unusually strong spin fluctuations.

  3. 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

  4. Covalent bonding and the nature of band gaps in some half-Heusler compounds

    NASA Astrophysics Data System (ADS)

    Kandpal, Hem Chandra; Felser, Claudia; Seshadri, Ram

    2006-03-01

    Half-Heusler compounds XYZ, also called semi-Heusler compounds, crystallize in the C1b MgAgAs structure, in the space group F\\bar{4}3m . We report a systematic examination of band gaps and the nature (covalent or ionic) of bonding in semiconducting 8- and 18-electron half-Heusler compounds through first-principles density functional calculations. We find that the most appropriate description of these compounds from the viewpoint of electronic structures is one of a YZ zinc blende lattice stuffed by the X ion. Simple valence rules are obeyed for bonding in the 8-electron compound. For example, LiMgN can be written Li+ + (MgN)- and (MgN)-, which is isoelectronic with (SiSi), forms a zinc blende lattice. The 18-electron compounds can similarly be considered as obeying valence rules. A semiconductor such as TiCoSb can be written Ti4+ + (CoSb)4-; the latter unit is isoelectronic and isostructural with zinc-blende GaSb. For both the 8- and the 18-electron compounds, when X is fixed as some electropositive cation, the computed band gap varies approximately as the difference in Pauling electronegativities of Y and Z. What is particularly exciting is that this simple idea of a covalently bonded YZ lattice can also be extended to the very important magnetic half-Heusler phases; we describe these as valence compounds, i.e. possessing a band gap at the Fermi energy albeit only in one spin direction. The local moment in these magnetic compounds resides on the X site.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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

  10. Superhard materials with low elastic moduli: Three-dimensional covalent bonding as the origin of superhardness in B6O

    NASA Astrophysics Data System (ADS)

    Zhang, R. F.; Lin, Z. J.; Zhao, Y. S.; Veprek, S.

    2011-03-01

    Using first-principles calculations, we show that, in spite of its relatively low shear modulus, boron suboxide (B6O) is superhard because of its high shear strength of ⩾38 GPa which originates from three-dimensional covalently bonded network of B12 icosahedral units connected by boron and oxygen atoms. We further demonstrate that the high shear resistance of B6O is related to strong B-B covalent bonds that connect the B12 units. These results challenge the concept of design intrinsically superhard materials based on high elastic moduli only.

  11. 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

  12. 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.

  13. 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.

  14. Polyvinylamine-graft-TEMPO adsorbs onto, oxidizes, and covalently bonds to wet cellulose.

    PubMed

    Pelton, Robert; Ren, Pengchao; Liu, Jieyi; Mijolovic, Darijo

    2011-04-11

    Described is a new, greener approach to increasing adhesion between wet cellulose surfaces. Polyvinylamine (PVAm) with grafted TEMPO spontaneously adsorbs onto cellulose and oxidizes the C6 hydroxyl to aldehyde groups that react to form covalent bonds with primary amines on PVAm. Grafted TEMPO offers two important advantages over solutions of low-molecular-weight water-soluble TEMPO derivatives. First, the oxidation of porous cellulose wood fibers is restricted to the exterior surfaces accessible to high-molecular-weight PVAm. Thus, fibers are not weakened by excessive oxidation of the interior fiber wall surfaces. The second advantage of tethered TEMPO is that the total dose of TEMPO required to oxidize dilute fiber suspensions is much less than that required by water-soluble TEMPO derivatives. PVAm-TEMPO is stable under oxidizing conditions. The oxidation activity of the immobilized TEMPO was demonstrated by the conversion of methylglyoxal to pyruvic acid.

  15. 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.

  16. Molecular single-bond covalent radii for elements 1-118.

    PubMed

    Pyykkö, Pekka; Atsumi, Michiko

    2009-01-01

    A self-consistent system of additive covalent radii, R(AB)=r(A) + r(B), is set up for the entire periodic table, Groups 1-18, Z=1-118. The primary bond lengths, R, are taken from experimental or theoretical data corresponding to chosen group valencies. All r(E) values are obtained from the same fit. Both E-E, E-H, and E-CH(3) data are incorporated for most elements, E. Many E-E' data inside the same group are included. For the late main groups, the system is close to that of Pauling. For other elements it is close to the methyl-based one of Suresh and Koga [J. Phys. Chem. A 2001, 105, 5940] and its predecessors. For the diatomic alkalis MM' and halides XX', separate fits give a very high accuracy. These primary data are then absorbed with the rest. The most notable exclusion are the transition-metal halides and chalcogenides which are regarded as partial multiple bonds. Other anomalies include H(2) and F(2). The standard deviation for the 410 included data points is 2.8 pm.

  17. 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.

  18. 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

  19. 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.

  20. A model ternary heparin conjugate by direct covalent bond strategy applied to drug delivery system.

    PubMed

    Wang, Ying; Xin, Dingcheng; Hu, Jiawen; Liu, Kaijian; Pan, Jiangao; Xiang, Jiannan

    2009-01-01

    A model ternary heparin conjugate by direct covalent bond strategy has been developed, in which modified heparin using active mix anhydride as intermediate conjugates with model drug molecule and model specific ligand, respectively. Designed ester bonds between model drug and heparin facilitate hydrolysis kinetics research. The strategy can be extended to design and synthesize a targeted drug delivery system. The key point is to use mixed anhydride groups as activating intermediates to mediate the synthesis of the ternary heparin conjugate. Formation of mixed anhydride is detected by the conductimetry experiment. The ternary heparin conjugate is characterized by (13)C NMR, FT-IR and GPC, respectively. The decreased trend on degree of substitution (DS) is consistent with that of introduced anticancer drug and specific ligand in drug delivery system. Moreover, their anticoagulant activity is evaluated by measuring activated partial thromboplastin time (APTT) and anti-factor Xa activity. The results show that model ternary heparin conjugate with reduced anticoagulant activity may avoid the risk of severe hemorrhagic complication during the administration and is potential to develop a safe and effective drug delivery system on anticancer research.

  1. 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…

  2. 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.

  3. 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.

  4. Ions colliding with clusters of fullerenes—Decay pathways and covalent bond formations

    NASA Astrophysics Data System (ADS)

    Seitz, F.; Zettergren, H.; Rousseau, P.; Wang, Y.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Rangama, J.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Domaracka, A.; Méry, A.; Maclot, S.; Vizcaino, V.; Schmidt, H. T.; Adoui, L.; Alcamí, M.; Tielens, A. G. G. M.; Martín, F.; Huber, B. A.; Cederquist, H.

    2013-07-01

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C60 molecules following collisions with Ar2 +, He2 +, and Xe20 + at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C60 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_{60}]_n^+ → C_{60}+ + (n-1)C_{60} evaporation model. Excitation energies in the range of only ˜0.7 eV per C60 molecule in a [C_{60}]_{13}^+ 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 Ar2 + and He2 + collisions, we observe very efficient C_{119}+ and C_{118}+ formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C_{59}+ or C_{58}+ and C60 during cluster fragmentation. In the Ar2 + case, it is possible to form even smaller C_{120-2m}+ molecules (m = 2-7), while no molecular fusion reactions are observed for the present Xe20 + collisions.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Immobilization of laminin peptide in molecularly aligned chitosan by covalent bonding.

    PubMed

    Matsuda, Atsushi; Kobayashi, Hisatoshi; Itoh, Soichiro; Kataoka, Kazunori; Tanaka, Junzo

    2005-05-01

    We developed a new biomaterial effective for nerve regeneration consisting of molecularly aligned chitosan with laminin peptides bonded covalently. Molecularly aligned chitosan was prepared from crab (Macrocheira kaempferi) tendons by ethanol treatment and 4 wt%-NaOH aqueous solutions to remove proteins and calcium phosphate, followed by deacetyl treatment using a 50 wt%-NaOH aqueous solution at 100 degrees C. Molecularly aligned tendon chitosan was chemically thiolated by reacting 4-thiobutyrolactone with the chitosan amino group. The introduction of thiol groups and their distribution to tendon chitosan and chitosan cast film were confirmed using ATR FT-IR, (1)H-NMR, and EDS. The 1.24 micromol/g of thiol groups introduced on the surface of tendon chitosan and the chitosan cast film was confirmed using ultraviolet (UV) spectra. Thiol groups of cysteine located at the end of synthetic laminin peptides were then reacted chemically with thiolated chitosan to form chitosan-S-S-laminin peptide. YIGSR estimated at 0.92 micromol/g and IKVAV estimated at 0.28 micromol/g on thiolated tendon chitosan were confirmed using UV spectra. YIGSR was estimated at 0.85 micromol/g and IKVAV was estimated at 0.34 micromol/g on the thiolated chitosan cast film.

  11. 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.

  12. 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

  13. Preparation of copolymer paclitaxel covalently linked via a disulfide bond and its application on controlled drug delivery.

    PubMed

    Chen, Wulian; Shi, Yuanlin; Feng, Hua; Du, Ming; Zhang, Jin Zhong; Hu, Jianhua; Yang, Dong

    2012-08-01

    A novel controlled drug delivery system based on copolymer covalently linked paclitaxel via a disulfide bond was constructed. Copolymer with poly(ethylene glycol) (PEG) side chains and carboxyl groups on the backbone was prepared by radical copolymerization of tert-butyl acrylate and poly(ethylene glycol) methyl ether acrylate, followed by selectively hydrolyzing tert-butyl groups to carboxyl groups. Utilizing the carboxyl group as an active reaction site, paclitaxel, a well-known chemotherapeutic drug, could be covalently linked to the backbone of a copolymer via a disulfide bond, and the loading content of paclitaxel could reach up to 32 wt %. In aqueous solution, this drug-loaded copolymer could self-assemble into a spherical micelle, with the hydrophobic drug as the core and hydrophilic PEG as the shell. The mean diameter of the micelles evaluated by transmission electron microscopy (TEM) and dynamic light scattering (DLS) was approximately 60 nm. The in vitro cytotoxicity experiments showed that the copolymer was biocompatible and suitable to use as a drug carrier. After covalently loading the drug, the copolymer showed apparent cytotoxicity to OS-RC-2 cells (kidney tumor cells) and low cytotoxicity to macrophage cells (human normal cells), indicating that the disulfide bond was stable in human normal cells, but would be broken in tumor cells. This selective bond scission behavior is potentially favorable for reducing the toxic and side effects of chemotherapeutic drugs. PMID:22774761

  14. 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.

  15. 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.

  16. Dynamic covalent bond based on reversible photo [4 + 4] cycloaddition of anthracene for construction of double-dynamic polymers.

    PubMed

    Xu, Jiang-Fei; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

    2013-12-20

    Dynamic covalent bonds supplied by reversible anthracene dimerization were combined with pillar[5]arene/imidazole host-guest interactions to construct double-dynamic polymers. Heating such polymers (in solution or as a gel) led to depolymerization by dissociation of either the host-guest complexes alone or the complexes and the anthracene dimers, depending on the extent of heating. The polymers reformed readily upon cooling or irradiation.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

    2016-07-22

    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

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Intrinsic carrier mobility of a single-layer graphene covalently bonded with single-walled carbon nanotubes

    SciTech Connect

    Li, Dian; Shao, Zhi-Gang; Hao, Qing; Zhao, Hongbo

    2014-06-21

    We report intrinsic carrier mobility calculations of a two-dimensional nanostructure that consists of porous single layer graphene covalently bonded with single-walled carbon nanotubes on both sides. We used first-principles calculation and found that the deformation potential of such system is about 25% of that of graphene, and the carrier mobility is about 5 × 10{sup 4} cm{sup 2} V{sup −1} s{sup −1} for both electrons and holes, about one order of magnitude lower than that of graphene. This nanostructure and its three-dimensional stacking could serve as novel organic electronic materials.

  11. 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.

  12. 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.

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

    PubMed

    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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets.

    PubMed

    Fonseca Guerra, Célia; Zijlstra, Hester; Paragi, Gábor; Bickelhaupt, F Matthias

    2011-11-01

    We show that the cooperative reinforcement between hydrogen bonds in guanine quartets is not caused by resonance-assisted hydrogen bonding (RAHB). This follows from extensive computational analyses of guanine quartets (G(4)) and xanthine quartets (X(4)) based on dispersion-corrected density functional theory (DFT-D). Our investigations cover the situation of quartets in the gas phase, in aqueous solution as well as in telomere-like stacks. A new mechanism for cooperativity between hydrogen bonds in guanine quartets emerges from our quantitative Kohn-Sham molecular orbital (MO) and corresponding energy decomposition analyses (EDA). Our analyses reveal that the intriguing cooperativity originates from the charge separation that goes with donor-acceptor orbital interactions in the σ-electron system, and not from the strengthening caused by resonance in the π-electron system. The cooperativity mechanism proposed here is argued to apply, beyond the present model systems, also to other hydrogen bonds that show cooperativity effects.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. Zigzag type magnetic structure of the spin J eff = ½ compound α-RuCl3 as determined by neutron powder diffraction

    NASA Astrophysics Data System (ADS)

    Ritter, C.

    2016-09-01

    Using high intensity powder neutron diffraction the magnetic structure of a-RuCl3 has been determined. Following the magnetic propagation vector κ = (½, 0, ½) the J eff = ½ spins of Ru3+ adopt a Zigzag type arrangement on the honeycomb lattice of the layered P3112 structure. The magnetic moments are oriented perpendicular to the trigonal axis. Similarities and differences to previously published single crystal data are discussed. The low value of the magnetic moments, μRu = 0.5(1) μB indicates a possible closeness of α-RuCl3 to the Kitaev spin liquid state.

  7. 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

  8. Covalent bond glued sulfur nanosheet-based cathode integration for long-cycle-life Li-S batteries.

    PubMed

    Wang, Lei; Dong, Zhihui; Wang, Dong; Zhang, Fengxing; Jin, Jian

    2013-01-01

    High-capacity electrochemical active material-based electrodes for lithium ion batteries (LIBs), such as sulfur (S), always face the collapse of the electrode due to the big volume change during insertion of the lithium (Li) ion and therefore shorten the cycle life of the cells. Herein, a series of design from the viewpoint of both individual components and the entire cathode in lithium-sulfur (Li-S) cell was introduced aiming at addressing the issues of poor conductivity, leakage of intermediate polysulphides, and large volumetric expansion upon insertion of the Li ion. In the designed electrode, polydopamine (PD)-coated S nanosheets (NSs) were used as active materials, carboxylic acid functionalized multiwall carbon nanotube (MWCNT-COOH) as conductive additives, and poly(acrylic acid) (PAA) as binders. Far different from the traditional hydrogen bond and/or van der Waals force linked electrodes, stronger covalent bonds formed by cross-linking of PD/MWCNT-COOH and PD/PAA into amide bonds, respectively, were built throughout the whole electrode to firmly integrate all of the individual components in the electrode together. As a result, the cathode demonstrated excellent cyclic performance with a charge capacity of 640 mAh/g after 500 cycles at a current density of 1 A/g. Besides, the charge capacity decay after 500 cycles is as small as 0.021% per cycle, which represents the best capacity retention so far.

  9. 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.

  10. 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

  11. 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.

  12. Covalent bonding of YIGSR and RGD to PEDOT/PSS/MWCNT-COOH composite material to improve the neural interface

    NASA Astrophysics Data System (ADS)

    Wang, Kun; Tang, Rong-Yu; Zhao, Xiao-Bo; Li, Jun-Jie; Lang, Yi-Ran; Jiang, Xiao-Xia; Sun, Hong-Ji; Lin, Qiu-Xia; Wang, Chang-Yong

    2015-11-01

    The development of coating materials for neural interfaces has been a pursued to improve the electrical, mechanical and biological performances. For these goals, a bioactive coating was developed in this work featuring a poly(3,4-ethylenedioxythiophene) (PEDOT)/carbon nanotube (CNT) composite and covalently bonded YIGSR and RGD. Its biological effect and electrical characteristics were assessed in vivo on microwire arrays (MWA). The coated electrodes exhibited a significantly higher charge storage capacity (CSC) and lower electrochemical impedance at 1 kHz which are desired to improve the stimulating and recording performances, respectively. Acute neural recording experiments revealed that coated MWA possess a higher signal/noise ratio capturing spikes undetected by uncoated electrodes. Moreover, coated MWA possessed more active sites and single units, and the noise floor of coated electrodes was lower than that of uncoated electrodes. There is little information in the literature concerning the chronic performance of bioactively modified neural interfaces in vivo. Therefore in this work, chronic in vivo tests were conducted and the PEDOT/PSS/MWCNT-polypeptide coated arrays exhibited excellent performances with the highest mean maximal amplitude from day 4 to day 12 during which the acute response severely compromised the performance of the electrodes. In brief, we developed a simple method of covalently bonding YIGSR and RGD to a PEDOT/PSS/MWCNT-COOH composite improving both the biocompatibility and electrical performance of the neural interface. Our findings suggest that YIGSR and RGD modified PEDOT/PSS/MWCNT is a promising bioactivated composite coating for neural recording and stimulating.

  13. Covalent bonding of YIGSR and RGD to PEDOT/PSS/MWCNT-COOH composite material to improve the neural interface.

    PubMed

    Wang, Kun; Tang, Rong-Yu; Zhao, Xiao-Bo; Li, Jun-Jie; Lang, Yi-Ran; Jiang, Xiao-Xia; Sun, Hong-Ji; Lin, Qiu-Xia; Wang, Chang-Yong

    2015-11-28

    The development of coating materials for neural interfaces has been a pursued to improve the electrical, mechanical and biological performances. For these goals, a bioactive coating was developed in this work featuring a poly(3,4-ethylenedioxythiophene) (PEDOT)/carbon nanotube (CNT) composite and covalently bonded YIGSR and RGD. Its biological effect and electrical characteristics were assessed in vivo on microwire arrays (MWA). The coated electrodes exhibited a significantly higher charge storage capacity (CSC) and lower electrochemical impedance at 1 kHz which are desired to improve the stimulating and recording performances, respectively. Acute neural recording experiments revealed that coated MWA possess a higher signal/noise ratio capturing spikes undetected by uncoated electrodes. Moreover, coated MWA possessed more active sites and single units, and the noise floor of coated electrodes was lower than that of uncoated electrodes. There is little information in the literature concerning the chronic performance of bioactively modified neural interfaces in vivo. Therefore in this work, chronic in vivo tests were conducted and the PEDOT/PSS/MWCNT-polypeptide coated arrays exhibited excellent performances with the highest mean maximal amplitude from day 4 to day 12 during which the acute response severely compromised the performance of the electrodes. In brief, we developed a simple method of covalently bonding YIGSR and RGD to a PEDOT/PSS/MWCNT-COOH composite improving both the biocompatibility and electrical performance of the neural interface. Our findings suggest that YIGSR and RGD modified PEDOT/PSS/MWCNT is a promising bioactivated composite coating for neural recording and stimulating.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Magnetic anisotropy in the Kitaev model systems Na2IrO3 and RuCl3

    NASA Astrophysics Data System (ADS)

    Chaloupka, Jiří; Khaliullin, Giniyat

    2016-08-01

    We study the ordered moment direction in the extended Kitaev-Heisenberg model relevant to honeycomb lattice magnets with strong spin-orbit coupling. We utilize numerical diagonalization and analyze the exact cluster ground states using a particular set of spin-coherent states, obtaining thereby quantum corrections to the magnetic anisotropy beyond conventional perturbative methods. It is found that the quantum fluctuations strongly modify the moment direction obtained at a classical level and are thus crucial for a precise quantification of the interactions. The results show that the moment direction is a sensitive probe of the model parameters in real materials. Focusing on the experimentally relevant zigzag phases of the model, we analyze the currently available neutron-diffraction and resonant x-ray-diffraction data on Na2IrO3 and RuCl3 and discuss the parameter regimes plausible in these Kitaev-Heisenberg model systems.

  20. 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

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

    SciTech Connect

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

    2014-05-28

    An analysis based on the variation principle shows that in the molecules H{sub 2}{sup +}, H{sub 2}, B{sub 2}, C{sub 2}, N{sub 2}, O{sub 2}, F{sub 2}, 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.

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

    PubMed

    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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. Covalent assembly of mouse immunoglobulin G subclasses in vitro: application of a theoretical model for interchain disulfide bond formation.

    PubMed

    Percy, M E; Baumal, R; Dorrington, K J; Percy, J R

    1976-08-01

    The pathways and kinetics of interchain disulfide bond formation have been determined in vitro for purified myeloma proteins representing the three major subclasses of mouse immunoglobulin G(IgG) using the reoxidation system described previously (Petersen, J.G.L. & Dorrington, K.J. (1974) J. Biol. Chem. 249, 5633-5641). Mixtures of oxidized and reduced glutathione were added to act as a disulfide interchange catalyst. The pathways of covalent assembly observed in vitro were qualitatively and quantitatively similar to those followed by the various subclasses in vivo. HH and HHL were the principle covalent intermediates seen with IgG1 (MOPC 31C) and IgG2a (MOPC 173 and clone 19). With IgG2b( MPC 11C), HL, HH and HHL were all prominant intermediates. The time courses of reoxidation were simulated using a theoretical model based on second-order reaction kinetics (Percy, J.R., Percy, M.E. & Dorrington, K.J. (1974) J. Biol. Chem. 250, 2398-2400). Two distinct phases were apparent in the reoxidation sequence. The first, which lasted for the initial 5-15 min, did not confirm to the theoretical model. The second phase could be accounted for by the model and represented the remainder of the covalent assembly process. The physico-chemical basis for this biphasic phenomenon was explored. Sedimentation velocity studies showed that noncovalent association was incomplete at the beginning of the reoxidation step for all proteins except IgG2b (MOPC 11C). No dissociation was apparent in the reduced and alkylated proteins at pH 5 in the absence of prior exposure to acid conditions. Thus, exposure to acid appears to affect the affinity between the subunits in the native proteins. Transfer of the proteins from pH 5 to pH 8.2 (the pH at which reoxidation proceeds) is accompanied by the generation of an absorption difference spectrum over an 8-10 min period. These data suggest that a pH-dependent conformational relaxation process may influence the early stages of reoxidation. PMID:953849

  9. Competition between covalent bonding and charge transfer at complex-oxide interfaces.

    PubMed

    Salafranca, Juan; Rincón, Julián; Tornos, Javier; León, Carlos; Santamaria, Jacobo; Dagotto, Elbio; Pennycook, Stephen J; Varela, Maria

    2014-05-16

    Here we study the electronic properties of cuprate-manganite interfaces. By means of atomic resolution electron microscopy and spectroscopy, we produce a subnanometer scale map of the transition metal oxidation state profile across the interface between the high Tc superconductor YBa2Cu3O7-δ and the colossal magnetoresistance compound (La,Ca)MnO3. A net transfer of electrons from manganite to cuprate with a peculiar nonmonotonic charge profile is observed. Model calculations rationalize the profile in terms of the competition between standard charge transfer tendencies (due to band mismatch), strong chemical bonding effects across the interface, and Cu substitution into the Mn lattice, with different characteristic length scales.

  10. 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.

  11. Pyridine derivative covalently bonded on chitosan pendant chains for textile dye removal.

    PubMed

    Oliveira, Cintia S; Airoldi, Claudio

    2014-02-15

    Chitosan was chemically modified through a sequence of four reactions with immobilized 2-aminomethylpyridine at the final stage, after prior protection of amino group with benzaldehyde. The characterized biopolymers containing free amino and hydroxyl active centers on the biopolymeric structure and pyridinic nitrogen on pendant chains showed combined hydrophobic properties that can potentially favor interactions. Reactive Yellow GR and Blue RN dyes gave the maximum sorption capacities of 2.13 and 1.61 mmol g(-1), which were performed as functions of contact time, concentration and dye structure. However, biopolymer/dye interactions are governed by effective hydrogen bond and van der Waals forces for such structural adjustments. The data obtained from the concentration isotherm were applied to non-linear regressions of the Langmuir, the Freundlich and the Sips models, with the best fit to the latter model. The kinetic data was fitted to non-linear regression of pseudo-second-order, indicating that the sorption phenomena are most likely to be controlled by chemisorption process.

  12. 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.

  13. Chemically fixed p-n heterojunctions for polymer electronics by means of covalent B-F bond formation

    NASA Astrophysics Data System (ADS)

    Hoven, Corey V.; Wang, Huiping; Elbing, Mark; Garner, Logan; Winkelhaus, Daniel; Bazan, Guillermo C.

    2010-03-01

    Widely used solid-state devices fabricated with inorganic semiconductors, including light-emitting diodes and solar cells, derive much of their function from the p-n junction. Such junctions lead to diode characteristics and are attained when p-doped and n-doped materials come into contact with each other. Achieving bilayer p-n junctions with semiconducting polymers has been hindered by difficulties in the deposition of thin films with independent p-doped and n-doped layers. Here we report on how to achieve permanently fixed organic p-n heterojunctions by using a cationic conjugated polyelectrolyte with fluoride counteranions and an underlayer composed of a neutral conjugated polymer bearing anion-trapping functional groups. Application of a bias leads to charge injection and fluoride migration into the neutral layer, where irreversible covalent bond formation takes place. After the initial charging and doping, one obtains devices with no delay in the turn on of light-emitting electrochemical behaviour and excellent current rectification. Such devices highlight how mobile ions in organic media can open opportunities to realize device structures in ways that do not have analogies in the world of silicon and promise new opportunities for integrating organic materials within technologies now dominated by inorganic semiconductors.

  14. 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.

  15. Crystal packing of TCNQ anion pi-radicals governed by intermolecular covalent pi-pi bonding: DFT calculations and statistical analysis of crystal structures.

    PubMed

    Huang, Jingsong; Kingsbury, Stephanie; Kertesz, Miklos

    2008-05-21

    On the basis of a thorough Cambridge Structural Database survey, we present a statistical analysis of the packing of TCNQ anion pi-radicals in TCNQ charge transfer salts, which reveals three packing motifs between neighboring TCNQs: one with a zero longitudinal offset and an approximate 1 A transversal offset, another with an approximate 2 A longitudinal offset and zero transversal offset, and the third with a relatively long sigma-bond in the length of r = 1.6-1.7 A connecting two TCNQ fragments. Along with the statistical analysis of the crystal structures, we also present density functional theory calculations of the total energy, covalent pi-pi bonding interaction energy, and Coulombic repulsion energy for the [TCNQ](2)(2-)pi-dimers with various packing geometries. We find that the interactions between TCNQ anion pi-radicals include contributions from intermolecular covalent pi-pi bonding interaction and local dipole repulsions, in addition to Coulombic repulsion, van der Waals and the attractive electrostatic forces between counter-cations and TCNQ anions pointed out recently by other groups for TCNE anion radicals. We describe an approximate formula for intermolecular interaction energy, E(int) = E(coul) + E(bond) + E(vdW), for systems in vacuum, while in the solid state E(coul) is compensated by the attractive electrostatic forces between counter-cations and TCNQ anions. We conclude that the crystal packing of TCNQ molecules in their charge transfer salts is predominantly determined by the intermolecular covalent pi-pi bonding term, E(bond).

  16. Efficient transfer of either one or two dithiolene ligands from nickel to ruthenium: synthesis and crystal structures of [Ru(SCR=CPhS)(2)(PPh(3))] and [RuCl(2)(SCR=CPhS)(PPh(3))(2)] (R = Ph, H).

    PubMed

    Adams, Harry; Coffey, Anna M; Morris, Michael J; Morris, Sarah A

    2009-12-21

    High yields of two different types of ruthenium dithiolene complex have been obtained by reactions that involve transfer of the dithiolene ligands from the nickel complexes [Ni(SCR=CPhS)(2)] (R = Ph, H) to [RuCl(2)(PPh(3))(3)]. At room temperature one dithiolene is rapidly transferred to yield [RuCl(2)(SCR=CPhS)(PPh(3))(2)], whereas under thermal conditions (refluxing toluene) two dithiolene ligands are incorporated to give [Ru(SCR=CPhS)(2)(PPh(3))]. The crystal structures of the ruthenium bis(dithiolene) complexes indicate that the dithiolene ligands are bonded in the monoanionic form, whereas in the monodithiolene complexes the dithioketone canonical form of the dithiolene ligand is more in evidence, as shown by the average C-S and C=C bond distances in the ligands. This is consistent with both complexes containing Ru(II) centers. The synthesis of the mixed-ligand bis(dithiolene) complex [Ru(SCH=CPhS)(S(2)C(2)Ph(2))(PPh(3))] has been achieved and it is shown that the bis(dithiolene) complexes undergo relatively slow scrambling of the dithiolene ligands in solution. The complex [Ru(SCH=CFcS)(2)(PPh(3))], containing two ferrocenyl-substituted dithiolene ligands, was also prepared, but attempts to establish the degree of electrochemical communication between them were hampered by instability and the irreversible nature of the redox processes.

  17. 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.

  18. 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

  19. The effect of covalently bonded conjugated linoleic acid on the reduction of oxidative stress and blood coagulation for polysulfone hemodialyzer membrane.

    PubMed

    Kung, Fu-Chen; Yang, Ming-Chine

    2006-05-30

    Conjugated linoleic acid (CLA) was covalently bonded to a layer of poly(acrylic acid) (PAA) grafted onto the surface of polysulfone (PSF) membranes. The effect of CLA-bonding on oxidative stress and blood coagulation was then evaluated. The surface was characterized with contact angle measurement and FTIR spectroscopy. Blood coagulation, platelet aggregation, and oxidative stress were evaluated using human blood. The complete blood count (CBC) and coagulation time (CT) were evaluated in vitro for hemocompatibility. The production of reactive oxygen species (ROS) was measured by the chemiluminescence (CL) method to evaluate the oxidative stress. The results showed that the CLA-bonding PSF membrane exhibited more stable CBC values, longer CT, and less adsorption of plasma proteins than the unmodified PSF membrane. In addition, the CL counts of hydrogen peroxide and superoxide values for CLA-bonding PSF membrane were more stable than for unmodified PSF membrane. These results demonstrate that CLA-bonding can improve the blood compatibility of PSF membrane. The CLA-bonding PSF membrane could offer protection for patients against oxidative stress and could also reduce the dosage of anticoagulant required during hemodialysis.

  20. 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.

  1. Building chemistry one atom at a time: An investigation of the effects of two curricula in students' understanding of covalent bonding and atomic size

    NASA Astrophysics Data System (ADS)

    Bull, Barbara Jeanne

    Chemists have to rely on models to aid in the explanation of phenomena they experience. Instruction of atomic theory has been used as the introduction and primary model for many concepts in chemistry. Therefore, it is important for students to have a robust understanding of the different atomic models, their relationships and their limitations. Previous research has shown that students have alternative conceptions concerning their interpretation of atomic models, but there is less exploration into how students apply their understanding of atomic structure to other chemical concepts. Therefore, this research concentrated on the development of three Model Eliciting Activities to investigate the most fundamental topic of the atom and how students applied their atomic model to covalent bonding and atomic size. Along with the investigation into students' use of their atomic models, a comparison was included between a traditional chemistry curriculum using an Atoms First approach and Chemistry, Life, the Universe and Everything (CLUE), a NSF-funded general chemistry curriculum. Treatment and Control groups were employed to determine the effectiveness of the curricula in conveying the relationship between atoms, covalent bonds and atomic size. The CLUE students developed a Cloud representation on the Atomic Model Eliciting Activity and maintained this depiction through the Covalent Bonding Model Eliciting Activity. The traditional students more often illustrated the atom using a Bohr representation and continued to apply the same model to their portrayal of covalent bonding. During the analysis of the Atomic Size Model Eliciting Activity, students had difficulty fully supporting their explanation of the atomic size trend. Utilizing the beSocratic platform, an activity was designed to aid students' construction of explanations using Toulmin's Argumentation Pattern. In order to study the effectiveness of the activity, the students were asked questions relating to a four

  2. 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

  3. 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.

  4. Hybrid materials of MCM-41 functionalized by lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes of modified meta-methylbenzoic acid: Covalently bonded assembly and photoluminescence

    SciTech Connect

    Li Ying; Yan Bing

    2008-05-15

    Novel organic-inorganic mesoporous hybrid materials were synthesized by linking lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes to the mesoporous MCM-41 through the modified meta-methylbenzoic acid (MMBA-Si) using co-condensation method in the presence of the cetyltrimethylammonium bromide (CTAB) surfactant as template. The luminescence properties of these resulting materials (denoted as Ln-MMBA-MCM-41, Ln=Tb, Eu) were characterized in detail, and the results reveal that luminescent mesoporous materials have high surface area, uniformity in the ordered mesoporous structure. Moreover, the mesoporous material covalently bonded Tb{sup 3+} complex (Tb-MMBA-MCM-41) exhibits the stronger characteristic emission of Tb{sup 3+} and longer lifetime than Eu-MMBA-MCM-41 due to the triplet state energy of organic legend MMBA-Si matches with the emissive energy level of Tb{sup 3+} very well. - Graphical abstract: Novel organic-inorganic mesoporous luminescent materials were synthesized by linking lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes to covalently bond the functionalized ordered mesoporous MCM-41 with modified meta-methylbenzoic acid (MMBA)-Si by co-condensation of tetraethoxysilane (TEOS) in the presence of the cetyltrimethylammonium bromide (CTAB) surfactant as template.

  5. Hydrolysis Mechanism of the NAMI-A-type Antitumor Complex (HL)[trans-RuCl4L(dmso-S)] (L=1-methyl-1,2,4-triazole)

    NASA Astrophysics Data System (ADS)

    Chen, Lan-mei; Chen, Jin-can; Liao, Si-yan; Liu, Jiang-qin; Luo, Hui; Zheng, Kang-cheng

    2011-08-01

    The hydrolysis process of Ru(III) complex (HL)[trans-RuCl4L(dmso-S)] (L=1-methyl-1,2,4-triazole and dmso-S=S-dimethyl sulfoxide) (1), a potential antitumor complex similar to the well-known antitumor agent (Him)[trans-RuCl4(dmso-S)(im)] (NAMI-A, im=imidazole), was investigated using density functional theory combined with the conductor-like polarizable continuum model approach. The structural characteristics and the detailed energy profiles for the hydrolysis processes of this complex were obtained. For the first hydrolysis step, complex 1 has slightly higher barrier energies than the reported anticancer drug NAMI-A, and the result is in accordance with the experimental evidence indicating larger half-life for complex 1. For the second hydrolysis step, the formation of cis-diaqua species is thermodynamic preferred to that of trans isomers. In addition, on the basis of the analysis of electronic characteristics of species in the hydrolysis process, the trend in nucleophilic attack abilities of hydrolysis products by pertinent biomolecules is revealed and predicted.

  6. Detection of antigens using a protein-DNA chimera developed by enzymatic covalent bonding with phiX gene A*.

    PubMed

    Akter, Farhima; Mie, Masayasu; Grimm, Sebastian; Nygren, Per-Åke; Kobatake, Eiry

    2012-06-01

    The chemical reactions used to make antibody-DNA conjugates in many immunoassays diminish antigen-binding activity and yield heterogeneous products. Here, we address these issues by developing an antibody-based rolling circle amplification (RCA) strategy using a fusion of φX174 gene A* protein and Z(mab25) (A*-Zmab). The φX174 gene A* protein is an enzyme that can covalently link with DNA, while the Z(mab25) protein moiety can bind to specific species of antibodies. The DNA in an A*-Zmab conjugate was attached to the A* protein at a site chosen to not interfere with protein function, as determined by enzyme-linked immunosorbent assay (ELISA) and gel mobility shift analysis. The novel A*-Zmab-DNA conjugate retained its binding capabilities to a specific class of murine immunoglobulin γ1 (IgG1) but not to rabbit IgG. This indicates the generality of the A*-Zmab-based immuno-RCA assay that can be used in-sandwich ELISA format. Moreover, the enzymatic covalent method dramatically increased the yields of A*-Zmab-DNA conjugates up to 80% after a 15 min reaction. Finally, sensitive detection of human interferon-γ (IFN-γ) was achieved by immuno-RCA using our fusion protein in sandwich ELISA format. This new approach of the use of site-specific enzymatic DNA conjugation to proteins should be applicable to fabrication of novel immunoassays for biosensing.

  7. 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).

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  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. 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.

  16. 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-Chien; Yang, Ping

    2013-01-28

    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 MO4x- anions 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 MO4- (M = Mn, Tc, Re) are evaluated for the first time by nonresonant inelastic X-ray scattering, X-ray absorption spectroscopy using fluorescence and transmission (via a scanning transmission X-ray microscope), and time-dependent density functional theory. The results suggest that moving from Group 6 to Group 7 or down the triads increases M-O e* (pi*) mixing; for example, it more than doubles in ReO4- relative to CrO42-. Mixing in the t(2)* orbitals (sigma* + pi*) remains relatively constant within the same Group, but increases on moving from Group 6 to Group 7. These unexpected changes in orbital energy and composition for formally isoelectronic tetraoxometalates are evaluated in terms of periodic trends in d orbital energy and radial extension.

  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. Anion-dependent self-assembly of silver(I) and diaminotriazines to coordination polymers: non-covalent bonds and role interchange between silver and hydrogen bonds.

    PubMed

    Manzano, Blanca R; Jalón, Félix A; Soriano, M Laura; Carrión, M Carmen; Carranza, M Pilar; Mereiter, Kurt; Rodríguez, Ana M; de la Hoz, Antonio; Sánchez-Migallón, Ana

    2008-10-01

    New coordination polymers have been obtained by the self-assembly of silver salts AgX (X = BF 4, PF 6, CF 3SO 3) and 2,4-diamino-6-R-1,3,5-triazines L (R = phenyl and p-tolyl) of formulas AgLX ( 1- 6). A complex of different stoichiometry, [Ag 3L 2(H 2O)(acetone) 2](BF 4) 3, 7 (R = phenyl), has also been synthesized. The three-dimensional structures of five compounds have been determined by X-ray diffraction studies. For the AgLX complexes, when X = BF 4 and R = phenyl or p-tolyl, chiral chains with alternating Ag and L are formed. The chains are cross-linked by the counteranions in a three-dimensional fashion through hydrogen bonds and weak Ag...F interactions giving rise to a structure with solvent-filled channels. Different and more compact structures have been found when the counteranion is CF 3SO 3 (OTf). When R = phenyl, sheets are formed which consist of [Ag 2(OTf) 2L 2] units with double triflate bridges and which contain columns of pi-pi stacked arenes. Hydrogen bonds connect the sheets. When AgOTf is used and R is p-tolyl, a different and unusual ladderlike structure is obtained in which the rungs are double asymmetric bridges consisting of the triflate groups bonded to Ag in kappa (2) O,mu 2- O and kappa (1) O,mu 2- O fashion. The ladders are parallel to each other and are mutually linked by N-H...N hydrogen bonds to give a 3D architecture. A very similar ladderlike structure has been found for 7 but with a water molecule and a BF 4 (-) group acting as bridges. The role played by the hydrogen bonds in complex 6 to form the 3-D structure is played in 7 by [Ag(acetone) 2] fragments. The noncovalent interactions play an important role in the different solid-state 3D structures. The behavior of the new derivatives in solution has also been analyzed. A new species has been detected at low temperatures, and this exhibits restricted rotation of the phenyl ring.

  19. C57BL/6 x BALB/c hybridomas produce IgA which assembles into molecules with covalent bonds between heavy chains (H) and light chains (L), and into molecules lacking covalent bonds between H and L.

    PubMed

    Wims, L A; Sharon, J; Newman, B; Kabat, E A; Morrison, S L

    1985-12-01

    Examination of the gel electrophoresis patterns of 14C-biosynthetically labeled immunoglobulin from C57BL/6 X BALB/c IgA hybridomas reveals that each of the monoclonal cell populations produces two different forms of IgA: molecules with heavy chains (H) and light chains (L) joined by disulfide bonds, as well as molecules with H and L being noncovalently associated. The possible origin of this was explored: Southern blot analysis of the hybridoma DNA indicated that only one alpha gene is expressed by each cell line; hybridoma cells labeled in the presence of the N-glycosylation inhibitor tunicamycin exhibit both forms; and electrophoresis of biosynthetically labeled spleen cell IgA from C57BL/6, BALB/c and (C57BL/6 X BALB/c) F1 mice shows that BALB/c mice produce only the noncovalently associated form, while C57BL/6 and (C57BL/6 X BALB/c) F1 mice produce both. Possible mechanisms by which two types of IgA may be assembled by the same hybridoma cell are discussed.

  20. Cyclometallation of arylimines and nitrogen-containing heterocycles via room-temperature C-H bond activation with arene ruthenium(II) acetate complexes.

    PubMed

    Li, Bin; Roisnel, Thierry; Darcel, Christophe; Dixneuf, Pierre H

    2012-08-28

    The reaction of [RuCl(2)(p-cymene)](2) with arylimines and 4 equiv. of KOAc in methanol at room temperature produces stable (N^C)-cyclometallated ruthenium(II) complexes via C-H bond activation/deprotonation. This method can be applied also to nitrogen-containing molecules: N-phenylpyrazole, 2-phenyl-2-oxazoline and benzo[h]quinoline. N-Phenyl-pyrazole, [RuCl(2)(p-cymene)](2) and diphenylacetylene directly lead to alkyne insertion into the metallacycle C-Ru bond. PMID:22890507

  1. Modeling the conformational preference of the carbon-bonded covalent adduct formed upon exposure of 2'-deoxyguanosine to ochratoxin A.

    PubMed

    Sharma, Purshotam; Manderville, Richard A; Wetmore, Stacey D

    2013-05-20

    The conformational flexibility of the C8-linked guanine adduct formed from attachment of ochratoxin A (OTA) was analyzed using a systematic computational approach and models ranging from the nucleobase to the adducted DNA helix. A focus was placed on the influence of the C8-modification of 2'-deoxyguanosine (dG) on the preferred relative arrangement of the nucleobase and the C8-substituent and, more importantly, the anti/syn conformational preference with respect to the glycosidic bond. Although OTA is twisted with respect to the base in the nucleobase model, addition of the deoxyribose sugar induces a further twist and restricts rotation about the C-C linkage due to close contacts between OTA and the sugar. The nucleoside model preferentially adpots a syn orientation (by 10-20 kJ mol(-1) depending on the OTA conformation) due to the presence of an O5'-H···N3 interaction. However, when this hydrogen bond is eliminated, which better mimics the DNA environment, a small (<5 kJ mol(-1)) anti/syn energy difference is predicted. Inclusion of the 5'-monophosphate group leads to an up to 20 kJ mol(-1) preference for the syn (nucleotide) conformation due to stabilizing base-phosphate interactions involving the amino group of guanine. Nevertheless, MD simulations and free energy analysis predict that both syn- and anti-conformations of OTB-dG are equally stable in helices when paired opposite cytosine. These results indicate that the adduct will likely adopt a syn conformation in an isolated nucleoside and nucleotide, while a mixture of syn and anti conformations will be observed in DNA duplexes. Since the syn conformation could stabilize base mismatches upon DNA replication or Z-DNA structures with varied biological outcomes, future computational and experimental work should elucidate the consequences of the conformational preference of this potentially harmful DNA lesion.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. Optimization of amino group density on surfaces of titanium dioxide nanoparticles covalently bonded to a silicone substrate for antibacterial and cell adhesion activities.

    PubMed

    Okada, Masahiro; Yasuda, Shoji; Kimura, Tsuyoshi; Iwasaki, Mitsunobu; Ito, Seishiro; Kishida, Akio; Furuzono, Tsutomu

    2006-01-01

    A composite consisting of titanium dioxide (TiO2) particle, the surface of which was modified with amino groups, and a silicone substrate through covalent bonding at their interface was developed, and antibacterial and cell adhesion activities of the composite were evaluated. The density of the amino groups on the TiO2 particle surface was controlled by the reaction time of the modification reaction. The degradation rate of CH3CHO in the presence of the TiO2 particles under UV irradiation decreased with an increase in the amino group density on the TiO2 surface. On the other hand, the number of L929 cells adhering on the TiO2/silicone composite increased with an increase in the amino group density. From the above two results, the optimum density of amino groups for both photoreactivity and cell adhesiveness was estimated to be 2.0-4.0 molecules/nm2. The optimum amino group-modified TiO2/silicone composite sheet (amino group density, 3.0 molecules/nm2) showed an effective antibacterial activity for Escherichia coli bacteria under UV irradiation.

  7. Reduction of lung metastasis by ImH[trans-RuCl4(DMSO)Im]: mechanism of the selective action investigated on mouse tumors.

    PubMed

    Sava, G; Clerici, K; Capozzi, I; Cocchietto, M; Gagliardi, R; Alessio, E; Mestroni, G; Perbellini, A

    1999-01-01

    NAMI-A (imidazolium trans-imidazoledimethylsulfoxidetetrachlororuthenate, ImH[trans-RuCl4(DMSO)Im]) is a new ruthenium compound active against lung metastasis of solid metastasizing tumors. We have tested this compound in mice with Lewis lung carcinoma or MCa mammary carcinoma in order to compare the effects on primary tumor and lung metastases with possible alterations of cell cycle distribution of tumor cells. We have also investigated whether there were unequal tissue accumulations of the compound itself at different dose levels ranging from 17.5 to 70 mg/kg/day given for six consecutive days. NAMI-A caused a reduction of metastasis weight larger than that of metastasis number; we explain this finding as the capacity of NAMI-A to selectively interfere with the growth of metastases already settled in the lungs. However, this specificity is not simply related to a larger concentration of NAMI-A in the lungs than in other tissues. Following i.p. treatment, NAMI-A rapidly disappeared from the peritoneal cavity; its low blood concentration may be caused by rapid renal clearance. These data provide further evidence for a selective anti-metastasis effect of the ruthenium complex NAMI-A. The reduction of lung metastasis is followed by a significant prolongation of the host's life-time expectancy, indicating a therapeutic benefit of NAMI-A on lung metastases from solid tumors.

  8. Synthesis, potentiometric titration, electrochemical investigation and biological properties of trans-[RuCl2(dinic)4] (dinic = 3,5-pyridinecarboxylic acid).

    PubMed

    Seifriz, I; Konzen, M; Paula, M M; Gonçalves, N S; Spoganickz, B; Creczynski-Pasa, T B; Bonetti, V R; Beirith, A; Calixto, J B; Franco, C V

    1999-09-30

    This work discusses both the synthesis of trans-[RuCl2(dinic)4], dinic = 3,5-pyridinecarboxylic acid, and its main characteristics including potentiometric titration, spectroscopic and electrochemical properties, and some biological properties. The complex was synthesized using ruthenium blue solution as the precursor in a synthetic route. The complex was characterized using electronic spectroscopy, vibrational FT-IR spectroscopy, and Raman spectroscopy, as well as 1H and 13C NMR. The results indicated that the complex exhibits a trans-geometry. Cyclic voltammetry carried out in water:acetone 1:1 solution revealed a quasi-reversible process centered on the Ru(II) atom, as well as a dependence of the redox potential, E1/2, on pH. An analysis of the electronic spectra revealed that the MLCT (metal ligand charge transfer) band underwent a hypsochromic shift as the pH increased. Spectroelectrochemical analysis indicated that the visible region band progressively faded out upon oxidation. The equilibrium constants for the eight protons of the complex were determined by potentiometric titration. The complex neither inhibits the activity of nitrogen monoxide synthase nor acts as a scavenger for nitrogen monoxide. Nevertheless, the complex shows antinociceptive properties and acts as a scavenger for hydroxyl radicals.

  9. Correlation of [RuCl3(dppb)(VPy)] cytotoxicity with its effects on the cell membranes: an investigation using Langmuir monolayers as membrane models.

    PubMed

    Sandrino, B; Tominaga, T T; Nobre, T M; Scorsin, L; Wrobel, E C; Fiorin, B C; de Araujo, M P; Caseli, L; Oliveira, O N; Wohnrath, K

    2014-09-11

    One of the major challenges in drug design is to identify compounds with potential toxicity toward target cells, preferably with molecular-level understanding of their mode of action. In this study, the antitumor property of a ruthenium complex, mer-[RuCl3(dppb)(VPy)] (dppb = 1,4-bis(diphenylphosphine)butane and VPy = 4-vinylpyridine) (RuVPy), was analyzed. Results showed that this compound led to a mortality rate of 50% of HEp-2 cell with 120 ± 10 μmol L(-1), indicating its high toxicity. Then, to prove if its mode of action is associated with its interaction with cell membranes, Langmuir monolayers were used as a membrane model. RuVPy had a strong effect on the surface pressure isotherms, especially on the elastic properties of both the zwitterionic dipalmitoylphosphatidylcholine (DPPC) and the negatively charged dipalmitoylphosphatidylglycerol (DPPG) phospholipids. These data were confirmed by polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS). In addition, interactions between the positive group from RuVPy and the phosphate group from the phospholipids were corroborated by density functional theory (DFT) calculations, allowing the determination of the Ru complex orientation at the air-water interface. Although possible contributions from receptors or other cell components cannot be discarded, the results reported here represent evidence for significant effects on the cell membranes which are probably associated with the high toxicity of RuVPy.

  10. Experimental visualization of covalent bonds and structural disorder in a gallium zinc oxynitride photocatalyst (Ga(1-x)Znx)(N(1-x)Ox): origin of visible light absorption.

    PubMed

    Yashima, Masatomo; Yamada, Hiroki; Maeda, Kazuhiko; Domen, Kazunari

    2010-04-14

    We present the experimental visualization of covalent bonding, positional disorders and split anion sites in visible-light responsive photocatalyst (Ga(0.885)Zn(0.115))(N(0.885)O(0.115)). ZnO alloying into GaN reduces the band gap, leading to the visible-light response. DFT calculations indicated no significant difference in band gap between structural models with and without split sites. PMID:20309458

  11. 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

  12. 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

  13. 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.

  14. Stochastic sensing through covalent interactions

    DOEpatents

    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.

  15. First-principles calculation of the 17O NMR parameters in Ca oxide and Ca aluminosilicates: the partially covalent nature of the Ca-O bond, a challenge for density functional theory.

    PubMed

    Profeta, Mickaël; Benoit, Magali; Mauri, Francesco; Pickard, Chris J

    2004-10-01

    We apply density functional theory (DFT) to the calculation of the (17)O NMR parameters in Ca and Mg oxides and aluminosilicates. We study the accuracy of the Perdew, Burke, and Ernzerhof (PBE) generalized-gradient approximation to DFT in the description of these systems and the origin of the experimentally observed large dependence of the (17)O chemical shift on the alkaline earth ion. We find that (i) the partially covalent nature of the Ca-O bond has a huge impact on the O chemical shifts. The Ca-O covalence alone explains why in Ca oxides and aluminosilicates the (17)O chemical shifts are much more deshielded than those of the corresponding Mg compounds. (ii) The Ca-O covalence is overestimated by the PBE functional. Thus PBE-DFT is not able to reproduce the measured (17)O NMR parameters in Ca oxide and Ca aluminosilicates. (iii) It is possible to correct for the PBE-DFT deficiency in a simple and transferable way and to predict very accurate (17)O NMR parameters. Such accuracy allows us to assign the (17)O NMR spectra of two important model systems: the grossite aluminate (CaAl(4)O(7)) and the wollastonite (CaSiO(3)) silicate.

  16. [Adenosine- and ethenoadenosine-5'-trimetaphosphates: the effect of covalent bond formation on the state of the affinity label in the complex with phenylalanyl-tRNA-synthetase].

    PubMed

    Nevinskiĭ, G A; Podust, V N; Khodyreva, S N; Gorshkova, I I; Lavrik, O I

    1984-01-01

    epsilon ATP is a substrate of phenylalanyl-tRNA synthetase and epsilon Ado is a competitive inhibitor of ATP in the reaction of tRNA aminoacylation (Ki = 1.6 mM). The association of phenylalanyl-tRNA synthetase with ATP or Ado results in synergistic binding of phenylalaninol and phenylalanine, respectively. However neither epsilon ATP nor epsilon Ado exhibit synergism. Adenosine- and ethenoadenosine-5'-trimethaphosphates are shown to be similar affinity reagents of phenylalanyl-tRNA synthetase. ATP being covalently bound to the enzyme shows essentially lower synergistic effect in comparison with free ATP. epsilon ATP-label is practically insensitive to the ligands namely ATP, Phe, phenylalaninol and is highly accessible for I- ions. The scheme of behaviour of affinity labels is assumed to be as follows: a) the formation of specific reagent-enzyme complex, b) the covalent attachment of the reagent to the enzyme, c) the covalent binding induced disruption of the specific complex formed before. PMID:6390177

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

    SciTech Connect

    Moore, k; schwartz, a; Wall, m; haire, d; der laan, g v

    2006-05-30

    Actinide physics and chemistry are of great interest due to the unique behavior of the 5f states that dominate the electronic structure. How these states evolve with changes in crystal structure, alloying, oxidation state, and radiation damage is of considerable importance to better understand these materials. Oxidations state: How are the f electrons bonding in actinide oxides? Radiation damage: U and Pu evolve with time due to self-induced radiation damage of the lattice. How does this affect the f states? Our goal here is to examine how oxidation and radiation damage influence the bonding behavior of the 5f electrons in U and Pu.

  18. 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.

  19. 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.

  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. Reversible Michael additions: covalent inhibitors and prodrugs.

    PubMed

    Johansson, Martin H

    2012-11-01

    Covalent inhibition is an efficient molecular mechanism for inhibiting enzymes or modulating the function of proteins and is found in the action of many drugs and biologically active natural products. However, it is has been less appreciated that the formation of covalent bonds can be reversible or irreversible. This review focuses on biologically active compounds that are Michael acceptors and how the reversible nature of the Michael addition reaction influences biological activity and how this can be exploited in designing prodrugs.

  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. Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations

    PubMed Central

    Bueren-Calabuig, Juan A.; Giraudon, Christophe; Galmarini, Carlos M.; Egly, Jean Marc; Gago, Federico

    2011-01-01

    The difference in melting temperature of a double-stranded (ds) DNA molecule in the absence and presence of bound ligands can provide experimental information about the stabilization brought about by ligand binding. By simulating the dynamic behaviour of a duplex of sequence 5′-d(TAATAACGGATTATT)·5′-d(AATAATCCGTTATTA) in 0.1 M NaCl aqueous solution at 400 K, we have characterized in atomic detail its complete thermal denaturation profile in <200 ns. A striking asymmetry was observed on both sides of the central CGG triplet and the strand separation process was shown to be strongly affected by bonding in the minor groove of the prototypical interstrand crosslinker mitomycin C or the monofunctional tetrahydroisoquinolines trabectedin (Yondelis®), Zalypsis® and PM01183®. Progressive helix unzipping was clearly interspersed with some reannealing events, which were most noticeable in the oligonucleotides containing the monoadducts, which maintained an average of 6 bp in the central region at the end of the simulations. These significant differences attest to the demonstrated ability of these drugs to stabilize dsDNA, stall replication and transcription forks, and recruit DNA repair proteins. This stabilization, quantified here in terms of undisrupted base pairs, supports the view that these monoadducts can functionally mimic a DNA interstrand crosslink. PMID:21727089

  5. Topology of electron charge density for chemical bonds from valence bond theory: a probe of bonding types.

    PubMed

    Zhang, Lixian; Ying, Fuming; Wu, Wei; Hiberty, Philippe C; Shaik, Sason

    2009-01-01

    To characterize the nature of bonding we derive the topological properties of the electron charge density of a variety of bonds based on ab initio valence bond methods. The electron density and its associated Laplacian are partitioned into covalent, ionic, and resonance components in the valence bond spirit. The analysis provides a density-based signature of bonding types and reveals, along with the classical covalent and ionic bonds, the existence of two-electron bonds in which most of the bonding arises from the covalent-ionic resonance energy, so-called charge-shift bonds. As expected, the covalent component of the Laplacian at the bond critical point is found to be largely negative for classical covalent bonds. In contrast, for charge-shift bonds, the covalent part of the Laplacian is small or positive, in agreement with the weakly attractive or repulsive character of the covalent interaction in these bonds. On the other hand, the resonance component of the Laplacian is always negative or nearly zero, and it increases in absolute value with the charge-shift character of the bond, in agreement with the decrease of kinetic energy associated with covalent-ionic mixing. A new interpretation of the topology of the total density at the bond critical point is proposed to characterize covalent, ionic, and charge-shift bonding from the density point of view.

  6. 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

  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.

  8. 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)

  9. 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.

  10. 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.

  11. 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

  12. 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)

  13. CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints.

    PubMed

    Ouyang, Xuchang; Zhou, Shuo; Su, Chinh Tran To; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

    2013-02-01

    Covalent linkage formation is a very important mechanism for many covalent drugs to work. However, partly due to the limitations of proper computational tools for covalent docking, most covalent drugs are not discovered systematically. In this article, we present a new covalent docking package, the CovalentDock, built on the top of the source code of Autodock. We developed an empirical model of free energy change estimation for covalent linkage formation, which is compatible with existing scoring functions used in docking, while handling the molecular geometry constrains of the covalent linkage with special atom types and directional grid maps. Integrated preparation scripts are also written for the automation of the whole covalent docking workflow. The result tested on existing crystal structures with covalent linkage shows that CovalentDock can reproduce the native covalent complexes with significant improved accuracy when compared with the default covalent docking method in Autodock. Experiments also suggest that CovalentDock is capable of covalent virtual screening with satisfactory enrichment performance. In addition, the investigation on the results also shows that the chirality and target selectivity along with the molecular geometry constrains are well preserved by CovalentDock, showing great capability of this method in the application for covalent drug discovery.

  14. 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…

  15. Cis-[RuCl(BzCN)(N-N)(P-P)]PF6 complexes: Synthesis and in vitro antitumor activity: (BzCN=benzonitrile; N-N=2,2'-bipyridine; 1,10-phenanthroline; P-P=1,4-bis(diphenylphosphino) butane, 1,2-bis(diphenylphosphino)ethane, or 1,1'-(diphenylphosphino)ferrocene).

    PubMed

    Pereira, Flávia de C; Lima, Benedicto A V; de Lima, Aliny P; Pires, Wanessa C; Monteiro, Thallita; Magalhães, Lorena F; Costa, Wanderson; Graminha, Angélica E; Batista, Alzir A; Ellena, Javier; Siveira-Lacerda, Elisângela de P

    2015-08-01

    The motivation to use ruthenium complexes in cancer treatment has led our research group to synthesize complexes with this metal and test them against several types of tumor cells, yielding promising results. In this paper the results of biological tests, assessed by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, were carried out on the complexes cis-[RuCl(BzCN)(bipy)(dppe)]PF6 (1), cis-[RuCl(BzCN)(bipy)(dppb)]PF6 (2), cis-[RuCl(BzCN)(bipy)(dppf)]PF6 (3) and cis-[RuCl(BzCN)(phen)(dppb)]PF6 (4) which are described [BzCN = b enzonitrile; bipy = 2,2'-bipyridine; phen = 1,10-phenanthroline; dppe = 1,2-bis(diphenylphosphino) ethane; dppb = 1,4-bis-(diphenylphosphino)butane; dppf = 1,1'-bis(diphenylphosphino)ferrocene]. The present study is focused on the cytotoxic activity of complexes (1)-(4) against four tumor cell lines and on the apoptosis and changes in the cell cycle and gene expression observed in the sarcoma 180 (S180) tumor cell line treated with complex (1). The results demonstrated that this complex inhibits S180 cell growth, with an IC50 of 17.02 ± 8.21 μM, while exhibiting lower cytotoxicity (IC50 = 53.73 ± 5.71 μM) towards lymphocytes (normal cells). Flow cytometry revealed that the complex inhibits the growth of tumor cells by inducing apoptosis as evidenced by an increase in the proportion of cells positive for annexin V staining and G0/G1 phase cell-cycle arrest. Further investigation showed that complex (1) induces a drop in the mitochondrial membrane potential and provokes a decrease in Bcl-2 protein expression and increase in caspase 3 activation, while the increased activation of caspase 8 caused a decrease in the gene expression in caspases 3 and 9. Increases in Tp53 and Bax expressions were also observed.

  16. 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.

  17. 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)

  18. 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.

  19. Non-Covalent Derivatives: Cocrystals and Eutectics.

    PubMed

    Stoler, Emily; Warner, John C

    2015-01-01

    Non-covalent derivatives (NCDs) are formed by incorporating one (or more) coformer molecule(s) into the matrix of a parent molecule via non-covalent forces. These forces can include ionic forces, Van der Waals forces, hydrogen bonding, lipophilic-lipophilic interactions and pi-pi interactions. NCDs, in both cocrystal and eutectic forms, possess properties that are unique to their supramolecular matrix. These properties include critical product performance factors such as solubility, stability and bioavailability. NCDs have been used to tailor materials for a variety of applications and have the potential to be used in an even broader range of materials and processes. NCDs can be prepared using little or no solvent and none of the reagents typical to synthetic modifications. Thus, NCDs represent a powerfully versatile, environmentally-friendly and cost-effective opportunity. PMID:26287141

  20. 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

  1. 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

  2. Photosensitive diazotized poly(ethylene glycol) covalent capillary coatings for analysis of proteins by capillary electrophoresis.

    PubMed

    Yu, Bing; Chen, Xin; Cong, Hailin; Shu, Xi; Peng, Qiaohong

    2016-09-01

    A new method for the fabrication of covalently cross-linked capillary coatings of poly(ethylene glycol) (PEG) is described using diazotized PEG (diazo-PEG) as a new photosensitive coating agent. The film of diazo-PEG depends on ionic bonding and was first prepared on the inner surface of capillary by self-assembly, and ionic bonding was converted into covalent bonding after reaction of ultraviolet light with diazo groups through unique photochemical reaction. The covalently bonded coating impedance adsorption of protein on the central surface of capillary and hence the four proteins ribonuclease A, cytochrome c, bovine serum albumin, and lysosome can be baseline separated by using capillary electrophoresis (CE). The covalently cross-linked diazo-PEG capillary column coatings not only improved the CE separation performance for proteins compared to non-covalently cross-linked coatings or bare capillary but also showed a remarkable chemical solidity and repeatability. Because photosensitive diazo-PEG took the place of the highly noxious and silane moisture-sensitive coating reagents in the fabrication of covalent coating, this technique shows the advantage of being environment-friendly and having a high efficiency for CE to make the covalently bonded capillaries. PMID:27475442

  3. Synthetic Covalent and Non-Covalent 2D Materials.

    PubMed

    Boott, Charlotte E; Nazemi, Ali; Manners, Ian

    2015-11-16

    The creation of synthetic 2D materials represents an attractive challenge that is ultimately driven by their prospective uses in, for example, electronics, biomedicine, catalysis, sensing, and as membranes for separation and filtration. This Review illustrates some recent advances in this diverse field with a focus on covalent and non-covalent 2D polymers and frameworks, and self-assembled 2D materials derived from nanoparticles, homopolymers, and block copolymers.

  4. 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

  5. The reactions of para-halo diaryl diselenides with halogens. A structural investigation of the CT compound (p-FC6H4)2Se2I2, and the first reported “RSeI3” compound, (p-ClC6H4)SeI·I2, which contains a covalent Se-I bond.

    PubMed

    Barnes, Nicholas A; Godfrey, Stephen M; Hughes, Jill; Khan, Rana Z; Mushtaq, Imrana; Ollerenshaw, Ruth T A; Pritchard, Robin G; Sarwar, Shamsa

    2013-02-28

    The reactions of the diaryl-diselenides (p-FC(6)H(4))(2)Se(2) and (p-ClC(6)H(4))(2)Se(2) with diiodine have been investigated. Species of stoichiometry "RSeI" are formed when the ratio employed is 1:1. The solid-state structure of "(p-FC(6)H(4))SeI" has been determined, and shown to be a charge-transfer (CT) adduct, (p-FC(6)H(4))(2)Se(2)I(2), where the Se-Se bond is retained and the diiodine molecule interacts with only one of the selenium atoms. The Se-I bond in (p-FC(6)H(4))(2)Se(2)I(2) is 2.9835(12) Å, which is typical for a (10-I-2) Se-I-I CT system. When diiodine is reacted in a 3:1 ratio with (p-XC(6)H(4))(2)Se(2) (X = F, Cl) species of stoichiometry "RSeI(3)" are formed. The structure of "(p-ClC(6)H(4))SeI(3)" reveals that this is not a selenium(IV) compound, but is better represented as a selenium(II) CT adduct, (p-ClC(6)H(4))SeI·I(2). The Se-I bond to the diiodine molecule is typical in magnitude for a CT adduct, Se-I: 2.8672(5) Å, whereas the other Se-I bond is much shorter, Se-I: 2.5590(6) Å, and is a genuine example of a rarely observed covalent Se-I bond, which appears to be stabilised by a weak Se···I interaction from a neighbouring iodine atom. The reaction of (p-ClC(6)H(4))SeI with Ph(3)P results in the formation of a CT adduct, Ph(3)PSe(p-ClC(6)H(4))I, which has a T-shaped geometry at selenium (10-Se-3). By contrast, the reaction of (p-FC(6)H(4))SeI with Ph(3)P does not form an adduct, but results in the formation of Ph(3)PI(2) and (p-FC(6)H(4))(2)Se(2).

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. Soft bond-deformation paths in superhard γ-boron.

    PubMed

    Zhou, Wei; Sun, Hong; Chen, Changfeng

    2010-11-19

    We report surprisingly soft covalent bond-deformation paths in recently discovered superhard γ-boron. First-principles calculations reveal an intriguing mechanism for bond transformation mediated by three-center bonding, which reduces considerably the rigidity and directionality of the two-center covalent bonds in γ-boron. It leads to much lower strength and large plastic deformation along the selected paths. These results establish a new type of bond-deformation pattern in γ-boron, which expands our knowledge about structural transformation in strong covalent solids.

  11. Soft Bond-Deformation Paths in Superhard γ-Boron

    NASA Astrophysics Data System (ADS)

    Zhou, Wei; Sun, Hong; Chen, Changfeng

    2010-11-01

    We report surprisingly soft covalent bond-deformation paths in recently discovered superhard γ-boron. First-principles calculations reveal an intriguing mechanism for bond transformation mediated by three-center bonding, which reduces considerably the rigidity and directionality of the two-center covalent bonds in γ-boron. It leads to much lower strength and large plastic deformation along the selected paths. These results establish a new type of bond-deformation pattern in γ-boron, which expands our knowledge about structural transformation in strong covalent solids.

  12. Novel hydroxyapatite biomaterial covalently linked to raloxifene.

    PubMed

    Meme, L; Santarelli, A; Marzo, G; Emanuelli, M; Nocini, P F; Bertossi, D; Putignano, A; Dioguardi, M; Lo Muzio, L; Bambini, F

    2014-01-01

    Since raloxifene, a drug used in osteoporosis therapy, inhibits osteoclast, but not osteoblast functions, it has been suggested to improve recovery during implant surgery. The present paper describes an effective method to link raloxifene, through a covalent bond, to a nano-Hydroxyapatite-based biomaterial by interfacing with (3-aminopropyl)-Triethoxysilane as assessed by Infra Red-Fourier Transformed (IR-FT) spectroscopy and Scanning Electron Microscope (SEM). To evaluate the safety of this modified new material, the vitality of osteoblast-like cells cultured with the new biomaterial was then investigated. Raloxifene-conjugated HAbiomaterial has been shown to be a safe material easy to obtain which could be an interesting starting point for the use of a new functional biomaterial suitable in bone regeneration procedures. PMID:25280036

  13. 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

  14. Covalent attachment of lactase to low-density polyethylene films.

    PubMed

    Goddard, J M; Talbert, J N; Hotchkiss, J H

    2007-01-01

    Polymer films to which bioactive compounds such as enzymes are covalently attached offer potential for in-package processing of food. Beta-galactosidase (lactase) was covalently attached to surface-functionalized low-density polyethylene films. A two-step wet chemical functionalization introduced 15.7 nmol/cm2 primary amines to the film surface. Contact angle, dye assays, X-ray photoelectron spectroscopy, and appropriate protein assays were used to characterize changes in film surface chemistry after each step in the process of attachment. Glutaraldehyde was used to covalently attach lactase to the surface at a density of 6.0 microg protein per cm2 via reductive amination. The bond between the covalently attached lactase and the functionalized polyethylene withstood heat treatment in the presence of an ionic denaturant with 74% enzyme retention, suggesting that migration of the enzyme into the food product would be unlikely. The resulting polyethylene had an enzyme activity of 0.020 lactase units (LU)/cm2 (approximately 4500 LU/g). These data suggest that enzymes that may have applications in foods can be covalently attached to inert polymer surfaces, retain significant activity, and thus have potential as a nonmigratory active packaging materials.

  15. 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…

  16. Strong covalent hydration of terephthalaldehyde.

    PubMed

    Baymak, Melek S; Vercoe, Kellie L; Zuman, Petr

    2005-11-24

    Spectrophotometric and electroanalytical studies indicate that one of the formyl groups of terephthalaldehyde in aqueous solution is present in about 23% as a geminal diol. Stronger covalent hydration of CHO in terephthalaldehyde than in p-nitrobenzaldehyde is attributed to a strong resonance interaction between the two formyl groups.

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

    PubMed Central

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

    2011-01-01

    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

  18. 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

  19. 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)

  20. Discovery of covalent inhibitors of glyceraldehyde-3-phosphate dehydrogenase, a target for the treatment of malaria.

    PubMed

    Bruno, Stefano; Pinto, Andrea; Paredi, Gianluca; Tamborini, Lucia; De Micheli, Carlo; La Pietra, Valeria; Marinelli, Luciana; Novellino, Ettore; Conti, Paola; Mozzarelli, Andrea

    2014-09-11

    We developed a new class of covalent inhibitors of Plasmodium falciparum glyceraldehyde-3-phosphate dehydrogenase, a validated target for the treatment of malaria, by screening a small library of 3-bromo-isoxazoline derivatives that inactivate the enzyme through a covalent, selective bond to the catalytic cysteine, as demonstrated by mass spectrometry. Substituents on the isoxazolinic ring modulated the potency up to 20-fold, predominantly due to an electrostatic effect, as assessed by computational analysis. PMID:25137375

  1. Equilibrium CO bond lengths

    NASA Astrophysics Data System (ADS)

    Demaison, Jean; Császár, Attila G.

    2012-09-01

    Based on a sample of 38 molecules, 47 accurate equilibrium CO bond lengths have been collected and analyzed. These ultimate experimental (reEX), semiexperimental (reSE), and Born-Oppenheimer (reBO) equilibrium structures are compared to reBO estimates from two lower-level techniques of electronic structure theory, MP2(FC)/cc-pVQZ and B3LYP/6-311+G(3df,2pd). A linear relationship is found between the best equilibrium bond lengths and their MP2 or B3LYP estimates. These (and similar) linear relationships permit to estimate the CO bond length with an accuracy of 0.002 Å within the full range of 1.10-1.43 Å, corresponding to single, double, and triple CO bonds, for a large number of molecules. The variation of the CO bond length is qualitatively explained using the Atoms in Molecules method. In particular, a nice correlation is found between the CO bond length and the bond critical point density and it appears that the CO bond is at the same time covalent and ionic. Conditions which permit the computation of an accurate ab initio Born-Oppenheimer equilibrium structure are discussed. In particular, the core-core and core-valence correlation is investigated and it is shown to roughly increase with the bond length.

  2. 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.

  3. 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.

  4. 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

  5. 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…

  6. Structure-based design of covalent Siah inhibitors.

    PubMed

    Stebbins, John L; Santelli, Eugenio; Feng, Yongmei; De, Surya K; Purves, Angela; Motamedchaboki, Khatereh; Wu, Bainan; Ronai, Ze'ev A; Liddington, Robert C; Pellecchia, Maurizio

    2013-08-22

    The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches. Ultimately, a rational structure-based design strategy was successful for the identification of Siah inhibitors in which peptide binding drives specific covalent bond formation with the target. X-ray crystallography, mass spectrometry, and functional data demonstrate that these peptide mimetics are efficient covalent inhibitors of Siah and antagonize Siah-dependent regulation of Erk and Hif signaling in the cell. The proposed strategy may result useful as a general approach to the design of peptide-based inhibitors of other protein-protein interactions.

  7. 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.

  8. Covalent biofunctionalization of silicon nitride surfaces.

    PubMed

    Arafat, Ahmed; Giesbers, Marcel; Rosso, Michel; Sudhölter, Ernst J R; Schroën, Karin; White, Richard G; Yang, Li; Linford, Matthew R; Zuilhof, Han

    2007-05-22

    Covalently attached organic monolayers on etched silicon nitride (SixN4; x >/= 3) surfaces were prepared by reaction of SixN4-coated wafers with neat or solutions of 1-alkenes and 1-alkynes in refluxing mesitylene. The surface modification was monitored by measurement of the static water contact angle, XPS, IRRAS, AFM, and ToF-SIMS, and evidence for the formation of Si-C bonds is presented. The etching can be achieved by dilute HF solutions and yields both Si-H and N-H moieties. The resulting etched SixN4 surfaces are functionalized by terminal carboxylic acid groups in either of two ways: (a) via attachment of a 10-undecenoic acid 2,2,2-trifluoroethyl ester (trifluoro ethanol ester) and subsequent thermal acid hydrolysis; (b) through attachment of a photocleavable ester, and subsequent photochemical cleavage, as this would allow photopatterned functionalized SixN4. The carboxylic acids are successfully used for the attachment of oligopeptides (aspartame) and complete proteins using EDC/NHS chemistry. Finally, an amino-terminated organic monolayer can be formed by reaction of HF-treated SixN4 surfaces with a N-(omega-undecylenyl)phthalimide, which yields an amino-terminated surface upon deprotection with hydrazine.

  9. 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

  10. 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.

  11. 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

  12. Facile synthesis of covalent probes to capture enzymatic intermediates during E1 enzyme catalysis.

    PubMed

    An, Heeseon; Statsyuk, Alexander V

    2016-02-11

    We report a facile synthetic strategy to prepare UBL-AMP electrophilic probes that form a covalent bond with the catalytic cysteine of cognate E1s, mimicking the tetrahedral intermediate of the E1-UBL-AMP complex. These probes enable the structural and biochemical study of both canonical- and non-canonical E1s.

  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. 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)

  15. 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.

  16. Lipid bilayers covalently anchored to carbon nanotubes.

    PubMed

    Dayani, Yasaman; Malmstadt, Noah

    2012-05-29

    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. Multiwalled 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.

  17. Learners' Mental Models of Chemical Bonding

    NASA Astrophysics Data System (ADS)

    Coll, Richard K.; Treagust, David F.

    2001-06-01

    The research reported in this inquiry consisted of a study involving two each of Year-12, undergraduate and postgraduate Australian students. The learners' mental models for chemical bonding were elicited using semi-structured interviews comprising a three-phase interview protocol. Each learner was presented with samples of metallic, ionic and covalent substances, and asked to describe the bonding in the substance. Second, they were shown prompts in the form of Interviews-About-Events (IAE) focus cards depicting events that involved the use of models of chemical bonding. Finally, each was shown prompts in the form of focus cards derived from curriculum material that showed ways in which the bonding in specific metallic, ionic and covalent substances had been depicted. Students' responses revealed that learners across all three academic levels prefer simple, realistic mental models for chemical bonding.

  18. Two supramolecular complexes based on polyoxometalates and Co-EDTA units via covalent connection or non-covalent interaction

    NASA Astrophysics Data System (ADS)

    Teng, Chunlin; Xiao, Hanxi; Cai, Qing; Tang, Jianting; Cai, Tiejun; Deng, Qian

    2016-11-01

    Two new 3D network organic-inorganic hybrid supramolecular complexes {[Na6(CoEDTA)2(H2O)13]·(H2SiW12O40)·xH2O}n (1) and [CoH4EDTA(H2O)]2(SiW12O40)·15H2O (2) (H4EDTA=Ethylenediamine tetraacetic acid) have been successfully synthesized by solution method, and characterized by infrared spectrum (IR), thermogravimetric-differential thermal analysis (TG-DTA), cyclic voltammetry (CV) and single-crystal X-ray diffraction (XRD). Both of the complexes are the supramolecules, but with different liking mode, they are two representative models of supramolecule. complex (1) is a 3D infinite network supramolecular coordination polymer with a rare multi-metal sturcture of sodium-cobalt-containing, which is mainly linked through coordinate-covalent bonds. While complex (2) is normal supramolecule, which linked by non-covalent interactions, such as H-bonding interaction, electrostatic interaction and van der waals force. Both of complex (1) and (2) exhibit good catalytic activities for catalytic oxidation of methanol, when the initial concentration of methanol is 3.0 g m-3, flow rate is 10 mL min-1, and the quality of catalyst is 0.2 g, for complex (1) and complex (2) the maximum elimination rates of methanol are 85% (150 °C) and 92% (120 °C), respectively.

  19. 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.

  20. Covalent assembly of molecular building blocks by ``on-surface-synthesis''

    NASA Astrophysics Data System (ADS)

    Grill, Leonhard; Lafferentz, Leif; Bombis, Christian; Dyer, Matthew; Persson, Mats; Peters, Maike; Yu, Hao; Hecht, Stefan

    2010-03-01

    A key challenge in the field of molecular electronics is the bottom-up construction of stable molecular networks with pre-defined topology and shape, whereas covalent bonds are desired due to stability and charge transport requirements. We have developed the method of ``on-surface-synthesis,'' which allows the formation of covalent bonds by controlling the synthetic process directly on the surface. This technique has been used successfully for the controlled formation of covalently bound networks of porphyrin molecules on a gold surface, which were then characterized by low temperature scanning tunnelling microscopy (STM). The covalent character of the intermolecular bonds has been proven by manipulation and spectroscopy and is in agreement with calculations. We demonstrate that the dimensions and shape of these nanostructures can be precisely engineered, because the resulting nanostructures directly reflect the chemical structure of the individual building blocks, which makes this method highly interesting for functional molecules. Very recently, we have deposited ultrathin NaCl films on the metallic surface in order to achieve the interesting hybrid configuration of molecular wires on insulating films.

  1. 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.

  2. 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

  3. Transcriptional template activity of covalently modified DNA.

    PubMed

    Tolwińska-Stańczyk, Z; Wilmańska, D; Studzian, K; Gniazdowski, M

    1997-03-01

    The transcriptional template activity of covalent modified DNA is compared. 8-Methoxypsoralen (MOP), 3,4'dimethyl-8-methoxypsoralen (DMMOP) and benzopsoralen (BP) forming with DNA covalent complexes upon UV irradiation and exhibiting preference to pyrimidines, mostly thymines, differ in their cross-linking potency. MOP and DMMOP form both monoadducts and diadducts while no cross-links are formed by BP. Nitracrine (NC) forms covalent complexes with DNA upon reductive activation with dithiothreitol exhibiting a preference to purines and low cross-linking potency. Semilogarithmic plots of the relative template activity against the number of the drugs molecules covalently bound per 10(3) DNA nucleotides fit to regression lines corresponding to one-hit inactivation characteristics. The number of drug molecules decreasing RNA synthesis to 37% differ from 0.25 to 1.26 depending on the template used and the base preference but no dependence on the cross-linking potency was found. PMID:9067423

  4. Contrasts in Structural and Bonding Representations among Polar Intermetallic Compounds. Strongly Differentiated Hamilton Populations for Three Related Condensed Cluster Halides of the Rare-Earth Elements

    SciTech Connect

    Gupta, Shalabh; Meyer, Gerd; Corbett, John D.

    2010-10-01

    The crystal and electronic structures of three related R{sub 3}TnX{sub 3} phases (R = rare-earth metal, Tn = transition metal, X = Cl, I) containing extended mixed-metal chains are compared and contrasted: (1) Pr{sub 3}RuI{sub 3} (P2{sub 1}/m), (2) Gd{sub 3}MnI{sub 3} (P2{sub 1}/m), and (3) Pr{sub 3}RuCl{sub 3} (Pnma). The structures all feature double chains built of pairs of condensed R{sub 6}(Tn) octahedral chains encased by halogen atoms. Pr{sub 3}RuI{sub 3} (1) lacks significant Ru-Ru bonding, evidently because of packing restrictions imposed by the large closed-shell size of iodine. However, the vertex Pr2 atoms on the chain exhibit a marked electronic differentiation. These are strongly bound to the central Ru (and to four I), but very little to four neighboring Pr in the cluster according to bond populations, in contrast to Pr2-Pr 'bond' distances that are very comparable to those elsewhere. In Gd{sub 3}MnI{sub 3} (2), the smaller metal atoms allow substantial distortions and Mn-Mn bonding. Pr{sub 3}RuCl{sub 3} (3), in contrast to the iodide (1), can be described in terms of a more tightly bound superstructure of (2) in which both substantial Ru-Ru bonding and an increased number of Pr-Cl contacts in very similar mixed-metal chains are favored by the smaller closed-shell contacts of chlorine. Local Spin Density Approximation (LSDA) Linearized Muffin-Tin Orbital (LMTO)-ASA calculations and Crystal Orbital Hamilton Population (COHP) analyses show that the customary structural descriptions in terms of condensed, Tn-stuffed, R-R bonded polyhedral frameworks are poor representations of the bonding in all. Hamilton bond populations (-ICOHP) for the polar mixed-metal R-Tn and the somewhat smaller R-X interactions account for 75-90% of the total populations in each of these phases, together with smaller contributions and variations for R-R and Tn-Tn interactions. The strength of such R-Tn contributions in polar intermetallics was first established or anticipated by

  5. Hydrogen bonded arrays: the power of multiple hydrogen bonds.

    PubMed

    Shokri, Alireza; Schmidt, Jacob; Wang, Xue-Bin; Kass, Steven R

    2012-02-01

    Hydrogen bond interactions in small covalent model compounds (i.e., deprotonated polyhydroxy alcohols) were measured by negative ion photoelectron spectroscopy. The experimentally determined vertical and adiabatic electron detachment energies for (HOCH(2)CH(2))(2)CHO(-)(2a), (HOCH(2)CH(2))(3)CO(-) (3a), and (HOCH(2)CH(2)CH(OH)CH(2))(3)CO(-) (4a)reveal that hydrogen-bonded networks can provide enormous stabilizations and that a single charge center not only can be stabilized by up to three hydrogen bonds but also can increase the interaction energy between noncharged OH groups by 5.8 kcal mol(-1) or more per hydrogen bond. This can lead to pK(a) values that are very different from those in water and can provide some of the impetus for catalytic processes.

  6. Halogen bonding in solution: thermodynamics and applications.

    PubMed

    Beale, Thomas M; Chudzinski, Michael G; Sarwar, Mohammed G; Taylor, Mark S

    2013-02-21

    Halogen bonds are noncovalent interactions in which covalently bound halogens act as electrophilic species. The utility of halogen bonding for controlling self-assembly in the solid state is evident from a broad spectrum of applications in crystal engineering and materials science. Until recently, it has been less clear whether, and to what extent, halogen bonding could be employed to influence conformation, binding or reactivity in the solution phase. This tutorial review summarizes and interprets solution-phase thermodynamic data for halogen bonding interactions obtained over the past six decades and highlights emerging applications in molecular recognition, medicinal chemistry and catalysis.

  7. Hydrogen bonding in ionic liquids.

    PubMed

    Hunt, Patricia A; Ashworth, Claire R; Matthews, Richard P

    2015-03-01

    Ionic liquids (IL) and hydrogen bonding (H-bonding) are two diverse fields for which there is a developing recognition of significant overlap. Doubly ionic H-bonds occur when a H-bond forms between a cation and anion, and are a key feature of ILs. Doubly ionic H-bonds represent a wide area of H-bonding which has yet to be fully recognised, characterised or explored. H-bonds in ILs (both protic and aprotic) are bifurcated and chelating, and unlike many molecular liquids a significant variety of distinct H-bonds are formed between different types and numbers of donor and acceptor sites within a given IL. Traditional more neutral H-bonds can also be formed in functionalised ILs, adding a further level of complexity. Ab initio computed parameters; association energies, partial charges, density descriptors as encompassed by the QTAIM methodology (ρBCP), qualitative molecular orbital theory and NBO analysis provide established and robust mechanisms for understanding and interpreting traditional neutral and ionic H-bonds. In this review the applicability and extension of these parameters to describe and quantify the doubly ionic H-bond has been explored. Estimating the H-bonding energy is difficult because at a fundamental level the H-bond and ionic interaction are coupled. The NBO and QTAIM methodologies, unlike the total energy, are local descriptors and therefore can be used to directly compare neutral, ionic and doubly ionic H-bonds. The charged nature of the ions influences the ionic characteristics of the H-bond and vice versa, in addition the close association of the ions leads to enhanced orbital overlap and covalent contributions. The charge on the ions raises the energy of the Ylp and lowers the energy of the X-H σ* NBOs resulting in greater charge transfer, strengthening the H-bond. Using this range of parameters and comparing doubly ionic H-bonds to more traditional neutral and ionic H-bonds it is clear that doubly ionic H-bonds cover the full range of weak

  8. Characterizing Covalently Sidewall-Functionalized SWCNTs by using 1H NMR Spectroscopy

    PubMed Central

    Nelson, Donna J.; Kumar, Ravi

    2013-01-01

    Unambiguous evidence for covalent sidewall functionalization of single-walled carbon nanotubes (SWCNTs) has been a difficult task, especially for nanomaterials in which slight differences in functionality structure produce significant changes in molecular characteristics. Nuclear magnetic resonance (NMR) spectroscopy provides clear information about the structural skeleton of molecules attached to SWCNTs. In order to establish the generality of proton NMR as an analytical technique for characterizing covalently functionalized SWCNTs, we have obtained and analyzed proton NMR data of SWCNT-substituted benzenes across a variety of para substituents. Trends obtained for differences in proton NMR chemical shifts and the impact of o-, p-, and m-directing effects of electrophilic aromatic substituents on phenyl groups covalently bonded to SWCNTs are discussed. PMID:24009779

  9. Graphene-like single-layered covalent organic frameworks: synthesis strategies and application prospects.

    PubMed

    Liu, Xuan-He; Guan, Cui-Zhong; Wang, Dong; Wan, Li-Jun

    2014-10-29

    Two-dimensional (2D) nanomaterials, such as graphene and transition metal chalcogenides, show many interesting dimension-related materials properties. Inspired by the development of 2D inorganic nanomaterials, single-layered covalent organic frameworks (sCOFs), featuring atom-thick sheets and crystalline extended organic structures with covalently bonded building blocks, have attracted great attention in recent years. With their unique graphene-like topological structure and the merit of structural diversity, sCOFs promise to possess novel and designable properties. However, the synthesis of sCOFs with well-defined structures remains a great challenge. Herein, the recent development of the bottom-up synthesis methods of 2D sCOFs, such as thermodynamic equilibrium control methods, growth-kinetics control methods, and surface-assisted covalent polymerization methods, are reviewed. Finally, some of the critical properties and application prospects of these materials are outlined.

  10. 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

  11. Effect of photocurrent enhancement in porphyrin-graphene covalent hybrids.

    PubMed

    Tang, Jianguo; Niu, Lin; Liu, Jixian; Wang, Yao; Huang, Zhen; Xie, Shiqiang; Huang, Linjun; Xu, Qingsong; Wang, Yuan; Belfiore, Laurence A

    2014-01-01

    Graphene oxide (GO) sheets were covalently functionalized with 5-p-aminophenyl-10,15,20-triphenylporphyrin (NH2TPP) by an amidation reaction between the amino group in NH2TPP and carboxyl groups in GO. The Fourier transform infrared spectroscopy, nuclear magnetic resonance, scanning and transmission electron microscopies reveal that NH2TPP covalent bonds form on the double surface of graphene oxide sheets, generating a unique nano-framework, i.e., NH2TPP-graphene-NH2TPP. Its UV-visible spectroscopy reveals that the absorption spectrum is not a linear superposition of the spectra of NH2TPP and graphene oxide, because a 59nm red shift of the strong graphene oxide absorption is observed from 238 to 297nm, with significant spectral broadening between 300 and 700nm. Fluorescence emission spectroscopy indicates efficient quenching of NH2TPP photoluminescence in this hybrid material, suggesting that photo-induced electron transfer occurs at the interface between NH2TPP and GO. A reversible on/off photo-current density of 47mA/cm(2) is observed when NH2TPP-graphene-NH2TPP hybrid sandwiches are subjected to pulsed white-light illumination. Covalently-bound porphyrins decrease the optical HOMO/LUMO band gap of graphene oxide by ≈1eV, according to UV-visible spectroscopy. Cyclic voltammetry predicts a small HOMO/LUMO band gap of 0.84eV for NH2TPP-graphene-NH2TPP hybrid sandwiches, which is consistent with efficient electron transfer and fluorescence quenching.

  12. Discovery of potent and selective covalent inhibitors of JNK

    PubMed Central

    Zhang, Tinghu; Inesta-Vaquera, Francisco; Niepel, Mario; Zhang, Jianming; Ficarro, Scott B.; Machleidt, Thomas; Xie, Ting; Marto, Jarrod A.; Kim, NamDoo; Sim, Taebo; Laughlin, John D; Park, Hajeung; LoGrasso, Philip V.; Patricelli, Matt; Nomanbhoy, Tyzoon K.; Sorger, Peter K.; Alessi, Dario R.; Gray, Nathanael S.

    2012-01-01

    The mitogen activated kinases JNK1/2/3 are key enzymes in signaling modules that transduce and integrate extracellular stimuli into coordinated cellular response. Here we report the discovery of the first irreversible inhibitors of JNK1/2/3. We describe two JNK3 co-crystal structures at 2.60 and 2.97 Å resolutions that show the compounds form covalent bonds with a conserved cysteine residue. JNK-IN-8 is a selective JNK inhibitor that inhibits phosphorylation of c-Jun, a direct substrate of JNK kinase, in cells exposed to sub-micromolar drug in a manner that depends on covalent modification of the conserved cysteine residue. Extensive biochemical, cellular and pathway-based profiling establish the selectivity of JNK-IN-8 for JNK and suggest that the compound will be broadly useful as a pharmacological probe of JNK-dependent signal transduction. Potential lead compounds have also been identified for kinases including IRAK1, PIK3C3, PIP4K2C, and PIP5K3. PMID:22284361

  13. 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

  14. 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.

  15. 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

  16. The Yeast Cell Fusion Protein Prm1p Requires Covalent Dimerization to Promote Membrane Fusion

    PubMed Central

    Engel, Alex; Aguilar, Pablo S.; Walter, Peter

    2010-01-01

    Prm1p is a multipass membrane protein that promotes plasma membrane fusion during yeast mating. The mechanism by which Prm1p and other putative regulators of developmentally controlled cell-cell fusion events facilitate membrane fusion has remained largely elusive. Here, we report that Prm1p forms covalently linked homodimers. Covalent Prm1p dimer formation occurs via intermolecular disulfide bonds of two cysteines, Cys-120 and Cys-545. PRM1 mutants in which these cysteines have been substituted are fusion defective. These PRM1 mutants are normally expressed, retain homotypic interaction and can traffic to the fusion zone. Because prm1-C120S and prm1-C545S mutants can form covalent dimers when coexpressed with wild-type PRM1, an intermolecular C120-C545 disulfide linkage is inferred. Cys-120 is adjacent to a highly conserved hydrophobic domain. Mutation of a charged residue within this hydrophobic domain abrogates formation of covalent dimers, trafficking to the fusion zone, and fusion-promoting activity. The importance of intermolecular disulfide bonding informs models regarding the mechanism of Prm1-mediated cell-cell fusion. PMID:20485669

  17. Hydrogen-bond reinforced vanadia nanofiber paper of high stiffness.

    PubMed

    Burghard, Zaklina; Leineweber, Andreas; van Aken, Peter A; Dufaux, Thomas; Burghard, Marko; Bill, Joachim

    2013-05-01

    Low-temperature, solution-based self-assembly of vanadia nanofibers yields a free-standing, ceramic paper with an outstanding combination of high strength, stiffness, and macroscopic flexibility. Its excellent mechanical performance results from a brick-and-mortar like architecture, which combines strong covalent bonding within the single-crystalline nanofibers with an intricate hydrogen bonding network between them. PMID:23468458

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

    PubMed Central

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

    2013-01-01

    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

  19. A QTAIM exploration of the competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

    NASA Astrophysics Data System (ADS)

    Huan, Guo; Xu, Tianlv; Momen, Roya; Wang, Lingling; Ping, Yang; Kirk, Steven R.; Jenkins, Samantha; van Mourik, Tanja

    2016-10-01

    Using QTAIM we show that the hydrogen bonding complexes of 5-halogenated-1-methyluracil (XmU; X = F, Cl, Br, I or At) with a water molecule were always stronger than the corresponding halogen bonds. The strength of the hydrogen bond decreased with increasing halogen size. The hydrogen bonds displayed an admixture of covalent character but all the halogen bonds were purely electrostatic in nature. An F---O halogen bond was found and was facilitated by an intermediate F---H bonding interaction. The metallicity ξ(rb) of the C = O bonds neighboring the hydrogen bonds and of the C-X bonds contiguous with the halogen bonds was explored.

  20. 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

  1. 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.

  2. Locking GTPases covalently in their functional states.

    PubMed

    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.

  3. 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.

  4. 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.

  5. 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…

  6. Sticker Bonding.

    ERIC Educational Resources Information Center

    Frazier, Laura Corbin

    2000-01-01

    Introduces a science activity on the bonding of chemical compounds. Assigns students the role of either a cation or anion and asks them to write the ions they may bond with. Assesses students' understanding of charge, bonding, and other concepts. (YDS)

  7. Covalent binding of single-walled carbon nanotubes to polyamide membranes for antimicrobial surface properties.

    PubMed

    Tiraferri, Alberto; Vecitis, Chad D; Elimelech, Menachem

    2011-08-01

    We propose an innovative approach to impart nanomaterial-specific properties to the surface of thin-film composite membranes. Specifically, biocidal properties were obtained by covalently binding single-walled carbon nanotubes (SWNTs) to the membrane surface. The SWNTs were first modified by purification and ozonolysis to increase their sidewall functionalities, maximize cytotoxic properties, and achieve dispersion in aqueous solution. A tailored reaction protocol was developed to exploit the inherent moieties of hand-cast polyamide membrane surfaces and create covalent amide bonds with the functionalized SWNTs. The reaction is entirely aqueous-based and entails activation of the carboxylate groups of both the membrane and the nanomaterials to maximize reaction with ethylenediamine. The presence of SWNTs was verified after sonication of the membranes, confirming the strength of the bond between the SWNTs and the membrane surface. Characterization of the SWNT-functionalized surfaces demonstrated the attainment of membranes with novel properties that continued to exhibit high performance in water separation processes. The presence of surface-bound antimicrobial SWNTs was confirmed by experiments using E. coli cells that demonstrated an enhanced bacterial cytotoxicity for the SWNT-coated membranes. The SWNT membranes were observed to achieve up to 60% inactivation of bacteria attached to the membrane within 1 h of contact time. Our results suggest the potential of covalently bonded SWNTs to delay the onset of membrane biofouling during operation.

  8. Supramolecular photocatalysis: combining confinement and non-covalent interactions to control light initiated reactions.

    PubMed

    Vallavoju, Nandini; Sivaguru, J

    2014-06-21

    Using non-bonding interactions to control photochemical reactions requires an understanding of not only thermodynamics and kinetics of ground state and excited state processes but also the intricate interactions that dictate the dynamics within the system of interest. This review is geared towards a conceptual understanding of how one can control the reactivity and selectivity in the excited state by employing confinement and non-covalent interactions. Photochemical reactivity of organic molecules within confined containers and organized assemblies as well as organic templates that interact through H-bonding and/or cation-carbonyl/cation-π interactions is reviewed with an eye towards understanding supramolecular effects and photocatalysis.

  9. Anthracene derivative covalently immobilized on sensing membrane as a fluorescent carrier for water assay.

    PubMed

    Jiao, Chen-Xu; Han, Yuan-Yuan; Xing, Bao-Yan

    2013-01-01

    This article describes an optical chemical sensor based on a fluorescent dye 1-allyloxy-4-hydroxyanthracene-9, 10-dione (AHD) with terminal double bond, which is covalently bonded to quartz glass plate surface treated with a silanizing agent to prevent its leakage. The purpose of this work was to characterize and optimize the sensor for determining the water content in the acetone organic solvent. The sensor is resistant to swelling; the membrane possesses relatively long lifetime, short response and recovering time. The reversibility and reproducibility of the sensor are adequate for practical measurements.

  10. Simultaneous Visualization of Covalent and Noncovalent Interactions Using Regions of Density Overlap

    PubMed Central

    2014-01-01

    We introduce a density-dependent bonding descriptor that enables simultaneous visualization of both covalent and noncovalent interactions. The proposed quantity is tailored to reveal the regions of space, where the total electron density results from a strong overlap of shell, atomic, or molecular densities. We show that this approach is successful in describing a variety of bonding patterns as well as nonbonding contacts. The Density Overlap Regions Indicator (DORI) analysis is also exploited to visualize and quantify the concept of electronic compactness in supramolecular chemistry. In particular, the scalar field is used to compare the compactness in molecular crystals, with a special emphasis on quaterthiophene derivatives with enhanced charge mobilities. PMID:25221443

  11. 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

  12. 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

  13. Covalent functionalization of graphene with reactive intermediates.

    PubMed

    Park, Jaehyeung; Yan, Mingdi

    2013-01-15

    Graphene, a material made exclusively of sp(2) carbon atoms with its π electrons delocalized over the entire 2D network, is somewhat chemically inert. Covalent functionalization can enhance graphene's properties including opening its band gap, tuning conductivity, and improving solubility and stability. Covalent functionalization of pristine graphene typically requires reactive species that can form covalent adducts with the sp(2) carbon structures in graphene. In this Account, we describe graphene functionalization reactions using reactive intermediates of radicals, nitrenes, carbenes, and arynes. These reactive species covalently modify graphene through free radical addition, CH insertion, or cycloaddition reactions. Free radical additions are among the most common reaction, and these radicals can be generated from diazonium salts and benzoyl peroxide. Electron transfer from graphene to aryl diazonium ion or photoactivation of benzoyl peroxide yields aryl radicals that subsequently add to graphene to form covalent adducts. Nitrenes, electron-deficient species generated by thermal or photochemical activation of organic azides, can functionalize graphene very efficiently. Because perfluorophenyl nitrenes show enhanced bimolecular reactions compared with alkyl or phenyl nitrenes, perfluorophenyl azides are especially effective. Carbenes are used less frequently than nitrenes, but they undergo CH insertion and C═C cycloaddition reactions with graphene. In addition, arynes can serve as a dienophile in a Diels-Alder type reaction with graphene. Further study is needed to understand and exploit the chemistry of graphene. The generation of highly reactive intermediates in these reactions leads to side products that complicate the product composition and analysis. Fundamental questions remain about the reactivity and regioselectivity of graphene. The differences in the basal plane and the undercoordinated edges of graphene and the zigzag versus arm-chair configurations

  14. On the activation of σ-bonds by electric fields: A Valence Bond perspective

    NASA Astrophysics Data System (ADS)

    Rincón, Luis; Mora, Jose R.; Torres, F. Javier; Almeida, Rafael

    2016-09-01

    The activation of non-polar σ -bonds induced by an electric field is studied from the perspective of the Valence Bond theory. As representative examples we study the dissociation of the H-H and C-H bonds of molecular hydrogen and methane, respectively, under the experience of an homogeneous as well as an heterogeneous field oriented along the bond axis. For all cases, the increase in the electric field have similar effects: (i) the stabilization of the potential energy, (ii) an increment of the equilibrium bond length and (iii) the transition from an homolytic dissociation mechanism to an heterolytic one when the bond is subjected under a strong enough field. These general observations are thoroughly explained using a simple Valence Bond model that involve the increment of the resonance energy between the covalent and the ionic structures, and the curve crossing between the two structures after some field strength.

  15. 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

  16. 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,…

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. Covalently networked monolayer-protected nanoparticle films.

    PubMed

    Tognarelli, D J; Miller, Robert B; Pompano, Rebecca R; Loftus, Andrew F; Sheibley, Daniel J; Leopold, Michael C

    2005-11-22

    Covalently networked films of nanoparticles can be assembled on various substrates from functionalized monolayer-protected clusters (MPCs) via ester coupling reactions. Exposure of a specifically modified substrate to alternating solutions of 11-mercaptoundecanoic acid exchanged and 11-mercaptoundecanol exchanged MPCs, in the presence of ester coupling reagents, 1,3-dicyclohexylcarbodiimide and 4-(dimethylamino)pyridine, results in the formation of a multilayer film with ester bridges between individual nanoparticles. These films can be grown in a controlled manner to various thicknesses and exhibit certain properties that are consistent with films having other types of interparticle connectivity, including chemical vapor response behavior and quantized double layer charging. Ester coupling of MPCs into assembled films is a straightforward and highly versatile approach that results in robust films that can endure harsher chemical environments than other types of films. The stability of these covalent films is assessed and compared to other more traditional MPC film assemblies.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. Phytochrome assembly. Defining chromophore structural requirements for covalent attachment and photoreversibility.

    PubMed

    Li, L; Lagarias, J C

    1992-09-25

    Assembly of holophytochrome in the plant cell requires covalent attachment of the linear tetrapyrrole chromophore precursor, phytochromobilin, to a unique cysteine in the nascent apoprotein. In this investigation we compare chromophore analogs with the natural chromophore precursor for their ability to attach covalently to recombinant oat apophytochrome and to form photoactive holoproteins. Ethylidene-containing analogs readily form covalent adducts with apophytochrome, whereas chromophores lacking this double bond are poor substrates for attachment. Kinetic measurements establish that although the chromophore binding site on apophytochrome is best tailored to phytochromobilin, apophytochrome will accommodate the two analogs with modified D-rings, phycocyanobilin and phycoerythrobilin. The phycocyanobilin-apophytochrome adduct is photoactive and undergoes a light-induced protein conformational change similar to the native holoprotein. By contrast, the phycoerythrobilin adduct is locked into a photochemically inactive protein conformation that is similar to the red light-absorbing Pr form of phytochrome. These results support the hypothesis that the photoconversion from Pr to Pfr, the far red light- absorbing form of phytochrome, involves the photoisomerization of the C15 double bond. Knowledge gained from these studies provides impetus for rational design of chromophore analogs whose insertion into apophytochrome should elicit profound changes in light-mediated plant growth and development.

  14. 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

  15. Tribology study of reduced graphene oxide sheets on silicon substrate synthesized via covalent assembly.

    PubMed

    Ou, Junfei; Wang, Jinqing; Liu, Sheng; Mu, Bo; Ren, Junfang; Wang, Honggang; Yang, Shengrong

    2010-10-19

    Reduced graphene oxide (RGO) sheets were covalently assembled onto silicon wafers via a multistep route based on the chemical adsorption and thermal reduction of graphene oxide (GO). The formation and microstructure of RGO were analyzed by X-ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, Raman spectroscopy, and water contact angle (WCA) measurements. Characterization by atomic force microscopy (AFM) was performed to evaluate the morphology and microtribological behaviors of the samples. Macrotribological performance was tested on a ball-on-plate tribometer. Results show that the assembled RGO possesses good friction reduction and antiwear ability, properties ascribed to its intrinsic structure, that is, the covalent bonding to the substrate and self-lubricating property of RGO.

  16. 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.

  17. 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

  18. 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.

  19. Spontaneous and specific activation of chemical bonds in macromolecular fluids.

    PubMed

    Park, Insun; Shirvanyants, David; Nese, Alper; Matyjaszewski, Krzysztof; Rubinstein, Michael; Sheiko, Sergei S

    2010-09-01

    Mechanical activation of chemical bonds typically involves the application of external forces, which implies a broad distribution of bond tensions. We demonstrate that controlling the flow profile of a macromolecular fluid generates and delineates mechanical force concentration, enabling a hierarchical activation of chemical bonds on different length scales from the macroscopic to the molecular. Bond tension is spontaneously generated within brushlike macromolecules as they spread on a solid substrate. The molecular architecture creates an uneven distribution of tension in the covalent bonds, leading to spatially controlled bond scission. By controlling the flow rate and the gradient of the film pressure, one can sever the flowing macromolecules with high precision. Specific chemical bonds are activated within distinct macromolecules located in a defined area of a thin film. Furthermore, the flow-controlled loading rate enables quantitative analysis of the bond activation parameters.

  20. 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

  1. LETTER TO THE EDITOR: Electronic structure and bonding properties in layered ternary carbide Ti3SiC2

    NASA Astrophysics Data System (ADS)

    Zhou, Yanchun; Sun, Zhimei

    2000-07-01

    Ab initio calculations based on the density-functional pseudopotential approach have been used to study the electronic structure and chemical bonding in layered machinable Ti3SiC2 ceramic. The calculations reveal that all three types of bonding - metallic, covalent and ionic - contribute to the bonding in Ti3SiC2. The high electric conductivity is attributed to the metallic bonding parallel to the basal plane and the high modulus and high melting point are attributed to the strong Ti-C-Ti-C-Ti covalent bond chains in the structure.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. An histidine covalent receptor and butenolide complex mediates strigolactone perception.

    PubMed

    de Saint Germain, Alexandre; Clavé, Guillaume; Badet-Denisot, Marie-Ange; Pillot, Jean-Paul; Cornu, David; Le Caer, Jean-Pierre; Burger, Marco; Pelissier, Frank; Retailleau, Pascal; Turnbull, Colin; Bonhomme, Sandrine; Chory, Joanne; Rameau, Catherine; Boyer, François-Didier

    2016-10-01

    Strigolactone plant hormones control plant architecture and are key players in both symbiotic and parasitic interactions. They contain an ABC tricyclic lactone connected to a butenolide group, the D ring. The DWARF14 (D14) strigolactone receptor belongs to the superfamily of α/β-hydrolases, and is known to hydrolyze the bond between the ABC lactone and the D ring. Here we characterized the binding and catalytic functions of RAMOSUS3 (RMS3), the pea (Pisum sativum) ortholog of rice (Oryza sativa) D14 strigolactone receptor. Using new profluorescent probes with strigolactone-like bioactivity, we found that RMS3 acts as a single-turnover enzyme that explains its apparent low enzymatic rate. We demonstrated the formation of a covalent RMS3-D-ring complex, essential for bioactivity, in which the D ring was attached to histidine 247 of the catalytic triad. These results reveal an undescribed mechanism of plant hormone reception in which the receptor performs an irreversible enzymatic reaction to generate its own ligand.

  7. An histidine covalent receptor and butenolide complex mediates strigolactone perception.

    PubMed

    de Saint Germain, Alexandre; Clavé, Guillaume; Badet-Denisot, Marie-Ange; Pillot, Jean-Paul; Cornu, David; Le Caer, Jean-Pierre; Burger, Marco; Pelissier, Frank; Retailleau, Pascal; Turnbull, Colin; Bonhomme, Sandrine; Chory, Joanne; Rameau, Catherine; Boyer, François-Didier

    2016-10-01

    Strigolactone plant hormones control plant architecture and are key players in both symbiotic and parasitic interactions. They contain an ABC tricyclic lactone connected to a butenolide group, the D ring. The DWARF14 (D14) strigolactone receptor belongs to the superfamily of α/β-hydrolases, and is known to hydrolyze the bond between the ABC lactone and the D ring. Here we characterized the binding and catalytic functions of RAMOSUS3 (RMS3), the pea (Pisum sativum) ortholog of rice (Oryza sativa) D14 strigolactone receptor. Using new profluorescent probes with strigolactone-like bioactivity, we found that RMS3 acts as a single-turnover enzyme that explains its apparent low enzymatic rate. We demonstrated the formation of a covalent RMS3-D-ring complex, essential for bioactivity, in which the D ring was attached to histidine 247 of the catalytic triad. These results reveal an undescribed mechanism of plant hormone reception in which the receptor performs an irreversible enzymatic reaction to generate its own ligand. PMID:27479744

  8. Arabinose 5-phosphate covalently inhibits transaldolase.

    PubMed

    Light, Samuel H; Anderson, Wayne F

    2014-03-01

    Arabinose 5-phosphate (A5P) is the aldopentose version of the ketohexose fructose 6-phosphate (F6P), having identical stereochemistry but lacking atoms corresponding to the 1-carbon and 1-hydroxyl. Despite structural similarity and conservation of the reactive portion of F6P, F6P acts as a substrate whereas A5P is reported to be an inhibitor of transaldolase. To address the lack of A5P reactivity we determined a crystal structure of the Francisella tularensis transaldolase in complex with A5P. This structure reveals that like F6P, A5P forms a covalent Schiff base with active site Lys135. Unlike F6P, A5P binding fails to displace an ordered active site water molecule. Retaining this water necessitates conformational changes at the A5P-protein linkage that possibly hinder reactivity. The findings presented here show the basis of A5P inhibition and suggest an unusual mechanism of competitive, reversible-covalent transaldolase regulation.

  9. Electronic structure and bonding in crystalline peroxides

    NASA Astrophysics Data System (ADS)

    Königstein, Markus; Sokol, Alexei A.; Catlow, C. Richard A.

    1999-08-01

    Hartree-Fock and density-functional PW91 theories as realized in the CRYSTAL95 code have been applied to investigate the structural and electronic properties of Ba, Sr, and Ca peroxide materials with the calcium carbide crystal structure, results for which are compared with those for the corresponding oxides. Special attention is paid to the stabilization of the peroxide molecular ion O2-2 in the ionic environment provided by the lattice, and to chemical bonding effects. In order to describe the covalent bonding within the O2-2 ion and the polarization of the O- ion in the crystal electrostatic field, it is essential to include an account of the effects of electron correlation. The PW91 density functional has allowed us to reproduce the crystallographic parameters within a 3% error. The chemical bonding within the peroxide molecular ion has a complex nature with a balance between the weak covalent bond of σz type and the strong electrostatic repulsion of the closed-shell electron groups occupying O 2s and O 2px and 2py states. Compression of the peroxide ion in the ionic crystals gives rise to an excessive overlap of the O 2s closed shells of the two O- ions of a peroxide molecular ion O2-2, which in turn determines the antibonding character of the interaction and chemical bonding in the O2-2 molecular ion.

  10. σ-Hole bonding: a physical interpretation.

    PubMed

    Politzer, Peter; Murray, Jane S; Clark, Timothy

    2015-01-01

    The anisotropic electronic densities of covalently-bonded Group IV-VII atoms frequently give rise to regions of positive electrostatic potential on the extensions of covalent bonds to these atoms. Through such positive "σ-holes," the atoms can interact attractively and highly directionally with negative sites such as the lone pairs of Lewis bases, anions, π electrons, etc. In the case of Group VII this is called "halogen bonding." Hydrogen bonding can be viewed as a less directional subset of σ-hole interactions. Since positive σ-holes often exist in conjunction with regions of negative potential, the atoms can also interact favorably with positive sites. In accordance with the Hellmann-Feynman theorem, all of these interactions are purely Coulombic in nature (which encompasses polarization and dispersion). The strength of σ-hole bonding increases with the magnitudes of the potentials of the positive σ-hole and the negative site; their polarizabilities must sometimes also be taken explicitly into account. PMID:25467532

  11. 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.

  12. Molecular marriage through partner preferences in covalent cage formation and cage-to-cage transformation.

    PubMed

    Acharyya, Koushik; Mukherjee, Sandip; Mukherjee, Partha Sarathi

    2013-01-16

    Unprecedented self-sorting of three-dimensional purely organic cages driven by dynamic covalent bonds is described. Four different cages were first synthesized by condensation of two triamines and two dialdehydes separately. When a mixture of all the components was allowed to react, only two cages were formed, which suggests a high-fidelity self-recognition. The issue of the preference of one triamine for a particular dialdehyde was further probed by transforming a non-preferred combination to either of the two preferred combinations by reacting it with the appropriate triamine or dialdehyde.

  13. Spectral and thermodynamic properties of electrons in mobility gap states of covalent glasses

    NASA Astrophysics Data System (ADS)

    Klinger, M. I.; Karpov, V. G.

    1981-07-01

    Spectral and thermodynamic properties of electrons (holes) in covalent semiconducting glasses are considered in which self-trapping of electron (hole) pairs is realized with negative effective correlation energy U -. Unlike the Anderson model, electron (hole) pairing is restricted to a small part of the glass bonds. Ranges of the U - values are found in which either pair effects (suppression of paramagnetism etc.) or single-particle effects predominate; the concentration of the pair states and of the occupied ones can roughly be estimated and can be fairly high. The problem of the coexistence of the Fermi level pinning and effective diamagnetism in glasses is discussed. Some related effects are briefly considered.

  14. Sub-ångström-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate

    NASA Astrophysics Data System (ADS)

    Lüdtke, Stefan; Neumann, Piotr; Erixon, Karl M.; Leeper, Finian; Kluger, Ronald; Ficner, Ralf; Tittmann, Kai

    2013-09-01

    It is recognized widely that enzymes promote reactions by providing a pathway that proceeds through a transition state of lower energy. In principle, further rate enhancements could be achieved if intermediates are prevented from relaxing to their lowest energy state, and thereby reduce the barrier to the subsequent transition state. Here, we report sub-ångström-resolution crystal structures of genuine covalent reaction intermediates of transketolase. These structures reveal a pronounced out-of-plane distortion of over 20° for the covalent bond that links cofactor and substrate, and a specific elongation of the scissile substrate carbon-carbon bond (d > 1.6 Å). To achieve these distortions, the protein's conformation appears to prevent relaxation of a substrate-cofactor intermediate. The results implicate a reduced barrier to the subsequent step that is consistent with an intermediate of raised energy and leads to a more efficient overall process.

  15. 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.

  16. Correlation effects in hydrogen-bonded polymer blends

    SciTech Connect

    Veytsman, B.; Painter, P. )

    1993-12-01

    In hydrogen-bonded polymer blends there are long range correlations that are a result of the combined covalent and hydrogen-bond connections. A mean field description of these mixtures is presented which indicates that there should be an infinite correlation length above some percolation threshold. There are various consequences of the compositional heterogeneities or clustering that results from these effects and these are discussed in this paper.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Biofunctional Paper via Covalent Modification of Cellulose

    PubMed Central

    Yu, Arthur; Shang, Jing; Cheng, Fang; Paik, Bradford A.; Kaplan, Justin M.; Andrade, Rodrigo B.; Ratner, Daniel M.

    2012-01-01

    Paper-based analytical devices are the subject of growing interest for the development of low-cost point-of-care diagnostics, environmental monitoring technologies and research tools for limited-resource settings. However, there are limited chemistries available for the conjugation of biomolecules to cellulose for use in biomedical applications. Herein, divinyl sulfone (DVS) chemistry was demonstrated to covalently immobilize small molecules, proteins and DNA onto the hydroxyl groups of cellulose membranes through nucleophilic addition. Assays on modified cellulose using protein-carbohydrate and protein-glycoprotein interactions as well as oligonucleotide hybridization showed that the membrane’s bioactivity was specific, dose-dependent, and stable over a long period of time. Use of an inkjet printer to form patterns of biomolecules on DVS-activated cellulose illustrates the adaptability of the DVS functionalization technique to pattern sophisticated designs, with potential applications in cellulose-based lateral flow devices. PMID:22708701

  3. Bonds Boom.

    ERIC Educational Resources Information Center

    Reynolds, Cathryn

    1989-01-01

    The combined effect of the "Serrano" decision and Proposition 13 left California school districts with aging, overcrowded facilities. Chico schools won a $18.5 million general obligation bond election for facilities construction. With $11 billion needed for new school construction, California will need to tap local sources. A sidebar outlines…

  4. 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.

  5. Characterization of C-alkyl amidines as bioavailable covalent reversible inhibitors of human DDAH-1.

    PubMed

    Lluis, Matthew; Wang, Yun; Monzingo, Arthur F; Fast, Walter; Robertus, Jon D

    2011-01-01

    C-Alkyl amidine analogues of asymmetric N(ω),N(ω)-dimethyl-L-arginine are dual-targeted inhibitors of both human DDAH-1 and nitric oxide (NO) synthase, and provide a promising scaffold for the development of therapeutics to control NO overproduction in a variety of pathologies including septic shock and some cancers. Using a two-part click-chemistry-mediated activity probe, a homologated series of C-alkyl amidines were ranked for their ability to inhibit DDAH-1 within cultured HEK 293T cells. N⁵-(1-Iminopentyl)-L-ornithine was determined to be the most potent compound in vitro (K(d)=7 μM) as well as in cultured cells, and the binding conformation and covalent reversible mode of inhibition was investigated by comparison of interactions made with DDAH-1 and a catalytically inactive C274S variant, as gauged by X-ray crystallography and isothermal titration calorimetry. By interrupting the ability of the inhibitor to form a covalent bond, the contribution of this interaction could be estimated. These results suggest that further stabilization of the covalent adduct is a promising strategy for lead optimization in the design of effective reagents to block NO synthesis.

  6. 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.

  7. Electron-deficient η1-Indenyl,η3-allylpalladium(II) complexes stabilized by fluxional non-covalent interactions.

    PubMed

    Werlé, Christophe; Hamdaoui, Mustapha; Bailly, Corinne; Le Goff, Xavier-Frédéric; Brelot, Lydia; Djukic, Jean-Pierre

    2013-02-01

    Highly fluxional, solution-persistent, and formally electron-deficient (32e(-)) binuclear Pd(II)-C(0) complexes of 2-methyl-1H-indene were synthesized and structurally characterized by X-ray diffraction analysis. DFT investigations combined with a number of theoretical analyses of the bond framework suggest that the polar intermetallic interaction possesses no major covalent character. Instead of bearing a static metal-metal bond as suggested by structural X-ray diffraction analysis, the complexes display in solution significant fluxionality through haptotropy, i.e., a formal "oscillation" of the Pd(η(3)-allyl) moiety between two limiting η(1)-indenyl configurations. PMID:23317421

  8. Analysis of Proton NMR in Hydrogen Bonds in Terms of Lone-Pair and Bond Orbital Contributions.

    PubMed

    Sutter, Kiplangat; Aucar, Gustavo A; Autschbach, Jochen

    2015-12-01

    NMR spectroscopic parameters of the proton involved in hydrogen bonding are studied theoretically. The set of molecules includes systems with internal resonance-assisted hydrogen bonds, internal hydrogen bonds but no resonance stabilization, the acetic acid dimer (AAD), a DNA base pair, and the hydrogen succinate anion (HSA). Ethanol and guanine represent reference molecules without hydrogen bonding. The calculations are based on zero-point vibrationally averaged molecular structures in order to include anharmonicity effects in the NMR parameters. An analysis of the calculated NMR shielding and J-coupling is performed in terms of "chemist's orbitals", that is, localized molecular orbitals (LMOs) representing lone-pairs, atomic cores, and bonds. The LMO analysis associates some of the strong de-shielding of the protons in resonance-assisted hydrogen bonds with delocalization involving the π-backbone. Resonance is also shown to be an important factor causing de-shielding of the OH protons for AAD and HSA, but not for the DNA base pair. Nitromalonamide (NMA) and HSA have particularly strong hydrogen bonds exhibiting signs of covalency in the associated J-couplings. The analysis results show how NMR spectroscopic parameters that are characteristic for hydrogen bonded protons are influenced by the geometry and degree of covalency of the hydrogen bond as well as intra- and intermolecular resonance.

  9. 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.

  10. 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.

  11. 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

  12. Disruption of heme-peptide covalent cross-linking in mammalian peroxidases by hypochlorous acid

    PubMed Central

    Abu-Soud, Husam M.; Maitra, Dhiman; Shaeib, Faten; Khan, Sana; Byun, Jaeman; Abdulhamid, Ibrahim; Yang, Zhe; Saed, Ghassan M.; Diamond, Michael P.; Andreana, Peter R.; Pennathur, Subramaniam

    2015-01-01

    Myeloperoxidase (MPO), lactoperoxidase (LPO) and eosinophil peroxidase (EPO) play a central role in oxidative damage in inflammatory disorders by utilizing hydrogen peroxide and halides/pseudo halides to generate the corresponding hypohalous acid. The catalytic sites of these enzymes contain a covalently modified heme group, which is tethered to the polypeptide chain at two ester linkages via the methyl group (MPO, EPO and LPO) and one sulfonium bond via the vinyl group (MPO only). Covalent cross-linking of the catalytic site heme to the polypeptide chain in peroxidases is thought to play a protective role, since it renders the heme moiety less susceptible to the oxidants generated by these enzymes. Mass-spectrometric analysis revealed the following possible pathways by which hypochlorous acid (HOCl) disrupts the heme-protein cross-linking: (1) the methyl-ester bond is cleaved to form an alcohol; (2) the alcohol group undergoes an oxygen elimination reaction via the formation of an aldehyde intermediate or undergoes a demethylation reaction to lose the terminal CH2 group; and (3) the oxidative cleavage of the vinyl-sulfonium linkage. Once the heme moiety is released it undergoes cleavage at the carbon-methyne bridge either along the δ-β or a α-γ axis to form different pyrrole derivatives. These results indicate that covalent cross-linking is not enough to protect the enzymes from HOCl mediated heme destruction and free iron release. Thus, the interactions of mammalian peroxidases with HOCl modulates their activity and sets a stage for initiation of the Fenton reaction, further perpetuating oxidative damage at sites of inflammation. PMID:25193127

  13. Covalent immobilization of p-selectin enhances cell rolling.

    PubMed

    Hong, Seungpyo; Lee, Dooyoung; Zhang, Huanan; Zhang, Jennifer Q; Resvick, Jennifer N; Khademhosseini, Ali; King, Michael R; Langer, Robert; Karp, Jeffrey M

    2007-11-20

    Cell rolling is an important physiological and pathological process that is used to recruit specific cells in the bloodstream to a target tissue. This process may be exploited for biomedical applications to capture and separate specific cell types. One of the most commonly studied proteins that regulate cell rolling is P-selectin. By coating surfaces with this protein, biofunctional surfaces that induce cell rolling can be prepared. Although most immobilization methods have relied on physisorption, chemical immobilization has obvious advantages, including longer functional stability and better control over ligand density and orientation. Here we describe chemical methods to immobilize P-selectin covalently on glass substrates. The chemistry was categorized on the basis of the functional groups on modified glass substrates: amine, aldehyde, and epoxy. The prepared surfaces were first tested in a flow chamber by flowing microspheres functionalized with a cell surface carbohydrate (sialyl Lewis(x)) that binds to P-selectin. Adhesion bonds between P-selectin and sialyl Lewis(x) dissociate readily under shear forces, leading to cell rolling. P-selectin immobilized on the epoxy glass surfaces exhibited enhanced long-term stability of the function and better homogeneity as compared to that for surfaces prepared by other methods and physisorbed controls. The microsphere rolling results were confirmed in vitro with isolated human neutrophils. This work is essential for the future development of devices for isolating specific cell types based on cell rolling, which may be useful for hematologic cancers and certain metastatic cancer cells that are responsive to immobilized selectins.

  14. Hapten-directed spontaneous disulfide shuffling: a universal technology for site-directed covalent coupling of payloads to antibodies.

    PubMed

    Dengl, Stefan; Hoffmann, Eike; Grote, Michael; Wagner, Cornelia; Mundigl, Olaf; Georges, Guy; Thorey, Irmgard; Stubenrauch, Kay-Gunnar; Bujotzek, Alexander; Josel, Hans-Peter; Dziadek, Sebastian; Benz, Joerg; Brinkmann, Ulrich

    2015-05-01

    Humanized hapten-binding IgGs were designed with an accessible cysteine close to their binding pockets, for specific covalent payload attachment. Individual analyses of known structures of digoxigenin (Dig)- and fluorescein (Fluo) binding antibodies and a new structure of a biotin (Biot)-binder, revealed a "universal" coupling position (52(+2)) in proximity to binding pockets but without contributing to hapten interactions. Payloads that carry a free thiol are positioned on the antibody and covalently linked to it via disulfides. Covalent coupling is achieved and driven toward complete (95-100%) payload occupancy by spontaneous redox shuffling between antibody and payload. Attachment at the universal position works with different haptens, antibodies, and payloads. Examples are the haptens Fluo, Dig, and Biot combined with various fluorescent or peptidic payloads. Disulfide-bonded covalent antibody-payload complexes do not dissociate in vitro and in vivo. Coupling requires the designed cysteine and matching payload thiol because payload or antibody without the Cys/thiol are not linked (<5% nonspecific coupling). Hapten-mediated positioning is necessary as hapten-thiol-payload is only coupled to antibodies that bind matching haptens. Covalent complexes are more stable in vivo than noncovalent counterparts because digoxigeninylated or biotinylated fluorescent payloads without disulfide-linkage are cleared more rapidly in mice (approximately 50% reduced 48 hour serum levels) compared with their covalently linked counterparts. The coupling technology is applicable to many haptens and hapten binding antibodies (confirmed by automated analyses of the structures of 140 additional hapten binding antibodies) and can be applied to modulate the pharmacokinetics of small compounds or peptides. It is also suitable to link payloads in a reduction-releasable manner to tumor- or tissue-targeting delivery vehicles.

  15. The halogen bond: an interim perspective.

    PubMed

    Legon, Anthony C

    2010-07-28

    There has been an upsurge of interest in the halogen bond during the last decade. This non-covalent interaction is less familiar than the hydrogen bond, but is similar to it in several respects. In this article, we first discuss the nature of the halogen bond in the gas phase, as established by systematic investigations of the rotational spectra of complexes B...XY, where B is a simple Lewis base and XY is a dihalogen molecule. The geometry of a given B...XY is found to be isomorphic with that of the corresponding hydrogen-bonded system B...HX, an observation that leads an interim definition of the halogen bond similar to that recently proposed for the hydrogen bond. Selected novel applications of the halogen bond made in the last decade in various areas of chemistry/materials (namely crystal engineering, liquid crystals, nano-materials, polymer chemistry and inorganic chemistry) are then reviewed. These applications generally involve molecules of the type XR (where R is an electron-withdrawing group) acting as the electron donor, rather than dihalogens XY.

  16. 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

  17. Chalcogen bond: a sister noncovalent bond to halogen bond.

    PubMed

    Wang, Weizhou; Ji, Baoming; Zhang, Yu

    2009-07-16

    A sister noncovalent bond to halogen bond, termed chalcogen bond, is defined in this article. By selecting the complexes H(2)CS...Cl(-), F(2)CS...Cl(-), OCS...Cl(-), and SCS...Cl(-) as models, the bond-length change, interaction energy, topological property of the electron charge density and its Laplacian, and the charge transfer of the chalcogen bond have been investigated in detail theoretically. It was found that the similar misshaped electron clouds of the chalcogen atom and the halogen atom result in the similar properties of the chalcogen bond and the halogen bond. Experimental results are in good agreement with the theoretical predictions.

  18. 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.

  19. 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

  20. 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)

  1. 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.

  2. 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.

  3. 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.

  4. Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons.

    PubMed

    Xiao, Chuanyun; Zhang, Yingkai

    2007-09-28

    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 pseudopotential 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 pseudopotentials 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  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

    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.

  12. 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

  13. Renaturation of denatured, covalently closed circular DNA.

    PubMed

    Strider, W; Camien, M N; Warner, R C

    1981-08-10

    The rate of renaturation of denatured, covalently closed, circular DNA (form Id DNA) of the phi X174 replicative form has been investigated as a function of pH, temperature, and ionic strength. The rate at a constant temperature is a sharply peaked function of pH in the range of pH 9 to 12. The position on the pH scale of the maximum rate decreases as the temperature is increased and as the ionic strength is increased. The kinetic course of renaturation is pseudo-first order: it is independent of DNA concentration, but falls off in rate from a first order relationship as the reaction proceeds. The rate of renaturation depends critically on the temperature at which the denaturation is carried out. Form Id, prepared at an alkaline pH at 0 degrees C, renatures from 5 to more than 100 times more rapidly than that similarly prepared at 50 degrees C. Both the heterogeneity in rate and the effect of the temperature of denaturation depend, in part, on the degree of supercoiling of the form I DNA from which the form Id is prepared. However, it is concluded that a much larger contribution to both arises from a configurational heterogeneity introduced in the denaturation reaction. The renaturation rate was determined by neutralization of the alkaline reaction and analytical ultracentrifugal analysis of the amounts of forms I and Id. The nature of the proximate renatured species at the temperature and alkaline pH of renaturation was investigated by spectrophotometric titration and analytical ultracentrifugation. It is concluded that the proximate species are the same as the intermediate species defined by an alkaline sedimentation titration of the kind first done by Vinograd et al. ((1965) Proc. Natl. Acad. Sci. U. S. A. 53, 1104-1111). Observations are included on the buoyant density of form Id and on depurination of DNA at alkaline pH values and high temperatures.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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

  19. A New Staple: Peptide-Targeted Covalent Inhibitors.

    PubMed

    Leverson, Joel D

    2016-09-22

    In this issue of Cell Chemical Biology, Huhn et al. (2016) unveil a clever strategy for selectively and irreversibly inhibiting an anti-apoptotic protein, BFL-1. The authors describe stapled peptides bearing carefully placed electrophiles that target a unique cysteine residue in BFL-1 via covalent modification, thus representing an extension of the stapled peptide concept into the covalent inhibitor space. PMID:27662249

  20. Non-covalent interactions between carbon nanotubes and conjugated polymers.

    PubMed

    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.

  1. 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 inhibitors in vitro and in vivo.

  2. 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.

  3. 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

  4. 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.

  5. Kinetics of reactions at an interface: functionalisation of silicate glass with porphyrins via covalent bonds.

    PubMed

    Fujimoto, Takahiro; Furuta, Nao; Mizutani, Tadashi

    2015-03-21

    Porphyrins carrying either a primary alcohol, a tertiary alcohol or a primary bromide linker group were allowed to react with the surface silanol groups on silicate glass thermally at 80-240 °C to obtain a monolayer film. The kinetics of the reaction was analysed based on the pseudo-second order equation. The tertiary alcohol and the primary bromide reacted much slower than the primary alcohol. Arrhenius plots indicated that higher activation energies can account for the slower reaction of both tertiary alcohol and primary bromide linkers. The introduction of six dodecyl chains into hydroxyporphyrin accelerated the anchoring reaction by a factor of 50 owing to the larger frequency factor of the reaction, demonstrating that the dynamics of the interface is one of the dominant factors regulating the reaction kinetics.

  6. Absence of edge states in covalently bonded zigzag edges of graphene on Ir(111).

    PubMed

    Li, Yan; Subramaniam, Dinesh; Atodiresei, Nicolae; Lazić, Predrag; Caciuc, Vasile; Pauly, Christian; Georgi, Alexander; Busse, Carsten; Liebmann, Marcus; Blügel, Stefan; Pratzer, Marco; Morgenstern, Markus; Mazzarello, Riccardo

    2013-04-11

    The zigzag edges of graphene on Ir(111) are studied by ab initio simulations and low-temperature scanning tunneling spectroscopy, providing information about their structural, electronic, and magnetic properties. No edge state is found to exist, which is explained in terms of the interplay between a strong geometrical relaxation at the edge and a hybridization of the d orbitals of Ir atoms with the graphene orbitals at the edge.

  7. 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

  8. 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.

  9. 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.

  10. Covalently coupled hybrid of graphitic carbon nitride with reduced graphene oxide as a superior performance lithium-ion battery anode.

    PubMed

    Fu, Yongsheng; Zhu, Junwu; Hu, Chong; Wu, Xiaodong; Wang, Xin

    2014-11-01

    An in situ chemical synthetic approach has been designed for the fabrication of a covalently coupled hybrid consisting of graphitic carbon nitride (g-C3N4) with reduced graphene oxide (rGO) with differing g-C3N4/rGO ratio. The epoxy groups of graphene oxide (GO) undergo a nucleophilic substitution reaction with dicyandiamide (C2H4N4) to form the C2H4N4-GO composite via a covalent C-N bond, and then both the in situ polymerization of C2H4N4 and the thermal reduction of GO can be achieved at higher temperatures, forming the covalently coupled g-C3N4-rGO. FT-IR, CP-MAS NMR and XPS analyses, clearly revealed a covalent interaction between the g-C3N4 and rGO sheets. The g-C3N4-rGO exhibits an unprecedented high, stable and reversible capacity of 1525 mA h g(-1) at a current density of 100 mA g(-1) after 50 cycles. Even at a large current density of 1000 mA g(-1), a reversible capacity of 943 mA h g(-1) can still be retained. The superior electrochemical performance of g-C3N4-rGO is attributed to the specific characteristics of the unique nanostructure of g-C3N4-rGO and the concerted effects of g-C3N4 and rGO, including covalent interactions between the two moieties, the good conductivity and high special surface area of the nanocomposite, as well as the template effect of the planar amino group of g-C3N4 for the dispersed decoration of Li(+) ions.

  11. 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

  12. 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.

  13. Hapten-directed spontaneous disulfide shuffling: a universal technology for site-directed covalent coupling of payloads to antibodies

    PubMed Central

    Dengl, Stefan; Hoffmann, Eike; Grote, Michael; Wagner, Cornelia; Mundigl, Olaf; Georges, Guy; Thorey, Irmgard; Stubenrauch, Kay-Gunnar; Bujotzek, Alexander; Josel, Hans-Peter; Dziadek, Sebastian; Benz, Joerg; Brinkmann, Ulrich

    2015-01-01

    Humanized hapten-binding IgGs were designed with an accessible cysteine close to their binding pockets, for specific covalent payload attachment. Individual analyses of known structures of digoxigenin (Dig)- and fluorescein (Fluo) binding antibodies and a new structure of a biotin (Biot)-binder, revealed a “universal” coupling position (52+2) in proximity to binding pockets but without contributing to hapten interactions. Payloads that carry a free thiol are positioned on the antibody and covalently linked to it via disulfides. Covalent coupling is achieved and driven toward complete (95–100%) payload occupancy by spontaneous redox shuffling between antibody and payload. Attachment at the universal position works with different haptens, antibodies, and payloads. Examples are the haptens Fluo, Dig, and Biot combined with various fluorescent or peptidic payloads. Disulfide-bonded covalent antibody-payload complexes do not dissociate in vitro and in vivo. Coupling requires the designed cysteine and matching payload thiol because payload or antibody without the Cys/thiol are not linked (<5% nonspecific coupling). Hapten-mediated positioning is necessary as hapten-thiol-payload is only coupled to antibodies that bind matching haptens. Covalent complexes are more stable in vivo than noncovalent counterparts because digoxigeninylated or biotinylated fluorescent payloads without disulfide-linkage are cleared more rapidly in mice (approximately 50% reduced 48 hour serum levels) compared with their covalently linked counterparts. The coupling technology is applicable to many haptens and hapten binding antibodies (confirmed by automated analyses of the structures of 140 additional hapten binding antibodies) and can be applied to modulate the pharmacokinetics of small compounds or peptides. It is also suitable to link payloads in a reduction-releasable manner to tumor- or tissue-targeting delivery vehicles.—Dengl, S., Hoffmann, E., Grote, M., Wagner, C., Mundigl, O

  14. Thermodynamic behavior of a model covalent material described by the environment-dependent interatomic potential

    NASA Astrophysics Data System (ADS)

    Keblinski, P.; Bazant, M. Z.; Dash, R. K.; Treacy, M. M.

    2002-08-01

    Using molecular-dynamics simulations we study the thermodynamic behavior of a single-component covalent material described by the recently proposed environment-dependent interatomic potential (EDIP). The parametrization of EDIP for silicon exhibits a range of unusual properties typically found in more complex materials, such as the existence of two structurally distinct disordered phases, a density increase upon melting of the low-temperature amorphous phase, and negative thermal-expansion coefficients for both the crystal (at high temperatures) and the amorphous phase (at all temperatures). Structural differences between the two disordered phases also lead to a first-order transition between them, which suggests the existence of a second critical point, as is believed to exist for amorphous forms of frozen water. For EDIP-Si, however, the unusual behavior is associated not only with the open nature of tetrahedral bonding but also with a competition between fourfold (covalent) and fivefold (metallic) coordination. The unusual behavior of the model and its unique ability to simulate the liquid/amorphous transition on molecular-dynamics time scales make it a suitable prototype for fundamental studies of anomalous thermodynamics in disordered systems.

  15. The effect of non-covalent functionalization on the thermal conductance of graphene/organic interfaces.

    PubMed

    Lin, Shangchao; Buehler, Markus J

    2013-04-26

    The intrinsic interfacial thermal resistance at graphene/organic interfaces, as a result of mismatches in the phonon vibrational spectra of the two materials, diminishes the overall heat transfer performance of graphene/organic nanocomposites. In this paper, we use molecular dynamics (MD) simulations to design alkyl-pyrene molecules that can non-covalently functionalize graphene surfaces in contact with a model organic phase composed of octane. The alkyl-pyrene molecules possess phonon-spectra features of both graphene and octane and, therefore, can serve as phonon-spectra linkers to bridge the vibrational mismatch at the graphene/octane interface. In support of this hypothesis, we find that the best linker candidate can enhance the out-of-plane graphene/organic interfacial thermal conductance by ~22%, attributed to its capability to compensate the low-frequency phonon mode of graphene. We also find that the length of the alkyl chain indirectly affects the interfacial thermal conductance through different orientations of these chains because they dictate the contribution of the out-of-plane high-frequency carbon-hydrogen bond vibrations to the overall phonon transport. This study advances our understanding of the less destructive non-covalent functionalization method and design principles of suitable linker molecules to enhance the thermal performance of graphene/organic nanocomposites while retaining the intrinsic chemical, thermal, and mechanical properties of pristine graphene.

  16. 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

  17. 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

  18. A new family of covalent inhibitors block nucleotide binding to the active site of pyruvate kinase

    PubMed Central

    Morgan, Hugh P.; Walsh, Martin J.; Blackburn, Elizabeth A.; Wear, Martin A.; Boxer, Matthew B.; Shen, Min; Mcnae, Iain W.; Nowicki, Matthew W.; Michels, Paul A. M.; Auld, Douglas S.; Fothergill-Gilmore, Linda A.; Walkinshaw, Malcolm D.

    2012-01-01

    SYNOPSIS Pyruvate kinase (PYK) plays a central role in the metabolism of many organisms and cell types, but the elucidation of the details of its function in a systems biology context has been hampered by the lack of specific high-affinity small molecule inhibitors. High-throughput screening has been used to identify a family of saccharin derivatives which inhibit Leishmania mexicana PYK (LmPYK) activity in a time- (and dose-) dependent manner; a characteristic of irreversible inhibition. The crystal structure of 4-[(1,1-dioxo-1,2-benzothiazol-3-yl)sulfanyl]benzoic acid (DBS) complexed with LmPYK shows that the saccharin moiety reacts with an active-site lysine residue (Lys335), forming a covalent bond and sterically hindering the binding of ADP/ATP. Mutation of the lysine residue to an arginine residue eliminated the effect of the inhibitor molecule, providing confirmation of the proposed inhibitor mechanism. This lysine residue is conserved in the active sites of the four human PYK isoenzymes, which were also found to be irreversibly inhibited by DBS. X-ray structures of PYK isoforms show structural differences at the DBS binding pocket, and this covalent inhibitor of PYK provides a chemical scaffold for the design of new families of potentially isoform-specific irreversible inhibitors. PMID:22906073

  19. 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

  20. 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

  1. 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.

  2. Theory of Covalent Adsorbate Frontier Orbital Energies on Functionalized Light-Absorbing Semiconductor Surfaces.

    PubMed

    Yu, Min; Doak, Peter; Tamblyn, Isaac; Neaton, Jeffrey B

    2013-05-16

    Functional hybrid interfaces between organic molecules and semiconductors are central to many emerging information and solar energy conversion technologies. Here we demonstrate a general, empirical parameter-free approach for computing and understanding frontier orbital energies - or redox levels - of a broad class of covalently bonded organic-semiconductor surfaces. We develop this framework in the context of specific density functional theory (DFT) and many-body perturbation theory calculations, within the GW approximation, of an exemplar interface, thiophene-functionalized silicon (111). Through detailed calculations taking into account structural and binding energetics of mixed-monolayers consisting of both covalently attached thiophene and hydrogen, chlorine, methyl, and other passivating groups, we quantify the impact of coverage, nonlocal polarization, and interface dipole effects on the alignment of the thiophene frontier orbital energies with the silicon band edges. For thiophene adsorbate frontier orbital energies, we observe significant corrections to standard DFT (∼1 eV), including large nonlocal electrostatic polarization effects (∼1.6 eV). Importantly, both results can be rationalized from knowledge of the electronic structure of the isolated thiophene molecule and silicon substrate systems. Silicon band edge energies are predicted to vary by more than 2.5 eV, while molecular orbital energies stay similar, with the different functional groups studied, suggesting the prospect of tuning energy alignment over a wide range for photoelectrochemistry and other applications.

  3. 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.

  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.

  5. The Nature of the Idealized Triple Bonds Between Principal Elements and the σ Origins of Trans-Bent Geometries-A Valence Bond Study.

    PubMed

    Ploshnik, Elina; Danovich, David; Hiberty, Philippe C; Shaik, Sason

    2011-04-12

    We describe herein a valence bond (VB) study of 27 triply bonded molecules of the general type X≡Y, where X and Y are main element atoms/fragments from groups 13-15 in the periodic table. The following conclusions were derived from the computational data: (a) Single π-bond and double π-bond energies for the entire set correlate with the "molecular electronegativity", which is the sum of the X and Y electronegativites for X≡Y. The correlation with the molecular electronegativity establishes a simple rule of periodicity: π-bonding strength generally increases from left to right in a period and decreases down a column in the periodic table. (b) The σ frame invariably prefers trans bending, while π-bonding gets destabilized and opposes the trans distortion. In HC≡CH, the π-bonding destabilization overrides the propensity of the σ frame to distort, while in the higher row molecules, the σ frame wins out and establishes trans-bent molecules with 2(1)/2 bonds, in accord with recent experimental evidence based on solid state (29)Si NMR of the Sekiguchi compound. Thus, in the trans-bent molecules "less bonds pay more". (c) All of the π bonds show significant bonding contributions from the resonance energy due to covalent-ionic mixing. This quantity is shown to correlate linearly with the corresponding "molecular electronegativity" and to reflect the mechanism required to satisfy the equilibrium condition for the bond. The π bonds for molecules possessing high molecular electronegativity are charge-shift bonds, wherein bonding is dominated by the resonance energy of the covalent and ionic forms, rather than by either form by itself.

  6. Nevirapine bioactivation and covalent binding in the skin.

    PubMed

    Sharma, Amy M; Klarskov, Klaus; Uetrecht, Jack

    2013-03-18

    Nevirapine (NVP) treatment is associated with serious skin rashes that appear to be immune-mediated. We previously developed a rat model of this skin rash that is immune-mediated and is very similar to the rash in humans. Treatment of rats with the major NVP metabolite, 12-OH-NVP, also caused the rash. Most idiosyncratic drug reactions are caused by reactive metabolites; 12-OH-NVP forms a benzylic sulfate, which was detected in the blood of animals treated with NVP or 12-OH-NVP. This sulfate is presumably formed in the liver; however, the skin also has significant sulfotransferase activity. In this study, we used a serum against NVP to detect covalent binding in the skin of rats. There was a large artifact band in immunoblots of whole skin homogenates that interfered with detection of covalent binding; however, when the skin was separated into dermal and epidermal fractions, covalent binding was clearly present in the epidermis, which is also the location of sulfotransferases. In contrast to rats, treatment of mice with NVP did not result in covalent binding in the skin or skin rash. Although the reaction of 12-OH-NVP sulfate with nucleophiles such as glutathione is slow, incubation of this sulfate with homogenized human and rat skin led to extensive covalent binding. Incubations of 12-OH-NVP with the soluble fraction from a 9,000g centrifugation (S9) of rat or human skin homogenate in the presence of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) produced extensive covalent binding, but no covalent binding was detected with mouse skin S9, which suggests that the reason mice do not develop a rash is that they lack the required sulfotransferase. This is the first study to report covalent binding of NVP to rat and human skin. These data provide strong evidence that covalent binding of NVP in the skin is due to 12-OH-NVP sulfate, which is likely responsible for NVP-induced skin rash. Sulfation may represent a bioactivation pathway for other drugs that cause a skin rash

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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

  15. Extra-electron induced covalent strengthening and generalization of intrinsic ductile-to-brittle criterion

    PubMed Central

    Niu, Haiyang; Chen, Xing-Qiu; Liu, Peitao; Xing, Weiwei; Cheng, Xiyue; Li, Dianzhong; Li, Yiyi

    2012-01-01

    Traditional strengthening ways, such as strain, precipitation, and solid-solution, come into effect by pinning the motion of dislocation. Here, through first-principles calculations we report on an extra-electron induced covalent strengthening mechanism, which alters chemical bonding upon the introduction of extra-valence electrons in the matrix of parent materials. It is responsible for the brittle and high-strength properties of Al12W-type compounds featured by the typical fivefold icosahedral cages, which are common for quasicrystals and bulk metallic glasses (BMGs). In combination with this mechanism, we generalize ductile-to-brittle criterion in a universal hyperbolic form by integrating the classical Pettifor's Cauchy pressure with Pugh's modulus ratio for a wide variety of materials with cubic lattices. This study provides compelling evidence to correlate Pugh's modulus ratio with hardness of materials and may have implication for understanding the intrinsic brittleness of quasicrystals and BMGs. PMID:23056910

  16. 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)

  17. Enhanced enzyme stability through site-directed covalent immobilization.

    PubMed

    Wu, Jeffrey Chun Yu; Hutchings, Christopher Hayden; Lindsay, Mark Jeffrey; Werner, Christopher James; Bundy, Bradley Charles

    2015-01-10

    Breakthroughs in enzyme immobilization have enabled increased enzyme recovery and reusability, leading to significant decreases in the cost of enzyme use and fueling biocatalysis growth. However, current enzyme immobilization techniques suffer from leaching, enzyme stability, and recoverability and reusability issues. Moreover, these techniques lack the ability to control the orientation of the immobilized enzymes. To determine the impact of orientation on covalently immobilized enzyme activity and stability, we apply our PRECISE (Protein Residue-Explicit Covalent Immobilization for Stability Enhancement) system to a model enzyme, T4 lysozyme. The PRECISE system uses non-canonical amino acid incorporation and the Huisgen 1,3-dipolar cycloaddition "click" reaction to enable directed enzyme immobilization at rationally chosen residues throughout an enzyme. Unlike previous site-specific systems, the PRECISE system is a truly covalent immobilization method. Utilizing this system, enzymes immobilized at proximate and distant locations from the active site were tested for activity and stability under denaturing conditions. Our results demonstrate that orientation control of covalently immobilized enzymes can provide activity and stability benefits exceeding that of traditional random covalent immobilization techniques. PRECISE immobilized enzymes were 50 and 73% more active than randomly immobilized enzymes after harsh freeze-thaw and chemical denaturant treatments.

  18. 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…

  19. 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

  20. 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.

  1. Carboxymethylchitosan covalently modified capillary column for open tubular capillary electrochromatography of basic proteins and opium alkaloids.

    PubMed

    Zhou, Sunying; Tan, Jingjing; Chen, Qinhua; Lin, Xucong; Lü, Haixia; Xie, Zenghong

    2010-12-24

    A novel open tubular (OT) column covalently modified with hydrophilic polysaccharide, carboxymethylchitosan (CMC) as stationary phase has been developed, and employed for the separations of basic proteins and opium alkaloids by capillary electrochromatography (CEC). With the procedures including the silanization of 3-aminopropyltrimethoxysilane (APTS) and the combination of glutaraldehyde with amino-silylated silica surface and CMC, CMC was covalently bonded on the capillary inner wall and exhibited a remarkable tolerance and chemical stability against 0.1 mol/L HCl, 0.1 mol/L NaOH or some organic solvents. By varying the pH values of running buffer, a cathodic or anodic EOF could be gained in CMC modified column. With anodic EOF mode (pH<4.3), favorable separations of basic proteins (trypsin, ribonuclease A, lysozyme and cytochrome C) were successfully achieved with high column efficiencies ranging from 97,000 to 182,000 plates/m, and the undesired adsorptions of basic proteins on the inter-wall of capillary could be avoided. Good repeatability was gained with RSD of the migration time less than 1.3% for run-to-run (n=5) and less than 3.2% for day-to-day (n=3), RSD of peak area was less than 5.6% for run-to-run (n=5) and less than 8.8% for day-to-day (n=3). With cathodic EOF mode (pH>4.3), four opium alkaloids were also baseline separated in phosphate buffer (50 mmol/L, pH 6.0) with column efficiencies ranging from 92,000 to 132,000 plates/m. CMC-bonded OT capillary column might be used as an alternative medium for the further analysis of basic proteins and alkaline analytes.

  2. Covalent functionalization of single-walled carbon nanotubes through attachment of aromatic diisocyanate molecules from first principles

    NASA Astrophysics Data System (ADS)

    Goclon, Jakub; Kozlowska, Mariana; Rodziewicz, Pawel

    2015-01-01

    We performed first-principle calculations of the covalent functionalization of metallic (6,0) and semiconducting (10,0) single-walled carbon nanotubes (SWCNTs) with aromatic diisocyanate molecules, namely, 4,4‧-methylene diphenyl diisocyanate (MDI) and toluene-2,4-diisocyanate (TDI). The corresponding binding energies of the attached molecules were scrutinized. We analyzed the changes in the electronic band structure of SWCNTs caused by the amide bond formation after the functionalization process. Furthermore, the MDI-MDI and TDI-TDI mutual interactions on the nanotube surface were investigated.

  3. Inter- and intramolecular non-covalent interactions in 1-methylimidazole-2-carbaldehyde complexes of copper, silver, and gold

    NASA Astrophysics Data System (ADS)

    Koskinen, Laura; Jääskeläinen, Sirpa; Hirva, Pipsa; Haukka, Matti

    2014-09-01

    Three new imidazole compounds, [CuBr2(mimc)2] (1), [Ag(mimc)2][CF3SO3] (2), and [AuCl3(mimc)] (3) (mimc = 1-methylimidazole-2-carbaldehyde), have been synthesized, structurally characterized, and further analyzed using the QTAIM analysis. The compounds exhibit self-assembled 3D networks arising from intermolecular non-covalent interactions such as metallophilic interactions, metal-π contacts, halogens-halogen interactions, and hydrogen bonds. These weak interactions have a strong impact on the coordination sphere of the metal atoms and on the packing of compounds 1, 2, and 3.

  4. 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.

  5. A Highly-Ordered 3D Covalent Fullerene Framework**

    PubMed Central

    Minar, Norma K; Hou, Kun; Westermeier, Christian; Döblinger, Markus; Schuster, Jörg; Hanusch, Fabian C; Nickel, Bert; Ozin, Geoffrey A; Bein, Thomas

    2015-01-01

    A highly-ordered 3D covalent fullerene framework is presented with a structure based on octahedrally functionalized fullerene building blocks in which every fullerene is separated from the next by six functional groups and whose mesoporosity is controlled by cooperative self-assembly with a liquid-crystalline block copolymer. The new fullerene-framework material was obtained in the form of supported films by spin coating the synthesis solution directly on glass or silicon substrates, followed by a heat treatment. The fullerene building blocks coassemble with a liquid-crystalline block copolymer to produce a highly ordered covalent fullerene framework with orthorhombic Fmmm symmetry, accessible 7.5 nm pores, and high surface area, as revealed by gas adsorption, NMR spectroscopy, small-angle X-ray scattering (SAXS), and TEM. We also note that the 3D covalent fullerene framework exhibits a dielectric constant significantly lower than that of the nonporous precursor material. PMID:25958846

  6. Nano-architectures by covalent assembly of molecular building blocks.

    PubMed

    Grill, Leonhard; Dyer, Matthew; Lafferentz, Leif; Persson, Mats; Peters, Maike V; Hecht, Stefan

    2007-11-01

    The construction of electronic devices from single molecular building blocks, which possess certain functions such as switching or rectifying and are connected by atomic-scale wires on a supporting surface, is an essential goal of molecular electronics. A key challenge is the controlled assembly of molecules into desired architectures by strong, that is, covalent, intermolecular connections, enabling efficient electron transport between the molecules and providing high stability. However, no molecular networks on surfaces 'locked' by covalent interactions have been reported so far. Here, we show that such covalently bound molecular nanostructures can be formed on a gold surface upon thermal activation of porphyrin building blocks and their subsequent chemical reaction at predefined connection points. We demonstrate that the topology of these nanostructures can be precisely engineered by controlling the chemical structure of the building blocks. Our results represent a versatile route for future bottom-up construction of sophisticated electronic circuits and devices, based on individual functionalized molecules.

  7. 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.

  8. 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.

  9. Theoretical investigation on multiple bonds in terminal actinide nitride complexes.

    PubMed

    Wu, Qun-Yan; Wang, Cong-Zhi; Lan, Jian-Hui; Xiao, Cheng-Liang; Wang, Xiang-Ke; Zhao, Yu-Liang; Chai, Zhi-Fang; Shi, Wei-Qun

    2014-09-15

    A series of actinide (An) species of L-An-N compounds [An = Pa-Pu, L = [N(CH2CH2NSiPr(i)3)3](3-), Pr(i) = CH(CH3)2] have been investigated using scalar relativistic density functional theory (DFT) without considering spin-orbit coupling effects. The ground state geometric and electronic structures and natural bond orbital (NBO) analysis of actinide compounds were studied systematically in neutral and anionic forms. It was found that with increasing actinide atomic number, the bond length of terminal multiple An-N1 bond decreases, in accordance with the actinide contraction. The Mayer bond order of An-N1 decreases gradually from An = Pa to Pu, which indicates a decrease in bond strength. The terminal multiple bond for L-An-N compounds contains one σ and two π molecular orbitals, and the contributions of the 6d orbital to covalency are larger in magnitude than the 5f orbital based on NBO analysis and topological analysis of electron density. This work may help in understanding of the bonding nature of An-N multiple bonds and elucidating the trends and electronic structure changes across the actinide series. It can also shed light on the construction of novel An-N multiple bonds.

  10. Robustly Engineering Thermal Conductivity of Bilayer Graphene by Interlayer Bonding.

    PubMed

    Zhang, Xiaoliang; Gao, Yufei; Chen, Yuli; Hu, Ming

    2016-02-25

    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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Temperature and Oxygen Sensing Properties of Ru(II) Covalently-Grafted Sol-Gel Derived Ormosil Hybrid Materials.

    PubMed

    Zhang, Haoran; Lei, Bingfu; Dong, Hanwu; Liu, Yingliang; Zheng, Mingtao; Xiao, Yong

    2016-04-01

    In this article, oxygen and temperature-sensing hybrid materials consisting of [Ru(Phen)3]2+ portions covalently-grafted onto the sol-gel derived ormosil network were prepared by co-condensation of tetraethoxysilane (TEOS) using n-octyltriethoxysilane as the network modifier. For comparison purposes, the hybrid materials in which [Ru(Phen)3]2+ were conventionally physically-incorporated into the matrix were also prepared. The obtained hybrid materials were characterized by Fourier transform infrared (FT-IR), luminescence intensity oxygen quenching Stern-Volmer plots, temperature quenching plots and excited-state lifetime. The near linear Stern-Volmer plots can be attributed to the approximate heterogeneous environment of the luminophore within the ormosil materials. The results reveal that the. covalently-grafted sample is more sensitive to 02, and has a higher sensing sensitivity and a higher thermal activation energy compared to the physically-incorporated one, since these Ru(II) molecules are strongly covalently-grafted onto the Si-O network via the CH2-Si bonds and less -OH group. PMID:27451760

  16. 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

  17. DFT investigation on dihydrogen-bonded amine-borane complexes.

    PubMed

    Yan, Shihai; Zou, Hongmei; Kang, Wukui; Sun, Lixiang

    2016-01-01

    The DFT method has been employed in the exploration on dihydrogen-bonded amine-borane complexes, with a special emphasis on the dimerization and substituent group effect. Stable dihydrogen bonded complexes can be generated from these amine-borane monomers with the appearance of NH(δ+)…H(δ-)B interactions. The binding energy decreases gradually with the increase of the steric effect of the substituents. The substituent group number mainly varies the C-N bond length. The dimerization generates close H…H and influences predominantly the N-B distance. The effect of dimerization on IR and vibrational circular dichroism (VCD) spectra is stronger than that of the number of substituent groups, which leads to distinct NBO charge variation on α-C. Both the substituent group number and dimerization enhance the chemical shift difference between hydrogen atoms covalently bonded to N and B, Δδ H-H, which can be hired as an index for structural determination. It is proposed that amine-borane complexes with more substituent groups in higher degree of polymerization are potentially interesting materials for hydrogen storage. Graphical Abstract Both the number of substituent group and dimerization enhance the chemical shift difference of hydrogen atoms covalently bonded on N and B, Δδ H-H, which can be employed as an index for the structural determination.

  18. The unexpected non-monotonic inter-layer bonding dependence of the thermal conductivity of bilayered boron nitride.

    PubMed

    Gao, Yufei; Zhang, Xiaoliang; Jing, Yuhang; Hu, Ming

    2015-04-28

    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.

  19. Unusual structure, bonding and properties in a californium borate

    NASA Astrophysics Data System (ADS)

    Polinski, Matthew J.; Garner, Edward B.; Maurice, Rémi; Planas, Nora; Stritzinger, Jared T.; Parker, T. Gannon; Cross, Justin N.; Green, Thomas D.; Alekseev, Evgeny V.; van Cleve, Shelley M.; Depmeier, Wulf; Gagliardi, Laura; Shatruk, Michael; Knappenberger, Kenneth L.; Liu, Guokui; Skanthakumar, S.; Soderholm, Lynda; Dixon, David A.; Albrecht-Schmitt, Thomas E.

    2014-05-01

    The participation of the valence orbitals of actinides in bonding has been debated for decades. Recent experimental and computational investigations demonstrated the involvement of 6p, 6d and/or 5f orbitals in bonding. However, structural and spectroscopic data, as well as theory, indicate a decrease in covalency across the actinide series, and the evidence points to highly ionic, lanthanide-like bonding for late actinides. Here we show that chemical differentiation between californium and lanthanides can be achieved by using ligands that are both highly polarizable and substantially rearrange on complexation. A ligand that suits both of these desired properties is polyborate. We demonstrate that the 5f, 6d and 7p orbitals are all involved in bonding in a Cf(III) borate, and that large crystal-field effects are present. Synthetic, structural and spectroscopic data are complemented by quantum mechanical calculations to support these observations.

  20. Unusual structure, bonding and properties in a californium borate.

    PubMed

    Polinski, Matthew J; Garner, Edward B; Maurice, Rémi; Planas, Nora; Stritzinger, Jared T; Parker, T Gannon; Cross, Justin N; Green, Thomas D; Alekseev, Evgeny V; Van Cleve, Shelley M; Depmeier, Wulf; Gagliardi, Laura; Shatruk, Michael; Knappenberger, Kenneth L; Liu, Guokui; Skanthakumar, S; Soderholm, Lynda; Dixon, David A; Albrecht-Schmitt, Thomas E

    2014-05-01

    The participation of the valence orbitals of actinides in bonding has been debated for decades. Recent experimental and computational investigations demonstrated the involvement of 6p, 6d and/or 5f orbitals in bonding. However, structural and spectroscopic data, as well as theory, indicate a decrease in covalency across the actinide series, and the evidence points to highly ionic, lanthanide-like bonding for late actinides. Here we show that chemical differentiation between californium and lanthanides can be achieved by using ligands that are both highly polarizable and substantially rearrange on complexation. A ligand that suits both of these desired properties is polyborate. We demonstrate that the 5f, 6d and 7p orbitals are all involved in bonding in a Cf(III) borate, and that large crystal-field effects are present. Synthetic, structural and spectroscopic data are complemented by quantum mechanical calculations to support these observations.

  1. 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

  2. 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.

  3. Covalent organic frameworks as pH responsive signaling scaffolds.

    PubMed

    Zhang, Yuwei; Shen, Xiaochen; Feng, Xiao; Xia, Hong; Mu, Ying; Liu, Xiaoming

    2016-09-25

    A β-ketoenamine based covalent organic framework, COF-JLU4, was synthesized by condensation of 2,5-dimethoxyterephthalohydrazide with triformylphloroglucinol under solvothermal conditions. This COF has strong crystallinity, good porosity, photoluminescence properties and wettability for water. It can serve as the first COF-based fluorescent pH sensor in aqueous solutions. PMID:27545686

  4. Fluoroquinolones as potential photochemotherapeutic agents: covalent addition to guanosine monophosphate.

    PubMed

    Fasani, Elisa; Manet, Ilse; Capobianco, Massimo L; Monti, Sandra; Pretali, Luca; Albini, Angelo

    2010-08-21

    The triplet aryl cation photochemically generated from fluoroquinolones bearing a fluoro atom at position 8 attacks guanosine monophosphate (k(r) > 10(9) M(-1)s(-1)) and forms covalent adducts. The reaction is a model for the implementation of oxygen-independent photochemotherapy. PMID:20571620

  5. Entanglement of protons in organic molecules: an attosecond neutron scattering study of C [bond] H bond breaking.

    PubMed

    Chatzidimitriou-Dreismann, C A; Abdul-Redah, T; Kolaric, B

    2001-12-01

    Interactions between adjacent particles of condensed phases can lead to quantum correlation phenomena, like quantum interference, entanglement, delocalization, and "Schrödinger's cat" states. Such correlations are theoretically expected to be extremely short-lived because of environmental disturbances. Here, we present experimental evidence for quantum entanglement between well localized protons of C [bond] H bonds of 2-isobutoxyethanol dissolved in D(2)O. The applied experimental method is neutron Compton scattering (NCS), which has a characteristic time window in the subfemtosecond time range. Our NCS results reveal that, in the subfemtosecond time scale, the measured cross-section density, and thus, in simple terms, the effectively present concentration, of the H atoms is "anomalously" reduced by approximately 20%. Affecting the microdynamics of protons of covalent C [bond] H bonds, this novel effect may have a broad range of chemical and biological applications.

  6. Molecular deformation mechanisms in cellulose allomorphs and the role of hydrogen bonds.

    PubMed

    Djahedi, Cyrus; Berglund, Lars A; Wohlert, Jakob

    2015-10-01

    Differences in tensile properties between cellulose crystal allomorphs cannot be rationalized by simply counting hydrogen bonds. From molecular dynamics computer simulations the cooperative nature of energy contributions to axial cellulose crystal modulus becomes apparent. Using a decomposition of inter and intramolecular forces as a function of tensile strain, the three allomorphs show dramatic differences in terms of how the contributions to elastic energy are distributed between covalent bonds, angles, dihedrals, electrostatic forces, dispersion and steric forces.

  7. Hyaluronic Acid-Based Hydrogels Containing Covalently Integrated Drug Depots: Implication for Controlling Inflammation in Mechanically Stressed Tissues

    PubMed Central

    Xiao, Longxi; Tong, Zhixiang; Chen, Yingchao; Pochan, Darrin J.; Sabanayagam, Chandran R.; Jia, Xinqiao

    2013-01-01

    Synthetic hydrogels containing covalently-integrated soft and deformable drug depots capable of releasing therapeutic molecules in response to mechanical forces are attractive candidates for the treatment of degenerated tissues that are normally load bearing. Herein, radically crosslinkable block copolymer micelles (xBCM) assembled from an amphiphilic block copolymer consisting of hydrophilic poly(acrylic acid) (PAA) partially modified with 2-hydroxyethyl acrylate, and hydrophobic poly(n-butyl acryclate) (PnBA) were employed as the drug depots and the microscopic crosslinkers for the preparation of hyaluronic acid (HA)-based, hydrogels. HA hydrogels containing covalently integrated micelles (HAxBCM) were prepared by radical polymerization of glycidyl methacrylate (GMA)-modified HA (HAGMA) in the presence of xBCMs. When micelles prepared from the parent PAA-b-PnBA without any polymerizable double bonds were used, hydrogels containing physically entrapped micelles (HApBCM) were obtained. The addition of xBCMs to a HAGMA precursor solution accelerated the gelation kinetics and altered the hydrogel mechanical properties. The resultant HAxBCM gels exhibit an elastic modulus of 847 ± 43 Pa and a compressive modulus of 9.2 ± 0.7 kPa. Diffusion analysis of Nile Red (NR)-labeled xBCMs employing fluorescence correlation spectroscopy confirmed the covalent immobilization of xBCMs in HA networks. Covalent integration of dexamethasone (DEX)-loaded xBCMs in HA gels significantly reduced the initial burst release and provided sustained release over a prolonged period. Importantly, DEX release from HAxBCM gels was accelerated by intermittently-applied external compression in a strain-dependent manner. Culturing macrophages in the presence of DEX-releasing HAxBCM gels significantly reduced cellular production of inflammatory cytokines. Incorporating mechano-responsive modules in synthetic matrices offers a novel strategy to harvest mechanical stress present in the healing wounds

  8. Supramolecular catalysis. Part 1: non-covalent interactions as a tool for building and modifying homogeneous catalysts.

    PubMed

    Raynal, Matthieu; Ballester, Pablo; Vidal-Ferran, Anton; van Leeuwen, Piet W N M

    2014-03-01

    Supramolecular catalysis is a rapidly expanding discipline which has benefited from the development of both homogeneous catalysis and supramolecular chemistry. The properties of classical metal and organic catalysts can now be carefully tailored by means of several suitable approaches and the choice of reversible interactions such as hydrogen bond, metal-ligand, electrostatic and hydrophobic interactions. The first part of these two subsequent reviews will be dedicated to catalytic systems for which non-covalent interactions between the partners of the reaction have been designed although mimicking enzyme properties has not been intended. Ligand, metal, organocatalyst, substrate, additive, and metal counterion are reaction partners that can be held together by non-covalent interactions. The resulting catalysts possess unique properties compared to analogues lacking the assembling properties. Depending on the nature of the reaction partners involved in the interactions, distinct applications have been accomplished, mainly (i) the building of bidentate ligand libraries (intra ligand-ligand), (ii) the building of di- or oligonuclear complexes (inter ligand-ligand), (iii) the alteration of the coordination spheres of a metal catalyst (ligand-ligand additive), and (iv) the control of the substrate reactivity (catalyst-substrate). More complex systems that involve the cooperative action of three reaction partners have also been disclosed. In this review, special attention will be given to supramolecular catalysts for which the observed catalytic activity and/or selectivity have been imputed to non-covalent interaction between the reaction partners. Additional features of these catalysts are the easy modulation of the catalytic performance by modifying one of their building blocks and the development of new catalytic pathways/reactions not achievable with classical covalent catalysts.

  9. Hyaluronic acid-based hydrogels containing covalently integrated drug depots: implication for controlling inflammation in mechanically stressed tissues.

    PubMed

    Xiao, Longxi; Tong, Zhixiang; Chen, Yingchao; Pochan, Darrin J; Sabanayagam, Chandran R; Jia, Xinqiao

    2013-11-11

    Synthetic hydrogels containing covalently integrated soft and deformable drug depots capable of releasing therapeutic molecules in response to mechanical forces are attractive candidates for the treatment of degenerated tissues that are normally load bearing. Herein, radically cross-linkable block copolymer micelles (xBCM) assembled from an amphiphilic block copolymer consisting of hydrophilic poly(acrylic acid) (PAA) partially modified with 2-hydroxyethyl acrylate, and hydrophobic poly(n-butyl acryclate) (PnBA) were employed as the drug depots and the microscopic cross-linkers for the preparation of hyaluronic acid (HA)-based, hydrogels. HA hydrogels containing covalently integrated micelles (HAxBCM) were prepared by radical polymerization of glycidyl methacrylate (GMA)-modified HA (HAGMA) in the presence of xBCMs. When micelles prepared from the parent PAA-b-PnBA without any polymerizable double bonds were used, hydrogels containing physically entrapped micelles (HApBCM) were obtained. The addition of xBCMs to a HAGMA precursor solution accelerated the gelation kinetics and altered the hydrogel mechanical properties. The resultant HAxBCM gels exhibit an elastic modulus of 847 ± 43 Pa and a compressive modulus of 9.2 ± 0.7 kPa. Diffusion analysis of Nile Red (NR)-labeled xBCMs employing fluorescence correlation spectroscopy confirmed the covalent immobilization of xBCMs in HA networks. Covalent integration of dexamethasone (DEX)-loaded xBCMs in HA gels significantly reduced the initial burst release and provided sustained release over a prolonged period. Importantly, DEX release from HAxBCM gels was accelerated by intermittently applied external compression in a strain-dependent manner. Culturing macrophages in the presence of DEX-releasing HAxBCM gels significantly reduced cellular production of inflammatory cytokines. Incorporating mechano-responsive modules in synthetic matrices offers a novel strategy to harvest mechanical stress present in the healing

  10. 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

  11. 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

  12. Efficiency of Polyoxometalate-Based Mesoporous Hybrids as Covalently Anchored Catalysts.

    PubMed

    Bentaleb, Faiza; Makrygenni, Ourania; Brouri, Dalil; Coelho Diogo, Cristina; Mehdi, Ahmad; Proust, Anna; Launay, Franck; Villanneau, Richard

    2015-08-01

    Polyoxometalate (POM) hybrids have been covalently immobilized through the formation of amide bonds on several types of mesoporous silica. This work allows the comparison of three POM-based mesoporous systems, obtained with three different silica supports in which either the organic functions of the support (amine vs carboxylic acid) and/or the structure of the support itself (SBA-15 vs mesocellular foams (MCF)) were varied. The resulting POM-based mesoporous systems have been studied in particular by high resolution transmission electronic microscopy (HR-TEM) in order to characterize the nanostructuration of the POMs inside the pores/cells of the different materials. We thus have shown that the best distribution and loading in POMs have been reached with SBA-15 functionalized with aminopropyl groups. In this case, the formation of amide bonds in the materials has led to the nonaggregation of the POMs inside the channels of the SBA-15. The catalytic activity of the anchored systems has been evaluated through the epoxidation of cyclooctene and cyclohexene with H2O2 in acetonitrile. The reactivity of the different grafted POMs hybrids has been compared to that in solution (homogeneous conditions). Parallels can be drawn between the distribution of the POMs and the activity of the supported systems. Furthermore, recycling tests together with catalyst filtration experiments during the reaction allowed us to preclude the hypothesis of a significant leaching of the supported catalyst. PMID:26161980

  13. Physical meaning of the QTAIM topological parameters in hydrogen bonding.

    PubMed

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

    2014-11-01

    This work examined the local topological parameters of charge density at the hydrogen bond (H-bond) critical points of a set of substituted formamide cyclic dimers and enolic tautomers. The analysis was performed not only on the total electron density of the hydrogen bonded complexes but also on the intermediate electron density differences derived from the Morokuma energy decomposition scheme. Through the connection between these intermediate electron density differences and the corresponding differences in topological parameters, the meaning of topological parameters variation due to hydrogen bonding (H-bonding) becomes evident. Thus, for example, we show in a plausible way that the potential energy density differences at the H-bond critical point properly describe the electrostatics of H-bonding, and local kinetic energy density differences account for the localization/delocalization degree of the electrons at that point. The results also support the idea that the total electronic energy density differences at the H-bond critical point describe the strength of the interaction rather than its covalent character as is commonly considered.

  14. 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

  15. Covalent disulfide-linked anti-CEA diabody allows site-specific conjugation and radiolabeling for tumor targeting applications

    PubMed Central

    Olafsen, Tove; Cheung, Chia-wei; Yazaki, Paul J.; Li, Lin; Sundaresan, Gobalakrishnan; Gambhir, Sanjiv S.; Sherman, Mark A.; Williams, Lawrence E.; Shively, John E.; Raubitschek, Andrew A.; Wu, Anna M.

    2014-01-01

    An engineered anti-carcinoembryonic antigen (CEA) diabody (scFv dimer, 55 kDa) was previously constructed from the murine anti-CEA T84.66 antibody. Tumor targeting, imaging and biodistribution studies in nude mice bearing LS174T xenografts with radiolabeled anti-CEA diabody demonstrated rapid tumor uptake and fast blood clearance, which are favorable properties for an imaging agent. Current radiolabeling approaches result in random modification of the protein surface, which may impair immunoreactivity especially for smaller antibody fragments. Site-specific conjugation approaches can direct modifications to reactive groups located away from the binding site. Here, cysteine residues were introduced into the anti-CEA diabody at three different locations, to provide specific thiol groups for chemical modification. One version (with a C-terminal Gly-Gly-Cys) existed exclusively as a disulfide-bonded dimer. This cysteine-modified diabody (Cys-diabody) retained high binding to CEA and demonstrated tumor targeting and biodistribution properties identical to the non-covalent diabody. Furthermore, following reduction of the disulfide bond, the Cys-diabody could be chemically modified using a thiol-specific bifunctional chelating agent, for radiometal labeling. Thus, the Cys-diabody provides a covalently linked alternative to conventional diabodies, which can be reduced and modified site-specifically. This format will provide a versatile platform for targeting a variety of agents to CEA-positive tumors. PMID:14985534

  16. Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand.

    PubMed

    Jiang, Yongying; Trnka, Michael J; Medzihradszky, Katalin F; Ouellet, Hugues; Wang, Yongqiang; Ortiz de Montellano, Paul R

    2009-03-01

    To characterize heme oxygenase with a selenocysteine (SeCys) as the proximal iron ligand, we have expressed truncated human heme oxygenase-1 (hHO-1) His25Cys, in which Cys-25 is the only cysteine, in the Escherichia coli cysteine auxotroph strain BL21(DE3)cys. Selenocysteine incorporation into the protein was demonstrated by both intact protein mass measurement and mass spectrometric identification of the selenocysteine-containing tryptic peptide. One selenocysteine was incorporated into approximately 95% of the expressed protein. Formation of an adduct with Ellman's reagent (DTNB) indicated that the selenocysteine in the expressed protein was in the reduced state. The heme-His25SeCys hHO-1 complex could be prepared by either (a) supplementing the overexpression medium with heme, or (b) reconstituting the purified apoprotein with heme. Under reducing conditions in the presence of imidazole, a covalent bond is formed by addition of the selenocysteine residue to one of the heme vinyl groups. No covalent bond is formed when the heme is replaced by mesoheme, in which the vinyls are replaced by ethyl groups. These results, together with our earlier demonstration that external selenolate ligands can transfer an electron to the iron [Y. Jiang, P.R. Ortiz de Montellano, Inorg. Chem. 47 (2008) 3480-3482 ], indicate that a selenyl radical is formed in the hHO-1 His25SeCys mutant that adds to a heme vinyl group.

  17. The role of delocalization error in non-covalent interactions from dispersion-corrected density-functional theory

    NASA Astrophysics Data System (ADS)

    Otero de La Roza, Alberto

    2015-03-01

    Extensive benchmarking of dispersion-corrected density functional theory (dcDFT) methods has shown that it is nowadays feasible to calculate, with great accuracy, binding energies of small dimers and lattice energies of molecular crystals. However, there are many outstanding questions that can only be answered by a proper understanding of the interplay between base functional and dispersion correction. In this talk, I explore how delocalization error from the exchange-correlation functional impacts the calculation of non-covalent donor-acceptor interactions. Delocalization error arises from the failure of most functionals to model the long-range behavior of the exchange-correlation hole. Its primary consequence for non-covalent interactions is that the stability of donor-acceptor interactions is overestimated. Errors caused by delocalization error are particularly harmful in systems with strong and extensive hydrogen-bonded networks (water clusters and ice) or strong donor-acceptor interactions (halogen bonding), and can not be corrected using a pairwise dispersion correction. In addition, I present how delocalization error affects real-life applications of dcDFT, such as molecular adsorption on iron-oxide nanoparticles and surfaces.

  18. Nondestructive covalent functionalization of carbon nanotubes by selective oxidation of the original defects with K2FeO4

    NASA Astrophysics Data System (ADS)

    Zhang, Zhao-yang; Xu, Xue-cheng

    2015-08-01

    Chemical oxidation is still the major approach to the covalent functionalization of carbon nanotubes (CNTs). Theoretically, the defects on CNTs are more reactive than skeletal hexagons and should be preferentially oxidized, but conventional oxidation methods, e.g., HNO3/H2SO4 treatment, have poor reaction selectivity and inevitably consume the Cdbnd C bonds in the hexagonal lattices, leading to structural damage, π-electrons loss and weight decrease. In this work, we realized the nondestructive covalent functionalization of CNTs by selective oxidation of the defects. In our method, potassium ferrate K2FeVIO4 was employed as an oxidant for CNTs in H2SO4 medium. The CNT samples, before and after K2FeO4/H2SO4 treatment, were characterized with colloid dispersibility, IR, Raman spectroscopy, FESEM and XPS. The results indicated that (i) CNTs could be effectively oxidized by Fe (VI) under mild condition (60 °C, 3 h), and hydrophilic CNTs with abundant surface sbnd COOH groups were produced; and (ii) Fe (VI) oxidation of CNTs followed a defect-specific oxidation process, that is, only the sp3-hybridized carbon atoms on CNT surface were oxidized while the Cdbnd C bonds remained unaffected. This selective/nondestructive oxidation afforded oxidized CNTs in yields of above 100 wt%. This paper shows that K2FeO4/H2SO4 is an effective, nondestructive and green oxidation system for oxidative functionalization of CNTs and probably other carbon materials as well.

  19. Covalent conjugation of tetrameric bovine liver catalase to liposome membranes for stabilization of the enzyme tertiary and quaternary structures.

    PubMed

    Yoshimoto, Makoto; Sakamoto, Hideyuki; Shirakami, Hiroshi

    2009-03-01

    Tetrameric bovine liver catalase (BLC) is unstable because of its dissociation into subunits at low enzyme concentrations and the conformational change of the subunits at high temperatures. In this work, for stabilization of BLC, the enzyme was covalently conjugated with liposome membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), cholesterol and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-glutaryl (NGPE). The NGPE, which was responsible for the BLC/membrane coupling, was altered from 0.05 to 0.2 in its liposomal mole fraction f(G). The catalase-conjugated liposome (CCL) with f(G) of 0.15 showed the maximum number of the conjugated BLC molecules of 28 per liposome. The reactivity of CCLs to H(2)O(2) was as high as that of free BLC at 25 degrees C in Tris-HCl buffer of pH 7.4. Among the CCLs, the catalyst with f(G) of 0.15 was the most stable at 55 degrees C in its enzyme activity in the buffer because the appropriate number of BLC/liposome covalent bonding prevented the dissociation-induced enzyme deactivation. Furthermore, the CCL showed much higher stability at 55 degrees C than the free BLC/enzyme-free liposome mixture and free BLC at the low BLC concentration of 340ng/mL. This was because BLC in the CCL was located in the vicinity of the host membrane regardless of the catalyst concentration, which could induce the effective stabilization effect of the membrane on the enzyme tertiary structure as indicated by the intrinsic tryptophan fluorescence analysis. The results obtained demonstrate the high structural stability of BLC in the CCL system, which was derived from the covalent bonding and interaction between BLC and liposomes. PMID:19131221

  20. The use of native chemical functional groups presented by wound beds for the covalent attachment of polymeric microcarriers of bioactive factors

    PubMed Central

    Jain, Rishabh; Agarwal, Ankit; Kierski, Patricia R.; Schurr, Michael J.; Murphy, Christopher J.; McAnulty, Jonathan F.; Abbott, Nicholas L.

    2012-01-01

    The development of versatile methods that provide spatial and temporal control over the presentation of physical and biochemical cues on wound beds can lead to new therapeutic approaches that expedite wound healing by favorably influencing cellular behaviors. Towards that goal, we report that native chemical functional groups presented by wound beds can be utilized for direct covalent attachment of polymeric microbeads. Specifically, we demonstrated the covalent attachment of maleimide-functionalized and catechol-functionalized microbeads, made of either polystyrene (non-degradable) or poly(lactic-co-glycolic acid) ((PLGA), degradable), to sulfhydryl and amine groups present on porcine dermis used here as an ex vivo model wound bed. A pronounced increase (10–70 fold) in the density and persistence of the covalently reactive microbeads was observed relative to microbeads that adsorb via non-covalent interactions. Complementary characterization of the surface chemistry of the ex vivo wound beds using Raman microspectroscopy provides support for our conclusion that the increased adherence of the maleimide-functionalized beads results from their covalent bond formation with sulfhydryl groups on the wound bed. The attachment of maleimide-functionalized microbeads to wounds created in live wild-type and diabetic mice led to observations of differential immobilization of microbeads on them and were consistent with anticipated differences in the presentation of sulfhydryl groups on the two different wound types. Finally, the incorporation of maleimide-functionalized microbeads in wounds created in wild-type mice did not impair the rate of wound closure relative to an untreated wound. Overall, the results presented in this paper enable a general and facile approach to the engineering of wound beds in which microbeads are covalently immobilized to wound beds. Such immobilized microbeads could be used in future studies to release bioactive factors (e.g., antimicrobial

  1. Hydroxide-catalyzed bonding

    NASA Technical Reports Server (NTRS)

    Gwo, Dz-Hung (Inventor)

    2003-01-01

    A method of bonding substrates by hydroxide-catalyzed hydration/dehydration involves applying a bonding material to at least one surface to be bonded, and placing the at least one surface sufficiently close to another surface such that a bonding interface is formed between them. A bonding material of the invention comprises a source of hydroxide ions, and may optionally include a silicate component, a particulate filling material, and a property-modifying component. Bonding methods of the invention reliably and reproducibly provide bonds which are strong and precise, and which may be tailored according to a wide range of possible applications. Possible applications for bonding materials of the invention include: forming composite materials, coating substrates, forming laminate structures, assembly of precision optical components, and preparing objects of defined geometry and composition. Bonding materials and methods of preparing the same are also disclosed.

  2. Diels-Alder attachment of a planar organic molecule to a dangling bond dimer on a hydrogenated semiconductor surface.

    PubMed

    Godlewski, Szymon; Kawai, Hiroyo; Engelund, Mads; Kolmer, Marek; Zuzak, Rafal; Garcia-Lekue, Aran; Novell-Leruth, Gerard; Echavarren, Antonio M; Sanchez-Portal, Daniel; Joachim, Christian; Saeys, Mark

    2016-06-22

    Construction of single-molecule electronic devices requires the controlled manipulation of organic molecules and their properties. This could be achieved by tuning the interaction between the molecule and individual atoms by local "on-surface" chemistry, i.e., the controlled formation of chemical bonds between the species. We demonstrate here the reversible attachment of a planar conjugated polyaromatic molecule to a pair of unpassivated dangling bonds on a hydrogenated Ge(001):H surface via a Diels-Alder [4+2] addition using the tip of a scanning tunneling microscope (STM). Due to the small stability difference between the covalently bonded and a nearly undistorted structure attached to the dangling bond dimer by long-range dispersive forces, we show that at cryogenic temperatures the molecule can be switched between both configurations. The reversibility of this covalent bond forming reaction may be applied in the construction of complex circuits containing organic molecules with tunable properties.

  3. Students' Reasoning about Basic Chemical Thermodynamics and Chemical Bonding: What Changes Occur during a Context-based Post-16 Chemistry Course?

    ERIC Educational Resources Information Center

    Barker, Vanessa; Millar, Robin

    2000-01-01

    A longitudinal study of students (n=250) following the Salters Advanced Chemistry course probed a range of chemical ideas including the exothermicity of bond formation and the development of thinking about covalent, ionic, and intermolecular bonds. At the start, many students demonstrated misunderstandings about these chemical ideas, but their…

  4. Mechanostereochemistry and the mechanical bond

    PubMed Central

    Barin, Gokhan; Forgan, Ross S.; Stoddart, J. Fraser

    2012-01-01

    The chemistry of mechanically interlocked molecules (MIMs), in which two or more covalently linked components are held together by mechanical bonds, has led to the coining of the term mechanostereochemistry to describe a new field of chemistry that embraces many aspects of MIMs, including their syntheses, properties, topologies where relevant and functions where operative. During the rapid development and emergence of the field, the synthesis of MIMs has witnessed the forsaking of the early and grossly inefficient statistical approaches for template-directed protocols, aided and abetted by molecular recognition processes and the tenets of self-assembly. The resounding success of these synthetic protocols, based on templation, has facilitated the design and construction of artificial molecular switches and machines, resulting more and more in the creation of integrated functional systems. This review highlights (i) the range of template-directed synthetic methods being used currently in the preparation of MIMs; (ii) the syntheses of topologically complex knots and links in the form of stable molecular compounds; and (iii) the incorporation of bistable MIMs into many different device settings associated with surfaces, nanoparticles and solid-state materials in response to the needs of particular applications that are perceived to be fair game for mechanostereochemistry. PMID:22977353

  5. COVALENT BINDING OF TRICHLOROETHYLENE TO PROTEINS IN HUMAN AND RAT HEPATOCYTES. (R826409)

    EPA Science Inventory

    The environmental contaminant and occupational solvent trichloroethylene is metabolized to a reactive intermediate that covalently binds to specific hepatic proteins in exposed mice and rats. In order to compare covalent binding between humans and rodents, primary hepatocyte c...

  6. Non-covalent modification of reduced graphene oxide by a chiral liquid crystalline surfactant

    NASA Astrophysics Data System (ADS)

    Lin, Pengcheng; Cong, Yuehua; Sun, Cong; Zhang, Baoyan

    2016-01-01

    In order to effectively disperse reduced graphene oxide (RGO) in functional materials and take full advantage of its exceptional physical and chemical properties, a novel and effective approach for non-covalent modification of RGO by a chiral liquid crystalline surfactant (CLCS) consisting of chiral mesogenic units, nematic mesogenic units with carboxyl groups and non-mesogenic units with a polycyclic conjugated structure is firstly established. The polycyclic conjugated structure can anchor onto the RGO surface via π-π interactions, the chiral mesogenic units possess affinity for chiral materials by joining the helical matrix of chiral material and the carboxyl groups in nematic mesogenic units are supposed to form coordination bonds with nano zinc oxide (ZnO) to fabricate functional nano hybrids. The transmittances of CLCS-RGO hybrids exhibit S-shaped nonlinear increase with the increase of wavelength, but the total transmittances from 220 nm to 800 nm show a linear decreasing trend with the increase of RGO content in the CLCS-RGO hybrid. Due to the superior thermal properties of RGO and the interactions between RGO and CLCS, the dispersed RGO can improve the glass transition and increase the thermal stability and decomposition activation energy of CLCS. The intercalation of RGO can decrease the thermochromism temperature and improve the pitch uniformity of CLCS. Furthermore, CLCS can promote the dispersion of RGO in chiral nematic liquid crystals (CNLCs), and the CNLC-RGO-CLCS hybrids present decreased driving voltage and accelerated electro-optical response. The CLCS non-covalently modified RGO can strengthen the photocatalytic degradation of ZnO by suppressing the aggregation of ZnO and RGO.In order to effectively disperse reduced graphene oxide (RGO) in functional materials and take full advantage of its exceptional physical and chemical properties, a novel and effective approach for non-covalent modification of RGO by a chiral liquid crystalline surfactant

  7. Non-covalent modification of reduced graphene oxide by a chiral liquid crystalline surfactant.

    PubMed

    Lin, Pengcheng; Cong, Yuehua; Sun, Cong; Zhang, Baoyan

    2016-01-28

    In order to effectively disperse reduced graphene oxide (RGO) in functional materials and take full advantage of its exceptional physical and chemical properties, a novel and effective approach for non-covalent modification of RGO by a chiral liquid crystalline surfactant (CLCS) consisting of chiral mesogenic units, nematic mesogenic units with carboxyl groups and non-mesogenic units with a polycyclic conjugated structure is firstly established. The polycyclic conjugated structure can anchor onto the RGO surface via π-π interactions, the chiral mesogenic units possess affinity for chiral materials by joining the helical matrix of chiral material and the carboxyl groups in nematic mesogenic units are supposed to form coordination bonds with nano zinc oxide (ZnO) to fabricate functional nano hybrids. The transmittances of CLCS-RGO hybrids exhibit S-shaped nonlinear increase with the increase of wavelength, but the total transmittances from 220 nm to 800 nm show a linear decreasing trend with the increase of RGO content in the CLCS-RGO hybrid. Due to the superior thermal properties of RGO and the interactions between RGO and CLCS, the dispersed RGO can improve the glass transition and increase the thermal stability and decomposition activation energy of CLCS. The intercalation of RGO can decrease the thermochromism temperature and improve the pitch uniformity of CLCS. Furthermore, CLCS can promote the dispersion of RGO in chiral nematic liquid crystals (CNLCs), and the CNLC-RGO-CLCS hybrids present decreased driving voltage and accelerated electro-optical response. The CLCS non-covalently modified RGO can strengthen the photocatalytic degradation of ZnO by suppressing the aggregation of ZnO and RGO. PMID:26754831

  8. Non-covalent modification of reduced graphene oxide by a chiral liquid crystalline surfactant.

    PubMed

    Lin, Pengcheng; Cong, Yuehua; Sun, Cong; Zhang, Baoyan

    2016-01-28

    In order to effectively disperse reduced graphene oxide (RGO) in functional materials and take full advantage of its exceptional physical and chemical properties, a novel and effective approach for non-covalent modification of RGO by a chiral liquid crystalline surfactant (CLCS) consisting of chiral mesogenic units, nematic mesogenic units with carboxyl groups and non-mesogenic units with a polycyclic conjugated structure is firstly established. The polycyclic conjugated structure can anchor onto the RGO surface via π-π interactions, the chiral mesogenic units possess affinity for chiral materials by joining the helical matrix of chiral material and the carboxyl groups in nematic mesogenic units are supposed to form coordination bonds with nano zinc oxide (ZnO) to fabricate functional nano hybrids. The transmittances of CLCS-RGO hybrids exhibit S-shaped nonlinear increase with the increase of wavelength, but the total transmittances from 220 nm to 800 nm show a linear decreasing trend with the increase of RGO content in the CLCS-RGO hybrid. Due to the superior thermal properties of RGO and the interactions between RGO and CLCS, the dispersed RGO can improve the glass transition and increase the thermal stability and decomposition activation energy of CLCS. The intercalation of RGO can decrease the thermochromism temperature and improve the pitch uniformity of CLCS. Furthermore, CLCS can promote the dispersion of RGO in chiral nematic liquid crystals (CNLCs), and the CNLC-RGO-CLCS hybrids present decreased driving voltage and accelerated electro-optical response. The CLCS non-covalently modified RGO can strengthen the photocatalytic degradation of ZnO by suppressing the aggregation of ZnO and RGO.

  9. Sequence specificity of formaldehyde-mediated covalent binding of anthracycline derivatives to DNA.

    PubMed

    Szulawska, Agata; Gniazdowski, Marek; Czyz, Malgorzata

    2005-01-01

    Daunorubicin (DRB) and doxorubicin (DOX) in the presence of formaldehyde (CH2O) form covalent adducts with DNA. A G-specific adduct is formed by producing an aminal bridge between the C-3' of daunosamine and the C-2 of guanine. New derivatives of DRB, DOX and epidoxorubicin (EDOX) with an amidine group bonded to the C-3' of the daunosamine moiety, with either a morpholine or hexamethyleneimine ring attached to the amidine group, were studied in this paper. DNase I footprinting and analyses with restriction endonucleases were applied to compare the specificity of adduct formed by the amidine derivatives and their parent compounds. These approaches provide consistent results, proving that a GC pair is required for covalent binding of anthracycline derivatives to DNA and that different flanking sequences are able to modify the sequence preference of the drugs. The 5'-GC-3', 5'-CG-3' and 5'-TC-3' sequences were protected most efficiently by the parent compounds and their morpholine derivatives and some increased protection of 5'-TC-3' sequence was observed for morpholine analogues. Hexamethyleneimine derivatives bind to DNA with much lower efficiency. Finally, the sequence specificity of anthracycline derivatives was correlated with their ability to inhibit binding of transcription factors Sp1 and AP-1 to their DNA recognition sequences. The anthracycline derivatives were more potent in inhibiting Sp1 binding to its cognate GC box than in preventing AP-1 from binding to its mixed A.T and G.C site. Overall, the results indicate that the amidine derivatives of anthracyclines show similar, but not identical sequence specificity as parent compounds, though they exert their effect at a higher concentration. PMID:15588709

  10. First-Principles Study of Thermoelectric Properties of Covalent Organic Frameworks

    NASA Astrophysics Data System (ADS)

    Chumakov, Yurii; Aksakal, Fatma; Dimoglo, Anatholy; Ata, Ali; Palomares-Sánchez, Salvador A.

    2016-07-01

    Covalent organic frameworks (COFs) are new emerging functional porous materials. Strong covalent bonds result in molecular building blocks that can be arranged in layered two-dimensional (2D) or three-dimensional (3D) periodic networks. However, to the best of our knowledge, there have been no reports on experimental and theoretical studies of thermoelectrical properties of COFs to date. Therefore, density functional theory (DFT) and the Boltzmann transport equation have been applied in this work to calculate the semiclassical transport coefficients for phthalocyanine (Pc)-based NiPc, NiPc-benzothiadiazole (BTDA), and Pc COFs. Owing to the well-ordered stacking of the phthalocyanine units and linkers in these compounds, charge-carrier transport is facilitated in the stacking direction. In all studied compounds, the highly directional character of π-orbitals provides band-structure engineering and produces a type of low-dimensional hole transport along the stacking direction. All studied compounds are indirect semiconductors. The low-dimensional transport of holes and the localized states in both valence and conduction bands prevent the electron-hole compensation effect in the Seebeck coefficients, correlating with the large Seebeck coefficients of the studied compounds. Insertion of the electron-deficient building block benzothiadiazole in the NiPc-BTDA COF leads to positive Seebeck coefficients along the a-, b-, and c-directions. The relaxation time was estimated in our investigations from DFT band-structure calculations and the experimentally defined mobility, leading to determination of the electrical conductivity and electronic contribution to the thermal conductivity, as well as figure of merit ( ZT) estimation. Ni atom provided greater electrical conductivity along the c-direction in comparison with metal-free Pc COF, and NiPc COF showed the highest thermoelectric performance among the studied COFs.

  11. Analysis of Cell-Surface Receptor Dynamics through Covalent Labeling by Catalyst-Tethered Antibody.

    PubMed

    Hayashi, Takahiro; Yasueda, Yuki; Tamura, Tomonori; Takaoka, Yousuke; Hamachi, Itaru

    2015-04-29

    A general technique for introducing biophysical probes into selected receptors in their native environment is valuable for the study of their structure, dynamics, function, and molecular interactions. A number of such techniques rely on genetic engineering, which is not applicable for the study of endogenous proteins, and such approaches often suffer from artifacts due to the overexpression and bulky size of the probes/protein tags used. Here we designed novel catalyst-antibody conjugates capable of introducing small chemical probes into receptor proteins such as epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) in a selective manner on the surface of living cells. Because of the selectivity and efficiency of this labeling technique, we were able to monitor the cellular dynamics and lifetime of HER2 endogenously expressed on cancer cells. More significantly, the current labeling technique comprises a stable covalent bond, which combined with a peptide mass fingerprinting analysis allowed epitope mapping of antibodies on living cells and identification of potential binding sites of anti-EGFR affibody. Although as yet unreported in the literature, the binding sites predicted by our labeling method were consistently supported by the subsequent mutation and binding assay experiments. In addition, this covalent labeling method provided experimental evidence that HER2 exhibits a more dynamic structure than expected on the basis of crystallographic analysis alone. Our novel catalyst-antibody conjugates are expected to provide a general tool for investigating the protein trafficking, fluctuation, and molecular interactions of an important class of cell-surface receptors on live cell surfaces. PMID:25853648

  12. Stable, Covalent Attachment of Laminin to Microposts Improves the Contractility of Mouse Neonatal Cardiomyocytes

    PubMed Central

    2015-01-01

    The mechanical output of contracting cardiomyocytes, the muscle cells of the heart, relates to healthy and disease states of the heart. Culturing cardiomyocytes on arrays of elastomeric microposts can enable inexpensive and high-throughput studies of heart disease at the single-cell level. However, cardiomyocytes weakly adhere to these microposts, which limits the possibility of using biomechanical assays of single cardiomyocytes to study heart disease. We hypothesized that a stable covalent attachment of laminin to the surface of microposts improves cardiomyocyte contractility. We cultured cells on polydimethylsiloxane microposts with laminin covalently bonded with the organosilanes 3-glycidoxypropyltrimethoxysilane and 3-aminopropyltriethoxysilane with glutaraldehyde. We measured displacement of microposts induced by the contractility of mouse neonatal cardiomyocytes, which attach better than mature cardiomyocytes to substrates. We observed time-dependent changes in contractile parameters such as micropost deformation, contractility rates, contraction and relaxation speeds, and the times of contractions. These parameters were affected by the density of laminin on microposts and by the stability of laminin binding to micropost surfaces. Organosilane-mediated binding resulted in higher laminin surface density and laminin binding stability. 3-glycidoxypropyltrimethoxysilane provided the highest laminin density but did not provide stable protein binding with time. Higher surface protein binding stability and strength were observed with 3-aminopropyltriethoxysilane with glutaraldehyde. In cultured cardiomyocytes, contractility rate, contraction speeds, and contraction time increased with higher laminin stability. Given these variations in contractile function, we conclude that binding of laminin to microposts via 3-aminopropyltriethoxysilane with glutaraldehyde improves contractility observed by an increase in beating rate and contraction speed as it occurs during the

  13. Contribution of flavin covalent linkage with histidine 99 to the reaction catalyzed by choline oxidase.

    PubMed

    Quaye, Osbourne; Cowins, Sharonda; Gadda, Giovanni

    2009-06-19

    The FAD-dependent choline oxidase has a flavin cofactor covalently attached to the protein via histidine 99 through an 8alpha-N(3)-histidyl linkage. The enzyme catalyzes the four-electron oxidation of choline to glycine betaine, forming betaine aldehyde as an enzyme-bound intermediate. The variant form of choline oxidase in which the histidine residue has been replaced with asparagine was used to investigate the contribution of the 8alpha-N(3)-histidyl linkage of FAD to the protein toward the reaction catalyzed by the enzyme. Decreases of 10-fold and 30-fold in the k(cat)/K(m) and k(cat) values were observed as compared with wild-type choline oxidase at pH 10 and 25 degrees C, with no significant effect on k(cat)/K(O) using choline as substrate. Both the k(cat)/K(m) and k(cat) values increased with increasing pH to limiting values at high pH consistent with the participation of an unprotonated group in the reductive half-reaction and the overall turnover of the enzyme. The pH independence of both (D)(k(cat)/K(m)) and (D)k(cat), with average values of 9.2 +/- 3.3 and 7.4 +/- 0.5, respectively, is consistent with absence of external forward and reverse commitments to catalysis, and the chemical step of CH bond cleavage being rate-limiting for both the reductive half-reaction and the overall enzyme turnover. The temperature dependence of the (D)k(red) values suggests disruption of the preorganization in the asparagine variant enzyme. Altogether, the data presented in this study are consistent with the FAD-histidyl covalent linkage being important for the optimal positioning of the hydride ion donor and acceptor in the tunneling reaction catalyzed by choline oxidase.

  14. Analysis of Cell-Surface Receptor Dynamics through Covalent Labeling by Catalyst-Tethered Antibody.

    PubMed

    Hayashi, Takahiro; Yasueda, Yuki; Tamura, Tomonori; Takaoka, Yousuke; Hamachi, Itaru

    2015-04-29

    A general technique for introducing biophysical probes into selected receptors in their native environment is valuable for the study of their structure, dynamics, function, and molecular interactions. A number of such techniques rely on genetic engineering, which is not applicable for the study of endogenous proteins, and such approaches often suffer from artifacts due to the overexpression and bulky size of the probes/protein tags used. Here we designed novel catalyst-antibody conjugates capable of introducing small chemical probes into receptor proteins such as epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) in a selective manner on the surface of living cells. Because of the selectivity and efficiency of this labeling technique, we were able to monitor the cellular dynamics and lifetime of HER2 endogenously expressed on cancer cells. More significantly, the current labeling technique comprises a stable covalent bond, which combined with a peptide mass fingerprinting analysis allowed epitope mapping of antibodies on living cells and identification of potential binding sites of anti-EGFR affibody. Although as yet unreported in the literature, the binding sites predicted by our labeling method were consistently supported by the subsequent mutation and binding assay experiments. In addition, this covalent labeling method provided experimental evidence that HER2 exhibits a more dynamic structure than expected on the basis of crystallographic analysis alone. Our novel catalyst-antibody conjugates are expected to provide a general tool for investigating the protein trafficking, fluctuation, and molecular interactions of an important class of cell-surface receptors on live cell surfaces.

  15. Covalent attachment of nanoparticles to copolymer surfaces to control structure-property relationships

    NASA Astrophysics Data System (ADS)

    McConnell, Marla D.

    Interest in functional nanoparticles has increased in recent years, because their small size gives them unique properties. Surface assembly of nanoparticles is particularly appealing, because it can create surfaces with tunable wetting and optical properties. This thesis presents a novel method for the covalent assembly of silica nanoparticles on random copolymer films via covalent bonding, and the subsequent analysis of the wetting and optical properties of these functionalized surfaces. First, the kinetics of the covalent attachment of amine-modified silica nanoparticles to poly(styrene-ran-acrylic acid) were investigated. The surface swelling of the copolymer films upon exposure to reaction solvents was studied with in situ AFM. The films' surface roughness controlled the nanoparticle attachment kinetics, as well as the final nanoparticle coverage. For particle diameters on the order of the roughness features, 70% surface coverage was achieved, while particles with diameters much larger than the surface features reached only 30% coverage. The wetting properties of the nanoparticle surfaces were investigated as a function of particle coverage and diameter. At low coverages of small particles, the surfaces exhibited Wenzel-type wetting behavior. At high particle coverages, the surfaces showed Cassie-type wetting. Finally, the particles were observed to sink into the polymer film with increasing reaction time. This sinking, as well as the magnitude of the contact angles achieved at high particle coverages, led to the hypothesis that polymer chains wet onto the surface of the silica particles. Core-shell Janus particles were prepared by electrostatic assembly of gold nanoparticles on the unprotected surfaces of the silica particles. The plasmon resonance absorption of the gold particles underwent a red shift upon formation of closely-packed networks on the silica particle surfaces. By applying gold, chromium, and gold:palladium coatings to the Janus particles and

  16. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry.

    PubMed

    Lee, Joongoo; Boersma, Arnold J; Boudreau, Marc A; Cheley, Stephen; Daltrop, Oliver; Li, Jianwei; Tamagaki, Hiroko; Bayley, Hagan

    2016-09-27

    Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level. PMID:27537396

  17. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry

    PubMed Central

    2016-01-01

    Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level. PMID:27537396

  18. Covalently Bound Nitroxyl Radicals in an Organic Framework.

    PubMed

    Hughes, Barbara K; Braunecker, Wade A; Bobela, David C; Nanayakkara, Sanjini U; Reid, Obadiah G; Johnson, Justin C

    2016-09-15

    A series of covalent organic framework (COF) structures is synthesized that possesses a tunable density of covalently bound nitroxyl radicals within the COF pores. The highest density of organic radicals produces an electron paramagnetic resonance (EPR) signal that suggests the majority of radicals strongly interact with other radicals, whereas for smaller loadings the EPR signals indicate the radicals are primarily isolated but with restricted motion. The dielectric loss as determined from microwave absorption of the framework structures compared with an amorphous control suggests that free motion of the radicals is inhibited when more than 25% of available sites are occupied. The ability to tune the mode of radical interactions and the subsequent effect on redox, electrical, and optical characteristics in a porous framework may lead to a class of structures with properties ideal for photoelectrochemistry or energy storage.

  19. Covalently Bound Nitroxyl Radicals in an Organic Framework.

    PubMed

    Hughes, Barbara K; Braunecker, Wade A; Bobela, David C; Nanayakkara, Sanjini U; Reid, Obadiah G; Johnson, Justin C

    2016-09-15

    A series of covalent organic framework (COF) structures is synthesized that possesses a tunable density of covalently bound nitroxyl radicals within the COF pores. The highest density of organic radicals produces an electron paramagnetic resonance (EPR) signal that suggests the majority of radicals strongly interact with other radicals, whereas for smaller loadings the EPR signals indicate the radicals are primarily isolated but with restricted motion. The dielectric loss as determined from microwave absorption of the framework structures compared with an amorphous control suggests that free motion of the radicals is inhibited when more than 25% of available sites are occupied. The ability to tune the mode of radical interactions and the subsequent effect on redox, electrical, and optical characteristics in a porous framework may lead to a class of structures with properties ideal for photoelectrochemistry or energy storage. PMID:27583443

  20. Significantly enhanced heme retention ability of myoglobin engineered to mimic the third covalent linkage by nonaxial histidine to heme (vinyl) in synechocystis hemoglobin.

    PubMed

    Uppal, Sheetal; Salhotra, Shikha; Mukhi, Nitika; Zaidi, Fatima Kamal; Seal, Manas; Dey, Somdatta Ghosh; Bhat, Rajiv; Kundu, Suman

    2015-01-23

    Heme proteins, which reversibly bind oxygen and display a particular fold originally identified in myoglobin (Mb), characterize the "hemoglobin (Hb) superfamily." The long known and widely investigated Hb superfamily, however, has been enriched by the discovery and investigation of new classes and members. Truncated Hbs typify such novel classes and exhibit a distinct two-on-two α-helical fold. The truncated Hb from the freshwater cyanobacterium Synechocystis exhibits hexacoordinate heme chemistry and bears an unusual covalent bond between the nonaxial His(117) and a heme porphyrin 2-vinyl atom, which remains tightly associated with the globin unlike any other. It seems to be the most stable Hb known to date, and His(117) is the dominant force holding the heme. Mutations of amino acid residues in the vicinity did not influence this covalent linkage. Introduction of a nonaxial His into sperm whale Mb at the topologically equivalent position and in close proximity to vinyl group significantly increased the heme stability of this prototype globin. Reversed phase chromatography, electrospray ionization-MS, and MALDI-TOF analyses confirmed the presence of covalent linkage in Mb I107H. The Mb mutant with the engineered covalent linkage was stable to denaturants and exhibited ligand binding and auto-oxidation rates similar to the wild type protein. This indeed is a novel finding and provides a new perspective to the evolution of Hbs. The successful attempt at engineering heme stability holds promise for the production of stable Hb-based blood substitute. PMID:25451928