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Sample records for ru-cl bond covalency

  1. 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.

  2. 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.

  3. Constructing covalent organic frameworks in water via dynamic covalent bonding

    PubMed Central

    Thote, Jayshri; Barike Aiyappa, Harshitha; Rahul Kumar, Raya; Kandambeth, Sharath; Biswal, Bishnu P.; Balaji Shinde, Digambar; Chaki Roy, Neha; Banerjee, Rahul

    2016-01-01

    The formation of keto-enamine based crystalline, porous polymers in water is investigated for the first time. Facile access to the Schiff base reaction in water has been exploited to synthesize stable porous structures using the principles of Dynamic Covalent Chemistry (DCC). Most credibly, the water-based Covalent Organic Frameworks (COFs) possess chemical as well as physical properties such as crystallinity, surface area and porosity, which is comparable to their solvothermal counterparts. The formation of COFs in water is further investigated by understanding the nature of the monomers formed using hydroxy and non-hydroxy analogues of the aldehyde. This synthetic route paves a new way to synthesize COFs using a viable, greener route by utilization of the DCC principles in conjunction with the keto–enol tautomerism to synthesize useful, stable and porous COFs in water. PMID:27840679

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

    SciTech Connect

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

    1995-09-13

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

  5. Covalent bonds in AlMnSi icosahedral quasicrystalline approximant

    PubMed

    Kirihara; Nakata; Takata; Kubota; Nishibori; Kimura; Sakata

    2000-10-16

    Electron density distributions were obtained using the maximum entropy method with synchrotron radiation powder data. In the metallic Al12Re, metallic bonding was observed for the icosahedral Al12 cluster with central Re atom. In the nonmetallic alpha-AlMnSi 1/1 approximant, covalent bonds were found in the electron density distribution of the Mackay icosahedral cluster without central atom. Rather than the Hume-Rothery mechanism, the covalency of Al (Si) icosahedron and that between Al (Si) and Mn atoms is considered to be the origin of the pseudogap and nonmetallic behavior of alpha-AlMnSi.

  6. 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).

  7. Design of a covalently bonded glycosphingolipid microarray.

    PubMed

    Arigi, Emma; Blixt, Ola; Buschard, Karsten; Clausen, Henrik; Levery, Steven B

    2012-01-01

    Glycosphingolipids (GSLs) are well known ubiquitous constituents of all eukaryotic cell membranes, yet their normal biological functions are not fully understood. As with other glycoconjugates and saccharides, solid phase display on microarrays potentially provides an effective platform for in vitro study of their functional interactions. However, with few exceptions, the most widely used microarray platforms display only the glycan moiety of GSLs, which not only ignores potential modulating effects of the lipid aglycone, but inherently limits the scope of application, excluding, for example, the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2-mercaptoethylamine, was also tested. Underivatized or linker-derivatized lyso-GSL were then immobilized on N-hydroxysuccinimide- or epoxide-activated glass microarray slides and probed with carbohydrate binding proteins of known or partially known specificities (i.e., cholera toxin B-chain; peanut agglutinin, a monoclonal antibody to sulfatide, Sulph 1; and a polyclonal antiserum reactive to asialo-G(M2)). Preliminary evaluation of the method indicated successful immobilization of the GSLs, and selective binding of test probes. The potential utility of this methodology for designing covalent microarrays that incorporate GSLs for serodiagnosis is discussed.

  8. 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

  9. 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.

  10. Anisotropic covalent bonding and photopolymerization of C[sub 70

    SciTech Connect

    Menon, M. ); Rao, A.M. ); Subbaswamy, K.R. ); Eklund, P.C. )

    1995-01-01

    We report theoretical and experimental results demonstrating covalent bonding between C[sub 70] molecules. Experimental results indicating the transformation of C[sub 70] films upon exposure to visible or ultraviolet radiation into a strongly bonded solid phase, similar to the transformation observed in solid C[sub 60] films are presented. Unlike C[sub 60] molecules, however, the covalent bonding between C[sub 70] molecules is found to be highly directional, strongly favoring certain relative intermolecular orientations. This theoretical finding is consistent with recent laser desorption mass spectroscopy results for visible or UV light irradiated C[sub 70] films which find the cross section for the phototransformation to a new toluene-insoluble solid phase to be considerably smaller than observed for solid C[sub 60]. The combined results suggest that the photochemical 2+2 cycloaddition reaction is responsible for the transformation.

  11. Covalent versus ionic bonding in alkalimetal fluoride oligomers.

    PubMed

    Bickelhaupt, F M; Solà, M; Guerra, C Fonseca

    2007-01-15

    The most polar bond in chemistry is that between a fluorine and an alkalimetal atom. Inspired by our recent finding that other polar bonds (C--M and H--M) have important covalent contributions (i.e., stabilization due to bond overlap), we herein address the question if covalency is also essential in the F--M bond. Thus, we have theoretically studied the alkalimetal fluoride monomers, FM, and (distorted) cubic tetramers, (FM)4, with M=Li, Na, K, and Rb, using density functional theory at the BP86/TZ2P level. Our objective is to determine how the structure and thermochemistry (e.g., F--M bond lengths and strengths, oligomerization energies, etc.) of alkalimetal fluorides depend on the metal atom, and to understand the emerging trends in terms of quantitative Kohn-Sham molecular orbital theory. The analyses confirm the extreme polarity of the F--M bond (dipole moment, Voronoi deformation density and Hirshfeld atomic charges), and they reveal that bond overlap-derived stabilization (ca. -6, -6, and -2 kcal/mol) contributes only little to the bond strength (-136, -112, and -114 kcal/mol) and the trend therein along Li, Na, and K. According to this and other criteria, the F--M bond is not only strongly polar, but also has a truly ionic bonding mechanism. Interestingly, the polarity is reduced on tetramerization. For the lithium and sodium fluoride tetramers, the F4 tetrahedron is larger than and surrounds the M4 cluster (i.e., F--F>M--M). But in the potassium and rubidium fluoride tetramers, the F4 tetrahedron is smaller than and inside the M4 cluster (i.e., F--F

  12. 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

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

    PubMed

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

    2016-05-07

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

  14. A covalent method of gentamicin bonding to silica supports.

    PubMed

    Ginalska, Grazyna; Osińska, Monika; Uryniak, Adam

    2004-04-01

    Results of a novel method of covalent bonding of an antibiotic (gentamicin) to silica bead supports are shown. Gentamicin was immobilized to four types of matrix: silica gel and porous glass beads activated by either silanization (APTES) or by adhesively bound keratin (with immobilization yield ranging from 36.5 to 91%). Gentamicin was immobilized to the supports after opening its carbohydrate ring in the molecule. This method of gentamicin activation before the immobilization process did not inhibit its antibiotic activity. The four gentamicin-containing immobilized preparations were stable, meaning that they did not release the antibiotic into the solution during the 30 days of incubation, not even during shaking experiments.

  15. 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.

  16. From covalent bonding to coalescence of metallic nanorods.

    PubMed

    Lee, Soohwan; Huang, Hanchen

    2011-10-25

    Growth of metallic nanorods by physical vapor deposition is a common practice, and the origin of their dimensions is a characteristic length scale that depends on the three-dimensional Ehrlich-Schwoebel (3D ES) barrier. For most metals, the 3D ES barrier is large so the characteristic length scale is on the order of 200 nm. Using density functional theory-based ab initio calculations, this paper reports that the 3D ES barrier of Al is small, making it infeasible to grow Al nanorods. By analyzing electron density distributions, this paper shows that the small barrier is the result of covalent bonding in Al. Beyond the infeasibility of growing Al nanorods by physical vapor deposition, the results of this paper suggest a new mechanism of controlling the 3D ES barrier and thereby nanorod growth. The modification of local degree of covalent bonding, for example, via the introduction of surfactants, can increase the 3D ES barrier and promote nanorod growth, or decrease the 3D ES barrier and promote thin film growth.

  17. Evidence for halogen bond covalency in acyclic and interlocked halogen-bonding receptor anion recognition

    DOE PAGES

    Robinson, Sean W.; Mustoe, Chantal L.; White, Nicholas G.; ...

    2014-12-05

    The synthesis and anion binding properties of novel halogen-bonding (XB) bis-iodotriazole-pyridinium-containing acyclic and [2]catenane anion host systems are described. The XB acyclic receptor displays selectivity for acetate over halides with enhanced anion recognition properties compared to the analogous hydrogen-bonding (HB) acyclic receptor. A reversal in halide selectivity is observed in the XB [2]catenane, in comparison to the acyclic XB receptor, due to the interlocked host’s unique three-dimensional binding cavity, and no binding is observed for oxoanions. Notable halide anion association constant values determined for the [2]catenane in competitive organic–aqueous solvent mixtures demonstrate considerable enhancement of anion recognition as compared tomore » the HB catenane analogue. X-ray crystallographic analysis of a series of halide catenane complexes reveal strong XB interactions in the solid state. These interactions were studied using Cl and Br K-edge X-ray Absorption Spectroscopy (XAS) indicating intense pre-edge features characteristic of charge transfer from the halide to its bonding partner (σAX←X–* ← X1s), and providing a direct measure of the degree of covalency in the halogen bond(s). Lastly, the data reveal that the degree of covalency is similar to that which is observed in transition metal coordinate covalent bonds. These results are supported by DFT results, which correlate well with the experimental data.« less

  18. Evidence for halogen bond covalency in acyclic and interlocked halogen-bonding receptor anion recognition

    SciTech Connect

    Robinson, Sean W.; Mustoe, Chantal L.; White, Nicholas G.; Brown, Asha; Thompson, Amber L.; Kennepohl, Pierre; Beer, Paul D.

    2014-12-05

    The synthesis and anion binding properties of novel halogen-bonding (XB) bis-iodotriazole-pyridinium-containing acyclic and [2]catenane anion host systems are described. The XB acyclic receptor displays selectivity for acetate over halides with enhanced anion recognition properties compared to the analogous hydrogen-bonding (HB) acyclic receptor. A reversal in halide selectivity is observed in the XB [2]catenane, in comparison to the acyclic XB receptor, due to the interlocked host’s unique three-dimensional binding cavity, and no binding is observed for oxoanions. Notable halide anion association constant values determined for the [2]catenane in competitive organic–aqueous solvent mixtures demonstrate considerable enhancement of anion recognition as compared to the HB catenane analogue. X-ray crystallographic analysis of a series of halide catenane complexes reveal strong XB interactions in the solid state. These interactions were studied using Cl and Br K-edge X-ray Absorption Spectroscopy (XAS) indicating intense pre-edge features characteristic of charge transfer from the halide to its bonding partner (σAX←X–* ← X1s), and providing a direct measure of the degree of covalency in the halogen bond(s). Lastly, the data reveal that the degree of covalency is similar to that which is observed in transition metal coordinate covalent bonds. These results are supported by DFT results, which correlate well with the experimental data.

  19. 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…

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

    PubMed

    Zheng, Peng; Li, Hongbin

    2011-05-04

    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.

  1. 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.

  2. Covalent bonds against magnetism in transition metal compounds

    PubMed Central

    Streltsov, Sergey V.; Khomskii, Daniel I.

    2016-01-01

    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

  3. Effective scheme for partitioning covalent bonds in density-functional embedding theory: From molecules to extended covalent systems

    NASA Astrophysics Data System (ADS)

    Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele

    2016-12-01

    Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.

  4. Effective scheme for partitioning covalent bonds in density-functional embedding theory: From molecules to extended covalent systems.

    PubMed

    Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele

    2016-12-28

    Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.

  5. The physical origin of large covalent-ionic resonance energies in some two-electron bonds.

    PubMed

    Hiberty, Philippe C; Ramozzi, Romain; Song, Lingchun; Wu, Wei; Shaik, Sason

    2007-01-01

    This study uses valence bond (VB) theory to analyze in detail the previously established finding that alongside the two classical bond families of covalent and ionic bonds, which describe the electron-pair bond, there exists a distinct class of charge-shift bonds (CS-bonds) in which the fluctuation of the electron pair density plays a dominant role. Such bonds are characterized by weak binding, or even a repulsive, covalent component, and by a large covalent-ionic resonance energy RE(cs) that is responsible for the major part, or even for the totality, of the bonding energy. In the present work, the nature of CS-bonding and its fundamental mechanisms are analyzed in detail by means of a VB study of some typical homonuclear bonds (H-H, H3C-CH3, H2N-NH2, HO-OH, F-F, and Cl-Cl), ranging from classical-covalent to fully charge-shift bonds. It is shown that CS-bonding is characterized by a covalent dissociation curve with a shallow minimum situated at long interatomic distances, or even a fully repulsive covalent curve. As the atoms that are involved in the bond are taken from left to right or from bottom to top of the periodic table, the weakening effect of the adjacent bonds or lone pairs increases, while at the same time the reduced resonance integral, that couples the covalent and ionic forms, increases. As a consequence, the weakening of the covalent interaction is gradually compensated by a strengthening of CS-bonding. The large RE(cs) quantity of CS-bonds is shown to be an outcome of the mechanism necessary to establish equilibrium and optimum bonding during bond formation. It is shown that the shrinkage of the orbitals in the covalent structure lowers the potential energy, V, but excessively raises the kinetic energy, T, thereby tipping the virial ratio off-balance. Subsequent addition of the ionic structures lowers T while having a lesser effect on V, thus restoring the requisite virial ratio (T/-V = 1/2). Generalizing to typically classical covalent bonds

  6. Excitation energy transfer in covalently bonded porphyrin heterodimers

    NASA Astrophysics Data System (ADS)

    Paschenko, V. Z.; Konovalova, N. V.; Bagdashkin, A. L.; Gorokhov, V. V.; Tusov, V. B.; Yuzhakov, V. I.

    2012-04-01

    We describe the photophysical properties of heterodimers that are formed by the free base 2-(2-carboxyvinyl)-5,10,15,20-tetraphenylporphyrin and the zinc complex of 5-( p-aminophenyl)-10,15,20-triphenylporphyrin and that are covalently bonded by the amide link. These dimers differ in the configuration of the double bond in the spacer group. We determine fluorescence quantum yields of heterodimers and their porphyrin components. The energy transfer rate constants have been estimated from the measured fluorescence lifetimes and fluorescence excitation spectra and, also, they have been calculated from the steady-state absorption and fluorescence spectra according to the Förster theory. We have found that the efficiency of the intramolecular energy transfer in heterodimers is 0.97-0.99, and the energy migration rate constants have been found to be (1.82-4.49) × 1010 s-1. The results of our investigation show that synthesized heterodimers can be used as efficient light-harvesting elements in solar energy conversion devices.

  7. 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

  8. Crystal structure of a mononuclear Ru(II) complex with a back-to-back terpyridine ligand: [RuCl(bpy)(tpy-tpy)](.).

    PubMed

    Rein, Francisca N; Chen, Weizhong; Scott, Brian L; Rocha, Reginaldo C

    2015-09-01

    We report the structural characterization of [6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine](2,2'-bi-pyridine)-chlorido-ruthenium(II) hexa-fluorido-phosphate, [RuCl(C10H8N2)(C30H20N6)]PF6, which contains the bidentate ligand 2,2'-bi-pyridine (bpy) and the tridendate ligand 6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine (tpy-tpy). The [RuCl(bpy)(tpy-tpy)](+) monocation has a distorted octa-hedral geometry at the central Ru(II) ion due to the restricted bite angle [159.32 (16)°] of the tridendate ligand. The Ru-bound tpy and bpy moieties are nearly planar and essentially perpendicular to each other with a dihedral angle of 89.78 (11)° between the least-squares planes. The lengths of the two Ru-N bonds for bpy are 2.028 (4) and 2.075 (4) Å, with the shorter bond being opposite to Ru-Cl. For tpy-tpy, the mean Ru-N distance involving the outer N atoms trans to each other is 2.053 (8) Å, whereas the length of the much shorter bond involving the central N atom is 1.936 (4) Å. The Ru-Cl distance is 2.3982 (16) Å. The free uncoordinated moiety of tpy-tpy adopts a trans,trans conformation about the inter-annular C-C bonds, with adjacent pyridyl rings being only approximately coplanar. The crystal packing shows significant π-π stacking inter-actions based on tpy-tpy. The crystal structure reported here is the first for a tpy-tpy complex of ruthenium.

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

    DOE PAGES

    Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian; ...

    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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  12. 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…

  13. 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…

  14. 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

    2016-06-08

    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.

  15. Interaction of Cis- and Trans-RuCl 2(DMSO)4 With Human Serum Albumin

    PubMed Central

    Kozlowski, Henryk; Katsaros, Nikolas

    2000-01-01

    The interaction between cis- and trans- RuCl2(DMSO)4 and human serum albumin have been investigated through UV-Vis, circular dichroism, fluorescence spectroscopy and inductively couplet plasma atomic emission spectroscopy (ICP(AES)) method Albumin can specifically bind 1 mole of cis-isomer and 2 moles of the trans-isomer RuCl2(DMSO)4 complex. The interaction of RuCl2(DMSO)4 with HSA causes: a conformational change with the loss of helical stability of protein; the strong quenching of the Trp 214 fluorescence indicating that the conformational change of the hydrophobic binding pocked in subdomain IIA takes place; a local perturbation of the warfarin binding site and induce some conformational changes at neighbour domains, a changing of the binding abilities towards heme. PMID:18475961

  16. 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.

  17. Metallic versus covalent bonding: Ga nanoparticles as a case study.

    PubMed

    Ghigna, Paolo; Spinolo, Giorgio; Parravicini, Giovanni Battista; Stella, Angiolino; Migliori, Andrea; Kofman, Richard

    2007-06-27

    A systematic X-ray absorption spectroscopy investigation of the local coordination in gallium nanostructures has been performed as a function of temperature and particle size. It is shown that the nanostructure strongly affects the polymorphism of solid gallium and the (meta)stability range of the liquid phase (in agreement with previous works) and that the surface tension acts in the same direction as hydrostatic pressure in stabilizing the Ga solid phases. The effect of surface free energy is first to favor the metallic arrangement of the delta phase and then to stabilize a liquid-like phase based on dimeric molecules even at 90 K. The Ga-Ga distance in the dimers is lower in the liquid phase than in the alpha solid. The experimental results are discussed in comparison with molecular dynamic calculations to assess the presence of covalent character of the dimeric Ga2 units in liquid nanostructured gallium.

  18. Superconductivity of MgB2: covalent bonds driven metallic.

    PubMed

    An, J M; Pickett, W E

    2001-05-07

    A series of calculations on MgB2 and related isoelectronic systems indicates that the layer of Mg2+ ions lowers the nonbonding B pi ( p(z)) bands relative to the bonding sigma ( sp(x)p(y)) bands compared to graphite, causing sigma-->pi charge transfer and sigma band doping of 0.13 holes/cell. Because of their two dimensionality the sigma bands contribute strongly to the Fermi level density of states. Calculated deformation potentials of gamma point phonons identify the B bond stretching modes as dominating the electron-phonon coupling. Superconductivity driven by sigma band holes is consistent with the report of destruction of superconductivity by doping with Al.

  19. 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

    2013-09-06

    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.

  20. The Analysis of Prospective Chemistry Teachers' Cognitive Structure: The Subject of Covalent and Ionic Bonding

    ERIC Educational Resources Information Center

    Temel, Senar; Özcan, Özgür

    2016-01-01

    This study aims to analyse prospective chemistry teachers' cognitive structure related to the subject of covalent and ionic bonding. Semi-structured interviews were conducted with the participants in order to determine their cognitive structure, and the interviews were audio recorded to prevent the loss of data. The data were transcribed and…

  1. Controls on Fe Isotope Fractionation During Organic Complexation: the Importance of Covalent Bonding

    NASA Astrophysics Data System (ADS)

    Domagal-Goldman, S. D.; Kubicki, J. D.

    2007-12-01

    Fe isotopes have been proposed as a tracer of changes to the redox state of the oceans (Rouxel et al., 2005), and for use as a biosignature (e.g., Johnson et al., 1999). Previous modeling work supports this, as they suggest redox fractionations are likely the main control over Fe isotopes.Fe isotopes have been proposed as a tracer of changes to the redox state of the oceans (Rouxel et al., 2005), and for use as a biosignature (e.g., Beard et al., 1999). Previous modeling work (Domagal-Goldman and Kubicki, submitted) that predicts greater equilibrium fractionations for redox reactions than for complexation reactions supports the former application. In this study, we try to ascertain the first-principles chemical drivers of fractionation of Fe isotopes. We do this by using Natural Bond Order (NBO) analyses and isotope fractionation predictions of Fe bound to various organic ligands at different Fe oxidation states and Fe:ligand ratios.NBO analysis re-assigns electrons in molecular orbitals to bond orbitals within a complex; this allows for the examination of the presence and strength of covalent bonding in a complex. By comparing the presence and strength of covalent Fe-O bonds in the studied complexes to other predicted variables such as bond lengths and predicted fractionation factors, we can assess the importance of these bonds to Fe isotope fractionation in nature. Byexamining the effect controlled variables such as Fe oxidation state and the number of Fe-ligand bonds have on the formation of covalent bonds, we will begin to understand what controls bonding for these types of complexes. Ultimately, this work is geared towards driving future research questions related to the isotopicfractionations of Fe and other transition metals.

  2. 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

  3. 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.

  4. Methacrylate-bonded covalent-organic framework monolithic columns for high performance liquid chromatography.

    PubMed

    Liu, Li-Hua; Yang, Cheng-Xiong; Yan, Xiu-Ping

    2017-01-06

    Covalent-organic frameworks (COFs) are a newfangled class of intriguing microporous materials. Considering their unique properties, COFs should be promising as packing materials for high performance liquid chromatography (HPLC). However, the irregular shape and sub-micrometer size of COFs synthesized via the traditional methods render the main obstacles for the application of COFs in HPLC. Herein, we report the preparation of methacrylate-bonded COF monolithic columns for HPLC to overcome the above obstacles. The prepared COF bonded monolithic columns not only show good homogeneity and permeability, but also give high column efficiency, good resolution and precision for HPLC separation of small molecules including polycyclic aromatic hydrocarbons, phenols, anilines, nonsteroidal anti-inflammatory drugs and benzothiophenes. Compared with the bare polymer monolithic column, the COF bonded monolithic columns show enhanced hydrophobic, π-π and hydrogen bond interactions in reverse phase HPLC. The results reveal the great potential of COF bonded monoliths for HPLC and COFs in separation sciences.

  5. A chiroptical switch based on supramolecular chirality transfer through alkyl chain entanglement and dynamic covalent bonding.

    PubMed

    Lv, Kai; Qin, Long; Wang, Xiufeng; Zhang, Li; Liu, Minghua

    2013-12-14

    Chirality transfer is an interesting phenomenon in Nature, which represents an important step to understand the evolution of chiral bias and the amplification of the chirality. In this paper, we report the chirality transfer via the entanglement of the alkyl chains between chiral gelator molecules and achiral amphiphilic Schiff base. We have found that although an achiral Schiff base amphiphile could not form organogels in any kind of organic solvents, it formed co-organogels when mixed with a chiral gelator molecule. Interestingly, the chirality of the gelator molecules was transferred to the Schiff base chromophore in the mixed co-gels and there was a maximum mixing ratio for the chirality transfer. Furthermore, the supramolecular chirality was also produced based on a dynamic covalent chemistry of an imine formed by the reaction between an aldehyde and an amine. Such a covalent bond of imine was formed reversibly depending on the pH variation. When the covalent bond was formed the chirality transfer occurred, when it was destroyed, the transfer stopped. Thus, a supramolecular chiroptical switch is obtained based on supramolecular chirality transfer and dynamic covalent chemistry.

  6. 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.

  7. Preparation of hexacoordinating benzimidazole containing ligand and hexakis(benzimidazole-ruthenium(II)) complex. Molecular structure of C6{CH2-(N-benzimidazole-RuCl2(p-cymene))}6.

    PubMed

    Požgan, Franc; Toupet, Loïc; Dixneuf, Pierre H

    2011-07-07

    A hexabenzimidazole ligand was synthesised and used to prepare a hexakis{benzimidazole-ruthenium(II)} complex containing six RuCl(2)(arene) units of which the X-ray structure analysis shows a helical arrangement with alternating up and down benzymidazole-ruthenium(II) branches attached to a central benzene ring. The reactivity of the prepared complex with phosphite and carbonate was investigated and revealed the weakness of (benzimidazole)N-Ru bonds and the release of the polydentate ligand.

  8. Coordinate covalent C --> B bonding in phenylborates and latent formation of phenyl anions from phenylboronic Acid.

    PubMed

    Glaser, Rainer; Knotts, Nathan

    2006-02-02

    The results are reported of a theoretical study of the addition of small nucleophiles Nu(-) (HO(-), F(-)) to phenylboronic acid Ph-B(OH)(2) and of the stability of the resulting complexes [Ph-B(OH)(2)Nu](-) with regard to Ph-B heterolysis [Ph-B(OH)(2)Nu](-) --> Ph(-) + B(OH)(2)Nu as well as Nu(-)/Ph(-) substitution [Ph-B(OH)(2)Nu](-) + Nu(-) --> Ph(-) + [B(OH)(2)Nu(2)](-). These reactions are of fundamental importance for the Suzuki-Miyaura cross-coupling reaction and many other processes in chemistry and biology that involve phenylboronic acids. The species were characterized by potential energy surface analysis (B3LYP/6-31+G*), examined by electronic structure analysis (B3LYP/6-311++G**), and reaction energies (CCSD/6-311++G**) and solvation energies (PCM and IPCM, B3LYP/6-311++G*) were determined. It is shown that Ph-B bonding in [Ph-B(OH)(2)Nu](-) is coordinate covalent and rather weak (<50 kcal.mol(-1)). The coordinate covalent bonding is large enough to inhibit unimolecular dissociation and bimolecular nucleophile-assisted phenyl anion liberation is slowed greatly by the negative charge on the borate's periphery. The latter is the major reason for the extraordinary differences in the kinetic stabilities of diazonium ions and borates in nucleophilic substitution reactions despite their rather similar coordinate covalent bond strengths.

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

    NASA Astrophysics Data System (ADS)

    Taneri, Sencer

    2013-05-01

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

  10. 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.

  11. Electronic Structure of the Kitaev Material α-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopies.

    PubMed

    Sinn, Soobin; Kim, Choong Hyun; Kim, Beom Hyun; Lee, Kyung Dong; Won, Choong Jae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

    2016-12-21

    Recently, α-RuCl3 has attracted much attention as a possible material to realize the honeycomb Kitaev model of a quantum-spin-liquid state. Although the magnetic properties of α-RuCl3 have been extensively studied, its electronic structure, which is strongly related to its Kitaev physics, is poorly understood. Here, the electronic structure of α-RuCl3 was investigated by photoemission (PE) and inverse-photoemission (IPE) spectroscopies. The band gap was directly measured from the PE and IPE spectra and was found to be 1.9 eV, much larger than previously estimated values. Local density approximation (LDA) calculations showed that the on-site Coulomb interaction U could open the band gap without spin-orbit coupling (SOC). However, the SOC should also be incorporated to reproduce the proper gap size, indicating that the interplay between U and SOC plays an essential role. Several features of the PE and IPE spectra could not be explained by the results of LDA calculations. To explain such discrepancies, we performed configuration-interaction calculations for a RuCl6(3-) cluster. The experimental data and calculations demonstrated that the 4d compound α-RuCl3 is a Jeff = 1/2 Mott insulator rather than a quasimolecular-orbital insulator. Our study also provides important physical parameters required for verifying the proposed Kitaev physics in α-RuCl3.

  12. Electronic Structure of the Kitaev Material α-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopies

    NASA Astrophysics Data System (ADS)

    Sinn, Soobin; Kim, Choong Hyun; Kim, Beom Hyun; Lee, Kyung Dong; Won, Choong Jae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

    2016-12-01

    Recently, α-RuCl3 has attracted much attention as a possible material to realize the honeycomb Kitaev model of a quantum-spin-liquid state. Although the magnetic properties of α-RuCl3 have been extensively studied, its electronic structure, which is strongly related to its Kitaev physics, is poorly understood. Here, the electronic structure of α-RuCl3 was investigated by photoemission (PE) and inverse-photoemission (IPE) spectroscopies. The band gap was directly measured from the PE and IPE spectra and was found to be 1.9 eV, much larger than previously estimated values. Local density approximation (LDA) calculations showed that the on-site Coulomb interaction U could open the band gap without spin-orbit coupling (SOC). However, the SOC should also be incorporated to reproduce the proper gap size, indicating that the interplay between U and SOC plays an essential role. Several features of the PE and IPE spectra could not be explained by the results of LDA calculations. To explain such discrepancies, we performed configuration-interaction calculations for a RuCl63‑ cluster. The experimental data and calculations demonstrated that the 4d compound α-RuCl3 is a Jeff = 1/2 Mott insulator rather than a quasimolecular-orbital insulator. Our study also provides important physical parameters required for verifying the proposed Kitaev physics in α-RuCl3.

  13. Electronic Structure of the Kitaev Material α-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopies

    PubMed Central

    Sinn, Soobin; Kim, Choong Hyun; Kim, Beom Hyun; Lee, Kyung Dong; Won, Choong Jae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

    2016-01-01

    Recently, α-RuCl3 has attracted much attention as a possible material to realize the honeycomb Kitaev model of a quantum-spin-liquid state. Although the magnetic properties of α-RuCl3 have been extensively studied, its electronic structure, which is strongly related to its Kitaev physics, is poorly understood. Here, the electronic structure of α-RuCl3 was investigated by photoemission (PE) and inverse-photoemission (IPE) spectroscopies. The band gap was directly measured from the PE and IPE spectra and was found to be 1.9 eV, much larger than previously estimated values. Local density approximation (LDA) calculations showed that the on-site Coulomb interaction U could open the band gap without spin-orbit coupling (SOC). However, the SOC should also be incorporated to reproduce the proper gap size, indicating that the interplay between U and SOC plays an essential role. Several features of the PE and IPE spectra could not be explained by the results of LDA calculations. To explain such discrepancies, we performed configuration-interaction calculations for a RuCl63− cluster. The experimental data and calculations demonstrated that the 4d compound α-RuCl3 is a Jeff = 1/2 Mott insulator rather than a quasimolecular-orbital insulator. Our study also provides important physical parameters required for verifying the proposed Kitaev physics in α-RuCl3. PMID:28000731

  14. An excursion from normal to inverted C-C bonds shows a clear demarcation between covalent and charge-shift C-C bonds.

    PubMed

    Shaik, Sason; Chen, Zhenhua; Wu, Wei; Stanger, Amnon; Danovich, David; Hiberty, Philippe C

    2009-10-19

    What is the nature of the C-C bond? Valence bond and electron density computations of 16 C-C bonds show two families of bonds that flesh out as a phase diagram. One family, involving ethane, cyclopropane and so forth, is typified by covalent C-C bonding wherein covalent spin-pairing accounts for most of the bond energy. The second family includes the inverted bridgehead bonds of small propellanes, where the bond is neither covalent nor ionic, but owes its existence to the resonance stabilization between the respective structures; hence a charge-shift (CS) bond. The dual family also emerges from calculated and experimental electron density properties. Covalent C-C bonds are characterized by negative Laplacians of the density, whereas CS-bonds display small or positive Laplacians. The positive Laplacian defines a region suffering from neighbouring repulsive interactions, which is precisely the case in the inverted bonding region. Such regions are rich in kinetic energy, and indeed the energy-density analysis reveals that CS-bonds are richer in kinetic energy than the covalent C-C bonds. The large covalent-ionic resonance energy is precisely the mechanism that lowers the kinetic energy in the bonding region and restores equilibrium bonding. Thus, different degrees of repulsive strain create two bonding families of the same chemical bond made from a single atomic constituent. It is further shown that the idea of repulsive strain is portable and can predict the properties of propellanes of various sizes and different wing substituents. Experimentally (M. Messerschmidt, S. Scheins, L. Bruberth, M. Patzel, G. Szeimies, C. Paulman, P. Luger, Angew. Chem. 2005, 117, 3993-3997; Angew. Chem. Int. Ed. 2005, 44, 3925-3928), the C-C bond families are beautifully represented in [1.1.1]propellane, where the inverted C-C is a CS-bond, while the wings are made from covalent C-C bonds. What other manifestations can we expect from CS-bonds? Answers from experiment have the potential

  15. Metallic-covalent bonding conversion and thermoelectric properties of Al-based icosahedral quasicrystals and approximants

    NASA Astrophysics Data System (ADS)

    Takagiwa, Yoshiki; Kimura, Kaoru

    2014-08-01

    In this article, we review the characteristic features of icosahedral cluster solids, metallic-covalent bonding conversion (MCBC), and the thermoelectric properties of Al-based icosahedral quasicrystals and approximants. MCBC is clearly distinguishable from and closely related to the well-known metal-insulator transition. This unique bonding conversion has been experimentally verified in 1/1-AlReSi and 1/0-Al12Re approximants by the maximum entropy method and Rietveld refinement for powder x-ray diffraction data, and is caused by a central atom inside the icosahedral clusters. This helps to understand pseudogap formation in the vicinity of the Fermi energy and establish a guiding principle for tuning the thermoelectric properties. From the electron density distribution analysis, rigid heavy clusters weakly bonded with glue atoms are observed in the 1/1-AlReSi approximant crystal, whose physical properties are close to icosahedral Al-Pd-TM (TM: Re, Mn) quasicrystals. They are considered to be an intermediate state among the three typical solids: metals, covalently bonded networks (semiconductor), and molecular solids. Using the above picture and detailed effective mass analysis, we propose a guiding principle of weakly bonded rigid heavy clusters to increase the thermoelectric figure of merit (ZT) by optimizing the bond strengths of intra- and inter-icosahedral clusters. Through element substitutions that mainly weaken the inter-cluster bonds, a dramatic increase of ZT from less than 0.01 to 0.26 was achieved. To further increase ZT, materials should form a real gap to obtain a higher Seebeck coefficient.

  16. Metallic-covalent bonding conversion and thermoelectric properties of Al-based icosahedral quasicrystals and approximants.

    PubMed

    Takagiwa, Yoshiki; Kimura, Kaoru

    2014-08-01

    In this article, we review the characteristic features of icosahedral cluster solids, metallic-covalent bonding conversion (MCBC), and the thermoelectric properties of Al-based icosahedral quasicrystals and approximants. MCBC is clearly distinguishable from and closely related to the well-known metal-insulator transition. This unique bonding conversion has been experimentally verified in 1/1-AlReSi and 1/0-Al12Re approximants by the maximum entropy method and Rietveld refinement for powder x-ray diffraction data, and is caused by a central atom inside the icosahedral clusters. This helps to understand pseudogap formation in the vicinity of the Fermi energy and establish a guiding principle for tuning the thermoelectric properties. From the electron density distribution analysis, rigid heavy clusters weakly bonded with glue atoms are observed in the 1/1-AlReSi approximant crystal, whose physical properties are close to icosahedral Al-Pd-TM (TM: Re, Mn) quasicrystals. They are considered to be an intermediate state among the three typical solids: metals, covalently bonded networks (semiconductor), and molecular solids. Using the above picture and detailed effective mass analysis, we propose a guiding principle of weakly bonded rigid heavy clusters to increase the thermoelectric figure of merit (ZT) by optimizing the bond strengths of intra- and inter-icosahedral clusters. Through element substitutions that mainly weaken the inter-cluster bonds, a dramatic increase of ZT from less than 0.01 to 0.26 was achieved. To further increase ZT, materials should form a real gap to obtain a higher Seebeck coefficient.

  17. 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.

  18. Interdigitated hydrogen bonds: electrophile activation for covalent capture and fluorescence turn-on detection of cyanide.

    PubMed

    Jo, Junyong; Olasz, András; Chen, Chun-Hsing; Lee, Dongwhan

    2013-03-06

    Hydrogen-bonding promoted covalent modifications are finding useful applications in small-molecule chemical synthesis and detection. We have designed a xanthene-based fluorescent probe 1, in which tightly held acylguanidine and aldehyde groups engage in multiple intramolecular hydrogen bonds within the concave side of the molecule. Such an interdigitated hydrogen bond donor-acceptor (HBD-HBA) array imposes significant energy barriers (ΔG(‡) = 10-16 kcal mol(-1)) for internal bond rotations to assist structural preorganization and effectively polarizes the electrophilic carbonyl group toward a nucleophilic attack by CN(-) in aqueous environment. This covalent modification redirects the de-excitation pathways of the cyanohydrin adduct 2 to elicit a large (>7-fold) enhancement in the fluorescence intensity at λmax = 440 nm. A remarkably faster (> 60-fold) response kinetics of 1, relative to its N-substituted (and therefore "loosely held") analogue 9, provided compelling experimental evidence for the functional role of HBD-HBA interactions in the "remote" control of chemical reactivity, the electronic and steric origins of which were investigated by DFT computational and X-ray crystallographic studies.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  20. Effect of laser soldering irradiation on covalent bonds of pure collagen.

    PubMed

    Constantinescu, Mihai A; Alfieri, Alex; Mihalache, George; Stuker, Florian; Ducray, Angélique; Seiler, Rolf W; Frenz, Martin; Reinert, Michael

    2007-03-01

    Laser tissue welding and soldering is being increasingly used in the clinical setting for defined surgical procedures. The exact induced changes responsible for tensile strength are not yet fully investigated. To further improve the strength of the bonding, a better understanding of the laser impact at the subcellular level is necessary. The goal of this study was to analyze whether the effect of laser irradiation on covalent bonding in pure collagen using irradiances typically applied for tissue soldering. Pure rabbit and equine type I collagen were subjected to laser irradiation. In the first part of the study, rabbit and equine collagen were compared using identical laser and irradiation settings. In the second part of the study, equine collagen was irradiated at increasing laser powers. Changes in covalent bonding were studied indirectly using the sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) technique. Tensile strengths of soldered membranes were measured with a calibrated tensile force gauge. In the first experiment, no differences between the species-specific collagen bands were noted, and no changes in banding were found on SDS-PAGE after laser irradiation. In the second experiment, increasing laser irradiation power showed no effect on collagen banding in SDS-PAGE. Finally, the laser tissue soldering of pure collagen membranes showed virtually no determinable tensile strength. Laser irradiation of pure collagen at typical power settings and exposure times generally used in laser tissue soldering does not induce covalent bonding between collagen molecules. This is true for both rabbit and equine collagen proveniences. Furthermore, soldering of pure collagen membranes without additional cellular components does not achieve the typical tensile strength reported in native, cell-rich tissues. This study is a first step in a better understanding of laser impact at the molecular level and might prove useful in engineering of combined

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

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

    SciTech Connect

    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.

    2016-06-23

    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 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.

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

    DOE PAGES

    Holt, Adam P.; Bocharova, Vera; Cheng, Shiwang; ...

    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

  5. Coexistence of covalent and metallic bonding in the boron intercalation superconductor MgB2

    NASA Astrophysics Data System (ADS)

    Belashchenko, K. D.; Schilfgaarde, M. Van; Antropov, V. P.

    2001-09-01

    Chemical bonding and electronic structure of MgB2, a boron-based newly discovered superconductor, is studied using self-consistent band-structure techniques. Analysis of the transformation of the band structure for the hypothetical series of graphite-primitive graphite-primitive graphitelike boron-intercalated boron, shows that the band structure of MgB2 is graphitelike, with π bands falling deeper than in ordinary graphite. These bands possess a typically delocalized and metallic, as opposed to covalent, character. The in-plane σ bands retain their two-dimensional (2D) covalent character, but exhibit a metallic hole-type conductivity. The coexistence of 2D covalent in-plane and three-dimensional (3D) metallic-type interlayer conducting bands is a peculiar feature of MgB2. We analyze the 2D and 3D features of the band structure of MgB2 and related compounds, and their contributions to conductivity.

  6. 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

    2013-12-02

    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.

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

    SciTech Connect

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

    1986-08-10

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

  8. 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…

  9. Engineering the bonding scheme in C-S-H: The iono-covalent framework

    SciTech Connect

    Pellenq, R.J.-M.; Lequeux, N.; Damme, H. van

    2008-02-15

    On the basis of recent molecular simulation and experimental studies, we discuss two possible strategies for tuning the mechanical properties of cementitious materials by modifying the bonding scheme in the hydrates at molecular level. We focus the discussion on the calcium silicate hydrates (C-S-H). A first strategy would be based on the strengthening of the network of cohesion forces acting between the individual C-S-H lamellae or between their crystallites. Atomic scale simulations by ab initio, molecular dynamics and energy minimization techniques show that the iono-covalent forces between individual C-S-H layers or C-S-H layer stacks, separated by strongly localized calcium ions and water molecules, are orders of magnitude larger than the ionic correlation forces acting between C-S-H surfaces separated by nm- or multi-nm-thick layers of mobile water molecules and ions. The elastic properties derived from this iono-covalent bonding scheme are in good agreement with experimental values obtained by ultrasonic or statistical ('grid') nanoindentation techniques. The concept picture for C-S-H which follows is that of a crystalline semi-continuum, with dense domains ('crystallites' or 'particles') iono-covalently bonded to each other, possibly entangled also, and embedded as long as the mesoscale porosity is water-saturated in a relatively weak attractive stress field due to fluctuating electrostatic forces. Depending on the size, the aspect ratio, and the turbostratic order of the crystallites, and also the composition of the interstitial solution, the relative importance of each contribution could be modified. This provides the basis for a better control of properties such as early age or long term strength development for instance. In this respect, the microstructure-properties relationships in clay minerals provide interesting leads, pointing to the importance of bonding continuity rather than bond strength. A second strategy to tune the mechanical properties of

  10. 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.

  11. Covalent-bonded immobilization of lipase on poly(phenylene sulfide) dendrimers and their hydrolysis ability.

    PubMed

    Yemul, Omprakash; Imae, Toyoko

    2005-01-01

    Covalent-bonded immobilization of lipase from burkholderia cepacia onto two poly(phenylene sulfide) (PPS) dendrimers with different generations (two and three) was achieved using carbodiimide as a coupling reagent. The hydrolysis activity of olive oil to fatty acid was studied on enzyme-immobilized PPS dendrimers. Enzyme activity was proportional to the enzyme loading, and highest recovered activity was obtained at the medium enzyme loading for both G2 and G3 dendrimers. The immobilization improved the optimum pH and caused the temperature range to widen. Immobilization of enzyme has enhanced the thermal stability of enzyme activity in comparison with free enzyme. The immobilized enzyme as a biocatalyst for batch hydrolysis of olive oil retained 80 approximately 90% activity even after 20 times of recycling. This retention of activity after recycle is very valuable and powerful in enzyme technology. The present noteworthy and vital availability on enzyme reaction of the covalently bonded immobilized lipase on dendrimer came from the structure of dendrimer with a large number of functional terminal groups, which are easily available for immobilization of many lipases at the situation keeping reactive enzymes on the surface of dendrimer.

  12. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin.

    PubMed

    Zakeri, Bijan; Fierer, Jacob O; Celik, Emrah; Chittock, Emily C; Schwarz-Linek, Ulrich; Moy, Vincent T; Howarth, Mark

    2012-03-20

    Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.

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

    DOE PAGES

    Tian, Yong-Hui; Huang, Jingsong; Sheng, Xiaolan; ...

    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

  14. 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.

  15. 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.

  16. 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.

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

    PubMed

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

    2015-12-01

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

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

    DOE PAGES

    Subedi, Alaska; Siegrist, Theo; Singh, David J.; ...

    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

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

    SciTech Connect

    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 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. 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.

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

    PubMed

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

    2016-05-19

    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 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.

  1. 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

  2. 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

  3. Graft polymerization of styrene initiated by covalently bonded peroxide groups on silica.

    PubMed

    Bachmann, Stefan; Wang, Hongyu; Albert, Klaus; Partch, Richard

    2007-05-01

    The graft polymerization of styrene initiated by immobilized peroxide groups was investigated. Three different types of modification reactions were used to introduce peroxide groups which are directly attached onto the surface of two different silica supports. Silanol groups were chlorinated using thionyl chloride or tetrachlorosilane. In another reaction pathway 1,3,5-benzenetricarbonyl chloride enabled the introduction of free acid chloride residues bonded onto the surface of silica. tert-Butyl hydroperoxide (TBHP) was used to transform the chlorosilyl and the acid chloride groups into peroxide residues. In a further reaction step the covalently bonded peroxides initiated the polymerization of styrene to form grafted polystyrene directly attached onto the silica support. Solid-state 13C CP/MAS NMR spectroscopy, and thermogravimetric and scanning electron microscope measurements enabled a clear structure and property elucidation of the different bonded phases. The highest amount of grafted polystyrene was achieved employing the acid chloride synthesis pathway with silica-gel, whereas modification of spherical silica only led to minor amounts of grafted polymer. The results contribute to the evolving need to understand particle surface modifications and may have positive impact on development of new HPLC stationary phases for improved elutant resolution.

  4. Ultrafast cooling by covalently bonded graphene-carbon nanotube hybrid immersed in water.

    PubMed

    Chen, Jie; Walther, Jens H; Koumoutsakos, Petros

    2016-11-18

    The increasing power density and the decreasing dimensions of transistors present severe thermal challenges to the design of modern microprocessors. Furthermore, new technologies such as three-dimensional chip-stack architectures require novel cooling solutions for their thermal management. Here, we demonstrate, through transient heat-dissipation simulations, that a covalently bonded graphene-carbon nanotube (G-CNT) hybrid immersed in water is a promising solution for the ultrafast cooling of such high-temperature and high heat-flux surfaces. The G-CNT hybrid offers a unique platform to integrate the superior axial heat transfer capability of individual CNTs via their parallel arrangement. The immersion of the G-CNT in water enables an additional heat dissipation path via the solid-liquid interaction, allowing for the sustainable cooling of the hot surface under a constant power input of up to 10 000 W cm(-2).

  5. Ultrafast cooling by covalently bonded graphene-carbon nanotube hybrid immersed in water

    NASA Astrophysics Data System (ADS)

    Chen, Jie; Walther, Jens H.; Koumoutsakos, Petros

    2016-11-01

    The increasing power density and the decreasing dimensions of transistors present severe thermal challenges to the design of modern microprocessors. Furthermore, new technologies such as three-dimensional chip-stack architectures require novel cooling solutions for their thermal management. Here, we demonstrate, through transient heat-dissipation simulations, that a covalently bonded graphene-carbon nanotube (G-CNT) hybrid immersed in water is a promising solution for the ultrafast cooling of such high-temperature and high heat-flux surfaces. The G-CNT hybrid offers a unique platform to integrate the superior axial heat transfer capability of individual CNTs via their parallel arrangement. The immersion of the G-CNT in water enables an additional heat dissipation path via the solid-liquid interaction, allowing for the sustainable cooling of the hot surface under a constant power input of up to 10 000 W cm-2.

  6. hcp metal nanoclusters with hexagonal A-A bilayer stacking stabilized by enhanced covalent bonding

    SciTech Connect

    Li, Shunfang; Li, Haisheng; Xue, Xinlian; Jia, Yu; Guo, Zheng Xiao; Zhang, Zhenyu; Gong, Xingao

    2010-01-01

    First-principles total energy calculations within density functional theory have been performed to study the geometric and electronic structures of Ru{sub n} nanoclusters of varying size n (14{<=}n{<=}42). Strikingly, for the size range of n=14 to 38, the clusters always prefer a hexagonal bilayer structure with A-A stacking, rather than some of the more closely packed forms, or bilayer with A-B stacking. Such an intriguing 'molecular double-wheel' form is stabilized by substantially enhanced interlayer covalent bonding associated with strong s-d hybridization. Similar A-A stacking is also observed in the ground states or low-lying isomers of the clusters composed of other hcp elements, such as Os, Tc, Re, and Co. Note that these 'molecular double-wheels' show enhanced chemical activity toward H{sub 2}O splitting relative to their bulk counterpart, implying its potential applications as nanocatalysts.

  7. Fabrication and characterization of magnetic mesoporous silica nanospheres covalently bonded with europium complex.

    PubMed

    Feng, Jing; Fan, Wei-Qiang; Song, Shu-Yan; Yu, Ying-Ning; Deng, Rui-Ping; Zhang, Hong-Jie

    2010-06-07

    A novel multifunctional nanocomposite has been developed by combining the magnetic (Fe3O4) cores encapsulated in the mesoporous silica nanospheres and the luminescent Eu(TTA)3phen complex covalently bonded to the framework of mesoporous silica through a chelate ligand 5-[N,N-bis-3-(triethoxysilyl)propyl]ureyl-1,10-phenanthroline (phen-Si). The obtained nanocomposite is denoted as Eu(TTA)3phen-MMS. It has been well characterized by field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), N2 adsorption/desorption, Quantum Design SQUID magnetometer and photoluminescence spectroscopy, respectively. The results demonstrated that Eu(TTA)3phen-MMS nanocomposite possess superparamagnetic behavior, intense red emission and mesostructures simultaneously.

  8. The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

    PubMed Central

    Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

    2012-01-01

    We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively. PMID:22844433

  9. 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

    2016-09-08

    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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

  12. Covalent and ionic nature of the dative bond and account of accurate ammonia borane binding enthalpies.

    PubMed

    Plumley, Joshua A; Evanseck, Jeffrey D

    2007-12-27

    The inherent difficulty in modeling the energetic character of the B-N dative bond has been investigated utilizing density functional theory and ab initio methods. The underlying influence of basis set size and functions, thermal corrections, and basis set superposition error (BSSE) on the predicted binding enthalpy of ammonia borane (H3B-NH3) and four methyl-substituted ammonia trimethylboranes ((CH3)3B-N(CH3)nH3-n; n = 0-3) has been evaluated and compared with experiment. HF, B3LYP, MPW1K, MP2, QCISD, and QCISD(T) have been utilized with a wide range of Pople and correlation-consistent basis sets, totaling 336 levels of theory. MPW1K, B3LYP, and HF result in less BSSE and converge to binding enthalpies with fewer basis functions than post-SCF techniques; however, the methods fail to model experimental binding enthalpies and trends accurately, producing mean absolute deviations (MADs) of 5.1, 10.8, and 16.3 kcal/mol, respectively. Despite slow convergence, MP2, QCISD, and QCISD(T) using the 6-311++G(3df,2p) basis set reproduce the experimental binding enthalpy trend and result in lower MADs of 2.2, 2.6, and 0.5 kcal/mol, respectively, when corrected for BSSE and a residual convergence error of ca. 1.3-1.6 kcal/mol. Accuracy of the predicted binding enthalpy is linked to correct determination of the bond's dative character given by charge-transfer frustration, QCTF = -(Delta QN + Delta QB). Frustration gauges the incompleteness of charge transfer between the donor and the acceptor. The binding enthalpy across ammonia borane and methylated complexes is correlated to its dative character (R2 = 0.91), where a more dative bond (less charge-transfer frustration) results in a weaker binding enthalpy. However, a balance of electronic and steric factors must be considered to explain trends in experimentally reported binding enthalpies. Dative bond descriptors, such as bond ionicity and covalency are important in the accurate characterization of the dative bond. The B

  13. 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.

  14. Dual responsive Pickering emulsions stabilized by constructed core crosslinked polymer nanoparticles via reversible covalent bonds.

    PubMed

    Guo, Huazhang; Yang, Duanguang; Yang, Mei; Gao, Yong; Liu, Yijiang; Li, Huaming

    2016-12-06

    In this study, pH- and glucose-responsive Pickering emulsions stabilized by core crosslinked polymer nanoparticles, which were constructed via reversible covalent bonds, were presented for the first time. Firstly, well-defined PDMA-b-PAPBA (poly(N,N-dimethylacrylamide)-b-poly(3-acrylamidophenylboronic acid)) diblock copolymers were synthesized via sequential reversible addition-fragmentation chain transfer (RAFT) polymerization reactions. By means of complexation of PBA units of PDMA-b-PAPBA with PVA in basic water, core crosslinked polymer nanoparticles (CCPNs) with a core-shell structure were formed. The PAPBA/PVA crosslinked network and PDMA acted as the core and shell, respectively. Because of the reversible B-O chemical bonds in the core, the as-produced CCPNs showed structural transitions in response to the external stimuli involving pH and glucose. Investigation of the interfacial activities revealed that CCPNs exhibited high emulsifying performances, and oil in water (o/w) Pickering emulsions could be formed at a low particle content. The formed Pickering emulsions showed high stability at room temperature without any disturbances, whereas de-emulsification was observed upon improving the pH or adding glucose at a given pH. This is the first report on a responsive Pickering emulsion whose stability can be manipulated by glucose, and this type of fabricated manipulative Pickering emulsions are expected to provide useful guidance in the fields of oil recovery, interfacial reactions, etc.

  15. 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.

  16. Thermomechanics of a temperature sensitive covalent adaptable polymer with bond exchange reactions.

    PubMed

    Sun, XiaoHao; Wu, HengAn; Long, Rong

    2016-11-04

    We study a covalent adaptable polymer that can rearrange its network topology through thermally activated bond exchange reactions. When the polymer is deformed, such a network rearrangement leads to macroscopic stress relaxation, which allows the polymer to be thermoformed without a mold. Based on a previously developed constitutive model, we investigate thermal-mechanical behaviors of this material under a non-uniform and evolving temperature field through numerical simulations. Our focus is on the complex coupling between mechanical deformation, heat conduction and bond exchange reactions. Several examples are presented to illustrate the effects of non-uniform heating: uniaxial tension under heat conduction, torsion of a thin strip with local heating and thermal imprinting. Our results show that during non-uniform heating the material in the high temperature region creeps. This causes a redistribution of the deformation field and thus results in a final shape that deviates from the prescribed shape. The final shapes after thermoforming can be tuned by controlling the extent of heat conduction through different combinations of heating temperature and time. For example, with high temperature and a short heating time, it is possible to approximately confine stress relaxation and thus shape fixity within the local heating region. This is not the case if low temperature and a long heating time are used. These results can be utilized to design the temporal and spatial sequences of local heating during thermoforming to achieve various complex final shapes.

  17. 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.

  18. 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. 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.

  19. Crystal structure of a mononuclear RuII complex with a back-to-back terpyridine ligand: [RuCl(bpy)(tpy–tpy)]+

    PubMed Central

    Rein, Francisca N.; Chen, Weizhong; Scott, Brian L.; Rocha, Reginaldo C.

    2015-01-01

    We report the structural characterization of [6′,6′′-bis­(pyridin-2-yl)-2,2′:4′,4′′:2′′,2′′′-quaterpyridine](2,2′-bi­pyridine)­chlorido­ruthenium(II) hexa­fluorido­phosphate, [RuCl(C10H8N2)(C30H20N6)]PF6, which contains the bidentate ligand 2,2′-bi­pyridine (bpy) and the tridendate ligand 6′,6′′-bis­(pyridin-2-yl)-2,2′:4′,4′′:2′′,2′′′-quaterpyridine (tpy–tpy). The [RuCl(bpy)(tpy–tpy)]+ monocation has a distorted octa­hedral geometry at the central RuII ion due to the restricted bite angle [159.32 (16)°] of the tridendate ligand. The Ru-bound tpy and bpy moieties are nearly planar and essentially perpendicular to each other with a dihedral angle of 89.78 (11)° between the least-squares planes. The lengths of the two Ru—N bonds for bpy are 2.028 (4) and 2.075 (4) Å, with the shorter bond being opposite to Ru—Cl. For tpy–tpy, the mean Ru—N distance involving the outer N atoms trans to each other is 2.053 (8) Å, whereas the length of the much shorter bond involving the central N atom is 1.936 (4) Å. The Ru—Cl distance is 2.3982 (16) Å. The free uncoordinated moiety of tpy–tpy adopts a trans,trans conformation about the inter­annular C—C bonds, with adjacent pyridyl rings being only approximately coplanar. The crystal packing shows significant π–π stacking inter­actions based on tpy–tpy. The crystal structure reported here is the first for a tpy–tpy complex of ruthenium. PMID:26396838

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

    PubMed Central

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

    2014-01-01

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

  1. 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.

  2. Enhancing peptide ligand binding to vascular endothelial growth factor by covalent bond formation.

    PubMed

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

    2012-05-16

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

  3. Modulation of aggregation-induced emission and electroluminescence of silole derivatives by a covalent bonding pattern.

    PubMed

    Nie, Han; Chen, Bin; Quan, Changyun; Zhou, Jian; Qiu, Huayu; Hu, Rongrong; Su, Shi-Jian; Qin, Anjun; Zhao, Zujin; Tang, Ben Zhong

    2015-05-26

    The deciphering of structure-property relationships is of high importance to rational design of functional molecules and to explore their potential applications. In this work, a series of silole derivatives substituted with benzo[b]thiophene (BT) at the 2,5-positions of the silole ring are synthesized and characterized. The experimental investigation reveals that the covalent bonding through the 2-position of BT (2-BT) with silole ring allows a better conjugation of the backbone than that achieved though the 5-position of BT (5-BT), and results in totally different emission behaviors. The silole derivatives with 5-BT groups are weakly fluorescent in solutions, but are induced to emit intensely in aggregates, presenting excellent aggregation-induced emission (AIE) characteristics. Those with 2-BT groups can fluoresce more strongly in solutions, but no obvious emission enhancements are found in aggregates, suggesting they are not AIE-active. Theoretical calculations disclose that the good conjugation lowers the rotational motions of BT groups, which enables the molecules to emit more efficiently in solutions. But the well-conjugated planar backbone is prone to form strong intermoelcular interactions in aggregates, which decreases the emission efficiency. Non-doped organic light-emitting diodes (OLEDs) are fabricated by using these siloles as emitters. AIE-active silole derivatives show much better elecroluminescence properties than those without the AIE characterisic, demonstrating the advantage of AIE-active emitters in OLED applications.

  4. Controllable synthesis, magnetism and solubility enhancement of graphene nanosheets/magnetite hybrid material by covalent bonding.

    PubMed

    Zhan, Yingqing; Yang, Xulin; Meng, Fanbin; Wei, Junji; Zhao, Rui; Liu, Xiaobo

    2011-11-01

    Hybrids of Fe(3)O(4) nanoparticles and surface-modified graphene nanosheets (GNs) were synthesized by a two-step process. First, graphene nanosheets were modified by SOCl(2) and 4-aminophenoxyphthalonitrile to introduce nitrile groups on their surface. Second, the nitrile groups of surface-modified graphene nanosheets were reacted with ferric ions on the surface of Fe(3)O(4) with the help of relatively high boiling point solvent ethylene glycol to form a GNs/Fe(3)O(4) hybrid. The covalent attachment of Fe(3)O(4) nanoparticles on the graphene nanosheet surface was confirmed by Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), energy-dispersive X-ray spectrometer (EDS) and scanning electron microscopy (SEM). TEM and HRTEM observations indicated that the sizes of the nanoparticles and their coverage density on GNs could be easily controlled by changing the concentration of the precursor and the weight ratio to GNs. Magnetic measurements showed that magnetization of the hybrid materials is strongly influenced by the reaction conditions. Chemically bonded by phthalocyanine, the solubility of as-synthesized GNs/Fe(3)O(4) hybrid materials was greatly enhanced, which was believed to have potential for applications in the fields of composites, wastewater treatment and biomaterials.

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

    PubMed

    Ma, Jichao; Ye, Nengsheng; Li, Jian

    2016-02-01

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

  6. 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.

  7. Spin-Wave Excitations Evidencing the Kitaev Interaction in Single Crystalline α-RuCl_{3}.

    PubMed

    Ran, Kejing; Wang, Jinghui; Wang, Wei; Dong, Zhao-Yang; Ren, Xiao; Bao, Song; Li, Shichao; Ma, Zhen; Gan, Yuan; Zhang, Youtian; Park, J T; Deng, Guochu; Danilkin, S; Yu, Shun-Li; Li, Jian-Xin; Wen, Jinsheng

    2017-03-10

    Kitaev interactions underlying a quantum spin liquid have long been sought, but experimental data from which their strengths can be determined directly, are still lacking. Here, by carrying out inelastic neutron scattering measurements on high-quality single crystals of α-RuCl_{3}, we observe spin-wave spectra with a gap of ∼2  meV around the M point of the two-dimensional Brillouin zone. We derive an effective-spin model in the strong-coupling limit based on energy bands obtained from first-principles calculations, and find that the anisotropic Kitaev interaction K term and the isotropic antiferromagnetic off-diagonal exchange interaction Γ term are significantly larger than the Heisenberg exchange coupling J term. Our experimental data can be well fit using an effective-spin model with K=-6.8  meV and Γ=9.5  meV. These results demonstrate explicitly that Kitaev physics is realized in real materials.

  8. Alkyne substituted mononuclear photocatalysts based on [RuCl(bpy)(tpy)]⁺.

    PubMed

    Davidson, Ross J; Wilson, Lucy E; Duckworth, Andrew R; Yufit, Dmitry S; Beeby, Andrew; Low, Paul J

    2015-07-07

    The ethynyl-phenylene substituted 2,2':6',2''-terpyridine (tpy) derivatives, 4-(phenyl-ethynyl)-2,2':6',2''-terpyridine (L(1)), 4-(methoxyphenyl-ethynyl)-2,2':6',2''-terpyridine (L(2)), 4-(tolyl-ethynyl)-2,2':6',2''-terpyridine (L(3)) and 4-(nitrophenyl-ethynyl)-2,2':6',2''-terpyridine (L(4)) have been used to synthesize four new [RuCl(2,2'-bipyridine)(L(n))]PF6 based complexes. Electronic absorption, resonance Raman, cyclic voltammetry and spectroelectrochemistry aided by DFT calculations were used to explore the influence of the alkynyl substituents on the electronic structures, photochemical and redox properties of the complexes. Furthermore, it is shown that the addition of ethynyl phenyl moieties to the 4-position of the tpy ligand does not have a detrimental effect on these complexes, or the analogous aqua complexes, with respect to their ability to photocatalyse the oxidation of 4-methoxybenzyl alcohol to the corresponding benzaldehyde.

  9. Spin-Wave Excitations Evidencing the Kitaev Interaction in Single Crystalline α -RuCl3

    NASA Astrophysics Data System (ADS)

    Ran, Kejing; Wang, Jinghui; Wang, Wei; Dong, Zhao-Yang; Ren, Xiao; Bao, Song; Li, Shichao; Ma, Zhen; Gan, Yuan; Zhang, Youtian; Park, J. T.; Deng, Guochu; Danilkin, S.; Yu, Shun-Li; Li, Jian-Xin; Wen, Jinsheng

    2017-03-01

    Kitaev interactions underlying a quantum spin liquid have long been sought, but experimental data from which their strengths can be determined directly, are still lacking. Here, by carrying out inelastic neutron scattering measurements on high-quality single crystals of α -RuCl3 , we observe spin-wave spectra with a gap of ˜2 meV around the M point of the two-dimensional Brillouin zone. We derive an effective-spin model in the strong-coupling limit based on energy bands obtained from first-principles calculations, and find that the anisotropic Kitaev interaction K term and the isotropic antiferromagnetic off-diagonal exchange interaction Γ term are significantly larger than the Heisenberg exchange coupling J term. Our experimental data can be well fit using an effective-spin model with K =-6.8 meV and Γ =9.5 meV . These results demonstrate explicitly that Kitaev physics is realized in real materials.

  10. ATOMIC-SCALE OBSERVATION OF STRUCTURAL AND ELECTRONIC ORDERS IN THE LAYERED COMPOUND -RuCl3

    DOE PAGES

    Ziatdinov, Maxim A; Banerjee, Arnab; Maksov, Artem B; ...

    2016-01-01

    A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, -RuCl3. Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of -RuCl3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at themore » nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of 0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual -RuCl3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface.« less

  11. ATOMIC-SCALE OBSERVATION OF STRUCTURAL AND ELECTRONIC ORDERS IN THE LAYERED COMPOUND -RuCl3

    SciTech Connect

    Ziatdinov, Maxim A; Banerjee, Arnab; Maksov, Artem B; Berlijn, Tom; Zhou, Wu; Cao, Huibo; Yan, Jiaqiang; Bridges, Craig A; Mandrus, D.; Nagler, Stephen E; Baddorf, Arthur P; Kalinin, Sergei V

    2016-01-01

    A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, -RuCl3. Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of -RuCl3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at the nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of 0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual -RuCl3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface.

  12. Atomic-scale observation of structural and electronic orders in the layered compound α-RuCl3

    PubMed Central

    Ziatdinov, M.; Banerjee, A.; Maksov, A.; Berlijn, T.; Zhou, W.; Cao, H. B.; Yan, J.-Q.; Bridges, C. A.; Mandrus, D. G.; Nagler, S. E.; Baddorf, A. P.; Kalinin, S. V.

    2016-01-01

    A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, α-RuCl3. Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of α-RuCl3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at the nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of ≈0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual α-RuCl3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface. PMID:27941761

  13. Atomic-scale observation of structural and electronic orders in the layered compound α-RuCl3

    NASA Astrophysics Data System (ADS)

    Ziatdinov, M.; Banerjee, A.; Maksov, A.; Berlijn, T.; Zhou, W.; Cao, H. B.; Yan, J.-Q.; Bridges, C. A.; Mandrus, D. G.; Nagler, S. E.; Baddorf, A. P.; Kalinin, S. V.

    2016-12-01

    A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, α-RuCl3. Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of α-RuCl3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at the nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of ~0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual α-RuCl3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface.

  14. When noncovalent interactions are stronger than covalent bonds: Bilayer graphene doped with second row atoms, aluminum, silicon, phosphorus and sulfur

    NASA Astrophysics Data System (ADS)

    Denis, Pablo A.

    2011-05-01

    Herein, we investigate bilayer graphene doped with second-row atoms using the LDA, M06-L, and VDW-DF functionals. For 2-3 at.% or lower Al and P dopings the structure with a short interlayer distance and without a covalent bond between the heteroatoms is more stable than that with a covalent bond and longer interlayer separation. However, for Si the linked structure is more stable. Doped bilayer-graphene is prone to the attachment of more heteroatoms, as reflected by the large adsorption energies, which decrease in the following order Al > Si > P. We show that it is feasible to tune the electronic properties, and the interlayer-interaction energy varying the type or amount of second row atoms.

  15. Face-centered-cubic K3B80 and Mg3B80 metals: Covalent and ionic bondings

    NASA Astrophysics Data System (ADS)

    Yan, Qing-Bo; Zheng, Qing-Rong; Su, Gang

    2009-09-01

    By means of first-principles calculations within the density-functional theory, we find that stable face-centered-cubic (fcc) K3B80 and Mg3B80 solids can be formed. For both solids, two possibly stable geometrical phases (identified as phase A and phase B ) with different lattice parameters can exist, where phase A has a lattice parameter smaller than phase B . In phase A , B80 clusters are significantly distorted and two or four intercluster covalent bonds are formed for K3B80 or Mg3B80 , respectively. In phase B , B80 units are slightly distorted and no intercluster covalent bonds exist. The phase A of Mg3B80 bears the largest cohesive energy among them and is more stable than the fcc B80 solid. The charge population analysis shows that K and Mg are ionized and donate electrons to the other boron atoms of K3B80 and Mg3B80 solids. The different ionic radii of K and Mg lead to major geometrical differences between K3B80 and Mg3B80 solids and the competition of the covalent and ionic bondings could explain the emergence of two different geometrical phases for both. The electronic structural calculations reveal that both fcc K3B80 and Mg3B80 solids are metals.

  16. 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

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

    DOE PAGES

    Cao, Huibo B.; Yan, Jiaqiang; Bridges, Craig 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

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

    SciTech Connect

    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 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 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.

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

    DOE PAGES

    Chen, Xinyue; Li, Hui; Yin, Panchao; ...

    2015-01-01

    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.

  20. Photoelectron imaging and spectroscopy of MI(2)(-) (M = Cs, Cu, Au): evolution from ionic to covalent bonding.

    PubMed

    Wang, Yi-Lei; Wang, Xue-Bin; Xing, Xiao-Peng; Wei, Fan; Li, Jun; Wang, Lai-Sheng

    2010-10-28

    We report a combined experimental and theoretical investigation of MI(2)(-) (M = Cs, Cu, Ag, Au) to explore the chemical bonding in the group IA and IB diiodide complexes. Both photoelectron imaging and low-temperature photoelectron spectroscopy are applied to MI(2)(-) (M = Cs, Cu, Au), yielding vibrationally resolved spectra for CuI(2)(-) and AuI(2)(-) and accurate electron affinities, 4.52 ± 0.02, 4.256 ± 0.010, and 4.226 ± 0.010 eV for CsI(2), CuI(2), and AuI(2), respectively. Spin-orbit coupling is found to be important in all the diiodide complexes and ab initio calculations including spin-orbit effects allow quantitative assignments of the observed photoelectron spectra. A variety of chemical bonding analyses (charge population, bond order, and electron localization functions) have been carried out, revealing a gradual transition from the expected ionic behavior in CsI(2)(-) to relatively strong covalent bonding in AuI(2)(-). Both relativistic effects and electron correlation are shown to enhance the covalency in the gold diiodide complex.

  1. How to make the ionic Si-O bond more covalent and the Si-O-Si linkage a better acceptor for hydrogen bonding.

    PubMed

    Grabowsky, Simon; Hesse, Maxie F; Paulmann, Carsten; Luger, Peter; Beckmann, Jens

    2009-05-18

    Variation of a bond angle can tune the reactivity of a chemical compound. To exemplify this concept, the nature of the siloxane linkage (Si-O-Si), the most abundant chemical bond in the earth's crust, was examined using theoretical calculations on the molecular model compounds H(3)SiOSiH(3), (H(3)Si)(2)OHOH, and (H(3)Si)(2)OHOSiH(3) and high-resolution synchrotron X-ray diffraction experiments on 5-dimethylhydroxysilyl-1,3-dihydro-1,1,3,3-tetramethyl-2,1,3-benzoxadisilole (1), a molecular compound that gives rise to the formation of very rare intermolecular hydrogen bonds between the silanol groups and the siloxane linkages. For theoretical calculations and experiment, electronic descriptors were derived from a topological analysis of the electron density (ED) distribution and the electron localization function (ELF). The topological analysis of an experimentally obtained ELF is a newly developed methodology. These descriptors reveal that the Si-O bond character and the basicity of the siloxane linkage strongly depend on the Si-O-Si angle. While the ionic bond character is dominant for Si-O bonds, covalent bond contributions become more significant and the basicity increases when the Si-O-Si angle is reduced from linearity to values near the tetrahedral angle. Thus, the existence of the exceptional intermolecular hydrogen bond observed for 1 can be explained by its very small strained Si-O-Si angle that adopts nearly a tetrahedral angle.

  2. 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

  3. 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.

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

    PubMed

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

    2013-11-19

    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.

  5. 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

  6. 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

    2015-11-07

    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 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.

  7. 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.

  8. 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.

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

    PubMed

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

    2015-03-11

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

  10. Effect of crystal anisotropy and adhesive forces on laser induced deformation patterns in covalently bonded thin films

    NASA Astrophysics Data System (ADS)

    Walgraef, D.; Ghoniem, N. M.

    2002-04-01

    The effect of crystal structure on laser induced deformation patterns in thin films and surfaces is analyzed within the framework of a dynamical model for the coupled evolution of defect densities and deformation fields. In crystals with covalent bonding, such as Si and SiC, preferential bond breaking may occur, as a result of the relative orientation of the laser electric field and crystallographic axes. We extend here our theoretical framework to incorporate the effects of anisotropic defect diffusion, and the influence of film-substrate adhesion on deformation pattern selection and stability of thin films subjected to laser beams. We also compare theoretical predictions to experimental observations on single crystal silicon wafer surfaces. Furthermore, it is predicted that the laser induced damage threshold for SiC single crystals can be in excess of 200 J/cm2.

  11. Covalent O-H bonds as electron traps in proton-rich rutile TiO2 nanoparticles.

    PubMed

    Zhang, Jing; Steigerwald, Michael; Brus, Louis; Friesner, Richard A

    2014-01-01

    The cation in the electrolyte of the dye-sensitized solar cell (DSSC) has a profound effect on electron trapping and transport behavior in TiO2 nanocrystalline film; this is one of the important factors that determines the overall efficiency of DSSCs. Here, we present a quantum mechanical investigation on the structures and energetics of proton-induced electron trap states and the thermodynamical barrier heights for the ambipolar diffusion of proton/electron pair using a large cluster model for the computations. Our calculations indicate that protons react with TiO2 to form covalent O-H bonds. This is in contrast to the reaction of Li(+) with TiO2, in which case the alkali metal is more accurately described as a simple coordinating cation. The covalent O-H bonding leads both to deeper electron trap states and to significantly higher barriers for the diffusion of carriers. These results are qualitatively consistent with experimental observations, and they extend our understanding of the cation effect in DSSCs at an atomic level of detail.

  12. 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

  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. Non-covalent bonding interaction of surfactants with functionalized carbon nanotubes in proton exchange membranes for fuel cell applications.

    PubMed

    Sayeed, M Abu; Kim, Young Ho; Park, Younjin; Gopalan, A I; Lee, Kwang-Pill; Choi, Sang-June

    2013-11-01

    Dispersion of functionalized multiwalled carbon nanotubes (MWCNTs) in proton exchange membranes (PEMs) was conducted via non-covalent bonding between benzene rings of various surfactants and functionalized MWCNTs. In the solution casting method, dispersion of functionalized MWCNTs in PEMs such as Nafion membranes is a critical issue. In this study, 1 wt.% pristine MWCNTs (p-MWCNTs) and oxidized MWCNTs (ox-MWCNTs) were reinforced in Nafion membranes by adding 0.1-0.5 wt.% of a surfactant such as benzalkonium chloride (BKC) as a cationic surfactant with a benzene ring, Tween-80 as a nonanionic surfactant without a benzene ring, sodium dodecylsulfonate (SDS) as an anionic surfactant without a benzene ring, or sodium dodecylben-zenesulfonate (SDBS) as an anionic surfactant with a benzene ring and their effects on the dispersion of nanocomposites were then observed. Among these surfactants, those with benzene rings such as BKC and SDBS produced enhanced dispersion via non-covalent bonding interaction between CNTs and surfactants. Specifically, the surfactants were adsorbed onto the surface of functionalized MWCNTs, where they prevented re-aggregation of MWCNTs in the nanocomposites. Furthermore, the prepared CNTs reinforced nanocomposite membranes showed reduced methanol uptake values while the ion exchange capacity values were maintained. The enhanced properties, including thermal property of the CNTs reinforced PEMs with surfactants, could be applicable to fuel cell applications.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  16. Selective covalent bond formation in polypeptide ions via gas-phase ion/ion reaction chemistry.

    PubMed

    Han, Hongling; McLuckey, Scott A

    2009-09-16

    Primary amines present in protonated polypeptides can be covalently modified via gas-phase ion/ion reactions using bifunctional reagent ions. The use of reagent anions with a charge-bearing site that leads to strong interactions with the polypeptide, such as sulfonic acid, gives rise to the formation of a long-lived adduct. A distinct reactive functional group, an aldehyde in the present case, can then undergo reaction with the peptide. Collisional activation of the adduct ion formed from a reagent with an aldehyde group and a peptide ion with a primary amine gives rise to water loss in conjunction with imine (Schiff base) formation. The covalently bound modification is retained upon subsequent collisional activation. This work demonstrates the ability to selectively modify polypeptide ions in the gas phase within the context of a multistage mass spectrometry experiment.

  17. In vivo inhibition of E. coli growth by a Ru(II)/Pt(II) supramolecule [(tpy)RuCl(dpp)PtCl2](PF6).

    PubMed

    Jain, Avijita; Winkel, Brenda S J; Brewer, Karen J

    2007-10-01

    Supramolecular complexes consisting of ruthenium chromophores and a cisplatin unit represent an emerging class of bioactive molecules of interest as anti-cancer agents. Although the ability of Ru(II)/Pt(II) heteronuclear complexes to bind to DNA has been demonstrated, the in vivo activity of these complexes has not yet been reported. In the present work, we report the anti-bacterial activity of the complex [(tpy)RuCl(dpp)PtCl(2)](PF(6)) (where dpp=2,3-bis(2-pyridyl)pyrazine, tpy=2,2':6',2''-terpyridine). The impact on bacterial cell growth of exposure to different concentrations of [(tpy)RuCl(dpp)PtCl(2)](PF(6)) and cisplatin was studied. The bioactivity of this complex was found to be due to the presence of the cis-PtCl(2) moiety, as the monometallic synthon [(tpy)RuCl(dpp)](PF(6)) did not inhibit bacterial cell growth.

  18. The roles of disulphide and non-covalent bonding in the functional properties of heat-induced whey protein gels.

    PubMed

    Havea, Palatasa; Carr, Alistair J; Creamer, Lawrence K

    2004-08-01

    Heat-induced gelation (80 degrees C, 30 min or 85 degrees C, 60 min) of whey protein concentrate (WPC) solutions was studied using transmission electron microscopy (TEM), dynamic rheology and polyacrylamide gel electrophoresis (PAGE). The WPC solutions (150 g/kg, pH 6.9) were prepared by dispersing WPC powder in water (control), 10 g/kg sodium dodecyl sulphate (SDS) solution or 10 mM-dithiothreitol (DTT) solution. The WPC gels containing SDS were more translucent than the control gels, which were slightly more translucent than the gels containing DTT. TEM analyses showed that the SDS-gels had finer aggregate structure (approximately equal to 10 nm) than the control gels (approximately equal to 100 nm), whereas the DTT-gels had a more particulate structure (approximately equal to 200 to 300 nm). Dynamic rheology measurements showed that the control WPC gels had storage modulus (G) values (approximately equal to 13,500 Pa) that were approximately equal to 25 times higher than those of the SDS-gels (approximately equal to 550 Pa) and less than half those of the DTT-gels after cooling. Compression tests showed that the DTT-gels were more rigid and more brittle than the control gels, whereas the SDS-gels were softer and more rubbery than either the control gels or the DTT-gels. PAGE analyses of WPC gel samples revealed that the control WPC solutions heated at 85 degrees C for 10 min contained both disulphide bonds and non-covalent linkages. In both the SDS-solutions and the DTT-solutions, the denatured whey protein molecules were in the form of monomers or small aggregates. It is likely that, on more extended heating, more disulphide linkages were formed in the SDS-gels whereas more hydrophobic aggregates were formed in the DTT-gels. These results demonstrate that the properties of heat-induced WPC gels are strongly influenced by non-covalent bonding. Intermolecular disulphide bonds appeared to give the rubbery nature of heat-induced WPC gels whereas non-covalent bonds

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

    PubMed

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

    2016-04-01

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

  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. 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.

  2. 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.

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

    DOE PAGES

    Zhao, X. J.; Xue, X. L.; Guo, Z. X.; ...

    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

  4. 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.

  5. 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.

  6. 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.

  7. Constructing safe and durable antibacterial textile surfaces using a robust graft-to strategy via covalent bond formation

    NASA Astrophysics Data System (ADS)

    He, Liang; Li, Sha; Chung, Cordelia T. W.; Gao, Chang; Xin, John H.

    2016-11-01

    Recently zwitterionic materials have been widely applied in the biomedical and bioengineering fields due to their excellent biocompatibility. Inspired by these, this study presents a graft-to strategy via covalent bond formation to fabricate safe and durable antibacterial textile surfaces. A novel zwitterionic sulfobetaine containing triazine reactive group was specifically designed and synthesized. MTT assay showed that it had no obvious cytotoxicity to human skin HaCaT cells as verified by ca. 89.9% relative viability at a rather high concentration of 0.8 mg·mL‑1. In the evaluation for its skin sensitization, the maximum score for symptoms of erythema and edema in all tests were 0 in all observation periods. The sulfobetaine had a hydrophilic nature and the hydrophilicity of the textiles was enhanced by 43.9% when it was covalently grafted onto the textiles. Moreover, the textiles grafted with the reactive sulfobetaine exhibited durable antibacterial activities, which was verified by the fact that they showed antibacterial rates of 97.4% against gram-positive S. aureus and 93.2% against gram-negative E. coli even after they were laundered for 30 times. Therefore, the titled zwitterionic sulfobetaine is safe to human for healthcare and wound dressing and shows a promising prospect on antibacterial textile application.

  8. 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

    2014-11-07

    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.

  9. Constructing safe and durable antibacterial textile surfaces using a robust graft-to strategy via covalent bond formation

    PubMed Central

    He, Liang; Li, Sha; Chung, Cordelia T. W.; Gao, Chang; Xin, John H.

    2016-01-01

    Recently zwitterionic materials have been widely applied in the biomedical and bioengineering fields due to their excellent biocompatibility. Inspired by these, this study presents a graft-to strategy via covalent bond formation to fabricate safe and durable antibacterial textile surfaces. A novel zwitterionic sulfobetaine containing triazine reactive group was specifically designed and synthesized. MTT assay showed that it had no obvious cytotoxicity to human skin HaCaT cells as verified by ca. 89.9% relative viability at a rather high concentration of 0.8 mg·mL−1. In the evaluation for its skin sensitization, the maximum score for symptoms of erythema and edema in all tests were 0 in all observation periods. The sulfobetaine had a hydrophilic nature and the hydrophilicity of the textiles was enhanced by 43.9% when it was covalently grafted onto the textiles. Moreover, the textiles grafted with the reactive sulfobetaine exhibited durable antibacterial activities, which was verified by the fact that they showed antibacterial rates of 97.4% against gram-positive S. aureus and 93.2% against gram-negative E. coli even after they were laundered for 30 times. Therefore, the titled zwitterionic sulfobetaine is safe to human for healthcare and wound dressing and shows a promising prospect on antibacterial textile application. PMID:27808248

  10. Constructing safe and durable antibacterial textile surfaces using a robust graft-to strategy via covalent bond formation.

    PubMed

    He, Liang; Li, Sha; Chung, Cordelia T W; Gao, Chang; Xin, John H

    2016-11-03

    Recently zwitterionic materials have been widely applied in the biomedical and bioengineering fields due to their excellent biocompatibility. Inspired by these, this study presents a graft-to strategy via covalent bond formation to fabricate safe and durable antibacterial textile surfaces. A novel zwitterionic sulfobetaine containing triazine reactive group was specifically designed and synthesized. MTT assay showed that it had no obvious cytotoxicity to human skin HaCaT cells as verified by ca. 89.9% relative viability at a rather high concentration of 0.8 mg·mL(-1). In the evaluation for its skin sensitization, the maximum score for symptoms of erythema and edema in all tests were 0 in all observation periods. The sulfobetaine had a hydrophilic nature and the hydrophilicity of the textiles was enhanced by 43.9% when it was covalently grafted onto the textiles. Moreover, the textiles grafted with the reactive sulfobetaine exhibited durable antibacterial activities, which was verified by the fact that they showed antibacterial rates of 97.4% against gram-positive S. aureus and 93.2% against gram-negative E. coli even after they were laundered for 30 times. Therefore, the titled zwitterionic sulfobetaine is safe to human for healthcare and wound dressing and shows a promising prospect on antibacterial textile application.

  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.

    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.

  13. 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.

  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

    2016-03-07

    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 effect of sulfur covalent bonding on the electronic shells of silver clusters.

    PubMed

    Pedicini, Anthony F; Reber, Arthur C; Khanna, Shiv N

    2013-10-28

    The nature of the bonding in Ag(n)S(m)(0∕-) clusters, n = 1-7; m = 1-4, has been analyzed to understand its effect on the electronic shell structure of silver clusters. First-principle investigations reveal that the sulfur atoms prefer 2 or 3-coordinate sites around a silver core, and that the addition of sulfur makes the planar structures compact. Molecular orbital analysis finds that the 3p orbitals of sulfur form a bonding orbital and two weakly bonding lone pairs with silver. We examine the electronic shell structures of Ag6Sm, which are two electrons deficient of a spherical closed electronic shell prior to the addition of sulfur, and Ag7S(m)(-) clusters that contain closed electronic shells prior to the addition of sulfur. The Ag6S4 cluster has a distorted octahedral silver core and an open shell with a multiplicity of 3, while the Ag7S(n_(-) clusters have compact geometries with enhanced stability, confirming that the clusters maintain their electronic shell structure after bonding with sulfur.

  17. Effect of Covalent Bonding on Magnetism and the Missing Neutron Intensity in Copper Oxide Compounds

    SciTech Connect

    Walters, A.C.; Gu, G.; Perring, T.G.; Caux, J.-S.; Savici, A.T.; Lee, C.-C.; Ku, W.; Zaliznyak, I.A.

    2009-10-04

    Theories involving highly energetic spin fluctuations are among the leading contenders for explaining high-temperature superconductivity in the cuprates. These theories could be tested by inelastic neutron scattering (INS), as a change in the magnetic scattering intensity that marks the entry into the superconducting state provides a precise quantitative measure of the spin-interaction energy involved in the superconductivity. However, the absolute intensities of spin fluctuations measured in neutron scattering experiments vary widely, and are usually much smaller than expected from fundamental sum rules, resulting in 'missing' INS intensity. Here, we solve this problem by studying magnetic excitations in the one-dimensional related compound, Sr{sub 2}CuO{sub 3}, for which an exact theory of the dynamical spin response has recently been developed. In this case, the missing INS intensity can be unambiguously identified and associated with the strongly covalent nature of magnetic orbitals. We find that whereas the energies of spin excitations in Sr{sub 2}CuO{sub 3} are well described by the nearest-neighbour spin-1/2 Heisenberg Hamiltonian, the corresponding magnetic INS intensities are modified markedly by the strong 2p-3d hybridization of Cu and O states. Hence, the ionic picture of magnetism, where spins reside on the atomic-like 3d orbitals of Cu{sup 2+} ions, fails markedly in the cuprates.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Unexpected Trend in Stability of Xe-F Compounds under Pressure Driven by Xe-Xe Covalent Bonds.

    PubMed

    Peng, Feng; Botana, Jorge; Wang, Yanchao; Ma, Yanming; Miao, Maosheng

    2016-11-17

    Xenon difluoride is the first and the most stable of hundreds of noble-gas (Ng) compounds. These compounds reveal the rich chemistry of Ng's. No stable compound that contains a Ng-Ng bond has been reported previously. Recent experiments have shown intriguing behaviors of this exemplar compound under high pressure, including increased coordination numbers and an insulator-to-metal transition. None of the behaviors can be explained by electronic-structure calculations with fixed stoichiometry. We therefore conducted a structure search of xenon-fluorine compounds with various stoichiometries and studied their stabilities under pressure using first-principles calculations. Our results revealed, unexpectedly, that pressure stabilizes xenon-fluorine compounds selectively, including xenon tetrafluoride, xenon hexafluoride, and the xenon-rich compound Xe2F. Xenon difluoride becomes unstable above 81 GPa and yields metallic products. These compounds contain xenon-xenon covalent bonds and may form intercalated graphitic xenon lattices, which stabilize xenon-rich compounds and promote the decomposition of xenon difluoride.

  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. S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity.

    PubMed

    Dey, Abhishek; Jiang, Yonging; Ortiz de Montellano, Paul; Hodgson, Keith O; Hedman, Britt; Solomon, Edward I

    2009-06-10

    Experimental covalencies of the Fe-S bond for the resting low-spin and substrate-bound high-spin active site of cytochrome P450 are reported. DFT calculations on the active site indicate that one H-bonding interaction from the protein backbone is needed to reproduce the experimental values. The H-bonding to the thiolate from the backbone decreases the anisotropic pi covalency of the Fe-S bond lowering the barrier of free rotation of the exchangeable axial ligand, which is important for reactivity. The anionic axial thiolate ligand is calculated to lower the Fe(III/II) reduction potential of the active site by more than 1 V compared to a neutral imidazole ligand. About half of this derives from its covalent bonding and half from its electrostatic interaction with the oxidized Fe. This axial thiolate ligand increases the pK(a) of compound 0 (Fe(III)-hydroperoxo) favoring its protonation which promotes O-O bond heterolysis forming compound I. The reactivity of compound I is calculated to be relatively insensitive to the nature of the axial ligand due to opposing reduction potential and proton affinity contributions to the H-atom abstraction energy.

  7. Activation of a Covalent Enzyme-Substrate Bond by Noncovalent Interaction with an Effector

    PubMed Central

    Malhotra, O. P.; Bernhard, Sidney A.

    1973-01-01

    The absorption spectrum of an activesite specific chromophoric acyl enzyme, sturgeon β-(2-furyl)-acryloyl-glyceraldehyde-3-phosphate dehydrogenase, is reported. This acyl enzyme undergoes all of the catalyzed reactions characteristic of the intermediate of the physiological acyl enzyme, 3-phospho-D-glyceroyl-glyceraldehyde-3-phosphate dehydrogenease. The rates of reactions of both these acyl enzymes depend strongly on the extent of interaction of the acyl enzyme with the oxidized coenzyme, NAD+, even where the “redox” properties of the coenzyme are not required. Likewise, the spectral properties of chromophoric acyl enzyme are affected by the extent of bound NAD. Under the pseudophysiological conditions reported herein, there is a stoichiometric limitation of two furylacryloyl-acyl groups per enzyme molecule containing four covalently-equivalent subunits. The binding of NAD both to the apoenzyme and to the diacyl enzyme is heterogeneous: at low extents of NAD occupancy, NAD binding is stronger. The binding to acyl enzyme can be quantitatively described by an enzyme model involving a tetramer with 2-fold symmetry, and consequently containing equal numbers of two classes of sites. NAD binding to difurylacryloyl-enzyme occurs virtually discretely, first to the two unmodified (tight-binding) sites, followed by looser binding to the two acyl-sites. NAD occupancy at these latter sites transforms the chromophoric acyl spectrum from that characteristic of a model furylacryloyl-thiol ester in H2O to a highly perturbed furylacryloyl spectrum characteristic of monomeric native “active-thiol” furylacryloyl-enzymes. Likewise the acyl reactivity towards arsenolysis depends on the extent of NAD bound to the loose sites. Elimination of the tight binding of NAD to the difurylacryloyl enzyme tetramer by alkylation of the remaining two free SH groups with iodoacetate has no apparent influence on the NAD-dependent furylacryloyl-spectral perturbation at the “two equivalent

  8. Covalent bonding of PMMA, PBMA, and poly(HEMA)to hydroxyapatite particles.

    PubMed

    Liu, Q; de Wijn, J R; van Blitterswijk, C A

    1998-05-01

    In our earlier study, we showed that the surface hydroxyl groups of hydroxyapatite have the ability to react with organic isocyanate groups. In this study, the feasibility of grafting poly(methyl methacrylate) (PMMA), poly(n-butyl methacrylate) (PBMA), and Poly(hydroxyethyl methacrylate) [poly(HEMA)] by using the reaction of isocyanate groups with the hydroxyl groups on the surface of HA was investigated. Double bonds were introduced to the surface of HA via the coupling reaction of isocyanateoethyl methacrylate (ICEM) with HA, or through hexamethylene diisocyanate (HMDI) with hydroxyethyl methacrylate (HEMA) and HA, followed by radical polymerization in MMA, BMA, or HEMA. Infrared spectra indicated the existence of polymers on the surfaces of HA. Thermogravimetric analysis also confirmed the presence of grafted polymers on the surface of HA powder particles (20-26 wt%). The polymers gave typical PMMA, PBMA, or poly(HEMA) infrared spectra, with the exception of amide bands, a result of the coupling reaction of ICEM or HMDI with hydroxy groups of HA or HEMA. Therefore it is concluded that the polymers were chemically bonded to the surface of HA through the isocyanate groups of ICEM or HMDI.

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

    SciTech Connect

    Clearfield, Abraham

    2014-11-01

    In this part of the proposal we have concentrated on the surface functionalization of α-zirconium phosphate of composition Zr(O3POH)2•H2O. It is a layered compound that can be prepared as particles as small as 30 nm to single crystals in the range of cm. This compound is an ion exchanger with a capacity of 6.64 meq per gram. It finds use as a catalyst, proton conductor, sensors, biosensors, in kidney dialysis and drug delivery. By functionalizing the surface additional uses are contemplated as will be described. The layers consist of the metal, with 4+ charge, that is positioned slightly above and below the mean layer plane and bridged by three of the four phosphate oxygens. The remaining POH groups point into the interlayer space creating double rows of POH groups but single arrays on the surface layers. The surface groups are reactive and we were able to bond silanes, isocyanates, epoxides, acrylates ` and phosphates to the surface POH groups. The layers are easily exfoliated or filled with ions by ion exchange or molecules by intercalation reactions. Highlights of our work include, in addition to direct functionalization of the surfaces, replacement of the protons on the surface with ions of different charge. This allows us to bond phosphates, biophosphates, phosphonic acids and alcohols to the surface. By variation of the ion charge of the ions that replace the surface protons, different surface structures are obtained. We have already shown that polymer fillers, catalysts and Janus particles may be prepared. The combination of surface functionalization with the ability to insert molecules and ions between the layers allow for a rich development of numerous useful other applications as well as nano-surface chemistry.

  11. Competition between covalent bonding and charge transfer tendencies at complex-oxides interfaces

    NASA Astrophysics Data System (ADS)

    Salafranca, J.; Tornos, J.; García-Barriocanal, J.; León, C.; Santamaria, J.; Rincón, J.; Álvarez, G.; Pennycook, S. J.; Dagotto, E.; Varela, M.

    2013-03-01

    Interfaces alter the subtle balance among different degrees of freedom responsible for exotic phenomena in complex oxides, such as cuprate-manganite interfaces. We study these interfaces by means of scanning transmission electron microscopy and theoretical calculations. Microscopy and EEL spectroscopy indicate that the interfaces are sharp, and the chemical profile is symmetric with two equivalent interfaces. Spectroscopy also allows us to establish an oxidation state profile with sub-nanometer resolution. We find an anomalous charge redistribution: a non-monotonic behavior of the occupancy of d orbitals in the manganite layers as a function of distance to the interface. Relying on model calculations, we establish that this profile is a result of the competition between standard charge transfer tendencies involving materials with different chemical potentials and strong bonding effects across the interface. The competition can be tuned by different factors (temperature, doping, magnetic fields...). As examples, we report different charge distributions as a function of doping of the manganite layers. ACKNOWLEDGEMENTS ORNL:U.S. DOE-BES, Material Sciences and Engineering Division & ORNL's ShaRE. UCM:Juan de la Cierva, Ramon y Cajal, & ERC Starting Investigator Award programs.

  12. 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.

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

    PubMed

    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. Small cycloalkane (CN)2C-C(CN)2 structures are highly directional non-covalent carbon-bond donors.

    PubMed

    Bauzá, Antonio; Mooibroek, Tiddo J; Frontera, Antonio

    2014-08-11

    High-level calculations (RI-MP2/def2-TZVP) disclosed that the σ-hole in between two C atoms of cycloalkane X2 CCX2 structures (X=F, CN) is increasingly exposed with decreasing ring size. The interacting energy of complexes of F(-) , HO(-) , N≡C(-) , and H2 CO with cyclopropane and cyclobutane X2 CCX2 derivatives was calculated. For X=F, these energies are small to positive, while for X=CN they are all negative, ranging from -6.8 to -42.3 kcal mol(-1) . These finding are corroborated by a thorough statistical survey of the Cambridge Structural Database (CSD). No clear evidence could be found in support of non-covalent carbon bonding between electron-rich atoms (El.R.) and F2 CCF2 structures. In marked contrast, El.R.⋅⋅⋅(CN)2 CC(CN)2 interactions are abundant and highly directional. Based on these findings, the hydrophobic electrophilic bowl formed by 1,1',2,2'-tetracyano cyclopropane or cyclobutane derivatives is proposed as a new and synthetically accessible supramolecular synthon.

  15. Kitaev exchange and field-induced quantum spin-liquid states in honeycomb α-RuCl3.

    PubMed

    Yadav, Ravi; Bogdanov, Nikolay A; Katukuri, Vamshi M; Nishimoto, Satoshi; van den Brink, Jeroen; Hozoi, Liviu

    2016-11-30

    Large anisotropic exchange in 5d and 4d oxides and halides open the door to new types of magnetic ground states and excitations, inconceivable a decade ago. A prominent case is the Kitaev spin liquid, host of remarkable properties such as protection of quantum information and the emergence of Majorana fermions. Here we discuss the promise for spin-liquid behavior in the 4d(5) honeycomb halide α-RuCl3. From advanced electronic-structure calculations, we find that the Kitaev interaction is ferromagnetic, as in 5d(5) iridium honeycomb oxides, and indeed defines the largest superexchange energy scale. A ferromagnetic Kitaev coupling is also supported by a detailed analysis of the field-dependent magnetization. Using exact diagonalization and density-matrix renormalization group techniques for extended Kitaev-Heisenberg spin Hamiltonians, we find indications for a transition from zigzag order to a gapped spin liquid when applying magnetic field. Our results offer a unified picture on recent magnetic and spectroscopic measurements on this material and open new perspectives on the prospect of realizing quantum spin liquids in d(5) halides and oxides in general.

  16. Kitaev exchange and field-induced quantum spin-liquid states in honeycomb α-RuCl3

    NASA Astrophysics Data System (ADS)

    Yadav, Ravi; Bogdanov, Nikolay A.; Katukuri, Vamshi M.; Nishimoto, Satoshi; van den Brink, Jeroen; Hozoi, Liviu

    2016-11-01

    Large anisotropic exchange in 5d and 4d oxides and halides open the door to new types of magnetic ground states and excitations, inconceivable a decade ago. A prominent case is the Kitaev spin liquid, host of remarkable properties such as protection of quantum information and the emergence of Majorana fermions. Here we discuss the promise for spin-liquid behavior in the 4d5 honeycomb halide α-RuCl3. From advanced electronic-structure calculations, we find that the Kitaev interaction is ferromagnetic, as in 5d5 iridium honeycomb oxides, and indeed defines the largest superexchange energy scale. A ferromagnetic Kitaev coupling is also supported by a detailed analysis of the field-dependent magnetization. Using exact diagonalization and density-matrix renormalization group techniques for extended Kitaev-Heisenberg spin Hamiltonians, we find indications for a transition from zigzag order to a gapped spin liquid when applying magnetic field. Our results offer a unified picture on recent magnetic and spectroscopic measurements on this material and open new perspectives on the prospect of realizing quantum spin liquids in d5 halides and oxides in general.

  17. Kitaev exchange and field-induced quantum spin-liquid states in honeycomb α-RuCl3

    PubMed Central

    Yadav, Ravi; Bogdanov, Nikolay A.; Katukuri, Vamshi M.; Nishimoto, Satoshi; van den Brink, Jeroen; Hozoi, Liviu

    2016-01-01

    Large anisotropic exchange in 5d and 4d oxides and halides open the door to new types of magnetic ground states and excitations, inconceivable a decade ago. A prominent case is the Kitaev spin liquid, host of remarkable properties such as protection of quantum information and the emergence of Majorana fermions. Here we discuss the promise for spin-liquid behavior in the 4d5 honeycomb halide α-RuCl3. From advanced electronic-structure calculations, we find that the Kitaev interaction is ferromagnetic, as in 5d5 iridium honeycomb oxides, and indeed defines the largest superexchange energy scale. A ferromagnetic Kitaev coupling is also supported by a detailed analysis of the field-dependent magnetization. Using exact diagonalization and density-matrix renormalization group techniques for extended Kitaev-Heisenberg spin Hamiltonians, we find indications for a transition from zigzag order to a gapped spin liquid when applying magnetic field. Our results offer a unified picture on recent magnetic and spectroscopic measurements on this material and open new perspectives on the prospect of realizing quantum spin liquids in d5 halides and oxides in general. PMID:27901091

  18. Synthesis, spectral, thermal, X-ray single crystal of new RuCl2(dppb)diamine complexes and their application in hydrogenation of Cinnamic aldehyde

    NASA Astrophysics Data System (ADS)

    Warad, Ismail; Al-Hussain, Hanan; Al-Far, Rawhi; Mahfouz, Refaat; Hammouti, Belkheir; Hadda, Taibi Ben

    The preparation of new three trans-[RuCl2(dppb)(N-N)] with mixed diamine (N-N) and 1,4-bis-(diphenylphosphino)butane (dppb) ligands, starting from RuCl2(PPh3)3 as precursor is presented. The complexes are characterized on the basis of elemental analysis, IR, 1H, 13C and 31P{1H}NMR, FAB-MS, TG/DTA and single crystal X-ray diffraction studies. Complex (2L1) crystallizes in the monoclinic unit cells with the space group P21. The catalysts are evaluated for their Cinnamic aldehyde hydrogenation. The catalysts show excellent activity and selectivity for the unsaturated carbonyl compound under mild conditions.

  19. 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.

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

    PubMed

    Mohr, Gerhard J

    2006-11-01

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

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

    PubMed Central

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

    2012-01-01

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

  2. UV-light exposure of insulin: pharmaceutical implications upon covalent insulin dityrosine dimerization and disulphide bond photolysis.

    PubMed

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

    2012-01-01

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

  3. The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine–Thymine (AT) Base Pairs and Their Mimics

    PubMed Central

    Guillaumes, Laia; Simon, Sílvia; Fonseca Guerra, Célia

    2015-01-01

    Invited for this issues cover are Dr. Célia Fonseca Guerra from the VU University of Amsterdam and her collaborators at the University of Girona. The cover picture shows H-bonds in the adenine–thymine Watson–Crick base pair. An essential part of these H-bonds is their covalent component arising from donor–acceptor interactions between N or O lone pairs and the N−H antibonding σ* acceptor orbital. This charge-transfer interaction is represented by green figures walking on the pedestrian crossing, connecting the bases. This covalent component is the reason why H-bonds between DNA and/or unsaturated model bases are significantly stronger than those between analogous saturated bases. This contrasts sharply with the classical picture of predominantly electrostatic H-bonds which is not only incomplete in terms of a proper bonding mechanism, but also fails to explain the trend in stability. For more details, see the Full Paper on p. 318 ff. PMID:26246979

  4. Racemization of alcohols catalyzed by [RuCl(CO)2(eta(5)-pentaphenylcyclopentadienyl)]--mechanistic insights from theoretical modeling.

    PubMed

    Nyhlén, Jonas; Privalov, Timofei; Bäckvall, Jan-E

    2009-01-01

    Two possible pathways of inner-sphere racemization of sec-alcohols by using the [RuCl(CO)(2)(eta(5)-pentaphenylcyclopentadienyl)] catalyst (1) have been thoroughly investigated by means of density function calculations. To be able to racemize alcohols, catalyst 1 needs to have a free coordination site on the metal. This can be achieved either by a eta(5)-->eta(3) ring slippage or by dissociation of a carbon monoxide (CO) ligand. The eta(5)-->eta(3) ring-slip pathway was found to have a high potential energy barrier, 42 kcal mol(-1), which can be explained by steric congestion in the transition state. On the other hand, CO dissociation to give a 16-electron complex has a barrier of only 22.6 kcal mol(-1). We have computationally discovered a mechanism involving CO participation that does not require eta(5)-->eta(3) ring slippage. The key features of this mechanism are 1) CO-assisted exchange of chloride for alkoxide, 2) alcohol-alkoxide exchange, and 3) generation of an active 16-electron complex through CO dissociation with subsequent beta-hydride elimination as the racemization step. We have found a low-energy pathway for reaction of 1 with potassium tert-butoxide and a pathway for fast alkoxide exchange with interaction between the incoming/leaving alcohol and one of the two CO ligands. We predict that dissociation of a Ru-bound CO ligand does not occur in these exchange reactions. Dissociation of one of the two Ru-bound CO ligands has been found necessary only at a later stage of the reaction. Though this barrier is still quite high, our results indicate that it is not necessary to cross the CO dissociation barrier for the racemization of each new alcohol. Thus, the dissociation of a CO ligand is interpreted as a rate-limiting reaction step in order to create a catalytically active 16-electron complex.

  5. Meaning and consequence of the coexistence of competitive hydrogen bond/salt forms on the dissociation orientation of non-covalent complexes.

    PubMed

    Darii, Ekaterina; Alves, Sandra; Gimbert, Yves; Perret, Alain; Tabet, Jean-Claude

    2017-03-15

    Non-covalent complexes (NCC) between hexose monophosphates (HexP) and arginine (R) were analyzed using ESI MS and MS/MS in negative mode under different (hard, HC and soft, SC) desolvation conditions. High resolution mass spectrometry (HRMS) revealed the presence of different ionic species, namely, homo- and heteromultimers of R and HexP. Deprotonated heterodimers and corresponding sodiated species were enhanced under HC likely due to a decrease in available charge number associated with the reduction of H(+)/Na(+) exchange. The quantum calculations showed that the formation of covalent systems is very little exothermic, therefore, such systems are disfavored. Desolvation dependent CID spectra of deprotonated [(HexP+R)‒H](-) complexes demonstrated that they can exist within the hydrogen bond (HB) and salt bridge (SB) forms, yielding either NCC separation or covalent bond cleavages, respectively. Although HB forms are the main species, they cannot survive under HC; therefore, the minor SB forms became detectable. Energy-resolved mass spectrometry (ERMS) experiments revealed diagnostic fragment ions from both SB and HB forms, providing evidence that these isomeric forms are inconvertible. SB formation should result from the ionic interactions of highly acidic group of HexP with strongly basic guanidine group of arginine and thus requires an arginine zwitterion (ZW) form. This was confirmed by quantum calculations. Ion-ion interactions are significantly affected by the presence of sodium cation as demonstrated by the fragmentation patterns of sodiated complex species. Regarding CID data, only SB between protonated amino group of R and deprotonated phosphate group of HexP could be suggested, but the primary amine is not enough basic then, the SB must be fleeting. Nevertheless, the observation of the covalent bond cleavages suggests the presence of structures with a free negative charge able to induce fragmentations. Indeed, according to quantum calculations, solvated

  6. Photoelectron Imaging and Spectroscopy of MI2- (M = Cs, Cu, Au): Evolution from Ionic to Covalent Bonding

    SciTech Connect

    Wang, Yi-Lei; Wang, Xue B; Xing, Xiaopeng; Wei, Fan; Li, Jun; Wang, Lai S

    2010-10-28

    We report a combined experimental and theoretical investigation on MI2- (M = Cs, Cu, Ag, Au) to explore the chemical bonding in the group IA and IB di-iodide complexes. Both photoelectron imaging and low-temperature photoelectron spectroscopy are applied to MI2- (M = Cs, Cu, Au), yielding vibrationally resolved spectra for CuI2- and AuI2- and accurate electron affinities, 4.52 ± 0.02, 4.256 ± 0.010, and 4.226 ± 0.010 eV for CsI2, CuI2, and AuI2, respectively. Spin-orbit coupling is found to be important in all the di-iodide complexes and ab initio calculations including spin-orbit effects allow quantitative assignments of the observed photoelectron spectra. A variety of chemical bonding analyses (charge population, bond order, and electron localization functions) have been carried out, revealing a gradual transition from the expected ionic behavior in CsI2- to strong covalent bonding in AuI2-. Both relativistic effects and electron correlation are shown to enhance the covalency in the gold di-iodide complex.

  7. Observation of covalent and electrostatic bonds in nitrogen-containing polycyclic ions formed by gas phase reactions of the benzene radical cation with pyrimidine.

    PubMed

    Attah, Isaac Kwame; Soliman, Abdel-Rahman; Platt, Sean P; Meot-Ner Mautner, Michael; Aziz, Saaudallah G; Samy El-Shall, M

    2017-03-01

    Polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocyclics (PANHs) are present in ionizing environments, including interstellar clouds and solar nebulae, where their ions can interact with neutral PAH and PANH molecules leading to the formation of a variety of complex organics including large N-containing ions. Herein, we report on the formation of a covalently-bonded (benzene·pyrimidine) radical cation dimer by the gas phase reaction of pyrimidine with the benzene radical cation at room temperature using the mass-selected ion mobility technique. No ligand exchange reactions with benzene and pyrimidine are observed indicating that the binding energy of the (benzene·pyrimidine)˙(+) adduct is significantly higher than both the benzene dimer cation and the proton-bound pyrimidine dimer. The (benzene·pyrimidine)˙(+) adduct shows thermal stability up to 541 K. Thermal dissociation of the (C6D6·C4H4N2)˙(+) adduct at temperatures higher than 500 K produces C4H4N2D(+) (m/z 82) suggesting the transfer of a D atom from the C6D6 moiety to the C4H4N2 moiety before the dissociation of the adduct. Mass-selected ion mobility of the (benzene·pyrimidine)˙(+) dimer reveals the presence of two families of isomers formed by electron impact ionization of the neutral (benzene·pyrimidine) dimer. The slower mobility peak corresponds to a non-covalent family of isomers with larger collision cross sections (76.0 ± 1.8 Å(2)) and the faster peak is consistent with a family of covalent isomers with more compact structures and smaller collision cross sections (67.7 ± 2.2 Å(2)). The mobility measurements at 509 K show only one peak corresponding to the family of stable covalently bonded isomers characterized by smaller collision cross sections (66.9 ± 1.9 Å(2) at 509 K). DFT calculations at the M06-2X/6-311++G** level show that the most stable (benzene·pyrimidine)˙(+) isomer forms a covalent C-N bond with a binding energy of 49.7 kcal mol(-1) and a

  8. Reactivity of [M2 (μ-Cl)2 (cod)2 ] (M=Ir, Rh) and [Ru(Cl)2 (cod)(CH3 CN)2 ] with Na[H2 B(bt)2 ]: Formation of Agostic versus Borate Complexes.

    PubMed

    Bakthavachalam, K; Yuvaraj, K; Zafar, Mohammad; Ghosh, Sundargopal

    2016-11-21

    Treatment of [M2 (μ-Cl)2 (cod)2 ] (M=Ir and Rh) with Na[H2 B(bt)2 ] (cod=1,5-cyclooctadiene and bt=2-mercaptobenzothiazolyl) at low temperature led to the formation of dimetallaheterocycles [(Mcod)2 (bt)2 ], 1 and 2 (1: M=Ir and 2: M=Rh) and a borate complex [Rh(cod){κ(2) -S,S'-H2 B(bt)2 }], 3. Compounds 1 and 2 are structurally characterized metal analogues of 1,5-cyclooctadiene. Metal-metal bond distances of 3.6195(9) Å in 1 and 3.6749(9) Å in 2 are too long to consider as bonding. In an attempt to generate the Ru analogue of 1 and 2, that is [(Rucod)2 (bt)2 ], we have carried out the reaction of [Ru(Cl)2 (cod)(CH3 CN)2 ] with Na[H2 B(bt)2 ]. Interestingly, the reaction yielded agostic complexes [Ru(cod)L{κ(3) -H,S,S'-H2 B(bt)2 }], 4 and 5 (4: L=Cl; 5: L=C7 H4 NS2 ). One of the key differences between 4 and 5 is the presence of different ancillary ligands at the metal center. The natural bond orbital (NBO) analysis of 1 and 2 shows that there is four lone pairs of electrons on each metal center with a significant amount of d character. Furthermore, the electronic structures and the bonding of these complexes have been established on the ground of quantum-chemical calculations. All of the new compounds were characterized by IR, (1) H, (11) B, (13) C NMR spectroscopy, and X-ray crystallographic analysis.

  9. 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.

  10. Dynamic covalent polymers

    PubMed Central

    García, Fátima

    2016-01-01

    ABSTRACT This Highlight presents an overview of the rapidly growing field of dynamic covalent polymers. This class of polymers combines intrinsic reversibility with the robustness of covalent bonds, thus enabling formation of mechanically stable, polymer‐based materials that are responsive to external stimuli. It will be discussed how the inherent dynamic nature of the dynamic covalent bonds on the molecular level can be translated to the macroscopic level of the polymer, giving access to a range of applications, such as stimuli‐responsive or self‐healing materials. A primary distinction will be made based on the type of dynamic covalent bond employed, while a secondary distinction will be based on the consideration whether the dynamic covalent bond is used in the main chain of the polymer or whether it is used to allow side chain modification of the polymer. Emphasis will be on the chemistry of the dynamic covalent bonds present in the polymer, in particular in relation to how the specific (dynamic) features of the bond impart functionality to the polymer material, and to the conditions under which this dynamic behavior is manifested. © 2016 The Authors. Journal of Polymer Science Part A: Polymer Chemistry Published by Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 3551–3577. PMID:27917019

  11. Dynamic covalent polymers.

    PubMed

    García, Fátima; Smulders, Maarten M J

    2016-11-15

    This Highlight presents an overview of the rapidly growing field of dynamic covalent polymers. This class of polymers combines intrinsic reversibility with the robustness of covalent bonds, thus enabling formation of mechanically stable, polymer-based materials that are responsive to external stimuli. It will be discussed how the inherent dynamic nature of the dynamic covalent bonds on the molecular level can be translated to the macroscopic level of the polymer, giving access to a range of applications, such as stimuli-responsive or self-healing materials. A primary distinction will be made based on the type of dynamic covalent bond employed, while a secondary distinction will be based on the consideration whether the dynamic covalent bond is used in the main chain of the polymer or whether it is used to allow side chain modification of the polymer. Emphasis will be on the chemistry of the dynamic covalent bonds present in the polymer, in particular in relation to how the specific (dynamic) features of the bond impart functionality to the polymer material, and to the conditions under which this dynamic behavior is manifested. © 2016 The Authors. Journal of Polymer Science Part A: Polymer Chemistry Published by Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 3551-3577.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  13. Tough, rapid-recovery composite hydrogels fabricated via synergistic core-shell microgel covalent bonding and Fe(3+) coordination cross-linking.

    PubMed

    Liang, Xuechen; Deng, Yukun; Pei, Xiaopeng; Zhai, Kankan; Xu, Kun; Tan, Ying; Gong, Xinyuan; Wang, Pixin

    2017-03-22

    We developed tough, rapid-recovery composite hydrogels that are fabricated via core-shell microgel covalent bonding and Fe(3+) dynamic metal coordination cross-linking. First, core-shell microgels are used as cross-linking agents and initiators to prepare homogeneous hydrogel networks with rapid recovery in the absence of an organic cross-linking agent. The toughness and recoverability of the composite hydrogels can be improved by adding the dynamic reversibility of ionic cross-linking. Owing to the synergistic effect of microgel covalent bonding, Fe(3+) coordination cross-linking, and H-bond cross-linking, the multi-cross-linked composite hydrogels exhibit excellent toughness and a fast recovery rate. These characteristics demonstrate that the dynamic reversibility of the ionic cross-linking can significantly improve the toughness and recoverability of the hydrogels. In addition, the core-shell microgels play a key role in toughening the hydrogels and accelerating their recovery by transferring stress to grafted polymer chains and homogenizing the hydrogel network.

  14. 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

  15. Self-assembly via (N$ctdot;I) non-covalent bonds between 1,4-diiodo-tetrafluoro-benzene and a tetra-imino ferrocenophane

    NASA Astrophysics Data System (ADS)

    Syssa-Magalé, Jean-Laurent; Boubekeur, Kamal; Palvadeau, Pierre; Meerschaut, Alain; Schöllhorn, Bernd

    2004-03-01

    The tetra-imino ferrocenophane ( 1) was cocrystallized with 1,4-diiodo-tetrafluoro-benzene (TFDIB). In the resulting compound 2, two of the four ferrocenophane nitrogens show interactions with the iodine atoms of TFDIB leading to a polymeric structure with extended linear alternating electron donor ( 1) and acceptor (TFDIB) molecule chains. For the first time, imino nitrogens are involved in this type of halogen bonding. The N⋯I non-covalent bonds (N⋯I distances 2.879(5) and 2.896(5) Å; N⋯I-C angles 171.1(2) and 178.1(2)°) are the directing interactions responsible for the observed self-assembly. The ferrocene fragments of the macrocycle are in an almost perpendicular conformation. Mössbauer spectroscopy indicates the sole presence of low spin iron (II). The temperature dependence of the magnetic susceptibility is corresponding to a quasi-diamagnetic compound.

  16. 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.

  17. Morphological effects of single-layer graphene oxide in the formation of covalently bonded polypyrrole composites using intermediate diisocyanate chemistry

    NASA Astrophysics Data System (ADS)

    Whitby, Raymond L. D.; Korobeinyk, Alina; Mikhalovsky, Sergey V.; Fukuda, Takahiro; Maekawa, Toru

    2011-10-01

    Single-layer graphene oxide (SLGO) possesses carboxylic and hydroxyl groups suitable for reactions with aliphatic or aromatic diisocyanate molecules. TEM analysis reveals that aliphatic diisocyanate molecules caused SLGO to scroll into star-like formations, whereas aromatic diisocyanate molecules retained SGLO in a flat-sheet morphology. TGA confirms the stabilisation of the formed urea and urethane groups on SLGO, but the onset of sheet pyrolysis occurs at a lower temperature due to isocyanate reactions with anhydride and epoxide groups embedded in the sheet. Pendant isocyanate groups act as bridging units to facilitate the attachment of pyrrole molecules, which are then used as anchor sites for the covalent polymerisation of pyrrole to polypyrrole (PPy). The use of FeCl3 as the polymerisation catalyst generated both covalent and free PPy, but also iron hydroxide nanoparticles were observed decorating the SLGO surface. When using ammonium persulfate as a catalyst and dodecylbenzenesulfonate as a dopant, free PPy could be removed under treatment with solvents to leave a purely covalent system. Discrete regions of SLGO were observed decorated with nanoparticles of PPy along the edge or across the surface of individual sheets. It was found that the flexibility of the SLGO sheet and the type of diisocyanate used directly affected the electrical resistance of the final composite.

  18. Syntheses and Crystal Structures of Ruthenium Complexes of 1,4,8,11-Tetraazacyclotetradecane, Tris(2-aminoethyl)amine (tren), and Bis(2-aminoethyl)(iminomethyl)amine. A Microporous Layered Structure Consisting of {[K(tren)](2)[RuCl(6)]}(n)()(n)()(-) and {(H(5)O(2))(4)[RuCl(6)]}(n)()(n)()(+).

    PubMed

    Sakai, Ken; Yamada, Yasutaka; Tsubomura, Taro

    1996-05-22

    The second method for the synthesis of cis-[Ru(III)Cl(2)(cyclam)]Cl (1) (cyclam = 1,4,8,11-tetraazacyclotetradecane), with use of cis-Ru(II)Cl(2)(DMSO)(4) (DMSO = dimethyl sulfoxide) as a starting complex, is reported together with the synthesis of [Ru(II)(cyclam)(bpy)](BF(4))(2).H(2)O (2) (bpy = 2,2'-bipyridine) from 1. The syntheses of Ru complexes of tris(2-aminoethyl)amine (tren) are also reported. A reaction between K(3)[Ru(III)(ox)(3)] (ox = oxalate) and tren affords fac-[Ru(III)Cl(3)(trenH)]Cl.(1)/(2)H(2)O (3) (trenH = bis(2-aminoethyl)(2-ammonioethyl)amine = monoprotonated tren) and (H(5)O(2))(2)[K(tren)][Ru(III)Cl(6)] (4) as major products and gives fac-[Ru(III)Cl(ox)(trenH)]Cl.(3)/(2)H(2)O (5) in very low reproducibility. A reaction between 3 and bpy affords [Ru(II)(baia)(bpy)](BF(4))(2) (6) (baia = bis(2-aminoethyl)(iminomethyl)amine), in which tren undergoes a selective dehydrogenation into baia. The crystal structures of 2-6 have been determined by X-ray diffraction, and their structural features are discussed in detail. Crystallographic data are as follows: 2, RuF(8)ON(6)C(20)B(2)H(34), monoclinic, space group P2(1)/c with a = 12.448(3) Å, b = 13.200(7) Å, c = 17.973(4) Å, beta = 104.28(2) degrees, V = 2862(2) Å(3), and Z = 4; 3, RuCl(4)O(0.5)N(4)C(6)H(20), monoclinic, space group P2(1)/a with a = 13.731(2) Å, b = 14.319(4) Å, c = 13.949(2) Å, beta = 90.77(1) degrees, V = 2742(1) Å(3), and Z = 8; 4, RuKCl(6)O(4)N(4)C(6)H(28), trigonal, space group R&thremacr; with a = 10.254(4), c = 35.03(1) Å, V = 3190(2) Å(3), and Z = 6; 5, RuCl(2)O(5.5)N(4)C(8)H(22), triclinic, space group P&onemacr; with a = 10.336(2) Å, b = 14.835(2) Å, c = 10.234(1) Å, alpha = 90.28(1) degrees, beta = 90.99(1) degrees, gamma = 92.07(1) degrees, V = 1567.9(4) Å(3), and Z = 4; 6, RuF(8)N(6)C(16)B(2)H(24), monoclinic, space group P2(1)/c, a = 10.779(2) Å, b = 14.416(3) Å, c = 14.190(2) Å, beta = 93.75(2) degrees, V = 2200.3(7) Å(3), and Z = 4. Compound 4 possesses

  19. Donor-Acceptor Interaction Determines the Mechanism of Photoinduced Electron Injection from Graphene Quantum Dots into TiO2: π-Stacking Supersedes Covalent Bonding.

    PubMed

    Long, Run; Casanova, David; Fang, Wei-Hai; Prezhdo, Oleg V

    2017-02-22

    Interfacial electron transfer (ET) constitutes the key step in conversion of solar energy into electricity and fuels. Required for fast and efficient charge separation, strong donor-acceptor interaction is typically achieved through covalent chemical bonding and leads to fast, adiabatic ET. Focusing on interfaces of pyrene, coronene, and a graphene quantum dot (GQD) with TiO2, we demonstrate the opposite situation: covalent bonding leads to weak coupling and nonadiabatic (NA) ET, while through-space π-electron interaction produces adiabatic ET. Using real-time time-dependent density functional theory combined with NA molecular dynamics, we simulate photoinduced ET into TiO2 from flat and vertically placed molecules and GQD containing commonly used carboxylic acid linkers. Both arrangements can be achieved experimentally with GQDs and other two-dimensional materials, such as MoS2. The weak through-bond donor-acceptor coupling is attributed to the π-electron withdrawing properties of the carboxylic acid group. The calculated ET time scales are in excellent agreement with pump-probe optical experiments. The simulations show that the ET proceeds faster than energy relaxation. The electron couples to a broad spectrum of vibrational modes, ranging from 100 cm(-1) large-scale motions to 1600 cm(-1) C-C stretches. Compared to graphene/TiO2 heterojunctions, the molecule/TiO2 and GQD/TiO2 systems exhibit energy gaps, allowing for longer-lived excited states and hot electron injection, facilitating charge separation and higher voltage. The reported state-of-the-art simulations generate a detailed time-domain, atomistic description of the interfacial charge and energy transfer and relaxation processes, and demonstrate that the fundamental principles leading to efficient charge separation in nanoscale materials depend strongly and often unexpectedly on the type of donor-acceptor interaction. Understanding these principles is critical to the development of highly efficient

  20. Rational Design of Fatty Acid Amide Hydrolase Inhibitors that Act by Covalently Bonding to Two Active Site Residues

    PubMed Central

    Otrubova, Katerina; Brown, Monica; McCormick, Michael S.; Han, Gye W.; O’Neal, Scott T.; Cravatt, Benjamin F.; Stevens, Raymond C.; Lichtman, Aron H.; Boger, Dale L.

    2013-01-01

    The design and characterization of α-ketoheterocycle fatty acid amide hydrolase (FAAH) inhibitors are disclosed that additionally and irreversibly target a cysteine (Cys269) found in the enzyme cytosolic port while maintaining the reversible covalent Ser241 attachment responsible for their rapid and initially reversible enzyme inhibition. Two α-ketooxazoles (3 and 4) containing strategically placed electrophiles at the C5 position of the pyridyl substituent of 2 (OL-135) were prepared and examined as inhibitors of FAAH. Consistent with the observed time-dependent non-competitive inhibition, the co-crystal X-ray structure of 3 bound to a humanized variant of rat FAAH revealed that 3 was not only covalently bound to the active site catalytic nucleophile Ser241 as a deprotonated hemiketal, but also to Cys269 through the pyridyl C5-substituent, thus providing an inhibitor with dual covalent attachment in the enzyme active site. In vivo characterization of the prototypical inhibitors in mice demonstrate that they raise endogenous brain levels of FAAH substrates to a greater extent and for a much longer duration (>6 h) than the reversible inhibitor 2, indicating that the inhibitors accumulate and persist in the brain to completely inhibit FAAH for a prolonged period. Consistent with this behavior and the targeted irreversible enzyme inhibition, 3 reversed cold allodynia in the chronic constriction injury model of neuropathic pain in mice for a sustained period (>6 h) beyond that observed with the reversible inhibitor 2, providing effects that were unchanged over the 1–6 h time course monitored. PMID:23581831

  1. Trans/cis isomerization of [RuCl2(diphosphine)(diamine)] complexes: Synthesis, X-ray structure and catalytic activity in hydrogenation

    NASA Astrophysics Data System (ADS)

    Warad, Ismail; AlHussen, Hanan; Alanazi, Hamdah; Mahfouz, Refaat; Hammouti, Belkheir; Al-Dosari, Mohammad A.; Al-Far, Rawhi; Ben Hadda, Taibi

    2013-03-01

    The diamine (Nsbnd N) co-ligand 2,2-dimethyl-1,3-propanediamine and 2,3-diaminophathalene react individually with [RuCl2(dppb)2(μ-dppb)] to afford complexes with kinetically stable trans-[Cl2Ru(dppb)(Nsbnd N)] as the favoured isomer. The thermodynamically stable cis-[Cl2Ru(dppb)(Nsbnd N)] isomer of complex 1 was formed from the trans-1 isomer. The trans to cis isomerization reaction was conducted in CHCl3 at RT and monitored by 31P{1H} NMR. The structures of the desired complexes were characterized via elemental analyses, IR and, UV-visible spectroscopy, FAB-MS and NMR. The structure of the cis-1 isomer was determined by single crystal X-ray measurements. Both the trans-1 and cis-1 isomers were shown to have a significant catalytic role in selective hydrogenation reactions under mild conditions using cinnamic aldehyde as typical model reaction.

  2. Ionic ASi2N3 (A=Li, Na, K and Rb) stabilized by the covalent Si-N bonding: First-principles calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Huijun; Ren, Jiadong; Wu, Lailei; Zhang, Jingwu

    2017-01-01

    The structural, elastic and electronic properties of LiSi2N3 and its substitutions by Na, K and Rb were investigated through first-principles computations. The expansion of lattice parameters of ASi2N3 from Li, Na, K to Rb is found to be determined by the bond angle of Si-N1-Si, which suggests a possible way to improve the lithium ionic conductivity by substitutions. ASi2N3 (A=Li, Na, K and Rb) shows the similar elastic behaviors, while the electronic band gap gradually decreases from 5.1 to 3.4 eV from LiSi2N3 to RbSi2N3. Interestingly, the analysis of electronic structure, crystal orbital Hamiltonian populations and Bader charges shows that the covalence of Si-N bonding is critical for the stability of ASi2N3 phase. Among ASi2N3 phases, there is a relatively high ionicity in NaSi2N3; the Si-N bond strength in [Si2N3]- net for KSi2N3 and RbSi2N3 is comparable to LiSi2N3, but stronger than NaSi2N3.

  3. Accurate determination of the reaction course in HY2 <−> Y + YH (Y = O, S): detailed analysis of the covalent- to hydrogen-bonding transition.

    PubMed

    Varandas, A J C

    2013-08-15

    The accurate prediction of a bond-breaking/bond-forming reaction course is useful but very difficult. Toward this goal, a cost-effective multireference scheme (A. J. C. Varandas, J. Chem. Theory Comput. 2012, 8, 428) is tested that provides a generalization of the Hartree-Fock plus dispersion model for closed-shell interactions, and hence is based on the popular but largely untested idea of performing single point calculations with a high-level method at stationary points or along paths located using a lower level method. The energetics so calculated for the reaction HO2 <−> O + OH is predicted in excellent agreement with the experimental data, whereas the reaction path shows a scar at the onset of hydrogen-bonding: a weak van der Waals type minimum separated from the deep covalent well by a small barrier, all below the O + OH asymptote. The O-OH long-range interaction potential is also examined and possible implications in reaction dynamics discussed. Corresponding attributes for the reaction HS2 <−> S + SH are predicted, in good agreement with the best theoretical and experimental results. A perspective on the general utility of the approach is presented.

  4. Determination of volatile compounds in cider apple juices using a covalently bonded ionic liquid coating as the stationary phase in gas chromatography.

    PubMed

    Pello-Palma, Jairo; González-Álvarez, Jaime; Gutiérrez-Álvarez, María Dolores; Dapena de la Fuente, Enrique; Mangas-Alonso, Juan José; Méndez-Sánchez, Daniel; Gotor-Fernández, Vicente; Arias-Abrodo, Pilar

    2017-04-01

    A chromatographic method for the separation of volatile compounds in Asturian cider apple juices has been developed. For this separation purpose, a monocationic imidazolium-based ionic liquid bearing a reactive terminal iodine atom was synthesized by a quaternization-anion exchange chemical sequence. Next, the gas chromatography (GC) stationary phase was prepared by covalently linking the imidazolium monolith to the reactive silanol groups of the inner capillary wall at 70 °C. This coated GC column exhibited good thermal stability (290 °C), as well as good efficiency (2000 plates/m) in the separation of volatile compounds from Asturian apple cider juices, and was characterized using the Abraham solvation parameter model. The intra-day and inter-day precision of the chromatographic method was evaluated, obtaining relative standard deviations from 3.7 to 12.9% and from 7.4 to 18.0%, respectively. Furthermore, recoveries from 82.5 to 122% were achieved. Graphical Abstract Covalent bonding of an ionic liquid to inner column wall led to a great improvement of the separation efficiencies of stationary phases in gas chromatography.

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

    PubMed

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

    2016-02-05

    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.

  6. Autocatalytic association of proteins by covalent bond formation: a Bio Molecular Welding toolbox derived from a bacterial adhesin

    PubMed Central

    Bonnet, J.; Cartannaz, J.; Tourcier, G.; Contreras-Martel, C.; Kleman, J. P.; Morlot, C.; Vernet, T.; Di Guilmi, A. M.

    2017-01-01

    Unusual intramolecular cross-links present in adhesins from Gram-positive bacteria have been used to develop a generic process amenable to biotechnology applications. Based on the crystal structure of RrgA, the Streptococcus pneumoniae pilus adhesin, we provide evidence that two engineered protein fragments retain their ability to associate covalently with high specificity, in vivo and in vitro, once isolated from the parent protein. We determined the optimal conditions for the assembly of the complex and we solved its crystal structure at 2 Å. Furthermore, we demonstrate biotechnological applications related to antibody production, nanoassembly and cell-surface labeling based on this process we named Bio Molecular Welding. PMID:28252635

  7. 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.

  8. 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.

  9. 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.

  10. Single-walled carbon nanotube modification on photograft-polymerized nation films via covalent and ionic bonding.

    PubMed

    Yamaguchi, Yoshifumi; Nakashima, Naotoshi

    2009-01-01

    Acrylic acid (AAc) and diallyldimethylammonium chloride (DADMAc) were photograft-polymerized onto the surfaces of perfluorosulfonic acid (Nafion) membranes using 2,2'-azobis[N-(2-carboxyethyl)-2-methylpropionamide (ACMP) or Mohr's salt as a polymerization initiator. The degree of photografting changed from 1 wt% to 13.7 wt% depending on the experimental conditions (monomer, initiator and UV-light irradiation time). Shortened single-walled carbon nanotubes (s-SWNTs) prepared by a mixed acid treatment were immobilized in the grafted Nafion films by two different methods (methods A and B). Method A is a covalent-modification of the s-SWNTs with an acrylic acid (AAc)-photografted Nafion membrane in the presence of a diamine and a condensation reagent. Method B uses ion-complexation between the s-SWNTs with an anionic charge and a DADMAc-photografted Nafion film with a cationic charge. Based on the characterization of the hybrid materials by Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), it was found the s-SWNTs were immobilized into the photografted-Nafion films by both methods.

  11. Covalent Chemistry beyond Molecules.

    PubMed

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

    2016-03-16

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

  12. Shift from covalent to ionic bonding in Al2MoO(y) (y = 2-4) anion and neutral clusters.

    PubMed

    Mann, Jennifer E; Waller, Sarah E; Jarrold, Caroline Chick

    2013-11-21

    The electronic and molecular structures of Al2MoO(y) (y = 2-4) anion and neutral complexes were studied using anion photoelectron spectroscopy and density functional theory calculations. The spectra are broad, reflecting significant structural changes in the transition from anion to neutral, and the neutral electron affinities determined from the spectra are similar for all three species. The calculations suggest that the lowest energy isomers of the neutral clusters can be described as predominantly (Al(+))2[MoO(y)(-2)] ionic complexes, in which the Al(+) cations bond with O(2-) anions in a way that minimizes repulsion with the positively charged Mo center. The anion structures for all three complexes favor closer Mo-Al and Al-Al internuclear distances, with the extra negative charge distributed more evenly among all three metal centers. Energetically, the fully occupied 3s orbitals on the Al centers are lower than the Mo-local 4d-like orbitals and above the O-local 2p-like orbitals. In the case of Al2MoO2(-), there is direct Al-Al covalent bonding. The calculated spectroscopic parameters for these species are consistent with the observed spectra, though definitive assignments are not possible due to the broad, unresolved spectra observed and predicted.

  13. Multifunctional nanocomposites of lanthanide (Eu3+, Tb3+) complexes functionalized magnetic mesoporous silica nanospheres covalently bonded with polymer modified ZnO.

    PubMed

    Yan, Bing; Shao, Yan-Fei

    2013-07-14

    Methacrylic-group-modified ZnO nanoparticles (designated ZnO-MAA) prepared through the sol-gel process are copolymerized with 2-hydroxyethyl methacrylate (HEMA) to form ZnO-MAA-PHEMA hybrid system. ZnO-MAA-PHEMA unit is functionalized with 3-(triethoxysilyl)-propyl isocyanate (TEPIC) to form ZnO-MAA-PHEMA-Si hybrids, and then is incorporated with oleic acid-modified Fe3O4 nanoparticles by co-condensation of tetraethoxysilane (TEOS) and ZnO-MAA-PHEMA-Si. Subsequently, ZnO-polymer covalently bonded mesoporous silica nanospheres are assembled using cetyltrimethylammonium bromide (CTAB) surfactant as template. Furthermore, lanthanide (Eu(3+), Tb(3+)) complexes with nicotinic acid (NTA), isonicotinic acid (INTA) and 2-chloronicotinic (CNTA) are introduced by coordination bonds, resulting in the final multifunctional nanocomposites. The detailed physical characterization of these hybrids is discussed in detail. It reveals that they possess both magnetic and luminescent properties. Especially Eu(ZnO-MMS)(CNTA)3 and Tb(ZnO-MMS)(NTA)3 present high quantum yield values of 32.2% and 68.5%, respectively. The results will lay the foundation for further application in biomedical and biopharmaceutical fields.

  14. 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.

  15. 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.

  16. Structures of heterogeneous proton-bond dimers with a high dipole moment monomer: covalent vs electrostatic interactions.

    PubMed

    Fridgen, Travis D

    2006-05-11

    A number of calculated structures of heterogeneous proton-bound dimers containing monomers such as acetonitrile, cyanamide, vinylene carbonate, and propiolactone, which have high dipole moments, are presented. These proton-bound dimers are predicted to have a structural anomaly pertaining to the bond distances between the central proton and the basic sites on each of the monomers. The monomers with the high dipole moments also have the larger proton affinity and, on the basis of difference in proton affinities, it would be expected that the proton would be closer to this monomer than the one with the lower proton affinity. However, the proton is found to lie substantially closer to the monomer with the lower proton affinity in most cases, unless the difference in proton affinity is too large. Simply stated, the difference in proton affinities is smaller than the difference in the affinity to form an ion-dipole complex for the two monomers and it is the larger affinity for the high dipole moment monomer (which also has the higher proton affinity) to form an ion-dipole complex that is responsible for the proton lying closer to the low proton affinity monomer. The bond distances between the central proton and the monomers are found to be related to the difference in proton affinity. It is found, though, that the proton-bound dimers can be grouped into two separate groups, one where the proton-bound dimer contains a high dipole moment monomer and one group where the proton-bound dimer does not contain a high dipole moment monomer. From these plots it has been determined that a high dipole moment monomer is one that has a dipole moment greater than 2.9 D.

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

    NASA Astrophysics Data System (ADS)

    Zheng, Xiang-Jun; Jin, Lin-Pei

    2003-07-01

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

  18. 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

  19. 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.

  20. Multi‐Pathway Consequent Chemoselectivities of CpRuCl(PPh3)2/MeI‐Catalysed Norbornadiene Alkyne Cycloadditions

    PubMed Central

    Fang, De‐Cai; Xia, Shu‐Ya; Cheng, Rui‐Jiao

    2016-01-01

    Abstract Chemoselectivities of five experimentally realised CpRuCl(PPh3)2/MeI‐catalysed couplings of 7‐azabenzo‐norbornadienes with selected alkynes were successfully resolved from multiple reaction pathway models. Density functional theory calculations showed the following mechanistic succession to be energetically plausible: (1) CpRuI catalyst activation; (2) formation of crucial metallacyclopentene intermediate; (3) cyclobutene product (P2) elimination (ΔG Rel(RDS)≈11.9–17.6 kcal mol−1). Alternative formation of dihydrobenzoindole products (P1) by isomerisation to azametalla‐cyclohexene followed by subsequent CpRuI release was much less favourable (ΔG Rel(RDS)≈26.5–29.8 kcal mol−1). Emergent stereoselectivities were in close agreement with experimental results for reactions a, b, e. Consequent investigations employing dispersion corrections similarly support the empirical findings of P1 dominating in reactions c and d through P2→P1 product transformations as being probable (ΔG≈25.3–30.1 kcal mol−1). PMID:27620274

  1. 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.

  2. Hybrids of [TSAO-T]-[foscarnet]: The first conjugate of foscarnet with a non-nucleoside reverse transcriptase inhibitor through a labile covalent ester bond.

    PubMed

    Velázquez, Sonsoles; Lobatón, Esther; De Clercq, Erik; Koontz, Dianna L; Mellors, John W; Balzarini, Jan; Camarasa, María-José

    2004-06-17

    This paper describes the first example of combination of non-nucleoside reverse transcriptase inhibitors such as TSAO derivatives and foscarnet (PFA) in a single molecule through a labile covalent ester bond. The essential criteria in the design of these hybrids [TSAO-T]-[PFA] was to explore if the conjugation of foscarnet with the highly lipophilic TSAO derivative may facilitate the penetration of the conjugates through the cell membrane and if the hybrids escape extracellular hydrolysis and regenerate the parent inhibitors intracellulary. Several [TSAO-T]-[PFA] conjugates proved markedly inhibitory to HIV-1. Some of them also showed potent activity against PFA-resistant HIV-1 strains but fewer had detectable inhibitory activity against TSAO-resistant HIV-1 strains. These results indicated a pivotal role of the TSAO component of the hybrid but not the PFA component in the activity of the conjugates. Moreover, stability studies of the [TSAO-T]-[PFA] conjugates demonstrated that the compounds were stable in PBS whereas some of the conjugates regenerated the parent inhibitors in extracts from CEM cells.

  3. Constructing monocrystalline covalent organic networks by polymerization

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  4. Sidewall Covalent Functionalization of Single Wall Carbon Nanotubes through C-N Bond Forming Reactions of Fluoronanotubes with Urea, Guanidine and Thiourea (Preprint)

    DTIC Science & Technology

    2007-04-01

    Journal article preprint 5a. CONTRACT NUMBER FA8650-05-D-1912-T06 5b. GRANT NUMBER 4. TITLE AND SUBTITLE SIDEWALL COVALENT FUNCTIONALIZATION OF...reactions15-17. These results have facilitated the use of the other substituted amino compounds, such as aminoalcohols, aminothiols, aminoacids , and

  5. 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.

  6. Valence bond/broken symmetry analysis of the exchange coupling constant in copper(II) dimers. Ferromagnetic contribution exalted through combined ligand topology and (singlet) covalent-ionic mixing.

    PubMed

    Onofrio, Nicolas; Mouesca, Jean-Marie

    2010-05-27

    In this paper we aim at presenting a full-VB (valence-bond) analysis of the DFT broken symmetry (BS) exchange coupling constant J(BS). We extend Kahn and Briat's "two sites-two electrons" VB original formalism (Kahn, O.; Briat, B. J. Chem. Soc. Farady Trans. II, 1976, 72, 268) by taking into account the covalent-ionic singlet state mixing, here translated into intersite magnetic orbital delocalization. In this way, two explicit contributions to the magnetic orbital overlap appear, one from the purely covalent state, and the other one from the covalent-ionic mixing. This scheme allows us to relax the strict orthogonality constraint of Kahn and Briat's chemically heuristic model resulting into ferromagnetism. Moreover, we show how DFT-BS calculations applied to various copper(II) dimers yield effective parameters that can be injected into the full-VB model, allowing for a breaking down of J(BS) into various contributions, one of which being either ferromagnetic or antiferromagnetic depending on the bridging ligand topology. Two classes of systems emerge from this analysis and the exceptional ferromagnetic coupling property of the "end-on" azido-bridged copper dimer is especially emphasized.

  7. Revealing Non-Covalent Interactions

    PubMed Central

    Johnson, Erin R.; Keinan, Shahar; Mori-Sánchez, Paula; Contreras-García, Julia; Cohen, Aron J.; Yang, Weitao

    2010-01-01

    Molecular structure does not easily identify the intricate non-covalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect non-covalent interactions in real space, based on the electron density and its derivatives. Our approach reveals underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of non-bonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands. PMID:20394428

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

    SciTech Connect

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

    2006-09-28

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

  9. Electro-oxidation of ethanol on PtRu/C electrocatalysts prepared from (η-C 2H 4)(Cl)Pt(μCl) 2Ru(Cl)(η 3,η 3-C 10H 16)

    NASA Astrophysics Data System (ADS)

    Spinacé, E. V.; Neto, A. O.; Linardi, M.

    PtRu/C electrocatalysts were prepared by impregnation of the complex (η-C 2H 4)(Cl)Pt(μCl) 2Ru(Cl)(η 3,η 3-C 10H 16) on to a carbon support. The complex/support was subjected to different thermal treatments and tested for ethanol electro-oxidation using the thin porous coating electrode technique. The electrocatalysts were characterized by transmission electron microscopy (TEM), EDAX and cyclic voltammetry. The electrocatalyst treated under hydrogen flow and subjected to an oxidative thermal treatment had a superior performance to that of a commercial catalyst, which could be attributed to the better control of the metallic platinum and oxidized ruthenium species on the PtRu nanoparticle surface.

  10. 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.

  11. In vitro and in vivo antitumor activity of a novel carbonyl ruthenium compound, the ct-[RuCl(CO)(dppb)(bipy)]PF-6[dppb=1,4-bis(diphenylphosphine)butane and bipy=2,2'-bipyridine].

    PubMed

    Carnizello, Andréa P; Barbosa, Marília I F; Martins, Monize; Ferreira, Natália H; Oliveira, Pollyanna F; Magalhães, Geórgia M; Batista, Alzir A; Tavares, Denise C

    2016-11-01

    This study performed in vitro and in vivo biological assays of the ruthenium (II) compound ct-[RuCl(CO)(dppb)(bipy)]PF6 (where, dppb=1,4-bis(diphenylphosphine)butane and bipy=2,2'-bipyridine). The cytotoxic activity of this compound was evaluated against different tumor cell lines (HeLa, human cervical adenocarcinoma; MCF7, human breast adenocarcinoma; MO59J, human glioblastoma; HepG2, hepatocellular carcinoma and B16F10, murine melanoma) and healthy cell line (V79, Chinese hamster lung fibroblasts), by XTT (sodium 2,3'-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)-carbonyl]-3,4-tetrazolium-bis(4-methoxy-6-nitro)benzene-sulfonic acid hydrate) method. A syngeneic murine melanoma tumor model (B16F10) was used to evaluate its antitumor activity. Additionally, experiments were performed to assess the interactions with ctDNA (calf thymus DNA) and BSA (bovine serum albumin). The results showed that ct-[RuCl(CO)(dppb)(bipy)]PF6 was cytotoxic against all tumor cell lines tested. Furthermore, the compound was more effective against tumor cells compared to the normal cell line, indicating selectivity, especially in B16F10 cells. Significant tumor growth reduction was observed in animals treated with the compound compared to the untreated control. Histopathological analysis of tumor tissue revealed a significant reduction of mitosis in animals treated with the compound compared to the untreated control. In the ctDNA and BSA interaction experiments, the compound in study showed weak interactions with ctDNA and hydrophobic interactions with BSA. The ruthenium compound investigated showed promising results in in vitro and in vivo biological assays.

  12. B-H bond activation using an electrophilic metal complex: insights into the reaction pathway.

    PubMed

    Kumar, Rahul; Jagirdar, Balaji R

    2013-01-07

    A highly electrophilic ruthenium center in the [RuCl(dppe)(2)][OTf] complex brings about the activation of the B-H bond in ammonia borane (H(3)N·BH(3), AB) and dimethylamine borane (Me(2)HN·BH(3), DMAB). At room temperature, the reaction between [RuCl(dppe)(2)][OTf] and AB or DMAB results in trans-[RuH(η(2)-H(2))(dppe)(2)][OTf], trans-[RuCl(η(2)-H(2))(dppe)(2)][OTf], and trans-[RuH(Cl)(dppe)(2)], as noted in the NMR spectra. Mixing the ruthenium complex and AB or DMAB at low temperature (198/193 K) followed by NMR spectral measurements as the reaction mixture was warmed up to room temperature allowed the observation of various species formed enroute to the final products that were obtained at room temperature. On the basis of the variable-temperature multinuclear NMR spectroscopic studies of these two reactions, the mechanistic insights for B-H bond activation were obtained. In both cases, the reaction proceeds via an η(1)-B-H moiety bound to the metal center. The detailed mechanistic pathways of these two reactions as studied by NMR spectroscopy are described.

  13. Theoretical investigation of paramagnetic NMR shifts in transition metal acetylacetonato complexes: analysis of signs, magnitudes, and the role of the covalency of ligand-metal bonding.

    PubMed

    Pritchard, Ben; Autschbach, Jochen

    2012-08-06

    Ligand chemical shifts are calculated and analyzed for three paramagnetic transition metal tris-acetylacetonato (acac) complexes, namely high-spin Fe(III) and Cr(III), and low-spin Ru(III), using scalar relativistic density functional theory (DFT). The signs and magnitudes of the paramagnetic NMR ligand chemical shifts are directly related to the extent of covalent acac oxygen-to-metal σ donation involving unoccupied metal valence d(σ) acceptor orbitals. The role of delocalization of metal-centered spin density over the ligand atoms plays a minor secondary role. Of particular interest is the origin of the sign and magnitude of the methyl carbon chemical shift in the acac ligands, and the role played by the DFT delocalization error when calculating such shifts. It is found that the α versus β spin balance of oxygen σ donation to metal valence d acceptor orbitals is responsible for the sign and the magnitude of the ligand methyl carbon chemical shift. A problematic case is the methyl carbon shift of Fe(acac)(3). Most functionals produce shifts in excess of 1400 ppm, whereas the experimental shift is approximately 279 ppm. Range-separated hybrid functionals that are optimally tuned for Fe(acac)(3) based on DFT energetic criteria predict a lower limit of about 2000 ppm for the methyl carbon shift of the high-spin electronic configuration. Since the experimental value is based on a very strongly broadened signal it is possibly unreliable.

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

    NASA Astrophysics Data System (ADS)

    Li, Yajuan; Yan, Bing; Li, Ying

    2010-04-01

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

  15. 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.

  16. Chalcohalide glasses: The effect of covalent versus ionic bonding in (CuI)0.6(Sb2Se3)0.4

    NASA Astrophysics Data System (ADS)

    Salmon, Philip S.; Xin, Shuqin

    2002-02-01

    The Cu-Cu partial structure factor and related difference functions were measured for the four-component chalcohalide glass (CuI)0.6(Sb2Se3)0.4 by using the method of isotopic substitution in neutron diffraction. The Cu-Cu nearest-neighbors reside at a large distance of 4.06(3) Å, by contrast with metal chalcogenide glasses of high modifier content, and the corresponding coordination number is 1.9(3). Local structural motifs centered on Cu and Sb are deduced using a scheme where there is exclusive heteropolar bonding but where Cu-Sb and Se-I contacts are disallowed.

  17. Influence of adduct stereochemistry and hydrogen-bonding solvents on photoinduced charge transfer in a covalent benzo[a]pyrene diol epoxide-nucleoside adduct on picosecond time scales

    SciTech Connect

    O'Connor, D. ); Shafirovich, V.Y.; Geacintov, N.E. )

    1994-09-29

    Photoinduced electron transfer occurs with different rate constants upon picosecond laser pulse excitation of the stereoisomeric (+)-trans- and (-)-cis-benzo[a]pyrene diol epoxide-N[sup 2]-deoxyguanosine covalently linked adducts (BPDE-N[sup 2]-dG, bond with 10S absolute configuration) in polar solvents (N,N[prime]-dimethylformamide (DMF), and the hydrogen-bonding liquids H[sub 2]O, D[sub 2]O, formamide (FA), and N-methylformamide (NMF)). In the case of (+)-trans-BPDE-dG in DMF, photoinduced electron transfer occurs in the normal Marcus region, from dG to the pyrenyl residue singlet with a rate constant k[sub s] = (9.1 [+-] 0.9) x 10[sup 9] s[sup [minus]1], which is followed by a slower recombination (k[sub r] = (1.8 + 0.5) x 10[sup 9] s[sup [minus]1]) in the inverted Marcus region. In the cis-stereoisomeric adduct, both rate constants are enhanced by a factor of approximately 5. The presence of the hydrogen-bonding network in NMF and FA exerts opposite effects on these rate constants, decreasing k[sub s] and increasing k[sub r] by factors of 2-5. In aqueous solutions these effects are even more pronounced, and radical ions are not observed since k[sub r] [much gt] k[sub s]. A kinetic isotope effect on the delay of the pyrenyl singlets in H[sub 2]O and D[sub 2]O (k[sub s](H[sub 2]O)/k[sub s](D[sub 2]O) = 1.3-1.5) suggests that a proton-coupled electron transfer mechanism may be operative in aqueous solutions. 51 refs., 10 figs., 2 tabs.

  18. Covalently Linked Tandem Lesions in DNA

    PubMed Central

    Patrzyc, Helen B.; Dawidzik, Jean B.; Budzinski, Edwin E.; Freund, Harold G.; Wilton, John H.; Box, Harold C.

    2013-01-01

    Reactive oxygen species (ROS) generate a type of DNA damage called tandem lesions, two adjacent nucleotides both modified. A subcategory of tandem lesions consists of adjacent nucleotides linked by a covalent bond. Covalently linked tandem lesions generate highly characteristic liquid chromotography-tandem mass spectrometry (LC-MS/MS) elution profiles. We have used this property to comprehensively survey X-irradiated DNA for covalently linked tandem lesions. A total of 15 tandem lesions were detected in DNA irradiated in deoxygenated aqueous solution, five tandem lesions were detected in DNA that was irradiated in oxygenated solution. PMID:23106212

  19. Covalent dependence of octahedral rotations in orthorhombic perovskite oxides.

    PubMed

    Cammarata, Antonio; Rondinelli, James M

    2014-09-21

    The compositional dependence of metal-oxygen BO6 octahedral distortions, including bond elongations and rotations, is frequently discussed in the ABO3 perovskite literature; structural distortions alleviate internal stresses driven by under- or over-coordinated bond environments. Here we identify the dependence of octahedral rotations from changes in metal-oxygen bond covalency in orthorhombic perovskites. Using density functional theory we formulate a covalency metric, which captures both the real and k-space interactions between the magnitude and sense, i.e., in-phase or out-of-phase, octahedral rotations, to explore the link between the ionic-covalent Fe-O bond and the interoctahedral Fe-O-Fe bond angles in Pbnm ferrates. Our survey finds that the covalency of the metal-oxygen bond is correlated with the rotation amplitude: We find the more covalent the Fe-O bond, the less distorted is the structure and the more important the long-range inter-octahedral (Fe-O-Fe bond angle) interactions. Finally, we show how to indirectly tune the B-O bond covalency by A-cation induced BO6 rotations independent of ionic size, facilitating design of targeted bonding interactions in complex perovskites.

  20. 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

  1. Covalent Metal-Metal-Bonded Mn4 Tetrahedron Inscribed within a Four-Coordinate Manganese Cubane Cluster, As Evidenced by Unexpected Temperature-Independent Diamagnetism.

    PubMed

    Vaddypally, Shivaiah; Jovinelli, Daniel J; McKendry, Ian G; Zdilla, Michael J

    2017-03-17

    The electronic structures of the manganese(IV) cubane cluster Mn(μ3-N(t)Bu)4(N(t)Bu)4 (1) and its one-electron-oxidized analogue, the 3:1 Mn(IV)/Mn(V) cluster [Mn(μ3-N(t)Bu)4(N(t)Bu)4](+)[PF6](-) (1(+)[PF6]), are described. The S = 0 spin quantum number of 1 is explained by a diamagnetic electronic structure where all metal-based d electrons are paired in Mn-Mn bonding orbitals. Temperature- and power-dependent studies of the S = (1)/2 electron paramagnetic resonance signal of 1(+) are consistent with an electronic structure described as a delocalized one-electron radical.

  2. Atomic covalent functionalization of graphene.

    PubMed

    Johns, James E; Hersam, Mark C

    2013-01-15

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

  3. The atom, the molecule, and the covalent organic framework.

    PubMed

    Diercks, Christian S; Yaghi, Omar M

    2017-03-03

    Just over a century ago, Lewis published his seminal work on what became known as the covalent bond, which has since occupied a central role in the theory of making organic molecules. With the advent of covalent organic frameworks (COFs), the chemistry of the covalent bond was extended to two- and three-dimensional frameworks. Here, organic molecules are linked by covalent bonds to yield crystalline, porous COFs from light elements (boron, carbon, nitrogen, oxygen, and silicon) that are characterized by high architectural and chemical robustness. This discovery paved the way for carrying out chemistry on frameworks without losing their porosity or crystallinity, and in turn achieving designed properties in materials. The recent union of the covalent and the mechanical bond in the COF provides the opportunity for making woven structures that incorporate flexibility and dynamics into frameworks.

  4. 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.

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

    PubMed

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

    2011-10-01

    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.

  6. 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

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

    PubMed

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

    2005-07-21

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

  8. Water-medium and solvent-free organic reactions over a bifunctional catalyst with Au nanoparticles covalently bonded to HS/SO3H functionalized periodic mesoporous organosilica.

    PubMed

    Zhu, Feng-Xia; Wang, Wei; Li, He-Xing

    2011-08-03

    An operationally simple approach for the preparation of a new class of bifunctional Au nanoparticle-acid catalysts has been developed. In situ reduction of Au(3+) with HS-functionalized periodic mesoporous organosilicas (PMOs) creates robust, fine Au nanoparticles and concomitantly produces a sulfonic acid moiety strongly bonded to PMOs. Characterizations of the nanostructures reveal that Au nanoparticles are formed with uniformed, narrow size distribution around 1-2 nm, which is very critical for essential catalytic activities. Moreover, the Au nanoparticles are mainly attached onto the pore surface rather than onto the outer surface with ordered mesoporous channels, allowing for maximal exposure to reaction substrates while minimizing Au nanoparticle leaching. Their higher S(BET), V(P), and D(P) than either the Au-HS-PMO(Et) or the Au/SO(3)H-PMO(Et) render the catalyst with comparably even higher catalytic efficiency than its homogeneous counterparts. Furthermore, the unique amphiphilic compartment of the Au-HS/SO(3)H-PMO(Et) nanostructures enables organic reactions to proceed efficiently in a pure aqueous solution without using any organic solvents or even without water. As demonstrated experimentally, remarkably, the unique bifunctional Au-HS/SO(3)H-PMO(Et) catalyst displays higher efficiencies in promoting water-medium alkyne hydration, intramolecular hydroamination, styrene oxidation, and three-component coupling reactions and even the solvent-free alkyne hydration process than its homogeneous catalysts. The robust catalyst can be easily recycled and used repetitively at least 10 times without loss of catalytic efficiency. These features render the catalyst particularly attractive in the practice of organic synthesis in an environmentally friendly manner.

  9. Novel photofunctional multicomponent rare earth (Eu3+, Tb3+, Sm3+ and Dy3+) hybrids with double cross-linking siloxane covalently bonding SiO2/ZnS nanocomposite.

    PubMed

    Yan, Bing; Zhao, Yan; Li, Ya-Juan

    2011-01-01

    Zinc sulfide (ZnS) quantum dot is modified with 3-mercaptopropyltrimethoxysilane (MPTMS) to obtain MPTMS functionalized SiO(2)/ZnS nanocomposite. Novel rare earth/inorganic/organic hybrid materials are prepared by using 3-(triethoxysilyl)-propyl isocyanate (TESPIC) as an organic bridge molecule that can both coordinate to rare earth ions (Eu(3+), Tb(3+), Sm(3+) and Dy(3+)) and form an inorganic Si-O-Si network with SiO(2) ZnS nanocomposite after cohydrolysis and copolycondensation through a sol-gel process. These multicomponent hybrids with double cross-linking siloxane (TESPIC-MPTMS) covalently bonding SiO(2)/ZnS and assistant ligands (Phen = 1,10-phenanthroline, Bipy = 2,2'-bipyridyl) are characterized and especially the photoluminescence properties of them are studied in detail. The luminescent spectra of the hybrids show the dominant excitation of TESPIC-MPTMS-SiO(2)/ZnS unit and the unique emission of rare earth ions, suggesting that TESPIC-MPTMS-SiO(2)/ZnS unit behaves as the main energy donor and effective energy transfer take place between it and rare earth ions. Besides, the luminescent performance of Bipy-RE-TESPIC-MPTM-SiO(2)/ZnS hybrids are superior to that of Phen-RE-TESPIC-MPTMS-SiO(2)/ZnS ones (RE=Eu, Tb, Sm, Dy), which reveals that Bipy or Phen only act as structural ligand within the hybrid systems.

  10. 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

    2016-04-06

    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.

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

    SciTech Connect

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

    1992-09-01

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

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

    SciTech Connect

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

    1992-01-01

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

  13. Dynamic exchange between the covalent and dative metal-metal bonded isomers of the heterodinuclear complex (NiPd(CNMe) sub 3 (dppm) sub 2 )(PF sub 6 ) sub 2 by sup 31 P l brace sup 1 H r brace NOESY

    SciTech Connect

    Ni, Jinfeng; Kubiak, C.P. )

    1990-10-17

    The first quantitative dynamic study by {sup 31}P({sup 1}H) Nuclear Overhauser enhancement spectroscopy (NOESY) is described herein. The exchange between a pair of isomers of the complex (NiPd(CNMe){sub 3}(dppm){sub 2})(PF{sub 6}){sub 2} that differ in their mode of metal-metal bonding has been measured. The {sup 31}P({sup 1}H) NOSEY for this complex is ascribed to the relatively slow interconversion between the covalent and dative Ni-Pd bonded isomers. 13 refs., 2 figs., 2 tabs.

  14. Remendable Polymeric Materials Using Reversible Covalent Bonds

    DTIC Science & Technology

    2008-12-01

    Novel Polymeric Dienes and Dienophiles: Synthesis of Reversibly Cross- Linked Elastomers . Macromolecules, 35, 7246- 7253. Goiti, E., M. Huglin, and J...Materials and Nanotechnology in Engineering. Edited by Du, 6423, 112. Liu, Y., and Y. Chen, 2007: Thermally Reversible Cross- Linked Polyamides with...High Toughness and Self- Repairing Ability from Maleimide- and Furan- Functionalized Aromatic Polyamides . Macromolecular Chemistry and Physics, 208

  15. Protonated alcohols are examples of complete charge-shift bonds.

    PubMed

    Anderson, Peter; Petit, Alban; Ho, Junming; Mitoraj, Mariusz Pawel; Coote, Michelle L; Danovich, David; Shaik, Sason; Braïda, Benoît; Ess, Daniel H

    2014-11-07

    Accurate gas-phase and solution-phase valence bond calculations reveal that protonation of the hydroxyl group of aliphatic alcohols transforms the C-O bond from a principally covalent bond to a complete charge-shift bond with principally "no-bond" character. All bonding in this charge-shift bond is due to resonance between covalent and ionic structures, which is a different bonding mechanism from that of traditional covalent bonds. Until now, charge-shift bonds have been previously identified in inorganic compounds or in exotic organic compounds. This work showcases that charge-shift bonds can occur in common organic species.

  16. Bulk modulus for polar covalent crystals

    PubMed Central

    Xu, Bo; Wang, Qianqian; Tian, Yongjun

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed

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

    2015-04-10

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

  19. 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)

  20. Covalent polymers of water.

    PubMed

    O'konski, C T

    1970-05-29

    A new covalent structural scheme for water polymers is proposed. The observed properties of "polywater" are related to the structures of the suggested homologous series of molecules. Mechanisms of formation are suggested.

  1. 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…

  2. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.

    PubMed

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-02-21

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular

  3. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

    PubMed Central

    2017-01-01

    Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition

  4. 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.

  5. Covalently linked organic networks

    NASA Astrophysics Data System (ADS)

    Tsotsalas, Manuel; Addicoat, Matthew

    2015-02-01

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

  6. Semiempirical formulae for elastic moduli and brittleness of diamondlike and zinc-blende covalent crystals

    SciTech Connect

    Kamran, Sami; Chen, Liang; Chen, Kuiying

    2008-03-01

    In the present work, semiempirical formulae for both bulk B and shear G moduli of diamondlike and zinc-blende covalent crystals are elaborated in terms of bond length and ionicity fraction of the bonding. The resulting expressions can be applied to a broad selection of covalent materials and their modulus predictions are in good agreement with the experimental data and those from ab initio calculations. Furthermore, the correlation between the ratio G/B and the aforementioned bonding parameters was investigated. The analysis of this relationship demonstrates that compared to the ionicity fraction, the bond length is the predominant parameter responsible for the brittle features of covalent materials.

  7. 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.

  8. 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)

  9. Molecular orbital calculations on atomic structures of Si-based covalent amorphous ceramics

    SciTech Connect

    Matsunaga, K.; Matsubara, H.

    1999-07-01

    The authors have performed ab-initio Hartree-Fock molecular orbital calculations of local atomic structures and chemical bonding states in Si-N covalent amorphous ceramics. Solute elements such as boron, carbon and oxygen were considered in the Si-N network, and the bonding characteristics around the solute elements were analyzed. When a nitrogen atom is substituted by a carbon atom, it was found that Si-C bonds reinforce the Si-N network due to strong covalency.

  10. 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.

  11. Non-Covalent Derivatives: Cocrystals and Eutectics.

    PubMed

    Stoler, Emily; Warner, John C

    2015-08-14

    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.

  12. 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

  13. 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.

  14. Dynamic covalent chemistry approaches toward macrocycles, molecular cages, and polymers.

    PubMed

    Jin, Yinghua; Wang, Qi; Taynton, Philip; Zhang, Wei

    2014-05-20

    The current research in the field of dynamic covalent chemistry includes the study of dynamic covalent reactions, catalysts, and their applications. Unlike noncovalent interactions utilized in supramolecular chemistry, the formation/breakage of covalent bonding has slower kinetics and usually requires the aid of a catalyst. Catalytic systems that enable efficient thermodynamic equilibrium are thus essential. In this Account, we describe the development of efficient catalysts for alkyne metathesis, and discuss the application of dynamic covalent reactions (mainly imine, olefin, and alkyne metathesis) in the development of organic functional materials. Alkyne metathesis is an emerging dynamic covalent reaction that offers robust and linear acetylene linkages. By introducing a podand motif into the catalyst ligand design, we have developed a series of highly active and robust alkyne metathesis catalysts, which, for the first time, enabled the one-step covalent assembly of ethynylene-linked functional molecular cages. Imine chemistry and olefin metathesis are among the most well-established reversible reactions, and have also been our main synthetic tools. Various shape-persistent macrocycles and covalent organic polyhedrons have been efficiently constructed in one-step through dynamic imine chemistry and olefin metathesis. The geometrical features and solubilizing groups of the building blocks as well as the reaction kinetics have significant effect on the outcome of a covalent assembly process. More recently, we explored the orthogonality of imine and olefin metatheses, and successfully synthesized heterosequenced macrocycles and molecular cages through one-pot orthogonal dynamic covalent chemistry. In addition to discrete molecular architectures, functional polymeric materials can also be accessed through dynamic covalent reactions. Defect-free solution-processable conjugated polyaryleneethynylenes and polydiacetylenes have been prepared through alkyne metathesis

  15. Electron tunneling through covalent and noncovalent pathways in proteins

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

  16. Hybrid materials based on novel 2D lanthanide coordination polymers covalently bonded to amine-modified SBA-15 and MCM-41: assembly, characterization, structural features, thermal and luminescence properties.

    PubMed

    Wang, Jun; Dou, Wei; Kirillov, Alexander M; Liu, Weisheng; Xu, Cailing; Fang, Ran; Yang, Lizi

    2016-11-22

    Three novel 2D coordination polymers [Tb2(μ4-L)2(μ-HL)(μ-HCOO)(DEF)]n (Tb-L), [Eu(μ4-L)(L)(H2O)2]n (Eu-L), and [Nd(μ4-L)(L)(H2O)2]n (Nd-L) were assembled from the corresponding lanthanide(iii) nitrates and 5 methoxy-(4-benzaldehyde)-1,3-benzenedicarboxylic acid (H2L) as a main multifunctional building block bearing carboxylate and aldehyde functional groups, using H2O/DEF {DEF = N,N-diethylformamide} as a reaction medium. The obtained coordination polymers were isolated as stable microcrystalline solids and fully characterized by elemental analysis, FT-IR spectroscopy, TGA, BET, PXRD, and single-crystal X-ray diffraction methods. Their structures feature intricate 2D metal-organic networks, which were topologically classified as underlying layers with the 4,6L26 (for Tb-L) or sql (for Eu-L and Nd-L) topologies. Besides, a novel series of mesoporous hybrid materials wherein the Tb-L, Eu-L, or Nd-L coordination polymers are covalently grafted into the amine-functionalized SBA-15-NH2 or MCM-41-NH2 matrices (via the formation of Schiff-base groups) was also synthesized and fully characterized. These hybrid materials show high thermal and photoluminescence stability, as well as remarkable chemical resistance to boiling water, and acidic or alkaline medium. Luminescent properties of the parent coordination polymers and derived hybrid materials are investigated in detail, showing that the latter combine the luminescent characteristics (intense green or red emissions and excellent stability) of lanthanide coordination polymers and structural features of ordered mesoporous silica molecular sieves. Moreover, light emitting devices were assembled, by coating the hybrid materials onto the surface of UV-LED bulbs, and showed excellent light emitting properties.

  17. 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

  18. 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.

  19. Colloidal Covalent Organic Frameworks

    PubMed Central

    2017-01-01

    Covalent organic frameworks (COFs) are two- or three-dimensional (2D or 3D) polymer networks with designed topology and chemical functionality, permanent porosity, and high surface areas. These features are potentially useful for a broad range of applications, including catalysis, optoelectronics, and energy storage devices. But current COF syntheses offer poor control over the material’s morphology and final form, generally providing insoluble and unprocessable microcrystalline powder aggregates. COF polymerizations are often performed under conditions in which the monomers are only partially soluble in the reaction solvent, and this heterogeneity has hindered understanding of their polymerization or crystallization processes. Here we report homogeneous polymerization conditions for boronate ester-linked, 2D COFs that inhibit crystallite precipitation, resulting in stable colloidal suspensions of 2D COF nanoparticles. The hexagonal, layered structures of the colloids are confirmed by small-angle and wide-angle X-ray scattering, and kinetic characterization provides insight into the growth process. The colloid size is modulated by solvent conditions, and the technique is demonstrated for four 2D boronate ester-linked COFs. The diameter of individual COF nanoparticles in solution is monitored and quantified during COF growth and stabilization at elevated temperature using in situ variable-temperature liquid cell transmission electron microscopy imaging, a new characterization technique that complements conventional bulk scattering techniques. Solution casting of the colloids yields a free-standing transparent COF film with retained crystallinity and porosity, as well as preferential crystallite orientation. Collectively this structural control provides new opportunities for understanding COF formation and designing morphologies for device applications. PMID:28149954

  20. 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).

  1. An equation to calculate internuclear distances of covalent, ionic and metallic lattices.

    PubMed

    Lang, Peter F; Smith, Barry C

    2015-02-07

    This paper briefly describes the many different sets of ionic and covalent radii available. A simple model of ionic and covalent bonding is proposed and an equation to calculate internuclear distances of covalent, ionic and metallic lattices is described. Derivation of covalent radii and the use of a proposed model of metallic structure and bonding to derive ionic radii are discussed. A brief summary of the development of the simple equation for calculating internuclear distances of ionic compounds is provided. Values of internuclear distances calculated from the derived radii are compared to observed values and give good agreement, showing strong evidence that ionic and covalent radii are not additive and electronegativity influences bonding and internuclear distances. Ionic radii derived from the proposed model are applied to calculate lattice energies which agree well with literature values/values calculated by the Born Haber cycle. Work functions of transition metals are shown to be simple inverse functions of the derived radii. Internuclear distances of inter-metallic compounds are calculated and compared with observed values to show good agreement. This work shows that the proposed model of metallic structure complements the band theory and expressions introduced in this work can be used to predict ionic and covalent bond lengths (in different environments) that have not yet been determined as well as being a method for resolving bond type.

  2. 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.

  3. Nucleic Acid Duplexes Incorporating a Dissociable Covalent Base Pair

    NASA Astrophysics Data System (ADS)

    Gao, Kui; Orgel, Leslie E.

    1999-12-01

    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.

  4. Hydrogen multicentre bonds.

    PubMed

    Janotti, Anderson; Van de Walle, Chris G

    2007-01-01

    The concept of a chemical bond stands out as a major development in the process of understanding how atoms are held together in molecules and solids. Lewis' classical picture of chemical bonds as shared-electron pairs evolved to the quantum-mechanical valence-bond and molecular-orbital theories, and the classification of molecules and solids in terms of their bonding type: covalent, ionic, van der Waals and metallic. Along with the more complex hydrogen bonds and three-centre bonds, they form a paradigm within which the structure of almost all molecules and solids can be understood. Here, we present evidence for hydrogen multicentre bonds-a generalization of three-centre bonds-in which a hydrogen atom equally bonds to four or more other atoms. When substituting for oxygen in metal oxides, hydrogen bonds equally to all the surrounding metal atoms, becoming fourfold coordinated in ZnO, and sixfold coordinated in MgO. These multicentre bonds are remarkably strong despite their large hydrogen-metal distances. The calculated local vibration mode frequency in MgO agrees with infrared spectroscopy measurements. Multicoordinated hydrogen also explains the dependence of electrical conductivity on oxygen partial pressure, resolving a long-standing controversy on the role of point defects in unintentional n-type conductivity of ZnO (refs 8-10).

  5. An azine-linked covalent organic framework.

    PubMed

    Dalapati, Sasanka; Jin, Shangbin; Gao, Jia; Xu, Yanhong; Nagai, Atsushi; Jiang, Donglin

    2013-11-20

    Condensation of hydrazine with 1,3,6,8-tetrakis(4-formylphenyl)pyrene under solvothermal conditions yields highly crystalline two-dimensional covalent organic frameworks. The pyrene units occupy the vertices and the diazabutadiene (-C═N-N═C-) linkers locate the edges of rohmbic-shaped polygon sheets, which further stack in an AA-stacking mode to constitute periodically ordered pyrene columns and one-dimensional microporous channels. The azine-linked frameworks feature permanent porosity with high surface area and exhibit outstanding chemical stability. By virtue of the pyrene columnar ordering, the azine-linked frameworks are highly luminescent, whereas the azine units serve as open docking sites for hydrogen-bonding interactions. These synergestic functions of the vertices and edge units endow the azine-linked pyrene frameworks with extremely high sensitivity and selectivity in chemosensing, for example, the selective detection of 2,4,6-trinitrophenol explosive. We anticipate that the extension of the present azine-linked strategy would not only increase the structural diversity but also expand the scope of functions based on this highly stable class of covalent organic frameworks.

  6. Covalent Organic Frameworks for CO2 Capture.

    PubMed

    Zeng, Yongfei; Zou, Ruqiang; Zhao, Yanli

    2016-04-20

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  8. Extracting covalent and ionic structures from usual delocalized wave functions: the electron-expansion methodology.

    PubMed

    Papanikolaou, P; Karafiloglou, P

    2008-09-18

    We present easily programmable expansions, allowing the calculation of the weights of local covalent and ionic structures of a chemical bond from usual delocalized wave functions; they are obtained in the framework of the electron-expansion methodology, in which the hole conditions (involved by definition in a covalent or ionic structure) are expanded in terms involving only electrons. From the derived relations, true for both HF and correlated levels, one can also express the covalency/ionicity and the localization of a usual two-electron two-center (2e/2c) bond in terms of electronic populations. The three-electron populations are crucial for bond localization. On the contrary, in 2e/2c bonding, and particularly in Charge-Shift bonds (which show enhanced covalent-ionic interactions) although the three-electron populations can be non-negligible, they are not important for the covalency/ionicity of these bonds. Numerical applications and discussion are given for correlated MO wave functions of butadiene, hexatriene, and pyrrole molecules on the basis of both natural atomic orbitals (NAOs) (orthogonal orbitals) and pre-NAOs (nonorthogonal orbitals).

  9. 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.

  10. 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

  11. 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.

  12. Hydrogen bonding. Part 25. The nature of the hydrogen bond in hydroxytropenylium chloride (tropone hydrochloride)

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; Cross, Joan E.; Toccalino, Patricia L.

    1988-08-01

    Hydroxytropenylium iodide and bromide contain normal electrostatic OH⋯X - hydrogen bonds. Hydroxytropenylium chloride, however, contains a hydrogen bond intermediate between the normal electrostatic type and the very strong covalent type, similar to the hydrogen bonds found in choline fluoride or the Type I C∞v hydrogen dihalide ions. Infrared comparisons with compounds previously studied demonstrate that the hydroxytropenylium ion is a stronger hydrogen bond donor than either choline cation or protonated betaine cation, and suggest that hydroxytropenylium fluoride, if it can be prepared, should contain a three-center covalent hydrogen bond.

  13. Dynamic Covalent Nanoparticle Building Blocks

    PubMed Central

    2016-01-01

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

  14. 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…

  15. 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)

  16. A multipolar approach to the interatomic covalent interaction energy.

    PubMed

    Francisco, Evelio; Menéndez Crespo, Daniel; Costales, Aurora; Martín Pendás, Ángel

    2017-04-30

    Interatomic exchange-correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities ρA(r) and ρB(r), we examine in this work the mp approach to approximate the interatomic exchange-correlation (xc) energies of the Interacting Quantum Atoms method. We show that the full xc mp series is quickly divergent for directly bonded atoms (1-2 pairs) albeit it works reasonably well most times for 1- n (n > 2) interactions. As with conventional perturbation theory, we show numerically that the xc series is asymptotically convergent and that, a truncated xc mp approximation retaining terms up to l1+l2=2 usually gives relatively accurate results, sometimes even for directly bonded atoms. Our findings are supported by extensive numerical analyses on a variety of systems that range from several standard hydrogen bonded dimers to typically covalent or aromatic molecules. The exact algebraic relationship between the monopole-monopole xc mp term and the inter-atomic bond order, as measured by the delocalization index of the quantum theory of atoms in molecules, is also established. © 2017 Wiley Periodicals, Inc.

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

    PubMed

    Bauer, Renato A

    2015-09-01

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

  18. 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

  19. Metallic Adhesion and Bonding

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  20. 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…

  1. 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.

  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-Bond Formation via On-Surface Chemistry.

    PubMed

    Held, Philipp Alexander; Fuchs, Harald; Studer, Armido

    2017-01-18

    In this Review article pioneering work and recent achievements in the emerging research area of on-surface chemistry is discussed. On-surface chemistry, sometimes also called two-dimensional chemistry, shows great potential for bottom-up preparation of defined nanostructures. In contrast to traditional organic synthesis, where reactions are generally conducted in well-defined reaction flasks in solution, on-surface chemistry is performed in the cavity of a scanning probe microscope on a metal crystal under ultrahigh vacuum conditions. The metal first acts as a platform for self-assembly of the organic building blocks and in many cases it also acts as a catalyst for the given chemical transformation. Products and hence success of the reaction are directly analyzed by scanning probe microscopy. This Review provides a general overview of this chemistry highlighting advantages and disadvantages as compared to traditional reaction setups. The second part of the Review then focuses on reactions that have been successfully conducted as on-surface processes. On-surface Ullmann and Glaser couplings are addressed. In addition, cyclodehydrogenation reactions and cycloadditions are discussed and reactions involving the carbonyl functionality are highlighted. Finally, the first examples of sequential on-surface chemistry are considered in which two different functionalities are chemoselectively addressed. The Review gives an overview for experts working in the area but also offers a starting point to non-experts to enter into this exciting new interdisciplinary research field.

  4. Surface and Defect Excitations in Covalently Bonded Solids

    DTIC Science & Technology

    1990-01-31

    Pseudopotentials for highly 5 Electronegative /rirst Row Elements’, C. Monte Carlo Study of the Quantum Heisenberg 7 Antiferromagnet D .- Magnetic ,Properties of...1989). 19. G. Gomez-Santos, J.D. Joannopoulos, and T. Negele, " Monte Carlo Study of the Quantum Heisenberg Antiferromagnet", Phys. Rev. B39, 4435...approaches. This paves the way for future studies of a variety of complex and important material systems. C. Monte Carlo Study of the Quantum

  5. Covalent magnetism and magnetic impurities.

    PubMed

    Gruber, C; Bedolla, P O; Mohn, P

    2013-05-08

    We use the model of covalent magnetism and its application to magnetic insulators applied to the case of insulating carbon doped BaTiO3. Since the usual Stoner mechanism is not applicable we study the possibility of the formation of magnetic order based on a mechanism favoring singly occupied orbitals. On the basis of our model parameters we formulate a criterion similar to the Stoner criterion but also valid for insulators. We describe the model of covalent magnetism using a molecular orbital picture and determine the occupation numbers for spin-up and spin-down states. Our model allows a simulation of the results of our ab initio calculations for E(ℳ) which are found to be in very good agreement.

  6. Covalent attachment of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) to enzymes: the current state of affairs.

    PubMed Central

    Mewies, M.; McIntire, W. S.; Scrutton, N. S.

    1998-01-01

    The first identified covalent flavoprotein, a component of mammalian succinate dehydrogenase, was reported 42 years ago. Since that time, more than 20 covalent flavoenzymes have been described, each possessing one of five modes of FAD or FMN linkage to protein. Despite the early identification of covalent flavoproteins, the mechanisms of covalent bond formation and the roles of the covalent links are only recently being appreciated. The main focus of this review is, therefore, one of mechanism and function, in addition to surveying the types of linkage observed and the methods employed for their identification. Case studies are presented for a variety of covalent flavoenzymes, from which general findings are beginning to emerge. PMID:9514256

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

    PubMed Central

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

    2010-01-01

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

  8. Novel covalently coated diazoresin/polyvinyl alcohol capillary column for the analysis of proteins by capillary electrophoresis.

    PubMed

    Yu, Bing; Liu, Peng; Cong, Hailin; Tang, Jianguo; Zhang, Lixin

    2012-10-01

    A novel method for the preparation of covalently linked capillary coatings of PVA was demonstrated using photosensitive diazoresin (DR) as coupling agents. Layer-by-layer self-assembly film of DR and PVA based on hydrogen bonding was first fabricated on the inner wall of capillary, then the hydrogen bonding was converted into covalent bonding after treatment with UV light through the unique photochemistry reaction of DR. The covalently bonded coatings suppressed basic protein adsorption on the inner surface of capillary, and thus a baseline separation of lysozyme, cytochrome c and BSA was achieved using CE. Compared with bare capillary or noncovalently bonded DR/PVA coatings, the covalently linked DR/PVA capillary coatings not only improved the CE separation performance for proteins, but also exhibited good stability and repeatability. Due to the replacement of highly toxic and moisture-sensitive silane coupling agent by DR in the covalent coating preparation, this method may provide a green and easy way to make the covalently coated capillaries for CE.

  9. Tetrel-bonding interaction: rediscovered supramolecular force?

    PubMed

    Bauzá, Antonio; Mooibroek, Tiddo J; Frontera, Antonio

    2013-11-18

    The w(hole) picture: A tetrel bond is a directional noncovalent interaction between a covalently bonded atom of Group IV and a negative site, for example, the lone pair of a Lewis base or an anion. It involves a region of positive electrostatic potential (σ hole), and energetically, they are comparable to hydrogen bonds and other σ-hole-based interactions.

  10. Hardness of covalent and ionic crystals: first-principle calculations.

    PubMed

    Simůnek, Antonín; Vackár, Jirí

    2006-03-03

    A new concept, the strength of bond, and a new form expressing the hardness of covalent and ionic crystals are presented. Hardness is expressed by means of quantities inherently coupled to the atomistic structure of matter, and, therefore, hardness can be determined by first-principles calculations. Good agreement between theory and experiment is observed in the range of 2 orders of magnitude. It is shown that a lower coordination number of atoms results in higher hardness, contrary to common opinion presented in general literature.

  11. 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.

  12. Simultaneous covalent and noncovalent hybrid polymerizations

    SciTech Connect

    Yu, Z.; Tantakitti, F.; Yu, T.; Palmer, L. C.; Schatz, G. C.; Stupp, S. I.

    2016-01-28

    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.

  13. Using the reactive dye method to covalently attach antibacterial compounds to cotton.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The antibacterial compounds used were sulfamethoxazole and trimethoprim. A version of the reactive dye method was used to react these two compounds chemically with the cotton fiber molecule. The two compounds were activated and then covalently bonded to cotton fabric, either separately or together...

  14. Two-Dimensional Covalent Organic Framework (COF) Membranes Fabricated via the Assembly of Exfoliated COF Nanosheets.

    PubMed

    Li, Gang; Zhang, Kai; Tsuru, Toshinori

    2017-03-15

    Exceptionally homogeneous and ultrathin COF membranes were successfully fabricated using exfoliated COF nanosheets with uniform perforations as membrane building blocks. The COF membranes showed highly permeable performance due to the ultrafast molecular diffusion through the perforations of the COF nanosheets and the excellent thermal stability due to the robust covalent bonds in the framework.

  15. Exploiting Noncovalent Interactions in an Imine-Based Covalent Organic Framework for Quercetin Delivery.

    PubMed

    Vyas, Vijay S; Vishwakarma, Medhavi; Moudrakovski, Igor; Haase, Frederik; Savasci, Gökcen; Ochsenfeld, Christian; Spatz, Joachim P; Lotsch, Bettina V

    2016-10-01

    Covalent organic frameworks (COFs) are a new class of nanoporous polymeric vector showing promise as drug-delivery vehicles with high loading capacity and biocompatibility. The interaction between the carrier and the cargo is specifically tailored on a molecular level by H-bonding. Cell-proliferation studies indicate higher efficacy of the drug in cancer cells by nanocarrier delivery mediated by the COF.

  16. 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.

  17. Exceptional ammonia uptake by a covalent organic framework

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

  18. Exceptional ammonia uptake by a covalent organic framework.

    PubMed

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

    2010-03-01

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

  19. 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)

  20. Covalence and ionicity in MgAgAs-type compounds.

    PubMed

    Bende, David; Grin, Yuri; Wagner, Frank R

    2014-07-28

    MgAgAs-type "half-Heusler" compounds are known to realize two out of three possible atomic arrangements of this structure type. The number of transition metal components typically determines which of the alternatives is favored. On the basis of DFT calculations for all three variants of 20 eight- and eighteen-valence-electron compounds, the experimentally observed structural variant was found to be determined by basically two different bonding patterns. They are quantified by employing two complementary position-space bonding measures. The Madelung energy E((M)(QTAIM)) calculated with the QTAIM effective charges reflects contributions of the ionic interactions to the total energy. The sum of nearest-neighbor delocalization indices ςnn characterizes the covalent interactions through electron sharing. With the aid of these quantities, the energetic sequence of the three atomic arrangements for each compound is rationalized. The resulting systematic is used to predict a scenario in which an untypical atomic arrangement becomes most favorable.

  1. 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.

  2. 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.

  3. VEGF internalization is not required for VEGFR-2 phosphorylation in bioengineered surfaces with covalently linked VEGF

    PubMed Central

    Anderson, Sean M.; Shergill, Bhupinder; Barry, Zachary T.; Manousiouthakis, Eleana; Chen, Tom T.; Botvinick, Elliot; Platt, Manu O.; Iruela-Arispe, M. Luisa; Segura, Tatiana

    2011-01-01

    Vascular endothelial growth factor (VEGF) is known to activate proliferation, migration, and survival pathways in endothelial cells through phosphorylation of VEGF receptor-2 (VEGFR-2). VEGF has been incorporated into biomaterials through encapsulation, electrostatic sequestration, and covalent attachment, but the effect of these immobilization strategies on VEGF signaling has not been thoroughly investigated. Further, although growth factor internalization along with the receptor generally occurs in a physiological setting, whether this internalization is needed for receptor phosphorylation is not entirely clear. Here we show that VEGF covalently bound through a modified heparin molecule elicits an extended response of pVEGFR-2 in human umbilical vein endothelial cells (HUVECs) and that the covalent linkage reduces internalization of the growth factor during receptor endocytosis. Optical tweezer measurements show that the rupture force required to disrupt the heparin-VEGF-VEGFR-2 interaction increases from 3–8 pN to 6–12 pN when a covalent bond is introduced between VEGF and heparin. Importantly, by covalently binding VEGF to a heparin substrate, the stability (half-life) of VEGF is extended over three-fold. Here, mathematical models support the biological conclusions, further suggesting that VEGF internalization is significantly reduced when covalently bound, and indicating that VEGF is available for repeated phosphorylation events. PMID:21826315

  4. 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.

  5. Conformational analysis of a covalently cross-linked Watson-Crick base pair model.

    PubMed

    Jensen, Erik A; Allen, Benjamin D; Kishi, Yoshito; O'Leary, Daniel J

    2008-11-15

    Low-temperature NMR experiments and molecular modeling have been used to characterize the conformational behavior of a covalently cross-linked DNA base pair model. The data suggest that Watson-Crick or reverse Watson-Crick hydrogen bonding geometries have similar energies and can interconvert at low temperatures. This low-temperature process involves rotation about the crosslink CH(2)C(5') (psi) carbon-carbon bond, which is energetically preferred over the alternate CH(2)N(3) (phi) carbon-nitrogen bond rotation.

  6. 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.

  7. Covalent and reversible short-range electrostatic imaging in noncontact atomic force microscopy.

    PubMed

    Dieska, Peter; Stich, Ivan; Pérez, Rubén

    2003-11-21

    We present a computational study of atomic-scale image formation in noncontact atomic force microscopy on metallic surfaces. We find two imaging scenarios: (1). atomic resolution arising due to very strong covalent tip-sample interaction exhibiting striking similarity with the imaging mechanism found on semiconductor surfaces, and (2). a completely new mechanism, reversible short-range electrostatic imaging, arising due to subtle charge-transfer interactions. Contrary to the strong covalent-bond imaging, the newly identified mechanism causes only negligible surface perturbation and can account for results recently observed experimentally.

  8. 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.

  9. Hydrogen Bonded Arrays: The Power of Multiple Hydrogen Bonds

    SciTech Connect

    Shokri, Alireza; Schmidt, Jacob C.; Wang, Xue B.; 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 (HOCH2CH2)2CHO (2a), (HOCH2CH2) 3CO (3a) and (HOCH2CH2CH(OH)CH2)3CO (4a) reveal that hydrogen-bonded networks can provide enormous stabilizations, and that a single charge center not only can be stabilized by up to 3 hydrogen bonds but it can increase the interaction energy between non-charged OH groups by 5.8 kcal mol1 or more per hydrogen bond. This can lead to pKa values that are very different than in water, and provide some of the impetus for catalytic processes.

  10. 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.

  11. Hydrogen bonding in ionic liquids.

    PubMed

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

    2015-03-07

    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

  12. Covalent bond or noncovalent bond: a supramolecular strategy for the construction of chemically synthesized vaccines.

    PubMed

    Gao, Yue; Sun, Zhan-Yi; Huang, Zhi-Hua; Chen, Pu-Guang; Chen, Yong-Xiang; Zhao, Yu-Fen; Li, Yan-Mei

    2014-10-13

    A novel noncovalent strategy to construct chemically synthesized vaccines has been designed to trigger a robust immune response and to dramatically improve the efficiency of vaccine preparation. Glycosylated MUC1 tripartite vaccines were constructed through host-guest interactions with cucurbit[8]uril. These vaccines elicited high levels of IgG antibodies that were recognized by transformed cells and induced the secretion of cytokines. The antisera also mediated complement-dependent cytotoxicity. This noncovalent strategy with good suitability, scalability, and feasibility can be applied as a universal strategy for the construction of chemically synthesized vaccines.

  13. 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

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

    PubMed

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

    2015-06-02

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

  15. 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.

  16. Estimation of bonding nature using diamagnetic susceptibility.

    PubMed

    Tomiyasu, Keisuke; Sato, Toyoto; Orimo, Shin-ichi

    2015-05-21

    A chemical bond includes both covalent and ionic characteristics. We develop an experimental method to estimate the degree of each contribution based on magnetic susceptibility measurements, in which Pascal's scheme for Larmor diamagnetism is combined with electronegativity. The applicability to metal hydrides is also shown.

  17. 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.

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

    PubMed

    Duffy, J A

    2006-12-14

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

  19. Prevention of sulfide mineral leaching through covalent coating

    SciTech Connect

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

    2007-09-15

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

  20. 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.

  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

    2016-05-05

    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. Non-covalent interactions in controlling pH-responsive behaviors of self-assembled nanosystems.

    PubMed

    Li, Yang; Wang, Zhaohui; Wei, Qi; Luo, Min; Huang, Gang; Sumer, Baran D; Gao, Jinming

    2016-10-14

    Self-assembly and associated dynamic and reversible non-covalent interactions are the basis of protein biochemistry (e.g., protein folding) and development of sophisticated nanomaterial systems that can respond to and amplify biological signals. In this study, we report a systematic investigation of non-covalent interactions that affect the pH responsive behaviors and resulting supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Increase of hydrophobic and π-π stacking interactions led to the decrease of pKa values. In contrast, enhancement of direct ionic binding between cationic ammonium groups and anionic counter ions gave rise to increased pKa. Moreover, hydration of hydrophobic surfaces and hydrogen bonding interactions may also play a role in the self-assembly process. The key parameters capable of controlling the subtle interplay of different non-covalent bonds in pH-triggered self-assembly of UPS copolymers are likely to offer molecular insights to understand other stimuli-responsive nanosystems. Selective and precise implementation of non-covalent interactions in stimuli-responsive self-assembly processes will provide powerful and versatile tools for the development of dynamic, complex nanostructures with predictable and tunable transitions.

  3. Covalent docking of large libraries for the discovery of chemical probes.

    PubMed

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

    2014-12-01

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

  4. Photofunctional hybrid silica microspheres covalently functionalized with metalloporphyrins

    NASA Astrophysics Data System (ADS)

    Guo, Lei; Fu, Lianshe; Ferreira, Rute A. S.; Carlos, Luis D.; Yan, Bing

    2012-10-01

    The entrapment of metalloporphyrins (with Zn2+ and Yb3+) in silica microspheres is achieved by modification of protoporphyrin IX (Pp-IX) molecules with three different organosilane precursors via the sol-gel method. The obtained hybrid materials are characterized by electronic absorption spectra, Fourier-transform infrared (FT-IR), X-ray diffraction (XRD), 29Si MAS NMR spectrum, scanning electron microscopy (SEM), nitrogen adsorption/desorption isotherms and thermogravimetric analysis (TGA), and their luminescence properties have also been determined. The results reveal that the obtained porphyrins networks are covalently bonded to the inorganic matrix through the bridging action of the functionalized silica microspheres. Furthermore, it has also been observed that porphyrins molecules located in different environments exhibit different photophysical properties in the visible and near-infrared regions.

  5. 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.

  6. 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.

  7. 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)

  8. Enhancing covalent mechanochemistry in bulk polymers using electrospun ABA triblock copolymers.

    PubMed

    Ramirez, A L Black; Schmitt, A K; Mahanthappa, M K; Craig, S L

    2014-01-01

    The mechanochemical activation of covalent bonds in bulk polymers is often characterized by low conversions. Here we report that the activation of gem-dibromocyclopropane (gDBC) mechanophores embedded in a poly(1,4-butadiene) (PB) is enhanced when a central gDBC-PB block is flanked by two polystyrene (PS) end blocks in an ABA-type triblock architecture. Electrospinning the PS-(gDBC)PB-PS leads to even greater activation in aligned fiber mats under tension.

  9. Tuning intermolecular non-covalent interactions for nanowires of organic semiconductors.

    PubMed

    Jiang, Lang; Gao, Jianhua; Fu, Yanyan; Dong, Huanli; Zhao, Huaping; Li, Hongxiang; Tang, Qingxin; Chen, Keqiu; Hu, Wenping

    2010-12-01

    Anthracene and its derivatives are used to demonstrate a simple way to cast assemble nanowires of organic semiconductors with tuning of intermolecular non-covalent interactions by molecular design. The tuning of intermolecular interactions could be achieved by (i) decreasing intermolecular hydrophobic interactions by linking hydrophilic side chains to anthracene rings, (ii) increasing intermolecular interaction for self-assembly with the assistance of hydrogen bonds, and (iii) enhancing molecular π-π interaction by increasing the conjugated dimension of the compounds.

  10. Tuning intermolecular non-covalent interactions for nanowires of organic semiconductors

    NASA Astrophysics Data System (ADS)

    Jiang, Lang; Gao, Jianhua; Fu, Yanyan; Dong, Huanli; Zhao, Huaping; Li, Hongxiang; Tang, Qingxin; Chen, Keqiu; Hu, Wenping

    2010-12-01

    Anthracene and its derivatives are used to demonstrate a simple way to cast assemble nanowires of organic semiconductors with tuning of intermolecular non-covalent interactions by molecular design. The tuning of intermolecular interactions could be achieved by (i) decreasing intermolecular hydrophobic interactions by linking hydrophilic side chains to anthracene rings, (ii) increasing intermolecular interaction for self-assembly with the assistance of hydrogen bonds, and (iii) enhancing molecular π-π interaction by increasing the conjugated dimension of the compounds.

  11. 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

    2015-07-16

    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.

  12. 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.

  13. 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.

  14. Blue shifts vs red shifts in sigma-hole bonding.

    PubMed

    Murray, Jane S; Concha, Monica C; Lane, Pat; Hobza, Pavel; Politzer, Peter

    2008-08-01

    Sigma-hole bonding is a noncovalent interaction between a region of positive electrostatic potential on the outer surface of a Group V, VI, or VII covalently-bonded atom (a sigma-hole) and a region of negative potential on another molecule, e.g., a lone pair of a Lewis base. We have investigated computationally the occurrence of increased vibration frequencies (blue shifts) and bond shortening vs decreased frequencies (red shifts) and bond lengthening for the covalent bonds to the atoms having the sigma-holes (the sigma-hole donors). Both are possible, depending upon the properties of the donor and the acceptor. Our results are consistent with models that were developed earlier by Hermansson and by Qian and Krimm in relation to blue vs red shifting in hydrogen bond formation. These models invoke the derivatives of the permanent and the induced dipole moments of the donor molecule.

  15. 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.

  16. Theoretical characterization of the sulfilimine bond: Double or single?

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2010-03-01

    Using quantum mechanical calculations in combination with AIM and NBO analyses, we investigate the properties of the sulfilimine bond, which has been recently detected in collagen IV [Vanacore et al., Science 325 (2009) 1230]. Contrary to the general belief that this is a double bond, -N dbnd S<, our analysis of the wavefunction of a model compound indicates it being a coordinate covalent (dative) single bond, -N ← S<, with a strong polarization towards nitrogen.

  17. 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.

  18. 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,…

  19. Charge-Shift Bonding Emerges as a Distinct Electron-Pair Bonding Family from Both Valence Bond and Molecular Orbital Theories.

    PubMed

    Zhang, Huaiyu; Danovich, David; Wu, Wei; Braïda, Benoît; Hiberty, Philippe C; Shaik, Sason

    2014-06-10

    The charge-shift bonding (CSB) concept was originally discovered through valence bond (VB) calculations. Later, CSB was found to have signatures in atoms-in-molecules and electron-localization-function and in experimental electron density measurements. However, the CSB concept has never been derived from a molecular orbital (MO)-based theory. We now provide a proof of principle that an MO-based approach enables one to derive the CSB family alongside the distinctly different classical family of covalent bonds. In this bridging energy decomposition analysis, the covalent-ionic resonance energy, RECS, of a bond is extracted by cloning an MO-based purely covalent reference state, which is a constrained two-configuration wave function. The energy gap between this reference state and the variational TCSCF ground state yields numerical values for RECS, which correlate with the values obtained at the VBSCF level. This simple MO-based method, which only takes care of static electron correlation, is already sufficient for distinguishing the classical covalent or polar-covalent bonds from charge-shift bonds. The equivalence of the VB and MO-based methods is further demonstrated when both methods are augmented by dynamic correlation. Thus, it is shown from both MO and VB perspectives that the bonding in the CSB family does not arise from electron correlation. Considering that the existence of the CSB family is associated also with quite a few experimental observations that we already reviewed ( Shaik , S. , Danovich , D. , Wu , W. , and Hiberty , P. C. Nat. Chem. , 2009 , 1 , 443 - 449 ), the new bonding concept has passed by now two stringent tests. This derivation, on the one hand, supports the new concept and on the other, it creates bridges between the two main theories of electronic structure.

  20. 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.

  1. 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.

  2. Covalent organic frameworks: Crossing the channel

    NASA Astrophysics Data System (ADS)

    Xu, Hong; Jiang, Donglin

    2014-07-01

    The ordered one-dimensional nanochannels found in covalent organic frameworks (COFs) could render them able to conduct protons. However, the frameworks' instability in acid has thus far precluded any practical implementations. Now, a strategy to overcome this instability has enabled proton conduction using a COF for the first time.

  3. 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

    2014-01-07

    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.

  4. 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

  5. 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.

  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. Surface-confined single-layer covalent organic framework on single-layer graphene grown on copper foil.

    PubMed

    Xu, Lirong; Zhou, Xin; Tian, Wei Quan; Gao, Teng; Zhang, Yan Feng; Lei, Shengbin; Liu, Zhong Fan

    2014-09-01

    The integration of 2D covalent organic frameworks (COFs) with atomic thickness with graphene will lead to intriguing two-dimensional materials. A surface-confined covalently bonded Schiff base network was prepared on single-layer graphene grown on copper foil and the dynamic reaction process was investigated with scanning tunneling microscopy. DFT simulations provide an understanding of the electronic structures and the interactions between the surface COF and graphene. Strong coupling between the surface COF and graphene was confirmed by the dispersive bands of the surface COF after interaction with graphene, and also by the experimental observation of tunneling condition dependent contrast of the surface COF.

  8. Structural and in vitro adhesion analysis of a novel covalently coupled bioactive composite.

    PubMed

    Khan, Abdul S; Hassan, Khawaja R; Bukhari, Syeda F; Wong, Ferranti S L; Rehman, Ihtesham U

    2012-01-01

    The interfacial adhesion between a restorative composite and tooth is one of the major factors that determine the ultimate performance of composite restoration. A novel polyurethane (PU) composite material was prepared by chemically binding the nano-hydroxyapatite (nHA) to the diisocyanate component in the PU backbone by utilizing solvent polymerization. The procedure involved stepwise addition of monomeric units of the PU and optimizing the reagent concentrations. The resultant materials were characterized structurally (Raman Spectroscopy) and in vitro bioactive analysis was conducted in modified-simulated body fluid for periodical time intervals. The in vitro study evaluated the push-out bond strength of existing obturating material and novel covalently linked PU/nHA composites to dentin after long-term storage in deionized water and artificial saliva. Human extracted molar roots were filled with experimental samples and analyzed at predetermined time intervals. The shear bond strength of samples was measured and surface morphologies were evaluated. Covalent bond formation was achieved between PU and nHA without intermediate coupling agent. With the increase in concentration of nHA, the composite showed more bioactivity and adhesion toward tooth structure. Bond strength of this new composite were in accordance with obutrating material, therefore, the material can be used as an obturating material because of its direct adhesion with tooth structure.

  9. 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.

  10. 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.

  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 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

  13. 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.

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

    PubMed

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

    2010-09-08

    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.

  15. 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

  16. Fusing tetrapyrroles to graphene edges by surface-assisted covalent coupling

    NASA Astrophysics Data System (ADS)

    He, Yuanqin; Garnica, Manuela; Bischoff, Felix; Ducke, Jacob; Bocquet, Marie-Laure; Batzill, Matthias; Auwärter, Willi; Barth, Johannes V.

    2017-01-01

    Surface-assisted covalent linking of precursor molecules enables the fabrication of low-dimensional nanostructures, which include graphene nanoribbons. One approach to building functional multicomponent systems involves the lateral anchoring of organic heteromolecules to graphene. Here we demonstrate the dehydrogenative coupling of single porphines to graphene edges on the same metal substrate as used for graphene synthesis. The covalent linkages are visualized by scanning probe techniques with submolecular resolution, which directly reveals bonding motifs and electronic features. Distinct configurations are identified that can be steered towards entities predominantly fused to graphene edges through two pyrrole rings by thermal annealing. Furthermore, we succeeded in the concomitant metallation of the macrocycle with substrate atoms and the axial ligation of adducts. Such processes combined with graphene-nanostructure synthesis has the potential to create complex materials systems with tunable functionalities.

  17. Conditional repair by locally switching the thermal healing capability of dynamic covalent polymers with light

    PubMed Central

    Fuhrmann, Anne; Göstl, Robert; Wendt, Robert; Kötteritzsch, Julia; Hager, Martin D.; Schubert, Ulrich S.; Brademann-Jock, Kerstin; Thünemann, Andreas F.; Nöchel, Ulrich; Behl, Marc; Hecht, Stefan

    2016-01-01

    Healable materials could play an important role in reducing the environmental footprint of our modern technological society through extending the life cycles of consumer products and constructions. However, as most healing processes are carried out by heat alone, the ability to heal damage generally kills the parent material's thermal and mechanical properties. Here we present a dynamic covalent polymer network whose thermal healing ability can be switched ‘on' and ‘off' on demand by light, thereby providing local control over repair while retaining the advantageous macroscopic properties of static polymer networks. We employ a photoswitchable furan-based crosslinker, which reacts with short and mobile maleimide-substituted poly(lauryl methacrylate) chains forming strong covalent bonds while simultaneously allowing the reversible, spatiotemporally resolved control over thermally induced de- and re-crosslinking. We reason that our system can be adapted to more complex materials and has the potential to impact applications in responsive coatings, photolithography and microfabrication. PMID:27941924

  18. 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

  19. 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.

  20. Conditional repair by locally switching the thermal healing capability of dynamic covalent polymers with light

    NASA Astrophysics Data System (ADS)

    Fuhrmann, Anne; Göstl, Robert; Wendt, Robert; Kötteritzsch, Julia; Hager, Martin D.; Schubert, Ulrich S.; Brademann-Jock, Kerstin; Thünemann, Andreas F.; Nöchel, Ulrich; Behl, Marc; Hecht, Stefan

    2016-12-01

    Healable materials could play an important role in reducing the environmental footprint of our modern technological society through extending the life cycles of consumer products and constructions. However, as most healing processes are carried out by heat alone, the ability to heal damage generally kills the parent material's thermal and mechanical properties. Here we present a dynamic covalent polymer network whose thermal healing ability can be switched `on' and `off' on demand by light, thereby providing local control over repair while retaining the advantageous macroscopic properties of static polymer networks. We employ a photoswitchable furan-based crosslinker, which reacts with short and mobile maleimide-substituted poly(lauryl methacrylate) chains forming strong covalent bonds while simultaneously allowing the reversible, spatiotemporally resolved control over thermally induced de- and re-crosslinking. We reason that our system can be adapted to more complex materials and has the potential to impact applications in responsive coatings, photolithography and microfabrication.

  1. 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.

  2. Interplays Between Covalent Modifications in the Endoplasmic Reticulum Increase Conformational Diversity in Nascent Prion Protein

    PubMed Central

    Orsi, Andrea

    2007-01-01

    Prion protein (PrP), the causative agent of transmissible spongiform encephalopathies, is synthesized in the endoplasmic reticulum (ER) where it undergoes numerous covalent modifications. Here we investigate the interdependence and regulation of PrP oxidative folding, N-glycosylation and GPI addition in diverse ER conditions. Our results show that formation of the single disulphide bond is a pivotal event, essential for PrP transport, and can occur post-translationally. Retarding its formation enhances N-glycosylation and GPI-anchoring. In contrast, lowering ER Ca2+ concentration inhibits N-glycosylation and GPI-anchoring. These data reveal tight interplays between the different ER covalent modifications, which collectively increase of PrP conformational diversity and may be important for its propagation. PMID:19164910

  3. Dynamic urea bond for the design of reversible and self-healing polymers.

    PubMed

    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-urea)s 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.

  4. Dynamic urea bond for the design of reversible and self-healing polymers

    NASA Astrophysics Data System (ADS)

    Ying, Hanze; Zhang, Yanfeng; Cheng, Jianjun

    2014-02-01

    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-urea)s 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.

  5. 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

  6. The Role of Wheat and Egg Constituents in the Formation of a Covalent and Non-covalent Protein Network in Fresh and Cooked Egg Noodles.

    PubMed

    Lambrecht, Marlies A; Rombouts, Ine; Nivelle, Mieke A; Delcour, Jan A

    2017-01-01

    Noodles of constant protein content and flour-to-egg protein ratio were made with whole egg, egg white, or egg yolk. The optimal cooking time, water absorption, and cooking loss of salted whole egg noodles was respectively lower and higher than of egg white and egg yolk noodles. However, cooked whole egg noodles showed the best Kieffer-rig extensibility. Differences in noodle properties were linked to protein network formation. Disulfide bonds in whole egg noodles developed faster and to a larger extent during cooking than in egg yolk noodles but slower and to a lower extent than in egg white noodles. The balance between the rate of protein cross-linking and starch swelling determines cooked noodle properties. Ionic and hydrophobic protein interactions increase the optimum cooking time and total work in Kieffer-rig extensibility testing of fresh noodles. Hydrogen bonds and covalent cross-links are probably the main determinants of the extensibility of cooked noodles.

  7. Agaricus meleagris pyranose dehydrogenase: Influence of covalent FAD linkage on catalysis and stability

    PubMed Central

    Krondorfer, Iris; Brugger, Dagmar; Paukner, Regina; Scheiblbrandner, Stefan; Pirker, Katharina F.; Hofbauer, Stefan; Furtmüller, Paul G.; Obinger, Christian; Haltrich, Dietmar; Peterbauer, Clemens K.

    2014-01-01

    Pyranose dehydrogenase (PDH) is a monomeric flavoprotein belonging to the glucose–methanol–choline (GMC) family of oxidoreductases. It catalyzes the oxidation of free, non-phosphorylated sugars to the corresponding keto sugars. The enzyme harbors an FAD cofactor that is covalently attached to histidine 103 via an 8α-N(3) histidyl linkage. Our previous work showed that variant H103Y was still able to bind FAD (non-covalently) and perform catalysis but steady-state kinetic parameters for several substrates were negatively affected. In order to investigate the impact of the covalent FAD attachment in Agaricus meleagris PDH in more detail, pre-steady-state kinetics, reduction potential and stability of the variant H103Y in comparison to the wild-type enzyme were probed. Stopped-flow analysis revealed that the mutation slowed down the reductive half-reaction by around three orders of magnitude whereas the oxidative half-reaction was affected only to a minor degree. This was reflected by a decrease in the standard reduction potential of variant H103Y compared to the wild-type protein. The existence of an anionic semiquinone radical in the resting state of both the wild-type and variant H103Y was demonstrated using electron paramagnetic resonance (EPR) spectroscopy and suggested a higher mobility of the cofactor in the variant H103Y. Unfolding studies showed significant negative effects of the disruption of the covalent bond on thermal and conformational stability. The results are discussed with respect to the role of covalently bound FAD in catalysis and stability. PMID:25043975

  8. Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase.

    PubMed

    Shi, Rong; McDonald, Laura; Cui, Qizhi; Matte, Allan; Cygler, Miroslaw; Ekiel, Irena

    2011-01-25

    The Escherichia coli dihydroxyacetone (Dha) kinase is an unusual kinase because (i) it uses the phosphoenolpyruvate carbohydrate: phosphotransferase system (PTS) as the source of high-energy phosphate, (ii) the active site is formed by two subunits, and (iii) the substrate is covalently bound to His218(K)* of the DhaK subunit. The PTS transfers phosphate to DhaM, which in turn phosphorylates the permanently bound ADP coenzyme of DhaL. This phosphoryl group is subsequently transferred to the Dha substrate bound to DhaK. Here we report the crystal structure of the E. coli Dha kinase complex, DhaK-DhaL. The structure of the complex reveals that DhaK undergoes significant conformational changes to accommodate binding of DhaL. Combined mutagenesis and enzymatic activity studies of kinase mutants allow us to propose a catalytic mechanism for covalent Dha binding, phosphorylation, and release of the Dha-phosphate product. Our results show that His56(K) is involved in formation of the covalent hemiaminal bond with Dha. The structure of H56N(K) with noncovalently bound substrate reveals a somewhat different positioning of Dha in the binding pocket as compared to covalently bound Dha, showing that the covalent attachment to His218(K) orients the substrate optimally for phosphoryl transfer. Asp109(K) is critical for activity, likely acting as a general base activating the γ-OH of Dha. Our results provide a comprehensive picture of the roles of the highly conserved active site residues of dihydroxyacetone kinases.

  9. Routes to Hydrogen Bonding Chain-End Functionalized Polymers.

    PubMed

    Bertrand, Arthur; Lortie, Frédéric; Bernard, Julien

    2012-12-21

    The contribution of supramolecular chemistry to polymer science opens new perspectives for the design of polymer materials exhibiting valuable properties and easier processability due to the dynamic nature of non-covalent interactions. Hydrogen bonding polymers can be used as supramolecular units for yielding larger assemblies that possess attractive features, arising from the combination of polymer properties and the responsiveness of hydrogen bonds. The post-polymerization modification of reactive end-groups is the most common procedure for generating such polymers. Examples of polymerizations mediated by hydrogen bonding-functionalized precursors have also recently been reported. This contribution reviews the current synthetic routes toward hydrogen bonding sticker chain-end functionalized polymers.

  10. 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.

  11. 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.

  12. Aerogen Bonding Interaction: A New Supramolecular Force?

    PubMed

    Bauzá, Antonio; Frontera, Antonio

    2015-06-15

    We report evidence of the favorable noncovalent interaction between a covalently bonded atom of Group 18 (known as noble gases or aerogens) and a negative site, for example, a lone pair of a Lewis base or an anion. It involves a region of positive electrostatic potential (σ-hole), therefore it is a totally new and unexplored σ-hole-based interaction, namely aerogen bonding. We demonstrate for the first time the existence of σ-hole regions in aerogen derivatives by means of high-level ab initio calculations. In addition, several crystal structures retrieved from the Cambridge Structural Database (CSD) give reliability to the calculations. Energetically, aerogen bonds are comparable to hydrogen bonds and other σ-hole-based interactions but less directional. They are expected to be important in xenon chemistry.

  13. DNA binding properties, histidine interaction and cytotoxicity studies of water soluble ruthenium(ii) terpyridine complexes.

    PubMed

    Lazić, Dejan; Arsenijević, Aleksandar; Puchta, Ralph; Bugarčić, Živadin D; Rilak, Ana

    2016-03-21

    In this study, two representatives of previously synthesized ruthenium(ii) terpyridine complexes, i.e., [Ru(Cl-tpy)(en)Cl][Cl] (1) and [Ru(Cl-tpy)(dach)Cl][Cl] (2), were chosen and a detailed study of the kinetic parameters of their reactivity toward l-histidine (l-His), using the UV-Vis and (1)H NMR techniques, was developed. The inner molecular rearrangement from N3-coordinated l-His to the N1 bound isomer, observable in the NMR data, was corroborated by DFT calculations favoring N1 coordination by nearly 4 kcal mol(-1). These two ruthenium(ii) terpyridine complexes were investigated for their interactions with DNA employing UV-Vis spectroscopy, DNA viscosity measurements and fluorescence quenching measurements. The high binding constants obtained in the DNA binding studies (Kb = 10(4)-10(5) M(-1)) suggest a strong binding of the complexes to calf thymus (CT) DNA. Competitive studies with ethidium bromide (EB) showed that the complexes can displace DNA-bound EB, suggesting strong competition with EB (Ksv = 1.5-2.5 × 10(4) M(-1)). In fact, the results indicate that these complexes can bind to DNA covalently and non-covalently. In order to gain insight of the behavior of a neutral compound, besides the four previously synthesized cationic complexes [Ru(Cl-tpy)(en)Cl][Cl] (1), [Ru(Cl-tpy)(dach)Cl][Cl] (2), [Ru(Cl-tpy)(bpy)Cl][Cl] (3) and [Ru(tpy)Cl3] (P2), a new complex, [Ru(Cl-tpy)(pic)Cl] (4), was used in the biological studies. Their cytotoxicity was investigated against three different tumor cell lines, i.e., A549 (human lung carcinoma cell line), HCT116 (human colon carcinoma cell line), and CT26 (mouse colon carcinoma cell line), by the MTT assay. Complexes 1 and 2 showed higher activity than complexes 3, 4 and P2 against all the selected cell lines. The results on in vitro anticancer activity confirmed that only compounds that hydrolyze the monodentate ligand at a reasonable rate show moderate activity, provided that the chelate ligand is a hydrogen bond

  14. Clustering of carboxylated magnetite nanoparticles through polyethylenimine: Covalent versus electrostatic approach

    NASA Astrophysics Data System (ADS)

    Tóth, Ildikó Y.; Nesztor, Dániel; Novák, Levente; Illés, Erzsébet; Szekeres, Márta; Szabó, Tamás; Tombácz, Etelka

    2017-04-01

    Carboxylated magnetite nanoparticles (MNPs) are frequently used to develop materials with enhanced properties for MRI and hyperthermia. The controlled clustering of MNPs via covalent or electrostatic approaches provides opportunity to prepare high quality materials. MNPs were prepared by co-precipitation and coated by poly(acrylic acid-co-maleic acid) (PAM@MNP). The clusters were synthesized from purified PAM@MNPs and polyethylenimine (PEI) solution via electrostatic interaction and covalent bond formation (ES-cluster and CB-cluster, respectively). The electrostatic adhesion (-NH3+ and -COO-) and the formed amide bond were confirmed by ATR-FTIR. The averaged area of CB-clusters was about twice as large as that of ES-cluster, based on TEM. The SAXS results showed that the surface of MNPs was smooth and the nanoparticles were close packed in both clusters. The pH-dependent aggregation state and zeta potential of clusters were characterized by DLS and electrophoresis measurements, the clusters were colloidally stable at pH>5. In hyperthermia experiments, the values of SAR were about two times larger for the chemically bonded cluster. The MRI studies showed exceptionally high transversion relaxivities, the r2 values are 457 mM-1 s-1 and 691 mM-1 s-1 for ES-cluster and CB-cluster, respectively. Based on these results, the chemically clustered product shows greater potential for feasible biomedical applications.

  15. Thermochemistry of non-covalent ion-molecule interactions.

    PubMed

    Armentrout, P B; Rodgers, M T

    2013-01-01

    The thermochemistry of non-covalent ion-molecule complexes has been examined by measuring quantitative bond dissociation energies using threshold collision-induced dissociation in guided ion beam tandem mass spectrometers (GIBMS). The methods used are briefly reviewed and several examples of the types of information and insight that can be obtained from such thermodynamic information are discussed. The hydration of metal cations, both singly and doubly charged, is reviewed and the trends elucidated, mainly on the basis of electrostatic contributions. The binding of alkali metal cations to amino acids has been examined for a range of systems, with both the overall polarizability of the amino acid and the local dipole moment of heteroatomic side-chains shown to be important contributors. The gas-phase interactions of the 12-crown-4 (12C4) polyether with alkali metal cations, classic molecular recognition systems in solution, have been newly compared to previous GIBMS work. These results validate the previous hypothesis that excited conformers were present for Rb(+)(12C4) and Cs(+)(12C4) and offer clues as to how and why they are formed.

  16. An histidine covalent receptor/butenolide complex mediates strigolactone perception

    PubMed Central

    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

    2016-01-01

    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 characterize the binding and catalytic functions of RAMOSUS3 (RMS3), the pea (Pisum sativum) ortholog of rice (Oryza sativa) D14 strigolactone receptor. Using novel profluorescent probes with strigolactone-like bioactivity, we show that RMS3 acts as a single-turnover enzyme that explains its apparent low enzymatic rate. We further demonstrate the formation of a covalent RMS3/D-ring complex, essential for bioactivity, in which the D-ring is attached to Histidine 247 of the catalytic triad. These results reveal an undescribed mechanism of plant hormone reception where the receptor performs an irreversible enzymatic reaction to generate its own ligand. PMID:27479744

  17. Thermochemistry of Non-Covalent Ion–Molecule Interactions

    PubMed Central

    Armentrout, P. B.; Rodgers, M. T.

    2013-01-01

    The thermochemistry of non-covalent ion–molecule complexes has been examined by measuring quantitative bond dissociation energies using threshold collision-induced dissociation in guided ion beam tandem mass spectrometers (GIBMS). The methods used are briefly reviewed and several examples of the types of information and insight that can be obtained from such thermodynamic information are discussed. The hydration of metal cations, both singly and doubly charged, is reviewed and the trends elucidated, mainly on the basis of electrostatic contributions. The binding of alkali metal cations to amino acids has been examined for a range of systems, with both the overall polarizability of the amino acid and the local dipole moment of heteroatomic side-chains shown to be important contributors. The gas-phase interactions of the 12-crown-4 (12C4) polyether with alkali metal cations, classic molecular recognition systems in solution, have been newly compared to previous GIBMS work. These results validate the previous hypothesis that excited conformers were present for Rb+(12C4) and Cs+(12C4) and offer clues as to how and why they are formed. PMID:24349924

  18. Building high-coverage monolayers of covalently bound magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Williams, Mackenzie G.; Teplyakov, Andrew V.

    2016-12-01

    This work presents an approach for producing a high-coverage single monolayer of magnetic nanoparticles using "click chemistry" between complementarily functionalized nanoparticles and a flat substrate. This method highlights essential aspects of the functionalization scheme for substrate surface and nanoparticles to produce exceptionally high surface coverage without sacrificing selectivity or control over the layer produced. The deposition of one single layer of magnetic particles without agglomeration, over a large area, with a nearly 100% coverage is confirmed by electron microscopy. Spectroscopic techniques, supplemented by computational predictions, are used to interrogate the chemistry of the attachment and to confirm covalent binding, rather than attachment through self-assembly or weak van der Waals bonding. Density functional theory calculations for the surface intermediate of this copper-catalyzed process provide mechanistic insight into the effects of the functionalization scheme on surface coverage. Based on this analysis, it appears that steric limitations of the intermediate structure affect nanoparticle coverage on a flat solid substrate; however, this can be overcome by designing a functionalization scheme in such a way that the copper-based intermediate is formed on the spherical nanoparticles instead. This observation can be carried over to other approaches for creating highly controlled single- or multilayered nanostructures of a wide range of materials to result in high coverage and possibly, conformal filling.

  19. Discovery of a novel covalent non-β-lactam inhibitor of the metallo-β-lactamase NDM-1.

    PubMed

    Christopeit, Tony; Albert, Anastasia; Leiros, Hanna-Kirsti S

    2016-07-01

    The inhibition of metallo-β-lactamases (MBL) can prevent the hydrolysis of β-lactam antibiotics and hence is a promising strategy for the treatment of antibiotic resistant infections. In this study, we present a novel reversible covalent inhibitor of the clinically relevant MBL New Delhi metallo-β-lactamase 1 (NDM-1). Electrospray ionization-mass spectrometry (ESI-MS) and single site directed mutagenesis were used to show that the inhibitor forms a covalent bond with Lys224 in the active site of NDM-1. The inhibitor was further characterized using an enzyme inhibition assay, a surface plasmon resonance (SPR) based biosensor assay and covalent docking. The determined inhibition constant (KI(∗)) was 580nM and the inhibition constant for the initial complex (KI) was 76μM. To our knowledge, this inhibitor is the first example for a reversible covalent non-β-lactam inhibitor targeting NDM-1 and a promising starting point for the design of potent covalent inhibitors.

  20. Compounds from Sichuan and Melegueta peppers activate, covalently and non-covalently, TRPA1 and TRPV1 channels

    PubMed Central

    Riera, CE; Menozzi-Smarrito, C; Affolter, M; Michlig, S; Munari, C; Robert, F; Vogel, H; Simon, SA; le Coutre, J

    2009-01-01

    Background and purpose: Oily extracts of Sichuan and Melegueta peppers evoke pungent sensations mediated by different alkylamides [mainly hydroxy-α-sanshool (α-SOH)] and hydroxyarylalkanones (6-shogaol and 6-paradol). We assessed how transient receptor potential ankyrin 1 (TRPA1) and TRP vanilloid 1 (TRPV1), two chemosensory ion channels, participate in these pungent sensations. Experimental approach: The structure–activity relationships of these molecules on TRPA1 and TRPV1 was measured by testing natural and synthetic analogues using calcium and voltage imaging on dissociated dorsal root ganglia neurons and human embryonic kidney 293 cells expressing the wild-type channels or specific cysteine mutants using glutathione trapping as a model to probe TRPA1 activation. In addition, using Trpv1 knockout mice, the compounds' aversive responses were measured in a taste brief-access test. Key results: For TRPA1 activation, the cis C6 double bond in the polyenic chain of α-SOH was critical, whereas no structural specificity was required for activation of TRPV1. Both 6-shogaol and 6-paradol were found to activate TRPV1 and TRPA1 channels, whereas linalool, an abundant terpene in Sichuan pepper, activated TRPA1 but not TRPV1 channels. Alkylamides and 6-shogaol act on TRPA1 by covalent bonding whereas none of these compounds activated TRPV1 through such interactions. Finally, TRPV1 mutant mice retained sensitivity to 6-shogaol but were not responsive to α-SOH. Conclusions and implications: The pungent nature of components of Sichuan and Melegueta peppers was mediated via interactions with TRPA1 and TRPV1 channels and may explain the aversive properties of these compounds. PMID:19594761

  1. Polarization-induced σ-holes and hydrogen bonding.

    PubMed

    Hennemann, Matthias; Murray, Jane S; Politzer, Peter; Riley, Kevin E; Clark, Timothy

    2012-06-01

    The strong collinear polarizability of the A-H bond in A-H···B hydrogen bonds is shown to lead to an enhanced σ-hole on the donor hydrogen atom and hence to stronger hydrogen bonding. This effect helps to explain the directionality of hydrogen bonds, the well known cooperative effect in hydrogen bonding, and the occurrence of blue-shifting. The latter results when significant additional electron density is shifted into the A-H bonding region by the polarization effect. The shift in the A-H stretching frequency is shown to depend essentially linearly on the calculated atomic charge on the donor hydrogen for all donors in which A belongs to the same row of the periodic table. A further result of the polarization effect, which is also expected for other σ-hole bonds, is that the strength of the non-covalent interaction depends strongly on external electric fields.

  2. Design Principles for Covalent Organic Frameworks as Efficient Electrocatalysts in Clean Energy Conversion and Green Oxidizer Production.

    PubMed

    Lin, Chun-Yu; Zhang, Lipeng; Zhao, Zhenghang; Xia, Zhenhai

    2017-02-23

    Covalent organic frameworks (COFs), an emerging class of framework materials linked by covalent bonds, hold potential for various applications such as efficient electrocatalysts, photovoltaics, and sensors. To rationally design COF-based electrocatalysts for oxygen reduction and evolution reactions in fuel cells and metal-air batteries, activity descriptors, derived from orbital energy and bonding structures, are identified with the first-principle calculations for the COFs, which correlate COF structures with their catalytic activities. The calculations also predict that alkaline-earth metal-porphyrin COFs could catalyze the direct production of H2 O2 , a green oxidizer and an energy carrier. These predictions are supported by experimental data, and the design principles derived from the descriptors provide an approach for rational design of new electrocatalysts for both clean energy conversion and green oxidizer production.

  3. ECL performance of ruthenium tris-bipyridyl complexes covalently linked with phenothiazine through different bridge.

    PubMed

    Sun, Shiguo; Yang, Yang; Liu, Fengyu; Fan, Jiangli; Kehr, Jan; Sun, Licheng; Peng, Xiaojun

    2010-10-07

    Three ruthenium complexes 1a, 1b and 1c were synthesized, in which the phenothiazine moiety was covalently linked to the ruthenium complex through a 4 carbon chain and amide bond, respectively. The results demonstrate that one PTZ moiety is preferred to reach a good ECL performance, and the 4 carbon chain linked complex 1a exhibits the highest ECL enhancement (up to about 9 times), in comparison with the commonly utilized parent Ru(bpy)(3)(2+), permitting a lower detection limit of 1.0 x 10(-14) M with signal to noise of 3 for 20 mM DBAE at Au electrode.

  4. Understanding the clean interface between covalent Si and ionic Al2O3.

    PubMed

    Xiang, H J; Da Silva, Juarez L F; Branz, Howard M; Wei, Su-Huai

    2009-09-11

    The atomic and electronic structures of the (001)-Si/(001)-gamma-Al(2)O(3) heterointerface are investigated by first principles total energy calculations combined with a newly developed "modified basin-hopping" method. It is found that all interface Si atoms are fourfold coordinated due to the formation of Si-O and unexpected covalent Si-Al bonds in the new abrupt interface model. And the interface has perfect electronic properties in that the unpassivated interface has a large LDA band gap and no gap levels. These results show that it is possible to have clean semiconductor-oxide interfaces.

  5. Understanding the Clean Interface Between Covalent Si and Ionic Al2O3

    SciTech Connect

    Xiang, H. J.; Da Silva, J. L. F.; Branz, H. M.; Wei, S. H.

    2009-09-11

    The atomic and electronic structures of the (001)-Si/(001)-{gamma}-Al{sub 2}O{sub 3} heterointerface are investigated by first principles total energy calculations combined with a newly developed 'modified basin-hopping' method. It is found that all interface Si atoms are fourfold coordinated due to the formation of Si-O and unexpected covalent Si-Al bonds in the new abrupt interface model. And the interface has perfect electronic properties in that the unpassivated interface has a large LDA band gap and no gap levels. These results show that it is possible to have clean semiconductor-oxide interfaces.

  6. 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.

  7. 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.

  8. The Bellamy relationship and the nature of the H-bond. Heteroassociates of alcohols

    NASA Astrophysics Data System (ADS)

    Vokin, A. I.; Sinegovskaya, L. M.; Shulunova, A. M.; Turchaninov, V. K.

    2013-05-01

    IR spectroscopic data are used to demonstrate that the donor ability of alcohols in H-bonds is determined by the molecular conformation and the universal interaction of subunits of the H-bond complex in homological series. The observed regularities can be employed for empirical separation of the contributions of electrostatic and covalent components in the formation energy of the H-complex.

  9. A robust and luminescent covalent organic framework as a highly sensitive and selective sensor for the detection of Cu(2+) ions.

    PubMed

    Li, Zhongping; Zhang, Yuwei; Xia, Hong; Mu, Ying; Liu, Xiaoming

    2016-05-05

    A hydrogen bond assisted azine-linked covalent organic framework, COF-JLU3, was synthesized under solvothermal conditions. Combining excellent crystallinity, porosity, stability and luminescence, it can be the first COF as a fluorescent sensor for toxic metal ions, exhibiting high sensitivity and selectivity to Cu(2+).

  10. Light-induced covalent immobilization of monolayers of magnetic nanoparticles on hydrogen-terminated silicon.

    PubMed

    Leem, Gyu; Zhang, Shishan; Jamison, Andrew C; Galstyan, Eduard; Rusakova, Irene; Lorenz, Bernd; Litvinov, Dmitri; Lee, T Randall

    2010-10-01

    Specifically tailored ω-alkenyl-1-carboxylic acids were synthesized for use as surfactants in the single-step preparation of manganese ferrite (MnFe2O4) nanoparticles (NPs). Monodisperse manganese ferrite NPs terminated with ω-alkenyl moieties were prepared via a one-pot reaction at high temperature without the need of ligand exchange. Using this approach, simple adjustment of the rate of heating allowed precise tuning of the size of the nanoparticles, which were characterized in bulk form by transmission electron microscopy (TEM), Fourier-transform infrared (FT-IR) spectroscopy, and X-ray diffraction (XRD). These surfactant-coated magnetic nanoparticles were then deposited onto hydrogen-terminated silicon(111) wafers and covalently anchored to the surface by UV-initiated covalent bonding. Analysis by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) confirmed that the UV treatment led to covalent immobilization of the NPs on the silicon surface with a consistent packing density across the surface. The magnetic properties of the stable, surface-bound nanoparticle arrays were characterized using a superconducting quantum interference device (SQUID) magnetometer. The materials and methods described here are being developed for use in bit-patterned ultrahigh density magnetic recording media and nanoscale biomagnetic sensing.

  11. Covalently linked chlorophyll a dimer: A biomimetic model of special pair chlorophyll

    PubMed Central

    Wasielewski, Michael R.; Studier, Martin H.; Katz, Joseph J.

    1976-01-01

    The synthesis of a covalent dimer of chlorophyll a which possesses properties strikingly similar to those exhibited by P700 special pair chlorophyll in vivo is described. The covalent dimer is characterized by several spectroscopic techniques. Hydrogen bonding nucleophiles, such as water, primary alcohols, and primary thiols, are effective in generating a species from solutions of 10 μM covalent dimer in hydrophobic solvents which absorbs light near 700 nm. Formation of this in vitro special pair is a rapid, spontaneous process at room temperature. The range of nucleophiles which promote this process suggests that amino acid residues may function in a similar fashion to form P700 in chlorophyll-protein complexes. The photochemical properties of this in vitro special pair mimic those of in vivo P700 species. The 697 nm absorption of the in vitro special pair undergoes photo-bleaching rapidly in the presence of iodine that results in the production of a cation radical which exhibits an electron spin resonance signal similar to that of oxidized P700 observed in Chlorella vulgaris. PMID:16592367

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

    PubMed Central

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

    2015-01-01

    To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI: http://dx.doi.org/10.7554/eLife.06638.001 PMID:26032562

  13. Inactivation of the Mycobacterium tuberculosis antigen 85 complex by covalent, allosteric inhibitors.

    PubMed

    Favrot, Lorenza; Lajiness, Daniel H; Ronning, Donald R

    2014-09-05

    The rise of multidrug-resistant and totally drug-resistant tuberculosis and the association with an increasing number of HIV-positive patients developing tuberculosis emphasize the necessity to find new antitubercular targets and drugs. The antigen 85 (Ag85) complex from Mycobacterium tuberculosis plays important roles in the biosynthesis of major components of the mycobacterial cell envelope. For this reason, Ag85 has emerged as an attractive drug target. Recently, ebselen was identified as an effective inhibitor of the Ag85 complex through covalent modification of a cysteine residue proximal to the Ag85 active site and is therefore a covalent, allosteric inhibitor. To expand the understanding of this process, we have solved the x-ray crystal structures of Ag85C covalently modified with ebselen and other thiol-reactive compounds, p-chloromercuribenzoic acid and iodoacetamide, as well as the structure of a cysteine to glycine mutant. All four structures confirm that chemical modification or mutation at this particular cysteine residue leads to the disruption of the active site hydrogen-bonded network essential for Ag85 catalysis. We also describe x-ray crystal structures of Ag85C single mutants within the catalytic triad and show that a mutation of any one of these three residues promotes the same conformational change observed in the cysteine-modified forms. These results provide evidence for active site dynamics that may afford new strategies for the development of selective and potent Ag85 inhibitors.

  14. Noxious compounds activate TRPA1 ion channels through covalent modification of cysteines.

    PubMed

    Macpherson, Lindsey J; Dubin, Adrienne E; Evans, Michael J; Marr, Felix; Schultz, Peter G; Cravatt, Benjamin F; Patapoutian, Ardem

    2007-02-01

    The nervous system senses peripheral damage through nociceptive neurons that transmit a pain signal. TRPA1 is a member of the Transient Receptor Potential (TRP) family of ion channels and is expressed in nociceptive neurons. TRPA1 is activated by a variety of noxious stimuli, including cold temperatures, pungent natural compounds, and environmental irritants. How such diverse stimuli activate TRPA1 is not known. We observed that most compounds known to activate TRPA1 are able to covalently bind cysteine residues. Here we use click chemistry to show that derivatives of two such compounds, mustard oil and cinnamaldehyde, covalently bind mouse TRPA1. Structurally unrelated cysteine-modifying agents such as iodoacetamide (IA) and (2-aminoethyl)methanethiosulphonate (MTSEA) also bind and activate TRPA1. We identified by mass spectrometry fourteen cytosolic TRPA1 cysteines labelled by IA, three of which are required for normal channel function. In excised patches, reactive compounds activated TRPA1 currents that were maintained at least 10 min after washout of the compound in calcium-free solutions. Finally, activation of TRPA1 by disulphide-bond-forming MTSEA is blocked by the reducing agent dithiothreitol (DTT). Collectively, our data indicate that covalent modification of reactive cysteines within TRPA1 can cause channel activation, rapidly signalling potential tissue damage through the pain pathway.

  15. Covalent heme attachment in Synechocystis hemoglobin is required to prevent ferrous heme dissociation

    PubMed Central

    Hoy, Julie A.; Smagghe, Benoit J.; Halder, Puspita; Hargrove, Mark S.

    2007-01-01

    Synechocystis hemoglobin contains an unprecedented covalent bond between a nonaxial histidine side chain (H117) and the heme 2-vinyl. This bond has been previously shown to stabilize the ferric protein against denaturation, and also to affect the kinetics of cyanide association. However, it is unclear why Synechocystis hemoglobin would require the additional degree of stabilization accompanying the His117–heme 2-vinyl bond because it also displays endogenous bis-histidyl axial heme coordination, which should greatly assist heme retention. Furthermore, the mechanism by which the His117–heme 2-vinyl bond affects ligand binding has not been reported, nor has any investigation of the role of this bond on the structure and function of the protein in the ferrous oxidation state. Here we report an investigation of the role of the Synechocystis hemoglobin His117–heme 2-vinyl bond on structure, heme coordination, exogenous ligand binding, and stability in both the ferrous and ferric oxidation states. Our results reveal that hexacoordinate Synechocystis hemoglobin lacking this bond is less stable in the ferrous oxidation state than the ferric, which is surprising in light of our understanding of pentacoordinate Hb stability, in which the ferric protein is always less stable. It is also demonstrated that removal of the His117–heme 2-vinyl bond increases the affinity constant for intramolecular histidine coordination in the ferric oxidation state, thus presenting greater competition for the ligand binding site and lowering the observed rate and affinity constants for exogenous ligands. PMID:17242429

  16. Covalent modification of DNA regulates memory formation.

    PubMed

    Miller, Courtney A; Sweatt, J David

    2007-03-15

    DNA methylation is a covalent chemical modification of DNA catalyzed by DNA methyltransferases (DNMTs). DNA methylation is associated with transcriptional silencing and has been studied extensively as a lifelong molecular information storage mechanism put in place during development. Here we report that DNMT gene expression is upregulated in the adult rat hippocampus following contextual fear conditioning and that DNMT inhibition blocks memory formation. In addition, fear conditioning is associated with rapid methylation and transcriptional silencing of the memory suppressor gene PP1 and demethylation and transcriptional activation of the synaptic plasticity gene reelin, indicating both methyltransferase and demethylase activity during consolidation. DNMT inhibition prevents the PP1 methylation increase, resulting in aberrant transcription of the gene during the memory-consolidation period. These results demonstrate that DNA methylation is dynamically regulated in the adult nervous system and that this cellular mechanism is a crucial step in memory formation.

  17. 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.

  18. A Photoresponsive Smart Covalent Organic Framework.

    PubMed

    Huang, Ning; Ding, Xuesong; Kim, Jangbae; Ihee, Hyotcherl; Jiang, Donglin

    2015-07-20

    Ordered π-columnar structures found in covalent organic frameworks (COFs) render them attractive as smart materials. However, external-stimuli-responsive COFs have not been explored. Here we report the design and synthesis of a photoresponsive COF with anthracene units as the photoresponsive π-building blocks. The COF is switchable upon photoirradiation to yield a concavo-convex polygon skeleton through the interlayer [4π+4π] cycloaddition of anthracene units stacked in the π-columns. This cycloaddition reaction is thermally reversible; heating resets the anthracene layers and regenerates the COF. These external-stimuli-induced structural transformations are accompanied by profound changes in properties, including gas adsorption, π-electronic function, and luminescence. The results suggest that COFs are useful for designing smart porous materials with properties that are controllable by external stimuli.

  19. 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.

  20. Classification of metal-oxide bonded interactions based on local potential- and kinetic-energy densities

    SciTech Connect

    Gibbs, Gerald V.; Cox, David; Crawford, T Daniel; Rosso, Kevin M.; Ross, Nancy; Downs, R. T.

    2006-02-28

    A classification of the HF bonded interactions comprising a large number of molecules has been proposed by Espinosa et al. [J. Chem. Phys. 117, 5529 (2002)] based on the ratio |V(rc)|/G(rc) where |V(rc)| is the magnitude of the local potential energy density and G(rc) is the local kinetic density evaluated at the bond critical points, rc. A calculation of the ratio for the MO bonded interactions comprising a relatively large number of molecules and earth materials, together with the constraints imposed by the values of Ñ2ρ(rc) and the local electronic energy density H(rc) = G(rc) + V(rc) in the HF study, yielded the same classification for the oxides as found for the fluorides. This is true despite the different trends of the bond critical point and local energy properties with the bond length displayed by the HF and MO bonded interactions. LiO, NaO and MgO bonded interactions classify as closed shell ionic bonds, BeO, AlO, SiO, BO and PO bonded interactions classify as bonds of intermediate character and NO bonded interactions classify as shared covalent bonds. CO and SO bonded interactions classify as both intermediate and covalent bonded interactions. The CO triple bonded interaction classifies as a bond of intermediate character and the CO single bonded interaction classifies as a covalent bond whereas their H(rc) value indicates that they are both covalent bonds. The |V(rc)|/G(rc) ratios for the BeO, AlO and SiO bonded interactions indicate that they have a substantial component of ionic character despite their classification as bonds of intermediate character. The trend between |V(rc)|/G(rc) and the character of the bonded interaction is consistent with trends expected from electronegativity considerations. The connection between the net charges and the experimental SiO bond length evaluated for the Si and O atoms comprising two orthosilicates are examined in terms of the |V(rc)|/G(rc) values.

  1. 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.

  2. Covalently modified silicon and diamond surfaces: resistance to nonspecific protein adsorption and optimization for biosensing.

    PubMed

    Lasseter, Tami L; Clare, Brian H; Abbott, Nicholas L; Hamers, Robert J

    2004-08-25

    We report the direct covalent functionalization of silicon and diamond surfaces with short ethylene glycol (EG) oligomers via photochemical reaction of the hydrogen-terminated surfaces with terminal vinyl groups of the oligomers, and the use of these monolayers to control protein binding at surfaces. Photochemical modification of Si(111) and polycrystalline diamond surfaces produces EG monolayers linked via Si-C bond formation (silicon) or C-C bond formation (diamond). X-ray photoelectron spectroscopy was used to characterize the monolayer composition. Measurements using fluorescently labeled proteins show that the EG-functionalized surfaces effectively resist nonspecific adsorption of proteins. Additionally, we demonstrate the use of mixed monolayers on silicon and diamond and apply these surfaces to control specific versus nonspecific binding to optimize a model protein sensing assay.

  3. 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.

  4. Nitrogen-tuned bonding mechanism of Li and Ti adatom embedded graphene

    SciTech Connect

    Lee, Sangho; Chung, Yong-Chae

    2013-09-15

    The effects of nitrogen defects on the bonding mechanism and resultant binding energy between the metal and graphene layer were investigated using density functional theory (DFT) calculations. For the graphitic N-doped graphene, Li adatom exhibited ionic bonding character, while Ti adatom showed features of covalent bonding similar to that of pristine graphene. However, in the cases of pyridinic and pyrrolic structures, partially covalent bonding characteristic occurred around N atoms in the process of binding with metals, and this particular bond formation enhanced the bond strength of metal on the graphene layer as much as it exceeded the cohesive energy of the metal bulk. Thus, Li and Ti metals are expected to be dispersed with atomic accuracy on the pyridinic and pyrrolic N-doped graphene layers. These results demonstrate that the bonding mechanism of metal–graphene complex can change according to the type of N defect, and this also affects the binding results. - Graphical abstract: Display Omitted - Highlights: • Nitrogen defects changed the bonding mechanism between metal and graphene. • Bonding character and binding results were investigated using DFT calculations. • Covalent bonding character occurred around pyridinic and pyrrolic N-doped graphene. • Pyridinic and pyrrolic N atoms are effective for metal dispersion on the graphene.

  5. 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

  6. Feynman force components: basis for a solution to the covalent vs. ionic dilemma.

    PubMed

    Dominikowska, Justyna; Jabłoński, Mirosław; Palusiak, Marcin

    2016-09-14

    The Hellmann-Feynman theorem, when applied to nuclear coordinates in a molecular system, states that Feynman forces, i.e. forces acting on a nucleus in a molecule, are solely of an electrostatic nature. This theorem is described by Slater as "the most powerful" theorem applicable to molecules. However, its possibilities have hardly been harnessed. This work presents the use of the Hellmann-Feynman theorem in conjunction with the partitioning of the molecular space into atoms in the spirit of the quantum theory of atoms in molecules (QTAIM). Homopolar and heteropolar diatomic molecules of varying polarity are studied in the context of Feynman force components, i.e. the components exerted on each nucleus by the other nucleus and by the electron density distributions of each of the atoms. These results are further related to electronegativity differences used in the differentiation between covalent and ionic bond. The approach based on the directions of Feynman force components gives physical fundamentals for covalent vs. ionic bond distinction without referring to the electronegativity concept.

  7. Covalent modification of calcium hydroxyapatite surface by grafting phenyl phosphonate moieties

    SciTech Connect

    Aissa, Abdallah; Debbabi, Mongi; Gruselle, Michel Thouvenot, Rene; Gredin, Patrick; Traksmaa, Rainer; Tonsuaadu, Kaia

    2007-08-15

    The reaction between phenyl phosphonic dichloride (C{sub 6}H{sub 5}P(O)Cl{sub 2}) and synthetic calcium hydroxy- and fluorapatite has been investigated. The presence of mono- or polymeric (C{sub 6}H{sub 5}PO) fragment bound to hydroxyapatite was evidenced by IR, and solid-state {sup 31}P NMR spectroscopy. X-ray powder analysis has shown that the apatitic structure remains unchanged during the reaction. In contrast, no reaction was found using fluorapatite. According to the results found for these two different apatites a mechanism was proposed for the formation of covalent P-O-P bonds as the result of a reaction between the C{sub 6}H{sub 5}P(O)Cl{sub 2} organic reagent and (HPO{sub 4}){sup -} and/or OH{sup -} ions of the hydroxyapatite. - Graphical abstract: Representation of the first step of the reaction between the phenyl phosphonic dichloride and the hydroxyl groups on the surface of the apatite, leading to covalent P-O-P bond with elimination of HCl.

  8. 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.

  9. 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

  10. 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)

  11. New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

    PubMed Central

    2016-01-01

    Hydrogen bond donor catalysis represents a rapidly growing subfield of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new organic catalysts for electrophile activation through the formation of C–H hydrogen bonds and C–X halogen bonds. PMID:28144357

  12. Self-assembled and covalently linked capillary coating of diazoresin and cyclodextrin-derived dendrimer for analysis of proteins by capillary electrophoresis.

    PubMed

    Yu, Bing; Chi, Ming; Han, Yuxing; Cong, Hailin; Tang, Jianbin; Peng, Qiaohong

    2016-05-15

    Self-assembled and covalently linked capillary coatings of cyclodextrin-derived (CD) dendrimer were prepared using photosensitive diazoresin (DR) as a coupling agent. Layer by layer (LBL) self-assembled DR/CD-dendrimer coatings based on ionic bonding was fabricated first on the inner surface of capillary, and subsequently converted into covalent bonding after treatment with UV light through a unique photochemistry reaction of DR. Protein adsorption on the inner surface of capillary was suppressed by the DR/CD-dendrimer coating, and thus a baseline separation of lysozyme (Lys), myoglobin (Mb), bovine serum albumin (BSA) and ribonuclease A (RNase A) was achieved using capillary electrophoresis (CE). Compared with the bare capillary, the DR/CD-dendrimer covalently linked capillary coatings showed excellent protein separation performance with good stability and repeatability. Because of the replacement of highly toxic and moisture sensitive silane coupling agent by DR in the covalent coating preparation, this method may provide an environmentally friendly and simple way to prepare the covalently coated capillaries for CE.

  13. 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.

  14. 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.

  15. OH-transition metal bonding

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.

    1986-01-01

    The bonding in both CuOH and AgOH has a covalent component that leads to a bent structure. The larger electrostatic stabilization in CuOH leads to a larger D(e) (2.83 eV) compared with AgOH (2.20 eV). Using Ni5OH to model chemisorption of OH on a Ni surface, it is found that OH adsorption in the fourfold hollow of Ni(100) leads to an OH normal to the surface, while adsorption directly above a Ni atom leads to a tilted OH. These qualitative Ni5OH calculations allow for speculation on the observed variation of OH on metal surfaces.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Ionic Covalent Organic Frameworks with Spiroborate Linkage.

    PubMed

    Du, Ya; Yang, Haishen; Whiteley, Justin Michael; Wan, Shun; Jin, Yinghua; Lee, Se-Hee; Zhang, Wei

    2016-01-26

    A novel type of ionic covalent organic framework (ICOF), which contains sp(3)  hybridized boron anionic centers and tunable countercations, was constructed by formation of spiroborate linkages. These ICOFs exhibit high BET surface areas up to 1259 m(2)  g(-1) and adsorb a significant amount of H2 (up to 3.11 wt %, 77 K, 1 bar) and CH4 (up to 4.62 wt %, 273 K, 1 bar). Importantly, the materials show good thermal stabilities and excellent resistance to hydrolysis, remaining nearly intact when immersed in water or basic solution for two days. The presence of permanently immobilized ion centers in ICOFs enables the transportation of lithium ions with room-temperature lithium-ion conductivity of 3.05×10(-5)  S cm(-1) and an average Li(+) transference number value of 0.80±0.02. Our approach thus provides a convenient route to highly stable COFs with ionic linkages, which can potentially serve as absorbents for alternative energy sources such as H2, CH4, and also as solid lithium electrolytes/separators for the next-generation lithium batteries.

  2. 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.

  3. 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.

  4. 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.

  5. Strategies to balance covalent and non-covalent biomolecule attachment within collagen-GAG biomaterials.

    PubMed

    Pence, Jacquelyn C; Gonnerman, Emily A; Bailey, Ryan C; Harley, Brendan A C

    2014-09-01

    Strategies to integrate instructive biomolecular signals into a biomaterial are becoming increasingly complex and bioinspired. While a large majority of reports still use repeated treatments with soluble factors, this approach can be prohibitively costly and difficult to translate in vivo for applications where spatial control over signal presentation is necessary. Recent efforts have explored the use of covalent immobilization of biomolecules to the biomaterial, via both bulk (ubiquitous) as well as spatially-selective light-based crosslinking, as a means to both enhance stability and bioactivity. However, little is known about how processing conditions during immobilization impact the degree of unintended non-covalent interactions, or fouling, that takes place between the biomaterial and the biomolecule of interest. Here we demonstrate the impact of processing conditions for bulk carbodiimide (EDC) and photolithography-based benzophenone (BP) crosslinking on specific attachment vs. fouling of a model protein (Concanavalin A, ConA) within collagen-glycosaminoglycan (CG) scaffolds. Collagen source significantly impacts the selectivity of biomolecule immobilization. EDC crosslinking intensity and ligand concentration significantly impacted selective immobilization. For benzophenone photoimmobilization we observed that increased UV exposure time leads to increased ConA immobilization. Immobilization efficiency for both EDC and BP strategies was maximal at physiological pH. Increasing ligand concentration during immobilization process led to enhanced immobilization for EDC chemistry, no impact on BP immobilization, but significant increases in non-specific fouling. Given recent efforts to covalently immobilize biomolecules to a biomaterial surface to enhance bioactivity, improved understanding of the impact of crosslinking conditions on selective attachment versus non-specific fouling will inform the design of instructive biomaterials for applications across tissue

  6. Drug discovery considerations in the development of covalent inhibitors.

    PubMed

    Mah, Robert; Thomas, Jason R; Shafer, Cynthia M

    2014-01-01

    In recent years, the number of drug candidates with a covalent mechanism of action progressing through clinical trials or being approved by the FDA has increased significantly. And as interest in covalent inhibitors has increased, the technical challenges for characterizing and optimizing these inhibitors have become evident. A number of new tools have been developed to aid this process, but these have not gained wide-spread use. This review will highlight a number of methods and tools useful for prosecuting covalent inhibitor drug discovery programs.

  7. Non-covalent interactions in ionic liquid ion pairs and ion pair dimers: a quantum chemical calculation analysis.

    PubMed

    Marekha, Bogdan A; Kalugin, Oleg N; Idrissi, Abdenacer

    2015-07-14

    Ionic liquids (ILs) being composed of bulky multiatomic ions reveal a plethora of non-covalent interactions which determine their microscopic structure. In order to establish the main peculiarities of these interactions in an IL-environment, we have performed quantum chemical calculations for a set of representative model molecular clusters. These calculations were coupled with advanced methods of analysis of the electron density distribution, namely, the quantum theory of atoms in molecules (QTAIM) and the non-covalent interaction (NCI; J. Am. Chem. Soc., 2010, 132, 6499) approaches. The former allows for profound quantitative characterization of non-covalent interactions between atoms while the latter gives an overview of spatial extent, delocalization, and relative strength of such interactions. The studied systems consist of 1-butyl-3-methylimidazolium (Bmim(+)) cations and different perfluorinated anions: tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), and bis(trifluoromethanesulfonyl)imide (TFSI(-)). IL ion pairs and ion pair dimers were considered as model structures for the neat ILs and large aggregates. Weak electrostatic hydrogen bonding was found between the anions and the imidazolium ring hydrogen atoms of cations. Weaker but still appreciable hydrogen bonding was also noted for hydrogen atoms adjacent to the imidazolium ring alkyl groups of Bmim(+). The relative strength of the hydrogen bonding is higher in BmimTfO and BmimBF4 ILs than in BmimPF6 and BmimTFSI, whereas BmimTfO and BmimTFSI reveal higher sensitivity of hydrogen bonding at the different hydrogen atoms of the imidazolium ring.

  8. Covalent Polymers Containing Discrete Heterocyclic Anion Receptors

    NASA Astrophysics Data System (ADS)

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

    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 noncovalent interactions (e.g., hydrogen bonding and electrostatic interactions) provides a route to not only sensitive but also selective polymeric materials. Furthermore, these systems have been utilized in the development of polymers capable of extracting anionic species from aqueous media. These latter materials may lead to advances in water purification and treatment of diseases resulting from surplus ions.

  9. Self-generated covalent cross-links in the cell-surface adhesins of Gram-positive bacteria.

    PubMed

    Baker, Edward N; Squire, Christopher J; Young, Paul G

    2015-10-01

    The ability of bacteria to adhere to other cells or to surfaces depends on long, thin adhesive structures that are anchored to their cell walls. These structures include extended protein oligomers known as pili and single, multi-domain polypeptides, mostly based on multiple tandem Ig-like domains. Recent structural studies have revealed the widespread presence of covalent cross-links, not previously seen within proteins, which stabilize these domains. The cross-links discovered so far are either isopeptide bonds that link lysine side chains to the side chains of asparagine or aspartic acid residues or ester bonds between threonine and glutamine side chains. These bonds appear to be formed by spontaneous intramolecular reactions as the proteins fold and are strategically placed so as to impart considerable mechanical strength.

  10. 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.

  11. 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.

  12. Correlation between the covalency and the thallium-205 nuclear magnetic resonance chemical shift in oxides and halides

    NASA Astrophysics Data System (ADS)

    Jouini, N.

    1986-07-01

    205Tl chemical shift measurements were carried out on thallium(I) oxides and halides. A correlation between the chemical shift and the stereochemical activity of the 6 s2 lone pair of Tl I was established; the greater this activity, the greater the absolute value of the chemical shift. For the halides, optical and chemical shift measurements gave access to the Tl- X bond ionicity via Ramsey's equation. In thallium(I) halides the absolute value of the chemical shift increases with the covalency. The work of Glaser on thallium(III) halides showed the chemical shift to decrease with increasing covalency. An explication of this difference is proposed. The hyperfine coupling constant A of the paramagnetic compound Tl 4MnI 6 was determined by the study of the chemical shift as a function of the susceptibility. This constant A is seen to be weak (-7 KG/μ B).

  13. Correlation between the covalency and the thallium-205 nuclear magnetic resonance chemical shift in oxides and halides

    SciTech Connect

    Jouini, N.

    1986-07-15

    /sup 205/Tl chemical shift measurements were carried out on thallium(I) oxides and halides. A correlation between the chemical shift and the stereochemical activity of the 6s/sup 2/ lone pair of Tl/sup I/ was established; the greater this activity, the greater the absolute value of the chemical shift. For the halides, optical and chemical shift measurements gave access to the Tl-X bond ionicity via Ramsey's equation. In thallium(I) halides the absolute value of the chemical shift increases with the covalency. The work of Glaser on thallium(III) halides showed the chemical shift to decrease with increasing covalency. An explication of this difference is proposed. The hyperfine coupling constant A of the paramagnetic compound Tl/sub 4/MnI/sub 6/ was determined by the study of the chemical shift as a function of the susceptibility. This constant A is seen to be weak (-7 KG/..mu../sub B/).

  14. Covalently functionalized hexagonal boron nitride nanosheets by nitrene addition.

    PubMed

    Sainsbury, Toby; Satti, Amro; May, Peter; O'Neill, Arlene; Nicolosi, Valeria; Gun'ko, Yurii K; Coleman, Jonathan N

    2012-08-27

    The covalent functionalization of exfoliated hexagonal boron nitride (h-BN) nanosheets by nitrene addition is described. Integration of functionalized h-BN nanosheets within a polycarbonate matrix is demonstrated and was found to afford significant increases in mechanical properties. This integration methodology was further extended by the covalent modification of the h-BN nanosheets with polymer chains of a polycarbonate analogue, and the integration of the polymer modified h-BN within the polymer matrix.

  15. Preparation and characterization of malonic acid cross-linked chitosan and collagen 3D scaffolds: an approach on non-covalent interactions.

    PubMed

    Mitra, Tapas; Sailakshmi, G; Gnanamani, A; Mandal, A B

    2012-05-01

    The present study emphasizes the influence of non-covalent interactions on the mechanical and thermal properties of the scaffolds of chitosan/collagen origin. Malonic acid (MA), a bifuncitonal diacid was chosen to offer non-covalent cross-linking. Three dimensional scaffolds was prepared using chitosan at 1.0% (w/v) and MA at 0.2% (w/v), similarly collagen 0.5% (w/v) and MA 0.2% (w/v) and characterized. Results on FT-IR, TGA, DSC, SEM and mechanical properties (tensile strength, stiffness, Young's modulus, etc.) assessment demonstrated the existence of non-covalent interaction between MA and chitosan/collagen, which offered flexibility and high strength to the scaffolds suitable for tissue engineering research. Studies using NIH 3T3 fibroblast cells suggested biocompatibility nature of the scaffolds. Docking simulation study further supports the intermolecular hydrogen bonding interactions between MA and chitosan/collagen.

  16. DOCKTITE-a highly versatile step-by-step workflow for covalent docking and virtual screening in the molecular operating environment.

    PubMed

    Scholz, Christoph; Knorr, Sabine; Hamacher, Kay; Schmidt, Boris

    2015-02-23

    The formation of a covalent bond with the target is essential for a number of successful drugs, yet tools for covalent docking without significant restrictions regarding warhead or receptor classes are rare and limited in use. In this work we present DOCKTITE, a highly versatile workflow for covalent docking in the Molecular Operating Environment (MOE) combining automated warhead screening, nucleophilic side chain attachment, pharmacophore-based docking, and a novel consensus scoring approach. The comprehensive validation study includes pose predictions of 35 protein/ligand complexes which resulted in a mean RMSD of 1.74 Å and a prediction rate of 71.4% with an RMSD below 2 Å, a virtual screening with an area under the curve (AUC) for the receiver operating characteristics (ROC) of 0.81, and a significant correlation between predicted and experimental binding affinities (ρ = 0.806, R(2) = 0.649, p < 0.005).

  17. Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach.

    PubMed

    Yurenko, Yevgen P; Novotný, Jan; Sklenář, Vladimir; Marek, Radek

    2014-02-07

    The study aimed to cast light on the structure and internal energetics of guanine- and xanthine-based model DNA quadruplexes and the physico-chemical nature of the non-covalent interactions involved. Several independent approaches were used for this purpose: DFT-D3 calculations, Quantum Theory of Atoms in Molecules, Natural Bond Orbital Analysis, Energy Decomposition Analysis, Compliance Constant Theory, and Non-Covalent Interaction Analysis. The results point to an excellent degree of structural and energetic compatibility between the two types of model quadruplexes. This fact stems from both the structural features (close values of van der Waals volumes, pore radii, geometrical parameters of the H-bonds) and the energetic characteristics (comparable values of the energies of formation). It was established that hydrogen bonding makes the greatest (∼50%) contribution to the internal stability of the DNA quadruplexes, whereas the aromatic base stacking and ion coordination terms are commensurable and account for the rest. Energy decomposition analysis performed for guanine (Gua) and xanthine (Xan) quartets B4 and higher-order structures consisting of two or three stacked quartets indicates that whereas Gua structures benefit from a high degree of H-bond cooperativity, Xan models are characterized by a more favorable and cooperative π-π stacking. The results of electron density topological analysis show that Na(+)/K(+) ion coordination deeply affects the network of non-covalent interactions in Gua models due to the change in the twist angle between the stacked tetrads. For Xan models, ion coordination makes tetrads in stacks more planar without changing the twist angle. Therefore, the presence of the ion seems to be essential for the formation of planar stacks in Xan-based DNA quadruplexes. Detailed study of the nature of ion-base coordination suggests that this interaction has a partially covalent character and cannot be considered as purely electrostatic

  18. 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

    2014-11-07

    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.

  19. 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.

  20. Covalently Bonded Three-Dimensional Carbon Nanotube Solids via Boron Induced Nanojunctions

    DTIC Science & Technology

    2012-04-13

    morphologies exploited to create 3D macroscale architectures. Theoretical studies had predicted that significant structural reorganization generates stable...Gogotsi25. These architectures had been studied theoretically as fas- cinating future materials with superior mechanical and electrical properties26. In...density material that wasmore soft and flexible. Microscopy characterization. The morphology and structural properties were extensively studied by SEM

  1. Superstrong nature of covalently bonded glass-forming liquids at select compositions

    NASA Astrophysics Data System (ADS)

    Gunasekera, K.; Bhosle, S.; Boolchand, P.; Micoulaut, M.

    2013-10-01

    Variation of fragility (m) of specially homogenized GexSe100-x melts is established from complex specific heat measurements and shows that m(x) has a global minimum at an extremely low value (m = 14.8(0.5)) in the 21.5% < x < 23% range of Ge. Outside of that compositional range, m(x) then increases first rapidly and then slowly to about m = 25-30. By directly mapping melt stoichiometry as a function of reaction time at a fixed temperature T > Tg, we observe a slowdown of melt-homogenization by the super-strong melt compositions, 21.5% < x < 23%. This range furthermore appears to be correlated to the one observed between the flexible and stressed rigid phase in network glasses. These spectacular features underscore the crucial role played by topology and rigidity in the properties of network-forming liquids and glasses which are highlighted when fragility is represented as a function of variables tracking the effect of rigidity. Finally, we investigate the fragility-glass transition temperature relationship, and find that reported scaling laws do not apply in the flexible phase, while being valid for intermediate and stressed rigid compositions.

  2. Preparation and characterization of monoliths covalently bonded chelating groups for capillary electrochromatographic separation of metal ions.

    PubMed

    Wang, Guan-Ren; Huang, Kuan-Pin; Huang, Bao-Yu; Liu, Chuen-Ying

    2009-08-21

    In this work, a novel polymer-based monolithic column was prepared using an o-phthalaldehyde-l-phenylalanine Schiff base complex as the reactive center and a mixture of methanol and n-propanol as the porogen. The monolithic column was employed for the separation of a metal ion mixture including Pb(II), Mn(II), Cu(II), Ni(II), Cr(III), Fe(III) and Cr(VI). Tetrabutylammonium bromide (TBAB) was used as a mobile phase additive to enhance the separation efficiency of metal ions by EDTA precomplexation. Using a phosphate buffer (20 mM, pH 3.0), TBAB (10 mM), MeOH (15%, v/v), an applied voltage of -15 kV, and detection at 220 nm, the metal ion mixture was satisfactorily resolved. The average theoretical plate number was 17,900 plates/m. The separation was also carried out in the absence of TBAB, leading to dissimilar elution order and shorter retention time. The separation behavior of the monolithic column was also compared with that of the blank polymer. The unique properties of the monolithic column might be mediated by a combination of electrophoretic behavior and chromatographic retention involving hydrophobic and hydrophilic interactions, as well as ligand exchange.

  3. Role of non-covalent and covalent interactions in cargo loading capacity and stability of polymeric micelles.

    PubMed

    Ke, Xiyu; Ng, Victor Wee Lin; Ono, Robert J; Chan, Julian M W; Krishnamurthy, Sangeetha; Wang, Ying; Hedrick, James L; Yang, Yi Yan

    2014-11-10

    Polymeric micelles self-assembled from biodegradable amphiphilic block copolymers have been proven to be effective drug delivery carriers that reduce the toxicity and enhance the therapeutic efficacy of free drugs. Several reviews have been reported in the literature to discuss the importance of size/size distribution, stability and drug loading capacity of polymeric micelles for successful in vivo drug delivery. This review is focused on non-covalent and covalent interactions that are employed to enhance cargo loading capacity and in vivo stability, and to achieve nanosize with narrow size distribution. In particular, this review analyzes various non-covalent and covalent interactions and chemistry applied to introduce these interactions to the micellar drug delivery systems, as well as the effects of these interactions on micelle stability, drug loading capacity and release kinetics. Moreover, the factors that influence these interactions and the future research directions of polymeric micelles are discussed.

  4. A designed P1 cysteine mimetic for covalent and non-covalent inhibitors of HCV NS3 protease.

    PubMed

    Narjes, Frank; Koehler, Konrad F; Koch, Uwe; Gerlach, Benjamin; Colarusso, Stefania; Steinkühler, Christian; Brunetti, Mirko; Altamura, Sergio; De Francesco, Raffaele; Matassa, Victor G

    2002-02-25

    The difluoromethyl group was designed by computational chemistry methods as a mimetic of the canonical P1 cysteine thiol for inhibitors of the hepatitis C virus NS3 protease. This modification led to the development of competitive, non-covalent inhibitor 4 (K(i) 30 nM) and reversible covalent inhibitors (6, K(i) 0.5 nM; and 8 K*(i) 10 pM).

  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. Digestibility and supramolecular structural changes of maize starch by non-covalent interactions with gallic acid.

    PubMed

    Chi, Chengdeng; Li, Xiaoxi; Zhang, Yiping; Chen, Ling; Li, Lin; Wang, Zhijiang

    2017-02-22

    The effects of non-covalent interactions between gallic acid (GA) and starch on starch digestibility and supramolecular structural changes (short-range ordered molecular structure, crystalline structure, lamellar structure and fractal structure) were investigated. The results indicated that the digestibility of both starches was substantially reduced in the rapidly digestible starch (RDS) content, but resistant starch (RS) was increased after interacting with GA. The RS content of starch-GA complexes ranged from 17.70 to 50.02%, which is much higher than that of high amylose starch (G50) (11.11%) and normal maize starch (NMS) (4.46%). Compared with native starches, starch-GA complexes possess more ordered and compact structures; furthermore, G50-GA complexes possessed more compact scattering objects, thicker crystalline lamellae and thinner amorphous lamellae than those of NMS-GA complexes. This revealed that more ordered multi-scale structures promote the RS formation. Docking studies were conducted to reveal the mechanism of digestibility variations. It showed that GA would non-covalently interact with starch molecules and contribute to ordered structure formation to somewhat extent; meanwhile, GA had higher binding affinities to α-amylase than to starch chains; during the hydrolytic process, GA could be released from the complex and was more likely to occupy the active sites of Asp197, Asp300, His299 and Glu233 by hydrogen bonds and van der Waals forces, which kept starch out of the active site pocket and reduced starch digestibility. These results demonstrate that the non-covalent interactions between GA and starch could be a promising method of controlling starch structures and starch digestion behaviors.

  7. 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

  8. 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)

  9. 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.

  10. 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.

  11. 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.

  12. 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…

  13. 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.

  14. Comparative study of the covalent diazotization of graphene and carbon nanotubes using thermogravimetric and spectroscopic techniques.

    PubMed

    Castelaín, Marta; Shuttleworth, Peter S; Marco, Carlos; Ellis, Gary; Salavagione, Horacio J

    2013-10-21

    The direct diazotization of the sp(2) carbon network of graphene and multi-walled carbon nanotubes (MWNTs) is one of the many methods employed to introduce functional groups into these nanostructures. Herein, a methodical study on solvent-free diazotization with ethynylaniline in the presence of isoamyl nitrite is reported. Thermogravimetric analysis and UV-visible, infrared and Raman spectroscopies are used to precisely determine the degree of modification, confirm the presence of physisorption and describe the mechanism of elimination of the modifying groups. The results suggest that the same synthetic protocol in both cases leads to a certain degree of covalent modification, whilst a proportion of the modifying groups remains adsorbed to the carbon nanostructure. A higher level of global modification was observed for MWNTs. It was found that the elimination mechanism of the covalently-linked modifiers is identical for both nanostructures and involves two steps; acetylenic-aromatic bond rupture in the modifier followed by modifier-carbon nanostructure cleavage.

  15. 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

  16. Modification of the adhesive properties of collagen by covalent grafting with RGD peptides.

    PubMed

    Myles, J L; Burgess, B T; Dickinson, R B

    2000-01-01

    Collagen, either alone or in combination with other materials, is an important natural biomaterial that is used in a variety of tissue-engineering applications. Cell adhesion and migration of cells within collagen-based biomaterials may be controlled by modifying the adhesive properties of collagen. Furthermore, spatially controlling the adhesiveness of the collagen may allow controlled localization or redistribution of cells. A method is presented for covalently coupling peptides that contain the well-characterized arginine-glycine-aspartic acid adhesion sequence directly to type I collagen monomers prior to fibrillogenesis. A heterobifunctional coupling agent was used to create stable amide and disulfide bonds with the lysine residues of the collagen monomers and the cysteine termini of the peptide molecules, respectively. The degree of conjugation could be controlled by changing the reaction conditions (ratios of reactants added and the length of incubation). The microstructure and gelation times of gels composed of covalently modified collagen were similar to those of unmodified gels. Cell adhesion on adsorbed monolayers of modified collagen was quantified using a well-established clonal cell line (K1735 murine melanoma). Cell adhesion was found to increase with both increasing degree of conjugation and increasing ratio of modified to unmodified collagen.

  17. 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.

  18. Coordination Covalent Frameworks: A New Route for Synthesis and Expansion of Functional Porous Materials

    SciTech Connect

    Elsaidi, Sameh K.; Mohamed, Mona H.; Loring, John S.; McGrail, Bernard. Pete; Thallapally, Praveen K.

    2016-10-26

    The synthetic approaches for fine-tuning the structural properties of coordination polymers or metal organic frameworks have exponentially grown during the last decade. This is due to the control over the properties of the resulting structures such as stability, pore size, pore chemis-try and surface area for myriad possible applications. Herein, we present a new class of porous materials called Covalent Coordination Frameworks (CCFs) that were designed and effectively synthesized using a two-step reticular chemistry approach. During the first step, trigonal prismatic molecular building block was isolated using 4-aminobenazoic acid and Cr (III) salt, subsequently in the second step the polymerization of the isolated molecular building blocks (MBBs) takes place by the formation of strong covalent bonds where small organic molecules can connect the MBBs forming extended porous CCF materials. All the isolated CCFs were found to be permanently porous while the discrete MBB were non-porous. This approach would inevitably open a feasible path for the applications of reticular chemistry and the synthesis of novel porous materials with various topologies under ambient conditions using simple organic molecules and versatile MBBs with different functionalities which would not be possible using the traditional one step approach

  19. Graphene Oxide Quantum Dots Covalently Functionalized PVDF Membrane with Significantly-Enhanced Bactericidal and Antibiofouling Performances.

    PubMed

    Zeng, Zhiping; Yu, Dingshan; He, Ziming; Liu, Jing; Xiao, Fang-Xing; Zhang, Yan; Wang, Rong; Bhattacharyya, Dibakar; Tan, Timothy Thatt Yang

    2016-02-02

    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.

  20. A review of the electrophilic reaction chemistry involved in covalent DNA binding.

    PubMed

    Enoch, S J; Cronin, M T D

    2010-09-01

    The need to assess the ability of a chemical to act as a mutagen or a genotoxic carcinogen (collectively termed genotoxicity) is one of the primary requirements in regulatory toxicology. Several pieces of legislation have led to an increased interest in the use of in silico methods, specifically the formation of chemical categories for the assessment of toxicological endpoints. A key step in the development of chemical categories for genotoxicity is defining the organic chemistry associated with the formation of a covalent bond between DNA and an exogenous chemical. This organic chemistry is typically defined as structural alerts. To this end, this article has reviewed the literature defining the structural alerts associated with covalent DNA binding. Importantly, this review article also details the mechanistic organic chemistry associated with each of the structural alerts. This information is extremely important in terms of meeting regulatory requirements for the acceptance of the chemical category approach. The structural alerts and associated mechanistic chemistry have been incorporated into the Organisation for Economic Co-operation and Development (OECD) (Q)SAR Application Toolbox.

  1. Surface functionalization of silica-coated magnetic nanoparticles for covalent attachment of cholesterol oxidase

    NASA Astrophysics Data System (ADS)

    Šulek, Franja; Drofenik, Miha; Habulin, Maja; Knez, Željko

    2010-01-01

    A systematic approach towards the fabrication of highly functionalized silica shell magnetic nanoparticles, presently used for enzyme immobilization, is herein fully presented. The synthesis of bare maghemite (γ-Fe 2O 3) nanoparticles was accomplished by thermal co-precipitation of iron ions in ammonia alkaline solution at harsh reaction conditions, respectively. Primary surface engineering of maghemite nanoparticles was successfully performed by the proper deposition of silica onto nanoparticles surface under strictly regulated reaction conditions. Next, the secondary surface functionalization of the particles was achieved by coating the particles with organosilane followed by glutaraldehyde activation in order to enhance protein immobilization. Covalent immobilization of cholesterol oxidase was attempted afterwards. The structural and magnetic properties of magnetic silica nanocomposites were characterized by TEM and vibrating sample magnetometer (VSM) instruments. X-ray diffraction measurements confirmed the spinel structure and average size of uncoated maghemite nanoparticles to be around 20 nm in diameter. SEM-EDS spectra indicated a strong signal for Si, implying the coating procedure of silica onto the particles surface to be successfully accomplished. Fourier transform infrared (FT-IR) spectra analysis confirmed the binding of amino silane molecules onto the surface of the maghemite nanoparticles mediated Si-O-Si chemical bonds. Compared to the free enzyme, the covalently bound cholesterol oxidase retained 50% of its activity. Binding of enzyme onto chemically modified magnetic nanoparticles via glutaraldehyde activation is a promising method for developing biosensing components in biomedicine.

  2. The structural and bonding evolution in cysteine-gold cluster complexes.

    PubMed

    Zhao, Yaxue; Zhou, Feng; Zhou, Huchen; Su, Haibin

    2013-02-07

    The bonding characteristics in cysteine-gold cluster complexes represented by thiolate (Au(n)·Cys(S) (n = 1, 3, 5, 7)) and thiol (Au(n)·Cys(SH) (n = 2, 4, 6, 8)) is investigated by density functional theory with 6-31G(d,p) and Lanl2DZ hybrid basis sets. The complexes exhibit very different bonding characteristic between these two forms. In the Au(n)·Cys(S) complexes, the charge transfers from gold clusters to sulfur atoms. The number of S-Au bonds in the Au(n)·Cys(S) complexes evolves from one to two when n is greater than three. For n equals three, i.e. Au(3)·Cys(S), its ground state only has one S-Au bond. While the only S-Au bond in Au(1)·Cys(S) is mainly covalent, the nature of the S-Au bond in other thiolates is featured with the combination of covalent and donor-acceptor interactions. In particular, one stable isomer of Au(3)·Cys(S) with two S-Au bonds, which is 2 kcal mol(-1) higher in energy than the corresponding ground state, consists of one covalent and one donor-acceptor S-Au bond explicitly. Moreover, the localized three center two electron bonds are formed within the Au clusters, which facilitates the formation of the two S-Au bonds in Au(5)·Cys(S) and Au(7)·Cys(S) complexes. In the Au(n)·Cys(SH) complexes, the donor-acceptor interaction prevails in the Au-SH bond by transferring lone pair electrons from the sulfur atom to the adjacent gold atom. Interestingly, the orbital with much more 6s-component in Au(4)·Cys(SH) enhances the donor-acceptor bonding character, thus yields the strongest bonding among all the Au(n)·Cys(SH) complexes studied in this paper. In general, the bonding strength between gold clusters and cysteine is positively correlated with the S-Au overlap-weighted bond order, but negatively correlated with the S-Au bond length. Lastly, the covalent and donor-acceptor S-Au bond strength is computed to be 48 and 18 kcal mol(-1), respectively.

  3. K3036.58 in the μ opioid (MOP) receptor is important in conferring selectivity for covalent binding of β-funaltrexamine (β-FNA)

    PubMed Central

    DiMattio, Kelly M.; Chen, Chongguang; Shi, Lei; Liu-Chen, Lee-Yuan

    2014-01-01

    β-funaltrexamine (β-FNA) is an irreversible μ opioid (MOP) receptor antagonist and a reversible agonist of κ opioid (KOP) receptor. β-FNA binds covalently to the MOP receptor at Lys2335.39, which is conserved among opioid receptors. Molecular docking of β-FNA showed that K3036.58 in the MOP receptor and E2976.58 in the KOP receptor played distinct roles in positioning β-FNA. K3036.58E MOP receptor and E2976.58K KOP receptor mutants were generated. The mutations did not affect β-FNA affinity or efficacy. K3036.58E mutation in the MOP receptor greatly reduced covalent binding of [3H]β-FNA; however, E2976.58K did not enable the KOP receptor to bind irreversibly to β-FNA. Molecular modeling demonstrated that the ε-amino group of K3036.58 in the MOP receptor interacted with C=O of the acetate group of β-FNA to facilitate covalent bond formation with Lys2335.39. Replacement of K3036.58 with Glu in the MOP receptor resulted in repulsion between the COOH of Glu and the C=O of β-FNA and increased the distance between K2335.39 and the fumarate group, making it impossible for covalent bond formation. These findings will be helpful for design of selective non-peptide MOP receptor antagonists. PMID:25481857

  4. Materials Data on K2RuCl6 (SG:225) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  5. Materials Data on Pr3RuCl3 (SG:62) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-10

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  6. Materials Data on RuCl3 (SG:193) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-04-22

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  7. Monolayer of Hydrazine Facilitates the Direct Covalent Attachment of C60 Fullerene to a Silicon Surface.

    PubMed

    Gao, Fei; Teplyakov, Andrew V

    2017-02-13

    The development of oxygen-free organic-inorganic interfaces has led to new schemes for the functionalization of silicon surfaces with nitrogen-based chemical groups. However, building layers of large structures directly on this functionalized surface has remained elusive. This work confirms the path to form a stable interface between silicon and buckminsterfullerene C60 based on covalent chemical bonds. The starting point for this modification is the hydrazine-reacted Si(111) surface with the diamine functionality, which is further reacted directly with the C60 molecules. The chemistry of this process is confirmed spectroscopically and microscopically and can be used to form organic-inorganic interfaces separated by a single layer of nitrogen.

  8. Nonlinear behavior of ionically and covalently cross-linked alginate hydrogels

    NASA Astrophysics Data System (ADS)

    Hashemnejad, Seyedmeysam; Zabet, Mahla; Kundu, Santanu

    2015-03-01

    Gels deform differently under applied load and the deformation behavior is related to their network structures and environmental conditions, specifically, strength and density of crosslinking, polymer concentration, applied load, and temperature. Here, we investigate the mechanical behavior of both ionically and covalent cross-linked alginate hydrogel using large amplitude oscillatory shear (LAOS) and cavitation experiments. Ionically-bonded alginate gels were obtained by using divalent calcium. Alginate volume fraction and alginate to calcium ratio were varied to obtain gels with different mechanical properties. Chemical gels were synthesized using adipic acid dihdrazide (AAD) as a cross-linker. The non-linear rheological parameters are estimated from the stress responses to elucidate the strain softening behavior of these gels. Fracture initiation and propagation mechanism during shear rheology and cavitation experiments will be presented. Our results provide a better understanding on the deformation mechanism of alginate gel under large-deformation.

  9. Antimicrobial peptide coatings for hydroxyapatite: electrostatic and covalent attachment of antimicrobial peptides to surfaces.

    PubMed

    Townsend, Leigh; Williams, Richard L; Anuforom, Olachi; Berwick, Matthew R; Halstead, Fenella; Hughes, Erik; Stamboulis, Artemis; Oppenheim, Beryl; Gough, Julie; Grover, Liam; Scott, Robert A H; Webber, Mark; Peacock, Anna F A; Belli, Antonio; Logan, Ann; de Cogan, Felicity

    2017-01-01

    The interface between implanted devices and their host tissue is complex and is often optimized for maximal integration and cell adhesion. However, this also gives a surface suitable for bacterial colonization. We have developed a novel method of modifying the surface at the material-tissue interface with an antimicrobial peptide (AMP) coating to allow cell attachment while inhibiting bacterial colonization. The technology reported here is a dual AMP coating. The dual coating consists of AMPs covalently bonded to the hydroxyapatite surface, followed by deposition of electrostatically bound AMPs. The dual approach gives an efficacious coating which is stable for over 12 months and can prevent colonization of the surface by both Gram-positive and Gram-negative bacteria.

  10. Stable, crystalline, porous, covalent organic frameworks as a platform for chiral organocatalysts

    NASA Astrophysics Data System (ADS)

    Xu, Hong; Gao, Jia; Jiang, Donglin

    2015-11-01

    The periodic layers and ordered nanochannels of covalent organic frameworks (COFs) make these materials viable open catalytic nanoreactors, but their low stability has precluded their practical implementation. Here we report the synthesis of a crystalline porous COF that is stable against water, strong acids and strong bases, and we demonstrate its utility as a material platform for structural design and functional development. We endowed a crystalline and porous imine-based COF with stability by incorporating methoxy groups into its pore walls to reinforce interlayer interactions. We subsequently converted the resulting achiral material into two distinct chiral organocatalysts, with the high crystallinity and porosity retained, by appending chiral centres and catalytically active sites on its channel walls. The COFs thus prepared combine catalytic activity, enantioselectivity and recyclability, which are attractive in heterogeneous organocatalysis, and were shown to promote asymmetric C-C bond formation in water under ambient conditions.

  11. Identification and characterization of a protein covalently bound to DNA of minute virus of mice.

    PubMed Central

    Chow, M; Bodnar, J W; Polvino-Bodnar, M; Ward, D C

    1986-01-01

    We identified a protein which is covalently linked to a fraction of the DNA synthesized in cells infected with minute virus of mice. This protein is specifically bound to the 5' terminus of the extended terminal conformers of the minute virus of mice replicative-form DNA species and of a variable fraction of single-stranded viral DNA. The chemical stability of the protein-DNA linkage is characteristic of a phosphodiester bond between a tyrosine residue in the protein and the 5' end of the DNA. The terminal protein (TP) bound on all DNA forms has a relative molecular weight of 60,000; it is also seen free in extracts from infected cells. Immunologic comparison of the TP with the other known viral proteins suggests that the TP is not related to the capsid proteins or NS-1. Images PMID:2936897

  12. 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.

  13. Antibody covalent immobilization on carbon nanotubes and assessment of antigen binding.

    PubMed

    Venturelli, Enrica; Fabbro, Chiara; Chaloin, Olivier; Ménard-Moyon, Cécilia; Smulski, Cristian R; Da Ros, Tatiana; Kostarelos, Kostas; Prato, Maurizio; Bianco, Alberto

    2011-08-08

    Controlling the covalent bonding of antibodies onto functionalized carbon nanotubes is a key step in the design and preparation of nanotube-based conjugates for targeting cancer cells. For this purpose, an anti-MUC1 antibody (Ab) is linked to both multi-walled (MWCNTs) and double-walled carbon nanotubes (DWCNTs) using different synthetic strategies. The presence of the Ab attached to the nanotubes is confirmed by gel electrophoresis and thermogravimetric analysis. Most importantly, molecular recognition of the antigen by surface plasmon resonance is able to determine similar Ab binding capacities for both Ab-DWCNTs and Ab-MWCNTs. These results are very relevant for the design of future receptor-targeting strategies using chemically functionalized carbon nanotubes.

  14. Probing the nature of chemical bonding in uranyl(VI) complexes with quantum chemical methods.

    PubMed

    Vallet, Valérie; Wahlgren, Ulf; Grenthe, Ingmar

    2012-12-20

    To assess the nature of chemical bonds in uranyl(VI) complexes with Lewis base ligands, such as F(-), Cl(-), OH(-), CO(3)(2-), and O(2)(2-), we have used quantum chemical observables, such as the bond distances, the internal symmetric/asymmetric uranyl stretch frequencies, and the electron density with its topology analyzed using the quantum theory of atoms-in-molecules. This analysis confirms that complex formation induces a weakening of the uranium-axial oxygen bond, reflected by the longer U-O(yl) bond distance and reduced uranyl-stretching frequencies. The strength of the ligand-induced effect increases in the order H(2)O < Cl(-) < F(-) < OH(-) < CO(3)(2-) < O(2)(2-). In-depth analysis reveals that the trend across the series does not always reflect an increasing covalent character of the uranyl-ligand bond. By using a point-charge model for the uranyl tetra-fluoride and tetra-chloride complexes, we show that a significant part of the uranyl bond destabilization arises from purely electrostatic interactions, the remaining part corresponding either to charge-transfer from the negatively charged ligands to the uranyl unit or a covalent interaction. The charge-transfer and the covalent interaction are qualitatively different due to the absence of a charge build up in the uranyl-halide bond region in the latter case. In all the charged complexes, the uranyl-ligand bond is best described as an ionic interaction. However, there are covalent contributions in the very stable peroxide complex and, to some extent, also in the carbonate complex. This study demonstrates that it is possible to describe the nature of chemical bond by observables rather than by ad hoc quantities such as atomic populations or molecular orbitals.

  15. Covalent agonists for studying G protein-coupled receptor activation

    PubMed Central

    Weichert, Dietmar; Kruse, Andrew C.; Manglik, Aashish; Hiller, Christine; Zhang, Cheng; Hübner, Harald; Kobilka, Brian K.; Gmeiner, Peter

    2014-01-01

    Structural studies on G protein-coupled receptors (GPCRs) provide important insights into the architecture and function of these important drug targets. However, the crystallization of GPCRs in active states is particularly challenging, requiring the formation of stable and conformationally homogeneous ligand-receptor complexes. Native hormones, neurotransmitters, and synthetic agonists that bind with low affinity are ineffective at stabilizing an active state for crystallogenesis. To promote structural studies on the pharmacologically highly relevant class of aminergic GPCRs, we here present the development of covalently binding molecular tools activating Gs-, Gi-, and Gq-coupled receptors. The covalent agonists are derived from the monoamine neurotransmitters noradrenaline, dopamine, serotonin, and histamine, and they were accessed using a general and versatile synthetic strategy. We demonstrate that the tool compounds presented herein display an efficient covalent binding mode and that the respective covalent ligand-receptor complexes activate G proteins comparable to the natural neurotransmitters. A crystal structure of the β2-adrenoreceptor in complex with a covalent noradrenaline analog and a conformationally selective antibody (nanobody) verified that these agonists can be used to facilitate crystallogenesis. PMID:25006259

  16. 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.

  17. Covalent layer-by-layer assemblies of polyelectrolytes and homobifunctional spacers.

    PubMed

    El Haitami, Alae E; Thomann, Jean-Sébastien; Jierry, Loïc; Parat, Audrey; Voegel, Jean-Claude; Schaaf, Pierre; Senger, Bernard; Boulmedais, Fouzia; Frisch, Benoît

    2010-07-20

    The step-by-step buildup of organic films through physical or covalent bonds is usually performed by the alternating adsorption of two types of polymeric chains. Overcompensation of the interacting groups after each deposition step (e.g., charge overcompensation in the case of polyelectrolyte multilayers) allows the buildup process to proceed. This overcompensation is intimately linked to the polymeric nature of the interacting species. We report here another type of film architecture also based on step-by-step construction but involving the covalent bonding, through the Sharpless click reaction, between polyelectrolytes (i.e., polyanions) and neutral bifunctional molecules. The films are built by the Cu(I)-catalyzed click reaction of poly(acrylic acid) (PAA) functionalized with ethylene glycol (EG) arms, each ending with either an alkyne or an azide group, and bifunctionalized EG spacers ended with either alkyne or azide functions. We prove that these systems lead to the regular buildup of films that cover the whole substrate surface and whose roughness varies as the thickness of the film core. The effects of various parameters on film buildup are investigated. The grafting density of reactive moieties along the PAA chains has no influence on the thickness increment per bilayer. EG spacers bifunctionalized with alkyne groups reacting with PAA chains functionalized with azide arms give films that grow more rapidly than those obtained with azide-functionalized EG spacers and alkyne-functionalized PAA chains. The influence of the length of the EG arm (grafted on PAA) and of the EG spacer on the film buildup is also investigated: longer arms or longer spacers lead to larger thickness increments per bilayer, except for very large spacers of 50 EG units for which the thickness is the smallest probably because of size exclusion effects during the deposition.

  18. 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

  19. 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.

  20. 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.