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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. Covalent bonding in heavy metal oxides

    NASA Astrophysics Data System (ADS)

    Bagus, Paul S.; Nelin, Connie J.; Hrovat, Dave A.; Ilton, Eugene S.

    2017-04-01

    Novel theoretical methods were used to quantify the magnitude and the energetic contributions of 4f/5f-O2p and 5d/6d-O2p interactions to covalent bonding in lanthanide and actinide oxides. Although many analyses have neglected the involvement of the frontier d orbitals, the present study shows that f and d covalencies are of comparable importance. Two trends are identified. As is expected, the covalent mixing is larger when the nominal oxidation state is higher. More subtly, the importance of the nf covalent mixing decreases sharply relative to (n + 1)d as the nf occupation increases. Atomic properties of the metal cations that drive these trends are identified.

  3. Magnetic and Crystal Structure of α-RuCl3

    NASA Astrophysics Data System (ADS)

    Sears, Jennifer

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

  4. Construct Polyoxometalate Frameworks through Covalent Bonds.

    PubMed

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

    2015-09-08

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

  5. Sharing in covalent and hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Perhacs, Pablo

    1998-11-01

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

  6. What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.

    PubMed

    Heuts, Dominic P H M; Scrutton, Nigel S; McIntire, William S; Fraaije, Marco W

    2009-07-01

    Many enzymes use one or more cofactors, such as biotin, heme, or flavin. These cofactors may be bound to the enzyme in a noncovalent or covalent manner. Although most flavoproteins contain a noncovalently bound flavin cofactor (FMN or FAD), a large number have these cofactors covalently linked to the polypeptide chain. Most covalent flavin-protein linkages involve a single cofactor attachment via a histidyl, tyrosyl, cysteinyl or threonyl linkage. However, some flavoproteins contain a flavin that is tethered to two amino acids. In the last decade, many studies have focused on elucidating the mechanism(s) of covalent flavin incorporation (flavinylation) and the possible role(s) of covalent protein-flavin bonds. These endeavors have revealed that covalent flavinylation is a post-translational and self-catalytic process. This review presents an overview of the known types of covalent flavin bonds and the proposed mechanisms and roles of covalent flavinylation.

  7. 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

  8. ARPES study of the Kitaev Candidate RuCl3

    NASA Astrophysics Data System (ADS)

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

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

  9. 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.

  10. Two Dimensional Antiferromagnetic Chern Insulator: NiRuCl6.

    PubMed

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

    2016-10-12

    Density functional theory (DFT) and Berry curvature calculations show that quantum anomalous Hall effect (QAHE) can be realized in two-dimensional(2D) antiferromagnetic (AFM) NiRuCl6. The results indicate that NiRuCl6 behaves as an AFM Chern insulator and its spin-polarized electronic structure and strong spin-orbit coupling (SOC) are responsible for the QAHE. By tuning SOC, we found that the topological property of NiRuCl6 arises from its energy band inversion. Considering the compatibility between the AFM and insulators, AFM Chern insulator provides a new way to archive high temperature QAHE in experiments due to its different magnetic coupling mechanism from that of ferromagnetic (FM) Chern insulator.

  11. Joining cross-stacked carbon nanotube architecture with covalent bonding

    NASA Astrophysics Data System (ADS)

    Li, Ru; Gong, Wenbin; He, Qiang; Li, Qingwen; Lu, Weibang; Zhu, Wenjun

    2017-05-01

    Carbon nanotubes (CNTs) have superior mechanical properties that make them highly attractive for high performance bulk structures such as CNT fibers and films; however, the weak wan der Waals interaction between CNTs gives degraded strength and modulus, forming covalent bonding between CNTs which is considered to be highly promising but remains a considerable challenge due to the inert nature of the carbon surface. An appropriate electron-beam, as yet, has been used to introduce covalent bonding but limited to CNT bundles. Here, we used a spinnable CNT array to form a cross-stacked CNT architecture first, a bulk film, and proved that sp3 covalent bonding can be directly formed between cross-stacked CNTs under high pressure at appropriate temperatures via a laser heated diamond anvil cell method. The Raman spectrum and molecular dynamic simulations were used to probe and interpret the bonding formation process, respectively. It was found that under 30 GPa with the temperature of 765-1345 K, sp3 covalent bonding was mainly formed in the cross-stacked region. We anticipate that the formation of sp3 covalent bonding between CNTs under high pressure could offer a general pathway to enhance the performance of nano-carbon based materials.

  12. Trimethyltin-mediated covalent gold-carbon bond formation.

    PubMed

    Batra, Arunabh; Kladnik, Gregor; Gorjizadeh, Narjes; Meisner, Jeffrey; Steigerwald, Michael; Nuckolls, Colin; Quek, Su Ying; Cvetko, Dean; Morgante, Alberto; Venkataraman, Latha

    2014-09-10

    We study the formation of covalent gold-carbon bonds in benzyltrimethylstannane (C10H16Sn) deposited on Au in ultra-high-vacuum conditions. Through X-ray photoemission spectroscopy and X-ray absorption measurements, we find that the molecule fragments at the Sn-benzyl bond when exposed to Au surfaces at temperatures as low as -110 °C. The resulting benzyl species is stabilized by the presence of Au(111) but only forms covalent Au-C bonds on more reactive Au surfaces like Au(110). We also present spectroscopic proof for the existence of an electronic "gateway" state localized on the Au-C bond that is responsible for its unique electronic properties. Finally, we use DFT-based nudged elastic band calculations to elucidate the crucial role played by the under-coordinated Au surface in the formation of Au-C bonds.

  13. 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.

  14. 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).

  15. 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.

  16. Factors Contributing to Students' Misconceptions in Learning Covalent Bonds

    ERIC Educational Resources Information Center

    Erman, Erman

    2017-01-01

    This study aims to identify students' misconceptions regarding covalent bonds. Seventy-seven graduate students in the middle of Indonesia participated in the study. Data were collected in three stages. First, misconceptions were identified by using the Semi Open Diagnostic Test. Ten students who experienced the worst misconceptions were…

  17. Polar covalent bonds: an AIM analysis of S,O bonds.

    PubMed

    Love, Ian

    2009-03-19

    The electron distribution for S,O bonds in a wide range of molecules is analyzed using Bader's atoms in molecules theory (AIM) and measures of bond order. It is shown that the electron density and other derived parameters at the bond critical point correlate very well with bond length. Measures of bond order show a more complex behavior, but a combination of bond order and polarity correlates well with bond length. The trends shown in the properties of derived parameters demonstrate clear characteristics for polar covalent bonds and for recognition of multiple bonding in many of the molecules.

  18. 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

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

    PubMed

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

    2014-03-10

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

  20. 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.

  1. 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.

  2. 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

  3. Covalent versus Ionic Bonding in Al-C Clusters.

    PubMed

    Du, Ning; Yang, Huihui; Chen, Hongshan

    2017-05-25

    The low-energy structures of AlnCm (n = 4, 6; m = 1-4) are determined by using the genetic algorithm combined with density functional theory and the QCISD models. The electronic structures and bonding features are analyzed through the density of states (DOS), valence molecular orbitals (MOs), and electron localization function (ELF). The results show that the carbon atoms tend to aggregate and sit at the center of the clusters. The C-C bond lengths in most cases agree with the double C═C bond. Because of the large difference between the electronegativities of carbon and aluminum atoms, almost all of the 3p electrons of Al transfer to C atoms. The 3s orbitals of Al and the 2s2p orbitals of C form bonding and antibonding orbitals; the bonding orbitals correspond to the covalent C-Al bonds, and the antibonding orbitals form lone pair electrons on the outer side of Al atoms. The lone pair electrons form large local dipole moments and enhance the electrostatic interactions between C and Al atoms. Planar geometry and multiconnection are prominent structural patterns in small AlnCm clusters. However, the multiconnection does not correspond to multicenter chemical bonding. There are multicenter bonds, but they are much weaker than the σ C-Al bonds.

  4. 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

  5. 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

  6. Hydrogen-bond-driven controlled molecular marriage in covalent cages.

    PubMed

    Acharyya, Koushik; Mukherjee, Partha Sarathi

    2014-02-03

    A supramolecular approach that uses hydrogen-bonding interaction as a driving force to accomplish exceptional self-sorting in the formation of imine-based covalent organic cages is discussed. Utilizing the dynamic covalent chemistry approach from three geometrically similar dialdehydes (A, B, and D) and the flexible triamine tris(2-aminoethyl)amine (X), three new [3+2] self-assembled nanoscopic organic cages have been synthesized and fully characterized by various techniques. When a complex mixture of the dialdehydes and triamine X was subjected to reaction, it was found that only dialdehyde B (which has OH groups for H-bonding) reacted to form the corresponding cage B3X2 selectively. Surprisingly, the same reaction in the absence of aldehyde B yielded a mixture of products. Theoretical and experimental investigations are in complete agreement that the presence of the hydroxyl moiety adjacent to the aldehyde functionality in B is responsible for the selective formation of cage B3X2 from a complex reaction mixture. This spectacular selection was further analyzed by transforming a nonpreferred (non-hydroxy) cage into a preferred (hydroxy) cage B3X2 by treating the former with aldehyde B. The role of the H-bond in partner selection in a mixture of two dialdehydes and two amines has also been established. Moreover, an example of unconventional imine bond metathesis in organic cage-to-cage transformation is reported. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

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

    2016-06-07

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

  8. 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.

  9. 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.

  10. 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.

  11. Covalent bond orders and atomic anisotropies from iterated stockholder atoms.

    PubMed

    Wheatley, Richard J; Gopal, Angelica A

    2012-02-14

    Iterated stockholder atoms are produced by dividing molecular electron densities into sums of overlapping, near-spherical atomic densities. It is shown that there exists a good correlation between the overlap of the densities of two atoms and the order of the covalent bond between the atoms (as given by simple valence rules). Furthermore, iterated stockholder atoms minimise a functional of the charge density, and this functional can be expressed as a sum of atomic contributions, which are related to the deviation of the atomic densities from spherical symmetry. Since iterated stockholder atoms can be obtained uniquely from the electron density, this work gives an orbital-free method for predicting bond orders and atomic anisotropies from experimental or theoretical charge density data.

  12. 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.

  13. Mechanically activated rupture of single covalent bonds: evidence of force induced bond hydrolysis.

    PubMed

    Schmidt, Sebastian W; Kersch, Alfred; Beyer, Martin K; Clausen-Schaumann, Hauke

    2011-04-07

    We have used temperature-dependent single molecule force spectroscopy to stretch covalently anchored carboxymethylated amylose (CMA) polymers attached to an amino-functionalized AFM cantilever. Using an Arrhenius kinetics model based on a Morse potential as a one-dimensional representation of covalent bonds, we have extracted kinetic and structural parameters of the bond rupture process. With 35.5 kJ mol(-1), we found a significantly smaller dissociation energy and with 9.0 × 10(2) s(-1) to 3.6 × 10(3) s(-1) also smaller Arrhenius pre-factors than expected for homolytic bond scission. One possible explanation for the severely reduced dissociation energy and Arrhenius pre-factors is the mechanically activated hydrolysis of covalent bonds. Both the carboxylic acid amide and the siloxane bond in the amino-silane surface linker are in principle prone to bond hydrolysis. Scattering, slope and curvature of the scattered data plots indicate that in fact two competing rupture mechanisms are observed.

  14. 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

  15. 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.

  16. 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…

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

    ERIC Educational Resources Information Center

    Green, Malcolm L. H.; Parkin, Gerard

    2014-01-01

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

  18. 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.

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

    PubMed

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

    2013-07-02

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

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

    PubMed

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

    2015-11-12

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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  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. Electronegativity effects and single covalent bond lengths of molecules in the gas phase.

    PubMed

    Lang, Peter F; Smith, Barry C

    2014-06-07

    This paper discusses in detail the calculation of internuclear distances of heteronuclear single bond covalent molecules in the gaseous state. It reviews briefly the effect of electronegativity in covalent bond length. A set of single bond covalent radii and electronegativity values are proposed. Covalent bond lengths calculated by an adapted form of a simple expression (which calculated internuclear separation of different Group 1 and Group 2 crystalline salts to a remarkable degree of accuracy) show very good agreement with observed values. A small number of bond lengths with double bonds as well as bond lengths in the crystalline state are calculated using the same expression and when compared with observed values also give good agreement. This work shows that covalent radii are not additive and that radii in the crystalline state are different from those in the gaseous state. The results also show that electronegativity is a major influence on covalent bond lengths and the set of electronegativity scale and covalent radii proposed in this work can be used to calculate covalent bond lengths in different environments that have not yet been experimentally measured.

  7. Novel covalent bond in proteins: calculations on model systems question the bond stability.

    PubMed

    Ončák, Milan; Berka, Karel; Slavíček, Petr

    2011-12-09

    We have investigated the sulfilimine covalent link between methionine (Met) and lysine (Lys), recently identified in collagen IV (R. Vanacore, A.-J. L. Ham, M. Voehler, C. R. Sanders, T. P. Conrads, T. D. Veenstra, K. B. Sharpless, P. E. Dawson, B. G. Hudson, Science 2009, 325, 1230), and have explored its stability with respect to both the redox processes and UV radiation by means of advanced computational methods. We have concluded that the bond should be present in a protonated state, (-NH=S-)(+). The bond is characterized by a relatively high standard reduction potential, that is, the bond should not be stable in a typical cell environment; if the sulfilimine bond exists (as suggested by the experiment) then the bond has to be supported by the protein environment. The sulfilimine bond then destabilizes the protein structure with respect to the alternative tertiary structure. We discuss conditions under which the bond could be formed as well as other possible structural arrangements consistent with the Met-Lys stoichiometry; some of the alternative bond motifs are more thermodynamically stable than the sulfilimine bond. We suggest that the character of the Met-Lys contact could be approached via NEXAFS spectroscopy. Finally, we show that the protonation brings photostability to the sulfilimine bond. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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.

  9. 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.

  10. 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

  11. Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity.

    PubMed

    Xiang, Zheng; Ren, Haiyan; Hu, Ying S; Coin, Irene; Wei, Jing; Cang, Hu; Wang, Lei

    2013-09-01

    Natural proteins often rely on the disulfide bond to covalently link side chains. Here we genetically introduce a new type of covalent bond into proteins by enabling an unnatural amino acid to react with a proximal cysteine. We demonstrate the utility of this bond for enabling irreversible binding between an affibody and its protein substrate, capturing peptide-protein interactions in mammalian cells, and improving the photon output of fluorescent proteins.

  12. 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

  13. Laser-Induced Fluorescence Spectroscopy of Two Ruthenium-Bearing Molecules: RuF and RuCl

    NASA Astrophysics Data System (ADS)

    Zarringhalam, Hanif; Adam, Allan G.; Linton, Colan; Tokaryk, Dennis W.

    2017-06-01

    This work extends the electronic spectroscopy of RuF, and reports on what we believe is the first observation of RuCl. Both molecules have been created in a laser-ablation molecular beam apparatus at UNB, and their spectra have been detected by laser-induced fluorescence. In the low-resolution survey of RuF from 400 to 770 nm, five bands were detected in the blue, green and infrared regions of the electromagnetic spectrum. Four of them were rotationally analyzed from high-resolution data. The three bands in the green region are associated with the ^4Γ_{11/2}-X^4Φ_{9/2} system first observed by Steimle et al. A new ^4Δ_{7/2}-X^4Φ_{9/2} transition in the blue region was also detected. Two high-resolution bands of RuCl were rotationally analyzed, and the ground state was also found to be X^4Φ_{9/2}. The data provide detailed structural information about the molecules, such as bond lengths, vibrational frequencies, isotopic structure, spin-orbit interactions and hyperfine interactions. T. C. Steimle, W. Virgo and T. Ma, J. Chem. Phys. 124 024309 (2006).

  14. Are One-Electron Bonds Any Different from Standard Two-Electron Covalent Bonds?

    PubMed

    Sousa, David Wilian Oliveira de; Nascimento, Marco Antonio Chaer

    2017-09-19

    The nature of the chemical bond is perhaps the central subject in theoretical chemistry. Our understanding of the behavior of molecules developed amazingly in the last century, mostly with the rise of quantum mechanics (QM) and QM-based theories such as valence bond theory and molecular orbital theory. Such theories are very successful in describing molecular properties, but they are not able to explain the origin of the chemical bond. This problem was first analyzed in the 1960s by Ruedenberg, who showed that covalent bonds are the direct result of quantum interference between one-electron states. The generality of this result and its quantification were made possible through the recent development of the generalized product function energy partitioning (GPF-EP) method by our group, which allows the partitioning of the electronic density and energy into their interference and quasi-classical (noninterference) contributions. Furthermore, with GPF wave functions these effects can be analyzed separately for each bond of a molecule. This interference energy analysis has been applied to a large variety of molecules, including diatomics and polyatomics, molecules with single, double, and triple bonds, molecules with different degrees of polarity, linear or branched molecules, cyclic or acyclic molecules, conjugated molecules, and aromatics, in order to verify the role played by quantum interference. In all cases the conclusion is exactly the same: for each bond in each of the molecules considered, the main contribution to its stability comes from the interference term. Two-center one-electron (2c1e) bonds are the simplest kind of chemical bonds. Yet they are often viewed as odd or unconventional cases of bonding. Are they any different from conventional (2c2e) bonds? If so, what differences can we expect in the nature of (2c1e) bonds relative to electron-pair bonds? In this Account, we extend the GPF-EP method to describe bonds involving N electrons in M orbitals (N < M

  15. 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.

  16. 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.

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

    PubMed

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

    2016-06-08

    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.

  18. Self-Assembly Can Direct Dynamic Covalent Bond Formation toward Diversity or Specificity.

    PubMed

    Komáromy, Dávid; Stuart, Marc C A; Monreal Santiago, Guillermo; Tezcan, Meniz; Krasnikov, Victor V; Otto, Sijbren

    2017-05-03

    With the advent of reversible covalent chemistry the study of the interplay between covalent bond formation and noncovalent interactions has become increasingly relevant. Here we report that the interplay between reversible disulfide chemistry and self-assembly can give rise either to molecular diversity, i.e., the emergence of a unprecedentedly large range of macrocycles or to molecular specificity, i.e., the autocatalytic emergence of a single species. The two phenomena are the result of two different modes of self-assembly, demonstrating that control over self-assembly pathways can enable control over covalent bond formation.

  19. 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.

  20. A new dynamic covalent bond of Se-N: towards controlled self-assembly and disassembly.

    PubMed

    Yi, Yu; Xu, Huaping; Wang, Lu; Cao, Wei; Zhang, Xi

    2013-07-15

    A new kind of Se-N dynamic covalent bond has been found that can form between the Se atom of a phenylselenyl halogen species and the N atom of a pyridine derivative, such as polystyrene-b-poly(4-vinylpyridine). This Se-N dynamic covalent bond can be reversibly and rapidly formed or cleaved under acidic or basic conditions, respectively. Furthermore, the bond can be dynamically cleaved by heating or treatment with stronger electron-donating pyridine derivatives. The multiple responses of Se-N bond to external stimuli has enriched the existing family of dynamic covalent bonds. It can be used for controlled and reversible self-assembly and disassembly, which may find potential applications in a number of areas, including self-healing materials and responsive assemblies. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. The covalent bonding interaction in the ferroelectric LuMnO3

    NASA Astrophysics Data System (ADS)

    Ahn, Suk-Jin; Kim, Jinyoung; Shin, Namsoo; Koo, Yang-Mo

    2011-10-01

    The electron density distributions of paraelectric and ferroelectric LuMnO3 are analyzed using high temperature synchrotron x-ray powder diffraction data with the Rietveld method, the maximum entropy method (MEM), and MEM-based pattern fitting. Bonding electrons due to orbital hybridization are clearly seen in the Lu1-O3 and Lu2-O4 bonds along the c-axis polarization direction. The Lu1-O3 bond was determined to be covalent due to hybridization below the ferroelectric transition temperature, and was identified as the driving force for ferroelectricity in LuMnO3. However, the Lu2-O4 bond shows covalent character in both paraelectric and ferroelectric states. Also, we suggest that the Lu2-O4 covalent bonding is responsible for large spontaneous polarization in LuMnO3, associated with the small radius of the Lu3+ ion.

  2. 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…

  3. 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…

  4. The intrinsic strength of the halogen bond: electrostatic and covalent contributions described by coupled cluster theory.

    PubMed

    Oliveira, Vytor; Kraka, Elfi; Cremer, Dieter

    2016-12-07

    36 halogen-bonded complexes YXARm (X: F, Cl, Br; Y: donor group; ARm acceptor group) have been investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Binding energies, geometries, NBO charges, charge transfer, dipole moments, electrostatic potential, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching and bending force constants, and relative bond strength orders n have been calculated and used to order the halogen bonds according to their intrinsic strength. Halogen bonding is found to arise from electrostatic and strong covalent contributions. It can be strengthened by H-bonding or lone pair delocalization. The covalent character of a halogen bond increases in the way 3c-4e (three-center-four-electron) bonding becomes possible. One can characterize halogen bonds by their percentage of 3c-4e bonding. FCl-phosphine complexes can form relatively strong halogen bonds provided electronegative substituents increase the covalent contributions in form of 3c-4e halogen bonding. Binding energies between 1 and 45 kcal mol(-1) are calculated, which reflects the large variety in halogen bonding.

  5. 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

  6. 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.

  7. 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…

  8. 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…

  9. Anisotropic magnetodielectric effect in the honeycomb-type magnet α -RuCl3

    NASA Astrophysics Data System (ADS)

    Aoyama, Takuya; Hasegawa, Yoshinao; Kimura, Shojiro; Kimura, Tsuyoshi; Ohgushi, Kenya

    2017-06-01

    The magnetoelectric coupling in possible Kitaev spin liquid α -RuCl3 with the layered honeycomb structure was examined. We observed a remarkable anisotropic magnetodielectric effect in the zigzag-type antiferromagnetic phase; there is a large suppression in dielectric constant, when both electric and magnetic fields were applied parallel to the in-plane direction. A possible origin of the observed anisotropic magnetodielectric effect is discussed in terms of a magnetically induced local electric polarization with antiferroelectric correlation. Our results stimulate the model calculation including not only exchange coupling but also magnetoelectric coupling to understand the ground state of the spin system in α -RuCl3 .

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

    PubMed

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

    2001-09-01

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

  11. Persistence of Covalent Bonding in Liquid Silicon Probed by Inelastic X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Okada, Junpei; Sit, P.; Wang, Y. J.; Barbiellini, B.; Watanabe, Y.; Bansil, A.; Sakurai, Y.; Itou, M.; Ishikawa, T.; Kimura, K.; Paradis, P.; Nanao, S.

    2012-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  13. Iron-sulfur bond covalency from electronic structure calculations for classical iron-sulfur clusters.

    PubMed

    Harris, Travis V; Szilagyi, Robert K

    2014-03-15

    The covalent character of iron-sulfur bonds is a fundamental electronic structural feature for understanding the electronic and magnetic properties and the reactivity of biological and biomimetic iron-sulfur clusters. Conceptually, bond covalency obtained from X-ray absorption spectroscopy (XAS) can be directly related to orbital compositions from electronic structure calculations, providing a standard for evaluation of density functional theoretical methods. Typically, a combination of functional and basis set that optimally reproduces experimental bond covalency is chosen, but its dependence on the population analysis method is often neglected, despite its important role in deriving theoretical bond covalency. In this study of iron tetrathiolates, and classical [2Fe-2S] and [4Fe-4S] clusters with only thiolate ligands, we find that orbital compositions can vary significantly depending on whether they are derived from frontier orbitals, spin densities, or electron sharing indexes from "Átoms in Molecules" (ÁIM) theory. The benefits and limitations of Mulliken, Minimum Basis Set Mulliken, Natural, Coefficients-Squared, Hirshfeld, and AIM population analyses are described using ab initio wave function-based (QCISD) and experimental (S K-edge XAS) bond covalency. We find that the AIM theory coupled with a triple-ζ basis set and the hybrid functional B(5%HF)P86 gives the most reasonable electronic structure for the studied Fe-S clusters. 2014 Wiley Periodicals, Inc.

  14. Characterization of covalent bond formation between PPARγ and oxo-fatty acids.

    PubMed

    Egawa, Daichi; Itoh, Toshimasa; Yamamoto, Keiko

    2015-04-15

    Covalent modification of proteins is important for normal cellular regulation. Here, we report on the covalent modification of peroxisome proliferator-activated receptor γ (PPARγ), an important drug target, by oxo-fatty acids. In this study, ESI mass spectroscopy showed that the reactivities of oxo-fatty acids with PPARγ are different from one another and that these behaviors are related to the structure of the fatty acids. X-ray crystallography showed that three oxo-fatty acids all bound to the same residue of PPARγ (Cys285), but displayed different hydrogen bonding modes. Moreover, fatty acids formed covalent bonds with both PPARγ moieties in the homodimer, one in an active conformation and the other in an alternative conformation. These two conformations may explain why covalently bound fatty acids show partial rather than full agonist activity.

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

    DOE PAGES

    Johnson, R. D.; Williams, S. C.; Haghighirad, A. A.; ...

    2015-12-10

    We have proposed the layered honeycomb magnet α - RuCl 3 as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled j eff = 1/2 Ru 3 + magnetic moments. We report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, inmore » contrast with the currently assumed trigonal three-layer stacking periodicity. We also report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the j eff = 1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below T N ≈ 13 K. Our analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in pulsed field up to 60 T show a single transition

  16. Dynamic covalent bond from first principles: Diarylbibenzofuranone structural, electronic, and oxidation studies.

    PubMed

    Schleder, Gabriel R; Fazzio, Adalberto; Arantes, Jeverson T

    2017-07-27

    A structure that can self-heal under standard conditions is a challenge faced nowadays and is one of the most promising areas in smart materials science. This can be achieved by dynamic bonds, of which diarylbibenzofuranone (DABBF) dynamic covalent bond is an appealing solution. In this report, we studied the DABBF bond formation against arylbenzofuranone (ABF) and O2 reaction (autoxidation). Our results show that the barrierless DABBF bond formation is preferred over autoxidation due to the charge transfer process that results in the weakly bonded superoxide. We calculated the electronic and structural properties using total energy density functional theory. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. Covalent bond between ligand and receptor required for efficient activation in rhodopsin.

    PubMed

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

    2010-03-12

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

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

    PubMed

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

    2014-01-01

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

  19. 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.

  20. 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.

  1. 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.

  2. Covalently Bonded Chitosan on Graphene Oxide via Redox Reaction

    PubMed Central

    Bustos-Ramírez, Karina; Martínez-Hernández, Ana L.; Martínez-Barrera, Gonzalo; de Icaza, Miguel; Castaño, Víctor M.; Velasco-Santos, Carlos

    2013-01-01

    Carbon nanostructures have played an important role in creating a new field of materials based on carbon. Chemical modification of carbon nanostructures through grafting has been a successful step to improve dispersion and compatibility in solvents, with biomolecules and polymers to form nanocomposites. In this sense carbohydrates such as chitosan are extremely valuable because their functional groups play an important role in diversifying the applications of carbon nanomaterials. This paper reports the covalent attachment of chitosan onto graphene oxide, taking advantage of this carbohydrate at the nanometric level. Grafting is an innovative route to modify properties of graphene, a two-dimensional nanometric arrangement, which is one of the most novel and promising nanostructures. Chitosan grafting was achieved by redox reaction using different temperature conditions that impact on the morphology and features of graphene oxide sheets. Transmission Electron Microscopy, Fourier Transform Infrared, Raman and Energy Dispersive spectroscopies were used to study the surface of chitosan-grafted-graphene oxide. Results show a successful modification indicated by the functional groups found in the grafted material. Dispersions of chitosan-grafted-graphene oxide samples in water and hexane revealed different behavior due to the chemical groups attached to the graphene oxide sheet. PMID:28809348

  3. Covalently Bonded Chitosan on Graphene Oxide via Redox Reaction.

    PubMed

    Bustos-Ramírez, Karina; Martínez-Hernández, Ana L; Martínez-Barrera, Gonzalo; Icaza, Miguel de; Castaño, Víctor M; Velasco-Santos, Carlos

    2013-03-07

    Carbon nanostructures have played an important role in creating a new field of materials based on carbon. Chemical modification of carbon nanostructures through grafting has been a successful step to improve dispersion and compatibility in solvents, with biomolecules and polymers to form nanocomposites. In this sense carbohydrates such as chitosan are extremely valuable because their functional groups play an important role in diversifying the applications of carbon nanomaterials. This paper reports the covalent attachment of chitosan onto graphene oxide, taking advantage of this carbohydrate at the nanometric level. Grafting is an innovative route to modify properties of graphene, a two-dimensional nanometric arrangement, which is one of the most novel and promising nanostructures. Chitosan grafting was achieved by redox reaction using different temperature conditions that impact on the morphology and features of graphene oxide sheets. Transmission Electron Microscopy, Fourier Transform Infrared, Raman and Energy Dispersive spectroscopies were used to study the surface of chitosan-grafted-graphene oxide. Results show a successful modification indicated by the functional groups found in the grafted material. Dispersions of chitosan-grafted-graphene oxide samples in water and hexane revealed different behavior due to the chemical groups attached to the graphene oxide sheet.

  4. 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…

  5. Self-assembly of a "double dynamic covalent" amphiphile featuring a glucose-responsive imine bond.

    PubMed

    Wu, Xin; Chen, Xuan-Xuan; Zhang, Miao; Li, Zhao; Gale, Philip A; Jiang, Yun-Bao

    2016-05-19

    Glucose binding via boronate ester linkages selectively triggers imine bond formation between 4-formylphenylboronic acid and octylamine, leading to the formation of vesicular aggregates in aqueous solutions. This "double dynamic covalent assembly" allows the facile selective sensing of glucose against the otherwise serious interferant fructose, without the need to resort to synthetic effort.

  6. 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…

  7. Is there any fundamental difference between ionic, covalent, and others types of bond? A canonical perspective on the question.

    PubMed

    Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

    2017-06-21

    The concept of chemical bonding is normally presented and simplified through two models: the covalent bond and the ionic bond. Expansion of the ideal covalent and ionic models leads chemists to the concepts of electronegativity and polarizability, and thus to the classification of polar and non-polar bonds. In addition, the intermolecular interactions are normally viewed as physical phenomena without direct correlation to the chemical bond in any simplistic model. Contrary to these traditional concepts of chemical bonding, recently developed canonical approaches demonstrate a unified perspective on the nature of binding in pairwise interatomic interactions. This new canonical model, which is a force-based approach with a basis in fundamental molecular quantum mechanics, confirms much earlier assertions that in fact there are no fundamental distinctions among covalent bonds, ionic bonds, and intermolecular interactions including the hydrogen bond, the halogen bond, and van der Waals interactions.

  8. 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.

  9. Neutron scattering in the proximate quantum spin liquid α-RuCl3

    NASA Astrophysics Data System (ADS)

    Banerjee, Arnab; Yan, Jiaqiang; Knolle, Johannes; Bridges, Craig A.; Stone, Matthew B.; Lumsden, Mark D.; Mandrus, David G.; Tennant, David A.; Moessner, Roderich; Nagler, Stephen E.

    2017-06-01

    The Kitaev quantum spin liquid (KQSL) is an exotic emergent state of matter exhibiting Majorana fermion and gauge flux excitations. The magnetic insulator α-RuCl3 is thought to realize a proximate KQSL. We used neutron scattering on single crystals of α-RuCl3 to reconstruct dynamical correlations in energy-momentum space. We discovered highly unusual signals, including a column of scattering over a large energy interval around the Brillouin zone center, which is very stable with temperature. This finding is consistent with scattering from the Majorana excitations of a KQSL. Other, more delicate experimental features can be transparently associated with perturbations to an ideal model. Our results encourage further study of this prototypical material and may open a window into investigating emergent magnetic Majorana fermions in correlated materials.

  10. Evidence for a Field-Induced Quantum Spin Liquid in α -RuCl3

    NASA Astrophysics Data System (ADS)

    Baek, S.-H.; Do, S.-H.; Choi, K.-Y.; Kwon, Y. S.; Wolter, A. U. B.; Nishimoto, S.; van den Brink, Jeroen; Büchner, B.

    2017-07-01

    We report a 35Cl nuclear magnetic resonance study in the honeycomb lattice α -RuCl3 , a material that has been suggested to potentially realize a Kitaev quantum spin liquid (QSL) ground state. Our results provide direct evidence that α -RuCl3 exhibits a magnetic-field-induced QSL. For fields larger than ˜10 T , a spin gap opens up while resonance lines remain sharp, evidencing that spins are quantum disordered and locally fluctuating. The spin gap increases linearly with an increasing magnetic field, reaching ˜50 K at 15 T, and is nearly isotropic with respect to the field direction. The unusual rapid increase of the spin gap with increasing field and its isotropic nature are incompatible with conventional magnetic ordering and, in particular, exclude that the ground state is a fully polarized ferromagnet. The presence of such a field-induced gapped QSL phase has indeed been predicted in the Kitaev model.

  11. Enhancing mechanical performance of a covalent self-healing material by sacrificial noncovalent bonds.

    PubMed

    Neal, James A; Mozhdehi, Davoud; Guan, Zhibin

    2015-04-15

    Polymers that repair themselves after mechanical damage can significantly improve their durability and safety. A major goal in the field of self-healing materials is to combine robust mechanical and efficient healing properties. Here, we show that incorporation of sacrificial bonds into a self-repairable network dramatically improves the overall mechanical properties. Specifically, we use simple secondary amide side chains to create dynamic energy dissipative hydrogen bonds in a covalently cross-linked polymer network, which can self-heal via olefin cross-metathesis. We envision that this straightforward sacrificial bonding strategy can be employed to improve mechanical properties in a variety of self-healing systems.

  12. 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

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

    PubMed

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

    2014-01-03

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

  14. Structural Model for Covalent Adhesion of the Streptococcus pyogenes Pilus through a Thioester Bond*

    PubMed Central

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

    2014-01-01

    The human pathogen Streptococcus pyogenes produces pili that are essential for adhesion to host surface receptors. Cpa, the adhesin at the pilus tip, was recently shown to have a thioester-containing domain. The thioester bond is believed to be important in adhesion, implying a mechanism of covalent attachment analogous to that used by human complement factors. Here, we have characterized a second active thioester-containing domain on Cpa, the N-terminal domain of Cpa (CpaN). Expression of CpaN in Escherichia coli gave covalently linked dimers. These were shown by x-ray crystallography and mass spectrometry to comprise two CpaN molecules cross-linked by the polyamine spermidine following reaction with the thioester bonds. This cross-linked CpaN dimer provides a model for the covalent attachment of Cpa to target receptors and thus the streptococcal pilus to host cells. Similar thioester domains were identified in cell wall proteins of other Gram-positive pathogens, suggesting that thioester domains are more widely used and provide a mechanism of adhesion by covalent bonding to target molecules on host cells that mimics that used by the human complement system to eliminate pathogens. PMID:24220033

  15. Self-assembly of nanostructured materials through irreversible covalent bond formation.

    PubMed

    Baek, Kangkyun; Hwang, Ilha; Roy, Indranil; Shetty, Dinesh; Kim, Kimoon

    2015-08-18

    Over the past decades, numerous efforts have been devoted to synthesizing nanostructured materials with specific morphology because their size and shape play an important role in determining their functions. Self-assembly using weak and reversible interactions or bonds has provided synthetic routes toward various nanostructures because it allows a "self-checking" and "self-error-correcting" process under thermodynamic control. By contrast, the use of irreversible covalent bonds, despite the potential to generate more robust structures, has been disfavored in the synthesis of well-defined nanomaterials largely due to the lack of such self-error-correcting mechanisms. To date, the use of irreversible bonds is largely limited to covalent fixation of preorganized building blocks on a template, which, though capable of producing shape-persistent and robust nanostructured materials, often requires a laborious and time-consuming multistep processes. Constructing well-defined nanostructures by self-assembly using irreversible covalent bonds without help of templates or preorganization of components remains a challenge. This Account describes our recent discoveries and progress in self-assembly of nanostructured materials through strong, practically irreversible covalent bond formation and their applications in various areas including drug delivery, anticancer therapy, and heterogeneous catalysis. The key to the success of this approach is the use of rationally designed building blocks possessing multiple in-plane reactive groups at the periphery. These blocks can then successfully grow into flat oligomeric patches through irreversible covalent bond formation without the aid of preorganization or templates. Further growth of the patches with or without curvature generation drives the system to the formation of polymer nanocapsules, two-dimensional (2D) polymer films, and toroidal nanotubular microrings. Remarkably, the final morphology can be specified by a few simple

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

    NASA Astrophysics Data System (ADS)

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

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

  17. 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.

  18. 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.

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

    PubMed

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

    2006-10-04

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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Formation of a covalent bond between a polyoxometalate and silica covered by SiH moieties.

    PubMed

    Grinenval, Eva; Bayard, François; Basset, Jean-Marie; Lefebvre, Frédéric

    2014-02-17

    Dehydroxylated silica was modified by grafting reaction of SiHMe2 groups. The resulting material was fully characterized by various methods including infrared and one- and two-dimensional solid-state NMR. This material can further react with dehydrated polyoxometalates (POMs), leading to the formation of a covalent POM-silica bond. In the case of H4PVMo11O40, hydrogen released during the grafting reaction reduces the POM. This leads to the formation of two surface species, which can be reoxidized in presence of oxygen. In the case of H3PW12O40, no reduction is observed. In both cases, (29)Si solid-state NMR shows that the POM-silica bond is covalent, contrary to what was observed in homogeneous conditions.

  6. Real-time electrochemical monitoring of covalent bond formation in solution via nanoparticle-electrode collisions.

    PubMed

    Li, Da; Kong, Na; Liu, Jingquan; Wang, Hongbin; Barrow, Colin J; Zhang, Shusheng; Yang, Wenrong

    2015-11-25

    We describe an alternative electrochemical technique to monitor covalent bond formation in real-time using nanoparticle-electrode collisions. The method is based on recognising the redox current when MP-11 functionalised chemical reduced graphene oxide (rGO) nanosheets collide with Lomant's reagent modified gold microelectrode. This facile and highly sensitive monitoring method can be useful for investigating the fundamental of single-molecule reactions.

  7. Comparison of Yarrowia lipolytica lipase immobilization yield of entrapment, adsorption, and covalent bond techniques.

    PubMed

    Alloue, Wazé Aimée Mireille; Destain, Jacqueline; El Medjoub, Thami; Ghalfi, Hakim; Kabran, Philomène; Thonart, Philippe

    2008-07-01

    The purpose of this study was to immobilize lipase from Yarrowia lipolytica using three methods including inclusion, adsorption, and covalent bond to study enzyme leaching, storage, and catalytic properties. Sodium alginate and chitosan were the polymers selected to immobilize lipase by inclusion. The beads of each polymer were dried by freeze drying and fluidization. The results show that chitosan was more adapted to the inclusion of lipase. Even though freeze dried, bead activity was low compared to that of fluidized beads. The freeze-drying process seems to produce suitable beads for storage at 4 and 20 degrees C. The immobilization by adsorption was carried out on both celite and silica gel. Maximum immobilization yield of 76% was obtained with celite followed by 43% in silica gel. The enzyme adsorbed on the two supports exhibited greater stability at a certain temperature (50 degrees C) and in no polar solvents (Isooctane, n-heptane, and n-hexane). In addition, the lipase immobilized by covalent bond retained residual activity equitable to 70%. It was demonstrated that the enzyme immobilized by covalent bond showed greater activity (80%) after 5 months of storage.

  8. Diazonium-derived aryl films on gold nanoparticles: evidence for a carbon-gold covalent bond.

    PubMed

    Laurentius, Lars; Stoyanov, Stanislav R; Gusarov, Sergey; Kovalenko, Andriy; Du, Rongbing; Lopinski, Gregory P; McDermott, Mark T

    2011-05-24

    Tailoring the surface chemistry of metallic nanoparticles is generally a key step for their use in a wide range of applications. There are few examples of organic films covalently bound to metal nanoparticles. We demonstrate here that aryl films are formed on gold nanoparticles from the spontaneous reduction of diazonium salts. The structure and the bonding of the film is probed with surface-enhanced Raman scattering (SERS). Extinction spectroscopy and SERS show that a nitrobenzene film forms on gold nanoparticles from the corresponding diazonium salt. Comparison of the SERS spectrum with spectra computed from density functional theory models reveals a band characteristic of a Au-C stretch. The observation of this stretch is direct evidence of a covalent bond. A similar band is observed in high-resolution electron energy loss spectra of nitrobenzene layers on planar gold. The bonding of these types of films through a covalent interaction on gold is consistent with their enhanced stability observed in other studies. These findings provide motivation for the use of diazonium-derived films on gold and other metals in applications where high stability and/or strong adsorbate-substrate coupling are required.

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

    PubMed

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

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature and have been extensively studied phenomenologically. However, little is known about the binding energies in non-covalent complexes containing these functional groups. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A(3)pXA(3)-NH(2) (X = S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. For systems examined in this study, covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  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. 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.

  19. 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.

  20. Density-decomposed orbital-free density functional theory for covalently bonded molecules and materials

    NASA Astrophysics Data System (ADS)

    Xia, Junchao; Carter, Emily A.

    2012-12-01

    We propose a density decomposition scheme using a Wang-Govind-Carter- (WGC-) based kinetic energy density functional (KEDF) to accurately and efficiently simulate various covalently bonded molecules and materials within orbital-free (OF) density functional theory (DFT). By using a local, density-dependent scale function, the total density is decomposed into a highly localized density within covalent bond regions and a flattened delocalized density, with the former described by semilocal KEDFs and the latter treated by the WGC KEDF. The new model predicts reasonable equilibrium volumes, bulk moduli, and phase-ordering energies for various semiconductors compared to Kohn-Sham (KS) DFT benchmarks. The decomposition formalism greatly improves numerical stability and accuracy, while retaining computational speed compared to simply applying the original WGC KEDF to covalent materials. The surface energy of Si(100) and various diatomic molecule properties can be stably calculated and also agree well with KSDFT benchmarks. This linear-scaled, computationally efficient, density-partitioned, multi-KEDF scheme opens the door to large-scale simulations of molecules, semiconductors, and insulators with OFDFT.

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

    PubMed Central

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

    2016-01-01

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

  2. Design of Modular Protein Tags for Orthogonal Covalent Bond Formation at Specific DNA Sequences.

    PubMed

    Nguyen, Thang Minh; Nakata, Eiji; Saimura, Masayuki; Dinh, Huyen; Morii, Takashi

    2017-06-28

    Simultaneous formation of specific covalent linkages at nucleotides in given DNA sequences demand distinct orthogonal reactivity of DNA modification agents. Such highly specific reactions require well-balanced reactivity and affinity of the DNA modification agents. Conjugation of a sequence-specific DNA binding zinc finger protein and a self-ligating protein tag provides a modular adaptor that expedites formation of a covalent bond between the protein tag and a substrate-modified nucleotide at a specific DNA sequence. The modular adaptor stably locates a protein of interest fused to it at the target position on DNA scaffold in its functional form. Modular adaptors with orthogonal selectivity and fast reaction kinetics to specific DNA sequences enable site-specific location of different protein molecules simultaneously. Three different modular adaptors consisting of zinc finger proteins with distinct DNA sequence specificities and self-ligating protein tags with different substrate specificities achieved orthogonal covalent bond formation at respective sequences on the same DNA scaffold with an overall coassembly yield over 90%. Application of this unique set of orthogonal modular adaptors enabled construction of a cascade reaction of three enzymes from xylose metabolic pathway on DNA scaffold.

  3. 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

  4. 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.

  5. Quantum confinement of the covalent bond beyond the Born-Oppenheimer approximation.

    PubMed

    Sarsa, A; Alcaraz-Pelegrina, J M; Le Sech, C; Cruz, S A

    2013-06-20

    Dirichlet boundary conditions with different symmetries, spherical and cylindrical impenetrable surfaces, are imposed on the covalent electron pair of a molecular bond. Accurate results for different observable like energy and interparticle distances are calculated using quantum Monte Carlo methods beyond the Born-Oppenheimer approximation. The spherical confinement induces a raise in the bond energy and shortens the internuclear distances even for a relatively soft confinement. When cylindrical symmetry is considered, similar qualitative behavior is observed though only the electrons are confined. A compression followed by a relaxation process of the confined bond is shown to induce a vibrationally excited state. Finally, a brief qualitative discussion based on a simplified picture of the role of compression/relaxation cycles in enzyme catalysis is given.

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  8. Hiding in Plain Sight: The Bimetallic Magnesium Covalent Bond in Enzyme Active Sites.

    PubMed

    Perera, Lalith; Beard, William A; Pedersen, Lee G; Wilson, Samuel H

    2017-01-03

    The transfer of phosphate groups is an essential function of many intracellular biological enzymes. The transfer is in many cases facilitated by a protein scaffold involving two closely spaced magnesium "ions". It has long been a mystery how these "ions" can retain their closely spaced positions throughout enzymatic phosphate transfer: Coulomb's law would dictate large repulsive forces between these ions at the observed distances. Here we show, however, that the electron density can be borrowed from nearby electron-rich oxygens to populate a bonding molecular orbital that is largely localized between the magnesium "ions". The result is that the Mg-Mg core of these phosphate transfer enzymes is surprisingly similar to a metastable [Mg2](2+) ion in the gas phase, an ion that has been identified experimentally and studied with high-level quantum-mechanical calculations. This similarity is confirmed by comparative computations of the electron densities of [Mg2](2+) in the gas phase and the Mg-Mg core in the structures derived from QM/MM studies of high-resolution X-ray crystal structures. That there is a level of covalent bonding between the two Mg "ions" at the core of these enzymes is a novel concept that enables an improved vision of how these enzymes function at the molecular level. The concept is broader than magnesium-other biologically relevant metals (e.g., Mn and Zn) can also form similar stabilizing covalent Me-Me bonds in both organometallic and inorganic crystals.

  9. Programmable Assembly of Peptide Amphiphile via Noncovalent-to-Covalent Bond Conversion.

    PubMed

    Sato, Kohei; Ji, Wei; Palmer, Liam C; Weber, Benjamin; Barz, Matthias; Stupp, Samuel I

    2017-07-05

    Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses revealed that hydrogen bonds between peptides were reinforced by covalent bond formation, enabling the fiber elongation. To examine these materials for their potential biomedical applications, cytotoxicity of nanofibers against C2C12 premyoblast cells was tested. We demonstrated that cell viability increased with an increase in fiber length, presumably because of the suppressed disruption of cell membranes by the fiber end-caps.

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

    SciTech Connect

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

    2011-04-21

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

  11. 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.

  12. 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.

  13. 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

  14. Supramolecular organic photochemistry: Control of covalent bond formation through noncovalent supramolecular interactions and magnetic effects

    PubMed Central

    Turro, Nicholas J.

    2002-01-01

    Supramolecular organic photochemistry, a field concerned with the interaction of light with supramolecular assemblies of organic molecules, has been inspired by the remarkable structural and dynamic features of guest@host chemistry, particularly as exemplified by enzymes. Exemplars of supramolecular organic photochemistry from soft-matter hosts (micelles) and hard-matter hosts (porous solids) are discussed with an emphasis on how noncovalent interactions, which are at the heart of supramolecular chemistry, can be systematically exploited to control the catalytic and magnetic effects on the formation of covalent bonds from photochemically produced pairs of radicals. PMID:11880603

  15. Bonding in gold-rare earth [Au2M] (M = Eu, Yb, Lu) ions. A strong covalent gold-lanthanide bond

    NASA Astrophysics Data System (ADS)

    Páez-Hernández, Dayán; Muñoz-Castro, Alvaro; Arratia-Perez, Ramiro

    2017-09-01

    The electronic structure and bonding nature of a series of intermetallic gold-lanthanide [Au2Ln] molecules, where Ln = Eu, Yb, Lu is predicted via the DFT and CASSCF/CASPT2 calculations. The 2c-2e bond model shows a good description of the intermetallic bonding which have a large covalent component with important contribution from bonding interaction between the 6s-Au and the 6s-Ln shell of orbitals.

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

    PubMed

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

    2015-09-08

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

  17. Bimodal supramolecular functionalization of carbon nanotubes triggered by covalent bond formation.

    PubMed

    Leret, Sofía; Pouillon, Yann; Casado, Santiago; Navío, Cristina; Rubio, Ángel; Pérez, Emilio M

    2017-03-01

    Many applications of carbon nanotubes require their chemical functionalization. Both covalent and supramolecular approaches have been extensively investigated. A less trodden path is the combination of both covalent and noncovalent chemistries, where the formation of covalent bonds triggers a particularly stable noncovalent interaction with the nanotubes. We describe a series of naphthalene diimide (NDI) bisalkene molecules that, upon mixing with single-walled carbon nanotubes (SWNTs) and Grubbs' catalyst, undergo two different reaction pathways. On one hand, they ring-close around the SWNTs to form rotaxane-like mechanically interlocked derivatives of SWNTs (MINTs). Alternatively, they oligomerize and then wrap around the SWNTs. The balance of MINTs to oligomer-wrapped SWNTs depends on the affinity of the NDI molecules for the SWNTs and the kinetics of the metathesis reactions, which can be controlled by varying the solvent. Thorough characterization of the products (TGA, TEM, AFM, Raman, UV-vis-NIR, PLE, XPS and UPS) confirms their structure and shows that each type of functionalization affects the electronic properties of the SWNTs differently.

  18. 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.

  19. 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.

  20. 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.

  1. Bolaform superamphiphile based on a dynamic covalent bond and its self-assembly in water.

    PubMed

    Wang, Guangtong; Wang, Chao; Wang, Zhiqiang; Zhang, Xi

    2011-10-18

    We have employed a dynamic covalent bond to fabricate a bolaform superamphiphile, which can be used as building blocks for controlled assembly and disassembly. In alkaline environment, one building block bearing a benzoic aldehyde group can react with the other building block bearing an amino group to form a bolaform superamphiphile. It is found that the bolaform superamphiphiles can self-assemble in water to form micellar aggregates. When the pH is tuned down to slightly acidic values, the benzoic imine bond can be hydrolyzed, leading to the dissociation of the superamphiphile. The micellar aggregates will also disassemble, and the loaded guest molecules are released subsequently. This line of research has enriched the family of bolaform amphiphiles, and the resulting assemblies may find application in the field of controlled and targetable drug-delivery in a biological environment. © 2011 American Chemical Society

  2. Direct imaging of covalent bond structure in single-molecule chemical reactions.

    PubMed

    de Oteyza, Dimas G; Gorman, Patrick; Chen, Yen-Chia; Wickenburg, Sebastian; Riss, Alexander; Mowbray, Duncan J; Etkin, Grisha; Pedramrazi, Zahra; Tsai, Hsin-Zon; Rubio, Angel; Crommie, Michael F; Fischer, Felix R

    2013-06-21

    Observing the intricate chemical transformation of an individual molecule as it undergoes a complex reaction is a long-standing challenge in molecular imaging. Advances in scanning probe microscopy now provide the tools to visualize not only the frontier orbitals of chemical reaction partners and products, but their internal covalent bond configurations as well. We used noncontact atomic force microscopy to investigate reaction-induced changes in the detailed internal bond structure of individual oligo-(phenylene-1,2-ethynylenes) on a (100) oriented silver surface as they underwent a series of cyclization processes. Our images reveal the complex surface reaction mechanisms underlying thermally induced cyclization cascades of enediynes. Calculations using ab initio density functional theory provide additional support for the proposed reaction pathways.

  3. 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

  4. 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…

  5. 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…

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  9. Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate.

    PubMed

    Lebedeva, Natalia V; Nese, Alper; Sun, Frank C; Matyjaszewski, Krzysztof; Sheiko, Sergei S

    2012-06-12

    Spontaneous degradation of bottlebrush macromolecules on aqueous substrates was monitored by atomic force microscopy. Scission of C ─ C covalent bonds in the brush backbone occurred due to steric repulsion between the adsorbed side chains, which generated bond tension on the order of several nano-Newtons. Unlike conventional chemical reactions, the rate of bond scission was shown to decrease with temperature. This apparent anti-Arrhenius behavior was caused by a decrease in the surface energy of the underlying substrate upon heating, which results in a corresponding decrease of bond tension in the adsorbed macromolecules. Even though the tension dropped minimally from 2.16 to 1.89 nN, this was sufficient to overpower the increase in the thermal energy (k(B)T) in the Arrhenius equation. The rate constant of the bond-scission reaction was measured as a function of temperature and surface energy. Fitting the experimental data by a perturbed Morse potential V = V(0)(1 - e(-βx))(2) - fx, we determined the depth and width of the potential to be V(0) = 141 ± 19 kJ/mol and β(-1) = 0.18 ± 0.03 Å, respectively. Whereas the V(0) value is in reasonable agreement with the activation energy E(a) = 80-220 kJ/mol of mechanical and thermal degradation of organic polymers, it is significantly lower than the dissociation energy of a C ─ C bond D(e) = 350 kJ/mol. Moreover, the force constant K(x) = 2β(2)V(0) = 1.45 ± 0.36 kN/m of a strained bottlebrush along its backbone is markedly larger than the force constant of a C ─ C bond K(l) = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains.

  10. 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.

  11. 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

  12. 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.

  13. H-shaped supra-amphiphiles based on a dynamic covalent bond.

    PubMed

    Wang, Guangtong; Wang, Chao; Wang, Zhiqiang; Zhang, Xi

    2012-10-16

    The imine bond, a kind of dynamic covalent bond, is used to bind two bolaform amphiphiles together with spacers, yielding H-shaped supra-amphiphiles. Micellar aggregates formed by the self-assembly of the H-shaped supra-amphiphiles are observed. When pH is tuned down from basic to slightly acidic, the benzoic imine bond can be hydrolyzed, leading to the dissociation of H-shaped supra-amphiphiles. Moreover, H-shaped supra-amphiphiles have a lower critical micelle concentration than their building blocks, which is very helpful in enhancing the stability of the benzoic imine bond being hydrolyzed by acid. The surface tension isotherms of the H-shaped supra-amphiphiles with different spacers indicate their twisty conformation at a gas-water interface. The study of H-shaped supra-amphiphiles can enrich the family of amphiphiles, and moreover, the pH-responsiveness may make them apply to controlled or targetable drug delivery in a biological environment.

  14. 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.

  15. 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.

  16. 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) .

  17. Optical probe of Heisenberg-Kitaev magnetism in α -RuCl3

    NASA Astrophysics Data System (ADS)

    Sandilands, Luke J.; Sohn, C. H.; Park, H. J.; Kim, So Yeun; Kim, K. W.; Sears, Jennifer A.; Kim, Young-June; Noh, Tae Won

    2016-11-01

    We report a temperature-dependent optical spectroscopic study of the Heisenberg-Kitaev magnet α -RuCl3 . Our measurements reveal anomalies in the optical response near the magnetic ordering temperature. At higher temperatures, we observe a redistribution of spectral weight over a broad energy range that is associated with nearest-neighbor spin-spin correlations. This finding is consistent with highly frustrated magnetic interactions and in agreement with theoretical expectations for this class of material. The optical data also reveal significant electron-hole interaction effects, including a bound excitonic state. These results demonstrate a clear coupling between charge and spin degrees of freedom and provide insight into the properties of thermally disordered Heisenberg-Kitaev magnets.

  18. Phase diagram of α -RuCl3 in an in-plane magnetic field

    NASA Astrophysics Data System (ADS)

    Sears, J. A.; Zhao, Y.; Xu, Z.; Lynn, J. W.; Kim, Young-June

    2017-05-01

    The low-temperature magnetic phases in the layered honeycomb lattice material α -RuCl3 have been studied as a function of in-plane magnetic field. In zero field this material orders magnetically below 7 K with a so-called zigzag order within the honeycomb planes. Neutron diffraction data show that a relatively small applied field of 2 T is sufficient to suppress the population of the magnetic domain in which the zigzag chains run along the field direction. We found that the intensity of the magnetic peaks due to zigzag order is continuously suppressed with increasing field until their disappearance at μoHc=8 T . At still higher fields (above 8 T) the zigzag order is destroyed, while bulk magnetization and heat capacity measurements suggest that the material enters a state with gapped magnetic excitations. We discuss the magnetic phase diagram obtained in our study in the context of a quantum phase transition.

  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

    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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. Malleable and Self-Healing Covalent Polymer Networks through Tunable Dynamic Boronic Ester Bonds.

    PubMed

    Cromwell, Olivia R; Chung, Jaeyoon; Guan, Zhibin

    2015-05-27

    Despite numerous strategies involving dynamic covalent bond exchange for dynamic and self-healing materials, it remains a challenge to be able to tune the malleability and self-healing properties of bulk materials through simple small molecule perturbations. Here we describe the use of tunable rates of boronic ester transesterification to tune the malleability and self-healing efficiencies of bulk materials. Specifically, we used two telechelic diboronic ester small molecules with variable transesterification kinetics to dynamically cross-link 1,2-diol-containing polymer backbones. The sample cross-linked with fast-exchanging diboronic ester showed enhanced malleability and accelerated healing compared to the slow-exchanging variant under the same conditions. Our report demonstrates the possibility of transferring small molecule kinetics to dynamic properties of bulk solid material and may serve as a guide for the rational design of tunable dynamic materials.

  8. 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.

  9. 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).

  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. 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.

  12. [Preparation of chiral monolithic column with covalently bonded cellulose and their application to rapid enantioseparation].

    PubMed

    Wang, Jiabin; Wang, Xiao; Li, Jianhua; Lü, Haixia; Lin, Xucong; Xie, Zenghong; Zhang, Qiqing

    2011-12-01

    A chiral monolithic capillary column for rapid enantioseparation was prepared by covalently bonding of cellulose tris(4-methylbenzoate) (CTMB) on N-acryloxysuccinimide-based monolith. The preparation and derivatization conditions of the monolithic column were optimized. The successful grafting of CTMB was confirmed on the characterizations of the infrared spectrum and the cathodic electroosmotic flow (EOF). The effects of acetic acid concentration and methanol content on the enantioseparation were studied. The solvent resistance, reproducibility and stability of the monolithic column have also been investigated. The rapid enantioseparation of the five solutes (phenylalanine, tyrosine, tryptophan, propranolol and phenylethanol) with resolution (R(s)) values up to 1.31 was achieved within 1.2 min on the prepared chiral capillary monolithic column by capillary electrochromatography.

  13. 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.

  14. In quest of a superhalogen supported covalent bond involving a noble gas atom.

    PubMed

    Chakraborty, Debdutta; Chattaraj, Pratim Kumar

    2015-03-26

    The possibility of having neutral Xe-bound compounds mediated by some representative transition metal fluorides of general formula MX3 (where M=Ru, Os, Rh, Ir, Pd, Pt, Ag, Au and X=F) has been investigated through density functional theory based calculations. Nature of interaction between MX3 and Xe moieties has been characterized through detailed electron density, charge density and bond energy decomposition analyses. The feasibility of having compounds of general formula XeMX3 at 298 K has been predicted through thermodynamic considerations. The nature of interaction in between Xe and M atoms is partly covalent in nature and the orbital interaction is the dominant contributor toward these interactions as suggested by energy decomposition analysis.

  15. 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

  16. 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.

  17. Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate

    PubMed Central

    Lebedeva, Natalia V.; Nese, Alper; Sun, Frank C.; Matyjaszewski, Krzysztof; Sheiko, Sergei S.

    2012-01-01

    Spontaneous degradation of bottlebrush macromolecules on aqueous substrates was monitored by atomic force microscopy. Scission of C─C covalent bonds in the brush backbone occurred due to steric repulsion between the adsorbed side chains, which generated bond tension on the order of several nano-Newtons. Unlike conventional chemical reactions, the rate of bond scission was shown to decrease with temperature. This apparent anti-Arrhenius behavior was caused by a decrease in the surface energy of the underlying substrate upon heating, which results in a corresponding decrease of bond tension in the adsorbed macromolecules. Even though the tension dropped minimally from 2.16 to 1.89 nN, this was sufficient to overpower the increase in the thermal energy (kBT) in the Arrhenius equation. The rate constant of the bond-scission reaction was measured as a function of temperature and surface energy. Fitting the experimental data by a perturbed Morse potential V = V0(1 - e-βx)2 - fx, we determined the depth and width of the potential to be V0 = 141 ± 19 kJ/mol and β-1 = 0.18 ± 0.03 Å, respectively. Whereas the V0 value is in reasonable agreement with the activation energy Ea = 80–220 kJ/mol of mechanical and thermal degradation of organic polymers, it is significantly lower than the dissociation energy of a C─C bond De = 350 kJ/mol. Moreover, the force constant Kx = 2β2V0 = 1.45 ± 0.36 kN/m of a strained bottlebrush along its backbone is markedly larger than the force constant of a C─C bond Kl = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains. PMID:22645366

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. Efficient Vibrational Energy Transfer through Covalent Bond in Indigo Carmine Revealed by Nonlinear IR Spectroscopy.

    PubMed

    He, Xuemei; Yu, Pengyun; Zhao, Juan; Wang, Jianping

    2017-09-28

    Ultrafast vibrational relaxation and structural dynamics of indigo carmine in dimethyl sulfoxide were examined using femtosecond pump-probe infrared and two-dimensional infrared (2D IR) spectroscopies. Using the intramolecularly hydrogen-bonded C═O and delocalized C═C stretching modes as infrared probes, local structural and dynamical variations of this blue dye molecule were observed. Energy relaxation of the vibrationally excited C═O stretching mode was found to occur through covalent bond to the delocalized aromatic vibrational modes on the time scale of a few picoseconds or less. Vibrational quantum beating was observed in magic-angle pump-probe, anisotropy, and 2D IR cross-peak dynamics, showing an oscillation period of ca. 1010 fs, which corresponds to the energy difference between the C═O and C═C transition frequency (33 cm(-1)). This confirms a resonant vibrational energy transfer happened between the two vibrators. However, a more efficient energy-accepting mode of the excited C═O stretching was believed to be a nearby combination and/or overtone mode that is more tightly connected to the C═O species. On the structural aspect, dynamical-time-dependent 2D IR spectra reveal an insignificant inhomogeneous contribution to time-correlation relaxation for both the C═O and C═C stretching modes, which is in agreement with the generally believed structural rigidity of such conjugated molecules.

  3. 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.

  4. 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

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

    ERIC Educational Resources Information Center

    Niaz, Mansoor

    2001-01-01

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

  6. Accurate frozen-density embedding potentials as a first step towards a subsystem description of covalent bonds

    NASA Astrophysics Data System (ADS)

    Fux, Samuel; Jacob, Christoph R.; Neugebauer, Johannes; Visscher, Lucas; Reiher, Markus

    2010-04-01

    The frozen-density embedding (FDE) scheme [Wesolowski and Warshel, J. Phys. Chem. 97, 8050 (1993)] relies on the use of approximations for the kinetic-energy component vT[ρ1,ρ2] of the embedding potential. While with approximations derived from generalized-gradient approximation kinetic-energy density functional weak interactions between subsystems such as hydrogen bonds can be described rather accurately, these approximations break down for bonds with a covalent character. Thus, to be able to directly apply the FDE scheme to subsystems connected by covalent bonds, improved approximations to vT are needed. As a first step toward this goal, we have implemented a method for the numerical calculation of accurate references for vT. We present accurate embedding potentials for a selected set of model systems, in which the subsystems are connected by hydrogen bonds of various strength (water dimer and F-H-F-), a coordination bond (ammonia borane), and a prototypical covalent bond (ethane). These accurate potentials are analyzed and compared to those obtained from popular kinetic-energy density functionals.

  7. Ions colliding with clusters of fullerenes--decay pathways and covalent bond formations.

    PubMed

    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

    2013-07-21

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C60 molecules following collisions with Ar(2+), He(2+), and Xe(20+) 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 [C60]n(+) → C60(+)+(n-1)C60 evaporation model. Excitation energies in the range of only ~0.7 eV per C60 molecule in a [C60]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 Ar(2+) and He(2+) collisions, we observe very efficient C119(+) and C118(+) formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C59(+) or C58(+) and C60 during cluster fragmentation. In the Ar(2+) case, it is possible to form even smaller C120-2m(+) molecules (m = 2-7), while no molecular fusion reactions are observed for the present Xe(20+) collisions.

  8. 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.

  9. 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.

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

    SciTech Connect

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

    2013-07-21

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

  11. Field-induced quantum criticality in the Kitaev system α -RuCl3

    NASA Astrophysics Data System (ADS)

    Wolter, A. U. B.; Corredor, L. T.; Janssen, L.; Nenkov, K.; Schönecker, S.; Do, S.-H.; Choi, K.-Y.; Albrecht, R.; Hunger, J.; Doert, T.; Vojta, M.; Büchner, B.

    2017-07-01

    α -RuCl3 has attracted enormous attention since it has been proposed as a prime candidate to study fractionalized magnetic excitations akin to Kitaev's honeycomb-lattice spin liquid. We have performed a detailed specific-heat investigation at temperatures down to 0.4 K in applied magnetic fields up to 9 T for fields parallel to the a b plane. We find a suppression of the zero-field antiferromagnetic order, together with an increase of the low-temperature specific heat, with increasing field up to μ0Hc≈6.9 T. Above Hc, the magnetic contribution to the low-temperature specific heat is strongly suppressed, implying the opening of a spin-excitation gap. Our data point toward a field-induced quantum critical point at Hc; this is supported by universal scaling behavior near Hc. Remarkably, the data also reveal the existence of a small characteristic energy scale well below 1 meV, above which the excitation spectrum changes qualitatively. We relate the data to theoretical calculations based on a J1-K1-Γ1-J3 honeycomb model.

  12. 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.

  13. 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.

  14. 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.

  15. Difference in chemical bonding between lithium and sodium salts: influence of covalency on their solubility.

    PubMed

    Chen, Su; Ishii, Jun; Horiuchi, Shunsuke; Yoshizawa-Fujita, Masahiro; Izgorodina, Ekaterina I

    2017-07-14

    Recent thermal runaways in lithium-ion batteries have reinforced the focus on the research of safer electrolytes based on ionic liquids. A simple switch from organic solvents to ionic liquids has been proven difficult due to the decreased efficiency of batteries caused by decreased conductivity and increased viscosity of ionic liquids upon addition of lithium salts. The new trend in replacing lithium salts with a cheaper alternative, sodium salts, has resulted in rather poor solubility of sodium salts in commonly used ionic liquids. This phenomenon has been left largely unexplained. Herein, we present a high-level quantum chemical study of the chemical bonding of lithium and sodium salts coupled with ionic liquid anions. Due to their proximity to the anion, the 1s(2) electrons on the lithium cation are found to become strongly polarized by the presence of the anion such that they start participating in the bonding, making it more covalent than originally thought. In sodium salts the 2s(2) orbitals are rather removed from the anion, making its influence weaker. This polarization results in 90 kJ mol(-1) of difference in the interaction magnitude between lithium and sodium salts. Theoretical results have confirmed that increasing covalency in lithium salts results in their excellent solubility since these dissolve as ion-paired complexes. The downside of this ability is decreased conductivity as lithium salts are unlikely to easily dissociate in ionic liquids. Sodium salts are shown to maintain a high degree of ionicity, thus decreasing their chances of being solvated by ionic liquids as a result of their low concentration of ions per unit volume. The theoretical results are further underpinned by solubility studies of MX salts, where M = Li or Na and X = bis(trifluoromethylsulfonyl)imide (NTf2), BF4(-) or PF6(-), conducted in six different ionic liquids. Lithium salts consisting of BF4(-) or PF6(-) exhibited significantly better solubility than their sodium

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

    SciTech Connect

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

    2016-12-12

    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.

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

    DOE PAGES

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

    2016-12-12

    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

  18. 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.

  19. 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

  20. Interplay of hydrogen-bond and coordinate covalent-bond interactions in self-assembly of NH3 molecules on the Si(001) surface.

    PubMed

    Kim, Yong-Sung; Koo, Ja-Yong; Kim, Hanchul

    2008-06-27

    An exchange of hydrogen-bond and coordinate covalent-bond (dative-bond) interactions is found to play a critical role in the self-assembly of NH3 molecules on the Si(001) surface. An NH3 molecule in the height of approximately 3-10 A above the surface is attracted toward the preadsorbed NH2 moiety through the long-range H-bond interaction. Within approximately 3 A, the H-bond interaction becomes repulsive, and instead the dative bond with the buckled-down Si atom governs the adsorption process. The interplay of the two interactions induces the clustering and the zigzag feature of the dissociatively adsorbed NH3 molecules on the Si(001) surface.

  1. 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

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

    PubMed

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

    2014-01-07

    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.

  3. 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.

  4. 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.

  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. 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.

  7. 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.

  8. Mucin Covalently Bonded to Microfibers Improves the Patency of Vascular Grafts

    PubMed Central

    Janairo, Randall Raphael R.; Zhu, YiQian; Chen, Timothy

    2014-01-01

    Due to high incidence of vascular bypass procedures, an unmet need for suitable vessel replacements exists, especially for small-diameter (<6 mm) vascular grafts. Here, we developed a novel, bilayered, synthetic vascular graft of 1-mm diameter that consisted of a microfibrous luminal layer and a nanofibrous outer layer, which was tailored to possess the same mechanical property as native arteries. We then chemically modified the scaffold with mucin, a glycoprotein lubricant on the surface of epithelial tissues, by either passive adsorption or covalent bonding using the di-amino-poly(ethylene glycol) linker to microfibers. Under static and physiological flow conditions, conjugated mucin was more stable than adsorbed mucin on the surfaces. Mucin could slightly inhibit blood clotting, and mucin coating suppressed platelet adhesion on microfibrous scaffolds. In the rat common carotid artery anastomosis model, grafts with conjugated mucin, but not adsorbed mucin, exhibited excellent patency and higher cell infiltration into the graft walls. Mucin, which can be easily obtained from autologous sources, offers a novel method for improving the hemocompatibility and surface lubrication of vascular grafts and many other implants. PMID:23962121

  9. Reaction of nitrosonium cation with resorc[4]arenes activated by supramolecular control: covalent bond formation.

    PubMed

    Ghirga, Francesca; D'Acquarica, Ilaria; Delle Monache, Giuliano; Mannina, Luisa; Molinaro, Carmela; Nevola, Laura; Sobolev, Anatoly P; Pierini, Marco; Botta, Bruno

    2013-07-19

    Resorc[4]arenes 1 and 2, which previously proved to entrap NO(+) cation within their cavities under conditions of host-to-guest excess, were treated with a 10-fold excess of NOBF4 salt in chloroform. Kinetic and spectral UV-visible analyses revealed the formation of isomeric 1:2 complexes as a direct evolution of the previously observed event. Accordingly, three-body 1-(NO(+))2 and 2-(NO(+))2 adducts were built by MM and fully optimized by DFT calculations at the B3LYP/6-31G(d) level of theory. Notably, covalent nitration products 4, 5 and 6, 7 were obtained by reaction of NOBF4 salt with host 1 and 2, respectively, involving macrocycle ring-opening and insertion of a nitro group in one of the four aromatic rings. In particular, compounds 4 and 6, both containing a trans-double bond in the place of the methine bridge, were oxidized to aldehydes 5 and 7, respectively, after addition of water to the reaction mixture. Calculation of the charge and frontier orbitals of the aromatic donor (HOMO) and the NO(+) acceptor (LUMO) clearly suggests an ipso electrophilic attack by a first NO(+) unit on the resorcinol ring, mediated by the second NO(+) unit.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Covalency of Fe{sup 3+}-O{sup 2{minus}} bonds and magnetic structure in mixed oxides

    SciTech Connect

    Lenglet, M.; Hochu, F.; Simsa, Z.

    1998-12-01

    Optical absorption and the Faraday rotation spectra of iron(III) in ferrimagnetic oxides may be interpreted using 3d crystal field and the pair excitation processes. Band assignments and ligand-field parameters are in agreement with the results of SCF-X{alpha}-SW molecular orbital calculations of (FeO{sub 4}){sup 5{minus}} and (FeO{sub 6}){sup 9{minus}} clusters. The pair excitation processes are strongly influenced by the nature and strength of the superexchange interactions. The presence of the ferrimagnetism in ferrites and garnets induces greater covalency effects of the Fe{sup 3+}-O{sup 2{minus}} bonds. The nephelauxetic ratios {beta}{sub 35} of iron(III) in hematite, ferrites, and garnets show that the greater covalency of the Fe{sup 3+}-O{sup 2{minus}} chemical bonds in these oxides is related to the magnetic structure.

  15. 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.

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

    PubMed

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

    2013-12-20

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

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

    PubMed

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

    2015-04-11

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

  18. An effective hierarchical model for the biomolecular covalent bond: an approach integrating artificial chemistry and an actual terrestrial life system.

    PubMed

    Oohashi, Tsutomu; Ueno, Osamu; Maekawa, Tadao; Kawai, Norie; Nishina, Emi; Honda, Manabu

    2009-01-01

    Under the AChem paradigm and the programmed self-decomposition (PSD) model, we propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the PSD mechanism of turning biological polymers (BPs) into biological monomers (BMs) as an efficient biomolecular recycling strategy We have examined the validity and effectiveness of the HBCB model by coordinating two complementary approaches: biological experiments using existent terrestrial life, and simulation experiments using an AChem system. Biological experiments have shown that terrestrial life possesses a PSD mechanism as an endergonic, genetically regulated process and that hydrolysis, which decomposes a BP into BMs, is one of the main processes of such a mechanism. In simulation experiments, we compared different virtual self-decomposition processes. The virtual species in which the self-decomposition process mainly involved covalent bond cleavage from a BP to BMs showed evolutionary superiority over other species in which the self-decomposition process involved cleavage from BP to classes lower than BM. These converging findings strongly support the existence of PSD and the validity and effectiveness of the HBCB model.

  19. 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.

  20. A macroscopic reaction: direct covalent bond formation between materials using a Suzuki-Miyaura cross-coupling reaction.

    PubMed

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

    2014-09-18

    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.

  1. [(p-Cymene)RuCl2 ]2 : an efficient catalyst for highly regioselective allylic alkylations of chelated amino acid ester enolates.

    PubMed

    Bayer, Anton; Kazmaier, Uli

    2014-08-11

    Chelated amino acid ester enolates are excellent nucleophiles for ruthenium-catalyzed allylic alkylations. Although [Cp*Ru(MeCN)3 ]PF6 was found to be the most reactive catalyst investigated, with the resulting allyl complexes reacting at temperatures as low as -78 °C, unfortunately the process took place with only moderate regio- and diastereoselectivity. In contrast, [(p-cymene)RuCl2 ]2 allowed allylations to be performed with a high degree of regioretention. Secondary allyl carboxylates with a terminal double bond were found to be the most reactive substrates, giving rise to the branched amino acids with perfect regioretention and chirality transfer. In this case, no isomerization of the Ru-allyl complex formed in situ was observed, in contrast to the analogues palladium complexes. This isomerization-free protocol can also be used for the synthesis of (Z)-configured γ,δ-unsaturated amino acid derivatives, starting from (Z)-allylic substrates. Here, the more reactive phosphates were found to be superior to the carboxylates, providing the required amino acids in almost quantitative yield with perfect regio- and stereoretention. Therefore, the Ru-catalyzed allylation reactions are well positioned to overcome the drawbacks of Pd-catalyzed processes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. 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.

  3. 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.

  4. 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.

  5. 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

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

    PubMed

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

    2015-03-23

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

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

    PubMed

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

    2010-12-10

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

  8. Tetrel, pnictogen and chalcogen bonds identified in the gas phase before they had names: a systematic look at non-covalent interactions.

    PubMed

    Legon, Anthony C

    2017-06-14

    The terms tetrel bond, pnictogen bond and chalcogen bond were coined recently to describe non-covalent interactions involving group 14, 15 and 16 atoms, respectively, acting as the electrophilic site that seeks a nucleophilic region of another molecule, for example a non-bonding electron pair or π-electron pair of a Lewis base. Many complexes containing these non-covalent bonds were identified and characterised in isolation in the gas phase by rotational and vibrational spectroscopy long before they were given these names. In this article, the geometries so determined for selected examples of complexes of each type are rationalised in terms of the molecular electrostatic surface potentials of the component molecules. Examples of chalcogen-bonded complexes considered are based mainly on sulfur dioxide, with the region near the sulfur atom as the electrophilic site that interacts with n-electron and π-electron pairs for a range of simple Lewis base molecules. For tetrel bonds, the examples discussed involve the carbon atom of carbon dioxide as the electrophilic centre, while for pnictogen bonds the central nitrogen of the closely related molecule nitrous oxide is chosen. Geometrical similarities within each series allow simple definitions of each type of non-covalent bond that are conformal with that recently advanced for the halogen bond, a related non-covalent interaction.

  9. 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.

  10. 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

  11. 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.

  12. A strategy to synthesize graphene-incorporated lignin polymer composite materials with uniform graphene dispersion and covalently bonded interface engineering

    NASA Astrophysics Data System (ADS)

    Wang, Mei; Duong, Le Dai; Ma, Yifei; Sun, Yan; Hong, Sung Yong; Kim, Ye Chan; Suhr, Jonghwan; Nam, Jae-Do

    2017-08-01

    Graphene-incorporated polymer composites have been demonstrated to have excellent mechanical and electrical properties. In the field of graphene-incorporated composite material synthesis, there are two main obstacles: Non-uniform dispersion of graphene filler in the matrix and weak interface bonding between the graphene filler and polymer matrix. To overcome these problems, we develop an in-situ polymerization strategy to synthesize uniformly dispersed and covalently bonded graphene/lignin composites. Graphene oxide (GO) was chemically modified by 4,4'-methylene diphenyl diisocyanate (MDI) to introduce isocyanate groups and form the urethane bonds with lignin macromonomers. Subsequential polycondensation reactions of lignin groups with caprolactone and sebacoyl chloride bring about a covalent network of modified GO and lignin-based polymers. The flexible and robust lignin polycaprolactone polycondensate/modified GO (Lig-GOm) composite membranes are achieved after vacuum filtration, which have tunable hydrophilicity and electrical resistance according to the contents of GOm. This research transforms lignin from an abundant biomass into film-state composite materials, paving a new way for the utilization of biomass wastes.

  13. Role of heme-protein covalent bonds in mammalian peroxidases. Protection of the heme by a single engineered heme-protein link in horseradish peroxidase.

    PubMed

    Huang, Liusheng; Wojciechowski, Grzegorz; Ortiz de Montellano, Paul R

    2006-07-14

    Oxidation of SCN-, Br-, and Cl- (X-) by horseradish peroxidase (HRP) and other plant and fungal peroxidases results in the addition of HOX to the heme vinyl group. This reaction is not observed with lactoperoxidase (LPO), in which the heme is covalently bound to the protein via two ester bonds between carboxylic side chains and heme methyl groups. To test the hypothesis that the heme of LPO and other mammalian peroxidases is protected from vinyl group modification by the hemeprotein covalent bonds, we prepared the F41E mutant of HRP in which the heme is attached to the protein via a covalent bond between Glu41 and the heme 3-methyl. We also examined the E375D mutant of LPO in which only one of the two normal covalent heme links is retained. The prosthetic heme groups of F41E HRP and E375D LPO are essentially not modified by the HOBr produced by these enzymes. The double E375D/D225E mutant of LPO that can form no covalent bonds is inactive and could not be examined. These results unambiguously demonstrate that a single heme-protein link is sufficient to protect the heme from vinyl group modification even in a protein (HRP) that is normally highly susceptible to this reaction. The results directly establish that one function of the covalent heme-protein bonds in mammalian peroxidases is to protect their prosthetic group from their highly reactive metabolic products.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. A catalyCEST MRI contrast agent that detects the enzyme-catalyzed creation of a covalent bond.

    PubMed

    Hingorani, Dina V; Randtke, Edward A; Pagel, Mark D

    2013-05-01

    CatalyCEST MRI can detect enzyme activity by employing contrast agents that are detected through chemical exchange saturation transfer (CEST). A CEST agent, Tm-DO3A-cadaverine, has been designed to detect the catalytic activity of transglutaminase (TGase), which creates a covalent bond between the agent and the side chain of a glutamine amino acid residue. CEST appeared at -9.2 ppm after TGase conjugated Tm-DO3A-cadaverine to albumin, which also caused a decrease in CEST from albumin at +4.6 ppm. Studies with model peptides revealed similar appearances and decreases in detectable CEST effects following TGase-catalyzed conjugation of the contrast agent and peptide. The MR frequencies and amplitudes of these CEST effects were dependent on the peptide sequence, which demonstrated the sensitivity of CEST agents to ligand conformations that may be exploited to create more responsive molecular imaging agents. The chemical exchange rates of the substrates and conjugated products were measured by fitting modified Bloch equations to CEST spectra, which demonstrated that changes in exchange rates can also be used to detect the formation of a covalent bond by catalyCEST MRI.

  3. 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.

  4. 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.

  5. 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.

  6. Charge-Shift Corrected Electronegativities and the Effect of Bond Polarity and Substituents on Covalent-Ionic Resonance Energy.

    PubMed

    James, Andrew M; Laconsay, Croix J; Galbraith, John Morrison

    2017-07-13

    Bond dissociation energies and resonance energies for HnA-BHm molecules (A, B = H, C, N, O, F, Cl, Li, and Na) have been determined in order to re-evaluate the concept of electronegativity in the context of modern valence bond theory. Following Pauling's original scheme and using the rigorous definition of the covalent-ionic resonance energy provided by the breathing orbital valence bond method, we have derived a charge-shift corrected electronegativity scale for H, C, N, O, F, Cl, Li, and Na. Atomic charge shift character is defined using a similar approach resulting in values of 0.42, 1.06, 1.43, 1.62, 1.64, 1.44, 0.46, and 0.34 for H, C, N, O, F, Cl, Li, and Na, respectively. The charge-shift corrected electronegativity values presented herein follow the same general trends as Pauling's original values with the exception of Li having a smaller value than Na (1.57 and 1.91 for Li and Na respectively). The resonance energy is then broken down into components derived from the atomic charge shift character and polarization effects. It is then shown that most of the resonance energy in the charge-shift bonds H-F, H3C-F, and Li-CH3 and borderline charge-shift H-OH is associated with polarity rather than the intrinsic atomic charge-shift character of the bonding species. This suggests a rebranding of these bonds as "polar charge-shift" rather than simply "charge-shift". Lastly, using a similar breakdown method, it is shown that the small effect the substituents -CH3, -NH2, -OH, and -F have on the resonance energy (<10%) is mostly due to changes in the charge-shift character of the bonding atom.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

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

    PubMed

    Kumar, Sandeep; Parks, David M

    2015-03-11

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

  14. 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.

  15. 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.

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  18. 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.

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

    PubMed

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

    2013-01-01

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

  20. 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.

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

    PubMed Central

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

    2014-01-01

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

  2. 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

  3. 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.

  4. 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.

  5. Covalency in resonance-assisted halogen bonds demonstrated with cooperativity in N-halo-guanine quartets.

    PubMed

    Wolters, Lando P; Smits, Nicole W G; Guerra, Célia Fonseca

    2015-01-21

    Halogen bonds are shown to possess the same characteristics as hydrogen bonds: charge transfer, resonance assistance and cooperativity. This follows from the computational analyses of the structure and bonding in N-halo-base pairs and quartets. The objective was to achieve an understanding of the nature of resonance-assisted halogen bonds (RAXB): how they resemble or differ from the better understood resonance-assisted hydrogen bonds (RAHB) in DNA. We present an accurate physical model of the RAXB based on the molecular orbital theory, which is derived from the corresponding energy decomposition analyses and study of the charge distribution. We show that the RAXB arise from classical electrostatic interaction and also receive strengthening from donor-acceptor interactions within the σ-electron system. Similar to RAHB, there is also a small stabilization by π-electron delocalization. This resemblance leads to prove cooperativity in N-halo-guanine quartets, which originates from the charge separation that occurs with donor-acceptor orbital interactions in the σ-electron system.

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

    SciTech Connect

    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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. Tuning of character of the N-O bond in HONO from covalent to protocovalent by different types of intramolecular interactions.

    PubMed

    Shishkina, Svitlana V; Slabko, Anzhelika I; Berski, Slawomir; Latajka, Zdzislaw; Shishkin, Oleg V

    2013-09-28

    Quantum-chemical calculations of the H-O-N=O molecule in the equilibrium and transition states and the complexes of the HONO with BH3, study of the intramolecular interactions using NBO theory, and investigation of the electron distribution on the basis of topological analysis of the ELF function clearly indicate the influence of the n-π* conjugation and n-σ* hyperconjugation interactions on a par with exchange repulsion of lone pairs the character of the N-O bond. It is shown that repulsion between lone pairs of oxygen and nitrogen atoms causes the elongation of the N-O bond only but character of this bond remains covalent. The interaction between lone pair of the terminal oxygen atom and antibonding orbital of the N-O bond (n-σ* hyperconjugation) coincides with influence of repulsion and reinforces it changing the character of the N-O bond from covalent to protocovalent. In contrary, the n-π* conjugation interaction between lone pairs of the bridged oxygen atom and π-orbital of the N=O double bond leads to the strengthening of the N-O bond making it more covalent.

  12. 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.

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

    NASA Technical Reports Server (NTRS)

    Kamaratos, E.

    1984-01-01

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

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

    PubMed

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

    2005-04-01

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

  15. Stilbene Boronic Acids Form a Covalent Bond with Human Transthyretin and Inhibit Its Aggregation.

    PubMed

    Smith, Thomas P; Windsor, Ian W; Forest, Katrina T; Raines, Ronald T

    2017-09-28

    Transthyretin (TTR) is a homotetrameric protein. Its dissociation into monomers leads to the formation of fibrils that underlie human amyloidogenic diseases. The binding of small molecules to the thyroxin-binding sites in TTR stabilizes the homotetramer and attenuates TTR amyloidosis. Herein, we report on boronic acid-substituted stilbenes that limit TTR amyloidosis in vitro. Assays of affinity for TTR and inhibition of its tendency to form fibrils were coupled with X-ray crystallographic analysis of nine TTR·ligand complexes. The ensuing structure-function data led to a symmetrical diboronic acid that forms a boronic ester reversibly with serine 117. This diboronic acid inhibits fibril formation by both wild-type TTR and a common disease-related variant, V30M TTR, as effectively as does tafamidis, a small-molecule drug used to treat TTR-related amyloidosis in the clinic. These findings establish a new modality for covalent inhibition of fibril formation and illuminate a path for future optimization.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

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

    SciTech Connect

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

    2014-05-28

    An analysis based on the variation principle shows that in the molecules H{sub 2}{sup +}, H{sub 2}, B{sub 2}, C{sub 2}, N{sub 2}, O{sub 2}, F{sub 2}, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

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

    PubMed 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

  3. 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.

  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. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    PubMed

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

    2016-05-11

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

  15. 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.

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

    PubMed Central

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

    1995-01-01

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

  17. Covalent bond formation between amino acids and lignin: cross-coupling between proteins and lignin.

    PubMed

    Cong, Fang; Diehl, Brett G; Hill, Joseph Lee; Brown, Nicole R; Tien, Ming

    2013-12-01

    The present study characterized the products formed from the reaction of amino acids and in turn, proteins, with lignin resulting in cross-coupling. When added to reaction mixtures containing coniferyl alcohol, horseradish peroxidase and H2O2, three amino acids (Cys, Tyr, and Thr) are able to form adducts. The low molecular weight products were analyzed by HPLC and from each reaction mixture, one product was isolated and analyzed by LC/MS. LC/MS results are consistent with bond formation between the polar side-chain of these amino acids with Cα. These results are consistent with the cross-coupling of Cys, Tyr and Thr through a quinone methide intermediate. In addition to the free amino acids, it was found that the cross-coupling of proteins with protolignin through Cys or Tyr residues. The findings provide a mechanism by which proteins and lignin can cross-couple in the plant cell wall. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. 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.

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

    PubMed

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

    2009-12-01

    Ruthenium(II) complexes are of great interest as a new class of cancerostatics with advantages over classical platinum compounds including lower toxicity. The stability of the [RuClCp(mPTA)2](OSO2CF3)2 complex (I) (Cp cyclopentadienyl, mPTA N-methyl 1,3,5-triaza-7-phosphaadamantane) in aqueous solution was studied using spectrophotometry, matrix-assisted laser desorption/ionization (MALDI) and laser desorption/ionization (LDI) time-of-flight (TOF) mass spectrometry (MS). Spectrophotometry proves that at least three different reactions take place in water. Dissolution of I leads to fast coordination of water molecules to the Ru(II) cation and then slow hydrolysis and ligand exchange of chloride and mPTA with water, hydroxide or with trifluoromethane sulfonate itself. Via MALDI and LDI of the hydrolyzed solutions the formation of singly positively charged ions of general formula RuCl(p)(Cp)(q)(mPTA)(r)(H2O)(s)(OH)(t) (p = 0-1, q = 0-1, r = 0-2, s = 0-5, t = 0-2) and of some fragment ions was shown. The stoichiometry was determined by analyzing the isotopic envelopes and computer modelling. The [RuClCp(mPTA)2](OSO2CF3)2 complex can be stabilized in dilute hydrochloric acid or in neutral 0.15 M isotonic sodium chloride solution. Copyright 2009 John Wiley & Sons, Ltd.

  20. Magnetization processes of zigzag states on the honeycomb lattice: Identifying spin models for α -RuCl3 and Na2IrO3

    NASA Astrophysics Data System (ADS)

    Janssen, Lukas; Andrade, Eric C.; Vojta, Matthias

    2017-08-01

    We study the field-induced magnetization processes of extended Heisenberg-Kitaev models on the honeycomb lattice, taking into account off-diagonal and longer-range exchange interactions, using a combination of Monte Carlo simulations, classical energy minimization, and spin-wave theory. We consider a number of different parameter sets, previously proposed to describe the magnetic behavior of α -RuCl3 and Na2IrO3 with their antiferromagnetic zigzag ground states. By classifying these parameter sets, we reveal the existence of three distinct mechanisms to stabilize zigzag states, which differ in the sign of the nearest-neighbor Kitaev interaction, the role of longer-range interactions, and the magnitude of the off-diagonal Γ1 interaction. While experimentally hardly distinguishable at zero field, we find that the three different scenarios lead to significantly different magnetization processes in applied magnetic fields. In particular, we show that a sizable off-diagonal interaction Γ1>0 naturally explains the strongly anisotropic field responses observed in α -RuCl3 without the need for a strong anisotropy in the effective g tensor. Moreover, for a generic field direction, it leads to a high-field state with a finite transversal magnetization, which should be observable in α -RuCl3 .

  1. Magnetic thermal conductivity far above the Néel temperature in the Kitaev-magnet candidate α -RuCl3

    NASA Astrophysics Data System (ADS)

    Hirobe, Daichi; Sato, Masahiro; Shiomi, Yuki; Tanaka, Hidekazu; Saitoh, Eiji

    2017-06-01

    We have investigated the longitudinal thermal conductivity of α -RuCl3 , the magnetic state of which is considered to be proximate to a Kitaev honeycomb model, along with the spin susceptibility and magnetic specific heat. We found that the temperature dependence of the thermal conductivity exhibits an additional peak around 100 K, which is well above the phonon peak temperature (˜50 K). The higher-temperature peak position is comparable to the temperature scale of the Kitaev couplings rather than the Néel temperatures below 15 K. Additional heat conduction was observed for all five samples used in this study, and was found to be rather immune to a structural phase transition of α -RuCl3 , which suggests its different origin from phonons. Combined with experimental results of the magnetic specific heat, our transport measurement suggests strongly that the higher-temperature peak in the thermal conductivity is attributed to itinerant spin excitations associated with the Kitaev couplings of α -RuCl3 . A kinetic approximation of the magnetic thermal conductivity yields a mean free path of ˜20 nm at 100 K, which is much longer than the nearest Ru-Ru distance (˜3 Å), suggesting the long-distance coherent propagation of magnetic excitations driven by the Kitaev couplings.

  2. 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.

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

    PubMed

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

    2016-07-05

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

  4. 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.

  5. A ruthenium tellurocarbonyl (CTe) complex with a cyclopentadienyl ligand: systematic studies of a series of chalcogenocarbonyl complexes [CpRuCl(CE)(H2IMes)] (E = O, S, Se, Te).

    PubMed

    Suzuki, Ayumi; Arai, Takahiro; Ikenaga, Kota; Mutoh, Yuichiro; Tsuchida, Noriko; Saito, Shinichi; Ishii, Youichi

    2016-12-20

    The first tellurocarbonyl complex with a half-sandwich structure [CpRuCl(CTe)(H2IMes)] was synthesized by a ligand substitution reaction. The practically complete series of the CpCE complexes [CpRuCl(CE)(H2IMes)] (E = O, S, Se, Te) were systematically explored. The tellurium atom in the CTe complex could be smoothly replaced with lighter chalcogen atoms.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. Higher impact energy in traumatic brain injury interferes with noncovalent and covalent bonds resulting in cytotoxic brain tissue edema as measured with computational simulation.

    PubMed

    von Holst, Hans; Li, Xiaogai

    2015-04-01

    Cytotoxic brain tissue edema is a complicated secondary consequence of ischemic injury following cerebral diseases such as traumatic brain injury and stroke. To some extent the pathophysiological mechanisms are known, but far from completely. In this study, a hypothesis is proposed in which protein unfolding and perturbation of nucleotide structures participate in the development of cytotoxic edema following traumatic brain injury (TBI). An advanced computational simulation model of the human head was used to simulate TBI. The consequences of kinetic energy transfer following an external dynamic impact were analyzed including the intracranial pressure (ICP), strain level, and their potential influences on the noncovalent and covalent bonds in folded protein structures. The result shows that although most of the transferred kinetic energy is absorbed in the skin and three bone layers, there is a substantial amount of energy reaching the gray and white matter. The kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent but also covalent bonds when high enough. The induced mechanical strain and pressure may further interfere with the proteins, which accumulate water molecules into the interior of the hydrophobic structures of unfolded proteins. Simultaneously, the noncovalent energy-rich bonds in nucleotide adenosine-triphosphates may be perturbed as well. Based on the analysis of the numerical simulation data, the kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent, but also with covalent bonds when high enough. The subsequent attraction of increased water molecules into the unfolded protein structures and disruption of adenosine-triphosphate bonds could to some extent explain the etiology to cytotoxic edema.

  13. 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, L; Simon, S; Fonseca Guerra, C

    2015-01-01

    Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine–thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson–Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp2 to sp3, does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn–Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor–acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers. PMID:26246994

  14. 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

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

    PubMed

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

    2016-05-01

    Anterior Gradient-2 (AGR2) is a component of a pro-oncogenic signalling pathway that can promote p53 inhibition, metastatic cell migration, limb regeneration, and cancer drug-resistance. AGR2 is in the protein-disulphide isomerase superfamily containing a single cysteine (Cys-81) that forms covalent adducts with its client proteins. We have found that mutation of Cysteine-81 attenuates its biochemical activity in its sequence-specific peptide docking function, reduces binding to Reptin, and reduces its stability in cells. As such, we evaluated how chemical oxidation of its cysteine affects its biochemical properties. Recombinant AGR2 spontaneously forms covalent dimers in the absence of reductant whilst DTT promotes dimer to monomer conversion. Mutation of Cysteine-81 to alanine prevents peroxide catalysed dimerization of AGR2 in vitro, suggesting a reactive cysteine is central to covalent dimer formation. Both biochemical assays and ESI mass spectrometry were used to demonstrate that low levels of a chemical oxidant promote an intermolecular disulphide bond through formation of a labile sulfenic acid intermediate. However, higher levels of oxidant promote sulfinic or sulfonic acid formation thus preventing covalent dimerization of AGR2. These data together identify the single cysteine of AGR2 as an oxidant responsive moiety that regulates its propensity for oxidation and its monomeric-dimeric state. This has implications for redox regulation of the pro-oncogenic functions of AGR2 protein in cancer cells. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. 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.

  17. Effects of Spin-Orbit Coupling on Covalent Bonding and the Jahn-Teller Effect Are Revealed with the Natural Language of Spinors.

    PubMed

    Zeng, Tao; Fedorov, Dmitri G; Schmidt, Michael W; Klobukowski, Mariusz

    2011-09-13

    The orbital-based natural language describing the complexity of chemistry ( Stowasser , R. ; Hoffmann , R. J. Am. Chem. Soc. 1999 , 121 , 3414 ) was extended by us recently to the definition of spin-orbit natural spinors ( Zeng , T. et al. J. Chem. Phys. 2011 , 134 , 214107 ). This novel method gives chemical insights into the role of spin-orbit coupling in covalent bonding and in the Jahn-Teller effect. The natural spinors are used to explain antibonding spin-orbit effects on TlH and Tl2: it is found that the spin-orbit induced charge transfer from the bonding to the nonbonding or antibonding orbitals has a large effect on the bond strength. The natural spinors are also used to explain the spin-orbit quenching of the Jahn-Teller effect in WF5: the spin-orbit interaction can stabilize the totally symmetric electron distribution so that the high-symmetry molecular structure becomes more stable than its distortions. A general discussion of the role of the spin-orbit coupling in covalent bonding and Jahn-Teller effect is given in terms of the competition between the rotational nature of the spin-orbit coupling and the directionality of the two effects. The natural spinors offer the advantage of providing a simple and clear pictorial explanation for the profound relativistic spin-dependent interactions in chemistry often appearing as a black box answer.

  18. 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.

  19. 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

  20. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. 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

  2. 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.

  3. 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

    2017-04-05

    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.

  4. 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

  5. Organic nonlinear optical materials: the mechanism of intermolecular covalent bonding interactions of Kekulé hydrocarbons with significant singlet biradical character.

    PubMed

    Liu, Jing; Xia, Jiarui; Song, Peng; Ding, Yong; Cui, Yanling; Liu, Xuemei; Dai, Yumei; Ma, Fengcai

    2014-08-25

    The ground- and excited-state properties of benzene-linked bisphenalenyl (B-LBP), naphthaline-linked bisphenalenyl (N-LBP), and anthracene-linked bisphenalenyl (A-LBP) Kekulé molecules and their respective one-dimensional (1D) stacks are investigated using time-dependent density functional theory (TD-DFT) and a range of extensive multidimensional visualization techniques. The results reveal a covalent π-π bonding interaction between overlapping phenalenyl radicals whose bond length is shorter than the van der Waals distance between carbon atoms. Increasing the linker length and/or number of molecules involved in the 1D stack decreases the HOMO-LUMO energy gap and increases the wavelength of the systems. The charge-transfer mechanism and electron coherence both differ with changes in the linker length and/or number of molecules involved in the 1D stack. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. 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.

  7. Resonance Raman, electron paramagnetic resonance, and density functional theory calculations of a phenolate-bound iron porphyrin complex: electrostatic versus covalent contribution to bonding.

    PubMed

    Das, Pradip Kumar; Dey, Abhishek

    2014-07-21

    Resonance Raman (rR), electron paramagnetic resonance (EPR), and density functional theory (DFT) calculations of a phenolate-bound iron porphyrin complex are reported. The complex is found to exist in a five-coordinate high-spin state in a noncoordinating solvent and in a six-coordinate low-spin state in a coordinating solvent. The vibrations originating from the iron phenolate-bound chromophores reproduced those reported for heme tyrosine active sites in nature. The EPR parameters and iron-pyrrole (Fe-Npyr) vibrations of phenolate, thiolate, and imidazole ligated iron porphyrin complexes indicate that the phenolate axial ligand acts as a π anisotropic ligand, which is more covalent than a neutral imidazole ligand but less covalent than a thiolate axial ligand. While the Fe(III/II) potential of the phenolate compound in a noncoordinating solvent is 500 mV more negative than that of the imidazole-bound complex, it is also 110 mV more negative than that of the thiolate-bound complex. DFT calculations reproduce the geometry and vibrational frequencies and show that while both phenolate and thiolate axial ligands bear π and σ interaction with the ferric center, the former is significantly less covalent than the thiolate. The higher covalency of the thiolate ligand is responsible for the lower Fe-Npyr vibration and higher V/λ (from EPR) of the thiolate-bound complexes relative to those of the phenolate-bound complex, whereas the greater electrostatic stabilization of the Fe(III)-OPh bond is responsible for lowering the Fe(III/II) E° of the phenolate-bound complex relative to that of the thiolate-bound complex in a medium having a reasonable dielectric constant.

  8. 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

  9. 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.

  10. Methamidophos, dichlorvos, O-methoate and diazinon pesticides used in Turkey make a covalent bond with butyrylcholinesterase detected by mass spectrometry.

    PubMed

    Tacal, Ozden; Lockridge, Oksana

    2010-07-01

    Organophosphorus pesticides used most commonly in Turkey include methamidophos, dichlorvos, O-methoate and diazinon. These toxic chemicals or their metabolites make a covalent bond with the active site serine of butyrylcholinesterase. Our goal was to identify the adducts that result from the reaction of human butyrylcholinesterase with these pesticides. Highly purified human butyrylcholinesterase was treated with a 20-fold molar excess of pesticide. The protein was denatured by boiling and digested with trypsin. MS and MSMS spectra of HPLC-purified peptides were acquired on a MALDI-TOF-TOF 4800 mass spectrometer. It was found that methamidophos added a mass of +93, consistent with addition of methoxy aminophosphate. A minor amount of adduct with an added mass of +109 was also found. Dichlorvos and O-methoate both made dimethoxyphosphate (+108) and monomethoxyphosphate adducts (+94). Diazinon gave a novel adduct with an added mass of +152 consistent with diethoxythiophosphate. Inhibition of enzyme activity in the presence of diazinon developed slowly (15 h), concomitant with isomerization of diazinon via a thiono-thiolo rearrangement. The isomer of diazinon yielded diethoxyphosphate and monoethoxyphosphate adducts with added masses of +136 and +108. MSMS spectra confirmed that each of the pesticides studied made a covalent bond with serine 198 of butyrylcholinesterase. These results can be used to identify the class of pesticides to which a patient was exposed. Copyright (c) 2010 John Wiley & Sons, Ltd.

  11. Methamidophos, Dichlorvos, O-methoate, and Diazinon Pesticides Used in Turkey Make a Covalent Bond with Butyrylcholinesterase Detected by Mass Spectrometry

    PubMed Central

    Tacal, Ozden; Lockridge, Oksana

    2010-01-01

    Organophosphorus pesticides used most commonly in Turkey include methamidophos, dichlorvos, O-methoate, and diazinon. These toxic chemicals or their metabolites make a covalent bond with the active site serine of butyrylcholinesterase. Our goal was to identify the adducts that result from the reaction of human butyrylcholinesterase with these pesticides. Highly purified human butyrylcholinesterase was treated with a 20-fold molar excess of pesticide. The protein was denatured by boiling and digested with trypsin. MS and MSMS spectra of HPLC-purified peptides were acquired on a MALDI-TOF-TOF 4800 mass spectrometer. It was found that methamidophos added a mass of +93, consistent with addition of methoxy aminophosphate. A minor amount of adduct with an added mass of +109 was also found. Dichlorvos and O-methoate both made dimethoxyphosphate (+108) and monomethoxyphosphate adducts (+94). Diazinon gave a novel adduct with an added mass of +152 consistent with diethoxythiophosphate. Inhibition of enzyme activity in the presence of diazinon developed slowly (15 h), concomitant with isomerization of diazinon via a thiono-thiolo rearrangement. The isomer of diazinon yielded diethoxyphosphate and monoethoxyphosphate adducts with added masses of +136 and +108. MSMS spectra confirmed that each of the pesticides studied made a covalent bond with serine 198 of butyrylcholinesterase. These results can be used to identify the class of pesticides to which a patient was exposed. PMID:20229498

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  15. 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

  16. Modeling covalent-modifier drugs.

    PubMed

    Awoonor-Williams, Ernest; Walsh, Andrew G; Rowley, Christopher N

    2017-05-18

    In this review, we present a summary of how computer modeling has been used in the development of covalent-modifier drugs. Covalent-modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein-ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent-modifier drugs. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. 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

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

    SciTech Connect

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

    2015-12-10

    We have proposed the layered honeycomb magnet α - RuCl 3 as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled j eff = 1/2 Ru 3 + magnetic moments. We report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, in contrast with the currently assumed trigonal three-layer stacking periodicity. We also report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the j eff = 1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below T N ≈ 13 K. Our analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in

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

    PubMed

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

    2017-03-02

    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.

  20. 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.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  3. 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.

  4. Experimental Evidence of Long-Range Intramolecular Vibrational Energy Redistribution through Eight Covalent Bonds: NIR Irradiation Induced Conformational Transformation of E-Glutaconic Acid.

    PubMed

    Kovács, Benjámin; Kuş, Nihal; Tarczay, György; Fausto, Rui

    2017-05-11

    Long-range intramolecular vibrational energy redistribution (IVR) driven conformational changes were investigated in a matrix-isolated open-chain, asymmetrical dicarboxylic acid, E-glutaconic acid. Although the analysis was challenging due to the presence of multiple backbone conformers and short lifetimes of the prepared higher energy cis conformers, it was shown that the selective excitation of the O-H stretching overtone of one of the carboxylic groups can induce the conformational change (trans to cis) of the other carboxylic group, located at the other end of the E-glutaconic acid molecule. This is a direct proof that the IVR process can act through eight covalent bonds in a flexible molecule before the excess energy completely dissipates into the matrix. The lifetime of the prepared higher energy conformers (averaged over the different backbones) was measured to be 12 s.

  5. The large variation in acidity of diethyl ether cation induced by internal rotation about a single covalent bond.

    PubMed

    Matsuda, Yoshiyuki; Endo, Tomoya; Mikami, Naohiko; Fujii, Asuka; Morita, Masato; Takahashi, Kaito

    2015-05-21

    In the IR spectrum of the diethyl ether cation, an extraordinarily intense band, with an extremely broad bandwidth, was observed at 2700 cm(-1), much lower frequency than normal CH stretch frequencies. This band is assigned to the stretch band of the CH bond, which is hyperconjugated with the singly occupied molecular orbital of the oxygen atom. The hyperconjugation causes the delocalization of the σ electron of the CH bond so that it enhances the acidity of the CH bond as well as the CH stretch band intensity. Theoretical simulation shows that the strength of hyperconjugation varies greatly with internal rotation of the ethyl group, and this is reflected in the large width of the observed CH stretch band. These results indicate that the DEE cation drastically changes its property from aprotic to highly acidic by the rotational isomerization of the ethyl group.

  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.

    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.

  8. Fluorescence properties of dansyl groups covalently bonded to the surface of oxidatively functionalized low-density polyethylene film

    NASA Astrophysics Data System (ADS)

    Holmes-Farley, S. R.; Whitesides, G. M.

    1985-12-01

    Brief oxidation of low-density polyethylene film with chromic acid in aqueous sulfuric acid introduced carboxylic acid and ketone and/or aldehyde groups onto the surface of the film. The carboxylic acid moieties can be used to attach more complex functionality to the polymer surface. We are developing this surface-functionalized polyethylene (named polyethylene carboxylic acid, PE-CO2H, to emphasize the functional group that dominates its surface properties) as a substrate with which to study problems in organic surface chemistry--especially wetting, polymer surface reconstruction, and adhesion--using physical-organic techniques. This document describes the preparation, characterization, and fluorescence properties of derivatives of PE-CO2H in which the Dansyl (5-dimethylaminonaphthalene-1-sulfonyl) group has been covalently attached by amide links to the surface carbonyl moieties.

  9. 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.

  10. Nature of the Ru−NO Coordination Bond: Kohn–Sham Molecular Orbital and Energy Decomposition Analysis

    PubMed Central

    Orenha, Renato P.; Rocha, Marcus V. J.; Poater, Jordi

    2017-01-01

    Abstract We have analyzed structure, stability, and Ru−NO bonding of the trans‐[RuCl(NO)(NH3)4]2+ complex by using relativistic density functional theory. First, we focus on the bond dissociation energies associated with the three canonical dissociation modes leading to [RuCl(NH3)4]++NO+, [RuCl(NH3)4]2++NO, and [RuCl(NH3)4]3++NO−. The main objective is to understand the Ru−NO+ bonding mechanism in the conceptual framework of Kohn–Sham molecular orbital theory in combination with a quantitative energy decomposition analysis. In our analyses, we have addressed the importance of the synergism between Ru−NO+ σ‐donation and π‐backdonation as well as the so‐called negative trans influence of the Cl− ligand on the Ru−NO bond. For completeness, the Ru−NO+ bonding mechanism is compared with that of the corresponding Ru−CO bond. PMID:28638774

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

    SciTech Connect

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

    2014-01-01

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

  12. Effects of covalent crosslinking and hydrogen bonding on the physical and mechanical properties of rigid-rod polymeric fibers

    NASA Astrophysics Data System (ADS)

    Jenkins, Shawn Eric

    The consequences of crosslinking pendant rigid-rod polymers have been presented. These systems were found to exhibit enhanced shrinkage, caused by pendant loss at elevated temperatures. The evidence suggests that crosslinking is likely to take place in these systems via the coupling of adjacent phenyl rings. Atomistic simulation suggests that this crosslink type would produce a substantial axial stress through a perturbation of the crystalline structure. Thermomechanical analysis and WAXD have observed the effects of this stress on a macroscopic and atomic level, respectively. In an effort to avoid the aforementioned strains on reaction, crosslinking methyl-pendant PBZT fibers via electron radiation, has been attempted and the results discussed. A new rigid-rod polymer, methyl-pendant poly(p-phenylene benzobisimidazole) (MePBI), having the capacity for intermolecular hydrogen bonding has been characterized and compared with analogous weakly interacting systems. MePBI shows marked improvement in compressive strength over MePBZT and other weakly associating rigid-rod polymers. The improvement in compressive strength is attributed to increased intermolecular association via the formation of intermolecular hydrogen bonds, as opposed to any differences in morphology. Finally, issues pertaining to the role of hydrogen bonding in effecting some physical and mechanical properties of rigid-rod polymeric systems have been discussed.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Acylhydrazone bond dynamic covalent polymer gel monolithic column online coupling to high-performance liquid chromatography for analysis of sulfonamides and fluorescent whitening agents in food.

    PubMed

    Zhang, Chengjiang; Luo, Xialin; Wei, Tianfu; Hu, Yufei; Li, Gongke; Zhang, Zhuomin

    2017-10-13

    A new dynamic covalent polymer (DCP) gel was well designed and constructed based on imine chemistry. Polycondensation of 4,4'-biphenyldicarboxaldehyde and 1,3,5-benzenetricarbohydrazide via Schiff-base reaction resulted in an acylhydrazone bond gel (AB-gel) DCP. AB-gel DCP had three-dimensional network of interconnected nanoparticles with hierarchically porous structure. AB-gel DCP was successfully fabricated as a monolithic column by an in-situ chemical bonding method for online enrichment and separation purpose with excellent permeability. AB-gel DCP based monolithic column showed remarkable adsorption affinity towards target analytes including sulfonamides (SAs) and fluorescent whitening agents (FWAs) due to its strong π-π affinity, hydrophobic effect and hydrogen bonding interaction. Then, AB-gel DCP based monolithic column was applied for online separation and analysis of trace SAs and FWAs in food samples coupled with high-performance liquid chromatography (HPLC). Sulfathiazole (ST) and sulfadimidine (SM2) in one positive weever sample were actually found and determined with concentrations of 273.8 and 286.3μg/kg, respectively. 2,5-Bis(5-tert-butyl-2-benzoxazolyl) thiophene (FWA184) was actually quantified in one tea infusion sample with the concentration of 268.5ng/L. The spiked experiments suggested the good recoveries in range of 74.5-110% for SAs in weever and shrimp samples with relative standard deviations (RSDs) less than 9.7% and in range of 74.0-113% for FWAs in milk and tea infusion samples with RSDs less than 9.0%. AB-gel DCP monolithic column was proved to be a promising sample preparation medium for online separation and analysis of trace analytes in food samples with complex matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Covalency in metal-oxygen multiple bonds evaluated using oxygen K-edge spectroscopy and electronic structure theory.

    PubMed

    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

    2013-02-06

    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 MO(4)(x-) anions have formed the basis for new M-O bonding theories. Herein, relative changes in M-O orbital mixing in MO(4)(2-) (M = Cr, Mo, W) and MO(4)(-) (M = Mn, Tc, Re) are evaluated for the first time by nonresonant inelastic X-ray scattering, X-ray absorption spectroscopy using fluorescence and transmission (via a scanning transmission X-ray microscope), and time-dependent density functional theory. The results suggest that moving from Group 6 to Group 7 or down the triads increases M-O e* (π*) mixing; for example, it more than doubles in ReO(4)(-) relative to CrO(4)(2-). Mixing in the t(2)* orbitals (σ* + π*) remains relatively constant within the same Group, but increases on moving from Group 6 to Group 7. These unexpected changes in orbital energy and composition for formally isoelectronic tetraoxometalates are evaluated in terms of periodic trends in d orbital energy and radial extension.

  1. 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.

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

    PubMed

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

    2016-05-11

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

  3. 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.

  4. 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

  5. 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.

  6. Binding energy curves from nonempirical density functionals. I. Covalent bonds in closed-shell and radical molecules.

    PubMed

    Ruzsinszky, Adrienn; Perdew, John P; Csonka, Gábor I

    2005-12-08

    Binding or potential energy curves have been calculated for the ground-state diatomics H(2)(+), He(2)(+), LiH(+), H(2), N(2), and C(2), for the transition state H(3), and for the triplet first excited state of H(2) using the nonempirical density functionals from the first three rungs of a ladder of approximations: the local spin density (LSD) approximation, the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA), and the Tao-Perdew-Staroverov-Scuseria (TPSS) meta GGA. Good binding energy curves in agreement with coupled cluster or configuration interaction calculations are found from the PBE GGA and especially from the TPSS meta GGA. Expected exceptions are the symmetric radicals H(2)(+) and He(2)(+), where the functionals suffer from self-interaction error, and the exotically bonded C(2). Although the energy barrier for the reaction H(2) + H --> H + H(2) is better in PBE than in TPSS, the transition state H(3) is a more properly positioned and curved saddle point of the energy surface in TPSS. The triplet first excited state of H(2) obeys the Aufbau principle and thus is one of the exceptional excited states that are computable in principle from the ground-state functional. The PBE GGA and TPSS meta GGA are useful not only for chemical applications but also for the construction of higher-rung nonempirical functionals that can further improve the binding energy curves.

  7. 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.

  8. 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

  9. Preparation of sodium cholate-based micelles through non-covalent ıbonding interaction and application as oral delivery systems for paclitaxel.

    PubMed

    Ge, Yanxiu; Zhao, Yanli; Li, Lingbing

    2016-09-01

    In present study, two types of micelles based on sodium cholate (NaC) were prepared through non-covalent bonding interaction and the potential of micelles as oral drug delivery systems for paclitaxel (PTX) was evaluated. Pluronic-chitosan (F127-CS) and Pluronic-poly (acrylic acid) (F127-PAA) copolymers were synthesized. Electrostatic interaction and hydrogen bond were used to prepare F127-CS/NaC micelles and F127-PAA/NaC micelles, respectively. The physicochemical characteristics of micelles were determined. An average diameter of 67.5 nm and unimodal pattern of size distribution were observed for F127-CS/NaC micelles. While for F127-PAA/NaC micelles, an average diameter of 85.89 nm and non-unimodal pattern of size distribution were observed. The results revealed that F127-CS/NaC micelles were more integrated than F127-PAA/NaC micelles. Further experiments showed that the F127-CS/NaC micelles had a higher drug-loading content of 12.8% and a lower critical micelle concentration (CMC) of 2.5 × 10(-3 )mol/L compared with F127-PAA/NaC micelles. In vitro cytotoxicity analysis demonstrated that the PTX-loaded F127-CS/NaC micelles were of great efficiency in inhibiting the growth of drug-resistant breast cancer MCF-7 cells (MCF-7/Adr). The intragastric administration of the PTX-loaded F127-CS/NaC micelles in rats provided a 4.33-fold higher absolute bioavailability compared to commercial Taxol®, indicating an efficient oral absorption of PTX delivered by micelles. These findings signify that F127-CS/NaC micelle may be a promising carrier for the delivery of PTX.

  10. 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.

  11. 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.

  12. A novel method for the sensitive detection of mutant proteins using a covalent-bonding tube-based proximity ligation assay.

    PubMed

    Jiang, Xuecheng; Zhou, Lixiao; Cheng, Jie; Zhang, Hua; Wang, Huixia; Chen, Zhixiong; Shi, Feng; Zhu, Chenggang

    2014-09-02

    Tumorigenesis is the cumulative result of multiple gene mutations. The mutant proteins that are expressed by mutant genes in cancer cells are secreted into the blood and are useful biomarkers for the early diagnosis of cancer. However, some difficulties exist; for example, the same gene will express different protein mutants in different patients, and early tumors secrete only small amounts of mutant protein. Thus, the presence of mutant proteins in plasma has not previously been exploited for the early diagnosis of cancer. Proximity ligation assay is a protein-detection method that has been developed in recent years and has been widely used because of its high sensitivity. However, this approach still suffers from some shortcomings that should be addressed. In this paper, we develop a covalent-bonding tube-based proximity ligation assay (TB-PLA). The limit of detection of TB-PLA for 0.001pM, and the method exhibited a broad dynamic range of up to seven orders of magnitude. Furthermore, we coupled the conformation-specific antibody PAb240 of p53 mutants to PCR tubes for TB-PLA. The assay was capable of detecting an approximately 500-fold lower concentration of mutant p53 in serum compared with sandwich ELISA. Thus, we demonstrate TB-PLA to be a highly sensitive and effective approach that is suitable for the early clinical diagnosis of cancer using the conformation-specific antibodies of protein mutants. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2016-07-13

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

  14. 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.

  15. Trimethylsilyl-terminated oligo(phenylene ethynylene)s: an approach to single-molecule junctions with covalent Au-C σ-bonds.

    PubMed

    Hong, Wenjing; Li, Hui; Liu, Shi-Xia; Fu, Yongchun; Li, Jianfeng; Kaliginedi, Veerabhadrarao; Decurtins, Silvio; Wandlowski, Thomas

    2012-11-28

    A new and efficient approach using cleaving of trimethylsilyl groups to create covalent Au-C anchoring sites has been developed for single-molecule junction conductance measurements. Employing the mechanically controllable break junction (MCBJ) technique in liquid, we demonstrate the formation of highly conducting single molecular junctions of several OPE derivatives. The created junctions are mechanically stable and exhibit conductances around one order of magnitude higher than those of their dithiol analogues. Extended assembly and reaction times lead to oligomerization. Combined STM imaging and gap-mode Raman experiments provide structure evidence to support the formation of covalent Au-C contacts and further oligomerization.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Urotensin-II peptidomimetic incorporating a non-reducible 1,5-triazole disulfide bond reveals a pseudo-irreversible covalent binding mechanism to the urotensin G-protein coupled receptor.

    PubMed

    Pacifico, Salvatore; Kerckhoffs, Aidan; Fallow, Andrew J; Foreman, Rachel E; Guerrini, Remo; McDonald, John; Lambert, David G; Jamieson, Andrew G

    2017-05-31

    The urotensin-II receptor (UTR) is a class A GPCR that predominantly binds to the pleiotropic cyclic peptide urotensin-II (U-II). U-II is constrained by a disulfide bridge that induces a β-turn structure and binds pseudo-irreversibly to UTR and is believed to result in a structural rearrangement of the receptor. However, it is not well understood how U-II binds pseudo-irreversibly and the nature of the reorganization of the receptor that results in G-protein activation. Here we describe a series of U-II peptidomimetics incorporating a non-reducible disulfide bond structural surrogate to investigate the feasibility that native U-II binds to the G protein-coupled receptor through disulfide bond shuffling as a mechanism of covalent interaction. Disubstituted 1,2,3-triazoles were designed with the aid of computational modeling as a non-reducible mimic of the disulfide bridge (Cys5-Cys10) in U-II. Solid phase synthesis using CuAAC or RuAAC as the key macrocyclisation step provided four analogues of U-II(4-11) incorporating either a 1,5-triazole bridge (5, 6) or 1,4-triazole bridge (9, 10). Biological evaluation of compounds 5, 6, 9 and 10 was achieved using in vitro [(125)I]UII binding and [Ca(2+)]i assays at recombinant human UTR. Compounds 5 and 6 demonstrated high affinity (KD ∼ 10 nM) for the UTR and were also shown to bind reversibly as predicted and activate the UTR to increase [Ca(2+)]i. Importantly, our results provide new insight into the mechanism of covalent binding of U-II with the UTR.

  5. Covalency in Americium(III) Hexachloride

    DOE PAGES

    Cross, Justin Neil; Su, Jing; Batista, Enrigue R.; ...

    2017-06-14

    Developing a better understanding of covalency (or orbital mixing) is of fundamental importance. Covalency occupies a central role in directing chemical and physical properties for almost any given compound or material. Hence, the concept of covalency has potential to generate broad and substantial scientific advances, ranging from biological applications to condensed matter physics. Given the importance orbital mixing combined with the difficultly in measuring covalency, estimating or inferring covalency often leads to fiery debate. Consider the 60-year controversy sparked by SEABORG and COWORKERS (1954) when it was proposed that covalency from 5f-orbitals contributed to the unique behavior of americium inmore » chloride matrixes. Herein, we describe the use of ligand K-edge X-ray absorption spectroscopy (XAS) and electronic structure calculations to quantify the extent of covalent bonding in – arguably – one of the most difficult systems to study, the Am–Cl interaction within AmCl63-. We observed both 5fand 6d-orbital mixing with the Cl-3p orbitals; however, contributions from the 6d-orbitals were more substantial. Comparisons with the isoelectronic EuCl63- indicated similar bonding for the AmIII 6d- and EuIII 5d-orbitals. Meanwhile, the results confirmed SEABORG’S 1954 hypothesis that AmIII 5f-orbital covalency was more substantial than 4forbital mixing for EuIII.« less

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

    PubMed

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

    2016-06-07

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

  7. Is HO3(-) multiple-minimum and floppy? Covalent to van der Waals isomerization and bond rupture of a peculiar anion.

    PubMed

    Varandas, A J C

    2014-08-28

    The singlet ground-state of the HO3(-) anion is studied with high level single- and multireference methods, and the scheme termed complete-active-space-dynamical-correlation, which has been previously used to study the neutral HO3 radical. It is found to have a planar cis isomeric structure with a long intermediate O-O bond (≈1.75 Å), as is now consensual in the literature. It also has a pyramidal-type branch-isomer, but its minimum lies ≈33 kcal mol(-1) above the cis minimum. Interestingly, another isomer is predicted here, with a planar geometry that can be even more stable than cis-HO3(-) at some levels of theory. It shows a hydrogen-bond (van der Waals) type structure, with an intermediate O-O bond of ≈2.59 Å. All such minima lie on the lowest adiabatic potential energy surface, with the two lowest planar ones (cis and vdW) connected by a saddle point whose structure, also planar, is unveiled. All these lie on the first third of the optimum path for bond-rupture in [HO-OO](-), which is predicted to yield ground state HO plus O2(-), an asymptote lying 30 kcal mol(-1) above the cis-HO3(-) minimum. Unprecedented in the literature on the key title anion, such features should bear strong implications for its preparation, spectroscopy, and role in chemistry.

  8. Spectroscopic and Electronic Structure Studies Probing Covalency Contributions to C-H Bond Activation and Transition State Stabilization in Xanthine Oxidase

    PubMed Central

    Sempombe, Joseph; Stein, Benjamin; Kirk, Martin L.

    2011-01-01

    A detailed EPR and computational study of a key paramagnetic form of xanthine oxidase (XO) has been performed which serves as a basis for developing a valence bond description of C-H activation and transition state stabilization along the reaction coordinate with aldehyde substrates. EPR spectra of aldehyde Inhibited XO have been analyzed in order to provide information regarding the relationship between the g-, 95,97Mo hyperfine (AMo), and the 13C hyperfine (AC) tensors. The analysis of the EPR spectra have allowed for greater insight into the electronic origin of key delocalizations within the Mo-Oeq-C fragment, and how these contribute to C-H bond activation/cleavage and transition state (TS) stabilization. A natural bond orbital analysis of the enzyme reaction coordinate with aldehyde substrates shows that both Mo=S π→C-H σ* (ΔE= 24.3 kcal/mol) and C-H σ → Mo=S π* (ΔE = 20.0 kcal/mol) back donation are important in activating the substrate for C-H bond for cleavage. Additional contributions to C-H activation derive from Oeq lp→C-H σ* (lp = lone pair; ΔE = 8.2 kcal/mol), and S lp→C-H σ* (ΔE = 13.2 kcal/mol) stabilizing interactions. The Oeq donor ligand that derives from water is part of the Mo-Oeq-C fragment probed in the EPR spectra of XO Inhibited, and the observation of Oeq lp→C-H σ* back donation indicates a key role for the Oeq in activating the substrate C-H bond for cleavage. We also show that the Oeq donor plays an even more important role in transition state (TS) stabilization. We find that Oeq→(Mo + C) charge transfer dominantly contributes to stabilization of the TS (ΔE = 89.5 kcal/mol) and the Mo-Oeq-C delocalization pathway reduces strong electronic repulsions that contribute to the classical TS energy barrier. The Mo-Oeq-C delocalization at the TS allows for the TS to be described in valence bond terms as a resonance hybrid of the reactant (R) and product (P) valence bond wavefunctions. PMID:21972782

  9. 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.

  10. 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.

  11. 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.

  12. K2 ZnSn3 Se8 : A Non-Centrosymmetric Zinc Selenidostannate(IV) Featuring Interesting Covalently Bonded [ZnSn3 Se8 ](2-) Layer and Exhibiting Intriguing Second Harmonic Generation Activity.

    PubMed

    Zhou, Molin; Jiang, Xingxing; Yang, Yi; Guo, Yangwu; Lin, Zheshuai; Yao, JJiyong; Wu, Yicheng

    2017-06-19

    Non-centrosymmetric zinc selenidostannate(IV) K2 ZnSn3 Se8 was synthesized. It features interesting covalently bonded [ZnSn3 Se8 ](2-) layers with K(+) cations filling in the interlayer voids. The phonon spectrum was calculated to clarify its structural stability. Based on the X-ray diffraction data along with the Raman spectrum, the major bonding features of the title compound were identified. According to the UV/vis-NIR spectroscopy, K2 ZnSn3 Se8 possesses a typical direct band gap of 2.10 eV, which is in good agreement with the band structure calculations. Moreover, our experimental measurements and detailed theoretical calculations reveal that K2 ZnSn3 Se8 is a new phase-matchable nonlinear optical material with a powder second harmonic generation (SHG) signal about 0.6 times of that of AgGaS2 . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Determining Cysteines Available for Covalent Inhibition Across the Human Kinome.

    PubMed

    Zhao, Zheng; Liu, Qingsong; Bliven, Spencer; Xie, Lei; Bourne, Philip E

    2017-04-13

    Covalently bound protein kinase inhibitors have been frequently designed to target noncatalytic cysteines at the ATP binding site. Thus, it is important to know if a given cysteine can form a covalent bond. Here we combine a function-site interaction fingerprint method and DFT calculations to determine the potential of cysteines to form a covalent interaction with an inhibitor. By harnessing the human structural kinome, a comprehensive structure-based binding site cysteine data set was assembled. The orientation of the cysteine thiol group indicates which cysteines can potentially form covalent bonds. These covalent inhibitor easy-available cysteines are located within five regions: P-loop, roof of pocket, front pocket, catalytic-2 of the catalytic loop, and DFG-3 close to the DFG peptide. In an independent test set these cysteines covered 95% of covalent kinase inhibitors. This study provides new insights into cysteine reactivity and preference which is important for the prospective development of covalent kinase inhibitors.

  14. 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.

  15. Covalently linked tandem lesions in DNA.

    PubMed

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

    2012-12-01

    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.

  16. 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

  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. 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.

  19. 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

  20. 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.

  1. 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

  2. Atomic Covalent Functionalization of Graphene

    PubMed Central

    Johns, James E.; Hersam, Mark C.

    2012-01-01

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

  3. 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.

  4. 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.

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

    PubMed

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

    2009-01-01

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

  6. Dynamic Conversion Between Se-N Covalent and Noncovalent Interactions.

    PubMed

    Xie, Meng; Wang, Lili; Liu, Fang; Zhang, Dongju; Gao, Jun

    2016-11-17

    Se-N dynamic covalent bond is a new dynamic covalent bond which has applications in the fabrication of stimuli responsive and self-healing functional materials. Although recent advances have been achieved in the experimental aspect, little is known about the formation mechanism of Se-N dynamic covalent bond. Here the structures and nature of Se-N dynamic covalent bond between three kinds of pyridine derivatives R-C5H4N, [pyridine (R = H), 4-methylpyridine (R = CH3), 4-dimethylamino-pyridine (R = N(CH3)2)] and phenylselenyl bromine (PhSeBr) have been analyzed using density functional theory. The interactions between Se atom in PhSeBr and N atom in pyridine or pyridine derivatives can be divided into three models: dissociation, nonbonding interaction and covalent bond interaction. Quantum chemical calculations on three series compounds show that these three models can convert mutually, which results in the generation of Se-N dynamic covalent bond. Solvent effects produced in polar solvents such as CH2Cl2 can make the conversion between Se-N covalent bond and Se···N nonbonding interactions easier. The kind of the substituents in pyridine ring can affect the conversion process: the stronger the electron-donating ability of the substituent, the easier the structure transformation.

  7. 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.

  8. 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

  9. 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.

  10. pH Switchable Emulsions Based on Dynamic Covalent Surfactants.

    PubMed

    Ren, Gaihuan; Wang, Lei; Chen, Qianqian; Xu, Zhenghe; Xu, Jian; Sun, Dejun

    2017-03-28

    Dynamic covalent surfactants were designed to prepare pH switchable emulsions. A dynamic covalent bond between nonamphiphilic building blocks (polyethylenimine (PEI) and benzaldehyde (B)) was introduced to form the dynamic covalent surfactant PEI-B. The dynamic nature of covalent bond in PEI-B was confirmed by (1)H NMR and fluorescence probe analysis. Stable emulsions were successfully prepared with interfacial active PEI-B at pH 7.8 with various water/paraffin oil ratios under sonication. When lowering the pH to 3.5, a complete phase separation was observed as a result of breaking dynamic covalent bond in the interfacial active PEI-B. After tuning the pH back to 7.8, stable emulsion was obtained again due to the reformation of the dynamic covalent bond and hence interfacial active PEI-B. The emulsification and demulsification were dependent on the formation and breaking of dynamic covalent bond in PEI-B. Such pH-triggered emulsification and demulsification can be switched at least three times. Application of dynamic covalent surfactants will open up a novel route for preparing responsive emulsions.

  11. 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.

  12. Construction of Hierarchically One-Dimensional Core-Shell CNT@Microporous Carbon by Covalent Bond-Induced Surface-Confined Cross-Linking for High-Performance Supercapacitor.

    PubMed

    Li, Zhenghui; Li, Zhaopeng; Li, Liuqing; Li, Chengfei; Zhong, Weihao; Zhang, Haiyan

    2017-05-10

    A covalent bond-induced surface-confined cross-linking is reported to construct one-dimensional coaxial CNT@microporous carbon composite (CNT@micro-C). Octaphenyl polyhedral oligomeric silsesquioxane (Ph-POSS) composed of eight phenyls and a -Si8O12 cage was selected as precursor for microporous carbon. The layer-by-layer cross-linking of phenyl anchored Ph-POSS on the surface of CNT; after carbonization and etching of -Si8O12 cages, CNT@micro-C including CNT core and microporous carbon shell was harvested. The thickness of microporous carbon shell can be well tailored from 6.0 to 20.0 nm, and the surface area of CNT@micro-C can reach 1306 m(2) g(-1). CNT@micro-C combines the structural advantages of CNT and microporous carbon, presenting large surface area, high electrical conductivity, fast ion transfer speed, and short ion transfer distance. When used as electrode material, CNT@micro-C reveals superior supercapacitive performance; for example, its capacitance can reach 243 F g(-1) at 0.5 A g(-1) and slightly decreases to 209 F g(-1) at 10 A g(-1), indicating a capacitance retention of 86%. Even at a very high scan rate of 50 A g(-1), a high capacitance of 177 F g(-1) is retained, giving a capacitance retention of 73%.

  13. 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.

  14. Covalent Protein Labeling at Glutamic Acids.

    PubMed

    Martín-Gago, Pablo; Fansa, Eyad K; Winzker, Michael; Murarka, Sandip; Janning, Petra; Schultz-Fademrecht, Carsten; Baumann, Matthias; Wittinghofer, Alfred; Waldmann, Herbert

    2017-05-18

    Covalent labeling of amino acids in proteins by reactive small molecules, in particular at cysteine SH and lysine NH groups, is a powerful approach to identify and characterize proteins and their functions. However, for the less-reactive carboxylic acids present in Asp and Glu, hardly any methodology is available. Employing the lipoprotein binding chaperone PDE6δ as an example, we demonstrate that incorporation of isoxazolium salts that resemble the structure and reactivity of Woodward's reagent K into protein ligands provides a novel method for selective covalent targeting of binding site carboxylic acids in whole proteomes. Covalent adduct formation occurs via rapid formation of enol esters and the covalent bond is stable even in the presence of strong nucleophiles. This new method promises to open up hitherto unexplored opportunities for chemical biology research. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    SciTech Connect

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

    1992-09-01

    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.

  16. 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.

  17. 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.

  18. Identification of Covalent Binding Sites Targeting Cysteines Based on Computational Approaches.

    PubMed

    Zhang, Yanmin; Zhang, Danfeng; Tian, Haozhong; Jiao, Yu; Shi, Zhihao; Ran, Ting; Liu, Haichun; Lu, Shuai; Xu, Anyang; Qiao, Xin; Pan, Jing; Yin, Lingfeng; Zhou, Weineng; Lu, Tao; Chen, Yadong

    2016-09-06

    Covalent drugs have attracted increasing attention in recent years due to good inhibitory activity and selectivity. Targeting noncatalytic cysteines with irreversible inhibitors is a powerful approach for enhancing pharmacological potency and selectivity because cysteines can form covalent bonds with inhibitors through their nucleophilic thiol groups. However, most human kinases have multiple noncatalytic cysteines within the active site; to accurately predict which cysteine is most likely to form covalent bonds is of great importance but remains a challenge when designing irreversible inhibitors. In this work, FTMap was first applied to check its ability in predicting covalent binding site defined as the region where covalent bonds are formed between cysteines and irreversible inhibitors. Results show that it has excellent performance in detecting the hot spots within the binding pocket, and its hydrogen bond interaction frequency analysis could give us some interesting instructions for identification of covalent binding cysteines. Furthermore, we proposed a simple but useful covalent fragment probing approach and showed that it successfully predicted the covalent binding site of seven targets. By adopting a distance-based method, we observed that the closer the nucleophiles of covalent warheads are to the thiol group of a cysteine, the higher the possibility that a cysteine is prone to form a covalent bond. We believe that the combination of FTMap and our distance-based covalent fragment probing method can become a useful tool in detecting the covalent binding site of these targets.

  19. Triply interlocked covalent organic cages.

    PubMed

    Hasell, Tom; Wu, Xiaofeng; Jones, James T A; Bacsa, John; Steiner, Alexander; Mitra, Tamoghna; Trewin, Abbie; Adams, Dave J; Cooper, Andrew I

    2010-09-01

    Interlocked molecules comprise two or more separate components that are joined by 'mechanical' rather than covalent bonds. In other words, these molecular assemblies cannot be dissociated without the cleavage of one or more chemical bonds. Although recent progress has enabled the preparation of such topologies through coordination or templating interactions, three-dimensional interlocked covalent architectures remain difficult to prepare. Here, we present a template-free one-pot synthesis of triply interlocked organic cages. These 20-component dimers consist of two tetrahedral monomeric cages each built from four nodes and six linkers. The monomers exhibit axial chirality, which is recognized by their partner cage during the template-free interlocking assembly process. The dimeric cages also include two well-defined cavities per assembly, which for one of the systems studied led to the formation of a supramolecular host-guest chain. These interlocked organic molecules may prove useful as part of a toolkit for the modular construction of complex porous solids and other supramolecular assemblies.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Single chain folding of synthetic polymers by covalent and non-covalent interactions: current status and future perspectives.

    PubMed

    Altintas, Ozcan; Barner-Kowollik, Christopher

    2012-06-14

    The present feature article highlights the preparation of polymeric nanoparticles and initial attempts towards mimicking the structure of natural biomacromolecules by single chain folding of well-defined linear polymers through covalent and non-covalent interactions. Initially, the discussion focuses on the synthesis and characterization of single chain self-folded structures by non-covalent interactions. The second part of the article summarizes the folding of single chain polymers by means of covalent interactions into nanoparticle systems. The current state of the art in the field of single chain folding indicates that covalent-bond-driven nanoparticle preparation is well advanced, while the first encouraging steps towards building reversible single chain folding systems by the use of mutually orthogonal hydrogen-bonding motifs have been made. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. 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)

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

    PubMed

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

    2015-08-01

    The motivation to use ruthenium complexes in cancer treatment has led our research group to synthesize complexes with this metal and test them against several types of tumor cells, yielding promising results. In this paper the results of biological tests, assessed by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, were carried out on the complexes cis-[RuCl(BzCN)(bipy)(dppe)]PF6 (1), cis-[RuCl(BzCN)(bipy)(dppb)]PF6 (2), cis-[RuCl(BzCN)(bipy)(dppf)]PF6 (3) and cis-[RuCl(BzCN)(phen)(dppb)]PF6 (4) which are described [BzCN = b enzonitrile; bipy = 2,2'-bipyridine; phen = 1,10-phenanthroline; dppe = 1,2-bis(diphenylphosphino) ethane; dppb = 1,4-bis-(diphenylphosphino)butane; dppf = 1,1'-bis(diphenylphosphino)ferrocene]. The present study is focused on the cytotoxic activity of complexes (1)-(4) against four tumor cell lines and on the apoptosis and changes in the cell cycle and gene expression observed in the sarcoma 180 (S180) tumor cell line treated with complex (1). The results demonstrated that this complex inhibits S180 cell growth, with an IC50 of 17.02 ± 8.21 μM, while exhibiting lower cytotoxicity (IC50 = 53.73 ± 5.71 μM) towards lymphocytes (normal cells). Flow cytometry revealed that the complex inhibits the growth of tumor cells by inducing apoptosis as evidenced by an increase in the proportion of cells positive for annexin V staining and G0/G1 phase cell-cycle arrest. Further investigation showed that complex (1) induces a drop in the mitochondrial membrane potential and provokes a decrease in Bcl-2 protein expression and increase in caspase 3 activation, while the increased activation of caspase 8 caused a decrease in the gene expression in caspases 3 and 9. Increases in Tp53 and Bax expressions were also observed. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. 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.

  9. 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…

  10. 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

  11. 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

  12. A Perspective on the Kinetics of Covalent and Irreversible Inhibition.

    PubMed

    Strelow, John M

    2017-01-01

    The clinical and commercial success of covalent drugs has prompted a renewed and more deliberate pursuit of covalent and irreversible mechanisms within drug discovery. A covalent mechanism can produce potent inhibition in a biochemical, cellular, or in vivo setting. In many cases, teams choose to focus on the consequences of the covalent event, defined by an IC50 value. In a biochemical assay, the IC50 may simply reflect the target protein concentration in the assay. What has received less attention is the importance of the rate of covalent modification, defined by kinact/KI. The kinact/KI is a rate constant describing the efficiency of covalent bond formation resulting from the potency (KI) of the first reversible binding event and the maximum potential rate (kinact) of inactivation. In this perspective, it is proposed that the kinact/KI should be employed as a critical parameter to identify covalent inhibitors, interpret structure-activity relationships (SARs), translate activity from biochemical assays to the cell, and more accurately define selectivity. It is also proposed that a physiologically relevant kinact/KI and an (unbound) AUC generated from a pharmacokinetic profile reflecting direct exposure of the inhibitor to the target protein are two critical determinants of in vivo covalent occupancy. A simple equation is presented to define this relationship and improve the interpretation of covalent and irreversible kinetics.

  13. 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.

  14. 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.

  15. 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.

  16. Comparative Analysis of Pharmacophore Features and Quantitative Structure-Activity Relationships for CD38 Covalent and Non-covalent Inhibitors.

    PubMed

    Zhang, Shuang; Xue, Xiwen; Zhang, Liangren; Zhang, Lihe; Liu, Zhenming

    2015-12-01

    In the past decade, the discovery, synthesis, and evaluation for hundreds of CD38 covalent and non-covalent inhibitors has been reported sequentially by our group and partners; however, a systematic structure-based guidance is still lacking for rational design of CD38 inhibitor. Here, we carried out a comparative analysis of pharmacophore features and quantitative structure-activity relationships for CD38 inhibitors. The results uncover that the essential interactions between key residues and covalent/non-covalent CD38 inhibitors include (i) hydrogen bond and hydrophobic interactions with residues Glu226 and Trp125, (ii) electrostatic or hydrogen bond interaction with the positively charged residue Arg127 region, and (iii) the hydrophobic interaction with residue Trp189. For covalent inhibitors, besides the covalent effect with residue Glu226, the electrostatic interaction with residue Arg127 is also necessary, while another hydrogen/non-bonded interaction with residues Trp125 and Trp189 can also be detected. By means of the SYBYL multifit alignment function, the best CoMFA and CoMSIA with CD38 covalent inhibitors presented cross-validated correlation coefficient values (q(2)) of 0.564 and 0.571, and non-cross-validated values (r(2)) of 0.967 and 0.971, respectively. The CD38 non-covalent inhibitors can be classified into five groups according to their chemical scaffolds, and the residues Glu226, Trp189, and Trp125 are indispensable for those non-covalent inhibitors binding to CD38, while the residues Ser126, Arg127, Asp155, Thr221, and Phe222 are also important. The best CoMFA and CoMSIA with the F12 analogues presented cross-validated correlation coefficient values (q(2)) of 0.469 and 0.454, and non-cross-validated values (r(2)) of 0.814 and 0.819, respectively. © 2015 John Wiley & Sons A/S.

  17. 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.

  18. Actinide covalency measured by pulsed electron paramagnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Formanuik, Alasdair; Ariciu, Ana-Maria; Ortu, Fabrizio; Beekmeyer, Reece; Kerridge, Andrew; Tuna, Floriana; McInnes, Eric J. L.; Mills, David P.

    2017-06-01

    Our knowledge of actinide chemical bonds lags far behind our understanding of the bonding regimes of any other series of elements. This is a major issue given the technological as well as fundamental importance of f-block elements. Some key chemical differences between actinides and lanthanides—and between different actinides—can be ascribed to minor differences in covalency, that is, the degree to which electrons are shared between the f-block element and coordinated ligands. Yet there are almost no direct measures of such covalency for actinides. Here we report the first pulsed electron paramagnetic resonance spectra of actinide compounds. We apply the hyperfine sublevel correlation technique to quantify the electron-spin density at ligand nuclei (via the weak hyperfine interactions) in molecular thorium(III) and uranium(III) species and therefore the extent of covalency. Such information will be important in developing our understanding of the chemical bonding, and therefore the reactivity, of actinides.

  19. 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)

  20. 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)

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. The Covalent Functionalization of Layered Black Phosphorus by Nucleophilic Reagents.

    PubMed

    Sofer, Zdeněk; Luxa, Jan; Bouša, Daniel; Sedmidubský, David; Lazar, Petr; Hartman, Tomáš; Hardtdegen, Hilde; Pumera, Martin

    2017-08-07

    Layered black phosphorus has been attracting great attention due to its interesting material properties which lead to a plethora of proposed applications. Several approaches are demonstrated here for covalent chemical modifications of layered black phosphorus in order to form P-C and P-O-C bonds. Nucleophilic reagents are highly effective for chemical modification of black phosphorus. Further derivatization approaches investigated were based on radical reactions. These reagents are not as effective as nucleophilic reagents for the surface covalent modification of black phosphorus. The influence of covalent modification on the electronic structure of black phosphorus was investigated using ab initio calculations. Covalent modification exerts a strong effect on the electronic structure including the change of band-gap width and spin polarization. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Hydrogen bonding and anaesthesia

    NASA Astrophysics Data System (ADS)

    Sándorfy, C.

    2004-12-01

    General anaesthetics act by perturbing intermolecular associations without breaking or forming covalent bonds. These associations might be due to a variety of van der Waals interactions or hydrogen bonding. Neurotransmitters all contain OH or NH groups, which are prone to form hydrogen bonds with those of the neurotransmitter receptors. These could be perturbed by anaesthetics. Aromatic rings in amino acids can act as weak hydrogen bond acceptors. On the other hand the acidic hydrogen in halothane type anaesthetics are weak proton donors. These two facts together lead to a probable mechanism of action for all general anaesthetics.

  7. Advanced Photonic Sensors Enabled by Semiconductor Bonding

    DTIC Science & Technology

    2010-05-31

    prior to bonding , (2) attempted argon and argon/hydrogen plasma treatment of the semiconductor surfaces prior to bonding , and (3) performed wet...sputtering on silicon surface for fusion bonding : Removal of hydrogen from silicon surface leaves active dangling bonds , which is known to...reconstruct the surface to a stable configuration by forming strong covalent bonds with each other. Hydrogen is known to terminate these dangling bonds while

  8. 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.

  9. Single-Molecule Covalent Chemistry in a Protein Nanoreactor

    NASA Astrophysics Data System (ADS)

    Bayley, Hagan; Luchian, Tudor; Shin, Seong-Ho; Steffensen, Mackay B.

    Covalent chemistry can be observed at the single-molecule level by using engineered protein pores as "nanoreactors". By recording the ionic current driven through single engineered alpha-hemolysin (αHL) pores in a transmembrane potential, individual bond-making and bond-breaking steps that occur within the pore and perturb the current are monitored with sub-millisecond time-resolution. Recently, a variety of covalent reactions of small molecules have been observed by this approach including irreversible light-activated chemistry, multiple turnovers of reversible reactions, the turnover of normally irreversible reactions in a twocompartment system and a step-by- step polymerization. These single-molecule experiments are revealing information about fundamental chemical processes that cannot be extracted from ensemble measurements. Further, the approach can be used to examine the effects of the local environment on chemistry and catalysis, and to construct sensors for reactive molecules based on covalent chemistry rather than non-covalent binding interactions. Alternative approaches to small molecule covalent chemistry at the single-molecule level are described in the review, as well as the problems and present limitations of the nanoreactor approach.

  10. 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

  11. The unprecedented bridging coordination mode of 1,1-cyclobutane dicarboxylate (mu-cbdc-O,O') stabilized by intramolecular hydrogen bonds in ruthenium(II) complexes.

    PubMed

    Bratsos, Ioannis; Zangrando, Ennio; Serli, Barbara; Katsaros, Nikos; Alessio, Enzo

    2005-12-21

    The 1,1-cyclobutane dicarboxylate ligand (cbdc), that normally binds to metal centres as a chelate (eta(2)-cbdc-O,O'), prefers to bind in an unprecedented bridging fashion (micro-cbdc-O,O') on cationic Ru(ii) centres bearing ancillary ligands (e.g. H(2)O, NH(3)) capable of making intramolecular H-bonds with the non-coordinated oxygen atoms of the carboxylate groups. Thus, the thermodynamic product of the reaction between cis,fac-[RuCl(2)(dmso-S)(3)(dmso-O)]() and cbdc in a number of different reaction conditions is the dinuclear species with two bridging cbdc units fac-[Ru(micro-cbdc-O,O')(dmso-S)(3)(H(2)O)](2) (2). Similarly, reaction of cis,fac-[RuCl(2)(dmso-S)(3)(NH(3))] (3) with cbdc yielded the corresponding dinuclear species fac-[Ru(micro-cbdc-O,O')(dmso-S)(3)(NH(3))](2) (4), in which ammonia occupies the position of the water molecule in 2. Both dinuclear species 2 and 4 were characterized by X-ray crystallography and have an anti geometry with respect to the H(2)O or NH(3) ligands. The results from the X-ray studies are consistent with the NMR spectroscopic data, indicating that the dinuclear structures observed in the solid state are maintained in solution. The mononuclear anionic complex with a chelating cbdc unit, K{fac-[RuCl(eta(2)-cbdc-O,O')(dmso-S)(3)]}(5), was isolated under appropriate conditions form the reaction of 1 with K(2)(cbdc) and was demonstrated to be an intermediate in the formation of 2.

  12. Electron tunneling through covalent and noncovalent pathways in proteins

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. The source of chemical bonding.

    PubMed

    Needham, Paul

    2014-03-01

    Developments in the application of quantum mechanics to the understanding of the chemical bond are traced with a view to examining the evolving conception of the covalent bond. Beginning with the first quantum mechanical resolution of the apparent paradox in Lewis's conception of a shared electron pair bond by Heitler and London, the ensuing account takes up the challenge molecular orbital theory seemed to pose to the classical conception of the bond. We will see that the threat of delocalisation can be overstated, although it is questionable whether this should be seen as reinstating the issue of the existence of the chemical bond. More salient are some recent developments in a longstanding discussion of how to understand the causal aspects of the bonding interaction--the nature of the force involved in the covalent link--which are taken up in the latter part of the paper.

  18. 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

  19. 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).

  20. 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.

  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 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.

  4. 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.

  5. Covalent enzyme-RNA complex: a tRNA modification that prevents a covalent enzyme interaction also prevents aminoacylation.

    PubMed Central

    Starzyk, R; Schoemaker, H; Schimmel, P

    1985-01-01

    Previous work indicates that aminoacyl-tRNA synthetases make a transient covalent adduct with cognate tRNAs, through Michael addition of an enzyme nucleophile to the carbon-6 position of uridine 8. We report the selective reduction of the 5,6 double bond of 4-thiouridine at position 8 in Escherichia coli tyrosine tRNA, so as to prevent formation of the presumed covalent enzyme-nucleic acid adduct. The completely reduced tRNA molecules are inactivated for aminoacylation. With partial reduction, a mixed pool of active and inactive molecules is created and the degree of inactivation exactly matches the extent of 4-thiouridine reduction. The active molecules recovered from this mixed pool are specifically unaltered at position 8. The results are consistent with the view that the covalent enzyme-RNA adduct is an obligatory intermediate for aminoacylation of this tRNA. Images PMID:3881761

  6. 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).

  7. 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.

  8. 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.

  9. Tough Self-Healing Elastomers by Molecular Enforced Integration of Covalent and Reversible Networks.

    PubMed

    Wu, Jinrong; Cai, Li-Heng; Weitz, David A

    2017-10-01

    Self-healing polymers crosslinked by solely reversible bonds are intrinsically weaker than common covalently crosslinked networks. Introducing covalent crosslinks into a reversible network would improve mechanical strength. It is challenging, however, to apply this concept to "dry" elastomers, largely because reversible crosslinks such as hydrogen bonds are often polar motifs, whereas covalent crosslinks are nonpolar motifs. These two types of bonds are intrinsically immiscible without cosolvents. Here, we design and fabricate a hybrid polymer network by crosslinking randomly branched polymers carrying motifs that can form both reversible hydrogen bonds and permanent covalent crosslinks. The randomly branched polymer links such two types of bonds and forces them to mix on the molecular level without cosolvents. This enables a hybrid "dry" elastomer that is very tough with fracture energy 13500 Jm(-2) comparable to that of natural rubber. Moreover, the elastomer can self-heal at room temperature with a recovered tensile strength 4 MPa, which is 30% of its original value, yet comparable to the pristine strength of existing self-healing polymers. The concept of forcing covalent and reversible bonds to mix at molecular scale to create a homogenous network is quite general and should enable development of tough, self-healing polymers of practical usage. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. 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).

  11. 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.

  12. Novel hydroxyapatite biomaterial covalently linked to raloxifene.

    PubMed

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

    2014-01-01

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

  13. Covalent Polymers Containing Discrete Heterocyclic Anion Receptors

    PubMed Central

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

    2010-01-01

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

  14. Photodissociation of Non-Covalent Peptide-Crown Ether Complexes

    PubMed Central

    Wilson, Jeffrey J.; Kirkovits, Gregory J.; Sessler, Jonathan L.; Brodbelt, Jennifer S.

    2008-01-01

    Highly chromogenic 18-crown-6-dipyrrolylquinoxaline coordinates primary amines of peptides, forming non-covalent complexes that can be transferred to the gas phase by electrospray ionization. The appended chromogenic crown ether facilitates efficient energy transfer to the peptide upon ultraviolet irradiation in the gas phase, resulting in diagnostic peptide fragmentation. Collisional activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) of these non-covalent complexes results only in their disassembly with the charge retained on either the peptide or crown ether, yielding no sequence ions. Upon UV photon absorption the intermolecular energy transfer is facilitated by the fast activation time scale of UVPD (< 10 ns) and by the collectively strong hydrogen bonding between the crown ether and peptide, thus allowing effective transfer of energy to the peptide moiety prior to disruption of the intermolecular hydrogen bonds. PMID:18077179

  15. Highly selective covalent organic functionalization of epitaxial graphene

    NASA Astrophysics Data System (ADS)

    Bueno, Rebeca A.; Martínez, José I.; Luccas, Roberto F.; Del Árbol, Nerea Ruiz; Munuera, Carmen; Palacio, Irene; Palomares, Francisco J.; Lauwaet, Koen; Thakur, Sangeeta; Baranowski, Jacek M.; Strupinski, Wlodek; López, María F.; Mompean, Federico; García-Hernández, Mar; Martín-Gago, José A.

    2017-05-01

    Graphene functionalization with organics is expected to be an important step for the development of graphene-based materials with tailored electronic properties. However, its high chemical inertness makes difficult a controlled and selective covalent functionalization, and most of the works performed up to the date report electrostatic molecular adsorption or unruly functionalization. We show hereafter a mechanism for promoting highly specific covalent bonding of any amino-terminated molecule and a description of the operating processes. We show, by different experimental techniques and theoretical methods, that the excess of charge at carbon dangling-bonds formed on single-atomic vacancies at the graphene surface induces enhanced reactivity towards a selective oxidation of the amino group and subsequent integration of the nitrogen within the graphene network. Remarkably, functionalized surfaces retain the electronic properties of pristine graphene. This study opens the door for development of graphene-based interfaces, as nano-bio-hybrid composites, fabrication of dielectrics, plasmonics or spintronics.

  16. Highly selective covalent organic functionalization of epitaxial graphene.

    PubMed

    Bueno, Rebeca A; Martínez, José I; Luccas, Roberto F; Del Árbol, Nerea Ruiz; Munuera, Carmen; Palacio, Irene; Palomares, Francisco J; Lauwaet, Koen; Thakur, Sangeeta; Baranowski, Jacek M; Strupinski, Wlodek; López, María F; Mompean, Federico; García-Hernández, Mar; Martín-Gago, José A

    2017-05-08

    Graphene functionalization with organics is expected to be an important step for the development of graphene-based materials with tailored electronic properties. However, its high chemical inertness makes difficult a controlled and selective covalent functionalization, and most of the works performed up to the date report electrostatic molecular adsorption or unruly functionalization. We show hereafter a mechanism for promoting highly specific covalent bonding of any amino-terminated molecule and a description of the operating processes. We show, by different experimental techniques and theoretical methods, that the excess of charge at carbon dangling-bonds formed on single-atomic vacancies at the graphene surface induces enhanced reactivity towards a selective oxidation of the amino group and subsequent integration of the nitrogen within the graphene network. Remarkably, functionalized surfaces retain the electronic properties of pristine graphene. This study opens the door for development of graphene-based interfaces, as nano-bio-hybrid composites, fabrication of dielectrics, plasmonics or spintronics.

  17. Covalent Organic Frameworks as a Platform for Multidimensional Polymerization

    PubMed Central

    2017-01-01

    The simultaneous polymerization and crystallization of monomers featuring directional bonding designs provides covalent organic frameworks (COFs), which are periodic polymer networks with robust covalent bonds arranged in two- or three-dimensional topologies. The range of properties characterized in COFs has rapidly expanded to include those of interest for heterogeneous catalysis, energy storage and photovoltaic devices, and proton-conducting membranes. Yet many of these applications will require materials quality, morphological control, and synthetic efficiency exceeding the capabilities of contemporary synthetic methods. This level of control will emerge from an improved fundamental understanding of COF nucleation and growth processes. More powerful characterization of structure and defects, improved syntheses guided by mechanistic understanding, and accessing diverse isolated forms, ranging from single crystals to thin films to colloidal suspensions, remain important frontier problems. PMID:28691064

  18. 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.

  19. 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

  20. 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…

  1. 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…

  2. 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)

  3. 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)

  4. 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.

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

    PubMed

    Bauer, Renato A

    2015-09-01

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

  6. 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

  7. 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.

  8. A Connection Between Empirical Bond Strength and the Localization of the Electron Density at the Bond Critical Points of the SiO Bonds in Silicates

    SciTech Connect

    Gibbs, Gerald V.; Cox, David F.; Rosso, Kevin M.

    2004-08-25

    The empirical bond strength of the SiO bond correlates with the value of the electron density at the bond critical point calculated for a large number of silicates and observed for the silica polymorphs stishovite and coesite. The greater the bond strength, the greater the localization of the electron density at the critical point, the shorter the bond, and the greater the covalent character of the bonded interaction. Bond strength and resonance bond number are considered to represent similar properties of the electronic structure of the bond.

  9. Both non-covalent and covalent interactions were involved in the mechanism of detoxifying effects of persimmon tannin on Chinese cobra PLA2.

    PubMed

    Zhang, Ying; Zhu, Wei; Deng, Xiang-Yi; Peng, Jin-Ming; Li, Chun-Mei

    2017-07-01

    Persimmon tannin (PT) has been shown to inhibit snake venom activities and toxicities both in vitro and in vivo. To clarify the detoxifying mechanism of PT on snake venom, the interaction of characteristic structural elements of PT (EGCG, ECG, EGCG dimer and ECG dimer) and Chinese cobra phospholipase A2 (PLA2) was studied. The results revealed that except non-covalent bonds like hydrogen bonds, hydrophobic bonds and iron bonds were formed between PT and PLA2, covalent interaction was also occurred. PT could bind with the key active residues of PLA2, such as lysine, histidine, tryptophan and tyrosine, restraining their activity and disturbing the structure of PLA2, thus showing detoxifying effects on snake venom. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Electronegativity and the Bond Triangle

    ERIC Educational Resources Information Center

    Meek, Terry L.; Garner, Leah D.

    2005-01-01

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

  11. 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…

  12. 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.

  13. Covalent bonding of polycations to small polymeric particles

    NASA Technical Reports Server (NTRS)

    Rembaum, A.

    1975-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

  15. Covalent-Bond Formation via On-Surface Chemistry.

    PubMed

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

    2017-05-02

    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. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. 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

  17. 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

  18. Structure-based design of covalent Siah inhibitors.

    PubMed

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

    2013-08-22

    The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches. Ultimately, a rational structure-based design strategy was successful for the identification of Siah inhibitors in which peptide binding drives specific covalent bond formation with the target. X-ray crystallography, mass spectrometry, and functional data demonstrate that these peptide mimetics are efficient covalent inhibitors of Siah and antagonize Siah-dependent regulation of Erk and Hif signaling in the cell. The proposed strategy may result useful as a general approach to the design of peptide-based inhibitors of other protein-protein interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. 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

  20. Recent advances in the covalent modification of graphene with polymers.

    PubMed

    Salavagione, Horacio J; Martínez, Gerardo; Ellis, Gary

    2011-11-15

    Covalent binding of polymers to graphene represents an interesting alternative for the development of novel composite materials with a compendium of interfacial interactions. Through covalent linking, the concept of interface changes from a traditional view of interactions between components, such as van der Waals, hydrogen bonding, and so on, that is to say, at a polymer-filler interface, to a single compound concept where graphene forms an integral part of the polymeric chains. This feature article provides an overview of the strategies currently employed to functionalize graphene with polymers. We focus on the grafting-from and grafting-to methods used to bind polymers to graphene. The advantages and drawbacks, as well as the influence of each method on the final properties, are highlighted. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.