Hydrolysis of Ketene Catalyzed by Formic Acid: Modification of Reaction Mechanism, Energetics, and Kinetics with Organic Acid Catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Louie, Matthew K.; Francisco, Joseph S.; Verdicchio, Marco

2015-05-14

The hydrolysis of ketene (H2C=C=O) to form acetic acid involving two water molecules and also separately in the presence of one to two water molecules and formic acid (FA) was investigated. Our results show that, while the currently accepted indirect mechanism, involving addition of water across the carbonyl C=O bond of ketene to form an ene-diol followed by tautomerization of the ene-diol to form acetic acid, is the preferred pathway when water alone is present, with formic acid as catalyst, addition of water across the ketene C=C double bond to directly produce acetic acid becomes the kinetically favored pathway formore » temperatures below 400 K. We find not only that the overall barrier for ketene hydrolysis involving one water molecule and formic acid (H2C2O + H2O + FA) is significantly lower than that involving two water molecules (H2C2O + 2H(2)O) but also that FA is able to reduce the barrier height for the direct path, involving addition of water across the C=C double bond, so that it is essentially identical with (6.4 kcal/mol) that for the indirect ene-diol formation path involving addition of water across the C=O bond. For the case of ketene hydrolysis involving two water molecules and formic acid (H2C2O + 2H(2)O + FA), the barrier for the direct addition of water across the C=C double bond is reduced even further and is 2.5 kcal/mol lower relative to the ene-diol path involving addition of water across the C=O bond. In fact, the hydrolysis barrier for the H2C2O + 2H(2)O + FA reaction through the direct path is sufficiently low (2.5 kcal/mol) for it to be an energetically accessible pathway for acetic acid formation under atmospheric conditions. Given the structural similarity between acetic and formic acid, our results also have potential implications for aqueous-phase chemistry. Thus, in an aqueous environment, even in the absence of formic acid, though the initial mechanism for ketene hydrolysis is expected to involve addition of water across the carbonyl bond as is currently accepted, the production and accumulation of acetic acid will likely alter the preferred pathway to one involving addition of water across the ketene C=C double bond as the reaction proceeds.« less

Regioselective Formation of α-Vinylpyrroles from the Ruthenium-Catalyzed Coupling Reaction of Pyrroles and Terminal Alkynes Involving C–H Bond Activation

PubMed Central

Gao, Ruili; Yi, Chae S.

2010-01-01

The cationic ruthenium catalyst, Ru3(CO)12/NH4PF6, was found to be highly effective for the intermolecular coupling reaction of pyrroles and terminal alkynes to give gem-selective α-vinylpyrroles. The carbon isotope effect on the α-pyrrole carbon and the Hammett correlation from a series of para-substituted N-arylpyrroles (ρ = −0.90) indicate a rate-limiting C–C bond formation step of the coupling reaction. PMID:20384382

Spontaneous grafting of diazonium salts: chemical mechanism on metallic surfaces.

PubMed

Mesnage, Alice; Lefèvre, Xavier; Jégou, Pascale; Deniau, Guy; Palacin, Serge

2012-08-14

The spontaneous reaction of diazonium salts on various substrates has been widely employed since it consists of a simple immersion of the substrate in the diazonium salt solution. As electrochemical processes involving the same diazonium salts, the spontaneous grafting is assumed to give covalently poly(phenylene)-like bonded films. Resistance to solvents and to ultrasonication is commonly accepted as indirect proof of the existence of a covalent bond. However, the most relevant attempts to demonstrate a metal-C interface bond have been obtained by an XPS investigation of spontaneously grafted films on copper. Similarly, our experiments give evidence of such a bond in spontaneously grafted films on nickel substrates in acetonitrile. In the case of gold substrates, the formation of a spontaneous film was unexpected but reported in the literature in parallel to our observations. Even if no interfacial bond was observed, formation of the films was explained by grafting of aryl cations or radicals on the surface arising from dediazoniation, the film growing later by azo coupling, radical addition, or cationic addition on the grafted phenyl layer. Nevertheless, none of these mechanisms fits our experimental results showing the presence of an Au-N bond. In this work, we present a fine spectroscopic analysis of the coatings obtained on gold and nickel substrates that allow us to propose a chemical structure of such films, in particular, their interface with the substrates. After testing the most probable mechanisms, we have concluded in favor of the involvement of two complementary mechanisms which are the direct reaction of diazonium salts with the gold surface that accounts for the observed Au-N interfacial bonds as well as the formation of aryl cations able to graft on the substrate through Au-C linkages.

Catalytic-site mapping of pyruvate formate lyase. Hypophosphite reaction on the acetyl-enzyme intermediate affords carbon-phosphorus bond synthesis (1-hydroxyethylphosphonate).

PubMed

Plaga, W; Frank, R; Knappe, J

1988-12-15

Pyruvate formate-lyase of Escherichia coli cells, a homodimeric protein of 2 x 85 kDa, is distinguished by the property of containing a stable organic free radical (g = 2.0037) in its resting state. The enzyme (E-SH) achieves pyruvate conversion to acetyl-CoA via two distinct half-reactions (E-SH + pyruvate in equilibrium E-S-acetyl + formate; E-S-acetyl + CoA in equilibrium E-SH + acetyl-CoA), the first of which has been proposed to involve reversible homolytic carbon-carbon bond cleavage [J. Knappe et al. (1984) Proc. Natl Acad. Sci. USA 81, 1332-1335]. Present studies identified Cys-419 as the covalent-catalytic cysteinyl residue via CNBr fragmentation of E-S-[14C]acetyl and radio-sequencing of the isolated peptide CB-Ac (amino acid residues 406-423). Reaction of the formate analogue hypophosphite with E-S-acetyl was investigated and found to produce 1-hydroxyethylphosphonate with a thioester linkage to the adjacent Cys-418. The structure was determined from the chymotryptic peptide CH-P (amino acid residues 415-425), using 31P-NMR spectroscopy (delta = 44 ppm) and by chemical characterisation through degradation into 1-hydroxyethylphosphonate with phosphodiesterase or bromine. This novel P-C-bond synthesis involves the enzyme-based free radical and is proposed to resemble the physiological C-C-bond synthesis (pyruvate production) from formate and E-S-acetyl. These findings are interpreted as proof of a radical mechanism for the action of pyruvate formate-lyase. The central Cys-418/Cys-419 pair of the active site shows a distinctive thiolate property even in the inactive (nonradical) form of the enzyme, as determined using an iodoacetate probe.

Formation of solvate structures by the ortho-, meta-, and para-isomers of hydroxybenzoic acid in supercritical fluid

NASA Astrophysics Data System (ADS)

Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Petrenko, V. E.

2017-04-01

The solvate structures formed by the ortho-, meta-, and para-isomers of hydroxybenzoic acid ( o-HBA, m-HBA, and p-HBA) with a polar co-solvent (methanol at a concentration of 0.030 and 0.035 mole fractions) in supercritical carbon dioxide at a constant density of 0.7 g/cm3 and temperatures of 318 and 328 K have been studied by the classic molecular dynamics. It has been determined that a stable hydrogen-bonded complex with the co-solvent forms via the hydrogen of the carboxyl group for all isomers. The probability of this complex existence is high at all temperatures and concentrations. In the o-HBA molecule, the other functional groups are engaged in the intramolecular hydrogen bond, but not involved in interactions with methanol. It has been found that m-HBA and p-HBA can be involved in hydrogen bonds with methanol via hydroxyl hydrogen and oxygen atoms; they are characterized by the presence of one more co-solvent molecule (rarely, two molecules) in their solvation shell and intermittent formations/breakages of hydrogen bonds via other functional groups. These bonds are far less stable, and their formation is sensitive to change of temperature and co-solvent concentration. It has been concluded that the degree of selective solvation of m-HBA and p-HBA by co-solvent molecules is approximately the same, but the rate of structural rearrangements in the nearest environment of m-HBA is higher than that of p-HBA.

Cross-dehydrogenative coupling for the intermolecular C–O bond formation

PubMed Central

Krylov, Igor B; Vil’, Vera A

2015-01-01

Summary The present review summarizes primary publications on the cross-dehydrogenative C–O coupling, with special emphasis on the studies published after 2000. The starting compound, which donates a carbon atom for the formation of a new C–O bond, is called the CH-reagent or the C-reagent, and the compound, an oxygen atom of which is involved in the new bond, is called the OH-reagent or the O-reagent. Alcohols and carboxylic acids are most commonly used as O-reagents; hydroxylamine derivatives, hydroperoxides, and sulfonic acids are employed less often. The cross-dehydrogenative C–O coupling reactions are carried out using different C-reagents, such as compounds containing directing functional groups (amide, heteroaromatic, oxime, and so on) and compounds with activated C–H bonds (aldehydes, alcohols, ketones, ethers, amines, amides, compounds containing the benzyl, allyl, or propargyl moiety). An analysis of the published data showed that the principles at the basis of a particular cross-dehydrogenative C–O coupling reaction are dictated mainly by the nature of the C-reagent. Hence, in the present review the data are classified according to the structures of C-reagents, and, in the second place, according to the type of oxidative systems. Besides the typical cross-dehydrogenative coupling reactions of CH- and OH-reagents, closely related C–H activation processes involving intermolecular C–O bond formation are discussed: acyloxylation reactions with ArI(O2CR)2 reagents and generation of O-reagents in situ from C-reagents (methylarenes, aldehydes, etc.). PMID:25670997

Nature and potency interactions of the hydrogen bond through the NBO analysis for charge transfer complex between 2-amino-4-hydroxy-6-methylpyrimidine and 2,3-pyrazinedicarboxylic acid

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Afroz, Ziya; Alam, Mohammad Jane; Bhat, Sheeraz Ahmad; Ahmad, Shabbir; Ahmad, Afaq

2018-05-01

The intermolecular interactions in complex formation between 2-amino-4-hydroxy-6-methylpyrimidine (AHMP) and 2,3-pyrazinedicarboxylicacid (PDCA) have been explored using density functional theory calculations. The isolated 1:1 molecular geometry of proton transfer (PT) complex between AHMP and PDCA has been optimized on a counterpoise corrected potential energy surface (PES) at DFT-B3LYP/6-31G(d,p) level of theory in the gaseous phase. Further, the formation of hydrogen bonded charge transfer (HBCT) complex between PDCA and AHMP has been also discussed. PT energy barrier between two extremes is calculated using potential energy surface (PES) scan by varying bond length. The intermolecular interactions have been analyzed from theoretical perspective of natural bond orbital (NBO) analysis. In addition, the interaction energy between molecular fragments involved in the complex formation has been also computed by counterpoise procedure at same level of theory.

Neural mechanisms of mother-infant bonding and pair bonding: Similarities, differences, and broader implications.

PubMed

Numan, Michael; Young, Larry J

2016-01-01

This article is part of a Special Issue "Parental Care". Mother-infant bonding is a characteristic of virtually all mammals. The maternal neural system may have provided the scaffold upon which other types of social bonds in mammals have been built. For example, most mammals exhibit a polygamous mating system, but monogamy and pair bonding between mating partners occur in ~5% of mammalian species. In mammals, it is plausible that the neural mechanisms that promote mother-infant bonding have been modified by natural selection to establish the capacity to develop a selective bond with a mate during the evolution of monogamous mating strategies. Here we compare the details of the neural mechanisms that promote mother-infant bonding in rats and other mammals with those that underpin pair bond formation in the monogamous prairie vole. Although details remain to be resolved, remarkable similarities and a few differences between the mechanisms underlying these two types of bond formation are revealed. For example, amygdala and nucleus accumbens-ventral pallidum (NA-VP) circuits are involved in both types of bond formation, and dopamine and oxytocin actions within NA appear to promote the synaptic plasticity that allows either infant or mating partner stimuli to persistently activate NA-VP attraction circuits, leading to an enduring social attraction and bonding. Further, although the medial preoptic area is essential for maternal behavior, its role in pair bonding remains to be determined. Our review concludes by examining the broader implications of this comparative analysis, and evidence is provided that the maternal care system may have also provided the basic neural foundation for other types of strong social relationships, beyond pair bonding, in mammals, including humans. Copyright © 2015 Elsevier Inc. All rights reserved.

Neural mechanisms of mother-infant bonding and pair bonding: Similarities, differences, and broader implications

PubMed Central

Numan, Michael; Young, Larry J.

2015-01-01

Mother-infant bonding is a characteristic of virtually all mammals. The maternal neural system may have provided the scaffold upon which other types of social bonds in mammals have been built. For example, most mammals exhibit a polygamous mating system, but monogamy and pair bonding between mating partners occurs in ∼5% of mammalian species. In mammals, it is plausible that the neural mechanisms that promote mother-infant bonding have been modified by natural selection to establish the capacity to develop a selective bond with a mate during the evolution of monogamous mating strategies. Here we compare the details of the neural mechanisms that promote mother-infant bonding in rats and other mammals with those that underpin pair bond formation in the monogamous prairie vole. Although details remain to be resolved, remarkable similarities and a few differences between the mechanisms underlying these two types of bond formation are revealed. For example, amygdala and nucleus accumbens-ventral pallidum (NA-VP) circuits are involved in both types of bond formation, and dopamine and oxytocin action within NA appears to promote the synaptic plasticity that allows either infant or mating partner stimuli to persistently activate NA-VP attraction circuits, leading to an enduring social attraction and bonding. Further, although the medial preoptic area is essential for maternal behavior, its role in pair bonding remains to be determined. Our review concludes by examining the broader implications of this comparative analysis, and evidence is provided that the maternal care system may have also provided the basic neural foundation for other types of strong social relationships, beyond pair bonding, in mammals, including humans. PMID:26062432

Mechanisms and time-resolved dynamics for trihydrogen cation (H 3 +) formation from organic molecules in strong laser fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ekanayake, Nagitha; Nairat, Muath; Kaderiya, Balram

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. Here, we present evidence for the existence of two different reaction pathways for H 3 + formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followedmore » by the abstraction of a proton from the remaining CHOH 2+ fragment by the roaming H 2 molecule. This reaction has similarities to the H 2+H 2 + mechanism leading to formation of H 3 + in the universe. These exotic chemical reaction mechanisms, involving roaming H 2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.« less

Mechanisms and time-resolved dynamics for trihydrogen cation (H 3 +) formation from organic molecules in strong laser fields

DOE PAGES

Ekanayake, Nagitha; Nairat, Muath; Kaderiya, Balram; ...

2017-07-05

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. Here, we present evidence for the existence of two different reaction pathways for H 3 + formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followedmore » by the abstraction of a proton from the remaining CHOH 2+ fragment by the roaming H 2 molecule. This reaction has similarities to the H 2+H 2 + mechanism leading to formation of H 3 + in the universe. These exotic chemical reaction mechanisms, involving roaming H 2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.« less

Oxytocin and mutual communication in mother-infant bonding

PubMed Central

Nagasawa, Miho; Okabe, Shota; Mogi, Kazutaka; Kikusui, Takefumi

2012-01-01

Mother-infant bonding is universal to all mammalian species. In this review, we describe the manner in which reciprocal communication between the mother and infant leads to mother-infant bonding in rodents. In rats and mice, mother-infant bond formation is reinforced by various social stimuli, such as tactile stimuli and ultrasonic vocalizations (USVs) from the pups to the mother, and feeding and tactile stimulation from the mother to the pups. Some evidence suggests that mother and infant can develop a cross-modal sensory recognition of their counterpart during this bonding process. Neurochemically, oxytocin in the neural system plays a pivotal role in each side of the mother-infant bonding process, although the mechanisms underlying bond formation in the brains of infants has not yet been clarified. Impairment of mother-infant bonding, that is, deprivation of social stimuli from the mother, strongly influences offspring sociality, including maternal behavior toward their own offspring in their adulthood, implying a “non-genomic transmission of maternal environment,” even in rodents. The comparative understanding of cognitive functions between mother and infants, and the biological mechanisms involved in mother-infant bonding may help us understand psychiatric disorders associated with mother-infant relationships. PMID:22375116

Affiliation, reward, and immune biomarkers coalesce to support social synchrony during periods of bond formation in humans.

PubMed

Ulmer-Yaniv, Adi; Avitsur, Ronit; Kanat-Maymon, Yaniv; Schneiderman, Inna; Zagoory-Sharon, Orna; Feldman, Ruth

2016-08-01

Social bonds are critical for survival and adaptation and periods of bond formation involve reorganization of neurobiological systems as mediated by social behavior. Theoretical accounts and animal studies suggest similarity between parent-infant and pair bonding, a hypothesis not yet directly tested in humans. In this study, we recruited three groups of human adults (N=189); parents who had their firstborn child in the last 4-6months, new lovers who began a romantic relationship within the past 4months, and non-attached singles. We measured plasma oxytocin (OT), beta endorphin (β-End), and interlukin-6 (IL-6), biomarkers of the affiliation, reward, and stress-response systems, and micro-coded gaze and affect synchrony between parents and infants and among new lovers during social interaction. OT significantly increased during periods of parental and romantic bonding and was highest in new lovers. In contrast, IL-6 and β-End were highest in new parents and lowest in singles. Biomarkers became more tightly coupled during periods of bond formation and inter-correlation among hormones was highest during romantic bonding. Structural equation modeling indicated that the effects of IL-6 and β-End on behavioral synchrony were mediated by their impact on OT, highlighting the integrative role of the oxytocinergic system in supporting human social affiliation. Findings suggest that periods of bond formation are accompanied by increased activity, as well as tighter cross-talk among systems underpinning affiliation, reward, and stress management and that research on the multidimensional process of bonding may shed further light on the effects of attachment on health. Copyright © 2016 Elsevier Inc. All rights reserved.

Grotthuss Transport of Iodide in EMIM/I3 Ionic Crystal.

PubMed

McDaniel, Jesse G; Yethiraj, Arun

2018-01-11

Highly ionic environments can mediate unusual chemical reactions that would otherwise be considered impossible based on chemical intuition. For example, the formation of a chemical bond between two iodide anions to form a divalent polyiodide anion is seemingly prohibited due to Coulombic repulsion. Using ab initio molecular dynamics simulations, we show that in the 1-ethyl-3-methylimidazolium (EMIM)/I 3 ionic crystal, the reactive formation of divalent and even trivalent polyiodide anions occurs with extremely small energetic barriers, due to the electrostatic field of the ionic lattice. A practical consequence of this anomalous reactivity is that iodide anions are efficiently transported within the crystal through a "Grotthuss-exchange" mechanism involving bond-breaking and forming events. We characterize two distinct transport pathways, involving both I 4 2- and I 7 3- intermediates, with fast transport of iodide resulting from the release of an I - anion on the opposite side of the intermediate species from the initial bond formation. The ordered cation arrangement in the crystal provides the necessary electrostatic screening for close approach of anions, suggesting a new counterintuitive approach to obtain high ionic conductivity. This new design principle could be used to develop better solid-state electrolytes for batteries, fuel cells, and supercapacitors.

Detailed reaction mechanism of macrophomate synthase. Extraordinary enzyme catalyzing five-step transformation from 2-pyrones to benzoates.

PubMed

Watanabe, K; Mie, T; Ichihara, A; Oikawa, H; Honma, M

2000-12-08

Macrophomate synthase from the fungus Macrophoma commelinae IFO 9570 is a Mg(II)-dependent dimeric enzyme that catalyzes an extraordinary, complex five-step chemical transformation from 2-pyrone and oxalacetate to benzoate involving decarboxylation, C-C bond formation, and dehydration. The catalytic mechanism of the whole pathway was investigated in three separate chemical steps. In the first decarboxylation step, the enzyme loses oxalacetate decarboxylation activity upon incubation with EDTA. Activity is fully restored by addition of Mg(II) and is not restored with other divalent metal cations. The dissociation constant of 0.93 x 10(-)(7) for Mg(II) and atomic absorption analysis established a 1:1 stoichiometric complex. Inhibition of pyruvate formation with 2-pyrone revealed that the actual product in the first step is a pyruvate enolate, which undergoes C-C bond formation in the presence of 2-pyrone. Incubation of substrate analogs provided aberrant adducts that were produced via C-C bond formation and rearrangement. This strongly indicates that the second step is two C-C bond formations, affording a bicyclic intermediate. Based on the stereospecificity, involvement of a Diels-Alder reaction at the second step is proposed. Incubation of the stereospecifically deuterium-labeled malate with 2-pyrones in the presence of malate dehydrogenase provided information for the stereochemical course of the reaction catalyzed by macrophomate synthase, indicating that the first decarboxylation provides pyruvate (Z)-[3-(2)H]enolate and that dehydration at the final step occurs with anti-elimination accompanied by concomitant decarboxylation. Examination of kinetic parameters in the individual steps suggests that the third step is the rate-determining step of the overall transformation.

New Physical Mechanism for Lightning

NASA Astrophysics Data System (ADS)

Artekha, Sergey N.; Belyan, Andrey V.

2018-02-01

The article is devoted to electromagnetic phenomena in the atmosphere. The set of experimental data on the thunderstorm activity is analyzed. It helps to identify a possible physical mechanism of lightning flashes. This mechanism can involve the formation of metallic bonds in thunderclouds. The analysis of the problem is performed at a microphysical level within the framework of quantum mechanics. The mechanism of appearance of metallic conductivity includes the resonant tunneling of electrons along resonance-percolation trajectories. Such bonds allow the charges from the vast cloud charged subsystems concentrate quickly in lightning channel. The formation of metal bonds in the thunderstorm cloudiness is described as the second-order phase transition. A successive mechanism for the process of formation and development of the lightning channel is suggested. This mechanism is associated with the change in the orientation of crystals in growing electric field. Possible consequences of the quantum-mechanical mechanism under discussion are compared with the results of observations.

Reversible hydrogen transfer reactions of cysteine thiyl radicals in peptides: the conversion of cysteine into dehydroalanine and alanine, and of alanine into dehydroalanine

PubMed Central

Mozziconacci, Olivier; Kerwin, Bruce A.; Schöneich, Christian

2013-01-01

The photodissociation of disulfide bonds in model peptides containing Ala and Ala-d3 generates a series of photoproducts following the generation of a CysS• thiyl radical pair. These photoproducts include transformations of Cys to dehydroalanine (Dha) and Ala, as well as Ala to Dha. Intramolecular Michael addition of an intact Cys with a photolytically generated Dha results in the formation of cyclic thioethers. The conversion of Cys into Dha likely involves a 1,3-H-shift from the Cys αC-H bond to the thiyl radical, followed by elimination of HS•. The conversion of Dha into Ala most likely involves hydrated electrons, which are generated through the photolysis of Cys, the photoproduct of disulfide photolysis. Prior to stable product formation, CysS• radicals engage in reversible hydrogen transfer reactions with αC-H and βC-H bonds of the surrounding amino acids. Especially for the βC-H bonds of Ala such hydrogen transfer reactions are unexpected based on thermodynamic grounds; however, the replacement of deuterons in Ala-d3 by hydrogens in H2O provides strong experimental evidence for such reactions. PMID:21895001

Molecular structures of N-ethylpiperidine betaine hydrate and its 1:1 complex with squaric acid

NASA Astrophysics Data System (ADS)

Dega-Szafran, Z.; Dutkiewicz, G.; Kosturkiewicz, Z.; Szafran, M.

2013-12-01

N-ethylpiperidine betaine, (N-carboxymethyl-N-ethylpiperidinium inner salt, EtPB) crystallizes as a hydrate. EtPB and water molecules are bonded by intermolecular OH⋯O hydrogen bonds of 2.817(1) and 2.863(1) Å, into a centrosymmetric dimer, in which only one carboxylate oxygen atom is involved in H-bonds formation. In the complex of EtPB with squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione, H2SQ) both carboxylate oxygen atoms are engaged in the hydrogen bonds which links molecules through two short, non-symmetric OH⋯O hydrogen bonds of 2.489(1) and 2.500(1) Å. The preferences of the conformation of the EtPB unit in the hydrogen bond formation have been studied by X-ray diffraction, FTIR and NMR spectroscopy and the results are supported by DFT calculations. EtPB, in hydrate and in the complex, has a chair conformation with the CH3CH2 group in the axial position and the CH2COO substituent in the equatorial position.

Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins

NASA Astrophysics Data System (ADS)

Steckmann, Timothy M.

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous alpha-helix or random-coil structure. The alpha-helices convert their structure to beta-strands that aggregate into beta-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis process from random coil to fibrils, including the molecular species that accelerate the conversions. The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process. To better understand the molecular basis of the protein structural transitions and aggregation, I report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccbeta, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow beta-hairpin proteins to straighten, and the subsequent formation of interchain hydrogen bonds during aggregation into amyloid fibrils. For my MD simulations, I found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccbeta protein experiences during the process of forming protofibrillar structures. Both the mathematical modeling of the kinetics and the MD simulations show that molecular structural heterogeneity is a major factor in the process. The MD simulations also show that intrachain and interchain hydrogen bonds breaking and forming is strongly correlated to the process of amyloid formation.

Damage mechanism of hydroxyl radicals toward adenine—thymine base pair

NASA Astrophysics Data System (ADS)

Tan, Rong-Ri; Wang, Dong-Qi; Zhang, Feng-Shou

2014-02-01

The adenine—thymine base pair was studied in the presence of hydroxyl radicals in order to probe the hydrogen bond effect. The results show that the hydrogen bonds have little effect on the hydroxylation and dehydrogenation happened at the sites, which are not involved in a hydrogen bond, while at the sites involved in hydrogen bond formation in the base pair, the reaction becomes more difficult, both in view of the free energy barrier and the exothermicity. With a 6-311++G(d,p) level of description, both B3LYP and MP2 methods confirm that the C8 site of isolated adenine has the highest possibility to form covalent bond with the hydroxyl radicals, though with different energetics: B3LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the dehydrogenation reactions, B3LYP method predicts that the free energy barrier increases in the order of HN9 < HN61 < HN62 < H2 < H8.

Oxidative 1,2-carboamination of alkenes with alkyl nitriles and amines toward γ-amino alkyl nitriles

NASA Astrophysics Data System (ADS)

Liu, Yan-Yun; Yang, Xu-Heng; Song, Ren-Jie; Luo, Shenglian; Li, Jin-Heng

2017-04-01

Difunctionalization of alkenes has become a powerful tool for quickly increasing molecular complexity in synthesis. Despite significant progress in the area of alkene difunctionalization involving the incorporation of a nitrogen atom across the C-C double bonds, approaches for the direct 1,2-carboamination of alkenes to produce linear N-containing molecules are scarce and remain a formidable challenge. Here we describe a radical-mediated oxidative intermolecular 1,2-alkylamination of alkenes with alkyl nitriles and amines involving C(sp3)-H oxidative functionalization catalysed by a combination of Ag2CO3 with iron Lewis acids. This three-component alkene 1,2-alkylamination method is initiated by the C(sp3)-H oxidative radical functionalization, which enables one-step formation of two new chemical bonds, a C-C bond and a C-N bond, to selectively produce γ-amino alkyl nitriles.

Importance of Nonclassical σ-Hole Interactions for the Reactivity of λ3-Iodane Complexes.

PubMed

Pinto de Magalhães, Halua; Togni, Antonio; Lüthi, Hans Peter

2017-11-17

Key for the observed reactivity of λ 3 -iodanes, powerful reagents for the selective transfer of functional groups to nucleophiles, are the properties of the 3-center-4-electron bond involving the iodine atom and the two linearly arranged ligands. This bond is also involved in the formation of the initial complex between the λ 3 -iodane and a nucleophile, which can be a solvent molecule or a reactant. The bonding in such complexes can be described by means of σ-hole interactions. In halogen compounds, σ-hole interaction was identified as a force in crystal packing or in the formation of supramolecular chains. More recently, σ-hole interactions were also shown to affect the reactivity of the iodine-based hypervalent reagents. Relative to their monovalent counterparts, where the σ-hole is located on the extension of the sigma-bond, in the hypervalent species our DFT calculations reveal the formation of a nonclassical σ-hole region with one or even two maxima. This observation is also made in fully relativistic calculations. The SAPT analysis shows that the σ-hole bond between the λ 3 -iodane and the nucleophile is not necessarily of purely electrostatic nature but may also contain a significant covalent component. This covalent component may facilitate chemical transformation of the compound by means of reductive elimination or other mechanisms and is therefore an indicator for its reactivity. Here, we also show that the shape, location, and strength of the σ-holes can be tuned by the choice of ligands and measures such as Brønsted activation of the iodane reagent. At the limit, the tuning transforms the nonclassical σ-hole regions into coordination sites, which allows us to control how a nucleophile will bind and react with the iodane.

Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II

NASA Astrophysics Data System (ADS)

Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi

2018-04-01

The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O-O sigma bond formation.

Prebiotic Peptide (Amide) Bond Synthesis Accelerated by Glycerol and Bicarbonate Under Neutral to Alkaline Dry-Down Conditions

NASA Technical Reports Server (NTRS)

Forsythe, J. G.; Weber, A. L.

2017-01-01

Past studies of prebiotic peptide bond synthesis have generally been carried out in the acidic to neutral pH range [1, 2]. Here we report a new process for peptide bond (amide) synthesis in the neutral to alkaline pH range that involves simple dry-down heating of amino acids in the presence of glycerol and bicarbonate. Glycerol was included in the reaction mixture as a solvent and to provide hydroxyl groups for possible formation of ester intermediates previously implicated in peptide bond synthesis under acidic to neutral conditions [1]. Bicarbonate was added to raise the reaction pH to 8-9.

O2-Promoted Allylic Acetoxylation of Alkenes: Assessment of "Push" vs. "Pull" Mechanisms and Comparison between O2 and Benzoquinone.

PubMed

Diao, Tianning; Stahl, Shannon S

2014-12-14

Palladium-catalyzed acetoxylation of allylic C-H bonds has been the subject of extensive study. These reactions proceed via allyl-palladium(II) intermediates that react with acetate to afford the allyl acetate product. Benzoquinone and molecular oxygen are two common oxidants for these reactions. Benzoquinone has been shown to promote allyl acetate formation from well-defined π-allyl palladium(II) complexes. Here, we assess the ability of O 2 to promote similar reactions with a series of "unligated" π-allyl palladium(II) complexes (i.e., in the absence of ancillary phosphorus, nitrogen or related donor ligands). Stoichiometric and catalytic allyl acetate formation is observed under aerobic conditions with several different alkenes. Mechanistic studies are most consistent with a "pull" mechanism in which O 2 traps the Pd 0 intermediate following reversible C-O bond-formation from an allyl-palladium(II) species. A "push" mechanism, involving oxidatively induced C-O bond formation, does not appear to participate. These results and conclusions are compared with benzoquinone-promoted allylic acetoxylation, in which a "push" mechanism seems to be operative.

Diethyl 2-{[(4-meth­oxy-3-pyrid­yl)amino]­methyl­idene}malonate

PubMed Central

Zhang, Zhi-Fang

2011-01-01

In the title mol­ecule, C14H8N2O5, the amino group is involved in the formation an intra­molecular N—H⋯O hydrogen bond. In the crystal, weak inter­molecular C—H⋯O and C—H⋯N hydrogen bonds link the mol­ecules into ribbons along the b axis. PMID:22090989

O–O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O–O radical coupling

DOE PAGES

Shaffer, David W.; Xie, Yan; Concepcion, Javier J.

2017-09-01

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

O–O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O–O radical coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaffer, David W.; Xie, Yan; Concepcion, Javier J.

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

O-O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O-O radical coupling.

PubMed

Shaffer, David W; Xie, Yan; Concepcion, Javier J

2017-10-16

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O-O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O-O bond formation step as the key step in water oxidation catalysis. The two main pathways to accomplish this step, single-site water nucleophilic attack and O-O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.

FTIR cryospectroscopic and ab initio studies of desflurane-dimethyl ether H-bonded complexes.

PubMed

Melikova, S M; Rutkowski, K S; Rospenk, M

2017-09-05

The IR spectra of mixtures of desflurane and dimethyl ether are studied with the help of FTIR cryospectroscopy in liquefied Kr at T~118-158K. Comparative analysis of the experimental data and results of ab initio calculations show that either of the two C-H groups of desflurane is involved in heterodimer formation of comparable strengths. The blue frequency shift is found for stretching vibrations of those C-H donors which directly participate in H-bond formation. Additionally the complexes are stabilized by weaker contacts between hydrogen atoms of dimethyl ether and fluorine atoms of desflurane. Copyright © 2017 Elsevier B.V. All rights reserved.

The enzymes associated with denitrification

NASA Technical Reports Server (NTRS)

Hochstein, L. I.; Tomlinson, G. A.

1988-01-01

The enzymes involved in the reduction of nitrogenous oxides are thought to be intermediates in denitrification processes. This review examines the roles of nitrate reductase, nitrite reductases, nitric oxide reductase, mechanisms of N-N bond formation, and nitrous oxide reductases.

Characterization of the hydrogen-bond network of water around sucrose and trehalose: H-O-H bending analysis

NASA Astrophysics Data System (ADS)

Shiraga, Keiichiro; Adachi, Aya; Ogawa, Yuichi

2017-06-01

The bioprotective properties of disaccharides have been linked to destructuring effect on the hydrogen-bond structure of the interfacial water around the disaccharide solute, but its detailed mechanisms are yet to be provided. In this study, we characterized the destructuring effect based on the complex dielectric constants of interfacial water around sucrose and trehalose in the H-O-H bending region. Our analysis showed that the destructuring effect around disaccharides involves substantial disordering of the hydrogen-bond structure and formation of strong disaccharide-water hydrogen-bond. Such a destructuring effect caused by disaccharides is totally distinct from what happens with temperature increases of neat water.

LAMMPS framework for dynamic bonding and an application modeling DNA

NASA Astrophysics Data System (ADS)

Svaneborg, Carsten

2012-08-01

We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Catalogue identifier: AEME_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Hours to days. The examples provided in the distribution take just seconds to run.

BF3·Et2O-promoted cleavage of the Csp-Csp2 bond of 2-propynolphenols/anilines: route to C2-alkenylated benzoxazoles and benzimidazoles.

PubMed

Song, Xian-Rong; Qiu, Yi-Feng; Song, Bo; Hao, Xin-Hua; Han, Ya-Ping; Gao, Pin; Liu, Xue-Yuan; Liang, Yong-Min

2015-02-20

A novel BF3·Et2O-promoted tandem reaction of easily prepared 2-propynolphenols/anilines and trimethylsilyl azide is developed to give C2-alkenylated benzoxazoles and benzimidazoles in moderate to good yields. Most reactions could be accomplished in 30 min at room temperature. This tandem process involves a Csp-Csp2 bond cleavage and a C-N bond formation. Moreover, both tertiary and secondary propargylic alcohols with diverse functional groups were tolerated under the mild conditions.

Linking Arsenic Metabolism and Toxic Effects

EPA Science Inventory

Although arsenic has been long recognized as a toxicant and a carcinogen, the molecular basis for few of its adverse effects are well understood. Like other metalloids, arsenic undergoes extensive metabolism involving oxidation state changes and formation of methyl-arsenic bonds ...

Orientation and Order of the Amide Group of Sphingomyelin in Bilayers Determined by Solid-State NMR

PubMed Central

Matsumori, Nobuaki; Yamaguchi, Toshiyuki; Maeta, Yoshiko; Murata, Michio

2015-01-01

Sphingomyelin (SM) and cholesterol (Chol) are considered essential for the formation of lipid rafts; however, the types of molecular interactions involved in this process, such as intermolecular hydrogen bonding, are not well understood. Since, unlike other phospholipids, SM is characterized by the presence of an amide group, it is essential to determine the orientation of the amide and its order in the lipid bilayers to understand the nature of the hydrogen bonds in lipid rafts. For this study, 1′-13C-2-15N-labeled and 2′-13C-2-15N-labeled SMs were prepared, and the rotational-axis direction and order parameters of the SM amide in bilayers were determined based on 13C and 15N chemical-shift anisotropies and intramolecular 13C-15N dipole coupling constants. Results revealed that the amide orientation was minimally affected by Chol, whereas the order was enhanced significantly in its presence. Thus, Chol likely promotes the formation of an intermolecular hydrogen-bond network involving the SM amide without significantly changing its orientation, providing a higher order to the SM amide. To our knowledge, this study offers new insight into the significance of the SM amide orientation with regard to molecular recognition in lipid rafts, and therefore provides a deeper understanding of the mechanism of their formation. PMID:26083921

Copper-Catalyzed Oxidative Reaction of β-Keto Sulfones with Alcohols via C-S Bond Cleavage: Reaction Development and Mechanism Study.

PubMed

Du, Bingnan; Wang, Wenmin; Wang, Yang; Qi, Zhenghang; Tian, Jiaqi; Zhou, Jie; Wang, Xiaochen; Han, Jianlin; Ma, Jing; Pan, Yi

2018-02-16

A Cu-catalyzed cascade oxidative radical process of β-keto sulfones with alcohols has been achieved by using oxygen as an oxidant. In this reaction, β-keto sulfones were converted into sulfinate esters under the oxidative conditions via cleavage of C-S bond. Experimental and computational studies demonstrate that a new pathway is involved in this reaction, which proceeds through the formation of the key four-coordinated Cu II intermediate, O-O bond homolysis induced C-S bond cleavage and Cu-catalyzed esterification to form the final products. This reaction provides a new strategy to sulfonate esters and enriches the research content of C-S bond cleavage and transformations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

2-(4-Hy-droxy-phen-yl)-1H-benzimidazol-3-ium chloride monohydrate.

PubMed

González-Padilla, Jazmin E; Rosales-Hernández, Martha Cecila; Padilla-Martínez, Itzia I; García-Báez, Efren V; Rojas-Lima, Susana

2013-01-01

The title mol-ecular salt, C13H11N2O(+)·Cl(-)·H2O, crystallizes as a monohydrate. In the cation, the phenol and benzimidazole rings are almost coplanar, making a dihedral angle of 3.18 (4)°. The chloride anion and benzimidazole cation are linked by two N(+)-H⋯Cl(-) hydrogen bonds, forming chains propagating along [010]. These chains are linked through O-H⋯Cl hydrogen bonds involving the water mol-ecule and the chloride anion, which form a diamond core, giving rise to the formation of two-dimensional networks lying parallel to (10-2). Two π-π inter-actions involving the imidazolium ring with the benzene and phenol rings [centroid-centroid distances = 3.859 (3) and 3.602 (3) Å, respectively], contribute to this second dimension. A strong O-H⋯O hydrogen bond involving the water mol-ecule and the phenol substituent on the benzimidazole unit links the networks, forming a three-dimensional structure.

Characterization of non-classical Csbnd Br⋯π interactions in (E)-1,3-dibromo-5-(2-(ferrocenyl)vinyl)benzene and related derivatives of ferrocene

NASA Astrophysics Data System (ADS)

Shukla, Rahul; Panini, Piyush; McAdam, C. John; Robinson, Brian H.; Simpson, Jim; Tagg, Tei; Chopra, Deepak

2017-03-01

Amongst the halogens, the involvement of bromine atoms in various types of intermolecular interactions is comparatively the least studied. In this manuscript, we report the formation of Csbnd Br⋯π interactions, with the π-rings being the cyclopentadienyl (Cp) rings of a ferrocene molecule in a newly synthesized compound (E)-1,3-dibromo-5-(2-(ferrocenyl)vinyl)benzene. We have also performed a detailed quantitative analysis on Csbnd Br⋯π interactions observed in the synthesized molecule and in several related molecules found in the Cambridge Structure Database (CSD) showing the presence of these interactions. A topological analysis based upon QTAIM theory and electrostatic potential ESP mapped on the Hirshfeld surface of these molecules confirm that these interactions are better described as "halogen bonds" wherein the electropositive region (σ-hole) on the Br-atom interacts with the electronegative region over the Cp-ring of the ferrocene. Further, the electronegative region on the bromine atom (perpendicular to the Csbnd Br bond) was observed to be involved in the formation of highly directional Csbnd H⋯Br interactions with the ∠Csbnd Br⋯H close to 90°. Thus the bromine atom is acting as both a "halogen bond donor" and "hydrogen bond acceptor" in the crystal packing with the two interactions being mutually orthogonal.

O2-Promoted Allylic Acetoxylation of Alkenes: Assessment of “Push” vs. “Pull” Mechanisms and Comparison between O2 and Benzoquinone

PubMed Central

Diao, Tianning

2014-01-01

Palladium-catalyzed acetoxylation of allylic C–H bonds has been the subject of extensive study. These reactions proceed via allyl-palladium(II) intermediates that react with acetate to afford the allyl acetate product. Benzoquinone and molecular oxygen are two common oxidants for these reactions. Benzoquinone has been shown to promote allyl acetate formation from well-defined π-allyl palladium(II) complexes. Here, we assess the ability of O2 to promote similar reactions with a series of “unligated” π-allyl palladium(II) complexes (i.e., in the absence of ancillary phosphorus, nitrogen or related donor ligands). Stoichiometric and catalytic allyl acetate formation is observed under aerobic conditions with several different alkenes. Mechanistic studies are most consistent with a “pull” mechanism in which O2 traps the Pd0 intermediate following reversible C–O bond-formation from an allyl-palladium(II) species. A “push” mechanism, involving oxidatively induced C–O bond formation, does not appear to participate. These results and conclusions are compared with benzoquinone-promoted allylic acetoxylation, in which a “push” mechanism seems to be operative. PMID:25435646

Asymmetric Methods for the Synthesis of Flavanones, Chromanones, and Azaflavanones

PubMed Central

Nibbs, Antoinette E.

2012-01-01

Flavanones, chromanones, and related structures are privileged natural products that display a wide variety of biological activities. Although flavanoids are abundant in nature, there are a limited number of available general and efficient synthetic methods for accessing molecules of this class in a stereoselective manner. Their structurally simple architectures belie the difficulties involved in installation and maintenance of the stereogenic configuration at the C2 position, which can be sensitive and can undergo epimerization under mildly acidic, basic, and thermal reaction conditions. This review presents the methods currently used to access these related structures. The synthetic methods include manipulation of the flavone/flavanone core, carbon-carbon bond formation, and carbon–heteroatom bond formation. PMID:22876166

Un-catalyzed peptide bond formation between two monomers of glycine, alanine, serine, threonine, and aspartic acid in gas phase: a density functional theory study

NASA Astrophysics Data System (ADS)

Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K.

2016-05-01

In the present report, un-catalyzed peptide bond formation between two monomers of glycine (Gly), alanine (Ala), serine (Ser), threonine (Thr), and aspartic acid (Asp) has been investigated in gas phase via two steps reaction mechanism and concerted mechanism at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. The peptide bond is formed through a nucleophilic reaction via transition states, TS1 and TS2 in stepwise mechanism. The TS1 reveals formation of a new C-N bond while TS2 illustrate the formation of C=O bond. In case of concerted mechanism, C-N bond is formed by a single four-centre transition state (TS3). The energy barrier is used to explain the involvement of energy at each step of the reaction. The energy barrier (20-48 kcal/mol) is required for the transformation of reactant state R1 to TS1 state and intermediate state I1 to TS2 state. The large value of energy barrier is explained in terms of distortion and interaction energies for stepwise mechanism. The energy barrier of TS3 in concerted mechanism is very close to the energy barrier of the first transition state (TS1) of the stepwise mechanism for the formation of Gly-Gly and Ala-Ala di- peptide. However, in case of Ser-Ser, Thr-Thr and Asp-Asp di-peptide, the energy barrier of TS3 is relatively high than that of the energy barrier of TS1 calculated at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. In both the mechanisms, the value of energy barrier calculated at B3LYP/6-31G(d,p) level of theory is greater than that of the value calculated at M062X/6-31G(d,p) level of theory.

Amide-Directed Photoredox Catalyzed C-C Bond Formation at Unactivated sp3 C-H Bonds

PubMed Central

Chu, John C. K.; Rovis, Tomislav

2017-01-01

Carbon-carbon (C-C) bond formation is paramount in the synthesis of biologically relevant molecules, modern synthetic materials and commodity chemicals such as fuels and lubricants. Traditionally, the presence of a functional group is required at the site of C-C bond formation. Strategies that allow C-C bond formation at inert carbon-hydrogen (C-H) bonds allow scientists to access molecules which would otherwise be inaccessible and to develop more efficient syntheses of complex molecules.1,2 Herein we report a method for the formation of C-C bonds by directed cleavage of traditionally non-reactive C-H bonds and their subsequent coupling with readily available alkenes. Our methodology allows for the selective C-C bond formation at single C-H bonds in molecules that contain a multitude of seemingly indifferentiable such bonds. Selectivity arises through a relayed photoredox catalyzed oxidation of an N-H bond. We anticipate our findings to serve as a starting point for functionalization at inert C-H bonds through a hydrogen atom transfer strategy. PMID:27732580

The mechanism of proton conduction in phosphoric acid

NASA Astrophysics Data System (ADS)

Vilčiauskas, Linas; Tuckerman, Mark E.; Bester, Gabriel; Paddison, Stephen J.; Kreuer, Klaus-Dieter

2012-06-01

Neat liquid phosphoric acid (H3PO4) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.

Body of Knowledge (BOK) for Copper Wire Bonds

NASA Technical Reports Server (NTRS)

Rutkowski, E.; Sampson, M. J.

2015-01-01

Copper wire bonds have replaced gold wire bonds in the majority of commercial semiconductor devices for the latest technology nodes. Although economics has been the driving mechanism to lower semiconductor packaging costs for a savings of about 20% by replacing gold wire bonds with copper, copper also has materials property advantages over gold. When compared to gold, copper has approximately: 25% lower electrical resistivity, 30% higher thermal conductivity, 75% higher tensile strength and 45% higher modulus of elasticity. Copper wire bonds on aluminum bond pads are also more mechanically robust over time and elevated temperature due to the slower intermetallic formation rate - approximately 1/100th that of the gold to aluminum intermetallic formation rate. However, there are significant tradeoffs with copper wire bonding - copper has twice the hardness of gold which results in a narrower bonding manufacturing process window and requires that the semiconductor companies design more mechanically rigid bonding pads to prevent cratering to both the bond pad and underlying chip structure. Furthermore, copper is significantly more prone to corrosion issues. The semiconductor packaging industry has responded to this corrosion concern by creating a palladium coated copper bonding wire, which is more corrosion resistant than pure copper bonding wire. Also, the selection of the device molding compound is critical because use of environmentally friendly green compounds can result in internal CTE (Coefficient of Thermal Expansion) mismatches with the copper wire bonds that can eventually lead to device failures during thermal cycling. Despite the difficult problems associated with the changeover to copper bonding wire, there are billions of copper wire bonded devices delivered annually to customers. It is noteworthy that Texas Instruments announced in October of 2014 that they are shipping microcircuits containing copper wire bonds for safety critical automotive applications. An evaluation of copper wire bond technology for applicability to spaceflight hardware may be warranted along with concurrently compiling a comprehensive understanding of the failure mechanisms involved with copper wire bonded semiconductor devices.

Nerve-gas destruction with metal organic frameworks

EPA Science Inventory

Chemical warfare agents (CWAs) such as saran, soman, and tabun have been developed since World War I. Their mode of action involves the rapid formation of phosphate ester bonds with acetylcholinesterase to attenuate activity. The cumulative result of this activity loss leads to a...

Copper-Catalyzed Domino Three-Component Approach for the Assembly of 2-Aminated Benzimidazoles and Quinazolines.

PubMed

Tran, Lam Quang; Li, Jihui; Neuville, Luc

2015-06-19

A copper-promoted three-component synthesis of 2-aminobenzimidazoles (1) or of 2-aminoquinazolines (2) involving cyanamides, arylboronic acids, and amines has been developed. The operationally simple oxidative process, performed in the presence of K2CO3, a catalytic amount of CuCl2·2H2O, 2,2'-bipyridine, and an O2 atmosphere (1 atm), allows the rapid assembly of either benzimidazoles or quinazolines starting from aryl- or benzyl-substituted cyanamides, respectively. In this process, the copper promotes the formation of three bonds, two C-N bonds, and an additional bond resulting from C-H functionalization event.

The Development, Implementation and Application of Accurate Quantum Chemical Methods for Molecular Structure, Spectra and Reaction Paths

DTIC Science & Technology

2016-02-02

Bartlett, Nigel G. J. Richards, Robert W. Molt, Alison M. Lecher. Facile Csp2 Csp2 bond cleavage in oxalic acid -derived radicals: Implications for...sway a strong bond link in oxalate can be broken by manganese containing enzymes. The intermediate steps involved the formation of either a radical or...catalysis by oxalate decarboxylase, Journal of the American Chemical Society, (03 2015): 3248. doi: 10.1021/ja510666r Erik Deumens, Victor F. Lotrich

An In Situ Directing Group Strategy for Chiral Anion Phase-Transfer Fluorination of Allylic Alcohols

PubMed Central

2015-01-01

An enantioselective fluorination of allylic alcohols under chiral anion phase-transfer conditions is reported. The in situ generation of a directing group proved crucial for achieving effective enantiocontrol. In the presence of such a directing group, a range of acyclic substrates underwent fluorination to afford highly enantioenriched α-fluoro homoallylic alcohols. Mechanistic studies suggest that this transformation proceeds through a concerted enantiodetermining transition state involving both C–F bond formation and C–H bond cleavage. PMID:25203796

Anodic Oxidative Modification of Egg White for Heat Treatment.

PubMed

Takahashi, Masahito; Handa, Akihiro; Yamaguchi, Yusuke; Kodama, Risa; Chiba, Kazuhiro

2016-08-31

A new functionalization of egg white was achieved by an electrochemical reaction. The method involves electron transfer from thiol groups of egg white protein to form disulfide bonds. The oxidized egg white produced less hydrogen sulfide during heat treatment; with sufficient application of electricity, almost no hydrogen sulfide was produced. In addition, gels formed by heating electrochemically oxidized egg white exhibited unique properties, such as a lower gelation temperature and a softened texture, presumably due to protein aggregation and electrochemically mediated intramolecular disulfide bond formation.

Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds

NASA Astrophysics Data System (ADS)

Oh, Yoo Jin; Hubauer-Brenner, Michael; Gruber, Hermann J.; Cui, Yidan; Traxler, Lukas; Siligan, Christine; Park, Sungsu; Hinterdorfer, Peter

2016-09-01

Many enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.

The Effect of Limited Diffusion and Wet-Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids.

PubMed

Higgs, Paul G

2016-06-08

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction.

The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids

PubMed Central

Higgs, Paul G.

2016-01-01

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction. PMID:27338479

Infrared spectra of SF6-.HCOOH.Arn (n=0-2): Infrared triggered reaction and Ar-induced reactive inhibition

NASA Astrophysics Data System (ADS)

Schneider, Holger; Takahashi, Kaito; Skodje, Rex T.; Weber, J. Mathias

2009-05-01

We present the infrared spectra of SF6-ṡHCOOHṡArm (m =0-2) complexes. We find that the binding motif involves a single hydrogen bond between the SF6- anion and the OH group of the formic acid, with the CH group weakly tethered to a neighboring F atom. Similar to the case of hydrated SF6-, the SF bond involved in the (OH-F) bond is significantly stretched and weakened by the attachment of the HCOOH ligand. The bare complex undergoes reaction upon infrared absorption in the CH/OH stretching region of the formic acid moiety, leading predominantly to the formation of SF4-+2HF+CO2. The reaction can be inhibited by attachment of two Ar atoms. We discuss a likely reaction mechanism in the framework of ab initio calculations, suggesting that reaction proceeds via tunneling through the potential barrier.

Atomic Scale Structure of (001) Hydrogen-Induced Platelets in Germanium

NASA Astrophysics Data System (ADS)

David, Marie-Laure; Pizzagalli, Laurent; Pailloux, Fréderic; Barbot, Jean François

2009-04-01

An accurate characterization of the structure of hydrogen-induced platelets is a prerequisite for investigating both hydrogen aggregation and formation of larger defects. On the basis of quantitative high resolution transmission electron microscopy experiments combined with extensive first principles calculations, we present a model for the atomic structure of (001) hydrogen-induced platelets in germanium. It involves broken Ge-Ge bonds in the [001] direction that are dihydride passivated, vacancies, and trapped H2 molecules, showing that the species involved in platelet formation depend on the habit plane. This model explains all previous experimental observations.

Theoretical investigation of the gas-phase reactions of CrO(+) with ethylene.

PubMed

Scupp, Thomas M; Dudley, Timothy J

2010-01-21

The potential energy surfaces associated with the reactions of chromium oxide cation (CrO(+)) with ethylene have been characterized using density functional, coupled-cluster, and multireference methods. Our calculations show that the most probable reaction involves the formation of acetaldehyde and Cr(+) via a hydride transfer involving the metal center. Our calculations support previous experimental hypotheses that a four-membered ring intermediate plays an important role in the reactivity of the system. We have also characterized a number of viable reaction pathways that lead to other products, including ethylene oxide. Due to the experimental observation that CrO(+) can activate carbon-carbon bonds, a reaction pathway involving C-C bond cleavage has also been characterized. Since many of the reactions involve a change in the spin state in going from reactants to products, locations of these spin surface crossings are presented and discussed. The applicability of methods based on Hartree-Fock orbitals is also discussed.

Formation, Migration, and Reactivity of Au CO Complexes on Gold Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jun; McEntee, Monica; Tang, Wenjie

2016-01-12

Here, we report experimental as well as theoretical evidence that suggests Au CO complex formation upon the exposure of CO to active sites (step edges and threading dislocations) on a Au(111) surface. Room-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, transmission infrared spectroscopy, and density functional theory calculations point to Au CO complex formation and migration. Room-temperature STM of the Au(111) surface at CO pressures in the range from 10^ 8 to 10^ 4 Torr (dosage up to 10^6 langmuir) indicates Au atom extraction from dislocation sites of the herringbone reconstruction, mobile Au CO complex formation and diffusion, and Aumore » adatom cluster formation on both elbows and step edges on the Au surface. The formation and mobility of the Au CO complex result from the reduced Au Au bonding at elbows and step edges leading to stronger Au CO bonding and to the formation of a more positively charged CO (CO +) on Au. These studies indicate that the mobile Au CO complex is involved in the Au nanoparticle formation and reactivity, and that the positive charge on CO increases due to the stronger adsorption of CO at Au sites with lower coordination numbers.« less

Computational study of the covalent bonding of microcystins to cysteine residues--a reaction involved in the inhibition of the PPP family of protein phosphatases.

PubMed

Pereira, Susana R; Vasconcelos, Vítor M; Antunes, Agostinho

2013-01-01

Microcystins (MCs) are cyclic peptides, produced by cyanobacteria, that are hepatotoxic to mammals. The toxicity mechanism involves the potent inhibition of protein phosphatases, as the toxins bind the catalytic subunits of five enzymes of the phosphoprotein phosphatase (PPP) family of serine/threonine-specific phosphatases: Ppp1 (aka PP1), Ppp2 (aka PP2A), Ppp4, Ppp5 and Ppp6. The interaction with the proteins includes the formation of a covalent bond with a cysteine residue. Although this reaction seems to be accessory for the inhibition of PPP enzymes, it has been suggested to play an important part in the biological role of MCs and furthermore is involved in their nonenzymatic conjugation to glutathione. In this study, the molecular interaction of microcystins with their targeted PPP catalytic subunits is reviewed, including the relevance of the covalent bond for overall inhibition. The chemical reaction that leads to the formation of the covalent bond was evaluated in silico, both thermodynamically and kinetically, using quantum mechanical-based methods. As a result, it was confirmed to be a Michael-type addition, with simultaneous abstraction of the thiol hydrogen by a water molecule, transfer of hydrogen from the water to the α,β-unsaturated carbonyl group of the microcystin and addition of the sulfur to the β-carbon of the microcystin moiety. The calculated kinetics are in agreement with previous experimental results that had indicated the reaction to occur in a second step after a fast noncovalent interaction that inhibited the enzymes per se. © 2011 The Authors Journal compilation © 2011 FEBS.

Rate-dependent inverse-addition beta-selective mannosylation and contiguous sequential glycosylation involving beta-mannosidic bond formation.

PubMed

Chang, Shih-Sheng; Shih, Che-Hao; Lai, Kwun-Cheng; Mong, Kwok-Kong Tony

2010-05-03

The beta-selectivity of mannosylation has been found to be dependent on the addition rate of the mannosyl trichloroacetimidate donor in an inverse-addition (I-A) procedure. This rate dependent I-A procedure can improve the selectivity of direct beta-mannosylation and is applicable to orthogonal glycosylations of thioglycoside acceptors. Further elaboration of this novel procedure enables the development of the contiguous sequential glycosylation strategy, which streamlines the preparation of oligosaccharides invoking beta-mannosidic bond formation. The synthetic utility of the contiguous glycosylation strategy was demonstrated by the preparation of the trisaccharide core of human N-linked glycoproteins and the trisaccharide repeating unit of the O-specific polysaccharide found in the cellular capsule of Salmonelle bacteria.

Visible-Light-Induced Nickel-Catalyzed Negishi Cross-Couplings by Exogenous-Photosensitizer-Free Photocatalysis.

PubMed

Abdiaj, Irini; Fontana, Alberto; Gomez, M Victoria; de la Hoz, Antonio; Alcázar, Jesús

2018-03-22

The merging of photoredox and transition-metal catalysis has become one of the most attractive approaches for carbon-carbon bond formation. Such reactions require the use of two organo-transition-metal species, one of which acts as a photosensitizer and the other one as a cross-coupling catalyst. We report herein an exogenous-photosensitizer-free photocatalytic process for the formation of carbon-carbon bonds by direct acceleration of the well-known nickel-catalyzed Negishi cross-coupling that is based on the use of two naturally abundant metals. This finding will open new avenues in cross-coupling chemistry that involve the direct visible-light absorption of organometallic catalytic complexes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simultaneous formation of 3-deoxy-d-threo-hexo-2-ulose and 3-deoxy-d-erythro-hexo-2-ulose during the degradation of d-glucose derived Amadori rearrangement products: Mechanistic considerations.

PubMed

Kaufmann, Martin; Krüger, Sophie; Mügge, Clemens; Kroh, Lothar W

2018-03-22

Analyzing classical model reaction systems of Amadori rearrangement products (ARP) it became apparent that the formation of 3-deoxy-d-threo-hexo-2-ulose (3-deoxygalactosone, 3-DGal) during the degradation of ARPs is highly dependent on pH and the amino acid residue of the respective ARP. Based on a detailed analysis of the NMR chemical shifts of the sugar moieties of different ARPs, it could be derived that the formation of 3-DGal is sensitive to the stability of a co-operative hydrogen bond network which involves HO-C3, the deprotonated carboxyl functionality and the protonated amino nitrogen of the amino acid substituent. Participating in this bond network, HO-C3 is partially protonated which facilitates the elimination of water at C3. Based on that, a new mechanism of 3-deoxyglycosone formation is proposed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Insights into the catalysis of a lysine-tryptophan bond in bacterial peptides by a SPASM domain radical S-adenosylmethionine (SAM) peptide cyclase.

PubMed

Benjdia, Alhosna; Decamps, Laure; Guillot, Alain; Kubiak, Xavier; Ruffié, Pauline; Sandström, Corine; Berteau, Olivier

2017-06-30

Radical S -adenosylmethionine (SAM) enzymes are emerging as a major superfamily of biological catalysts involved in the biosynthesis of the broad family of bioactive peptides called ribosomally synthesized and post-translationally modified peptides (RiPPs). These enzymes have been shown to catalyze unconventional reactions, such as methyl transfer to electrophilic carbon atoms, sulfur to C α atom thioether bonds, or carbon-carbon bond formation. Recently, a novel radical SAM enzyme catalyzing the formation of a lysine-tryptophan bond has been identified in Streptococcus thermophilus , and a reaction mechanism has been proposed. By combining site-directed mutagenesis, biochemical assays, and spectroscopic analyses, we show here that this enzyme, belonging to the emerging family of SPASM domain radical SAM enzymes, likely contains three [4Fe-4S] clusters. Notably, our data support that the seven conserved cysteine residues, present within the SPASM domain, are critical for enzyme activity. In addition, we uncovered the minimum substrate requirements and demonstrate that KW cyclic peptides are more widespread than anticipated, notably in pathogenic bacteria. Finally, we show a strict specificity of the enzyme for lysine and tryptophan residues and the dependence of an eight-amino acid leader peptide for activity. Altogether, our study suggests novel mechanistic links among SPASM domain radical SAM enzymes and supports the involvement of non-cysteinyl ligands in the coordination of auxiliary clusters. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Formation of oligonucleotide-PNA-chimeras by template-directed ligation

NASA Technical Reports Server (NTRS)

Koppitz, M.; Nielsen, P. E.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

DNA sequences have previously been reported to act as templates for the synthesis of PNA, and vice versa. A continuous evolutionary transition from an informational replicating system based on one polymer to a system based on the other would be facilitated if it were possible to form chimeras, that is molecules that contain monomers of both types. Here we show that ligation to form chimeras proceeds efficiently both on PNA and on DNA templates. The efficiency of ligation is primarily determined by the number of backbone bonds at the ligation site and the relative orientation of template and substrate strands. The most efficient reactions result in the formation of chimeras with ligation junctions resembling the structures of the backbones of PNA and DNA and with antiparallel alignment of both components of the chimera with the template, that is, ligations involving formation of 3'-phosphoramidate and 5'-ester bonds. However, double helices involving PNA are stable both with antiparallel and parallel orientation of the two strands. Ligation on PNA but not on DNA templates is, therefore, sometimes possible on templates with reversed orientation. The relevance of these findings to discussions of possible transitions between genetic systems is discussed.

Cooperative Light-Activated Iodine and Photoredox Catalysis for the Amination of Csp3 -H Bonds.

PubMed

Becker, Peter; Duhamel, Thomas; Stein, Christopher J; Reiher, Markus; Muñiz, Kilian

2017-06-26

An unprecedented method that makes use of the cooperative interplay between molecular iodine and photoredox catalysis has been developed for dual light-activated intramolecular benzylic C-H amination. Iodine serves as the catalyst for the formation of a new C-N bond by activating a remote Csp3 -H bond (1,5-HAT process) under visible-light irradiation while the organic photoredox catalyst TPT effects the reoxidation of the molecular iodine catalyst. To explain the compatibility of the two involved photochemical steps, the key N-I bond activation was elucidated by computational methods. The new cooperative catalysis has important implications for the combination of non-metallic main-group catalysis with photocatalysis. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Peptide Bond Synthesis by a Mechanism Involving an Enzymatic Reaction and a Subsequent Chemical Reaction*

PubMed Central

Abe, Tomoko; Hashimoto, Yoshiteru; Zhuang, Ye; Ge, Yin; Kumano, Takuto; Kobayashi, Michihiko

2016-01-01

We recently reported that an amide bond is unexpectedly formed by an acyl-CoA synthetase (which catalyzes the formation of a carbon-sulfur bond) when a suitable acid and l-cysteine are used as substrates. DltA, which is homologous to the adenylation domain of nonribosomal peptide synthetase, belongs to the same superfamily of adenylate-forming enzymes, which includes many kinds of enzymes, including the acyl-CoA synthetases. Here, we demonstrate that DltA synthesizes not only N-(d-alanyl)-l-cysteine (a dipeptide) but also various oligopeptides. We propose that this enzyme catalyzes peptide synthesis by the following unprecedented mechanism: (i) the formation of S-acyl-l-cysteine as an intermediate via its “enzymatic activity” and (ii) subsequent “chemical” S → N acyl transfer in the intermediate, resulting in peptide formation. Step ii is identical to the corresponding reaction in native chemical ligation, a method of chemical peptide synthesis, whereas step i is not. To the best of our knowledge, our discovery of this peptide synthesis mechanism involving an enzymatic reaction and a subsequent chemical reaction is the first such one to be reported. This new process yields peptides without the use of a thioesterified fragment, which is required in native chemical ligation. Together with these findings, the same mechanism-dependent formation of N-acyl compounds by other members of the above-mentioned superfamily demonstrated that all members most likely form peptide/amide compounds by using this novel mechanism. Each member enzyme acts on a specific substrate; thus, not only the corresponding peptides but also new types of amide compounds can be formed. PMID:26586916

SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm

PubMed Central

2012-01-01

Background Production of correctly disulfide bonded proteins to high yields remains a challenge. Recombinant protein expression in Escherichia coli is the popular choice, especially within the research community. While there is an ever growing demand for new expression strains, few strains are dedicated to post-translational modifications, such as disulfide bond formation. Thus, new protein expression strains must be engineered and the parameters involved in producing disulfide bonded proteins must be understood. Results We have engineered a new E. coli protein expression strain named SHuffle, dedicated to producing correctly disulfide bonded active proteins to high yields within its cytoplasm. This strain is based on the trxB gor suppressor strain SMG96 where its cytoplasmic reductive pathways have been diminished, allowing for the formation of disulfide bonds in the cytoplasm. We have further engineered a major improvement by integrating into its chromosome a signal sequenceless disulfide bond isomerase, DsbC. We probed the redox state of DsbC in the oxidizing cytoplasm and evaluated its role in assisting the formation of correctly folded multi-disulfide bonded proteins. We optimized protein expression conditions, varying temperature, induction conditions, strain background and the co-expression of various helper proteins. We found that temperature has the biggest impact on improving yields and that the E. coli B strain background of this strain was superior to the K12 version. We also discovered that auto-expression of substrate target proteins using this strain resulted in higher yields of active pure protein. Finally, we found that co-expression of mutant thioredoxins and PDI homologs improved yields of various substrate proteins. Conclusions This work is the first extensive characterization of the trxB gor suppressor strain. The results presented should help researchers design the appropriate protein expression conditions using SHuffle strains. PMID:22569138

Catalytic enantioselective alkene aminohalogenation/cyclization involving atom transfer.

PubMed

Bovino, Michael T; Chemler, Sherry R

2012-04-16

Problem solved: the title reaction was used for the synthesis of chiral 2-bromo, chloro, and iodomethyl indolines and 2-iodomethyl pyrrolidines. Stereocenter formation is believed to occur by enantioselective cis aminocupration and C-X bond formation is believed to occur by atom transfer. The ultility of the products as versatile synthetic intermediates was demonstrated, as was a radical cascade cyclization sequence. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

2-(4-Hy­droxy­phen­yl)-1H-benzimidazol-3-ium chloride monohydrate

PubMed Central

González-Padilla, Jazmin E.; Rosales-Hernández, Martha Cecila; Padilla-Martínez, Itzia I.; García-Báez, Efren V.; Rojas-Lima, Susana

2013-01-01

The title mol­ecular salt, C13H11N2O+·Cl−·H2O, crystallizes as a monohydrate. In the cation, the phenol and benzimidazole rings are almost coplanar, making a dihedral angle of 3.18 (4)°. The chloride anion and benzimidazole cation are linked by two N+—H⋯Cl− hydrogen bonds, forming chains propagating along [010]. These chains are linked through O—H⋯Cl hydrogen bonds involving the water mol­ecule and the chloride anion, which form a diamond core, giving rise to the formation of two-dimensional networks lying parallel to (10-2). Two π–π inter­actions involving the imidazolium ring with the benzene and phenol rings [centroid–centroid distances = 3.859 (3) and 3.602 (3) Å, respectively], contribute to this second dimension. A strong O—H⋯O hydrogen bond involving the water mol­ecule and the phenol substituent on the benzimidazole unit links the networks, forming a three-dimensional structure. PMID:24427105

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

PubMed Central

2017-01-01

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M–1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor–acceptor sequences are avoided. PMID:28857551

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

PubMed

Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

2017-10-01

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp 2 -H...F-Csp 2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp 2 -F...F-Csp 2 contacts.

Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons.

PubMed

Bythell, Benjamin J; Suhai, Sándor; Somogyi, Arpád; Paizs, Béla

2009-10-07

The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

Elucidation of metal-ion accumulation induced by hydrogen bonds on protein surfaces by using porous lysozyme crystals containing Rh(III) ions as the model surfaces.

PubMed

Ueno, Takafumi; Abe, Satoshi; Koshiyama, Tomomi; Ohki, Takahiro; Hikage, Tatsuo; Watanabe, Yoshihito

2010-03-01

Metal-ion accumulation on protein surfaces is a crucial step in the initiation of small-metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh(III) ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino-acid residues to capture Rh(III) ions. ii) Water molecules pre-organized by hydrogen bonds can stabilize Rh(III) coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino-acid residues can be replaced by Rh(III) ions to form polynuclear structures with the residues. iv) Rh(III) aqua complexes are retained on amino-acid residues through stabilizing hydrogen bonds even at low pH (approximately 2). These metal-protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.

Formation of Annular Protofibrillar Assembly by Cysteine Tripeptide: Unraveling the Interactions with NMR, FTIR, and Molecular Dynamics.

PubMed

Banerji, Biswadip; Chatterjee, Moumita; Pal, Uttam; Maiti, Nakul C

2017-07-06

Both hydrogen-bonding and hydrophobic interactions play a significant role in molecular assembly, including self-assembly of proteins and peptides. In this study, we report the formation of annular protofibrillar structure (diameter ∼500 nm) made of a newly synthesized s-benzyl-protected cysteine tripeptide, which was primarily stabilized by hydrogen-bonding and hydrophobic interactions. Atomic force microscopy and field emission scanning electron microscopy analyses found small oligomers (diameter ∼60 nm) to bigger annular (outer diameter ∼300 nm; inner diameter, 100 nm) and protofibrillar structures after 1-2 days of incubation. Rotating-frame Overhauser spectroscopic (ROESY) analysis revealed the presence of several nonbonded proton-proton interactions among the residues, such as amide protons with methylene group, aromatic protons with tertiary butyl group, and methylene protons with tertiary butyl group. These added significant stability to bring the peptides closer to form a well-ordered assembled structure. Hydrogen-deuterium exchange NMR measurement further suggested that two individual amide protons among the three amide groups were strongly engaged with the adjacent tripeptide via H-bond interaction. However, the remaining amide proton was found to be exposed to solvent and remained noninteracting with other tripeptide molecules. In addition to chemical shift values, a significant change in amide bond vibrations of the tripeptide was found due to the formation of the self-assembled structure. The amide I mode of vibrations involving two amide linkages appeared at 1641 and 1695 cm -1 in the solid state. However, in the assembled state, the stretching band at 1695 cm -1 became broad and slightly shifted to ∼1689 cm -1 . On the contrary, the band at 1641 cm -1 shifted to 1659 cm -1 and indicated that the -C═O bond associated with this vibration became stronger in the assembled state. These changes in Fourier transform infrared spectroscopy frequency clearly indicated changes in the amide backbone conformation and the associated hydrogen-bonding pattern due to the formation of the assembled structure. In addition to hydrogen bonding, molecular dynamics simulation indicated that the number of π-π interactions also increased with increasing number of tripeptides participated in the self-assembly process. Combined results envisaged a cross β-sheet assembly unit consisting of four intermolecular hydrogen bonds. Such noncovalent peptide assemblies glued by hydrogen-bonding and other weak forces may be useful in developing nanocapsule and related materials.

Biofilm formation on stainless steel and gold wires for bonded retainers in vitro and in vivo and their susceptibility to oral antimicrobials.

PubMed

Jongsma, Marije A; Pelser, Floris D H; van der Mei, Henny C; Atema-Smit, Jelly; van de Belt-Gritter, Betsy; Busscher, Henk J; Ren, Yijin

2013-05-01

Bonded retainers are used in orthodontics to maintain treatment result. Retention wires are prone to biofilm formation and cause gingival recession, bleeding on probing and increased pocket depths near bonded retainers. In this study, we compare in vitro and in vivo biofilm formation on different wires used for bonded retainers and the susceptibility of in vitro biofilms to oral antimicrobials. Orthodontic wires were exposed to saliva, and in vitro biofilm formation was evaluated using plate counting and live/dead staining, together with effects of exposure to toothpaste slurry alone or followed by antimicrobial mouthrinse application. Wires were also placed intra-orally for 72 h in human volunteers and undisturbed biofilm formation was compared by plate counting and live/dead staining, as well as by denaturing gradient gel electrophoresis for compositional differences in biofilms. Single-strand wires attracted only slightly less biofilm in vitro than multi-strand wires. Biofilms on stainless steel single-strand wires however, were much more susceptible to antimicrobials from toothpaste slurries and mouthrinses than on single-strand gold wires and biofilms on multi-strand wires. Also, in vivo significantly less biofilm was found on single-strand than on multi-strand wires. Microbial composition of biofilms was more dependent on the volunteer involved than on wire type. Biofilms on single-strand stainless steel wires attract less biofilm in vitro and are more susceptible to antimicrobials than on multi-strand wires. Also in vivo, single-strand wires attract less biofilm than multi-strand ones. Use of single-strand wires is preferred over multi-strand wires, not because they attract less biofilm, but because biofilms on single-strand wires are not protected against antimicrobials as in crevices and niches as on multi-strand wires.

Straightforward Entry toward Highly Substituted 2,3-Dihydrobenz[ b]oxepines by Ring Expansion of Benzopyryliums with Donor-Acceptor Diazo Compounds.

PubMed

Courant, Thibaut; Pasco, Morgane; Lecourt, Thomas

2018-05-04

Ylide-type reactivity of diazo compounds is exploited in a new way to prepare benzo[ b]oxepines thanks to the formation of three chemical bonds and two contiguous and highly substituted stereocenters in a single pot. This cationic reaction cascade first involves addition of a donor-acceptor-substituted diazo compound to a benzopyrylium. Selective 1,2 migration of the endocyclic C-C bond then results in a ring-expansion and generates a second oxocarbenium that is trapped by a nucleophile added sequentially.

Computational Study of the Adsorption of Dimethyl Methylphosphonate (DMMP) on the (010) Surface of Anatase TiO2 With and Without Faceting

DTIC Science & Technology

2009-12-05

surface area of anatase nanocrystals [6] and to be es- pecially active in photocatalysis [7]. Recent work by Dzwigaj et al. [8] has clearly shown that the...two-fold-coordinated (O2c) sites can also be involved in hydrogen bond (H-bond) formation. The effects, on the structure of the (100) and other...To reduce the computational cost , geometry optimization was done at the restricted Hartree Fock (RHF) level. This has previously been shown [36,37

Possible Evidence of Amide Bond Formation Between Sinapinic Acid and Lysine-Containing Bacterial Proteins by Matrix-Assisted Laser Desorption/Ionization (MALDI) at 355 nm

NASA Astrophysics Data System (ADS)

Fagerquist, Clifton K.; Sultan, Omar; Carter, Michelle Q.

2012-12-01

We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, Hde, and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALDI) time-of-flight-time-of-flight tandem mass spectrometry (TOF-TOF-MS/MS) and post-source decay (PSD). We also reported the absence of adduct formation when using α-cyano-4-hydroxycinnamic acid (CHCA) matrix. Further mass spectrometric analysis of disulfide-intact and disulfide-reduced over-expressed HdeA and HdeB proteins from lysates of gene-inserted E. coli plasmids suggests covalent attachment of SA occurs not at cysteine residues but at lysine residues. In this revised hypothesis, the attachment of SA is preceded by formation of a solid phase ammonium carboxylate salt between SA and accessible lysine residues of the protein during sample preparation under acidic conditions. Laser irradiation at 355 nm of the dried sample spot results in equilibrium retrogradation followed by nucleophilic attack by the amine group of lysine at the carbonyl group of SA and subsequent amide bond formation and loss of water. The absence of CHCA adducts suggests that the electron-withdrawing effect of the α-cyano group of this matrix may inhibit salt formation and/or amide bond formation. This revised hypothesis is supported by dissociative loss of SA (-224 Da) and the amide-bound SA (-206 Da) from SA-adducted HdeA and HdeB ions by MS/MS (PSD). It is proposed that cleavage of the amide-bound SA from the lysine side-chain occurs via rearrangement involving a pentacyclic transition state followed by hydrogen abstraction/migration and loss of 3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-ynal (-206 Da).

Platinum anti-cancer drugs: Free radical mechanism of Pt-DNA adduct formation and anti-neoplastic effect.

PubMed

Fong, Clifford W

2016-06-01

The literature on the anti-neoplastic effects of Pt drugs provides substantial evidence that free radical may be involved in the formation of Pt-DNA adducts and other cytotoxic effects. The conditions specific to cancerous tumours are more conducive to free radical mechanisms than the commonly accepted hydrolysis nucleophilic-electrophilic mechanism of Pt-DNA adduct formation. Molecular orbital studies of the adiabatic attachment of hydrated electrons to Pt drugs reveal that there is a significant lengthening of the Pt-X bond (where X is Cl, O in cisplatin, carboplatin and some pyrophosphate-Pt drugs but not oxaliplatin) in the anion radical species. This observation is consistent with a dissociative electron transfer (DET) mechanism for the formation of Pt-DNA adducts. A DET reaction mechanism is proposed for the reaction of Pt drugs with guanine which involves a quasi-inner sphere 2 electron transfer process involving a transient intermediate 5 co-ordinated activated anion radical species {R2Pt---Cl(G)(Cl)•}*(-) (where R is an ammine group, and G is guanine) and the complex has an elongated Pt---Cl (or Pt---O) bond. A DET mechanism is also proposed when Pt drugs are activated by reaction with free radicals such as HO•, CO3•(-), O2•(-) but do not react with DNA bases to form adducts, but form Pt-protein adducts with proteins such ezrin, FAS, DR5, TNFR1 etc. The DET mechanism may not occur with oxaliplatin. Copyright © 2016 Elsevier Inc. All rights reserved.

Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Gao-Lei; Valiev, Marat; Wang, Xue-Bin

Dicarboxylic acids represent an important class of water-soluble organic compounds found in the atmosphere. In this work we are studying properties of dicarboxylic acid homodimer complexes (HO 2(CH 2) nCO 2 -[HO 2(CH 2) nCO 2H], n = 0-12), as potentially important intermediates in aerosol formation processes. Our approach is based on experimental data from negative ion photoelectron spectra of the dimer complexes combined with updated measurements of the corresponding monomer species. These results are analyzed with quantum-mechanical calculations, which provide further information about equilibrium structures, thermochemical parameters associated with the complex formation, and evaporation rates. We find that uponmore » formation of the dimer complexes the electron binding energies increase by 1.3–1.7 eV (30.0–39.2 kcal/mol), indicating increased stability of the dimerized complexes. Calculations indicate that these dimer complexes are characterized by the presence of strong intermolecular hydrogen bonds with high binding energies and are thermodynamically favorable to form with low evaporation rates. Comparison with previously studied HSO 4 -[HO 2(CH 2) 2CO 2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO 2(CH 2) 2CO 2 -[HO 2(CH 2) 2CO 2H] has very similar thermochemical properties. These results imply that dicarboxylic acids not only can contribute to the heterogeneous complexes formation involving sulfuric acid and dicarboxylic acids, but also can promote the formation of homogenous complexes by involving dicarboxylic acids themselves.« less

Liquid phase diffusion bonding of A1070 by using metal formate coated Zn sheet

NASA Astrophysics Data System (ADS)

Ozawa, K.; Koyama, S.; shohji, I.

2017-05-01

Aluminium alloy have high strength and easily recycle due to its low melting point. Therefore, aluminium is widely used in the manufacturing of cars and electronic devices. In recent years, the most common way for bonding aluminium alloy is brazing and friction stir welding. However, brazing requires positional accuracy and results in the formation of voids by the flax residue. Moreover, aluminium is an excellent heat radiating and electricity conducting material; therefore, it is difficult to bond together using other bonding methods. Because of these limitations, liquid phase diffusion bonding is considered to the suitable method for bonding aluminium at low temperature and low bonding pressure. In this study, the effect of metal formate coating processing of zinc surface on the bond strength of the liquid phase diffusion bonded interface of A1070 has been investigated by SEM observation of the interfacial microstructures and fractured surfaces after tensile test. Liquid phase diffusion bonding was carried out under a nitrogen gas atmosphere at a bonding temperature of 673 K and 713 K and a bonding load of 6 MPa (bonding time: 15 min). As a result of the metal formate coating processing, a joint having the ultimate tensile strength of the base aluminium was provided. It is hypothesized that this is because metallic zinc is generated as a result of thermal decomposition of formate in the bonded interface at lower bonding temperatures.

On the mechanism of the palladium catalyzed intramolecular Pauson-Khand-type reaction.

PubMed

Lan, Yu; Deng, Lujiang; Liu, Jing; Wang, Can; Wiest, Olaf; Yang, Zhen; Wu, Yun-Dong

2009-07-17

Density functional theory calculations and experimental studies have been carried out on the intramolecular Pauson-Khand-Type reaction mediated by a PdCl(2)-thiourea catalyst, which proceeds under mild reaction conditions and provides a useful alternative to traditional Pauson-Khand reactions. The classical mechanism of the Pauson-Khand reaction involving the alkyne/alkene C-C bond formation as the key step has been found to be energetically unfavorable and is not in line with the experimental observations. A novel reaction mechanism has been proposed for the reaction. The first step involves the cis-halometalation of the alkyne, followed by sequential alkene and carbonyl insertion. The rate-determining fourth step is an intramolecular C-Cl oxidative addition, leading to a Pd(IV) intermediate. A C-C bond formation by reductive elimination completes the reaction. The mechanism is in agreement with the key experimental observations including (1) the need of a chloride for catalytic activity and the absence of catalysis with Pd(OAc)(2) alone; (2) the rate acceleration by the addition of LiCl; both with PdCl(2) and Pd(OAc)(2) catalysts; and (3) the preferred formation of the trans diastereomer in substituted cases. The cis halometalation and the formation and stability of the Pd(IV) intermediate is studied in detail and provides general insights into these novel steps.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO reversible reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HNO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X double bond H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate (Delta)H(sub f, sup o) value for HNO using state-of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +/- 0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

Formation of conjugated delta8,delta10-double bonds by delta12-oleic-acid desaturase-related enzymes: biosynthetic origin of calendic acid.

PubMed

Cahoon, E B; Ripp, K G; Hall, S E; Kinney, A J

2001-01-26

Divergent forms of the plant Delta(12)-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Delta(11),Delta(13)-double bonds by modification of an existing Delta(12)-double bond in C(18) fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Delta(9)-double bond to produce the conjugated trans-Delta(8),trans-Delta(10)-double bonds found in calendic acid (18:3Delta(8trans,10trans,12cis)), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40-50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Delta(9cis,12cis)). These results are thus consistent with a route of calendic acid synthesis involving modification of the Delta(9)-double bond of linoleic acid. Regiospecificity for Delta(9)-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.

Alkyl Aryl Ether Bond Formation with PhenoFluor**

PubMed Central

Shen, Xiao; Neumann, Constanze N.; Kleinlein, Claudia; Claudia, Nathaniel W.; Ritter, Tobias

2015-01-01

An alkyl aryl ether bond formation reaction between phenols and primary and secondary alcohols with PhenoFluor has been developed. The reaction features a broad substrate scope and tolerates many functional groups, and substrates that are challenging for more conventional ether bond forming processes may be coupled. A preliminary mechanistic study indicates reactivity distinct from conventional ether bond formation. PMID:25800679

Importance of mother-infant communication for social bond formation in mammals.

PubMed

Okabe, Shota; Nagasawa, Miho; Mogi, Kazutaka; Kikusui, Takefumi

2012-06-01

Mother-infant bonding is a universal relationship of all mammalian species. Here, we describe the role of reciprocal communication between mother and infant in the formation of bonding for several mammalian species. Mother-infant bond formation is reinforced by various social cues or stimuli, including communicative signals, such as odor and vocalizations, or tactile stimuli. The mother also develops cross-modal sensory recognition of the infant, during bond formation. Many studies have indicated that the oxytocin neural system plays a pivotal role in bond formation by the mother; however, the underlying neural mechanisms for infants have not yet been clarified. The comparative understanding of cognitive functions of mother and infants may help us understand the biological significance of mother-infant communication in mammalian species. © 2012 The Authors. Animal Science Journal © 2012 Japanese Society of Animal Science.

Characterization of the Amicetin Biosynthesis Gene Cluster from Streptomyces vinaceusdrappus NRRL 2363 Implicates Two Alternative Strategies for Amide Bond Formation

PubMed Central

Zhang, Gaiyun; Zhang, Haibo; Li, Sumei; Xiao, Ji; Zhang, Guangtao; Zhu, Yiguang; Niu, Siwen; Ju, Jianhua

2012-01-01

Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis. PMID:22267658

Mechanisms for Flow-Enhanced Cell Adhesion

PubMed Central

Zhu, Cheng; Yago, Tadayuki; Lou, Jizhong; Zarnitsyna, Veronika I.; McEver, Rodger P.

2009-01-01

Cell adhesion is mediated by specific receptor—ligand bonds. In several biological systems, increasing flow has been observed to enhance cell adhesion despite the increasing dislodging fluid shear forces. Flow-enhanced cell adhesion includes several aspects: flow augments the initial tethering of flowing cells to a stationary surface, slows the velocity and increases the regularity of rolling cells, and increases the number of rollingly adherent cells. Mechanisms for this intriguing phenomenon may include transport-dependent acceleration of bond formation and force-dependent deceleration of bond dissociation. The former includes three distinct transport modes: sliding of cell bottom on the surface, Brownian motion of the cell, and rotational diffusion of the interacting molecules. The latter involves a recently demonstrated counterintuitive behavior called catch bonds where force prolongs rather than shortens the lifetimes of receptor—ligand bonds. In this article, we summarize our recently published data that used dimensional analysis and mutational analysis to elucidate the above mechanisms for flow-enhanced leukocyte adhesion mediated by L-selectinligand interactions. PMID:18299992

A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions

NASA Astrophysics Data System (ADS)

Solimannejad, Mohammad; Massahi, Shokofeh; Alkorta, Ibon

2009-07-01

Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH⋯N and NH⋯O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4-8 kJ mol -1 and 12-19 kJ mol -1, respectively. Blue shift of NH bond upon complex formation in the ranges between 30-80 and 14,114 cm -1 is predicted for dimers and trimers, respectively.

Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond

PubMed Central

Le Bailly, Bryden A. F.; Byrne, Liam

2016-01-01

Abstract Small changes in the structure of a foldamer may lead to gross changes in conformational preference. We show that the simple insertion or deletion of a single hydrogen bond by changes in pH or by photochemical deprotection is sufficient to refold a helical oligomer, interconverting M and P screw‐sense preference. As a consequence of the switch, information may be transmitted to a remote catalytic site, selectively directing the formation of either of two enantiomeric products by a reaction involving 1,22‐remote intermolecular asymmetric induction. PMID:26762559

Reactions in trifluoroacetic acid (CF 3COOH) induced by low energy electron attachment

NASA Astrophysics Data System (ADS)

Langer, Judith; Stano, Michal; Gohlke, Sascha; Foltin, Victor; Matejcik, Stefan; Illenberger, Eugen

2006-02-01

Dissociative electron attachment to trifluoroacetic acid (CF 3COOH) is characterized by an intense low energy shape resonance located near 1 eV and a comparatively weaker core excited resonance located near 7 eV. The shape resonance decomposes into the fragment ions CF 3COO -, CF 2COO -, and CF2-. The underlying reactions include simple bond cleavage but also more complex sequences involving multiple bond cleavages, rearrangement in the precursor ion and formation of new molecules (HF, CO 2). The core excited resonance additionally decomposes into F -, CF3- and probably metastable CO2-.

5-Chloro-2-nitro-phenol.

PubMed

Ren, Dong-Mei

2012-05-01

The asymmetric unit of the title compound, C(6)H(4)ClNO(3), contains two independent mol-ecules in which the dihedral angles between the benzene ring and the nitro groups are 2.5 (1) and 8.5 (1)°. Intra-molecular O-H⋯O hydrogen bonds involving the hy-droxy and nitro substituents result in the formation of S(6) six-membered rings. In the crystal, O-H⋯O, O-H⋯Cl and C-H⋯O hydrogen bonds together with Cl⋯O contacts [3.238 (3) and 3.207 (3) Å] generate a three-dimensional network.

Lanthanum-mediated dehydrogenation of butenes: Spectroscopy and formation of La(C4H6) isomers

NASA Astrophysics Data System (ADS)

Cao, Wenjin; Hewage, Dilrukshi; Yang, Dong-Sheng

2018-01-01

La atom reactions with 1-butene, 2-butene, and isobutene are carried out in a laser-vaporization molecular beam source. The three reactions yield the same La-hydrocarbon products from the dehydrogenation and carbon-carbon bond cleavage and coupling of the butenes. The dehydrogenated species La(C4H6) is the major product, which is characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectrum of La(C4H6) produced from the La+1-butene reaction exhibits two band systems, whereas the MATI spectra produced from the La+2-butene and isobutene reactions display only a single band system. Each of these spectra shows a strong origin band and several vibrational progressions. The two band systems from the spectrum of the 1-butene reaction are assigned to the ionization of two isomers: La[C(CH2)3] (Iso A) and La(CH2CHCHCH2) (Iso B), and the single band system from the spectra of the 2-butene and isobutene reactions is attributed to Iso B and Iso A, respectively. The ground electronic states are 2A1 (C3v) for Iso A and 2A' (Cs) for Iso B. The ionization of the doublet state of each isomer removes a La 6s-based electron and leads to the 1A1 ion of Iso A and the 1A' ion of Iso B. The formation of both isomers consists of La addition to the C=C double bond, La insertion into two C(sp3)—H bonds, and H2 elimination. In addition to these steps, the formation of Iso A from the La+1-butene reaction may involve the isomerization of 1-butene to isobutene prior to the C—H bond activation, whereas the formation of Iso B from the La+trans-2-butene reaction may include the trans- to cis-butene isomerization after the C—H bond activation.

Well-Defined Heterobimetallic Reactivity at Unsupported Ruthenium-Indium Bonds.

PubMed

Riddlestone, Ian M; Rajabi, Nasir A; Macgregor, Stuart A; Mahon, Mary F; Whittlesey, Michael K

2018-02-01

The hydride complex [Ru(IPr) 2 (CO)H][BAr F 4 ], 1, reacts with InMe 3 with loss of CH 4 to form [Ru(IPr) 2 (CO)(InMe)(Me)][BAr F 4 ], 4, featuring an unsupported Ru-In bond with unsaturated Ru and In centres. 4 reacts with H 2 to give [Ru(IPr) 2 (CO)(η 2 -H 2 )(InMe)(H)][BAr F 4 ], 5, while CO induces formation of the indyl complex [Ru(IPr) 2 (CO) 3 (InMe 2 )][BAr F 4 ], 7. These observations highlight the ability of Me to shuttle between Ru and In centres and are supported by DFT calculations on the mechanism of formation of 4 and its reactions with H 2 and CO. An analysis of Ru-In bonding in these species is also presented. Reaction of 1 with GaMe 3 also involves CH 4 loss but, in contrast to its In congener, sees IPr transfer from Ru to Ga to give a gallyl complex featuring an η 6 interaction of one aryl substituent with Ru. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen Bonding-Mediated Microphase Separation during the Formation of Mesoporous Novolac-Type Phenolic Resin Templated by the Triblock Copolymer, PEO-b-PPO-b-PEO

PubMed Central

Chu, Wei-Cheng; Chiang, Shih-Fan; Li, Jheng-Guang; Kuo, Shiao-Wei

2013-01-01

After blending the triblock copolymer, poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) (PEO-b-PPO-b-PEO) with novolac-type phenolic resin, Fourier transform infrared spectroscopy revealed that the ether groups of the PEO block were stronger hydrogen bond acceptors for the OH groups of phenolic resin than were the ether groups of the PPO block. Thermal curing with hexamethylenetetramine as the curing agent resulted in the triblock copolymer being incorporated into the phenolic resin, forming a nanostructure through a mechanism involving reaction-induced microphase separation. Mild pyrolysis conditions led to the removal of the PEO-b-PPO-b-PEO triblock copolymer and formation of mesoporous phenolic resin. This approach provided a variety of composition-dependent nanostructures, including disordered wormlike, body-centered-cubic spherical and disorder micelles. The regular mesoporous novolac-type phenolic resin was formed only at a phenolic content of 40–60 wt %, the result of an intriguing balance of hydrogen bonding interactions among the phenolic resin and the PEO and PPO segments of the triblock copolymer. PMID:28788378

Maternal and paternal plasma, salivary, and urinary oxytocin and parent-infant synchrony: considering stress and affiliation components of human bonding.

PubMed

Feldman, Ruth; Gordon, Ilanit; Zagoory-Sharon, Orna

2011-07-01

Studies in mammals have implicated the neuropeptide oxytocin (OT) in processes of bond formation and stress modulation, yet the involvement of OT in human bonding throughout life remains poorly understood. We assessed OT in the plasma, saliva, and urine of 112 mothers and fathers interacting with their 4-6-month-old infants. Parent-infant interactions were micro-coded for parent and child's social behaviors and for the temporal coordination of their socio-affective cues. Parents were interviewed regarding their attachment to the infant and reported on bonding to own parents, romantic attachment, and parenting stress. Results indicated that OT in plasma (pOT) and saliva (sOT) were inter-related and were unrelated to OT in urine (uOT). pOT and sOT in mothers and fathers were associated with parent and child's social engagement, affect synchrony, and positive communicative sequences between parent and child. uOT was related to moments of interactive stress among mothers only, indexed by the co-occurrence of infant negative engagement and mother re-engagement attempts. pOT and sOT were associated with mothers' and fathers' attachment relationships throughout life: to own parents, partner, and infant, whereas uOT correlated with relationship anxiety and parenting stress among mothers only. Similar to other mammals, OT is involved in human attachment and contingent parenting. The dual role of OT in stress and affiliation underscores its complex involvement in processes of social bonding throughout life. © 2010 Blackwell Publishing Ltd.

Bonded exciplex formation: electronic and stereoelectronic effects.

PubMed

Wang, Yingsheng; Haze, Olesya; Dinnocenzo, Joseph P; Farid, Samir; Farid, Ramy S; Gould, Ian R

2008-12-18

As recently proposed, the singlet-excited states of several cyanoaromatics react with pyridine via bonded-exciplex formation, a novel concept in photochemical charge transfer reactions. Presented here are electronic and steric effects on the quenching rate constants, which provide valuable support for the model. Additionally, excited-state quenching in poly(vinylpyridine) is strongly inhibited both relative to that in neat pyridine and also to conventional exciplex formation in polymers, consistent with a restrictive orientational requirement for the formation of bonded exciplexes. Examples of competing reactions to form both conventional and bonded exciplexes are presented, which illustrate the delicate balance between these two processes when their reaction energetics are similar. Experimental and computational evidence is provided for the formation of a bonded exciplex in the reaction of the singlet excited state of 2,6,9,10-tetracyanoanthracene (TCA) with an oxygen-substituted donor, dioxane, thus expanding the scope of bonded exciplexes.

Theoretical Studies of Chemical Reactions following Electronic Excitation

NASA Technical Reports Server (NTRS)

Chaban, Galina M.

2003-01-01

The use of multi-configurational wave functions is demonstrated for several processes: tautomerization reactions in the ground and excited states of the DNA base adenine, dissociation of glycine molecule after electronic excitation, and decomposition/deformation of novel rare gas molecules HRgF. These processes involve bond brealung/formation and require multi-configurational approaches that include dynamic correlation.

Clarification of the Mechanism of Acylation Reaction and Origin of Substrate Specificity of the Serine-Carboxyl Peptidase Sedolisin through QM/MM Free Energy Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Qin; Yao, Jianzhuang; Wiodawer, Alexander

2011-01-01

Quantum mechanical/molecular mechanical (QM/MM) free energy simulations are applied for understanding the mechanism of the acylation reaction catalyzed by sedolisin, a representative serine-carboxyl peptidase, leading to the acyl-enzyme (AE) and first product from the enzyme-catalyzed reaction. One of the interesting questions to be addressed in this work is the origin of the substrate specificity of sedolisin that shows a relatively high activity on the substrates with Glu at P1 site. It is shown that the bond making and breaking events of the acylation reaction involving a peptide substrate (LLE*FL) seem to be accompanied by local conformational changes, proton transfers asmore » well as the formation of alternative hydrogen bonds. The results of the simulations indicate that the conformational change of Glu at P1 site and its formation of a low barrier hydrogen bond with Asp-170 (along with the transient proton transfer) during the acylation reaction might play a role in the relatively high specificity for the substrate with Glu at P1 site. The role of some key residues in the catalysis is confirmed through free energy simulations. Glu-80 is found to act as a general base to accept a proton from Ser-287 during the nucleophilic attack and then as a general acid to protonate the leaving group (N H of P1 -Phe) during the cleavage of the scissile peptide bond. Another acidic residue, Asp-170, acts as a general acid catalyst to protonate the carbonyl of P1-Glu during the formation of the tetrahedral intermediate and as a general base for the formation of the acyl-enzyme. The energetic results from the free energy simulations support the importance of proton transfer from Asp-170 to the carbonyl of P1-Glu in the stabilization of the tetrahedral intermediate and the formation of a low-barrier hydrogen bond between the carboxyl group of P1-Glu and Asp-170 in the lowering of the free energy barrier for the cleavage of the peptide bond. Detailed analyses of the proton transfers during acylation are also given.« less

Effect of vacancies on the mechanical properties of phosphorene nanotubes.

PubMed

Sorkin, V; Zhang, Y W

2018-06-08

Using density functional tight-binding method, we studied the mechanical properties, deformation and failure of armchair (AC) and zigzag (ZZ) phosphorene nanotubes (PNTs) with monovacancies and divacancies subjected to uniaxial tensile strain. We found that divacancies in AC PNTs and monovacancies in ZZ PNTs possess the lowest vacancy formation energy, which decreases with the tube diameter in AC PNTs and increases in ZZ PNTs. The Young's modulus is reduced, while the radial and thickness Poisson's ratios are increased by hosted vacancies. In defective AC PNTs, deformation involves fracture of the intra-pucker bonds and formation of the new inter-pucker bonds at a critical strain, and the most stretched bonds around the vacancy rupture first, triggering a sequence of the structural transformations terminated by the ultimate failure. The critical strain of AC PNTs is reduced significantly by hosted vacancies, whereas their effect on the critical stress is relatively weaker. Defective ZZ PNTs fail in a brittle-like manner once the most stretched bonds around a vacancy rupture, and vacancies are able to significantly reduce the failure strain but only moderately reduce the failure stress of ZZ PNTs. The understandings revealed here on the mechanical properties and the deformation and failure mechanisms of PNTs provide useful guidelines for their design and fabrication as building blocks in nanodevices.

Effect of vacancies on the mechanical properties of phosphorene nanotubes

NASA Astrophysics Data System (ADS)

Sorkin, V.; Zhang, Y. W.

2018-06-01

Using density functional tight-binding method, we studied the mechanical properties, deformation and failure of armchair (AC) and zigzag (ZZ) phosphorene nanotubes (PNTs) with monovacancies and divacancies subjected to uniaxial tensile strain. We found that divacancies in AC PNTs and monovacancies in ZZ PNTs possess the lowest vacancy formation energy, which decreases with the tube diameter in AC PNTs and increases in ZZ PNTs. The Young’s modulus is reduced, while the radial and thickness Poisson’s ratios are increased by hosted vacancies. In defective AC PNTs, deformation involves fracture of the intra-pucker bonds and formation of the new inter-pucker bonds at a critical strain, and the most stretched bonds around the vacancy rupture first, triggering a sequence of the structural transformations terminated by the ultimate failure. The critical strain of AC PNTs is reduced significantly by hosted vacancies, whereas their effect on the critical stress is relatively weaker. Defective ZZ PNTs fail in a brittle-like manner once the most stretched bonds around a vacancy rupture, and vacancies are able to significantly reduce the failure strain but only moderately reduce the failure stress of ZZ PNTs. The understandings revealed here on the mechanical properties and the deformation and failure mechanisms of PNTs provide useful guidelines for their design and fabrication as building blocks in nanodevices.

Supramolecular interactions of oxidative stress biomarker glutathione with fluorone black.

PubMed

Hepel, Maria; Stobiecka, Magdalena

2018-03-05

Oxidative stress biomarkers, including glutathione (GSH) and related compounds, are involved in a variety of interactions enabling redox potential maintenance in living cells and protection against radicals. Since the oxidative stress is promoting and, in many cases, inducing serious illnesses, monitoring of GSH levels can aid in diagnostics and disease prevention. Herein, we report on the discovery of the formation of a supramolecular ensemble of GSH with fluorone black (9-phenyl fluorone, FB) which is optically active and enables sensitive determination of GSH by resonance elastic light scattering (RELS). We have found that supramolecular interactions of GSH with FB can be probed with spectroscopic, RELS, and electrochemical methods. Our investigations show that RELS intensity for FB solutions increases with GSH concentration while fluorescence emission of FB is not affected, as quenching begins only above 0.8mM GSH. The UV-Vis difference spectra show a positive peak at 383nm and a negative peak at 458nm, indicating a higher-energy absorbing complex in comparison to the non-bonded FB host. Supramolecular interactions of FB with GSH have also been corroborated by electrochemical measurements involving two configurations of FB-GSH ensembles on electrodes: (i) an inverted orientation on Au-coated quartz crystal piezoelectrode (Au@SG-FB), with strong thiolate bonding to gold, and (ii) a non-inverted orientation on glassy carbon electrode (GCE@FB-GS), with weak π-π stacking attachment and efficient charge mediation through the ensemble. The formation of a supramolecular ensemble with hydrogen bonding has also been confirmed by quantum mechanical calculations. The discovery of supramolecular FB-GSH ensemble formation enables elucidating the mechanisms of strong RELS responses, changes in UV-Vis absorption spectra, and the electrochemical reactivity. Also, it provides new insights to the understanding of the efficient charge-transfer in redox potential homeostasis which is likely based on an intermediate formation of a similar type of supramolecular ensembles. Copyright © 2017 Elsevier B.V. All rights reserved.

Supramolecular interactions of oxidative stress biomarker glutathione with fluorone black

NASA Astrophysics Data System (ADS)

Hepel, Maria; Stobiecka, Magdalena

2018-03-01

Oxidative stress biomarkers, including glutathione (GSH) and related compounds, are involved in a variety of interactions enabling redox potential maintenance in living cells and protection against radicals. Since the oxidative stress is promoting and, in many cases, inducing serious illnesses, monitoring of GSH levels can aid in diagnostics and disease prevention. Herein, we report on the discovery of the formation of a supramolecular ensemble of GSH with fluorone black (9-phenyl fluorone, FB) which is optically active and enables sensitive determination of GSH by resonance elastic light scattering (RELS). We have found that supramolecular interactions of GSH with FB can be probed with spectroscopic, RELS, and electrochemical methods. Our investigations show that RELS intensity for FB solutions increases with GSH concentration while fluorescence emission of FB is not affected, as quenching begins only above 0.8 mM GSH. The UV-Vis difference spectra show a positive peak at 383 nm and a negative peak at 458 nm, indicating a higher-energy absorbing complex in comparison to the non-bonded FB host. Supramolecular interactions of FB with GSH have also been corroborated by electrochemical measurements involving two configurations of FB-GSH ensembles on electrodes: (i) an inverted orientation on Au-coated quartz crystal piezoelectrode (Au@SG-FB), with strong thiolate bonding to gold, and (ii) a non-inverted orientation on glassy carbon electrode (GCE@FB-GS), with weak π-π stacking attachment and efficient charge mediation through the ensemble. The formation of a supramolecular ensemble with hydrogen bonding has also been confirmed by quantum mechanical calculations. The discovery of supramolecular FB-GSH ensemble formation enables elucidating the mechanisms of strong RELS responses, changes in UV-Vis absorption spectra, and the electrochemical reactivity. Also, it provides new insights to the understanding of the efficient charge-transfer in redox potential homeostasis which is likely based on an intermediate formation of a similar type of supramolecular ensembles.

One-shot preparation of an inherently chiral trifunctional calix[4]arene from an easily available cone-triformylcalix[4]arene.

PubMed

Ciaccia, Maria; Tosi, Irene; Cacciapaglia, Roberta; Casnati, Alessandro; Baldini, Laura; Di Stefano, Stefano

2013-06-14

Via selective 1,3-distal intramolecular Cannizzaro disproportionation of an easily available cone-triformylcalix[4]arene, an inherently chiral trifunctional cone-calix[4]arene derivative has been prepared. The presence of three different functional groups (-CH2OH, -CHO and -COOH) at the upper rim of the calixarene scaffold makes this compound a versatile intermediate for the development of multifunctional devices. Interesting chiral discrimination of serine derivatives has been observed, presumably thanks to a multipoint-interaction involving the reversible imine bond formation and the hydrogen bonding of the hydroxyl group of the amino acid side-chain with the upper rim functional groups. Consistently, chiral discrimination was not observed with alanine and valine derivatives, lacking hydrogen bonding groups on the side-chain.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO rev. reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X=H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate(DELTA)H(sup o)(sub f) value for HNO using state of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

Carbon-hydrogen bond activation, C-N bond coupling, and cycloaddition reactivity of a three-coordinate nickel complex featuring a terminal imido ligand.

PubMed

Mindiola, Daniel J; Waterman, Rory; Iluc, Vlad M; Cundari, Thomas R; Hillhouse, Gregory L

2014-12-15

The three-coordinate imidos (dtbpe)Ni═NR (dtbpe = (t)Bu2PCH2CH2P(t)Bu2, R = 2,6-(i)Pr2C6H3, 2,4,6-Me3C6H2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni-N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6-(i)Pr2C6H3, reductive carbonylation results in formation of the (dtbpe)Ni(CO)2 along with the N-C coupled product keteneimine PhCH═C═N(2,6- (i)Pr2C6H3). Given the ability of the Ni═N bond to have biradical character as suggested by theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni═N{2,6-(i)Pr2C6H3} when this species is treated with HSn((n)Bu)3. Likewise, the microscopic reverse reaction--conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6-(i)Pr2C6H3)} to the imido (dtbpe)Ni═N{2,6-(i)Pr2C6H3}--is promoted when using the radical Mes*O(•) (Mes* = 2,4,6-(t)Bu3C6H2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni═N{2,6-(i)Pr2C6H3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C-N and N-N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni═N{2,6-(i)Pr2C6H3}.

Carbon–hydrogen bond activation, C–N bond coupling, and cycloaddition reactivity of a three-coordinate nickel complex featuring a terminal imido ligand

DOE PAGES

Mindiola, Daniel J.; Waterman, Rory; Iluc, Vlad M.; ...

2014-12-01

Here, the three-coordinate imidos (dtbpe)Ni=NR (dtbpe = tBu 2PCH 2CH 2PtBu 2, R = 2,6- iPr 2C 6H 3, 2,4,6-Me 3C 6H 2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni–N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6- iPr 2C 6H 3, reductive carbonylation results in formation of the (dtbpe)Ni(CO) 2 along with the N–C coupled product keteneimine PhCH=C=N(2,6- iPr 2C 6H 3). Given the ability of the Ni=N bond to have biradical character as suggested bymore » theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni=N{2,6- iPr 2C 6H 3} when this species is treated with HSn( nBu) 3. Likewise, the microscopic reverse reaction—conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6- iPr 2C 6H 3)} to the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}—is promoted when using the radical Mes*O • (Mes* = 2,4,6- tBu 3C 6H 2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni=N{2,6- iPr 2C 6H 3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C–N and N–N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}.« less

Carbon–Hydrogen Bond Activation, C–N Bond Coupling, and Cycloaddition Reactivity of a Three-Coordinate Nickel Complex Featuring a Terminal Imido Ligand

PubMed Central

2015-01-01

The three-coordinate imidos (dtbpe)Ni=NR (dtbpe = tBu2PCH2CH2PtBu2, R = 2,6-iPr2C6H3, 2,4,6-Me3C6H2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni–N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6-iPr2C6H3, reductive carbonylation results in formation of the (dtbpe)Ni(CO)2 along with the N–C coupled product keteneimine PhCH=C=N(2,6- iPr2C6H3). Given the ability of the Ni=N bond to have biradical character as suggested by theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni=N{2,6-iPr2C6H3} when this species is treated with HSn(nBu)3. Likewise, the microscopic reverse reaction—conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6-iPr2C6H3)} to the imido (dtbpe)Ni=N{2,6-iPr2C6H3}—is promoted when using the radical Mes*O• (Mes* = 2,4,6-tBu3C6H2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni=N{2,6-iPr2C6H3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C–N and N–N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni=N{2,6-iPr2C6H3}. PMID:25437507

Carbon–hydrogen bond activation, C–N bond coupling, and cycloaddition reactivity of a three-coordinate nickel complex featuring a terminal imido ligand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mindiola, Daniel J.; Waterman, Rory; Iluc, Vlad M.

Here, the three-coordinate imidos (dtbpe)Ni=NR (dtbpe = tBu 2PCH 2CH 2PtBu 2, R = 2,6- iPr 2C 6H 3, 2,4,6-Me 3C 6H 2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni–N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6- iPr 2C 6H 3, reductive carbonylation results in formation of the (dtbpe)Ni(CO) 2 along with the N–C coupled product keteneimine PhCH=C=N(2,6- iPr 2C 6H 3). Given the ability of the Ni=N bond to have biradical character as suggested bymore » theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni=N{2,6- iPr 2C 6H 3} when this species is treated with HSn( nBu) 3. Likewise, the microscopic reverse reaction—conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6- iPr 2C 6H 3)} to the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}—is promoted when using the radical Mes*O • (Mes* = 2,4,6- tBu 3C 6H 2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni=N{2,6- iPr 2C 6H 3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C–N and N–N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}.« less

Pairing Increases Activation of V1aR, but not OTR, in Auditory Regions of Zebra Finches: The Importance of Signal Modality in Nonapeptide-Social Behavior Relationships.

PubMed

Tomaszycki, Michelle L; Atchley, Derek

2017-10-01

Social relationships are complex, involving the production and comprehension of signals, individual recognition, and close coordination of behavior between two or more individuals. The nonapeptides oxytocin and vasopressin are widely believed to regulate social relationships. These findings come largely from prairie voles, in which nonapeptide receptors in olfactory neural circuits drive pair bonding. This research is assumed to apply to all species. Previous reviews have offered two competing hypotheses. The work of Sarah Newman has implicated a common neural network across species, the Social Behavior Network. In contrast, others have suggested that there are signal modality-specific networks that regulate social behavior. Our research focuses on evaluating these two competing hypotheses in the zebra finch, a species that relies heavily on vocal/auditory signals for communication, specifically the neural circuits underlying singing in males and song perception in females. We have demonstrated that the quality of vocal interactions is highly important for the formation of long-term monogamous bonds in zebra finches. Qualitative evidence at first suggests that nonapeptide receptor distributions are very different between monogamous rodents (olfactory species) and monogamous birds (vocal/auditory species). However, we have demonstrated that social bonding behaviors are not only correlated with activation of nonapeptide receptors in vocal and auditory circuits, but also involve regions of the common Social Behavior Network. Here, we show increased Vasopressin 1a receptor, but not oxytocin receptor, activation in two auditory regions following formation of a pair bond. To our knowledge, this is the first study to suggest a role of nonapeptides in the auditory circuit in pair bonding. Thus, we highlight converging mechanisms of social relationships and also point to the importance of studying multiple species to understand mechanisms of behavior. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Carrier-envelope phase dependence of the directional fragmentation and hydrogen migration in toluene in few-cycle laser fields.

PubMed

Li, Hui; Kling, Nora G; Förg, Benjamin; Stierle, Johannes; Kessel, Alexander; Trushin, Sergei A; Kling, Matthias F; Kaziannis, Spyros

2016-07-01

The dissociative ionization of toluene initiated by a few-cycle laser pulse as a function of the carrier envelope phase (CEP) is investigated using single-shot velocity map imaging. Several ionic fragments, CH3 (+), H2 (+), and H3 (+), originating from multiply charged toluene ions present a CEP-dependent directional emission. The formation of H2 (+) and H3 (+) involves breaking C-H bonds and forming new bonds between the hydrogen atoms within the transient structure of the multiply charged precursor. We observe appreciable intensity-dependent CEP-offsets. The experimental data are interpreted with a mechanism that involves laser-induced coupling of vibrational states, which has been found to play a role in the CEP-control of molecular processes in hydrocarbon molecules, and appears to be of general importance for such complex molecules.

Metal-Free Oxidative C-C Bond Formation through C-H Bond Functionalization.

PubMed

Narayan, Rishikesh; Matcha, Kiran; Antonchick, Andrey P

2015-10-12

The formation of C-C bonds embodies the core of organic chemistry because of its fundamental application in generation of molecular diversity and complexity. C-C bond-forming reactions are well-known challenges. To achieve this goal through direct functionalization of C-H bonds in both of the coupling partners represents the state-of-the-art in organic synthesis. Oxidative C-C bond formation obviates the need for prefunctionalization of both substrates. This Minireview is dedicated to the field of C-C bond-forming reactions through direct C-H bond functionalization under completely metal-free oxidative conditions. Selected important developments in this area have been summarized with representative examples and discussions on their reaction mechanisms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanism of Oxidation of Ethane to Ethanol at Iron(IV)-Oxo Sites in Magnesium-Diluted Fe2(dobdc).

PubMed

Verma, Pragya; Vogiatzis, Konstantinos D; Planas, Nora; Borycz, Joshua; Xiao, Dianne J; Long, Jeffrey R; Gagliardi, Laura; Truhlar, Donald G

2015-05-06

The catalytic properties of the metal-organic framework Fe2(dobdc), containing open Fe(II) sites, include hydroxylation of phenol by pure Fe2(dobdc) and hydroxylation of ethane by its magnesium-diluted analogue, Fe0.1Mg1.9(dobdc). In earlier work, the latter reaction was proposed to occur through a redox mechanism involving the generation of an iron(IV)-oxo species, which is an intermediate that is also observed or postulated (depending on the case) in some heme and nonheme enzymes and their model complexes. In the present work, we present a detailed mechanism by which the catalytic material, Fe0.1Mg1.9(dobdc), activates the strong C-H bonds of ethane. Kohn-Sham density functional and multireference wave function calculations have been performed to characterize the electronic structure of key species. We show that the catalytic nonheme-Fe hydroxylation of the strong C-H bond of ethane proceeds by a quintet single-state σ-attack pathway after the formation of highly reactive iron-oxo intermediate. The mechanistic pathway involves three key transition states, with the highest activation barrier for the transfer of oxygen from N2O to the Fe(II) center. The uncatalyzed reaction, where nitrous oxide directly oxidizes ethane to ethanol is found to have an activation barrier of 280 kJ/mol, in contrast to 82 kJ/mol for the slowest step in the iron(IV)-oxo catalytic mechanism. The energetics of the C-H bond activation steps of ethane and methane are also compared. Dehydrogenation and dissociation pathways that can compete with the formation of ethanol were shown to involve higher barriers than the hydroxylation pathway.

From Ruthenium to Copper: A la carte Tools for the Synthesis of Molecules of Interest.

PubMed

Monnier, Florian; Taillefer, Marc

2016-01-01

Well-defined ruthenium complexes and simple copper-ligand systems proved to be powerful catalysts for the construction of complex molecules from simple and abundant organic sources. In this account, chosen examples of reactions involving C-C bond formation catalyzed by [Ru(η(5)-C(5)H(5))-(CH(3)CN)(3)][PF(6)] will be presented. A practical synthesis of the versatile catalyst [Ru(η(5)-C(5)H(5))-(CH(3)CN)(3)][PF(6)] is also described via a simple and easy-handled procedure discovered in Geneva ten years ago. The second part of this review is focused on methodologies catalyzed by an association of a copper salt and a simple ligand for the formation of C-N, C-O and C-C bonds developed in our group in Montpellier. A brief overview of applications in life sciences and materials will conclude this article.

Correlation of the protein structure and gelling properties in dried egg white products.

PubMed

Handa, A; Hayashi, K; Shidara, H; Kuroda, N

2001-08-01

The relationship between protein structure and aggregation, as well as heat-induced gelling properties, of seven dried egg white (DEW) products was investigated. Strong correlations were found between average molecular weight and hydrophobicity plus surface SH groups of DEW-soluble protein aggregate (SPA). This suggests that hydrophobic interactions and disulfide bond formation between protein molecules were involved in the aggregation. The average molecular weight of DEW products with alkaline pHs was relatively higher than those with neutral pHs and the same degree of protein unfolding, probably because of more disulfide bond formation between protein molecules. In addition, strong correlations were found between hydrophobicity, surface SH groups plus average molecular weight of DEW-SPA, and physical properties of the gels from DEW products. These data indicated that controlling the aggregation of DEW proteins in the dry state is crucial to controlling the gelling properties of DEW.

Dipentaerythritol penta-acrylate phosphate - an alternative phosphate ester monomer for bonding of methacrylates to zirconia

NASA Astrophysics Data System (ADS)

Chen, Ying; Tay, Franklin R.; Lu, Zhicen; Chen, Chen; Qian, Mengke; Zhang, Huaiqin; Tian, Fucong; Xie, Haifeng

2016-12-01

The present work examined the effects of dipentaerythritol penta-acrylate phosphate (PENTA) as an alternative phosphate ester monomer for bonding of methacrylate-based resins to yttria-stabilized tetragonal zirconia polycrystals (Y-TZP) and further investigated the potential bonding mechanism involved. Shear bond strength testing was performed to evaluate the efficacy of experimental PENTA-containing primers (5, 10, 15, 20 or 30 wt% PENTA in acetone) in improving resin-Y-TZP bond strength. Bonding without the use of a PENTA-containing served as the negative control, and a Methacryloyloxidecyl dihydrogenphosphate(MDP)-containing primer was used as the positive control. Inductively coupled plasma-mass spectrometry (ICP-MS), X-ray photoelectron spectroscopy (XPS) and Fourier-transform infrared spectroscopy (FTIR) were used to investigate the potential existence of chemical affinity between PENTA and Y-TZP. Shear bond strengths were significant higher in the 15 and 20 wt% PENTA groups. The ICP-MS, XPS and FTIR data indicated that the P content on the Y-TZP surface increased as the concentration of PENTA increased in the experimental primers, via the formation of Zr-O-P bond. Taken together, the results attest that PENTA improves resin bonding of Y-TZP through chemical reaction with Y-TZP. Increasing the concentration of PENTA augments its binding affinity but not its bonding efficacy with zirconia.

Preparation of water-soluble magnetic nanocrystals using aryl diazonium salt chemistry.

PubMed

Griffete, Nébéwia; Herbst, Frédéric; Pinson, Jean; Ammar, Souad; Mangeney, Claire

2011-02-16

A novel and facile methodology for the in situ surface functionalization of Fe(3)O(4) nanoparticles is proposed, based on the use of aryl diazonium salts chemistry. The grafting reaction involves the formation of diazoates in a basic medium. These species are unstable and dediazonize along a homolytic pathway to give aryl radicals which further react with the Fe(3)O(4) NPs during their formation and stop their growth. Advantages of the present approach rely not only on the simplicity, rapidity, and efficiency of the procedure but also on the formation of strong Fe(3)O(4)-aryl surface bonds, highly suitable for further applications.

Cooperative structural transitions in amyloid-like aggregation

NASA Astrophysics Data System (ADS)

Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

2017-04-01

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.

Chemisorbed monolayers of corannulene penta-thioethers on gold.

PubMed

Angelova, Polina; Solel, Ephrath; Parvari, Galit; Turchanin, Andrey; Botoshansky, Mark; Gölzhäuser, Armin; Keinan, Ehud

2013-02-19

Penta(tert-butylthio)corannulene and penta(4-dimethylaminophenylthio)corannulene form highly stable monolayers on gold surfaces, as indicated by X-ray photoelectron spectroscopy (XPS). Formation of these homogeneous monolayers involves multivalent coordination of the five sulfur atoms to gold with the peripheral alkyl or aryl substituents pointing away from the surface. No dissociation of C-S bonds upon binding could be observed at room temperature. Yet, the XPS experiments reveal strong chemical bonding between the thioether groups and gold. Temperature-dependent XPS study shows that the thermal stability of the monolayers is higher than the typical stability of self-assembled monolayers (SAMs) of thiolates on gold.

Detection of OH on photolysis of styrene oxide at 193 nm in gas phase

NASA Astrophysics Data System (ADS)

Kumar, Awadhesh; SenGupta, Sumana; Pushpa, K. K.; Naik, P. D.; Bajaj, P. N.

2006-10-01

Photodissociation of styrene oxide at 193 nm in gas phase generates OH, as detected by laser-induced fluorescence technique. Under similar conditions, OH was not observed from ethylene and propylene oxides, primarily because of their low absorption cross-sections at 193 nm. Mechanism of OH formation involves first opening of the three-membered ring from the ground electronic state via cleavage of either of two C sbnd O bonds, followed by isomerization to enolic forms of phenylacetaldehyde and acetophenone, and finally scission of the C sbnd OH bond of enols. Ab initio molecular orbital calculations support the proposed mechanism.

Regioselective Cu(I)-catalyzed tandem A3-coupling/decarboxylative coupling to 3-amino-1,4-enynes.

PubMed

Feng, Huangdi; Ermolat'ev, Denis S; Song, Gonghua; Van der Eycken, Erik V

2012-04-06

An efficient and novel copper-mediated protocol for the synthesis of 3-amino-1,4-enynes from glyoxylic acid, an amine, and an alkyne was developed. This new reaction involving two sequential C-C bond formations is air and moisture tolerant and proceeds via a tandem A(3)-coupling and a selective decarboxylative coupling.

The Surface Layer of a Crystal and Its Specific Role in the Process of Melt Formation

NASA Astrophysics Data System (ADS)

Sobolev, R. N.

2018-04-01

A crystal becomes melted in a few stages. The structure of the crystal surface differs from that of its interior. Therefore, as its interior is gradually involved in the melting process, the phase transition temperature becomes higher. The melting point becomes constant when all atoms have the same number of unsaturated bonds.

Infrared and Raman studies of hydrogen bonded complexes involving acetone, acetophenone and benzophenone—I. Thermodynamic constants and frequency shifts of the ν OH and ν CO stretching vibrations

NASA Astrophysics Data System (ADS)

Thijs, R.; Zeegers-Huyskens, Th.

The hydrogen bonded complexes between phenol derivatives and acetone ( I), acetophenone ( II) and benzophenone ( III) have been studied in carbon tetrachloride solution by i.r. spectroscopy. The formation constants, the enthalpies of complex formation, the Δν OH and Δν CO values have been determined. For a given phenol derivative, the thermodynamic constants and Δν OH are ordered according to I > II > III and the influence of a substituent implanted on the phenolic ring can be expressed by the Hammett relationship. The ϱ coefficients of the Hammett equation are related to the complexation enthalpies. The Badger—Bauer relation is valid for the three bases. The comparison with complexes involving other carbonyl bases allows to precise the influence of the substituent implanted on the carbonyl group. The Δν OH values obey the dual substituent parameter equation using σ I and σ +R; the ϱ I/ϱ R ratio is higher than one. The Δν CO values are shown to depend on the complexation enthalpy and on the delocalization effect of the substituents.

Interconnect mechanisms in microelectronic packaging

NASA Astrophysics Data System (ADS)

Roma, Maria Penafrancia C.

Global economic, environmental and market developments caused major impact in the microelectronics industry. Astronomical rise of gold metal prices over the last decade shifted the use of copper and silver alloys as bonding wires. Environmental legislation on the restriction of the use of Pb launched worldwide search for lead-free solders and platings. Finally, electrical and digital uses demanded smaller, faster and cheaper devices. Ultra-fine pitch bonding, decreasing bond wire sizes and hard to bond substrates have put the once-robust stitch bond in the center of reliability issues due to stitch bond lift or open wires .Unlike the ball bond, stitch bonding does not lead to intermetallic compound formation but adhesion is dependent on mechanical deformation, interdiffusion, solid solution formation, void formation and mechanical interlocking depending on the wire material, bond configuration, substrate type , thickness and surface condition. Using Au standoff stitch bonds on NiPdAu plated substrates eliminated stitch bond lift even when the Au and Pd layers are reduced. Using the Matano-Boltzmann analysis on a STEM (Scanning Transmission Analysis) concentration profile the interdiffusion coefficient is measured to be 10-16 cm 2/s. Wire pull strength data showed that the wire pull strength is 0.062N and increases upon stress testing. Meanwhile, coating the Cu wire with Pd, not only increases oxidation resistance but also improved adhesion due to the formation of a unique interfacial adhesion layers. Adhesion strength as measured by pull showed the Cu wire bonded to Ag plated Cu substrate (0.132N) to be stronger than the Au wire bonded on the same substrate (0.124N). Ag stitch bonded to Au is predicted to be strong but surface modification made the adhesion stronger. However, on the Ag ball bonded to Al showed multiple IMC formation with unique morphology exposed by ion milling and backscattered scanning electron microscopy. Adding alloying elements in the Ag wire alloy showed differences in adhesion strength and IMC formation. Bond strength by wire pull testing showed the 95Ag alloy with higher values while shear bond testing showed the 88Ag higher bond strength. Use of Cu pillars in flip chips and eutectic bonding in wafer level chip scale packages are direct consequences of diminishing interconnect dimension as a result of the drive for miniaturization. The combination of Cu-Sn interdiffusion, Kirkendall mechanism and heterogeneous vacancy precipitation are the main causes of IMC and void formation in Cu pillar - Sn solder - Cu lead frame sandwich structure. However, adding a Ni barrier agent showed less porous IMC layer as well as void formation as a result of the modified Cu and Sn movement well as the void formation. Direct die to die bonding using Al-Ge eutectic bonds is necessary when 3D integration is needed to reduce the footprint of a package. Hermeticity and adhesion strength are a function of the Al/Ge thickness ratio, bonding pressure, temperature and time. Scanning Electron Microscope (SEM) and Focused Ion Beam (FIB) allowed imaging of interfacial microstructures, porosity, grain morphology while Scanning Transmission Electron microscope (STEM) provided diffusion profile and confirmed interdiffusion. Ion polishing technique provided information on porosity and when imaged using backscattered mode, grain structure confirmed mechanical deformation of the bonds. Measurements of the interfacial bond strength are made by wire pull tests and ball shear tests based on existing industry standard tests. However, for the Al-Ge eutectic bonds, no standard strength is available so a test is developed using the stud pull test method using the Dage 4000 Plus to yield consistent results. Adhesion strengths of 30-40 MPa are found for eutectic bonded packages however, as low as 20MPa was measured in low temperature bonded areas.

The eighth fibronectin type III domain of protein tyrosine phosphatase receptor J influences the formation of protein complexes and cell localization.

PubMed

Iuliano, Rodolfo; Raso, Cinzia; Quintiero, Alfina; Pera, Ilaria Le; Pichiorri, Flavia; Palumbo, Tiziana; Palmieri, Dario; Pattarozzi, Alessandra; Florio, Tullio; Viglietto, Giuseppe; Trapasso, Francesco; Croce, Carlo Maria; Fusco, Alfredo

2009-03-01

Regulation of receptor-type phosphatases can involve the formation of higher-order structures, but the exact role played in this process by protein domains is not well understood. In this study we show the formation of different higher-order structures of the receptor-type phosphatase PTPRJ, detected in HEK293A cells transfected with different PTPRJ expression constructs. In the plasma membrane PTPRJ forms dimers detectable by treatment with the cross-linking reagent BS(3) (bis[sulfosuccinimidyl]suberate). However, other PTPRJ complexes, dependent on the formation of disulfide bonds, are detected by treatment with the oxidant agent H(2)O(2) or by a mutation Asp872Cys, located in the eighth fibronectin type III domain of PTPRJ. A deletion in the eighth fibronectin domain of PTPRJ impairs its dimerization in the plasma membrane and increases the formation of PTPRJ complexes dependent on disulfide bonds that remain trapped in the cytoplasm. The deletion mutant maintains the catalytic activity but is unable to carry out inhibition of proliferation on HeLa cells, achieved by the wild type form, since it does not reach the plasma membrane. Therefore, the intact structure of the eighth fibronectin domain of PTPRJ is critical for its localization in plasma membrane and biological function.

Dynamic corticostriatal activity biases social bonding in monogamous female prairie voles

PubMed Central

Amadei, Elizabeth A.; Johnson, Zachary V.; Kwon, Yong Jun; Shpiner, Aaron C.; Saravanan, Varun; Mays, Wittney D.; Ryan, Steven J.; Walum, Hasse; Rainnie, Donald G.; Young, Larry J.; Liu, Robert C.

2017-01-01

Summary paragraph Adult pair bonding involves dramatic changes in the perception and valuation of another individual1. One key change is that partners come to reliably activate the brain's reward system2-6, though the precise neural mechanisms by which partners become rewarding during sociosexual interactions leading to a bond remain unclear. Using a prairie vole model of social bonding7, we show how a functional circuit from medial prefrontal cortex (mPFC) to nucleus accumbens (NAcc) is dynamically modulated to enhance females' affiliative behavior towards a partner. Individual variation in the strength of this functional connectivity, particularly after the first mating encounter, predicts how quickly animals begin affiliative huddling with their partner. Rhythmically activating this circuit in a social context without mating biases later preference towards a partner, indicating that this circuit's activity is not just correlated with how quickly animals become affiliative but causally accelerates it. These results provide the first dynamic view of corticostriatal activity during bond formation, revealing how social interactions can recruit brain reward systems to drive changes in affiliative behavior. PMID:28562592

The role of hydrogen bonds in the crystals of 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate and 4-hydroxybenzenesulfonate - X-ray and spectroscopic studies.

PubMed

Bryndal, I; Marchewka, M; Wandas, M; Sąsiadek, W; Lorenc, J; Lis, T; Dymińska, L; Kucharska, E; Hanuza, J

2014-04-05

Two new organic-organic salts, 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate (AMNP-TFA), and 2-amino-4-methyl-5-nitropyridinium 4-hydroxybenzenesulfonate (AMNP-HBS), were obtained and characterized by means of FT-IR, FT-Raman and single crystal X-ray crystallography. In the former crystal, the cations, anions and water molecules are linked into layers by three types of hydrogen bonds, NPH⋯O, NAH⋯O and OH⋯O. These layers are connected by weaker CH⋯O hydrogen bonds. In the latter crystal, the cations and anions form one-dimensional structure through a number of hydrogen-bonding interactions involving the OH, NH(+) and NH2 groups as donors. In this case the NPH⋯O and NAH⋯O hydrogen bonds are formed. The combination of interactions between cations and anions results in the formation of columns. Additionally, there are π-π stacking interactions between the columns. The obtained X-ray structural data are related to the vibrational spectra of the studied crystals. Copyright © 2013 Elsevier B.V. All rights reserved.

Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.

PubMed

Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C; Nicolet, Yvain

2016-05-01

Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE

NASA Astrophysics Data System (ADS)

Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C.; Nicolet, Yvain

2016-05-01

Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5‧-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

Investigating intermolecular forces associated with thrombus initiation using optical tweezers

NASA Astrophysics Data System (ADS)

Arya, Maneesh; Lopez, Jose A.; Romo, Gabriel M.; Dong, Jing-Fei; McIntire, Larry V.; Moake, Joel L.; Anvari, Bahman

2002-05-01

Thrombus formation occurs when a platelet membrane receptor, glycoprotein (GP) Ib-IX-V complex, binds to its ligand, von Willebrand factor (vWf), in the subendothelium or plasma. To determine which GP Ib-IX-V amino acid sequences are critical for bond formation, we have used optical tweezers to measure forces involved in the binding of vWf to GP Ib-IX-V variants. Inasmuch as GP Ib(alpha) subunit is the primary component in human GP Ib-IX-V complex that binds to vWf, and that canine GP Ib(alpha) , on the other hand, does not bind to human vWf, we progressively replaced human GP Ib(alpha) amino acid sequences with canine GP Ib(alpha) sequences to determine the sequences essential for vWf/GP Ib(alpha) binding. After measuring the adhesive forces between optically trapped, vWf-coated beads and GP Ib(alpha) variants expressed on mammalian cells, we determined that leucine- rich repeat 2 of GP Ib(alpha) was necessary for vWf/GP Ib-IX- V bond formation. We also found that deletion of the N- terminal flanking sequence and leucine-rich repeat 1 reduced adhesion strength to vWf but did not abolish binding. While divalent cations are known to influence binding of vWf, addition of 1mM CaCl2 had no effect on measured vWf/GP Ib(alpha) bond strengths.

Crystal structure of cis-aqua­chlorido­bis­(1,10-phenanthroline-κ2 N,N′)chromium(III) tetra­chlorido­zincate monohydrate from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2015-01-01

The structure of the title compound, [CrCl(C12H8N2)2(H2O)][ZnCl4]·H2O, has been determined from synchrotron data. The CrIII ion is bonded to four N atoms from two 1,10-phenanthroline (phen) ligands, one water mol­ecule and a Cl atom in a cis arrangement, displaying an overall distorted octa­hedral coordination environment. The Cr—N(phen) bond lengths are in the range of 2.0495 (18) to 2.0831 (18) Å, while the Cr—Cl and Cr—(OH2) bond lengths are 2.2734 (7) and 1.9986 (17) Å, respectively. The tetra­hedral [ZnCl4]2− anion is slightly distorted owing to its involvement in O—H⋯Cl hydrogen bonding with coordinating and non-coordinating water mol­ecules. The two types of water mol­ecules also inter­act through O—H⋯O hydrogen bonds. The observed hydrogen-bonding pattern leads to the formation of a three-dimensional network structure. PMID:25844190

Carrier-envelope phase dependence of the directional fragmentation and hydrogen migration in toluene in few-cycle laser fields

PubMed Central

Li, Hui; Kling, Nora G.; Förg, Benjamin; Stierle, Johannes; Kessel, Alexander; Trushin, Sergei A.; Kling, Matthias F.; Kaziannis, Spyros

2016-01-01

The dissociative ionization of toluene initiated by a few-cycle laser pulse as a function of the carrier envelope phase (CEP) is investigated using single-shot velocity map imaging. Several ionic fragments, CH3+, H2+, and H3+, originating from multiply charged toluene ions present a CEP-dependent directional emission. The formation of H2+ and H3+ involves breaking C-H bonds and forming new bonds between the hydrogen atoms within the transient structure of the multiply charged precursor. We observe appreciable intensity-dependent CEP-offsets. The experimental data are interpreted with a mechanism that involves laser-induced coupling of vibrational states, which has been found to play a role in the CEP-control of molecular processes in hydrocarbon molecules, and appears to be of general importance for such complex molecules. PMID:26958589

Food Antioxidants: Chemical Insights at the Molecular Level.

PubMed

Galano, Annia; Mazzone, Gloria; Alvarez-Diduk, Ruslán; Marino, Tiziana; Alvarez-Idaboy, J Raúl; Russo, Nino

2016-01-01

In this review, we briefly summarize the reliability of the density functional theory (DFT)-based methods to accurately predict the main antioxidant properties and the reaction mechanisms involved in the free radical-scavenging reactions of chemical compounds present in food. The analyzed properties are the bond dissociation energies, in particular those involving OH bonds, electron transfer enthalpies, adiabatic ionization potentials, and proton affinities. The reaction mechanisms are hydrogen-atom transfer, proton-coupled electron transfer, radical adduct formation, single electron transfer, sequential electron proton transfer, proton-loss electron transfer, and proton-loss hydrogen-atom transfer. Furthermore, the chelating ability of these compounds and its role in decreasing or inhibiting the oxidative stress induced by Fe(III) and Cu(II) are considered. Comparisons between theoretical and experimental data confirm that modern theoretical tools are not only able to explain controversial experimental facts but also to predict chemical behavior.

Amyloid Hydrogen Bonding Polymorphism Evaluated by (15)N{(17)O}REAPDOR Solid-State NMR and Ultra-High Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

Wei, Juan; Antzutkin, Oleg N; Filippov, Andrei V; Iuga, Dinu; Lam, Pui Yiu; Barrow, Mark P; Dupree, Ray; Brown, Steven P; O'Connor, Peter B

2016-04-12

A combined approach, using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and solid-state NMR (Nuclear Magnetic Resonance), shows a high degree of polymorphism exhibited by Aβ species in forming hydrogen-bonded networks. Two Alzheimer's Aβ peptides, Ac-Aβ(16-22)-NH2 and Aβ(11-25), selectively labeled with (17)O and (15)N at specific amino acid residues were investigated. The total amount of peptides labeled with (17)O as measured by FTICR-MS enabled the interpretation of dephasing observed in (15)N{(17)O}REAPDOR solid-state NMR experiments. Specifically, about one-third of the Aβ peptides were found to be involved in the formation of a specific >C═(17)O···H-(15)N hydrogen bond with their neighbor peptide molecules, and we hypothesize that the rest of the molecules undergo ± n off-registry shifts in their hydrogen bonding networks.

6-[(Dimethyl­amino)methyl­ene­amino]-1,3-dimethyl­pyrimidine-2,4(1H,3H)-dione dihydrate

PubMed Central

Das, Subrata; Saikia, Binoy K.; Sridhar, B.; Thakur, Ashim J.

2008-01-01

Uracil, the pyrimidine nucleobase, which combined with adenine forms one of the major motifs present in the biopolymer RNA, is also involved in the self-assembly of RNA. In the title compound, C9H14N4O2·2H2O, the asymmetric unit contains one dimethyl­amino­uracil group and two water mol­ecules. The plane of the N=C—NMe2 side chain is inclined at 27.6 (5)° to the plane of the uracil ring. Both water mol­ecules form O—H⋯O hydrogen bonds with the carbonyl O atoms of the uracil group. Additional water–water hydrogen-bond inter­actions are also observed in the crystal structure. The O—H⋯O hydrogen bonds lead to the formation of a two-dimensional hydrogen-bonded network cage consisting of two dimethyl­amino­uracil groups and six water mol­ecules. PMID:21201655

Regioselectivity of enzymatic and photochemical single electron transfer promoted carbon-carbon bond fragmentation reactions of tetrameric lignin model compounds.

PubMed

Cho, Dae Won; Latham, John A; Park, Hea Jung; Yoon, Ung Chan; Langan, Paul; Dunaway-Mariano, Debra; Mariano, Patrick S

2011-04-15

New types of tetrameric lignin model compounds, which contain the common β-O-4 and β-1 structural subunits found in natural lignins, have been prepared and carbon-carbon bond fragmentation reactions of their cation radicals, formed by photochemical (9,10-dicyanoanthracene) and enzymatic (lignin peroxidase) SET-promoted methods, have been explored. The results show that cation radical intermediates generated from the tetrameric model compounds undergo highly regioselective C-C bond cleavage in their β-1 subunits. The outcomes of these processes suggest that, independent of positive charge and odd-electron distributions, cation radicals of lignins formed by SET to excited states of sensitizers or heme-iron centers in enzymes degrade selectively through bond cleavage reactions in β-1 vs β-O-4 moieties. In addition, the findings made in the enzymatic studies demonstrate that the sterically large tetrameric lignin model compounds undergo lignin peroxidase-catalyzed cleavage via a mechanism involving preliminary formation of an enzyme-substrate complex.

δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

PubMed Central

2015-01-01

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

Many Mg-Mg bonds form the core of the Mg16Cp*8Br4K cluster anion: the key to a reassessment of the Grignard reagent (GR) formation process?

PubMed

Kruczyński, T; Henke, F; Neumaier, M; Bowen, K H; Schnöckel, H

2016-02-01

It caused a sensation eight years ago, when the first room temperature stable molecular compound with a Mg-Mg bond (LMgMgL, L = chelating ligand) containing magnesium in the oxidation state +1 was prepared. Here, we report the preparation of a [Mg 16 Cp*8Br 4 K] - cluster anion (Cp* = pentamethylcyclopentadiene) with 27 Mg-Mg bonds. It has been obtained through the reaction of KCp* with a metastable solution of MgBr in toluene. A highly-resolved Fourier transform mass spectrum (FT-MS) of this cluster anion, brought into vacuum by electrospraying its solution in THF, provides the title cluster's stoichiometry. This Mg 16 cluster together with experiments on the metastable solution of MgBr show that: during the formation process of GRs (Grignard reagents) which are involved in most of sophisticated syntheses of organic products, not the highly reactive MgBr radical as often presumed, but instead the metalloid Mg 16 Cp*8Br 4 cluster anion and its related cousins that are the operative intermediates along the pathway from Mg metal to GRs ( e.g. Cp*MgBr).

Multicomponent hollow tubules formed using phytosterol and gamma-oryzanol-based compounds: an understanding of their molecular embrace.

PubMed

Rogers, Michael A; Bot, Arjen; Lam, Ricky Sze Ho; Pedersen, Tor; May, Tim

2010-08-19

The formation kinetics of self-assembling tubules composed of phytosterol:gamma-oryzanol mixtures were investigated at the Canadian Light Source on the mid-IR beamline using synchrotron radiation and Fourier transform infrared spectroscopy (FT-IR). The Avrami model was fitted to the changing hydrogen bonding density occurring at 3450 cm(-1). The nucleation process was found to be highly dependent on the molecular structure of the phytosterol. The nucleation event for cholesterol:gamma-oryzanol was determined to be sporadic whereas 5alpha-cholestan-3beta-ol:gamma-oryzanol and beta-sitosterol:gamma-oryzanol underwent instantaneous nucleation. One-dimensional growth occurred for each phytosterol:gamma-oryzanol mixture and involved the evolution of highly specific intermolecular hydrogen bonds. More detailed studies on the cholesterol:gamma-oryzanol system indicated that the nucleation activation energy, determined from multiple rate constants, obtained using the Avrami model, was at a minimum when the two compounds were at a 1:1 weight ratio. This resulted in drastic differences to the microscopic structures and affected the macroscopic properties such as turbidity. The formation of the phytosterol:gamma-oryzanol complex was due to intermolecular hydrogen bonding, which was in agreement with the infrared spectroscopic evidence.

Gold-catalyzed sequential annulations towards 3,4-fused bi/tri-cyclic furans involving a [3+2+2]-cycloaddition.

PubMed

Liu, Suna; Yang, Pu; Peng, Shiyong; Zhu, Chenghao; Cao, Shengyu; Li, Jian; Sun, Jiangtao

2017-01-17

A gold-catalyzed sequential annulation reaction to prepare 3,4-fused bicyclic furan compounds has been realized by employing 2-(1-alkynyl)-2-alken-1-ones and 1,3,5-triazines as the starting materials under mild reaction conditions. This protocol features multiple bond formation in a single operation with the incorporation of two nitrogen and two carbon atoms into the final products. A mechanistic investigation reveals that the sequential annulations involved an unprecedented stepwise [3+2+2]-cycloaddition.

Can Csbnd H⋯Fsbnd C hydrogen bonds alter crystal packing features in the presence of Nsbnd H⋯Odbnd C hydrogen bond?

NASA Astrophysics Data System (ADS)

Yadav, Hare Ram; Choudhury, Angshuman Roy

2017-12-01

Intermolecular interactions involving organic fluorine have been the contemporary field of research in the area of organic solid state chemistry. While a group of researchers had refuted the importance of "organic fluorine" in guiding crystal structures, others have provided evidences for in favor of fluorine mediated interactions in the solid state. Many systematic studies have indicated that the "organic fluorine" is capable of offering weak hydrogen bonds through various supramolecular synthons, mostly in the absence of other stronger hydrogen bonds. Analysis of fluorine mediated interaction in the presence of strong hydrogen bonds has not been highlighted in detail. Hence a thorough structural investigation is needed to understand the role of "organic fluorine" in crystal engineering of small organic fluorinated molecules having the possibility of strong hydrogen bond formation in the solution and in the solid state. To fulfil this aim, we have synthesized a series of fluorinated amides using 3-methoxyphenylacetic acid and fluorinated anilines and studied their structural properties through single crystal and powder X-ray diffraction methods. Our results indicated that the "organic fluorine" plays a significant role in altering the packing characteristics of the molecule in building specific crystal lattices even in the presence of strong hydrogen bond.

Theoretical Study of the Mechanism of Oxoiron(IV) Formation from H2O2 and a Nonheme Iron(II) Complex: O–O Cleavage Involving Proton-Coupled Electron Transfer

PubMed Central

Hirao, Hajime; Li, Feifei; Que, Lawrence; Morokuma, Keiji

2011-01-01

It has recently been shown that the nonheme oxoiron(IV) species supported by the 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane ligand (TMC) can be generated in near-quantitative yield by reacting [FeII(TMC)(OTf)2] with a stoichiometric amount of H2O2 in CH3CN in the presence of 2,6-lutidine (Li, F.; England, J.; Que L., Jr. J. Am. Chem. Soc. 2010, 132, 2134–2135). This finding has major implications for O–O bond cleavage events in both Fenton chemistry and nonheme iron enzymes. To understand the mechanism of this process, especially the intimate details of the O–O bond cleavage step, a series of density functional theory (DFT) calculations and analyses have been carried out. Two distinct reaction paths (A and B) were identified. Path A consists of two principal steps: (1) coordination of H2O2 to Fe(II) and (2) a combination of partial homolytic O–O bond cleavage and proton-coupled electron transfer (PCET). The latter combination renders the rate-limiting O–O cleavage effectively a heterolytic process. Path B proceeds via a simultaneous homolytic O–O bond cleavage of H2O2 and Fe–O bond formation. This is followed by H-abstraction from the resultant Fe(III)–OH species by an •OH radical. Calculations suggest that path B is plausible in the absence of base. However, once 2,6-lutidine is added to the reacting system, the reaction barrier is lowered and more importantly the mechanistic path switches to path A, where 2,6-lutidine plays an essential role as an acid-base catalyst in a manner similar to how the distal histidine or glutamate residue assists in Compound I formation in heme peroxidases. The reaction was found to proceed predominantly on the quintet spin state surface, and a transition to the triplet state, the experimentally known ground state for the TMC-oxoiron(IV) species, occurs in the last stage of the oxoiron(IV) formation process. PMID:21678930

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

PubMed

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape

PubMed Central

Manibog, Kristine; Sankar, Kannan; Kim, Sun-Ae; Zhang, Yunxiang; Jernigan, Robert L.; Sivasankar, Sanjeevi

2016-01-01

Classical cadherin cell–cell adhesion proteins are essential for the formation and maintenance of tissue structures; their primary function is to physically couple neighboring cells and withstand mechanical force. Cadherins from opposing cells bind in two distinct trans conformations: strand-swap dimers and X-dimers. As cadherins convert between these conformations, they form ideal bonds (i.e., adhesive interactions that are insensitive to force). However, the biophysical mechanism for ideal bond formation is unknown. Here, we integrate single-molecule force measurements with coarse-grained and atomistic simulations to resolve the mechanistic basis for cadherin ideal bond formation. Using simulations, we predict the energy landscape for cadherin adhesion, the transition pathways for interconversion between X-dimers and strand-swap dimers, and the cadherin structures that form ideal bonds. Based on these predictions, we engineer cadherin mutants that promote or inhibit ideal bond formation and measure their force-dependent kinetics using single-molecule force-clamp measurements with an atomic force microscope. Our data establish that cadherins adopt an intermediate conformation as they shuttle between X-dimers and strand-swap dimers; pulling on this conformation induces a torsional motion perpendicular to the pulling direction that unbinds the proteins and forms force-independent ideal bonds. Torsional motion is blocked when cadherins associate laterally in a cis orientation, suggesting that ideal bonds may play a role in mechanically regulating cadherin clustering on cell surfaces. PMID:27621473

Elucidating Protein Involvement in the Stabilization of the Biogenic Silver Nanoparticles

NASA Astrophysics Data System (ADS)

Ballottin, Daniela; Fulaz, Stephanie; Souza, Michele L.; Corio, Paola; Rodrigues, Alexandre G.; Souza, Ana O.; Gaspari, Priscyla M.; Gomes, Alexandre F.; Gozzo, Fábio; Tasic, Ljubica

2016-06-01

Silver nanoparticles (AgNPs) have been broadly used as antibacterial and antiviral agents. Further, interests for green AgNP synthesis have increased in recent years and several results for AgNP biological synthesis have been reported using bacteria, fungi and plant extracts. The understanding of the role and nature of fungal proteins, their interaction with AgNPs and the subsequent stabilization of nanosilver is yet to be deeply investigated. Therefore, in an attempt to better understand biogenic AgNP stabilization with the extracellular fungal proteins and to describe these supramolecular interactions between proteins and silver nanoparticles, AgNPs, produced extracellularly by Aspergillus tubingensis—isolated as an endophytic fungus from Rizophora mangle—were characterized in order to study their physical characteristics, identify the involved proteins, and shed light into the interactions among protein-NPs by several techniques. AgNPs of around 35 nm in diameter as measured by TEM and a positive zeta potential of +8.48 mV were obtained. These AgNPs exhibited a surface plasmon resonance (SPR) band at 440 nm, indicating the nanoparticles formation, and another band at 280 nm, attributed to the electronic excitations in tryptophan, tyrosine, and/or phenylalanine residues in fungal proteins. Fungal proteins were covalently bounded to the AgNPs, mainly through S-Ag bonds due to cysteine residues (HS-) and with few N-Ag bonds from H2N- groups, as verified by Raman spectroscopy. Observed supramolecular interactions also occur by electrostatic and other protein-protein interactions. Furthermore, proteins that remain free on AgNP surface may perform hydrogen bonds with other proteins or water increasing thus the capping layer around the AgNPs and consequently expanding the hydrodynamic diameter of the particles (~264 nm, measured by DLS). FTIR results enabled us to state that proteins adsorbed to the AgNPs did not suffer relevant secondary structure alteration upon their physical interaction with the AgNPs or when covalently bonded to them. Eight proteins in the AgNP dispersion were identified by mass spectrometry analyses. All these proteins are involved in metabolic pathways of the fungus and are important for carbon, phosphorous and nitrogen uptake, and for the fungal growth. Thereby, important proteins for fungi are also involved in the formation and stabilization of the biogenic AgNPs.

Pair bond formation leads to a sustained increase in global cerebral glucose metabolism in monogamous male titi monkeys (Callicebus cupreus).

PubMed

Maninger, Nicole; Hinde, Katie; Mendoza, Sally P; Mason, William A; Larke, Rebecca H; Ragen, Benjamin J; Jarcho, Michael R; Cherry, Simon R; Rowland, Douglas J; Ferrer, Emilio; Bales, Karen L

2017-04-21

Social bonds, especially attachment relationships, are crucial to our health and happiness. However, what we know about the neural substrates of these bonds is almost exclusively limited to rodent models and correlational experiments in humans. Here, we used socially monogamous non-human primates, titi monkeys (Callicebus cupreus) to experimentally examine changes in regional and global cerebral glucose metabolism (GCGM) during the formation and maintenance of pair bonds. Baseline positron emission tomography (PET) scans were taken of thirteen unpaired male titi monkeys. Seven males were then experimentally paired with females, scanned and compared, after one week, to six age-matched control males. Five of the six control males were then also paired and scanned after one week. Scans were repeated on all males after four months of pairing. PET scans were coregistered with structural magnetic resonance imaging (MRI), and region of interest (ROI) analysis was carried out. A primary finding was that paired males showed a significant increase in [ 18 F]-fluorodeoxyglucose (FDG) uptake in whole brain following one week of pairing, which is maintained out to four months. Dopaminergic, "motivational" areas and those involved in social behavior showed the greatest change in glucose uptake. In contrast, control areas changed only marginally more than GCGM. These findings confirm the large effects of social bonds on GCGM. They also suggest that more studies should examine how social manipulations affect whole-brain FDG uptake, as opposed to assuming that it does not change across condition. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

Electronic excited state paths of Stone-Wales rearrangement in pyrene: roles of conical intersections.

PubMed

Yamazaki, Kaoru; Niitsu, Naoyuki; Nakamura, Kosuke; Kanno, Manabu; Kono, Hirohiko

2012-11-26

We investigated the reaction paths of Stone-Wales rearrangement (SWR), i.e., π/2 rotation of two carbon atoms with respect to the midpoint of the bond, in graphene and carbon nanotube quantum chemically. Our particular attention is focused on the roles of electronic excitations and conical intersections (CIs) in the reaction mechanism. We used pyrene as a model system. The reaction paths were determined by constructing potential energy surfaces at the MS-CASPT2//SA-CASSCF level of theory. We found that there are no CIs involved in SWR when both of C-C bond cleavage and formation occur simultaneously (concerted mechanism). In contrast, for the reaction path with stepwise cleavage and formation of C-C bonds, C-C bond breaking and making processes proceed through two CIs. When SWR starts from the ground (S(0)) state, the concerted and stepwise paths have an equivalent reaction barrier ΔE(‡) (9.5-9.6 eV). For the reaction path starting from excited states, only the stepwise mechanism is energetically preferable. This path contains a nonadabatic transition between the S(1) and S(0) states via a CI associated with the first stage of C-C bond cleavage and has ΔE(‡) as large as in the S(0) paths. We confirmed that the main active molecular orbitals and electron configurations for the low-lying electronic states of larger nanocarbons are the same as those in pyrene. This result suggests the importance of the nonadiabatic transitions through CIs in the photochemical reactions in large nanocarbons.

Pair bond Formation Leads to a Sustained Increase in Global Cerebral Glucose Metabolism in Monogamous Male Titi Monkeys (Callicebus cupreus)

PubMed Central

Maninger, Nicole; Hinde, Katie; Mendoza, Sally P.; Mason, William A.; Larke, Rebecca H.; Ragen, Benjamin J; Jarcho, Michael R.; Cherry, Simon R.; Rowland, Douglas J.; Ferrer, Emilio; Bales, Karen L.

2017-01-01

Social bonds, especially attachment relationships, are crucial to our health and happiness. However, what we know about the neural substrates of these bonds is almost exclusively limited to rodent models and correlational experiments in humans. Here, we used socially monogamous non-human primates, titi monkeys (Callicebus cupreus) to experimentally examine changes in regional and global cerebral glucose metabolism during the formation and maintenance of pair bonds. Baseline positron emission tomography (PET) scans were taken of thirteen unpaired male titi monkeys. Seven males were then experimentally paired with females, scanned and compared, after one week, to six age-matched control males. Five of the six control males were then also paired and scanned after one week. Scans were repeated on all males after four months of pairing. PET scans were coregistered with structural magnetic resonance imaging (MRI), and region of interest (ROI) analysis was carried out. A primary finding was that paired males showed a significant increase in FDG uptake in whole brain following one week of pairing, which is maintained out to four months. Dopaminergic, “motivational” areas and those involved in social behavior showed the greatest change in glucose uptake. In contrast, control areas changed only marginally more than GCGM. These findings confirm the large effects of social bonds on global cerebral glucose metabolism. They also suggest that more studies should examine how social manipulations affect whole brain FDG uptake, as opposed to assuming that it does not change across condition. PMID:28242440

Conserved Cysteine Residues Provide a Protein-Protein Interaction Surface in Dual Oxidase (DUOX) Proteins*

PubMed Central

Meitzler, Jennifer L.; Hinde, Sara; Bánfi, Botond; Nauseef, William M.; Ortiz de Montellano, Paul R.

2013-01-01

Intramolecular disulfide bond formation is promoted in oxidizing extracellular and endoplasmic reticulum compartments and often contributes to protein stability and function. DUOX1 and DUOX2 are distinguished from other members of the NOX protein family by the presence of a unique extracellular N-terminal region. These peroxidase-like domains lack the conserved cysteines that confer structural stability to mammalian peroxidases. Sequence-based structure predictions suggest that the thiol groups present are solvent-exposed on a single protein surface and are too distant to support intramolecular disulfide bond formation. To investigate the role of these thiol residues, we introduced four individual cysteine to glycine mutations in the peroxidase-like domains of both human DUOXs and purified the recombinant proteins. The mutations caused little change in the stabilities of the monomeric proteins, supporting the hypothesis that the thiol residues are solvent-exposed and not involved in disulfide bonds that are critical for structural integrity. However, the ability of the isolated hDUOX1 peroxidase-like domain to dimerize was altered, suggesting a role for these cysteines in protein-protein interactions that could facilitate homodimerization of the peroxidase-like domain or, in the full-length protein, heterodimeric interactions with a maturation protein. When full-length hDUOX1 was expressed in HEK293 cells, the mutations resulted in decreased H2O2 production that correlated with a decreased amount of the enzyme localized to the membrane surface rather than with a loss of activity or with a failure to synthesize the mutant proteins. These results support a role for the cysteine residues in intermolecular disulfide bond formation with the DUOX maturation factor DUOXA1. PMID:23362256

Rhodium(i)-catalyzed asymmetric [4 + 2] cycloaddition reactions of 2-alkylenecyclobutanols with cyclic enones through C–C bond cleavage: efficient access to trans-bicyclic compounds† †Electronic supplementary information (ESI) available. CCDC 1575240. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04784c

PubMed Central

Zheng, Xinxin; Guo, Rui

2018-01-01

We report a rhodium-catalyzed asymmetric formal intermolecular [4 + 2] cycloaddition reaction of 2-alkylenecyclobutanols with α,β-unsaturated cyclic ketones leading to synthetically useful trans-bicyclic molecules. Three consecutive stereogenic centers are formed in a highly enantio- and diastereoselective manner. Stepwise C–C bond cleavage and annulation are likely involved in the reaction pathway. Here, iPr-Duphos is the viable chiral ligand that promotes excellent enantio-control. PMID:29675233

Ion Transport via Structural Relaxations in Polymerized Ionic Liquids

NASA Astrophysics Data System (ADS)

Ganesan, Venkat; Mogurampelly, Santosh

We study the mechanisms underlying ion transport in poly(1-butyl-3-vinylimidazolium-hexafluorophosphate) polymer electrolytes. We consider polymer electrolytes of varying polymerized ionic liquid to ionic liquid (polyIL:IL) ratios and use atomistic molecular dynamics (MD) simulations to probe the dynamical and structural characteristics of the electrolyte. Our results reveal that anion diffusion along polymer backbone occurs primarily viathe formation and breaking of ion-pairs involving threepolymerized cationic monomers of twodifferent polymer chains. Moreover, we observe that the ionic diffusivities exhibit a direct correlation with the structural relaxation times of the ion-pairs and hydrogen bonds (H-bonds). These results provide new insights into the mechanisms underlying ion transport in polymerized ionic liquid electrolytes.

Biophysical insights into the interaction of hen egg white lysozyme with therapeutic dye clofazimine: modulation of activity and SDS induced aggregation of model protein.

PubMed

Ajmal, Mohammad Rehan; Chaturvedi, Sumit Kumar; Zaidi, Nida; Alam, Parvez; Zaman, Masihuz; Siddiqi, Mohammad Khursheed; Nusrat, Saima; Jamal, Mohammad Sarwar; Mahmoud, Mohamed H; Badr, Gamal; Khan, Rizwan Hasan

2017-08-01

The present study details the binding process of clofazimine to hen egg white lysozyme (HEWL) using spectroscopy, dynamic light scattering, transmission electron microscopy (TEM), and molecular docking techniques. Clofazimine binds to the protein with binding constant (K b ) in the order of 1.57 × 10 4 at 298 K. Binding process is spontaneous and exothermic. Molecular docking results suggested the involvement of hydrogen bonding and hydrophobic interactions in the binding process. Bacterial cell lytic activity in the presence of clofazimine increased to more than 40% of the value obtained with HEWL only. Interaction of the drug with HEWL induced ordered secondary structure in the protein and molecular compaction. Clofazimine also effectively inhibited the sodium dodecyl sulfate (SDS) induced amyloid formation in HEWL and caused disaggregation of preformed fibrils, reinforcing the notion that there is involvement of hydrophobic interactions and hydrogen bonding in the binding process of clofazimine with HEWL and clofazimine destabilizes the mature fibrils. Further, TEM images confirmed that fibrillar species were absent in the samples where amyloid induction was performed in the presence of clofazimine. As clofazimine is a drug less explored for the inhibition of fibril formation of the proteins, this study reports the inhibition of SDS-induced amyloid formation of HEWL by clofazimine, which will help in the development of clofazimine-related molecules for the treatment of amyloidosis.

Identification of the formation of metal-vinylidene interfacial bonds of alkyne-capped platinum nanoparticles by isotopic labeling.

PubMed

Hu, Peiguang; Chen, Limei; Deming, Christopher P; Bonny, Lewis W; Lee, Hsiau-Wei; Chen, Shaowei

2016-10-07

Stable platinum nanoparticles were prepared by the self-assembly of 1-dodecyne and dodec-1-deuteroyne onto bare platinum colloid surfaces. The nanoparticles exhibited consistent core size and optical properties. FTIR and NMR measurements confirmed the formation of Pt-vinylidene (Pt[double bond, length as m-dash]C[double bond, length as m-dash]CH-) interfacial linkages rather than Pt-acetylide (Pt-C[triple bond, length as m-dash]C-) and platinum-hydride (Pt-H) bonds.

Formation of Gas-Phase Formate in Thermal Reactions of Carbon Dioxide with Diatomic Iron Hydride Anions.

PubMed

Jiang, Li-Xue; Zhao, Chongyang; Li, Xiao-Na; Chen, Hui; He, Sheng-Gui

2017-04-03

The hydrogenation of carbon dioxide involves the activation of the thermodynamically very stable molecule CO 2 and formation of a C-H bond. Herein, we report that HCO 2 - and CO can be formed in the thermal reaction of CO 2 with a diatomic metal hydride species, FeH - . The FeH - anions were produced by laser ablation, and the reaction with CO 2 was analyzed by mass spectrometry and quantum-chemical calculations. Gas-phase HCO 2 - was observed directly as a product, and its formation was predicted to proceed by facile hydride transfer. The mechanism of CO 2 hydrogenation in this gas-phase study parallels similar behavior of a condensed-phase iron catalyst. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cross-dehydrogenative coupling and oxidative-amination reactions of ethers and alcohols with aromatics and heteroaromatics

PubMed Central

Vuram, Prasanna K.

2017-01-01

Cross-dehydrogenative coupling (CDC) is a process in which, typically, a C–C bond is formed at the expense of two C–H bonds, either catalyzed by metals or other organic compounds, or via uncatalyzed processes. In this perspective, we present various modes of C–H bond-activation at sp3 centers adjacent to ether oxygen atoms, followed by C–C bond formation with aromatic systems as well as with heteroaromatic systems. C–N bond-formation with NH-containing heteroaromatics, leading to hemiaminal ethers, is also an event that can occur analogously to C–C bond formation, but at the expense of C–H and N–H bonds. A large variety of hemiaminal ether-forming reactions have recently appeared in the literature and this perspective also includes this complementary chemistry. In addition, the participation of C–H bonds in alcohols in such processes is also described. Facile access to a wide range of compounds can be attained through these processes, rendering such reactions useful for synthetic applications via Csp3 bond activations. PMID:28970941

Structure and Reaction Mechanism of Basil Eugenol Synthase

PubMed Central

Louie, Gordon V.; Baiga, Thomas J.; Bowman, Marianne E.; Koeduka, Takao; Taylor, John H.; Spassova, Snejina M.; Pichersky, Eran; Noel, Joseph P.

2007-01-01

Phenylpropenes, a large group of plant volatile compounds that serve in multiple roles in defense and pollinator attraction, contain a propenyl side chain. Eugenol synthase (EGS) catalyzes the reductive displacement of acetate from the propenyl side chain of the substrate coniferyl acetate to produce the allyl-phenylpropene eugenol. We report here the structure determination of EGS from basil (Ocimum basilicum) by protein x-ray crystallography. EGS is structurally related to the short-chain dehydrogenase/reductases (SDRs), and in particular, enzymes in the isoflavone-reductase-like subfamily. The structure of a ternary complex of EGS bound to the cofactor NADP(H) and a mixed competitive inhibitor EMDF ((7S,8S)-ethyl (7,8-methylene)-dihydroferulate) provides a detailed view of the binding interactions within the EGS active site and a starting point for mutagenic examination of the unusual reductive mechanism of EGS. The key interactions between EMDF and the EGS-holoenzyme include stacking of the phenyl ring of EMDF against the cofactor's nicotinamide ring and a water-mediated hydrogen-bonding interaction between the EMDF 4-hydroxy group and the side-chain amino moiety of a conserved lysine residue, Lys132. The C4 carbon of nicotinamide resides immediately adjacent to the site of hydride addition, the C7 carbon of cinnamyl acetate substrates. The inhibitor-bound EGS structure suggests a two-step reaction mechanism involving the formation of a quinone-methide prior to reduction. The formation of this intermediate is promoted by a hydrogen-bonding network that favors deprotonation of the substrate's 4-hydroxyl group and disfavors binding of the acetate moiety, akin to a push-pull catalytic mechanism. Notably, the catalytic involvement in EGS of the conserved Lys132 in preparing the phenolic substrate for quinone methide formation through the proton-relay network appears to be an adaptation of the analogous role in hydrogen bonding played by the equivalent lysine residue in other enzymes of the SDR family. PMID:17912370

4-alkyl-L-(Dehydro)proline biosynthesis in actinobacteria involves N-terminal nucleophile-hydrolase activity of γ-glutamyltranspeptidase homolog for C-C bond cleavage

NASA Astrophysics Data System (ADS)

Zhong, Guannan; Zhao, Qunfei; Zhang, Qinglin; Liu, Wen

2017-07-01

γ-Glutamyltranspeptidases (γ-GTs), ubiquitous in glutathione metabolism for γ-glutamyl transfer/hydrolysis, are N-terminal nucleophile (Ntn)-hydrolase fold proteins that share an autoproteolytic process for self-activation. γ-GT homologues are widely present in Gram-positive actinobacteria where their Ntn-hydrolase activities, however, are not involved in glutathione metabolism. Herein, we demonstrate that the formation of 4-Alkyl-L-(dehydro)proline (ALDP) residues, the non-proteinogenic α-amino acids that serve as vital components of many bioactive metabolites found in actinobacteria, involves unprecedented Ntn-hydrolase activity of γ-GT homologue for C-C bond cleavage. The related enzymes share a key Thr residue, which acts as an internal nucleophile for protein hydrolysis and then as a newly released N-terminal nucleophile for carboxylate side-chain processing likely through the generation of an oxalyl-Thr enzyme intermediate. These findings provide mechanistic insights into the biosynthesis of various ALDP residues/associated natural products, highlight the versatile functions of Ntn-hydrolase fold proteins, and particularly generate interest in thus far less-appreciated γ-GT homologues in actinobacteria.

Enzymatic and free radical formation of cis- and trans- epoxyeicosatrienoic acids in vitro and in vivo.

PubMed

Aliwarga, Theresa; Raccor, Brianne S; Lemaitre, Rozenn N; Sotoodehnia, Nona; Gharib, Sina A; Xu, Libin; Totah, Rheem A

2017-11-01

Epoxyeicosatrienoic acids (EETs) are metabolites of arachidonic acid (AA) oxidation that have important cardioprotective and signaling properties. AA is an ω-6 polyunsaturated fatty acid (PUFA) that is prone to autoxidation. Although hydroperoxides and isoprostanes are major autoxidation products of AA, EETs are also formed from the largely overlooked peroxyl radical addition mechanism. While autoxidation yields both cis- and trans-EETs, cytochrome P450 (CYP) epoxygenases have been shown to exclusively catalyze the formation of all regioisomer cis-EETs, on each of the double bonds. In plasma and red blood cell (RBC) membranes, cis- and trans-EETs have been observed, and both have multiple physiological functions. We developed a sensitive ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay that separates cis- and trans- isomers of EETs and applied it to determine the relative distribution of cis- vs. trans-EETs in reaction mixtures of AA subjected to free radical oxidation in benzene and liposomes in vitro. We also determined the in vivo distribution of EETs in several tissues, including human and mouse heart, and RBC membranes. We then measured EET levels in heart and RBC of young mice compared to old. Formation of EETs in free radical reactions of AA in benzene and in liposomes exhibited time- and AA concentration-dependent increase and trans-EET levels were higher than cis-EETs under both conditions. In contrast, cis-EET levels were overall higher in biological samples. In general, trans-EETs increased with mouse age more than cis-EETs. We propose a mechanism for the non-enzymatic formation of cis- and trans-EETs involving addition of the peroxyl radical to one of AA's double bonds followed by bond rotation and intramolecular homolytic substitution (S H i). Enzymatic formation of cis-EETs by cytochrome P450 most likely occurs via a one-step concerted mechanism that does not allow bond rotation. The ability to accurately measure circulating EETs resulting from autoxidation or enzymatic reactions in plasma and RBC membranes will allow for future studies investigating how these important signaling lipids correlate with heart disease outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

Nowa, a novel protein with minicollagen Cys-rich domains, is involved in nematocyst formation in Hydra.

PubMed

Engel, Ulrike; Ozbek, Suat; Streitwolf-Engel, Ruth; Petri, Barbara; Lottspeich, Friedrich; Holstein, Thomas W; Oezbek, Suat; Engel, Ruth

2002-10-15

The novel protein Nowa was identified in nematocysts, explosive organelles of Hydra, jellyfish, corals and other CNIDARIA: Biogenesis of these organelles is complex and involves assembly of proteins inside a post-Golgi vesicle to form a double-layered capsule with a long tubule. Nowa is the major component of the outer wall, which is formed very early in morphogenesis. The high molecular weight glycoprotein has a modular structure with an N-terminal sperm coating glycoprotein domain, a central C-type lectin-like domain, and an eightfold repeated cysteine-rich domain at the C-terminus. Interestingly, the cysteine-rich domains are homologous to the cysteine-rich domains of minicollagens. We have previously shown that the cysteines of these minicollagen cysteine-rich domains undergo an isomerization process from intra- to intermolecular disulfide bonds, which mediates the crosslinking of minicollagens to networks in the inner wall of the capsule. The minicollagen cysteine-rich domains present in both proteins provide a potential link between Nowa in the outer wall and minicollagens in the inner wall. We propose a model for nematocyst formation that integrates cytoskeleton rearrangements around the post-Golgi vesicle and protein assembly inside the vesicle to generate a complex structure that is stabilized by intermolecular disulfide bonds.

Splitting of the O–O bond at the heme-copper catalytic site of respiratory oxidases

PubMed Central

Poiana, Federica; von Ballmoos, Christoph; Gonska, Nathalie; Blomberg, Margareta R. A.; Ädelroth, Pia; Brzezinski, Peter

2017-01-01

Heme-copper oxidases catalyze the four-electron reduction of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier experimental studies have shown that the O–O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR; Fe4+=O2−, CuB2+–OH−). We show that with the Thermus thermophilus ba3 oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the PR ferryl (τ ≅110 μs), which indicates that O2 is reduced before the splitting of the O–O bond. Application of density functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe3+–O−–O−(H+)], which is formed before the PR ferryl. The rates of heme b oxidation and PR ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined experimental and theoretical data suggest a general mechanism for O2 reduction by heme-copper oxidases. PMID:28630929

Tuning the reactivity of Fe(V)(O) toward C-H bonds at room temperature: effect of water.

PubMed

Singh, Kundan K; Tiwari, Mrityunjay k; Ghosh, Munmun; Panda, Chakadola; Weitz, Andrew; Hendrich, Michael P; Dhar, Basab B; Vanka, Kumar; Sen Gupta, Sayam

2015-02-16

The presence of an Fe(V)(O) species has been postulated as the active intermediate for the oxidation of both C-H and C═C bonds in the Rieske dioxygenase family of enzymes. Understanding the reactivity of these high valent iron-oxo intermediates, especially in an aqueous medium, would provide a better understanding of these enzymatic reaction mechanisms. The formation of an Fe(V)(O) complex at room temperature in an aqueous CH3CN mixture that contains up to 90% water using NaOCl as the oxidant is reported here. The stability of Fe(V)(O) decreases with increasing water concentration. We show that the reactivity of Fe(V)(O) toward the oxidation of C-H bonds, such as those in toluene, can be tuned by varying the amount of water in the H2O/CH3CN mixture. Rate acceleration of up to 60 times is observed for the oxidation of toluene upon increasing the water concentration. The role of water in accelerating the rate of the reaction has been studied using kinetic measurements, isotope labeling experiments, and density functional theory (DFT) calculations. A kinetic isotope effect of ∼13 was observed for the oxidation of toluene and d8-toluene showing that C-H abstraction was involved in the rate-determining step. Activation parameters determined for toluene oxidation in H2O/CH3CN mixtures on the basis of Eyring plots for the rate constants show a gain in enthalpy with a concomitant loss in entropy. This points to the formation of a more-ordered transition state involving water molecules. To further understand the role of water, we performed a careful DFT study, concentrating mostly on the rate-determining hydrogen abstraction step. The DFT-optimized structure of the starting Fe(V)(O) and the transition state indicates that the rate enhancement is due to the transition state's favored stabilization over the reactant due to enhanced hydrogen bonding with water.

Rhodium-Catalyzed C-C Bond Formation via Heteroatom-Directed C-H Bond Activation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colby, Denise; Bergman, Robert; Ellman, Jonathan

2010-05-13

Once considered the 'holy grail' of organometallic chemistry, synthetically useful reactions employing C-H bond activation have increasingly been developed and applied to natural product and drug synthesis over the past decade. The ubiquity and relative low cost of hydrocarbons makes C-H bond functionalization an attractive alternative to classical C-C bond forming reactions such as cross-coupling, which require organohalides and organometallic reagents. In addition to providing an atom economical alternative to standard cross - coupling strategies, C-H bond functionalization also reduces the production of toxic by-products, thereby contributing to the growing field of reactions with decreased environmental impact. In the areamore » of C-C bond forming reactions that proceed via a C-H activation mechanism, rhodium catalysts stand out for their functional group tolerance and wide range of synthetic utility. Over the course of the last decade, many Rh-catalyzed methods for heteroatom-directed C-H bond functionalization have been reported and will be the focus of this review. Material appearing in the literature prior to 2001 has been reviewed previously and will only be introduced as background when necessary. The synthesis of complex molecules from relatively simple precursors has long been a goal for many organic chemists. The ability to selectively functionalize a molecule with minimal pre-activation can streamline syntheses and expand the opportunities to explore the utility of complex molecules in areas ranging from the pharmaceutical industry to materials science. Indeed, the issue of selectivity is paramount in the development of all C-H bond functionalization methods. Several groups have developed elegant approaches towards achieving selectivity in molecules that possess many sterically and electronically similar C-H bonds. Many of these approaches are discussed in detail in the accompanying articles in this special issue of Chemical Reviews. One approach that has seen widespread success involves the use of a proximal heteroatom that serves as a directing group for the selective functionalization of a specific C-H bond. In a survey of examples of heteroatom-directed Rh catalysis, two mechanistically distinct reaction pathways are revealed. In one case, the heteroatom acts as a chelator to bind the Rh catalyst, facilitating reactivity at a proximal site. In this case, the formation of a five-membered metallacycle provides a favorable driving force in inducing reactivity at the desired location. In the other case, the heteroatom initially coordinates the Rh catalyst and then acts to stabilize the formation of a metal-carbon bond at a proximal site. A true test of the utility of a synthetic method is in its application to the synthesis of natural products or complex molecules. Several groups have demonstrated the applicability of C-H bond functionalization reactions towards complex molecule synthesis. Target-oriented synthesis provides a platform to test the effectiveness of a method in unique chemical and steric environments. In this respect, Rh-catalyzed methods for C-H bond functionalization stand out, with several syntheses being described in the literature that utilize C-H bond functionalization in a key step. These syntheses are highlighted following the discussion of the method they employ.« less

H-Bond Self-Assembly: Folding versus Duplex Formation.

PubMed

Núñez-Villanueva, Diego; Iadevaia, Giulia; Stross, Alexander E; Jinks, Michael A; Swain, Jonathan A; Hunter, Christopher A

2017-05-17

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

The Strength of Hydrogen Bonds between Fluoro-Organics and Alcohols, a Theoretical Study.

PubMed

Rosenberg, Robert E

2018-05-10

Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. There are only a few published examples of the strengths of these bonds. This study provides a high level ab initio study of inter- and intramolecular hydrogen bonds between RF and R'OH, where R and R' are aryl, vinyl, alkyl, and cycloalkyl. Intermolecular binding energies average near 5 kcal/mol, while intramolecular binding energies average about 3 kcal/mol. Inclusion of zero-point energies and applying a counterpoise correction lessen the difference. In both series, modest increases in binding energies are seen with increased acidity of R'OH and increased electron donation of R in RF. In the intramolecular compounds, binding energy increases with the rigidity of the F-(C) n -OH ring. Inclusion of free energy corrections at 298 K results in exoergic binding energies for the intramolecular compounds and endoergic binding energies for the intermolecular compounds. Parameters such as bond lengths, vibrational frequencies, and atomic populations are consistent with formation of a hydrogen bond and with slightly stronger binding in the intermolecular cases over the intramolecular cases. However, these parameters correlated poorly with binding energies.

Improving strand pairing prediction through exploring folding cooperativity

PubMed Central

Jeong, Jieun; Berman, Piotr; Przytycka, Teresa M.

2008-01-01

The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. At the same time, finding the correct partners is very difficult due to long range interactions involved in strand pairing. Additionally, patterns of aminoacids observed in β-sheet formations are very general and therefore difficult to use for computational recognition of specific contacts between strands. In this work, we report a new strand pairing algorithm. To address above mentioned difficulties, our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming hydrogen bonds between other pairs of strand. We demonstrate that this approach provides an improvement over previously proposed algorithms. We also compare the performance of this method to that of a global optimization algorithm that poses the problem as integer linear programming optimization problem and solves it using ILOG CPLEX™ package. PMID:18989036

Oxytocin promotes social bonding in dogs.

PubMed

Romero, Teresa; Nagasawa, Miho; Mogi, Kazutaka; Hasegawa, Toshikazu; Kikusui, Takefumi

2014-06-24

Recent evidence suggests that enduring social bonds have fitness benefits. However, very little is known about the neural circuitry and neurochemistry underlying the formation and maintenance of stable social bonds outside reproductive contexts. Oxytocin (OT), a neuropeptide synthetized by the hypothalamus in mammals, regulates many complex forms of social behavior and cognition in both human and nonhuman animals. Animal research, however, has concentrated on monogamous mammals, and it remains unknown whether OT also modulates social bonds in nonreproductive contexts. In this study we provide behavioral evidence that exogenous OT promotes positive social behaviors in the domestic dog toward not only conspecifics but also human partners. Specifically, when sprayed with OT, dogs showed higher social orientation and affiliation toward their owners and higher affiliation and approach behaviors toward dog partners than when sprayed with placebo. Additionally, the exchange of socio-positive behaviors with dog partners triggered the release of endogenous OT, highlighting the involvement of OT in the development of social relationships in the domestic dog. These data provide new insight into the mechanisms that facilitate the maintenance of close social bonds beyond immediate reproductive interest or genetic ties and complement a growing body of evidence that identifies OT as one of the neurochemical foundations of sociality in mammalian species.

New insights into a hot environment for early life.

PubMed

Dai, Jianghong

2017-06-01

Investigating the physical-chemical setting of early life is a challenging task. In this contribution, the author attempted to introduce a provocative concept from cosmology - cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe - to the field. For this purpose, the author revisited a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB. In vivo, the formation process of the 1,6-anhydro bond of sugars on the peptidoglycan of prokaryotic cell wall is parallel to in vitro processes, suggesting that the 1,6-anhydro bond is an ideal CMB-like analogue that suggests a hot setting for early life. The CMB-like 1,6-anhydro bond is involved in the life cycle of viruses and the metabolism of eukaryotes, underlying this notion. From a novel perspective, the application of the concept of the CMB to microbial ecology may give new insights into a hot environment, such as hydrothermal vents, supporting early life and providing hypotheses to test in molecular palaeontology. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Ammonolysis of ketene as a potential source of acetamide in the troposphere: a quantum chemical investigation.

PubMed

Sarkar, Saptarshi; Mallick, Subhasish; Kumar, Pradeep; Bandyopadhyay, Biman

2018-05-16

Quantum chemical calculations at the CCSD(T)/CBS//MP2/aug-cc-pVTZ levels of theory have been carried out to investigate a potential new source of acetamide in Earth's atmosphere through the ammonolysis of the simplest ketene. It was found that the reaction can occur via the addition of ammonia at either the C[double bond, length as m-dash]C or C[double bond, length as m-dash]O bond of ketene. The potential energy surface as well as calculated rate coefficients indicate that under tropospheric conditions, ammonolysis would occur almost exclusively via ammonia addition at the C[double bond, length as m-dash]O bond with negligible contribution from addition at the C[double bond, length as m-dash]C bond. The reaction of ketene with water has also been investigated in order to compare between hydrolysis and ammonolysis, as the former is known to be responsible for the formation of acetic acid. The rate coefficient for the formation of acetamide was found to be ∼106 to 109 times higher than that for the formation of acetic acid from the same ketene source in the troposphere. By means of the relative rate of ammonolysis with respect to hydrolysis, it was shown that acetamide formation would dominate over acetic acid formation at various altitudes in the troposphere.

Assigning Peptide Disulfide Linkage Pattern Among Regio-Isomers via Methoxy Addition to Disulfide and Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Durand, Kirt L.; Tan, Lei; Stinson, Craig A.; Love-Nkansah, Chasity B.; Ma, Xiaoxiao; Xia, Yu

2017-06-01

Pinpointing disulfide linkage pattern is critical in the characterization of proteins and peptides consisting of multiple disulfide bonds. Herein, we report a method based on coupling online disulfide modification and tandem mass spectrometry (MS/MS) to distinguish peptide disulfide regio-isomers. Such a method relies on a new disulfide bond cleavage reaction in solution, involving methanol as a reactant and 254 nm ultraviolet (UV) irradiation. This reaction leads to selective cleavage of a disulfide bond and formation of sulfenic methyl ester (-SOCH3) at one cysteine residue and a thiol (-SH) at the other. Under low energy collision-induced dissociation (CID), cysteine sulfenic methyl ester motif produces a signature methanol loss (-32 Da), allowing its identification from other possible isomeric structures such as S-hydroxylmethyl (-SCH2OH) and methyl sulfoxide (-S(O)-CH3). Since disulfide bond can be selectively cleaved and modified upon methoxy addition, subsequent MS2 CID of the methoxy addition product provides enhanced sequence coverage as demonstrated by the analysis of bovine insulin. More importantly, this reaction does not induce disulfide scrambling, likely due to the fact that radical intermediates are not involved in the process. An approach based on methoxy addition followed by MS3 CID has been developed for assigning disulfide linkage patterns in peptide disulfide regio-isomers. This methodology was successfully applied to characterizing peptide systems having two disulfide bonds and three disulfide linkage isomers: side-by-side, overlapped, and looped-within-a-loop configurations. [Figure not available: see fulltext.

Hydrogen bonded binary molecular adducts derived from exobidentate N-donor ligand with dicarboxylic acids: Acid⋯imidazole hydrogen-bonding interactions in neutral and ionic heterosynthons

NASA Astrophysics Data System (ADS)

Kathalikkattil, Amal Cherian; Damodaran, Subin; Bisht, Kamal Kumar; Suresh, Eringathodi

2011-01-01

Four new binary molecular compounds between a flexible exobidentate N-heterocycle and a series of dicarboxylic acids have been synthesized. The N-donor 1,4-bis(imidazol-1-ylmethyl)benzene (bix) was reacted with flexible and rigid dicarboxylic acids viz., cyclohexane-1,4-dicarboxylic acid (H 2chdc), naphthalene-1,4-dicarboxylic acid (H 2npdc) and 1H-pyrazole-3,5-dicarboxylic acid (H 2pzdc), generating four binary molecular complexes. X-ray crystallographic investigation of the molecular adducts revealed the primary intermolecular interactions carboxylic acid⋯amine (via O-H⋯N) as well as carboxylate⋯protonated amine (via N-H +⋯O -) within the binary compounds, generating layered and two-dimensional sheet type H-bonded networks involving secondary weak interactions (C-H⋯O) including the solvent of crystallization. Depending on the differences in p Ka values of the selected base/acid (Δp Ka), diverse H-bonded supramolecular assemblies could be premeditated. This study demonstrates the H-bonding interactions between imidazole/imidazolium cation and carboxylic acid/carboxylate anion in providing sufficient driving force for the directed assembly of binary molecular complexes. In the two-component solid form of hetero synthons involving bix and dicarboxylic acid, only H 2chdc exist as cocrystal with bix, while all the other three compounds crystallized exclusively as salt, in agreement with the Δp Ka values predicted for the formation of salts/cocrystals from the base and acid used in the synthesis of supramolecular solids.

Preparation of phosphines through C–P bond formation

PubMed Central

Wauters, Iris; Debrouwer, Wouter

2014-01-01

Summary Phosphines are an important class of ligands in the field of metal-catalysis. This has spurred the development of new routes toward functionalized phosphines. Some of the most important C–P bond formation strategies were reviewed and organized according to the hybridization of carbon in the newly formed C–P bond. PMID:24991257

Protonation of a peroxodiiron(III) complex and conversion to a diiron(III/IV) intermediate: implications for proton-assisted O-O bond cleavage in nonheme diiron enzymes.

PubMed

Cranswick, Matthew A; Meier, Katlyn K; Shan, Xiaopeng; Stubna, Audria; Kaizer, Jószef; Mehn, Mark P; Münck, Eckard; Que, Lawrence

2012-10-01

Oxygenation of a diiron(II) complex, [Fe(II)(2)(μ-OH)(2)(BnBQA)(2)(NCMe)(2)](2+) [2, where BnBQA is N-benzyl-N,N-bis(2-quinolinylmethyl)amine], results in the formation of a metastable peroxodiferric intermediate, 3. The treatment of 3 with strong acid affords its conjugate acid, 4, in which the (μ-oxo)(μ-1,2-peroxo)diiron(III) core of 3 is protonated at the oxo bridge. The core structures of 3 and 4 are characterized in detail by UV-vis, Mössbauer, resonance Raman, and X-ray absorption spectroscopies. Complex 4 is shorter-lived than 3 and decays to generate in ~20% yield of a diiron(III/IV) species 5, which can be identified by electron paramagnetic resonance and Mössbauer spectroscopies. This reaction sequence demonstrates for the first time that protonation of the oxo bridge of a (μ-oxo)(μ-1,2-peroxo)diiron(III) complex leads to cleavage of the peroxo O-O bond and formation of a high-valent diiron complex, thereby mimicking the steps involved in the formation of intermediate X in the activation cycle of ribonucleotide reductase.

Active Thermochemical Tables: Sequential Bond Dissociation Enthalpies of Methane, Ethane, and Methanol and the Related Thermochemistry

DOE PAGES

Ruscic, Branko

2015-03-31

Active Thermochemical Tables (ATcT) thermochemistry for the sequential bond dissociations of methane, ethane, and methanol systems were obtained by analyzing and solving a very large thermochemical network (TN). Values for all possible C–H, C–C, C–O, and O–H bond dissociation enthalpies at 298.15 K (BDE 298) and bond dissociation energies at 0 K (D 0) are presented. The corresponding ATcT standard gas-phase enthalpies of formation of the resulting CH n, n = 4–0 species (methane, methyl, methylene, methylidyne, and carbon atom), C 2H n, n = 6–0 species (ethane, ethyl, ethylene, ethylidene, vinyl, ethylidyne, acetylene, vinylidene, ethynyl, and ethynylene), and COHmore » n, n = 4–0 species (methanol, hydroxymethyl, methoxy, formaldehyde, hydroxymethylene, formyl, isoformyl, and carbon monoxide) are also presented. The ATcT thermochemistry of carbon dioxide, water, hydroxyl, and carbon, oxygen, and hydrogen atoms is also included, together with the sequential BDEs of CO 2 and H 2O. The provenances of the ATcT enthalpies of formation, which are quite distributed and involve a large number of relevant determinations, are analyzed by variance decomposition and discussed in terms of principal contributions. The underlying reasons for periodic appearances of remarkably low and/or unusually high BDEs, alternating along the dissociation sequences, are analyzed and quantitatively rationalized. The present ATcT results are the most accurate thermochemical values currently available for these species.« less

A theoretical investigation into the strength of N-NO2 bonds, ring strain and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX.

PubMed

Wang, Bao-Guo; Ren, Fu-de; Shi, Wen-Jing

2015-11-01

Changes in N-NO2 bond strength, ring strain energy and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX were investigated using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. Analysis of electron density shifts was also carried out. The results indicate that H-bonding energy correlates well with the increment of ring strain energy. Upon complex formation, the strength of the N-NO2 trigger-bond is enhanced, suggesting reduced sensitivity, while judged by the increased ring strain energy, sensitivity is increased. However, some features of the molecular surface electrostatic potential, such as a local maximum above the N-NO2 bond and ring, σ + (2) and electrostatic balance parameter ν, remain essentially unchanged upon complex formation, and only a small change in the impact sensitivity h 50 is suggested. It is not sufficient to determine sensitivity solely on the basis of trigger bond or ring strain; as a global feature of a molecule, the molecular surface electrostatic potential is available to help judge the change of sensitivity in H-bonded complexes. Graphical Abstract The strengthened N-NO2 bond suggests reduced sensitivity, while it is reverse by theincreased ring strain energy upon the complex formation. However, the molecular surfaceelectrostatic potential (V S) shows the little change of h 50. The V S should be taken into accountin the analysis of explosive sensitivity in the H-bonded complex.

Mesoscopic Modeling of Blood Clotting: Coagulation Cascade and Platelets Adhesion

NASA Astrophysics Data System (ADS)

Yazdani, Alireza; Li, Zhen; Karniadakis, George

2015-11-01

The process of clot formation and growth at a site on a blood vessel wall involve a number of multi-scale simultaneous processes including: multiple chemical reactions in the coagulation cascade, species transport and flow. To model these processes we have incorporated advection-diffusion-reaction (ADR) of multiple species into an extended version of Dissipative Particle Dynamics (DPD) method which is considered as a coarse-grained Molecular Dynamics method. At the continuum level this is equivalent to the Navier-Stokes equation plus one advection-diffusion equation for each specie. The chemistry of clot formation is now understood to be determined by mechanisms involving reactions among many species in dilute solution, where reaction rate constants and species diffusion coefficients in plasma are known. The role of blood particulates, i.e. red cells and platelets, in the clotting process is studied by including them separately and together in the simulations. An agonist-induced platelet activation mechanism is presented, while platelets adhesive dynamics based on a stochastic bond formation/dissociation process is included in the model.

Resolving the molecular mechanism of cadherin catch bond formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manibog, Kristine; Li, Hui; Rakshit, Sabyasachi

2014-06-02

Classical cadherin Ca(2+)-dependent cell-cell adhesion proteins play key roles in embryogenesis and in maintaining tissue integrity. Cadherins mediate robust adhesion by binding in multiple conformations. One of these adhesive states, called an X-dimer, forms catch bonds that strengthen and become longer lived in the presence of mechanical force. Here we use single-molecule force-clamp spectroscopy with an atomic force microscope along with molecular dynamics and steered molecular dynamics simulations to resolve the molecular mechanisms underlying catch bond formation and the role of Ca(2+) ions in this process. Our data suggest that tensile force bends the cadherin extracellular region such that theymore » form long-lived, force-induced hydrogen bonds that lock X-dimers into tighter contact. When Ca(2+) concentration is decreased, fewer de novo hydrogen bonds are formed and catch bond formation is eliminated« less

Selective Formation of Ser-His Dipeptide via Phosphorus Activation

NASA Astrophysics Data System (ADS)

Shu, Wanyun; Yu, Yongfei; Chen, Su; Yan, Xia; Liu, Yan; Zhao, Yufen

2018-04-01

The Ser-His dipeptide is the shortest active peptide. This dipeptide not only hydrolyzes proteins and DNA but also catalyzes the formation of peptides and phosphodiester bonds. As a potential candidate for the prototype of modern hydrolase, Ser-His has attracted increasing attention. To explore if Ser-His could be obtained efficiently in the prebiotic condition, we investigated the reactions of N-DIPP-Ser with His or other amino acids in an aqueous system. We observed that N-DIPP-Ser incubated with His can form Ser-His more efficiently than with other amino acids. A synergistic effect involving the two side chains of Ser and His is presumed to be the critical factor for the selectivity of this specific peptide formation.

Oxidative acylation using thioacids

NASA Technical Reports Server (NTRS)

Liu, R.; Orgel, L. E.

1997-01-01

Several important prebiotic reactions, including the coupling of amino acids into polypeptides by the formation of amide linkages, involve acylation. Theae reactions present a challenge to the understanding of prebiotic synthesis. Condensation reactions relying on dehydrating agents are either inefficient in aqueous solution or require strongly acidic conditions and high temperatures. Activated amino acids such as thioester derivatives have therefore been suggested as likely substrates for prebiotic peptide synthesis. Here we propose a closely related route to amide bond formation involving oxidative acylation by thioacids. We find that phenylalanine, leucine and phenylphosphate are acylated efficiently in aqueous solution by thioacetic acid and an oxidizing agent. From a prebiotic point of view, oxidative acylation has the advantage of proceeding efficiently in solution and under mild conditions. We anticipate that oxidative acylation should prove to be a general method for activating carboxylic acids, including amino acids.

Effect of Dangling Bond Spins on the Dark Exciton Recombination and Spin Polarization in CdSe Colloidal Nanostructures

NASA Astrophysics Data System (ADS)

Rodina, A. V.; Golovatenko, A. A.; Shornikova, E. V.; Yakovlev, D. R.; Efros, Al. L.

2018-04-01

We present theoretical aspects of the exchange interaction between the ground optically-forbidden "dark" exciton state and surface dangling bonds in colloidal CdSe spherical nanocrystals and nanoplatelets. The influence of the dangling bond spins on the radiative recombination and spin splitting of the dark exciton is shown. Processes of optically-driven and external magnetic field-driven formation of the dangling bond magnetic polaron (DBMP) are considered. Thermodynamic and dynamic polarization mechanisms of the DBMP formation within these two processes and corresponding critical temperatures are compared. Experimental manifestations of the DBMP formation in CdSe nanocrystals and nanoplatelets are discussed.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation.

PubMed

Chernia, Zelig; Tsori, Yoav

2018-03-14

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

Involvement of DPP-IV catalytic residues in enzyme–saxagliptin complex formation

PubMed Central

Metzler, William J.; Yanchunas, Joseph; Weigelt, Carolyn; Kish, Kevin; Klei, Herbert E.; Xie, Dianlin; Zhang, Yaqun; Corbett, Martin; Tamura, James K.; He, Bin; Hamann, Lawrence G.; Kirby, Mark S.; Marcinkeviciene, Jovita

2008-01-01

The inhibition of DPP-IV by saxagliptin has been proposed to occur through formation of a covalent but reversible complex. To evaluate further the mechanism of inhibition, we determined the X-ray crystal structure of the DPP-IV:saxagliptin complex. This structure reveals covalent attachment between S630 and the inhibitor nitrile carbon (C–O distance <1.3 Å). To investigate whether this serine addition is assisted by the catalytic His-Asp dyad, we generated two mutants of DPP-IV, S630A and H740Q, and assayed them for ability to bind inhibitor. DPP-IVH740Q bound saxagliptin with an ∼1000-fold reduction in affinity relative to DPP-IVWT, while DPP-IVS630A showed no evidence for binding inhibitor. An analog of saxagliptin lacking the nitrile group showed unchanged binding properties to the both mutant proteins, highlighting the essential role S630 and H740 play in covalent bond formation between S630 and saxagliptin. Further supporting mechanism-based inhibition by saxagliptin, NMR spectra of enzyme–saxagliptin complexes revealed the presence of three downfield resonances with low fractionation factors characteristic of short and strong hydrogen bonds (SSHB). Comparison of the NMR spectra of various wild-type and mutant DPP-IV:ligand complexes enabled assignment of a resonance at ∼14 ppm to H740. Two additional DPP-IV mutants, Y547F and Y547Q, generated to probe potential stabilization of the enzyme–inhibitor complex by this residue, did not show any differences in inhibitor binding either by ITC or NMR. Together with the previously published enzymatic data, the structural and binding data presented here strongly support a histidine-assisted covalent bond formation between S630 hydroxyl oxygen and the nitrile group of saxagliptin. PMID:18227430

Involvement of DPP-IV Catalytic Residues in Enzyme-Saxagliptin Complex Formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metzler,W.; Yanchunas, J.; Weigelt, C.

The inhibition of DPP-IV by saxagliptin has been proposed to occur through formation of a covalent but reversible complex. To evaluate further the mechanism of inhibition, we determined the X-ray crystal structure of the DPP-IV:saxagliptin complex. This structure reveals covalent attachment between S630 and the inhibitor nitrile carbon (C-O distance <1.3 Angstroms). To investigate whether this serine addition is assisted by the catalytic His-Asp dyad, we generated two mutants of DPP-IV, S630A and H740Q, and assayed them for ability to bind inhibitor. DPP-IVH740Q bound saxagliptin with an {approx}1000-fold reduction in affinity relative to DPP-IVWT, while DPP-IVS630A showed no evidence formore » binding inhibitor. An analog of saxagliptin lacking the nitrile group showed unchanged binding properties to the both mutant proteins, highlighting the essential role S630 and H740 play in covalent bond formation between S630 and saxagliptin. Further supporting mechanism-based inhibition by saxagliptin, NMR spectra of enzyme-saxagliptin complexes revealed the presence of three downfield resonances with low fractionation factors characteristic of short and strong hydrogen bonds (SSHB). Comparison of the NMR spectra of various wild-type and mutant DPP-IV:ligand complexes enabled assignment of a resonance at {approx}14 ppm to H740. Two additional DPP-IV mutants, Y547F and Y547Q, generated to probe potential stabilization of the enzyme-inhibitor complex by this residue, did not show any differences in inhibitor binding either by ITC or NMR. Together with the previously published enzymatic data, the structural and binding data presented here strongly support a histidine-assisted covalent bond formation between S630 hydroxyl oxygen and the nitrile group of saxagliptin.« less

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation

NASA Astrophysics Data System (ADS)

Chernia, Zelig; Tsori, Yoav

2018-03-01

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

Effect of heparin bonding on catheter-induced fibrin formation and platelet activation.

PubMed

Nichols, A B; Owen, J; Grossman, B A; Marcella, J J; Fleisher, L N; Lee, M M

1984-11-01

Pathologic and experimental evidence indicates that platelet activation and fibrin formation contribute to the pathogenesis of angina pectoris, coronary vasospasm and myocardial infarction. Detection of localized intravascular platelet activation and fibrin formation in vivo by selective blood sampling requires catheters that do not induce coagulation ex vivo. We studied the effect of heparin bonding of catheter surfaces on activation of the coagulation system by cardiovascular catheters. Woven Dacron, polyvinylchloride, and polyurethane catheters were tested and compared with identical catheters with heparin-bonded surfaces in 47 patients undergoing percutaneous cardiac catheterization. Platelet activation was measured by radioimmunoassay of plasma platelet factor 4 (PF4), beta-thromboglobulin (BTG), and thromboxane B2 (TXB2) in blood samples withdrawn through catheters, and fibrin formation was assessed by determination of fibrinopeptide A (FPA) levels. In blood samples collected through conventional catheters, FPA, PF4, BTG, and TXB2 levels were markedly elevated; blood sampling through heparin-bonded catheters had no significant effect on FPA, PF4, BTG, or TXB2 levels. Scanning electron microscopy disclosed extensive platelet aggregates and fibrin strands adherent to the surface of conventional catheters but not to heparin-bonded catheter surfaces. This study demonstrates that (1) collection of blood samples through cardiovascular catheters causes artifactual elevation of FPA, PF4, BTG, and TXB2 levels, and (2) heparin-bonded catheter surfaces effectively prevent catheter-induced platelet alpha-granule release and fibrin formation on catheter surfaces. Heparin-bonded catheters will facilitate investigation of the role of intravascular coagulation in coronary artery disease by eliminating catheter-induced fibrin formation and platelet activation.

Structure-Activity Correlations with Compounds Related to Abscisic Acid 1

PubMed Central

Sondheimer, Ernest; Walton, Daniel C.

1970-01-01

Inhibition of cell expansion of excised embryonic axes of Phaseolus vulgaris was used to evaluate the growth-inhibiting activity of abscisic acid and related compounds. None of the 13 compounds tested was as active as abscisic acid. 4-Hydroxyisophorone, a substance representative of the abscisic acid ring system was essentially inactive; cis, trans-3-methylsorbic acid, a compound resembling the side chain of abscisic acid, had low activity; and cis, trans-β-ionylideneacetic acid was one-sixth as active. Loss of the ring double bond results in a drastic decrease in biological activity. Comparison of our results with those reported previously leads to the suggestion that the double bond of the cyclohexyl moiety may have an important function in determining the degree of activity of cis, trans-ionylideneacetic acids. Two modes of action are discussed. It seems possible that the ring double bond is involved in covalent bonding in binding of the abscisic acid analogue to macromolecules. This may require formation of an intermediate epoxide. It can also be argued that stereochemical differences between cyclohexane derivatives are important factors in determining the degree of biological activity. PMID:5423465

Clustering mechanism of oxocarboxylic acids involving hydration reaction: Implications for the atmospheric models

NASA Astrophysics Data System (ADS)

Liu, Ling; Kupiainen-Määttä, Oona; Zhang, Haijie; Li, Hao; Zhong, Jie; Kurtén, Theo; Vehkamäki, Hanna; Zhang, Shaowen; Zhang, Yunhong; Ge, Maofa; Zhang, Xiuhui; Li, Zesheng

2018-06-01

The formation of atmospheric aerosol particles from condensable gases is a dominant source of particulate matter in the boundary layer, but the mechanism is still ambiguous. During the clustering process, precursors with different reactivities can induce various chemical reactions in addition to the formation of hydrogen bonds. However, the clustering mechanism involving chemical reactions is rarely considered in most of the nucleation process models. Oxocarboxylic acids are common compositions of secondary organic aerosol, but the role of oxocarboxylic acids in secondary organic aerosol formation is still not fully understood. In this paper, glyoxylic acid, the simplest and the most abundant atmospheric oxocarboxylic acid, has been selected as a representative example of oxocarboxylic acids in order to study the clustering mechanism involving hydration reactions using density functional theory combined with the Atmospheric Clusters Dynamic Code. The hydration reaction of glyoxylic acid can occur either in the gas phase or during the clustering process. Under atmospheric conditions, the total conversion ratio of glyoxylic acid to its hydration reaction product (2,2-dihydroxyacetic acid) in both gas phase and clusters can be up to 85%, and the product can further participate in the clustering process. The differences in cluster structures and properties induced by the hydration reaction lead to significant differences in cluster formation rates and pathways at relatively low temperatures.

Chemoselective ligation

DOEpatents

Saxon, Eliana [Albany, CA; Bertozzi, Carolyn Ruth [Berkeley, CA

2011-12-13

The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Chemoselective ligation

DOEpatents

Saxon, Eliana; Bertozzi, Carolyn

2006-10-17

The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Chemoselective ligation

DOEpatents

Saxon, Eliana [Albany, CA; Bertozzi, Carolyn R [Berkeley, CA

2011-05-10

The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Chemoselective ligation

DOEpatents

Saxon, Eliana; Bertozzi, Carolyn Ruth

2010-11-23

The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Chemoselective ligation

DOEpatents

Saxon, Eliana [Albany, CA; Bertozzi, Carolyn R [Berkeley, CA

2011-04-12

The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Chemoselective ligation

DOEpatents

Saxon, Eliana; Bertozzi, Carolyn R.

2010-02-23

The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g. on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Chemoselective ligation

DOEpatents

Saxon, Eliana [Albany, CA; Bertozzi, Carolyn [Berkeley, CA

2003-05-27

The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Csbnd N bond formation in alicyclic and heterocyclic compounds by amine-modified nanoclay

NASA Astrophysics Data System (ADS)

Zarnegar, Zohre; Alizadeh, Roghayeh; Ahmadzadeh, Majid; Safari, Javad

2017-09-01

In the current protocol, amine functionalized montmorillonite K10 nanoclay (NH2-MMT) was applied to catalyze the formation of Csbnd N bonds in the synthesis of azines and 2-aminothiazoles at room temperature. In comparison with the current methods of Csbnd N bond formation, this approach displays specific advantages include atom economy, clean conversion, design for energy efficiency, the use of nontoxic and heterogeneous catalyst, higher purity and yields, safer solvent and reagents for this organic transformation.

Inactivation of neurotensin by rat brain synaptic membranes. Cleavage at the Pro10-Tyr11 bond by endopeptidase 24.11 (enkephalinase) and a peptidase different from proline-endopeptidase.

PubMed

Checler, F; Emson, P C; Vincent, J P; Kitabgi, P

1984-11-01

It was shown previously that the tridecapeptide neurotensin is inactivated by rat brain synaptic membranes and that one of the primary inactivating cleavages occurs at the Pro10-Try11 peptide bond, leading to the formation of NT1-10 and NT11-13. The present study was designed to investigate the possibility that this cleavage was catalyzed by proline endopeptidase and/or endopeptidase 24.11 (enkephalinase). Purified rat brain synaptic membranes were found to contain a N-benzyloxycarbonyl-Gly-Pro-4-methyl-coumarinyl-7-amide-hydrolyzin g activity that was markedly inhibited (93%) by the proline endopeptidase inhibitor N-benzyloxycarbonyl-Pro-Prolinal and partially blocked (25%) by an antiproline endopeptidase antiserum. In contrast, the cleavage of neurotensin at the Pro10-Tyr11 bond by synaptic membranes was not affected by N-benzyloxycarbonyl-Pro-Prolinal and the antiserum. When the conversion of NT1-10 to NT1-8 by angiotensin converting enzyme was blocked by captopril and when the processing of NT11-13 by aminopeptidase(s) was inhibited by bestatin, it was found that thiorphan, a potent endopeptidase 24.11 inhibitor, partially decreased the formation of NT1-10 and NT11-13 by synaptic membranes. (1) proline endopeptidase, although it is present in synaptic membranes, is not involved in the cleavage of neurotensin at the Pro10-Tyr11 bond; (2) endopeptidase 24.11 only partially contributes to this cleavage; (3) there exists in rat brain synaptic membranes a peptidase different from proline endopeptidase and endopeptidase 24.11 that is mainly responsible for inactivating neurotensin by cleaving at the Pro10-Tyr11 bond.

The Cremeomycin Biosynthetic Gene Cluster Encodes a Pathway for Diazo Formation.

PubMed

Waldman, Abraham J; Pechersky, Yakov; Wang, Peng; Wang, Jennifer X; Balskus, Emily P

2015-10-12

Diazo groups are found in a range of natural products that possess potent biological activities. Despite longstanding interest in these metabolites, diazo group biosynthesis is not well understood, in part because of difficulties in identifying specific genes linked to diazo formation. Here we describe the discovery of the gene cluster that produces the o-diazoquinone natural product cremeomycin and its heterologous expression in Streptomyces lividans. We used stable isotope feeding experiments and in vitro characterization of biosynthetic enzymes to decipher the order of events in this pathway and establish that diazo construction involves late-stage N-N bond formation. This work represents the first successful production of a diazo-containing metabolite in a heterologous host, experimentally linking a set of genes with diazo formation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Acyl silicates and acyl aluminates as activated intermediates in peptide formation on clays

NASA Technical Reports Server (NTRS)

White, D. H.; Kennedy, R. M.; Macklin, J.

1984-01-01

Glycine reacts with heating on dried clays and other minerals to give peptides in much better yield than in the absence of mineral. This reaction was proposed to occur by way of an activated intermediate such as an acyl silicate or acyl aluminate analogous to acyl phosphates involved in several biochemical reactions including peptide bond synthesis. The proposed mechanism has been confirmed by trapping the intermediate, as well as by direct spectroscopic observation of a related intermediate. The reaction of amino acids on periodically dried mineral surfaces represents a widespead, geologically realistic setting for prebiotic peptide formation via in situ activation.

Replacement of Ser108 in Plasmodium falciparum enolase results in weak Mg(II) binding: role of a parasite-specific pentapeptide insert in stabilizing the active conformation of the enzyme.

PubMed

Dutta, Sneha; Mukherjee, Debanjan; Jarori, Gotam K

2015-06-01

A distinct structural feature of Plasmodium falciparum enolase (Pfeno) is the presence of a five amino acid insert -104EWGWS108- that is not found in host enolases. Its conservation among apicomplexan enolases has raised the possibility of its involvement in some important physiological function(s). Deletion of this sequence is known to lower k(cat)/K(m), increase K(a) for Mg(II) and convert dimer into monomers (Vora HK, Shaik FR, Pal-Bhowmick I, Mout R & Jarori GK (2009) Arch Biochem Biophys 485, 128-138). These authors also raised the possibility of the formation of an H-bond between Ser108 and Leu49 that could stabilize the apo-Pfeno in an active closed conformation that has high affinity for Mg(II). Here, we examined the effect of replacement of Ser108 with Gly/Ala/Thr on enzyme activity, Mg(II) binding affinity, conformational states and oligomeric structure and compared it with native recombinant Pfeno. The results obtained support the view that Ser108 is likely to be involved in the formation of certain crucial H-bonds with Leu49. The presence of these interactions can stabilize apo-Pfeno in an active closed conformation similar to that of Mg(II) bound yeast enolase. As predicted, S108G/A-Pfeno variants (where Ser108-Leu49 H-bonds are likely to be disrupted) were found to exist in an open conformation and had low affinity for Mg(II). They also required Mg(II) induced conformational changes to acquire the active closed conformational state essential for catalysis. The possible physiological relevance of apo-Pfeno being in such an active state is discussed. © 2015 FEBS.

A local difference in Hedgehog signal transduction increases mechanical cell bond tension and biases cell intercalations along the Drosophila anteroposterior compartment boundary.

PubMed

Rudolf, Katrin; Umetsu, Daiki; Aliee, Maryam; Sui, Liyuan; Jülicher, Frank; Dahmann, Christian

2015-11-15

Tissue organization requires the interplay between biochemical signaling and cellular force generation. The formation of straight boundaries separating cells with different fates into compartments is important for growth and patterning during tissue development. In the developing Drosophila wing disc, maintenance of the straight anteroposterior (AP) compartment boundary involves a local increase in mechanical tension at cell bonds along the boundary. The biochemical signals that regulate mechanical tension along the AP boundary, however, remain unknown. Here, we show that a local difference in Hedgehog signal transduction activity between anterior and posterior cells is necessary and sufficient to increase mechanical tension along the AP boundary. This difference in Hedgehog signal transduction is also required to bias cell rearrangements during cell intercalations to keep the characteristic straight shape of the AP boundary. Moreover, severing cell bonds along the AP boundary does not reduce tension at neighboring bonds, implying that active mechanical tension is upregulated, cell bond by cell bond. Finally, differences in the expression of the homeodomain-containing protein Engrailed also contribute to the straight shape of the AP boundary, independently of Hedgehog signal transduction and without modulating cell bond tension. Our data reveal a novel link between local differences in Hedgehog signal transduction and a local increase in active mechanical tension of cell bonds that biases junctional rearrangements. The large-scale shape of the AP boundary thus emerges from biochemical signals inducing patterns of active tension on cell bonds. © 2015. Published by The Company of Biologists Ltd.

Disulfide Bond Formation and ToxR Activity in Vibrio cholerae

PubMed Central

Fengler, Vera H. I.; Boritsch, Eva C.; Tutz, Sarah; Seper, Andrea; Ebner, Hanna; Roier, Sandro; Schild, Stefan; Reidl, Joachim

2012-01-01

Virulence factor production in Vibrio cholerae is complex, with ToxRS being an important part of the regulatory cascade. Additionally, ToxR is the transcriptional regulator for the genes encoding the major outer membrane porins OmpU and OmpT. ToxR is a transmembrane protein and contains two cysteine residues in the periplasmic domain. This study addresses the influence of the thiol-disulfide oxidoreductase system DsbAB, ToxR cysteine residues and ToxR/ToxS interaction on ToxR activity. The results show that porin production correlates with ToxR intrachain disulfide bond formation, which depends on DsbAB. In contrast, formation of ToxR intrachain or interchain disulfide bonds is dispensable for virulence factor production and in vivo colonization. This study further reveals that in the absence of ToxS, ToxR interchain disulfide bond formation is facilitated, whereat cysteinyl dependent homo- and oligomerization of ToxR is suppressed if ToxS is coexpressed. In summary, new insights into gene regulation by ToxR are presented, demonstrating a mechanism by which ToxR activity is linked to a DsbAB dependent intrachain disulfide bond formation. PMID:23144706

Critical Hydrogen Bond Formation for Activation of the Angiotensin II Type 1 Receptor*

PubMed Central

Cabana, Jérôme; Holleran, Brian; Beaulieu, Marie-Ève; Leduc, Richard; Escher, Emanuel; Guillemette, Gaétan; Lavigne, Pierre

2013-01-01

G protein-coupled receptors contain selectively important residues that play central roles in the conformational changes that occur during receptor activation. Asparagine 111 (N1113.35) is such a residue within the angiotensin II type 1 (AT1) receptor. Substitution of N1113.35 for glycine leads to a constitutively active receptor, whereas substitution for tryptophan leads to an inactivable receptor. Here, we analyzed the AT1 receptor and two mutants (N111G and N111W) by molecular dynamics simulations, which revealed a novel molecular switch involving the strictly conserved residue D742.50. Indeed, D742.50 forms a stable hydrogen bond (H-bond) with the residue in position 1113.35 in the wild-type and the inactivable receptor. However, in the constitutively active mutant N111G-AT1 receptor, residue D74 is reoriented to form a new H-bond with another strictly conserved residue, N461.50. When expressed in HEK293 cells, the mutant N46G-AT1 receptor was poorly activable, although it retained a high binding affinity. Interestingly, the mutant N46G/N111G-AT1 receptor was also inactivable. Molecular dynamics simulations also revealed the presence of a cluster of hydrophobic residues from transmembrane domains 2, 3, and 7 that appears to stabilize the inactive form of the receptor. Whereas this hydrophobic cluster and the H-bond between D742.50 and W1113.35 are more stable in the inactivable N111W-AT1 receptor, the mutant N111W/F77A-AT1 receptor, designed to weaken the hydrophobic core, showed significant agonist-induced signaling. These results support the potential for the formation of an H-bond between residues D742.50 and N461.50 in the activation of the AT1 receptor. PMID:23223579

Protein-protein interactions during high-moisture extrusion for fibrous meat analogues and comparison of protein solubility methods using different solvent systems.

PubMed

Liu, KeShun; Hsieh, Fu-Hung

2008-04-23

Soy protein, mixed with gluten and starch, was extruded into fibrous meat analogues under high-moisture and high-temperature conditions. The protein solubility of samples collected at different extruder zones and extrudates made with different moistures was determined by 11 extraction solutions consisting of 6 selective reagents and their combinations: phosphate salts, urea, DTT, thiourea, Triton X-100, and CHAPS. Protein solubility by most extractants showed decreasing patterns as the material passed through the extruder, but the solution containing all 6 reagents, known as isoelectric focus (IEF) buffer, solubilized the highest levels and equal amounts of proteins in all samples, indicating that there are no other covalent bonds involved besides disulfide bonds. With regard to relative importance between disulfide bonds and non-covalent interactions, different conclusions could be made from protein solubility patterns, depending on the type of extracting systems and a baseline used for comparison. The observation points out pitfalls and limitation of current protein solubility methodology and explains why controversy exists in the literature. Using the IEF buffer system with omission of one or more selective reagents is considered to be the right methodology to conduct protein solubility study and thus recommended. Results obtained with this system indicate that disulfide bonding plays a more important role than non-covalent bonds in not only holding the rigid structure of extrudates but also forming fibrous texture. The sharpest decrease in protein solubility occurred when the mix passed through the intermediate section of the extruder barrel, indicating formation of new disulfide bonds during the stage of dramatic increase in both temperature and moisture. After this stage, although the physical form of the product might undergo change and fiber formation might occur as it passed through the cooling die, the chemical nature of the product did not change significantly.

Aggregation of nitroaniline in tetrahydrofuran through intriguing H-bond formation by sodium borohydride.

PubMed

Ganguly, Mainak; Mondal, Chanchal; Pal, Anjali; Pratik, Saied Md; Pal, Jaya; Pal, Tarasankar

2014-07-07

The participation of sodium borohydride (NaBH4) in hydrogen bonding interactions and transient anion radical formation has been proved. Thus, the properties of NaBH4 are extended beyond the purview of its normal reducing capability and nucleophilic property. It is reported that ortho- and para-nitroanilines (NAs) form stable aggregates only in tetrahydrofuran (THF) in the presence of NaBH4 and unprecedented orange/red colorations are observed. The same recipe with nitrobenzene instead of nitroanilines (NAs) in the presence of NaBH4 evolves a transient rose red solution due to the formation of a highly fluorescent anion radical. Spectroscopic studies (UV-vis, fluorescence, RLS, Raman, NMR etc.) as well as theoretical calculations supplement the J-aggregate formation of NAs due to extensive hydrogen bonding. This is the first report where BH4(-) in THF has been shown to support such an aggregation process through H-bonding. It is further confirmed that stable intermolecular hydrogen bond-induced aggregation requires a geometrical match in both the nitro- and amino-functionalities attached to the phenyl ring with proper geometry. On the contrary, meta-nitroaniline remains as the odd man out and does not take part in such aggregation. Surprisingly, Au nanoparticles dismantle the J-aggregates of NA in THF. Explicit hydrogen bond formation in NA has been confirmed experimentally considering its promising applications in different fields including non-linear optics.

Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry.

PubMed

Baum, Bernhard; Muley, Laveena; Smolinski, Michael; Heine, Andreas; Hangauer, David; Klebe, Gerhard

2010-04-09

Additivity of functional group contributions to protein-ligand binding is a very popular concept in medicinal chemistry as the basis of rational design and optimized lead structures. Most of the currently applied scoring functions for docking build on such additivity models. Even though the limitation of this concept is well known, case studies examining in detail why additivity fails at the molecular level are still very scarce. The present study shows, by use of crystal structure analysis and isothermal titration calorimetry for a congeneric series of thrombin inhibitors, that extensive cooperative effects between hydrophobic contacts and hydrogen bond formation are intimately coupled via dynamic properties of the formed complexes. The formation of optimal lipophilic contacts with the surface of the thrombin S3 pocket and the full desolvation of this pocket can conflict with the formation of an optimal hydrogen bond between ligand and protein. The mutual contributions of the competing interactions depend on the size of the ligand hydrophobic substituent and influence the residual mobility of ligand portions at the binding site. Analysis of the individual crystal structures and factorizing the free energy into enthalpy and entropy demonstrates that binding affinity of the ligands results from a mixture of enthalpic contributions from hydrogen bonding and hydrophobic contacts, and entropic considerations involving an increasing loss of residual mobility of the bound ligands. This complex picture of mutually competing and partially compensating enthalpic and entropic effects determines the non-additivity of free energy contributions to ligand binding at the molecular level. (c) 2010 Elsevier Ltd. All rights reserved.

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach

NASA Astrophysics Data System (ADS)

Suresh, D. M.; Amalanathan, M.; Sebastian, S.; Sajan, D.; Hubert Joe, I.; Bena Jothy, V.; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.

Carbopalladation of nitriles: synthesis of 3,4-disubstituted 2-aminonaphthalenes and 1,3-benzoxazine derivatives by the palladium-catalyzed annulation of alkynes by (2-Iodophenyl)acetonitrile.

PubMed

Tian, Qingping; Pletnev, Alexandre A; Larock, Richard C

2003-01-24

Intramolecular carbopalladation of the cyano group has been employed for the synthesis of 3,4-disubstituted 2-aminonaphthalenes. (2-Iodophenyl)acetonitrile reacts with a variety of internal alkynes to afford 2-aminonaphthalenes in high yields with good regioselectivity. The scope and limitations of this process, which proceeds by the intramolecular addition of a vinylpalladium species to the triple bond of the cyano group, have been studied. The annulation of certain hindered propargylic alcohols affords 1,3-benzoxazine derivatives, rather than the expected 2-aminonaphthalenes. The involvement of trialkylamine bases in the formation of these heterocyclic compounds has been established. A proposed mechanism for the synthesis of 1,3-benzoxazine derivatives involves the formation of the expected 2-amino-3-(1-hydroxyalkyl)naphthalenes, followed by their condensation with an iminium ion species formed from the trialkylamine base used in the reaction.

Dioxygen Activation and O–O Bond Formation Reactions by Manganese Corroles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Mian; Lee, Yong-Min; Gupta, Ranjana

Activation of dioxygen (O 2) in enzymatic and biomimetic reactions has been intensively investigated over the past several decades. More recently, O–O bond formation, which is the reverse of the O 2-activation reaction, has been the focus of current research. Herein, we report the O 2-activation and O–O bond formation reactions by manganese corrole complexes. In the O 2-activation reaction, Mn(V)-oxo and Mn(IV)-peroxo intermediates were formed when Mn(III) corroles were exposed to O 2 in the presence of base (e.g., OH –) and hydrogen atom (H atom) donor (e.g., THF or cyclic olefins); the O 2-activation reaction did not occurmore » in the absence of base and H atom donor. Moreover, formation of the Mn(V)-oxo and Mn(IV)-peroxo species was dependent on the amounts of base present in the reaction solution. The role of the base was proposed to lower the oxidation potential of the Mn(III) corroles, thereby facilitating the binding of O 2 and forming a Mn(IV)-superoxo species. The putative Mn(IV)-superoxo species was then converted to the corresponding Mn(IV)-hydroperoxo species by abstracting a H atom from H atom donor, followed by the O–O bond cleavage of the putative Mn(IV)-hydroperoxo species to form a Mn(V)-oxo species. We have also shown that addition of hydroxide ion to the Mn(V)-oxo species afforded the Mn(IV)-peroxo species via O–O bond formation and the resulting Mn(IV)-peroxo species reverted to the Mn(V)-oxo species upon addition of proton, indicating that the O–O bond formation and cleavage reactions between the Mn(V)-oxo and Mn(IV)-peroxo complexes are reversible. The present paper reports the first example of using the same manganese complex in both O 2-activation and O–O bond formation reactions.« less

Dioxygen Activation and O–O Bond Formation Reactions by Manganese Corroles

DOE PAGES

Guo, Mian; Lee, Yong-Min; Gupta, Ranjana; ...

2017-10-22

Activation of dioxygen (O 2) in enzymatic and biomimetic reactions has been intensively investigated over the past several decades. More recently, O–O bond formation, which is the reverse of the O 2-activation reaction, has been the focus of current research. Herein, we report the O 2-activation and O–O bond formation reactions by manganese corrole complexes. In the O 2-activation reaction, Mn(V)-oxo and Mn(IV)-peroxo intermediates were formed when Mn(III) corroles were exposed to O 2 in the presence of base (e.g., OH –) and hydrogen atom (H atom) donor (e.g., THF or cyclic olefins); the O 2-activation reaction did not occurmore » in the absence of base and H atom donor. Moreover, formation of the Mn(V)-oxo and Mn(IV)-peroxo species was dependent on the amounts of base present in the reaction solution. The role of the base was proposed to lower the oxidation potential of the Mn(III) corroles, thereby facilitating the binding of O 2 and forming a Mn(IV)-superoxo species. The putative Mn(IV)-superoxo species was then converted to the corresponding Mn(IV)-hydroperoxo species by abstracting a H atom from H atom donor, followed by the O–O bond cleavage of the putative Mn(IV)-hydroperoxo species to form a Mn(V)-oxo species. We have also shown that addition of hydroxide ion to the Mn(V)-oxo species afforded the Mn(IV)-peroxo species via O–O bond formation and the resulting Mn(IV)-peroxo species reverted to the Mn(V)-oxo species upon addition of proton, indicating that the O–O bond formation and cleavage reactions between the Mn(V)-oxo and Mn(IV)-peroxo complexes are reversible. The present paper reports the first example of using the same manganese complex in both O 2-activation and O–O bond formation reactions.« less

A DFT study of ethanol adsorption and decomposition on α-Al2O3(0 0 0 1) surface

NASA Astrophysics Data System (ADS)

Chiang, Hsin-Ni; Nachimuthu, Santhanamoorthi; Cheng, Ya-Chin; Damayanti, Nur Pradani; Jiang, Jyh-Chiang

2016-02-01

Ethanol adsorption and decomposition on the clean α-Al2O3(0 0 0 1) surface have been systematically investigated by density functional theory calculations. The nature of the surface-ethanol bonding has studied through the density of states (DOS) and the electron density difference (EDD) contour plots. The DOS patterns confirm that the lone pair electrons of EtOH are involved in the formation of a surface Alsbnd O dative bond and the EDD plots provide evidences for the bond weakening/forming, which are consistent with the DOS analysis. Our ethanol decomposition results indicate that ethanol dehydration to ethylene (CH3CH2OH(a) → C2H4(g) + OH(a) + H(a)), is the main reaction pathway with the energy barrier of 1.46 eV. Although the cleavage of the hydroxyl group of ethanol has lower energy barrier, the further decomposition of ethoxy owns much higher energy barrier.

Oxytocin enhances brain reward system responses in men viewing the face of their female partner.

PubMed

Scheele, Dirk; Wille, Andrea; Kendrick, Keith M; Stoffel-Wagner, Birgit; Becker, Benjamin; Güntürkün, Onur; Maier, Wolfgang; Hurlemann, René

2013-12-10

The biological mechanisms underlying long-term partner bonds in humans are unclear. The evolutionarily conserved neuropeptide oxytocin (OXT) is associated with the formation of partner bonds in some species via interactions with brain dopamine reward systems. However, whether it plays a similar role in humans has as yet not been established. Here, we report the results of a discovery and a replication study, each involving a double-blind, placebo-controlled, within-subject, pharmaco-functional MRI experiment with 20 heterosexual pair-bonded male volunteers. In both experiments, intranasal OXT treatment (24 IU) made subjects perceive their female partner's face as more attractive compared with unfamiliar women but had no effect on the attractiveness of other familiar women. This enhanced positive partner bias was paralleled by an increased response to partner stimuli compared with unfamiliar women in brain reward regions including the ventral tegmental area and the nucleus accumbens (NAcc). In the left NAcc, OXT even augmented the neural response to the partner compared with a familiar woman, indicating that this finding is partner-bond specific rather than due to familiarity. Taken together, our results suggest that OXT could contribute to romantic bonds in men by enhancing their partner's attractiveness and reward value compared with other women.

Assessing the issue of instability due to Michael adduct formation in novel chemical entities possessing a carbon-carbon double bond during early drug development--applicability of common laboratory analytical protocols.

PubMed

Polepally, Akshanth Reddy; Kumar, Venkata V Pavan; Bhamidipati, Ravikanth; Kota, Jagannath; Naveed, Shaik Abdul; Reddy, Karnati Harinder; Mamidi, Rao N V S; Selvakumar, N; Mullangi, Ramesh; Srinivas, Nuggehally R

2008-09-01

The discovery of small-molecule novel chemical entities (NCEs) is often a complex play between appropriate structural requirements and optimization of the desired efficacy, safety and pharmacokinetic properties. One of the typical structural variants such as having an active carbon-carbon double bond (alpha, beta-unsaturated carbonyl group) in xenobiotics may lead to stability issues. Such functionalities are extremely reactive, paving way to nucleophilic attack by endogenously occurring and ubiquitous nucleophiles like thiols. While it is easy to make a unilateral decision to not pursue the development of xenobiotics with such functionalities, we question the wisdom of such a decision. In this report, we present in vitro methodologies with appropriate examples to illustrate the ease of assessing the reactivity of the xenobiotics containing double bonds with a known nucleophile. The protocols involve simple reaction procedures followed by measurements using standard laboratory equipments (UV spectrophotometer, HPLC and LC-MS). Our data suggests that not all xenobiotics with carbon-carbon double bonds readily form a Michael's adduct product with glutathione. Hence, the criterion for dropping discovery compounds because of alpha,beta-unsaturated double bonds needs to be reconsidered.

Oxytocin enhances brain reward system responses in men viewing the face of their female partner

PubMed Central

Scheele, Dirk; Wille, Andrea; Kendrick, Keith M.; Stoffel-Wagner, Birgit; Becker, Benjamin; Güntürkün, Onur; Maier, Wolfgang; Hurlemann, René

2013-01-01

The biological mechanisms underlying long-term partner bonds in humans are unclear. The evolutionarily conserved neuropeptide oxytocin (OXT) is associated with the formation of partner bonds in some species via interactions with brain dopamine reward systems. However, whether it plays a similar role in humans has as yet not been established. Here, we report the results of a discovery and a replication study, each involving a double-blind, placebo-controlled, within-subject, pharmaco-functional MRI experiment with 20 heterosexual pair-bonded male volunteers. In both experiments, intranasal OXT treatment (24 IU) made subjects perceive their female partner's face as more attractive compared with unfamiliar women but had no effect on the attractiveness of other familiar women. This enhanced positive partner bias was paralleled by an increased response to partner stimuli compared with unfamiliar women in brain reward regions including the ventral tegmental area and the nucleus accumbens (NAcc). In the left NAcc, OXT even augmented the neural response to the partner compared with a familiar woman, indicating that this finding is partner-bond specific rather than due to familiarity. Taken together, our results suggest that OXT could contribute to romantic bonds in men by enhancing their partner's attractiveness and reward value compared with other women. PMID:24277856

Controlling formation of single-molecule junctions by electrochemical reduction of diazonium terminal groups.

PubMed

Hines, Thomas; Díez-Pérez, Ismael; Nakamura, Hisao; Shimazaki, Tomomi; Asai, Yoshihiro; Tao, Nongjian

2013-03-06

We report controlling the formation of single-molecule junctions by means of electrochemically reducing two axialdiazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in situ between the molecule and gold electrodes. We report a yield enhancement in molecular junction formation as the electrochemical potential of both junction electrodes approach the reduction potential of the diazonium terminal groups. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond.

A heterobimetallic complex featuring a Ti–Co multiple bond and its application to the reductive coupling of ketones to alkenes† †Electronic supplementary information (ESI) available: Experimental procedures, additional spectroscopic data for 1–4, and computational details of 2 and 3. CCDC 1037714–1037716. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03772c Click here for additional data file. Click here for additional data file.

PubMed Central

Wu, Bing; Bezpalko, Mark W.; Foxman, Bruce M.

2015-01-01

To explore metal–metal multiple bonds between first row transition metals, Ti/Co complexes supported by two phosphinoamide ligands have been synthesized and characterized. The Ti metalloligand Cl2Ti(XylNPiPr2)2 (1) was treated with CoI2 under reducing conditions, permitting isolation of the Ti/Co complex [(μ-Cl)Ti(XylNPiPr2)2CoI]2 (2). One electron reduction of complex 2 affords ClTi(XylNPiPr2)2CoPMe3 (3), which features a metal–metal triple bond and an unprecedentedly short Ti–Co distance of 2.0236(9) Å. This complex is shown to promote the McMurry coupling reaction of aryl ketones into alkenes, with concomitant formation of the tetranuclear complex [Ti(μ3-O)(NXylPiPr2)2CoI]2 (4). A cooperative mechanism involving bimetallic C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 O bond activation and a cobalt carbene intermediate is proposed. PMID:29142672

IMPACT OF PHYSICAL AND CHEMICAL MUD CONTAMINATION ON WELLBORE CEMENT- FORMATION SHEAR BOND STRENGTH Authors: Arome Oyibo1 and Mileva Radonjic1 * 1. Craft and Hawkins Department of Petroleum Engineering, 2131 Patrick F. Taylor Hall, Louisiana State University, Baton Rouge, LA 70803, aoyibo1@tigers.lsu.edu, mileva@lsu.edu

NASA Astrophysics Data System (ADS)

Oyibo, A. E.

2013-12-01

Wellbore cement has been used to provide well integrity through zonal isolation in oil & gas wells and geothermal wells. Cementing is also used to provide mechanical support for the casing and protect the casing from corrosive fluids. Failure of cement could be caused by several factors ranging from poor cementing, failure to completely displace the drilling fluids to failure on the path of the casing. A failed cement job could result in creation of cracks and micro annulus through which produced fluids could migrate to the surface which could lead to sustained casing pressure, contamination of fresh water aquifer and blow out in some cases. In addition, cement failures could risk the release of chemicals substances from hydraulic fracturing into fresh water aquifer during the injection process. To achieve proper cementing, the drilling fluid should be completely displaced by the cement slurry. However, this is hard to achieve in practice, some mud is usually left on the wellbore which ends up contaminating the cement afterwards. The purpose of this experimental study is to investigate the impact of both physical and chemical mud contaminations on cement-formation bond strength for different types of formations. Physical contamination occurs when drilling fluids (mud) dries on the surface of the formation forming a mud cake. Chemical contamination on the other hand occurs when the drilling fluids which is still in the liquid form interacts chemically with the cement during a cementing job. We investigated the impact of the contamination on the shear bond strength and the changes in the mineralogy of the cement at the cement-formation interface to ascertain the impact of the contamination on the cement-formation bond strength. Berea sandstone and clay rich shale cores were bonded with cement cores with the cement-formation contaminated either physically or chemically. For the physically contaminated composite cores, we have 3 different sample designs: clean/not contaminated, scrapped and washed composite cores. Similarly, for the chemically contaminated samples we had 3 different sample designs: 0%, 5% and 10% mud contaminated composite cores. Shear test were performed on the composite cores to determine the shear bond strength and the results suggested that the detrimental impact of the contamination is higher when the cores are physically contaminated i.e. when we have mud cake present at the surface of the wellbore before a cement job is performed. Also, the results showed that shear bond strength is higher for sandstone formations as compared to shale formations. Material characterization analysis was carried out to determine the micro structural changes at the cement-formation interface. The results obtained from the SEM and micro CT images taken at the bond interface confirmed that chemical contamination caused substantial changes in the spatial distribution of minerals that impacted bond strength. Keywords: Cement-Formation bond strength, mud contamination, shale, sandstone and material characterization *Corresponding author

Simultaneous bond degradation and bond formation during phenol-formaldehyde curing with wood

Treesearch

Daniel J. Yelle; John Ralph

2016-01-01

Bonding of wood using phenol–formaldehyde adhesive develops highly durable bonds. Phenol– formaldehyde is believed to form primary bonds with wood cell wall polymers (e.g., lignin). However, it is unclear how this adhesive interacts and bonds to lignin. Through wood solubilisation methodologies, earlywood and latewood bonded assemblies were characterized using two-...

Formation of Irreversible H-bonds in Cellulose Materials

Treesearch

Umesh P. Agarwal; Sally A. Ralph; Rick S. Reiner; Nicole M. Stark

2015-01-01

Understanding of formation of irreversible Hbonds in cellulose is important in a number of fields. For example, fields as diverse as pulp and paper and enzymatic saccharification of cellulose are affected. In the present investigation, the phenomenon of formation of irreversible H-bonds is studied in a variety of celluloses and under two different drying conditions....

UV-induced effects on chlorination of creatinine.

PubMed

Weng, Shih Chi; Li, Jing; Wood, Karl V; Kenttämaa, Hilkka I; Williams, Peggy E; Amundson, Lucas M; Blatchley, Ernest R

2013-09-15

Ultraviolet (UV) irradiation is commonly employed for water treatment in swimming pools to complement conventional chlorination, and to reduce the concentration of inorganic chloramine compounds. The approach of combining UV irradiation and chlorination has the potential to improve water quality, as defined by microbial composition. However, relatively little is known about the effects of this process on water chemistry. To address this issue, experiments were conducted to examine the effects of sequential UV254 irradiation/chlorination, as will occur in recirculating system of swimming pools, on disinfection byproduct (DBP) formation. Creatinine, which is present in human sweat and urine, was selected as the target precursor for these experiments. Enhanced formation of dichloromethylamine (CH3NCl2) and inorganic chloramines was observed to result from post-chlorination of UV-irradiated samples. Chlorocreatinine was found to be more sensitive to UV254 irradiation than creatinine; UV254 irradiation of chlorocreatinine resulted in opening of the ring structure, thereby yielding a series of intermediates that were more susceptible to free chlorine attack than their parent compound. The quantum yields for photodegradation of creatinine and chlorocreatinine at 254 nm were estimated at 0.011 ± 0.002 mol/E and 0.144 ± 0.011 mol/E, respectively. The N-Cl bond was found to be common to UV-sensitive chlorinated compounds (e.g., inorganic chloramines, CH3NCl2, and chlorocreatinine); compounds that were less susceptible to UV-based attack generally lacked the N-Cl bond. This suggested that the N-Cl bond is susceptible to UV254 irradiation, and cleavage of the N-Cl bond appears to open or promote reaction pathways that involve free chlorine, thereby enhancing formation of some DBPs and promoting loss of free chlorine. Proposed reaction mechanisms to describe this behavior based on creatinine as a precursor are presented. Copyright © 2013 Elsevier Ltd. All rights reserved.

A theoretical study of the hydrogen bonding between the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride

NASA Astrophysics Data System (ADS)

Rusu, Victor H.; da Silva, João Bosco P.; Ramos, Mozart N.

2009-04-01

MP2/6-31++G(d,p) and B3LYP/6-31++G(d,p) theoretical calculations have been employed to investigate the hydrogen bonding formation involving the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride. Our calculations have revealed for each isomer the preferential existence of two possible hydrogen-bonded complexes: a non-cyclic complex and a cyclic complex. For all the three isomers the binding energies for the non-cyclic and cyclic hydrogen complexes are essentially equal using both the MP2 and B3LYP calculations, being that the cyclic structure is slightly more stable. For instance, the binding energies including BSSE and ZPE corrections for the non-cyclic and cyclic structures of cis-C 2H 2F···HF are 8.7 and 9.0 kJ mol -1, respectively, using B3LYP calculations. The cyclic complex formation reduces the polarity, in contrast to what occurs with the non-cyclic complex. This result is more accentuated in vic-C 2H 2F 2···HF. In this latter, Δ μ(cyclic) is -3.07 D, whereas Δ μ(non-cyclic) is +1.92 D using B3LYP calculations. Their corresponding MP2 values are +0.44 D and -1.89 D, respectively. As expected, the complexation produces an H sbnd F stretching frequency downward shift, whereas its IR intensity is enhanced. On the other hand, the vibrational modes of the vic-, cis- and trans-C 2H 2F 2 isomers are little affected by complexation. The new vibrational modes due to hydrogen bonding formation show several interesting features, in particular the HF bending modes which are pure rotations in the free molecule.

Impact of Supramolecular Aggregation on the Crystallization Kinetics of Organic Compounds from the Supercooled Liquid State.

PubMed

Kalra, Arjun; Tishmack, Patrick; Lubach, Joseph W; Munson, Eric J; Taylor, Lynne S; Byrn, Stephen R; Li, Tonglei

2017-06-05

Despite numerous challenges in their theoretical description and practical implementation, amorphous drugs are of growing importance to the pharmaceutical industry. One such challenge is to gain molecular level understanding of the propensity of a molecule to form and remain as a glassy solid. In this study, a series of structurally similar diarylamine compounds was examined to elucidate the role of supramolecular aggregation on crystallization kinetics from supercooled liquid state. The structural similarity of the compounds makes it easier to isolate the molecular features that affect crystallization kinetics and glass forming ability of these compounds. To examine the role of hydrogen-bonded aggregation and motifs on crystallization kinetics, a combination of thermal and spectroscopic techniques was employed. Using variable temperature FTIR, Raman, and solid-state NMR spectroscopies, the presence of hydrogen bonding in the melt and glassy state was examined and correlated with observed phase transition behaviors. Spectroscopic results revealed that the formation of hydrogen-bonded aggregates involving carboxylic acid and pyridine nitrogen (acid-pyridine aggregates) between neighboring molecules in the melt state impedes crystallization, while the presence of carboxylic acid dimers (acid-acid dimers) in the melt favors crystallization. This study suggests that glass formation of small molecules is influenced by the type of intermolecular interactions present in the melt state and the kinetics associated with the molecules to assemble into a crystalline lattice. For the compounds that form acid-pyridine aggregates, the formation of energy degenerate chains, produced due to conformational flexibility of the molecules, presents a kinetic barrier to crystallization. The poor crystallization tendency of these aggregates stems from the highly directional hydrogen-bonding interactions needed to form the acid-pyridine chains. Conversely, for the compounds that form acid-acid dimers, the nondirectional van der Waals forces needed to construct a nucleus promote rapid assembly and crystallization.

Three different product types from reactions of lithiated cyclic aminals with trivalent organometal chlorides.

PubMed

Hellmann, Benjamin J; Kamps, Ina; Mix, Andreas; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

2010-09-21

The reaction of 2-lithio-1,3,5-trimethyl-1,3,5-triazacyclohexane with YCp(2)Cl leads to the formation of a donor-functionalised mono-anionic amide ligand, 1,3,5-trimethyl-2-(methylamidomethyl)-1,3,5-triazacyclohexane, bonded to the YCp(2) unit. The reaction involves a cleavage of the 1,3,5-triazacyclohexane ring and such a cleavage is also observed in the analogous reaction with (Me(3)C)(2)GaCl, where a MeN[double bond, length as m-dash]CH(-) fragment is formed. No such cleavage occurs in the reaction of the related dilithiated bicyclic bis(3-methyl-1,3-diazacyclohex-1-yl)methane with YCpCl(2).3thf, which affords a mixed lithium-yttrium organyl.

(Z)-N,N-Dimethyl-2-[phen­yl(pyridin-2-yl)methyl­idene]hydrazinecarbothio­amide

PubMed Central

Jayakumar, K.; Sithambaresan, M.; Prathapachandra Kurup, M. R.

2011-01-01

The title compound, C15H16N4S, exists in the Z conformation with the thionyl S atom lying cis to the azomethine N atom. The shortening of the N—N distance [1.3697 (17) Å] is due to extensive delocalization with the pyridine ring. The hydrazine–carbothio­amide unit is almost planar, with a maximum deviation of 0.013 (2) Å for the amide N atom. The stability of this conformation is favoured by the formation of an intra­molecular N—H⋯N hydrogen bond. The packing of the mol­ecules involves no classical inter­molecular hydrogen-bonding inter­actions; however, a C—H⋯π inter­action occurs. PMID:22199715

Thermodynamic aspects of dicarboxylate recognition by simple artificial receptors.

PubMed

Linton, B R; Goodman, M S; Fan, E; van Arman, S A; Hamilton, A D

2001-11-02

Recognition of dicarboxylates by bis-functional hydrogen-bonding receptors displays divergent thermodynamics in different solvent systems. NMR titration and isothermal titration calorimetry indicated that neutral bis-urea and bis-thiourea receptors form exothermic complexes with dicarboxylates in DMSO, with a near zero entropic contribution to binding. The increased binding strength of bis-guanidinium receptors precluded quantitative measurement of binding constants in DMSO, but titration calorimetry offered a qualitative picture of the association. Formation of these 1:1 complexes was also exothermic, but additional endothermic events occurred at both lower and higher host-guest ratios. These events indicated multiple binding equilibria but did not always occur at a discrete 2:1 or 1:2 host-guest molar ratio, suggesting higher aggregates. With increasing amounts of methanol as solvent, bis-guanidinium receptors form more endothermic complexes with dicarboxylates, with a favorable entropy of association. This switch from association driven by enthalpy to one driven by entropy may reflect a change from complexation involving the formation of hydrogen bonds to that promoted by solvent liberation from binding sites.

Eu(III) sorption to TiO2 (anatase and rutile): batch, XPS, and EXAFS studies.

PubMed

Tan, Xiaoli; Fan, Qiaohui; Wang, Xiangke; Grambow, Bernd

2009-05-01

The sorption of Eu(III) on anatase and rutile was studied as a function of ionic strength, humic acid (HA, 7.5 mg/L), and electrolyte anions over a large range of pH (2-12). The presence of HA significantly affected Eu(III) sorption to anatase and rutile. The sorption of Eu(III) on anatase and rutile was independent of ionic strength. Results of an X-ray photoelectron spectroscopy (XPS) analysis showed that Eu(III) was chemically present within the near-surface of TiO2 due to the formation of triple bond SOEu and triple bond SOHAEu complexes. An extended X-ray absorption fine structure (EXAFS) technique was applied to characterize the local structural environment of the adsorbed Eu(III), and the results indicated that Eu(III) was bound to about seven or eight O atoms at a distance of about 2.40 A. The functional groups of surface-bound HA were expected to be involved in the sorption process. The measured Eu-Ti distance confirmed the formation of inner-sphere sorption complexes on a TiO2 surface.

Solvent extraction: the coordination chemistry behind extractive metallurgy.

PubMed

Wilson, A Matthew; Bailey, Phillip J; Tasker, Peter A; Turkington, Jennifer R; Grant, Richard A; Love, Jason B

2014-01-07

The modes of action of the commercial solvent extractants used in extractive hydrometallurgy are classified according to whether the recovery process involves the transport of metal cations, M(n+), metalate anions, MXx(n-), or metal salts, MXx into a water-immiscible solvent. Well-established principles of coordination chemistry provide an explanation for the remarkable strengths and selectivities shown by most of these extractants. Reagents which achieve high selectivity when transporting metal cations or metal salts into a water-immiscible solvent usually operate in the inner coordination sphere of the metal and provide donor atom types or dispositions which favour the formation of particularly stable neutral complexes that have high solubility in the hydrocarbons commonly used in recovery processes. In the extraction of metalates, the structures of the neutral assemblies formed in the water-immiscible phase are usually not well defined and the cationic reagents can be assumed to operate in the outer coordination spheres. The formation of secondary bonds in the outer sphere using, for example, electrostatic or H-bonding interactions are favoured by the low polarity of the water-immiscible solvents.

Remote carboxylation of halogenated aliphatic hydrocarbons with carbon dioxide

NASA Astrophysics Data System (ADS)

Juliá-Hernández, Francisco; Moragas, Toni; Cornella, Josep; Martin, Ruben

2017-05-01

Catalytic carbon-carbon bond formation has enabled the streamlining of synthetic routes when assembling complex molecules. It is particularly important when incorporating saturated hydrocarbons, which are common motifs in petrochemicals and biologically relevant molecules. However, cross-coupling methods that involve alkyl electrophiles result in catalytic bond formation only at specific and previously functionalized sites. Here we describe a catalytic method that is capable of promoting carboxylation reactions at remote and unfunctionalized aliphatic sites with carbon dioxide at atmospheric pressure. The reaction occurs via selective migration of the catalyst along the hydrocarbon side-chain with excellent regio- and chemoselectivity, representing a remarkable reactivity relay when compared with classical cross-coupling reactions. Our results demonstrate that site-selectivity can be switched and controlled, enabling the functionalization of less-reactive positions in the presence of a priori more reactive ones. Furthermore, we show that raw materials obtained in bulk from petroleum processing, such as alkanes and unrefined mixtures of olefins, can be used as substrates. This offers an opportunity to integrate a catalytic platform en route to valuable fatty acids by transforming petroleum-derived feedstocks directly.

Reconstruction of low-index graphite surfaces

NASA Astrophysics Data System (ADS)

Thinius, Sascha; Islam, Mazharul M.; Bredow, Thomas

2016-07-01

The low-index graphite surfaces (10 1 -0), (10 1 -1), (11 2 -0) and (11 2 - 1) have been studied by density functional theory (DFT) including van-der-Waals (vdW) corrections. Different from the (0001) surface which has been extensively investigated both experimentally and theoretically, there is no comprehensive study on the (10 1 -0)- (10 1 -1)-, (11 2 -0)- and (11 2 - 1)-surfaces available, although they are of relevance for Li insertion processes, e.g. in Li-ion batteries. In this study the structure and stability of all non-(0001) low-index surfaces were calculated with RPBE-D3 and converged slab models. In all cases reconstruction involving bond formation between unsaturated carbon atoms of two neighboring graphene sheets reduces the surface energy dramatically. Two possible reconstruction patterns have been considered. The first possibility leads to formation of oblong nanotubes. Alternatively, the graphene sheets form bonds to different neighboring sheets at the upper and lower sides and sinusoidal structures are formed. Both structure types have similar stabilities. Based on the calculated surface energies the Gibbs-Wulff theorem was applied to construct the macroscopic shape of graphite single crystals.

27 CFR 24.126 - Change in proprietorship involving a bonded wine warehouse.

Code of Federal Regulations, 2010 CFR

2010-04-01

... involving a bonded wine warehouse. 24.126 Section 24.126 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS WINE Establishment and Operations Changes Subsequent to Original Establishment § 24.126 Change in proprietorship involving a bonded wine warehouse...

Hydrogen bonds between the alpha and beta subunits of the F1-ATPase allow communication between the catalytic site and the interface of the beta catch loop and the gamma subunit.

PubMed

Boltz, Kathryn W; Frasch, Wayne D

2006-09-19

F(1)-ATPase mutations in Escherichia coli that changed the strength of hydrogen bonds between the alpha and beta subunits in a location that links the catalytic site to the interface between the beta catch loop and the gamma subunit were examined. Loss of the ability to form the hydrogen bonds involving alphaS337, betaD301, and alphaD335 lowered the k(cat) of ATPase and decreased its susceptibility to Mg(2+)-ADP-AlF(n) inhibition, while mutations that maintain or strengthen these bonds increased the susceptibility to Mg(2+)-ADP-AlF(n) inhibition and lowered the k(cat) of ATPase. These data suggest that hydrogen bonds connecting alphaS337 to betaD301 and betaR323 and connecting alphaD335 to alphaS337 are important to transition state stabilization and catalytic function that may result from the proper alignment of catalytic site residues betaR182 and alphaR376 through the VISIT sequence (alpha344-348). Mutations betaD301E, betaR323K, and alphaR282Q changed the rate-limiting step of the reaction as determined by an isokinetic plot. Hydrophobic mutations of betaR323 decreased the susceptibility to Mg(2+)-ADP-AlF(n)() inhibition and lowered the number of interactions required in the rate-limiting step yet did not affect the k(cat) of ATPase, suggesting that betaR323 is important to transition state formation. The decreased rate of ATP synthase-dependent growth and decreased level of lactate-dependent quenching observed with alphaD335, betaD301, and alphaE283 mutations suggest that these residues may be important to the formation of an alternative set of hydrogen bonds at the interface of the alpha and beta subunits that permits the release of intersubunit bonds upon the binding of ATP, allowing gamma rotation in the escapement mechanism.

Diffusion Bonding of Silicon Carbide Ceramics using Titanium Interlayers

NASA Technical Reports Server (NTRS)

Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, James D.

2006-01-01

Robust joining approaches for silicon carbide ceramics are critically needed to fabricate leak free joints with high temperature mechanical capability. In this study, titanium foils and physical vapor deposited (PVD) titanium coatings were used to form diffusion bonds between SiC ceramics using hot pressing. Silicon carbide substrate materials used for bonding include sintered SiC and two types of CVD SiC. Microscopy results show the formation of well adhered diffusion bonds. The bond strengths as determined from pull tests are on the order of several ksi, which is much higher than required for a proposed application. Microprobe results show the distribution of silicon, carbon, titanium, and other minor elements across the diffusion bond. Compositions of several phases formed in the joint region were identified. Potential issues of material compatibility and optimal bond formation will also be discussed.

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins1[W

PubMed Central

Campos, Bruna Medéia; Sforça, Mauricio Luis; Ambrosio, Andre Luis Berteli; Domingues, Mariane Noronha; Brasil de Souza, Tatiana de Arruda Campos; Barbosa, João Alexandre Ribeiro Gonçalvez; Leme, Adriana Franco Paes; Perez, Carlos Alberto; Whittaker, Sara Britt-Marie; Murakami, Mario Tyago; Zeri, Ana Carolina de Matos; Benedetti, Celso Eduardo

2013-01-01

The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism. PMID:23709667

Importance of vaginocervical stimulation for the formation of maternal bonding in primiparous and multiparous parturient ewes.

PubMed

Kendrick, K M; Lévy, F; Keverne, E B

1991-09-01

The importance of vaginocervical stimulation for the formation of the maternal bond between a ewe and its lambs was investigated by studying the ability of artificial mechanical vaginocervical stimulation to induce adoption of an alien lamb after the selective bond with the ewe's own lambs had been formed. Results showed that for both multiparous and primiparous ewes, 5 min of mechanical VCS (using a hand) was effective in inducing complete acceptance of an alien lamb (6-48 h old) between 6.5 and 7.5 h postpartum in the majority of animals (8/10 multiparous, 8/9 primiparous) without interfering with the bond between the ewe and its own lambs. In a second group of multiparous animals, 6 out of 7 animals were also induced to completely accept an alien lamb between 26.5 and 27.5 h postpartum. It was found that the most critical aspect of the VCS was pressure on, and stretching the neck of, the cervix. Results show that VCS is not only important for the stimulation of maternal behavior, but also for the formation of the selective maternal bond. The ability of VCS to trigger the formation of a new maternal bond extends for at least 27.5 h post-partum.

Trichostatin A (TSA) facilitates formation of partner preference in male prairie voles (Microtus ochrogaster).

PubMed

Duclot, F; Wang, H; Youssef, C; Liu, Y; Wang, Z; Kabbaj, M

2016-05-01

In the socially monogamous prairie voles (Microtus ochrogaster), the development of a social bonding is indicated by the formation of partner preference, which involves a variety of environmental and neurochemical factors and brain structures. In a most recent study in female prairie voles, we found that treatment with the histone deacetylase inhibitor trichostatin A (TSA) facilitates the formation of partner preference through up-regulation of oxytocin receptor (OTR) and vasopressin V1a receptor (V1aR) genes expression in the nucleus accumbens (NAcc). In the present study, we tested the hypothesis that TSA treatment also facilitates partner preference formation and alters OTR and V1aR genes expression in the NAcc in male prairie voles. We thus observed that central injection of TSA dose-dependently promoted the formation of partner preference in the absence of mating in male prairie voles. Interestingly, TSA treatment up-regulated OTR, but not V1aR, gene expression in the NAcc similarly as they were affected by mating - an essential process for naturally occurring partner preference. These data, together with others, not only indicate the involvement of epigenetic events but also the potential role of NAcc oxytocin in the regulation of partner preference in both male and female prairie voles. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparison of group transfer, inner sphere and outer sphere electron transfer mechanisms for organometallic complexes

NASA Astrophysics Data System (ADS)

Our studies of reactions of metal carbonyl cations and anions have shown that metal carbonyl cations can catalyze CO exchange reactions on metal carbonyl anions. This result provides further evidence for a mechanism involving attack of the metal carbonyl anion on a carbon of the metal carbonyl cation in CO(exp 2+) transfer reactions. Reaction of metal carbonyl anions with metal carbonyl halides is a common approach to formation of metal-metal bonds. We have begun to use kinetic data and product analysis to understand the formation of homobimetallic versus heterobimetallic products in such reactions. Initial data indicate a nucleophilic attack, possibly through a ring-slippage mechanism.

Acid-promoted Bicyclization of Diaryl Alkynes: Synthesis of 2H-Indazoles with in situ Generated Diazonium Salt as Nitrogen Source.

PubMed

Zhang, Cheng; Chang, Sailan; Dong, Shanliang; Qiu, Lihua; Xu, Xinfang

2018-06-08

An unprecedented transition-metal-free tandem bicyclization of diaryl alkynes has been disclosed, which provides a streamlined access to a range of polycyclic 2H-indazoles in high to excellent yields. The salient features of this reaction include readily available starting materials, good functional group compatibility, mild reaction conditions, no column chromatography, high bond-formation efficiency, and ease in further transformations. Notably, this is the first example for the synthesis of 2H-indazoles with in situ generated diazonium salt as the nitrogen source, and a mechanistic rationale involving an acid-promoted tandem diazonium salt formation/bicyclization process is discussed.

Different routes to the glass transition: A comparison between chemical and physical vitrification

NASA Astrophysics Data System (ADS)

Caponi, Silvia; Corezzi, Silvia

2012-07-01

Despite the differences in the molecular processes involved in chemical and physical vitrification, surprising similarities are observed in the dynamics and in the thermodynamical properties of the resulting glasses. We report on a systematic study of reactive glass-formers undergoing a process of progressive polymerization of the constituent molecules via the formation of irreversible chemical bonds. The formation of most of the materials used in engineering plastics and the hardening of natural and synthetic resins, including epoxy resins, are based on chemical vitrification. The clear analogies characterizing the dynamic evolution of physical and chemical glass-formers, on the time scale of the structural and the low-frequency vibrational dynamics, are briefly reviewed.

On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes.

PubMed

Tâme Parreira, Renato Luis; Galembeck, Sérgio Emanuel; Hobza, Pavel

2007-01-08

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less

Influence of heat-pretreatments on the microstructural and mechanical properties of galfan-coated metal bonds

NASA Astrophysics Data System (ADS)

Hordych, Illia; Rodman, Dmytro; Nürnberger, Florian; Schmidt, Hans Christian; Orive, Alejandro Gonzalez; Homberg, Werner; Grundmeier, Guido; Maier, Hans Jürgen

2018-05-01

In the present study, heat-treatment assisted bonding of galfan-coated low-carbon steel sheets was investigated. Steel sheets were bonded by cold rolling subsequently to a heat treatment in the temperature range from 400 °C to 550°C. The reduction ratio during cold rolling was varied in the range from 50% to 80%. Such high reduction ratios were achieved by splitting the bonding process into three stages. By employing heat-treatments, the mechanical properties of the bonds were improved. The heat-pretreatment allowed the formation of brittle intermetallic phases that were easily fractured in the rolling gap during the bonding process. Thus, juvenile non-oxidized surfaces were formed, which facilitated the bonding between the steel layers, and thus increased the bond strength. The intermetallic phases were actively formed at temperatures of 450 °C and above; however increasing temperatures resulted in decreasing mechanical properties due to oxidation processes. The local microstructure was analyzed by scanning electron microscopy in order to characterize the contact zone on the micro level with a focus on the formation of intermetallic phases. The mechanical properties were determined in tensile shear tests. Interestingly, it was found that the galfan coating allowed for bonding at room temperature, and the aluminum fraction was primarily responsible for the enhanced oxide formation during the heat-pretreatment.

Real-time Monitoring of Intermediates Reveals the Reaction Pathway in the Thiol-Disulfide Exchange between Disulfide Bond Formation Protein A (DsbA) and B (DsbB) on a Membrane-immobilized Quartz Crystal Microbalance (QCM) System*

PubMed Central

Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

2013-01-01

Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre

2018-05-01

Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

Effect of contact time and force on monocyte adhesion to vascular endothelium.

PubMed Central

Rinker, K D; Prabhakar, V; Truskey, G A

2001-01-01

In this study we examined whether monocytic cell attachment to vascular endothelium was affected by elevating shear stress at a constant shear rate. Contact time, which is inversely related to the shear rate, was fixed and viscosity elevated with dextran to increase the shear stress (and hence the net force on the cell) independently of shear rate. At a fixed contact time, tethering frequencies increased, rolling velocities decreased, and median arrest durations increased with increasing shear stress. Rolling and short arrests (< 0.2 s) were well fit by a single exponential consistent with adhesion via the formation of a single additional bond. The cell dissociation constant, k(off), increased when the shear stress was elevated at constant shear rate. Firmly adherent cells arresting for at least 0.2 s were well fit by a stochastic model involving dissociation from multiple bonds. Therefore, at a fixed contact time and increasing shear stress, bonds formed more frequently for rolling cells resulting in more short arrests, and more bonds formed for firmly arresting cells resulting in longer arrest durations. Possible mechanisms for this increased adhesion include greater monocyte deformation and/or more frequent penetration of microvilli through steric and charge barriers. PMID:11259286

Detection of thermally grown oxides in thermal barrier coatings by nondestructive evaluation

NASA Astrophysics Data System (ADS)

Fahr, A.; Rogé, B.; Thornton, J.

2006-03-01

The thermal-barrier coatings (TBC) sprayed on hot-section components of aircraft turbine engines commonly consist of a partially stabilized zirconia top-coat and an intermediate bond-coat applied on the metallic substrate. The bond-coat is made of an aluminide alloy that at high engine temperatures forms thermally grown oxides (TGO). Although formation of a thin layer of aluminum oxide at the interface between the ceramic top-coat and the bond-coat has the beneficial effect of protecting the metallic substrate from hot gases, oxide formation at splat boundaries or pores within the bond-coat is a source of weakness. In this study, plasma-sprayed TBC specimens are manufactured from two types of bond-coat powders and exposed to elevated temperatures to form oxides at the ceramic-bond-coat boundary and within the bond-coat. The specimens are then tested using nondestructive evaluation (NDE) and destructive metallography and compared with the as-manufactured samples. The objective is to determine if NDE can identify the oxidation within the bond-coat and give indication of its severity. While ultrasonic testing can provide some indication of the degree of bond-coat oxidation, the eddy current (EC) technique clearly identifies severe oxide formation within the bond-coat. Imaging of the EC signals as the function of probe location provides information on the spatial variations in the degree of oxidation, and thereby identifies which components or areas are prone to premature damage.

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

NASA Technical Reports Server (NTRS)

Oie, T.; Loew, G. H.; Burt, S. K.; MacElroy, R. D.

1984-01-01

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

Extended reaction scope of thiamine diphosphate dependent cyclohexane-1,2-dione hydrolase: from C-C bond cleavage to C-C bond ligation.

PubMed

Loschonsky, Sabrina; Wacker, Tobias; Waltzer, Simon; Giovannini, Pier Paolo; McLeish, Michael J; Andrade, Susana L A; Müller, Michael

2014-12-22

ThDP-dependent cyclohexane-1,2-dione hydrolase (CDH) catalyzes the CC bond cleavage of cyclohexane-1,2-dione to 6-oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH-H28A is much less able to catalyze the CC bond formation, while the ability for CC bond cleavage is still intact. The double variant CDH-H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane-1,2-dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54-94 % enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane-2,3-dione are alternative donor substrates for CC bond formation. Thus, the very rare aldehyde-ketone cross-benzoin reaction has been solved by design of an enzyme variant. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation of {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]} Dimers Bonded by Single C-C Bonds and Bridging η(2)-Coordinated Cobalt Atoms.

PubMed

Konarev, Dmitri V; Troyanov, Sergey I; Ustimenko, Kseniya A; Nakano, Yoshiaki; Shestakov, Alexander F; Otsuka, Akihiro; Yamochi, Hideki; Saito, Gunzi; Lyubovskaya, Rimma N

2015-05-18

Coordination of two bridging cobalt atoms to fullerenes by the η(2) type in {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]}·3C6H4Cl2 [1; dppe = 1,2-bis(diphenylphosphino)ethane] triggers fullerene dimerization with the formation of two intercage C-C bonds of 1.571(4) Å length. Coordination-induced fullerene dimerization opens a path to the design of fullerene structures bonded by both covalent C-C bonds and η(2)-coordination-bridged metal atoms.

Discovery of a diazo-forming enzyme in cremeomycin biosynthesis.

PubMed

Waldman, Abraham J; Balskus, Emily P

2018-05-17

The molecular architectures and potent bioactivities of diazo-containing natural products have attracted the interest of synthetic and biological chemists. Despite this attention, the biosynthetic enzymes involved in diazo group construction have not been identified. Here, we show the ATP-dependent enzyme CreM installs the diazo group in cremeomycin via late-stage N-N bond formation using nitrite. This finding should inspire efforts to use diazo-forming enzymes in biocatalysis and synthetic biology and enable genome-based discovery of new diazo-containing metabolites.

Addition of CF3 across unsaturated moieties: a powerful functionalization tool

PubMed Central

2014-01-01

In the last few years, the efficient introduction of trifluoromethyl groups in organic molecules has become a major research focus. This review highlights the recent developments enabling the incorporation of CF3 groups across unsaturated moieties, preferentially alkenes, and the mechanistic scenarios governing these transformations. We have specially focused on methods involving the simultaneous formation of C–CF3 and C–C or C–heteroatom bonds by formal addition reactions across π-systems, as such difunctionalization processes hold valuable synthetic potential. PMID:24789472

Reusable ionic liquid-catalyzed oxidative coupling of azoles and benzylic compounds via sp(3) C-N bond formation under metal-free conditions.

PubMed

Liu, Wenbo; Liu, Chenjiang; Zhang, Yonghong; Sun, Yadong; Abdukadera, Ablimit; Wang, Bin; Li, He; Ma, Xuecheng; Zhang, Zengpeng

2015-07-14

The heterocyclic ionic liquid-catalyzed direct oxidative amination of benzylic sp(3) C-H bonds via intermolecular sp(3) C-N bond formation for the synthesis of N-alkylated azoles under metal-free conditions is reported for the first time. The catalyst 1-butylpyridinium iodide can be recycled and reused with similar efficacies for at least eight cycles.

Unexpected formation of (E)-4-alkene 1,3-diketones from the three-component reaction of lithium selenolates with 1-(1-alkynyl)cyclopropyl ketones and aldehydes.

PubMed

Xu, Jianfeng; Wu, Luling; Huang, Xian

2011-07-15

A novel three-component stereoselective synthesis of (E)-4-alkene 1,3-diketones from lithium selenolates, 1-(1-alkynyl)cyclopropyl ketones, and aldehydes is reported. This reaction afforded the products in moderate to good yields with the formation of a new C-Se single bond, a new C-C double bond, and a new C-O double bond.

Formation of C-C and C-O bonds and oxygen removal in reactions of alkanediols, alkanols, and alkanals on copper catalysts.

PubMed

Sad, María E; Neurock, Matthew; Iglesia, Enrique

2011-12-21

This study reports evidence for catalytic deoxygenation of alkanols, alkanals, and alkanediols on dispersed Cu clusters with minimal use of external H(2) and with the concurrent formation of new C-C and C-O bonds. These catalysts selectively remove O-atoms from these oxygenates as CO or CO(2) through decarbonylation or decarboxylation routes, respectively, that use C-atoms present within reactants or as H(2)O using H(2) added or formed in situ from CO/H(2)O mixtures via water-gas shift. Cu catalysts fully convert 1,3-propanediol to equilibrated propanol-propanal intermediates that subsequently form larger oxygenates via aldol-type condensation and esterification routes without detectable involvement of the oxide supports. Propanal-propanol-H(2) equilibration is mediated by their chemisorption and interconversion at surfaces via C-H and O-H activation and propoxide intermediates. The kinetic effects of H(2), propanal, and propanol pressures on turnover rates, taken together with measured selectivities and the established chemical events for base-catalyzed condensation and esterification reactions, indicate that both reactions involve kinetically relevant bimolecular steps in which propoxide species, acting as the base, abstract the α-hydrogen in adsorbed propanal (condensation) or attack the electrophilic C-atom at its carbonyl group (esterification). These weakly held basic alkoxides render Cu surfaces able to mediate C-C and C-O formation reactions typically catalyzed by basic sites inherent in the catalyst, instead of provided by coadsorbed organic moieties. Turnover rates for condensation and esterification reactions decrease with increasing Cu dispersion, because low-coordination corner and edge atoms prevalent on small clusters stabilize adsorbed intermediates and increase the activation barriers for the bimolecular kinetically relevant steps required for both reactions. © 2011 American Chemical Society

Involvement of the host DNA-repair enzyme TDP2 in formation of the covalently closed circular DNA persistence reservoir of hepatitis B viruses.

PubMed

Königer, Christian; Wingert, Ida; Marsmann, Moritz; Rösler, Christine; Beck, Jürgen; Nassal, Michael

2014-10-07

Hepatitis B virus (HBV), the causative agent of chronic hepatitis B and prototypic hepadnavirus, is a small DNA virus that replicates by protein-primed reverse transcription. The product is a 3-kb relaxed circular DNA (RC-DNA) in which one strand is linked to the viral polymerase (P protein) through a tyrosyl-DNA phosphodiester bond. Upon infection, the incoming RC-DNA is converted into covalently closed circular (ccc) DNA, which serves as a viral persistence reservoir that is refractory to current anti-HBV treatments. The mechanism of cccDNA formation is unknown, but the release of P protein is one mandatory step. Structural similarities between RC-DNA and cellular topoisomerase-DNA adducts and their known repair by tyrosyl-DNA-phosphodiesterase (TDP) 1 or TDP2 suggested that HBV may usurp these enzymes for its own purpose. Here we demonstrate that human and chicken TDP2, but only the yeast ortholog of TDP1, can specifically cleave the Tyr-DNA bond in virus-adapted model substrates and release P protein from authentic HBV and duck HBV (DHBV) RC-DNA in vitro, without prior proteolysis of the large P proteins. Consistent with TPD2's having a physiological role in cccDNA formation, RNAi-mediated TDP2 depletion in human cells significantly slowed the conversion of RC-DNA to cccDNA. Ectopic TDP2 expression in the same cells restored faster conversion kinetics. These data strongly suggest that TDP2 is a first, although likely not the only, host DNA-repair factor involved in HBV cccDNA biogenesis. In addition to establishing a functional link between hepadnaviruses and DNA repair, our results open new prospects for directly targeting HBV persistence.

Controlled formation of closed-edge nanopores in graphene

NASA Astrophysics Data System (ADS)

He, Kuang; Robertson, Alex W.; Gong, Chuncheng; Allen, Christopher S.; Xu, Qiang; Zandbergen, Henny; Grossman, Jeffrey C.; Kirkland, Angus I.; Warner, Jamie H.

2015-07-01

Dangling bonds at the edge of a nanopore in monolayer graphene make it susceptible to back-filling at low temperatures from atmospheric hydrocarbons, leading to potential instability for nanopore applications, such as DNA sequencing. We show that closed edge nanopores in bilayer graphene are robust to back-filling under atmospheric conditions for days. A controlled method for closed edge nanopore formation starting from monolayer graphene is reported using an in situ heating holder and electron beam irradiation within an aberration-corrected transmission electron microscopy. Tailoring of closed-edge nanopore sizes is demonstrated from 1.4-7.4 nm. These results should provide mechanisms for improving the stability of nanopores in graphene for a wide range of applications involving mass transport.Dangling bonds at the edge of a nanopore in monolayer graphene make it susceptible to back-filling at low temperatures from atmospheric hydrocarbons, leading to potential instability for nanopore applications, such as DNA sequencing. We show that closed edge nanopores in bilayer graphene are robust to back-filling under atmospheric conditions for days. A controlled method for closed edge nanopore formation starting from monolayer graphene is reported using an in situ heating holder and electron beam irradiation within an aberration-corrected transmission electron microscopy. Tailoring of closed-edge nanopore sizes is demonstrated from 1.4-7.4 nm. These results should provide mechanisms for improving the stability of nanopores in graphene for a wide range of applications involving mass transport. Electronic supplementary information (ESI) available: Low magnification images, image processing techniques employed, modelling and simulation of closed edge nanoribbon, comprehensive AC-TEM dataset, and supporting analysis. See DOI: 10.1039/c5nr02277k

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach.

PubMed

Suresh, D M; Amalanathan, M; Sebastian, S; Sajan, D; Hubert Joe, I; Bena Jothy, V; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Comprehensive analysis of individual pulp fiber bonds quantifies the mechanisms of fiber bonding in paper

PubMed Central

Hirn, Ulrich; Schennach, Robert

2015-01-01

The process of papermaking requires substantial amounts of energy and wood consumption, which contributes to larger environmental costs. In order to optimize the production of papermaking to suit its many applications in material science and engineering, a quantitative understanding of bonding forces between the individual pulp fibers is of importance. Here we show the first approach to quantify the bonding energies contributed by the individual bonding mechanisms. We calculated the impact of the following mechanisms necessary for paper formation: mechanical interlocking, interdiffusion, capillary bridges, hydrogen bonding, Van der Waals forces, and Coulomb forces on the bonding energy. Experimental results quantify the area in molecular contact necessary for bonding. Atomic force microscopy experiments derive the impact of mechanical interlocking. Capillary bridges also contribute to the bond. A model based on the crystal structure of cellulose leads to values for the chemical bonds. In contrast to general believe which favors hydrogen bonding Van der Waals bonds play the most important role according to our model. Comparison with experimentally derived bond energies support the presented model. This study characterizes bond formation between pulp fibers leading to insight that could be potentially used to optimize the papermaking process, while reducing energy and wood consumption. PMID:26000898

METHOD OF SOLID STATE WELDING

DOEpatents

Storchheim, S.

1958-07-10

An improved method is described for pressure bonding of dissimilar metals, particularly nickel and aluminum. Using ordinary techniques for the pressure bonding of these metals, an alloy zone is usually formed between the metals, and this alloy zone exhibits undesirable brittleness and lack of tensile strengh. Formation of this alloy zone can be inhibited or prevented by heating the metals being bonded to a temperature below the melting point of either of the metals and using very high pressures for short periods of time. In this manner a bond is formed without the formation of the undesirable alloy zone.

Amide Bond Formation Assisted by Vicinal Alkylthio Migration in Enaminones: Metal- and CO-Free Synthesis of α,β-Unsaturated Amides.

PubMed

Liu, Zhuqing; Huang, Fei; Wu, Ping; Wang, Quannan; Yu, Zhengkun

2018-05-18

Amide bond formation is one of the most important transformations in organic synthesis, drug development, and materials science. Efficient construction of amides has been among the most challenging tasks for organic chemists. Herein, we report a concise methodology for amide bond (-CONH-) formation assisted by vicinal group migration in alkylthio-functionalized enaminones (α-oxo ketene N, S-acetals) under mild conditions. Simple treatment of such enaminones with PhI(OAc) 2 at ambient temperature in air afforded diverse multiply functionalized α,β-unsaturated amides including β-cyclopropylated acrylamides, in which a wide array of functional groups such as aryl, (hetero)aryl, alkenyl, and alkyl can be conveniently introduced to a ketene moiety. The reaction mechanism was investigated by exploring the origins of the amide oxygen and carbon atoms as well as isolation and structural characterization of the reaction intermediates. The amide bond formation reactions could also be efficiently performed under solventless mechanical milling conditions.

The mechanism of transition-metal (Cu or Pd)-catalyzed synthesis of benzimidazoles from amidines: theoretical investigation.

PubMed

Li, Juan; Gu, Honghong; Wu, Caihong; Du, Lijuan

2014-11-28

In this study, the Cu(OAc)2- and [PdCl2(PhCN)2]-catalyzed syntheses of benzimidazoles from amidines were theoretically investigated using density functional theory calculations. For the Cu-catalyzed system, our calculations supported a four-step-pathway involving C-H activation of an arene with Cu(II) via concerted metalation-deprotonation (CMD), followed by oxidation of the Cu(II) intermediate and deprotonation of the imino group by Cu(III), and finally reductive elimination from Cu(III). In our calculations, the barriers for the CMD step and the oxidation step are the same. The results are different from the ones reported by Fu et al. in which the whole reaction mechanism includes three steps and the CMD step is rate determining. On the basis of the calculation results for the [PdCl2(PhCN)2]-catalyzed system, C-H bond breaking by CMD occurs first, followed by the rate-determining C-N bond formation and N-H deprotonation. Pd(III) species is not involved in the [PdCl2(PhCN)2]-catalyzed syntheses of benzimidazoles from amidines.

E2-EPF UCP Possesses E3 Ubiquitin Ligase Activity via Its Cysteine 118 Residue.

PubMed

Lim, Jung Hwa; Shin, Hee Won; Chung, Kyung-Sook; Kim, Nam-Soon; Kim, Ju Hee; Jung, Hong-Ryul; Im, Dong-Soo; Jung, Cho-Rok

Here, we show that E2-EPF ubiquitin carrier protein (UCP) elongated E3-independent polyubiquitin chains on the lysine residues of von Hippel-Lindau protein (pVHL) and its own lysine residues both in vitro and in vivo. The initiation of the ubiquitin reaction depended on not only Lys11 linkage but also the Lys6, Lys48 and Lys63 residues of ubiquitin, which were involved in polyubiquitin chain formation on UCP itself. UCP self-association occurred through the UBC domain, which also contributed to the interaction with pVHL. The polyubiquitin chains appeared on the N-terminus of UCP in vivo, which indicated that the N-terminus of UCP contains target lysines for polyubiquitination. The Lys76 residue of UCP was the most critical site for auto-ubiquitination, whereas the polyubiquitin chain formation on pVHL occurred on all three of its lysines (Lys159, Lys171 and Lys196). A UCP mutant in which Cys118 was changed to alanine (UCPC118A) did not form a polyubiquitin chain but did strongly accumulate mono- and di-ubiquitin via auto-ubiquitination. Polyubiquitin chain formation required the coordination of Cys95 and Cys118 between two interacting molecules. The mechanism of the polyubiquitin chain reaction of UCP may involve the transfer of ubiquitin from Cys95 to Cys118 by trans-thiolation, with polyubiquitin chains forming at Cys118 by reversible thioester bonding. The polyubiquitin chains are then moved to the lysine residues of the substrate by irreversible isopeptide bonding. During the elongation of the ubiquitin chain, an active Cys118 residue is required in both parts of UCP, namely, the catalytic enzyme and the substrate. In conclusion, UCP possesses not only E2 ubiquitin conjugating enzyme activity but also E3 ubiquitin ligase activity, and Cys118 is critical for polyubiquitin chain formation.

E2-EPF UCP Possesses E3 Ubiquitin Ligase Activity via Its Cysteine 118 Residue

PubMed Central

Lim, Jung Hwa; Shin, Hee Won; Chung, Kyung-Sook; Kim, Nam-Soon; Kim, Ju Hee; Jung, Hong-Ryul; Im, Dong-Soo; Jung, Cho-Rok

2016-01-01

Here, we show that E2-EPF ubiquitin carrier protein (UCP) elongated E3-independent polyubiquitin chains on the lysine residues of von Hippel-Lindau protein (pVHL) and its own lysine residues both in vitro and in vivo. The initiation of the ubiquitin reaction depended on not only Lys11 linkage but also the Lys6, Lys48 and Lys63 residues of ubiquitin, which were involved in polyubiquitin chain formation on UCP itself. UCP self-association occurred through the UBC domain, which also contributed to the interaction with pVHL. The polyubiquitin chains appeared on the N-terminus of UCP in vivo, which indicated that the N-terminus of UCP contains target lysines for polyubiquitination. The Lys76 residue of UCP was the most critical site for auto-ubiquitination, whereas the polyubiquitin chain formation on pVHL occurred on all three of its lysines (Lys159, Lys171 and Lys196). A UCP mutant in which Cys118 was changed to alanine (UCPC118A) did not form a polyubiquitin chain but did strongly accumulate mono- and di-ubiquitin via auto-ubiquitination. Polyubiquitin chain formation required the coordination of Cys95 and Cys118 between two interacting molecules. The mechanism of the polyubiquitin chain reaction of UCP may involve the transfer of ubiquitin from Cys95 to Cys118 by trans-thiolation, with polyubiquitin chains forming at Cys118 by reversible thioester bonding. The polyubiquitin chains are then moved to the lysine residues of the substrate by irreversible isopeptide bonding. During the elongation of the ubiquitin chain, an active Cys118 residue is required in both parts of UCP, namely, the catalytic enzyme and the substrate. In conclusion, UCP possesses not only E2 ubiquitin conjugating enzyme activity but also E3 ubiquitin ligase activity, and Cys118 is critical for polyubiquitin chain formation. PMID:27685940

Ester versus polyketone formation in the palladium-diphosphine catalyzed carbonylation of ethene.

PubMed

Zuidema, Erik; Bo, Carles; van Leeuwen, Piet W N M

2007-04-04

The origin of the chemoselectivity of palladium catalysts containing bidentate phosphine ligands toward either methoxycarbonylation of ethene or the copolymerization of ethene and carbon monoxide was investigated using density functional theory based calculations. For a palladium catalyst containing the electron-donating bis(dimethylphosphino)ethane (dmpe) ligand, the rate determining step for chain propagation is shown to be the insertion of ethene into the metal-acyl bond. The high barrier for chain propagation is attributed to the low stability of the ethene intermediate, (dmpe)Pd(ethene)(C(O)CH3). For the competing methanolysis process, the most likely pathway involves the formation of (dmpe)Pd(CH3OH)(C(O)CH3) via dissociative ligand exchange, followed by a solvent mediated proton-transfer/reductive- elimination process. The overall barrier for this process is higher than the barrier for ethene insertion into the palladium-acetyl bond, in line with the experimentally observed preference of this type of catalyst toward the formation of polyketone. Electronic bite angle effects on the rates of ethene insertion and ethanoyl methanolysis were evaluated using four electronically and sterically related ligands (Me)2P(CH2)nP(Me)2 (n = 1-4). Steric effects were studied for larger tert-butyl substituted ligands using a QM/MM methodology. The results show that ethene coordination to the metal center and subsequent insertion into the palladium-ethanoyl bond are disfavored by the addition of steric bulk around the metal center. Key intermediates in the methanolysis mechanism, on the other hand, are stabilized because of electronic effects caused by increasing the bite angle of the diphosphine ligand. The combined effects explain successfully which ligands give polymer and which ones give methyl propionate as the major products of the reaction.

Silica, Alumina and Clay Catalyzed Peptide Bond Formation: Enhanced Efficiency of Alumina Catalyst

NASA Astrophysics Data System (ADS)

Bujdák, Juraj; Rode, Bernd M.

1999-10-01

Catalytic efficiencies of clay (hectorite), silica and alumina were tested in peptide bond formation reactions of glycine (Gly), alanine (Ala), proline (Pro), valine (Val) and leucine (Leu). The reactions were performed as drying/wetting (hectorite) and temperature fluctuation (silica and alumina) experiments at 85 °C. The reactivity of amino acids decreased in order Gly > Ala > Pro ~ Val ~ Leu. The highest catalytic efficiency was observed for alumina, the only catalyst producing oligopeptides in all investigated reaction systems. The peptide bond formation on alumina is probably catalyzed by the same sites and via similar reaction mechanisms as some alumina-catalyzed dehydration reactions used in industrial chemistry.

Single and double carbon vacancies in pyrene as first models for graphene defects: A survey of the chemical reactivity toward hydrogen

NASA Astrophysics Data System (ADS)

Nieman, Reed; Das, Anita; Aquino, Adélia J. A.; Amorim, Rodrigo G.; Machado, Francisco B. C.; Lischka, Hans

2017-01-01

Graphene is regarded as one of the most promising materials for nanoelectronics applications. Defects play an important role in modulating its electronic properties and also enhance its chemical reactivity. In this work the reactivity of single vacancies (SV) and double vacancies (DV) in reaction with a hydrogen atom Hr is studied. Because of the complicated open shell electronic structures of these defects due to dangling bonds, multireference configuration interaction (MRCI) methods are being used in combination with a previously developed defect model based on pyrene. Comparison of the stability of products derived from Csbnd Hr bond formation with different carbon atoms of the different polyaromatic hydrocarbons is made. In the single vacancy case the most stable structure is the one where the incoming hydrogen is bound to the carbon atom carrying the dangling bond. However, stable Csbnd Hr bonded structures are also observed in the five-membered ring of the single vacancy. In the double vacancy, most stable bonding of the reactant Hr atom is found in the five-membered rings. In total, Csbnd Hr bonds, corresponding to local energy minimum structures, are formed with all carbon atoms in the different defect systems and the pyrene itself. Reaction profiles for the four lowest electronic states show in the case of a single vacancy a complex picture of curve crossings and avoided crossings which will give rise to a complex nonadiabatic reaction dynamics involving several electronic states.

Analysis of factors influencing the bond strength in roll bonding processes

NASA Astrophysics Data System (ADS)

Khaledi, Kavan; Wulfinghoff, Stephan; Reese, Stefanie

2018-05-01

Cold Roll Bonding (CRB) is recognized as an industrial technique in which the metal sheets are joined together in order to produce laminate metal composites. In this technique, a metallurgical bond resulting from severe plastic deformation is formed between the rolled metallic layers. The main objective of this paper is to analyse different factors which may affect the bond formation in rolling processes. To achieve this goal, first, an interface model is employed which describes both the bonding and debonding. In this model, the bond strength evolution between the metallic layers is calculated based on the film theory of bonding. On the other hand, the debonding process is modelled by means of a bilinear cohesive zone model. In the numerical section, different scenarios are taken into account to model the roll bonding process of metal sheets. The numerical simulation includes the modelling of joining during the roll bonding process followed by debonding in a Double Cantilever Beam (DCB) peeling test. In all simulations, the metallic layers are regarded as elastoplastic materials subjected to large plastic deformations. Finally, the effects of some important factors on the bond formation are numerically investigated.

The possible participation of esters as well as amides in prebiotic polymers.

NASA Technical Reports Server (NTRS)

Rich, A.

1971-01-01

Demonstration that alpha-hydroxy acids may have participated in the formation of prebiological polymers in a manner similar to the participation of alpha-amino acids. Ex periments are described which indicate that the system for forming peptide bonds in present-day biological organisms is equally competent in forming ester and polyester bonds. In particular, the experiments described are directed toward answering questions regarding the action of peptidyl transferase in ester formation. Also, an attempt is made to determine whether a complete protein synthetic system can operate with transfer RNA molecules which have alpha-hydroxyl acids attached to them instead of alpha-amino acids, using both synthetic and natural mRNA. The ability of ribosomal peptidyl transferase to catalyze the formation of an ester bond as well as its normal product, the peptide bond, is demonstrated.

Disulfide Bond Formation and Activation of Escherichia coli β-Galactosidase under Oxidizing Conditions

PubMed Central

Seras-Franzoso, Joaquin; Affentranger, Roman; Ferrer-Navarro, Mario; Daura, Xavier; Villaverde, Antonio

2012-01-01

Escherichia coli β-galactosidase is probably the most widely used reporter enzyme in molecular biology, cell biology, and biotechnology because of the easy detection of its activity. Its large size and tetrameric structure make this bacterial protein an interesting model for crystallographic studies and atomic mapping. In the present study, we investigate a version of Escherichia coli β-galactosidase produced under oxidizing conditions, in the cytoplasm of an Origami strain. Our data prove the activation of this microbial enzyme under oxidizing conditions and clearly show the occurrence of a disulfide bond in the β-galactosidase structure. Additionally, the formation of this disulfide bond is supported by the analysis of a homology model of the protein that indicates that two cysteines located in the vicinity of the catalytic center are sufficiently close for disulfide bond formation. PMID:22286993

Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network☆

PubMed Central

Kaiser, Alexander; Ismailova, Oksana; Koskela, Antti; Huber, Stefan E.; Ritter, Marcel; Cosenza, Biagio; Benger, Werner; Nazmutdinov, Renat; Probst, Michael

2014-01-01

Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions. PMID:24748697

Selective Hydrogen Atom Abstraction through Induced Bond Polarization: Direct α-Arylation of Alcohols through Photoredox, HAT, and Nickel Catalysis.

PubMed

Twilton, Jack; Christensen, Melodie; DiRocco, Daniel A; Ruck, Rebecca T; Davies, Ian W; MacMillan, David W C

2018-05-04

The combination of nickel metallaphotoredox catalysis, hydrogen atom transfer catalysis, and a Lewis acid activation mode, has led to the development of an arylation method for the selective functionalization of alcohol α-hydroxy C-H bonds. This approach employs zinc-mediated alcohol deprotonation to activate α-hydroxy C-H bonds while simultaneously suppressing C-O bond formation by inhibiting the formation of nickel alkoxide species. The use of Zn-based Lewis acids also deactivates other hydridic bonds such as α-amino and α-oxy C-H bonds. This approach facilitates rapid access to benzylic alcohols, an important motif in drug discovery. A 3-step synthesis of the drug Prozac exemplifies the utility of this new method. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

PubMed

Mills, Jamie E; Whitford, Paul C; Shaffer, Jennifer; Onuchic, Jose N; Adams, Joseph A; Jennings, Patricia A

2007-02-02

The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of the SH2 domain were investigated. The kinase activity of full-length Csk decreases by an order of magnitude upon formation of the disulfide bond in the distal SH2 domain. NMR spectra of the fully oxidized and fully reduced SH2 domains exhibit similar chemical shift patterns and are indicative of similar, well-defined tertiary structures. The solvent-accessible disulfide bond in the isolated SH2 domain is highly stable and far from the small lobe of the kinase domain. However, reduction of this bond results in chemical shift changes of resonances that map to a cluster of residues that extend from the disulfide bond across the molecule to a surface that is in direct contact with the small lobe of the kinase domain in the intact molecule. Normal mode analyses and molecular dynamics calculations suggest that disulfide bond formation has large effects on residues within the kinase domain, most notably within the active-site cleft. Overall, the data indicate that reversible cross-linking of two cysteine residues in the SH2 domain greatly impacts catalytic function and interdomain communication in Csk.

The Selector Gene apterous and Notch Are Required to Locally Increase Mechanical Cell Bond Tension at the Drosophila Dorsoventral Compartment Boundary

PubMed Central

Michel, Marcus; Aliee, Maryam; Rudolf, Katrin; Bialas, Lisa; Jülicher, Frank; Dahmann, Christian

2016-01-01

The separation of cells with distinct fates and functions is important for tissue and organ formation during animal development. Regions of different fates within tissues are often separated from another along straight boundaries. These compartment boundaries play a crucial role in tissue patterning and growth by stably positioning organizers. In Drosophila, the wing imaginal disc is subdivided into a dorsal and a ventral compartment. Cells of the dorsal, but not ventral, compartment express the selector gene apterous. Apterous expression sets in motion a gene regulatory cascade that leads to the activation of Notch signaling in a few cell rows on either side of the dorsoventral compartment boundary. Both Notch and apterous mutant clones disturb the separation of dorsal and ventral cells. Maintenance of the straight shape of the dorsoventral boundary involves a local increase in mechanical tension at cell bonds along the boundary. The mechanisms by which cell bond tension is locally increased however remain unknown. Here we use a combination of laser ablation of cell bonds, quantitative image analysis, and genetic mutants to show that Notch and Apterous are required to increase cell bond tension along the dorsoventral compartment boundary. Moreover, clonal expression of the Apterous target gene capricious results in cell separation and increased cell bond tension at the clone borders. Finally, using a vertex model to simulate tissue growth, we find that an increase in cell bond tension at the borders of cell clones, but not throughout the cell clone, can lead to cell separation. We conclude that Apterous and Notch maintain the characteristic straight shape of the dorsoventral compartment boundary by locally increasing cell bond tension. PMID:27552097

Reliable aluminum contact formation by electrostatic bonding

NASA Astrophysics Data System (ADS)

Kárpáti, T.; Pap, A. E.; Radnóczi, Gy; Beke, B.; Bársony, I.; Fürjes, P.

2015-07-01

The paper presents a detailed study of a reliable method developed for aluminum fusion wafer bonding assisted by the electrostatic force evolving during the anodic bonding process. The IC-compatible procedure described allows the parallel formation of electrical and mechanical contacts, facilitating a reliable packaging of electromechanical systems with backside electrical contacts. This fusion bonding method supports the fabrication of complex microelectromechanical systems (MEMS) and micro-opto-electromechanical systems (MOEMS) structures with enhanced temperature stability, which is crucial in mechanical sensor applications such as pressure or force sensors. Due to the applied electrical potential of  -1000 V the Al metal layers are compressed by electrostatic force, and at the bonding temperature of 450 °C intermetallic diffusion causes aluminum ions to migrate between metal layers.

Both the stroma and thylakoid lumen of tobacco chloroplasts are competent for the formation of disulphide bonds in recombinant proteins.

PubMed

Bally, Julia; Paget, Eric; Droux, Michel; Job, Claudette; Job, Dominique; Dubald, Manuel

2008-01-01

Plant chloroplasts are promising vehicles for recombinant protein production, but the process of protein folding in these organelles is not well understood in comparison with that in prokaryotic systems, such as Escherichia coli. This is particularly true for disulphide bond formation which is crucial for the biological activity of many therapeutic proteins. We have investigated the capacity of tobacco (Nicotiana tabacum) chloroplasts to efficiently form disulphide bonds in proteins by expressing in this plant cell organelle a well-known bacterial enzyme, alkaline phosphatase, whose activity and stability strictly depend on the correct formation of two intramolecular disulphide bonds. Plastid transformants have been generated that express either the mature enzyme, localized in the stroma, or the full-length coding region, including its signal peptide. The latter has the potential to direct the recombinant alkaline phosphatase into the lumen of thylakoids, giving access to this even less well-characterized organellar compartment. We show that the chloroplast stroma supports the formation of an active enzyme, unlike a normal bacterial cytosol. Sorting of alkaline phosphatase to the thylakoid lumen occurs in the plastid transformants translating the full-length coding region, and leads to larger amounts and more active enzyme. These results are compared with those obtained in bacteria. The implications of these findings on protein folding properties and competency of chloroplasts for disulphide bond formation are discussed.

4-(4-Meth­oxy­phen­yl)-2-methyl­but-3-yn-2-ol

PubMed Central

Eissmann, Frank; Kafurke, Uwe; Weber, Edwin

2010-01-01

The mol­ecular structure of the title compound, C12H14O2, features a nearly coplanar arrangement including the aromatic ring, the C C—C group and the ether O atom. The maximum deviation from the least-squares plane of these ten atoms is 0.0787 (8) Å for the ether O atom. In the crystal, mol­ecules are connected via O—H⋯O hydrogen bonds (involving the hy­droxy O atom both as hydrogen-bond donor and acceptor) and weaker (ar­yl)C—H⋯π(ar­yl) contacts, leading to the formation of strands running parallel to the b axis. Further stabilization results from weaker (meth­yl)C—H⋯π(acetyl­ene) inter­actions between different strands. PMID:21588063

Strained-layer epitaxy of germanium-silicon alloys

NASA Astrophysics Data System (ADS)

Bean, J. C.

1985-10-01

Strained-layer epitaxy is presented as a developing technique for combining Si with other materials in order to obtain semiconductors with enhanced electronic properties. The method involves applying layers sufficiently thin so that the atoms deposited match the bonding configurations of the substrate crystal. When deposited on Si, a four-fold bonding pattern is retained, with a lowered interfacial energy and augmented stored strain energy in the epitaxial layer. The main problem which remains is building an epitaxial layer thick enough to yield desired epitaxial properties while avoiding a reversion to an unstrained structure. The application of a Ge layer to Si using MBE is described, along with the formation of heterojunction multi-layer superlattices, which can reduce the dislocation effects in some homojunctions. The technique shows promise for developing materials of use as bipolar transistors, optical detectors and fiber optic transmission devices.

Rapid reversible borane to boryl hydride exchange by metal shuttling on the carborane cluster surface† †Electronic supplementary information (ESI) available. CCDC 1545735 and 1545736. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc01846k

PubMed Central

Eleazer, Bennett J.; Smith, Mark D.

2017-01-01

In this work, we introduce a novel concept of a borane group vicinal to a metal boryl bond acting as a supporting hemilabile ligand in exohedrally metalated three-dimensional carborane clusters. The (POBOP)Ru(Cl)(PPh3) pincer complex (POBOP = 1,7-OP(i-Pr)2-m-2-carboranyl) features extreme distortion of the two-center-two-electron Ru–B bond due to the presence of a strong three-center-two-electron B–H···Ru vicinal interaction. Replacement of the chloride ligand with a hydride afforded the (POBOP)Ru(H)(PPh3) pincer complex, which possesses B–Ru, B–H···Ru, and Ru–H bonds. This complex was found to exhibit a rapid exchange between hydrogen atoms of the borane and the terminal hydride through metal center shuttling between two boron atoms of the carborane cage. This exchange process, which involves sequential cleavage and formation of strong covalent metal–boron and metal–hydrogen bonds, is unexpectedly facile at temperatures above –50 °C corresponding to an activation barrier of 12.2 kcal mol–1. Theoretical calculations suggested two equally probable pathways for the exchange process through formally Ru(0) or Ru(iv) intermediates, respectively. The presence of this hemilabile vicinal B–H···Ru interaction in (POBOP)Ru(H)(PPh3) was found to stabilize a latent coordination site at the metal center promoting efficient catalytic transfer dehydrogenation of cyclooctane under nitrogen and air at 170 °C. PMID:28970919

Critical evaluation of dipolar, acid-base and charge interactions I. Electron displacement within and between molecules, liquids and semiconductors.

PubMed

Rosenholm, Jarl B

2017-09-01

Specific dipolar, acid-base and charge interactions involve electron displacements. For atoms, single bonds and molecules electron displacement is characterized by electronic potential, absolute hardness, electronegativity and electron gap. In addition, dissociation, bonding, atomization, formation, ionization, affinity and lattice enthalpies are required to quantify the electron displacement in solids. Semiconductors are characterized by valence and conduction band energies, electron gaps and average Fermi energies which in turn determine Galvani potentials of the bulk, space charge layer and surface states. Electron displacement due to interaction between (probe) molecules, liquids and solids are characterized by parameters such as Hamaker constant, solubility parameter, exchange energy density, surface tension, work of adhesion and immersion. They are determined from permittivity, refractive index, enthalpy of vaporization, molar volume, surface pressure and contact angle. Moreover, acidic and basic probes may form adducts which are adsorbed on target substrates in order to establish an indirect measure of polarity, acidity, basicity or hydrogen bonding. Acidic acceptor numbers (AN), basic donor numbers (DN), acidic and basic "electrostatic" (E) and "covalent" (C) parameters determined by enthalpy of adduct formation are considered as general acid-base scales. However, the formal grounds for assignments as dispersive, Lifshitz-van der Waals, polar, acid, base and hydrogen bond interactions are inconsistent. Although correlations are found no of the parameters are mutually fully compatible and moreover the enthalpies of acid-base interaction do not correspond to free energies. In this review the foundations of different acid-base parameters relating to electron displacement within and between (probe) molecules, liquids and (semiconducting) solids are thoroughly investigated and their mutual relationships are evaluated. Copyright © 2017 Elsevier B.V. All rights reserved.

S K-edge XAS and DFT Calculations on Square Planar NiII-thiolate Complexes: Effects of Active and Passive H-bonding

PubMed Central

Dey, Abhishek; Green, Kayla N.; Jenkins, Roxanne M.; Jeffrey, Stephen P.; Darensbourg, Marcetta; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

2008-01-01

S K-edge XAS for a low-spin NiII-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high spin FeIII-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc.; 2005; 127, 12046-12053.). These differences were analyzed using DFT calculations and the results indicate that two different types of H-bonding interactions are possible in metal-thiolate systems. In the high-spin FeIII-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin NiII-thiolate the orbital involved in H-bonding is non-bonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated. PMID:17949080

Self-Healing of Unentangled Polymer Networks with Reversible Bonds

PubMed Central

Stukalin, Evgeny B.; Cai, Li-Heng; Kumar, N. Arun; Leibler, Ludwik; Rubinstein, Michael

2013-01-01

Self-healing polymeric materials are systems that after damage can revert to their original state with full or partial recovery of mechanical strength. Using scaling theory we study a simple model of autonomic self-healing of unentangled polymer networks. In this model one of the two end monomers of each polymer chain is fixed in space mimicking dangling chains attachment to a polymer network, while the sticky monomer at the other end of each chain can form pairwise reversible bond with the sticky end of another chain. We study the reaction kinetics of reversible bonds in this simple model and analyze the different stages in the self-repair process. The formation of bridges and the recovery of the material strength across the fractured interface during the healing period occur appreciably faster after shorter waiting time, during which the fractured surfaces are kept apart. We observe the slowest formation of bridges for self-adhesion after bringing into contact two bare surfaces with equilibrium (very low) density of open stickers in comparison with self-healing. The primary role of anomalous diffusion in material self-repair for short waiting times is established, while at long waiting times the recovery of bonds across fractured interface is due to hopping diffusion of stickers between different bonded partners. Acceleration in bridge formation for self-healing compared to self-adhesion is due to excess non-equilibrium concentration of open stickers. Full recovery of reversible bonds across fractured interface (formation of bridges) occurs after appreciably longer time than the equilibration time of the concentration of reversible bonds in the bulk. PMID:24347684

Effect of Particle Size and Impact Velocity on Collision Behaviors Between Nano-Scale TiN Particles: MD Simulation.

PubMed

Yao, Hai-Long; Hu, Xiao-Zhen; Yang, Guan-Jun

2018-06-01

Inter-particle bonding formation which determines qualities of nano-scale ceramic coatings is influenced by particle collision behaviors during high velocity collision processes. In this study, collision behaviors between nano-scale TiN particles with different diameters were illuminated by using Molecular Dynamics simulation through controlling impact velocities. Results show that nano-scale TiN particles exhibit three states depending on particle sizes and impact velocities, i.e., bonding, bonding with localized fracturing, and rebounding. These TiN particles states are summarized into a parameter selection map providing an overview of the conditions in terms of particle sizes and velocities. Microstructure results show that localized atoms displacement and partial fracture around the impact region are main reasons for bonding formation of nano-scale ceramic particles, which shows differences from conventional particles refining and amorphization. A relationship between the adhesion energy and the rebound energy is established to understand bonding formation mechanism for nano-scale TiN particle collision. Results show that the energy relationship is depended on the particle sizes and impact velocities, and nano-scale ceramic particles can be bonded together as the adhesion energy being higher than the rebound energy.

Collapsed tetragonal phase as a strongly covalent and fully nonmagnetic state: Persistent magnetism with interlayer As-As bond formation in Rh-doped Ca0 .8Sr0 .2Fe2As2

NASA Astrophysics Data System (ADS)

Zhao, K.; Glasbrenner, J. K.; Gretarsson, H.; Schmitz, D.; Bednarcik, J.; Etter, M.; Sun, J. P.; Manna, R. S.; Al-Zein, A.; Lafuerza, S.; Scherer, W.; Cheng, J. G.; Gegenwart, P.

2018-02-01

A well-known feature of the CaFe2As2 -based superconductors is the pressure-induced collapsed tetragonal phase that is commonly ascribed to the formation of an interlayer As-As bond. Using detailed x-ray scattering and spectroscopy, we find that Rh-doped Ca0.8Sr0.2Fe2As2 does not undergo a first-order phase transition and that local Fe moments persist despite the formation of interlayer As-As bonds. Our density functional theory calculations reveal that the Fe-As bond geometry is critical for stabilizing magnetism and the pressure-induced drop in the c lattice parameter observed in pure CaFe2As2 is mostly due to a constriction within the FeAs planes. The collapsed tetragonal phase emerges when covalent bonding of strongly hybridized Fe 3 d and As 4 p states completely wins out over their exchange splitting. Thus the collapsed tetragonal phase is properly understood as a strong covalent phase that is fully nonmagnetic with the As-As bond forming as a by-product.

SK-Edge XAS And DFT Calculations on Square-Planar NiII-Thiolate Complexes: Effects of Active And Passive H-Bonding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dey, A.; Green, K.N.; Jenkins, R.M.

S K-edge XAS for a low-spin Ni{sup II}-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high-spin Fe{sup III}-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc. 2005, 127, 12046-12053). These differences were analyzed using DFT calculations, and the results indicate that two different types of H-bonding interactions are possiblemore » in metal-thiolate systems. In the high-spin Fe{sup III}-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin Ni{sup II}-thiolate, the orbital involved in H-bonding is nonbonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated.« less

A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis.

PubMed

Huang, Kai-Fa; Wang, Yu-Ruei; Chang, En-Cheng; Chou, Tsung-Lin; Wang, Andrew H-J

2008-04-01

QCs (glutaminyl cyclases; glutaminyl-peptide cyclotransferases, EC 2.3.2.5) catalyse N-terminal pyroglutamate formation in numerous bioactive peptides and proteins. The enzymes were reported to be involved in several pathological conditions such as amyloidotic disease, osteoporosis, rheumatoid arthritis and melanoma. The crystal structure of human QC revealed an unusual H-bond (hydrogen-bond) network in the active site, formed by several highly conserved residues (Ser(160), Glu(201), Asp(248), Asp(305) and His(319)), within which Glu(201) and Asp(248) were found to bind to substrate. In the present study we combined steady-state enzyme kinetic and X-ray structural analyses of 11 single-mutation human QCs to investigate the roles of the H-bond network in catalysis. Our results showed that disrupting one or both of the central H-bonds, i.e., Glu(201)...Asp(305) and Asp(248)...Asp(305), reduced the steady-state catalysis dramatically. The roles of these two COOH...COOH bonds on catalysis could be partly replaced by COOH...water bonds, but not by COOH...CONH(2) bonds, reminiscent of the low-barrier Asp...Asp H-bond in the active site of pepsin-like aspartic peptidases. Mutations on Asp(305), a residue located at the centre of the H-bond network, raised the K(m) value of the enzyme by 4.4-19-fold, but decreased the k(cat) value by 79-2842-fold, indicating that Asp(305) primarily plays a catalytic role. In addition, results from mutational studies on Ser(160) and His(319) suggest that these two residues might help to stabilize the conformations of Asp(248) and Asp(305) respectively. These data allow us to propose an essential proton transfer between Glu(201), Asp(305) and Asp(248) during the catalysis by animal QCs.

Mitochondrial protein import: Mia40 facilitates Tim22 translocation into the inner membrane of mitochondria.

PubMed

Wrobel, Lidia; Trojanowska, Agata; Sztolsztener, Malgorzata E; Chacinska, Agnieszka

2013-03-01

The mitochondrial intermembrane space assembly (MIA) pathway is generally considered to be dedicated to the redox-dependent import and biogenesis of proteins localized to the intermembrane space of mitochondria. The oxidoreductase Mia40 is a central component of the pathway responsible for the transfer of disulfide bonds to intermembrane space precursor proteins, causing their oxidative folding. Here we present the first evidence that the function of Mia40 is not restricted to the transport and oxidative folding of intermembrane space proteins. We identify Tim22, a multispanning membrane protein and core component of the TIM22 translocase of inner membrane, as a protein with cysteine residues undergoing oxidation during Tim22 biogenesis. We show that Mia40 is involved in the biogenesis and complex assembly of Tim22. Tim22 forms a disulfide-bonded intermediate with Mia40 upon import into mitochondria. Of interest, Mia40 binds the Tim22 precursor also via noncovalent interactions. We propose that Mia40 not only is responsible for disulfide bond formation, but also assists the Tim22 protein in its integration into the inner membrane of mitochondria.

High performance low cost interconnections for flip chip attachment with electrically conductive adhesive. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-05-01

This final report is a compilation of final reports from each of the groups participating in the program. The main three groups involved in this effort are the Thomas J. Watson Research Center of IBM Corporation in Yorktown Heights, New York, Assembly Process Design of IBM Corporation in Endicott, New York, and SMT Laboratory of Universal Instruments Corporation in Binghamton, New York. The group at the research center focused on the conductive adhesive materials development and characterization. The group in process development focused on processing of the Polymer-Metal-Solvent Paste (PMSP) to form conductive adhesive bumps, formation of the Polymer-Metal Compositemore » (PMC) on semiconductor devices and study of the bonding process to circuitized organic carriers, and the long term durability and reliability of joints formed using the process. The group at Universal Instruments focused on development of an equipment set and bonding parameters for the equipment to produce bond assembly tooling. Reports of each of these individual groups are presented here reviewing their technical efforts and achievements.« less

Sacrificial adhesive bonding: a powerful method for fabrication of glass microchips

PubMed Central

Lima, Renato S.; Leão, Paulo A. G. C.; Piazzetta, Maria H. O.; Monteiro, Alessandra M.; Shiroma, Leandro Y.; Gobbi, Angelo L.; Carrilho, Emanuel

2015-01-01

A new protocol for fabrication of glass microchips is addressed in this research paper. Initially, the method involves the use of an uncured SU-8 intermediate to seal two glass slides irreversibly as in conventional adhesive bonding-based approaches. Subsequently, an additional step removes the adhesive layer from the channels. This step relies on a selective development to remove the SU-8 only inside the microchannel, generating glass-like surface properties as demonstrated by specific tests. Named sacrificial adhesive layer (SAB), the protocol meets the requirements of an ideal microfabrication technique such as throughput, relatively low cost, feasibility for ultra large-scale integration (ULSI), and high adhesion strength, supporting pressures on the order of 5 MPa. Furthermore, SAB eliminates the use of high temperature, pressure, or potential, enabling the deposition of thin films for electrical or electrochemical experiments. Finally, the SAB protocol is an improvement on SU-8-based bondings described in the literature. Aspects such as substrate/resist adherence, formation of bubbles, and thermal stress were effectively solved by using simple and inexpensive alternatives. PMID:26293346

Observation of structure transition as a function of temperature in depositing hydrogenated sp2-rich carbon films

NASA Astrophysics Data System (ADS)

Wang, Yongfu; Gao, Kaixiong; Zhang, Junyan

2018-05-01

In this study, we carried out the transition experiments of graphite-like (GL) to fullerene-like (FL) structures by placing high temperature steel substrates in the depositing environment which can form FL hydrogenated carbon films. We investigated the changes of bond mixtures, H content, aromatic clusters and internal stress at the transition process, and proposed the transformation mechanism inferred from Raman, TEM cross-section, FTIR and XPS results. It was found that the size of aromatic clusters and accordingly graphene planes and the formation of edge dangling bonds were the key steps. H+ bombardment leaded to the splitting of large graphene planes (at GL stage) into more and smaller planes (at FL stage) and the formation of edge dangling bonds; Some of these dangling bonds were reduced by the formation of pentagons and subsequent curving of the smaller planes, which were an indicator of FL structures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yuzhan; Zhang, Yuehong; Rios, Orlando

In this study, a liquid crystalline epoxy network (LCEN) with exchangeable disulfide bonds is synthesized by polymerizing a biphenyl-based epoxy monomer with an aliphatic dicarboxylic acid curing agent containing a disulfide bond. The effect of disulfide bonds on curing behavior and liquid crystalline (LC) phase formation of the LCEN is investigated. The presence of the disulfide bonds results in an increase in the reaction rate, leading to a reduction in liquid crystallinity of the LCEN. In order to promote LC phase formation and stabilize the self-assembled LC domains, a similar aliphatic dicarboxylic acid without the disulfide bond is used asmore » a co-curing agent to reduce the amount of exchangeable disulfide bonds in the system. After optimizing the molar ratio of the two curing agents, the resulting LCEN exhibits improved reprocessability and recyclability because of the disulfide exchange reactions, while preserving LC properties, such as the reversible LC phase transition and macroscopic LC orientation, for shape memory applications.« less

Liquid crystalline epoxy networks with exchangeable disulfide bonds

DOE PAGES

Li, Yuzhan; Zhang, Yuehong; Rios, Orlando; ...

2017-06-09

In this study, a liquid crystalline epoxy network (LCEN) with exchangeable disulfide bonds is synthesized by polymerizing a biphenyl-based epoxy monomer with an aliphatic dicarboxylic acid curing agent containing a disulfide bond. The effect of disulfide bonds on curing behavior and liquid crystalline (LC) phase formation of the LCEN is investigated. The presence of the disulfide bonds results in an increase in the reaction rate, leading to a reduction in liquid crystallinity of the LCEN. In order to promote LC phase formation and stabilize the self-assembled LC domains, a similar aliphatic dicarboxylic acid without the disulfide bond is used asmore » a co-curing agent to reduce the amount of exchangeable disulfide bonds in the system. After optimizing the molar ratio of the two curing agents, the resulting LCEN exhibits improved reprocessability and recyclability because of the disulfide exchange reactions, while preserving LC properties, such as the reversible LC phase transition and macroscopic LC orientation, for shape memory applications.« less

Photochemical activity of a key donor-acceptor complex can drive stereoselective catalytic α-alkylation of aldehydes.

PubMed

Arceo, Elena; Jurberg, Igor D; Alvarez-Fernández, Ana; Melchiorre, Paolo

2013-09-01

Asymmetric catalytic variants of sunlight-driven photochemical processes hold extraordinary potential for the sustainable preparation of chiral molecules. However, the involvement of short-lived electronically excited states inherent to any photochemical reaction makes it challenging for a chiral catalyst to dictate the stereochemistry of the products. Here, we report that readily available chiral organic catalysts, with well-known utility in thermal asymmetric processes, can also confer a high level of stereocontrol in synthetically relevant intermolecular carbon-carbon bond-forming reactions driven by visible light. A unique mechanism of catalysis is proposed, wherein the catalyst is involved actively in both the photochemical activation of the substrates (by inducing the transient formation of chiral electron donor-acceptor complexes) and the stereoselectivity-defining event. We use this approach to enable transformations that are extremely difficult under thermal conditions, such as the asymmetric α-alkylation of aldehydes with alkyl halides, the formation of all-carbon quaternary stereocentres and the control of remote stereochemistry.

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains.

PubMed

Krieger, Florian; Möglich, Andreas; Kiefhaber, Thomas

2005-03-16

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.

Electronic structure and mechanical properties of plasma nitrided ferrous alloys

NASA Astrophysics Data System (ADS)

Portolan, E.; Baumvol, I. J. R.; Figueroa, C. A.

2009-04-01

The electronic structures of the near-surface regions of two different nitrided steels (AISI 316 and 4140) were investigated using X-ray photoelectron spectroscopy. Photoelectron groups from all main chemical elements involved were addressed for steel samples with implanted-N concentrations in the range 16-32 at.%. As the implanted-N concentrations were increased, rather contrasting behaviors were observed for the two kinds of steel. The N1s photoelectrons had spectral shifts toward lower (nitrided AISI 316) or higher (nitrided AISI 4140) binding energies, whereas the Fe2p 3/2 photoelectron spectrum remains at a constant binding energy (nitrided AISI 316) or shifts toward higher binding energies (AISI 4140). These trends are discussed in terms of the metallic nitride formation and the overlapping of atomic orbitals. For nitrided AISI 316, a semi-classical approach of charge transfer between Cr and N is used to explain the experimental facts (formation of CrN), while for nitrided AISI 4140 we propose that the interaction between orbitals 4s from Fe and 2p from N promotes electrons to the conduction band increasing the electrical attraction of the N1s and Fe2p electrons in core shells (formation of FeN x). The increase in hardness of the steel upon N implantation is attributed to the localization of electrons in specific bonds, which diminishes the metallic bond character.

Oligomerization reactions for precursors to secondary organic aerosol: Comparison between two formation mechanisms for the oligomeric hydroxyalkyl hydroperoxides

NASA Astrophysics Data System (ADS)

Zhao, Qiangli; Wang, Weina; Liu, Fengyi; Lü, Jian; Wang, Wenliang

2017-10-01

To better understand the formation mechanism of oligomeric hydroxyalkyl hydroperoxides HOROO(SCI)nH composed of stabilized Criegee intermediate (SCI) as a chain unit, the reactions of SCI with hydroxyalkyl hydroperoxides (HOROOH) and hydroxyalkylperoxy radical (HORO2) as well as HO2 radical were investigated. For the reactions of HORO2 + SCI, two preferred pathways involving a SCI insertion in HOROOH hydroperoxide bond can be found, and the formation of HOROO(SCI)H is the dominant pathway in the reaction of HOCH2(CH3)2COOH + (CH3)2COO. The structures of the HORO2, HOROOH as well as the SCIs play a crucial role in determining the reactivity of the oligomerization. Both the reactions of HORO2 + SCI + HO2 and HOROOH + SCI could be the source of the processors to the formation of secondary organic aerosol (SOA). But from the point of free energy barriers, the formation of HOROO(SCI)H prefers to follow the mechanism involving initiation by the reaction of a HORO2 and a SCI, sequential addition of SCIs, and termination by reaction with the HO2 radical. The rate coefficients show negative temperature dependence and vary in different systems depending on the reactants. The reaction process and constituents of the products can be regulated by temperature and reactants.

The H2O-CH3F Complex: a Combined Microwave and Infrared Spectroscopic Study Supported by Structure Calculations

NASA Astrophysics Data System (ADS)

Gnanasekar, Sharon Priya; Goubet, Manuel; Arunan, Elangannan; Georges, Robert; Soulard, Pascale; Asselin, Pierre; Huet, T. R.; Pirali, Olivier

2015-06-01

The H2O-CH3F complex could have two geometries, one with a hydrogen bond and one with the newly proposed carbon bond. While in general carbon bonds are weaker than hydrogen bonds, this complex appears to have comparable energies for the two structures. Infrared (IR) and microwave (MW) spectroscopic measurements using, respectively, the Jet-AILES apparatus and the FTMW spectrometer at the PhLAM laboratory, have been carried out to determine the structure of this complex. The IR spectrum shows the formation of the CH3F- H2O hydrogen bonded complex and small red-shifts in OH frequency most probably due to (CH3F)m-(H2O)n clusters. Noticeably, addition of CH_3F in the mixture promotes the formation of small water clusters. Preliminary MW spectroscopic measurements indicate the formation of the hydrogen bonded complex. So far, we have no experimental evidence for the carbon bonded structure. However, calculations of the Ar-CH3F complex show three energetically equivalent structures: a T-shape, a "fluorine" bond and a carbon bond. The MW spectrum of the (Ar)n-CH3F complexes is currently under analysis. Mani, D; Arunan, E. Phys. Chem. Chem. Phys. 2013, 15, 14377. Cirtog, M; Asselin, P; Soulard, P; Tremblay, B; Madebene, B; Alikhani, M. E; Georges, R; Moudens, A; Goubet, M; Huet, T.R; Pirali, O; Roy, P. J. Phys. Chem. A. 2011, 115, 2523 Kassi, S; Petitprez, D; Wlodarczak, G. J. Mol. Struct. 2000, 517-518, 375

The 8-Pyrrole-Benzothiazinones Are Noncovalent Inhibitors of DprE1 from Mycobacterium tuberculosis

PubMed Central

Makarov, Vadim; Neres, João; Hartkoorn, Ruben C.; Ryabova, Olga B.; Kazakova, Elena; Šarkan, Michal; Huszár, Stanislav; Piton, Jérémie; Kolly, Gaëlle S.; Vocat, Anthony; Conroy, Trent M.; Mikušová, Katarína

2015-01-01

8-Nitro-benzothiazinones (BTZs), such as BTZ043 and PBTZ169, inhibit decaprenylphosphoryl-β-d-ribose 2′-oxidase (DprE1) and display nanomolar bactericidal activity against Mycobacterium tuberculosis in vitro. Structure-activity relationship (SAR) studies revealed the 8-nitro group of the BTZ scaffold to be crucial for the mechanism of action, which involves formation of a semimercaptal bond with Cys387 in the active site of DprE1. To date, substitution of the 8-nitro group has led to extensive loss of antimycobacterial activity. Here, we report the synthesis and characterization of the pyrrole-benzothiazinones PyrBTZ01 and PyrBTZ02, non-nitro-benzothiazinones that retain significant antimycobacterial activity, with MICs of 0.16 μg/ml against M. tuberculosis. These compounds inhibit DprE1 with 50% inhibitory concentration (IC50) values of <8 μM and present favorable in vitro absorption-distribution-metabolism-excretion/toxicity (ADME/T) and in vivo pharmacokinetic profiles. The most promising compound, PyrBTZ01, did not show efficacy in a mouse model of acute tuberculosis, suggesting that BTZ-mediated killing through DprE1 inhibition requires a combination of both covalent bond formation and compound potency. PMID:25987616

Subunit arrangement in P2X receptors.

PubMed

Jiang, Lin-Hua; Kim, Miran; Spelta, Valeria; Bo, Xuenong; Surprenant, Annmarie; North, R Alan

2003-10-01

ATP-gated ionotropic receptors (P2X receptors) are distributed widely in the nervous system. For example, a hetero-oligomeric receptor containing both P2X2 and P2X3 subunits is involved in primary afferent sensation. Each subunit has two membrane-spanning domains. We have used disulfide bond formation between engineered cysteines to demonstrate close proximity between the outer ends of the first transmembrane domain of one subunit and the second transmembrane domain of another. After expression in HEK 293 cells of such modified P2X2 or P2X4 subunits, the disulfide bond formation is evident because an ATP-evoked channel opening requires previous reduction with dithiothreitol. In the hetero-oligomeric P2X2/3 receptor the coexpression of doubly substituted subunits with wild-type partners allows us to deduce that the hetero-oligomeric channel contains adjacent P2X3 subunits but does not contain adjacent P2X2 subunits. The results suggest a "head-to-tail" subunit arrangement in the quaternary structure of P2X receptors and show that a trimeric P2X2/3 receptor would have the composition P2X2(P2X3)2.

Theoretical Study on the Catalytic Reduction Mechanism of NO by CO on Tetrahedral Rh4 Subnanocluster.

PubMed

Yang, Hua-Qing; Fu, Hong-Quan; Su, Ben-Fang; Xiang, Bo; Xu, Qian-Qian; Hu, Chang-Wei

2015-11-25

The catalytic mechanism of 2NO + 2CO → N2 + 2CO2 on Rh4 cluster has been systematically investigated on the ground and first excited states at the B3LYP/6-311+G(2d),SDD level. For the overall reaction of 2NO + 2CO → N2 + 2CO2, the main reaction pathways take place on the facet site rather than the edge site of the Rh4 cluster. The turnover frequency (TOF) determining transition states are characteristic of the second N-O bond cleavage with rate constant k4 = 1.403 × 10(11) exp (-181 203/RT) and the N-N bond formation for the intermediate N2O formation with rate constant k2 = 3.762 × 10(12) exp (-207 817/RT). The TOF-determining intermediates of (3)N(b)Rh4NO and (3)N(b)Rh4O(b)(NO) are associated with the nitrogen-atom molecular complex, which is in agreement with the experimental observation of surface nitrogen. On the facet site of Rh4 cluster, the formation of CO2 stems solely from the recombination of CO and O atom, while N2 originates partly from the recombination of two N atoms and partly from the decomposition of N2O. For the N-O bond cleavage or the synchronous N-O bond cleavage and C-O bond formation, the neutral Rh4 cluster exhibits better catalytic performance than the cationic Rh4(+) cluster. Alternatively, for N-N bond formation, the cationic Rh4(+) cluster possesses better catalytic performance than the neutral Rh4 cluster.

The Kringle-like Domain Facilitates Post-endoplasmic Reticulum Changes to Premelanosome Protein (PMEL) Oligomerization and Disulfide Bond Configuration and Promotes Amyloid Formation*

PubMed Central

Ho, Tina; Watt, Brenda; Spruce, Lynn A.; Seeholzer, Steven H.; Marks, Michael S.

2016-01-01

The formation of functional amyloid must be carefully regulated to prevent the accumulation of potentially toxic products. Premelanosome protein (PMEL) forms non-toxic functional amyloid fibrils that assemble into sheets upon which melanins ultimately are deposited within the melanosomes of pigment cells. PMEL is synthesized in the endoplasmic reticulum but forms amyloid only within post-Golgi melanosome precursors; thus, PMEL must traverse the secretory pathway in a non-amyloid form. Here, we identified two pre-amyloid PMEL intermediates that likely regulate the timing of fibril formation. Analyses by non-reducing SDS-PAGE, size exclusion chromatography, and sedimentation velocity revealed two native high Mr disulfide-bonded species that contain Golgi-modified forms of PMEL. These species correspond to disulfide bond-containing dimeric and monomeric PMEL isoforms that contain no other proteins as judged by two-dimensional PAGE of metabolically labeled/immunoprecipitated PMEL and by mass spectrometry of affinity-purified complexes. Metabolic pulse-chase analyses, small molecule inhibitor treatments, and evaluation of site-directed mutants suggest that the PMEL dimer forms around the time of endoplasmic reticulum exit and is resolved by disulfide bond rearrangement into a monomeric form within the late Golgi or a post-Golgi compartment. Mutagenesis of individual cysteine residues within the non-amyloid cysteine-rich Kringle-like domain stabilizes the disulfide-bonded dimer and impairs fibril formation as determined by electron microscopy. Our data show that the Kringle-like domain facilitates the resolution of disulfide-bonded PMEL dimers and promotes PMEL functional amyloid formation, thereby suggesting that PMEL dimers must be resolved to monomers to generate functional amyloid fibrils. PMID:26694611

Comparing Ullmann Coupling on Noble Metal Surfaces: On-Surface Polymerization of 1,3,6,8-Tetrabromopyrene on Cu(111) and Au(111).

PubMed

Pham, Tuan Anh; Song, Fei; Nguyen, Manh-Thuong; Li, Zheshen; Studener, Florian; Stöhr, Meike

2016-04-18

The on-surface polymerization of 1,3,6,8-tetrabromopyrene (Br4 Py) on Cu(111) and Au(111) surfaces under ultrahigh vacuum conditions was investigated by a combination of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) calculations. Deposition of Br4 Py on Cu(111) held at 300 K resulted in a spontaneous debromination reaction, generating the formation of a branched coordination polymer network stabilized by C-Cu-C bonds. After annealing at 473 K, the C-Cu-C bonds were converted to covalent C-C bonds, leading to the formation of a covalently linked molecular network of short oligomers. In contrast, highly ordered self-assembled two-dimensional (2D) patterns stabilized by both Br-Br halogen and Br-H hydrogen bonds were observed upon deposition of Br4 Py on Au(111) held at 300 K. Subsequent annealing of the sample at 473 K led to a dissociation of the C-Br bonds and the formation of disordered metal-coordinated molecular networks. Further annealing at 573 K resulted in the formation of covalently linked disordered networks. Importantly, we found that the chosen substrate not only plays an important role as catalyst for the Ullmann reaction, but also influences the formation of different types of intermolecular bonds and thus, determines the final polymer network morphology. DFT calculations further support our experimental findings obtained by STM and XPS and add complementary information on the reaction pathway of Br4 Py on the different substrates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Helicobacter pylori protein oxidation influences the colonization process.

PubMed

Godlewska, Renata; Dzwonek, Artur; Mikuła, Michał; Ostrowski, Jerzy; Pawłowski, Marcin; Bujnicki, Janusz M; Jagusztyn-Krynicka, Elzbieta K

2006-08-01

Dsb proteins control the formation and rearrangement of disulfide bonds during the folding of membrane and exported proteins. Here we examined the role of DsbI protein in Helicobacter pylori pathogenesis and demonstrated that a dsbI mutant impaired in disulfide bond formation revealed a greatly reduced ability to colonize mice gastric mucosa.

MICROWAVE-ASSISTED CHEMISTRY: SYNTHESIS OF AMINES AND HETEROCYCLES VIA CARBON-NITROGEN BOND FORMATION IN AQUEOUS MEDIA

EPA Science Inventory

Improved C-N bond formation under MW influence is demonstrated by a) solventless three-component coupling reaction to generate propargyl amines that uses only Cu (I); b) aqueous N-alkylation of amines by alkyl halides that proceeds expeditiously in the presence of NaOH to deliver...

Interfacial crystalline structures in injection over-molded polypropylene and bond strength.

PubMed

Yan, Bowen; Wu, Hong; Jiang, Genjie; Guo, Shaoyun; Huang, Jian

2010-11-01

This paper describes interfacial crystalline structures found in injection overmolded polypropylene components and the relationship of these structures to bond strength between the components. The combined effects of the development of hierarchical gradient structures and the particular thermomechanical environment near the interface on the interfacial crystalline structures were investigated in detail by PLM, SEM, DSC, WAXD, and infrared dichroism spectroscopy. The experimental results showed that during molding there was competitive formation of interfacial crystalline structures consisted of "shish-kebab" layer (SKL) and a transcrystalline layers (TCL). Variation in shear stress (controlled by injection pressure and injection speed) plays an important role in the formation of the SKL. The formation of TCL is influenced by the thermal environment, namely melt temperature and mold temperature. Increasing within certain limits, interfacial temperature and the thermal gradient near the interface promotes β-iPP growth. The relationship between interfacial crystalline structures and interfacial bond strength was established by lap shear measurement. The interfacial bond strength is improved by enhancing the formation of TCL, but reduced if SKL predominates.

Spectroscopic Identification of the Au-C Bond Formation upon Electroreduction of an Aryl Diazonium Salt on Gold.

PubMed

Guo, Limin; Ma, Lipo; Zhang, Yelong; Cheng, Xun; Xu, Ye; Wang, Jin; Wang, Erkang; Peng, Zhangquan

2016-11-08

Electroreduction of aryl diazonium salts on gold can produce organic films that are more robust than their analogous self-assembled monolayers formed from chemical adsorption of organic thiols on gold. However, whether the enhanced stability is due to the Au-C bond formation remains debated. In this work, we report the electroreduction of an aryl diazonium salt of 4,4'-disulfanediyldibenzenediazonium on gold forming a multilayer of Au-(Ar-S-S-Ar) n , which can be further degraded to a monolayer of Au-Ar-S - by electrochemical cleavage of the S-S moieties within the multilayer. By conducting an in situ surface-enhanced Raman spectroscopic study of both the multilayer formation/degradation and the monolayer reduction/oxidation processes, coupled to density functional theory calculations, we provide compelling evidence that an Au-C bond does form upon electroreduction of aryl diazonium salts on gold and that the enhanced stability of the electrografted organic films is due to the Au-C bond being intrinsically stronger than the Au-S bond for a given phenylthiolate compound by ca. 0.4 eV.

Plasticity in the Oxidative Folding Pathway of the High Affinity Nerita Versicolor Carboxypeptidase Inhibitor (NvCI).

PubMed

Esperante, Sebastián A; Covaleda, Giovanni; Trejo, Sebastián A; Bronsoms, Sílvia; Aviles, Francesc X; Ventura, Salvador

2017-07-14

Nerita Versicolor carboxypeptidase inhibitor (NvCI) is the strongest inhibitor reported so far for the M14A subfamily of carboxypeptidases. It comprises 53 residues and a protein fold composed of a two-stranded antiparallel β sheet connected by three loops and stabilized by three disulfide bridges. Here we report the oxidative folding and reductive unfolding pathways of NvCI. Much debate has gone on whether protein conformational folding guides disulfide bond formation or instead they are disulfide bonds that favour the arrangement of local or global structural elements. We show here that for NvCI both possibilities apply. Under physiological conditions, this protein folds trough a funnelled pathway involving a network of kinetically connected native-like intermediates, all sharing the disulfide bond connecting the two β-strands. In contrast, under denaturing conditions, the folding of NvCI is under thermodynamic control and follows a "trial and error" mechanism, in which an initial quasi-stochastic population of intermediates rearrange their disulfide bonds to attain the stable native topology. Despite their striking mechanistic differences, the efficiency of both folding routes is similar. The present study illustrates thus a surprising plasticity in the folding of this extremely stable small disulfide-rich inhibitor and provides the basis for its redesign for biomedical applications.

Periodic density functional theory study of ethylene hydrogenation over Co3O4 (1 1 1) surface: The critical role of oxygen vacancies

NASA Astrophysics Data System (ADS)

Lu, Jinhui; Song, JiaJia; Niu, Hongling; Pan, Lun; Zhang, Xiangwen; Wang, Li; Zou, Ji-Jun

2016-05-01

Recently, metal oxides are attracting increasing interests as hydrogenation catalyst. Herein we studied the hydrogenation of ethylene on perfect and oxygen defective Co3O4 (1 1 1) using periodic density functional theory. The energetics and pathways of ethylene hydrogenation to ethane were determined. We have demonstrated that (i) H2 dissociation on Co3O4 is a complicated two-step process through a heterolytic cleavage, followed by the migration of H atom and finally yields the homolytic product on both perfect and oxygen defective Co3O4 (1 1 1) surfaces easily. (ii) After introducing the surface oxygen vacancy, the stepwise hydrogenation of ethylene by atomic hydrogen is much easier than that on perfect surface due to the weaker bond strength of OH group. The strength of Osbnd H bond is a crucial factor for the hydrogenation reaction which involves the breakage of Osbnd H bond. The formation of oxygen vacancy increases the electronic charges at the adjacent surface O, which reduces its capability of further gaining electrons from adsorbed atomic hydrogen and then weakens the strength of Osbnd H bond. These results emphasize the importance of the oxygen vacancies for hydrogenation on metal oxides.

MALDI In-Source Decay of Protein: The Mechanism of c-Ion Formation

PubMed Central

Takayama, Mitsuo

2016-01-01

The in-source decay (ISD) phenomenon, the fragmentation at an N–Cα bond of a peptide backbone that occurs within several tens of nanoseconds in the ion-source in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), is discussed from the standpoints of the discovery and early publications dealing with MALDI-ISD, the formation of c-ions in energy-sudden desorption/ionization methods, the formation of radical species in a MALDI, model construction for ISD, and matrix materials that are suitable for use in MALDI-ISD. The formation of c-ions derived from peptides and proteins in MALDI-ISD can be rationalized by a mechanism involving intermolecular hydrogen transfer, denoted as the “Takayama’s model” by De Pauw’s group (Anal. Chem. 79: 8678–8685, 2007). It should be emphasized that the model for MALDI-ISD was constructed on the basis of X-ray crystallography and scanning probe microscopy (SPM) analyses of matrix crystals, as well as the use of isotopically-labelled peptides. PMID:27162707

Role of ring-constrained γ-amino acid residues in α/γ-peptide folding: single-conformation UV and IR spectroscopy.

PubMed

Kusaka, Ryoji; Zhang, Di; Walsh, Patrick S; Gord, Joseph R; Fisher, Brian F; Gellman, Samuel H; Zwier, Timothy S

2013-10-24

The capped α/γ-peptide foldamers Ac-γACHC-Ala-NH-benzyl (γα) and Ac-Ala-γACHC-NH-benzyl (αγ) were studied in the gas phase under jet-cooled conditions using single-conformation spectroscopy. These molecules serve as models for local segments of larger heterogeneous 1:1 α/γ-peptides that have recently been synthesized and shown to form a 12-helix composed of repeating C12 H-bonded rings both in crystalline form and in solution [Guo, L.; et al. J. Am. Chem. Soc. 2009, 131, 16018]. The γα and αγ peptide subunits are structurally constrained at the Cβ-Cγ bond of the γ-residue with a cis-cyclohexyl ring and by an ethyl group at the Cα position. These triamides are the minimum length necessary for the formation of the C12 H-bond. Resonant two-photon ionization (R2PI) provides ultraviolet spectra that have contributions from all conformational isomers, while IR-UV hole-burning (IR-UV HB) and resonant ion-dip infrared (RIDIR) spectroscopies are used to record single-conformation UV and IR spectra, respectively. Four and six conformers are identified in the R2PI spectra of the γα and αγ peptides, respectively. RIDIR spectra in the NH stretch, amide I (C═O stretch), and amide II (NH bend) regions are compared with the predictions of density functional theory (DFT) calculations at the M05-2X/6-31+G* level, leading to definite assignments for the H-bonding architectures of the conformers. While the C12 H-bond is present in both γα and αγ, C9 rings are more prevalent, with seven of ten conformers incorporating a C9 H-bond involving in the γ-residue. Nevertheless, comparison of the assigned structures of gas-phase γα and αγ with the crystal structures for γα and larger α/γ-peptides reveals that the constrained γ-peptide backbone formed by the C9 ring is structurally similar to that formed by the larger C12 ring present in the 12-helix. These results confirm that the ACHC/ethyl constrained γ-residue is structurally preorganized to play a significant role in promoting C12 H-bond formation in larger α/γ-peptides.

DFT studies on the heterogeneous oxidation of SO2 by oxygen functional groups on graphene.

PubMed

He, Guangzhi; He, Hong

2016-11-23

The heterogeneous oxidation of SO 2 has been the subject of intense scrutiny in atmospheric chemistry because of the adverse effects of sulfate particles. Although it has been found that the soot particles with a graphene-like structure play an important role in the oxidation of SO 2 , little is known about the atomic-level mechanism involved. Here, we studied the oxidation of SO 2 on oxygen-functionalized graphene using density functional theory (DFT) calculation. The results showed that SO 2 is oxidized by the epoxide group via a two-step mechanism, where the C-O bond away from the SO 2 is broken first, followed by the breaking of the other C-O bond and the synchronous formation of a new S-O bond. The energy barriers are significantly decreased when solvation free energies are involved, suggesting that humidity is favorable for promoting the oxidation by reducing the reaction barrier. The energy barriers for H 2 SO 3 oxidation are much higher than that for SO 2 oxidation, indicating that the direct conversion of SO 2 to SO 3 is the main pathway for the oxidation of SO 2 by oxygen-functionalized graphene sheets in both the gas phase and solution. The reduced density gradient (RDG) analysis showed that the hydrogen bond formed between H 2 SO 3 and epoxide groups enhances the stability of the reaction complex, and is responsible for the high energy barrier that has to be overcome for the reaction to proceed. These atomistic studies proposed a two-step mechanism for the oxidation of SO 2 on the oxygen-functionalized graphene-like carbonaceous surfaces under ambient conditions.

Heterogeneous catalytic reactions of carbon dioxide

NASA Astrophysics Data System (ADS)

Krylov, Oleg V.; Mamedov, A. Kh

1995-09-01

The most important classes of heterogeneous catalytic reactions involving CO2 are examined: the incorporation of CO2 in the C-C, C-H, and C-N bonds with formation of carbonyl- and carboxyl-containing compounds and oxidation of other compounds by CO2. Reactions of the second class are more promising from the standpoint of the utilisation of carbon dioxide as a chemical raw material and from the standpoint of the solution of the ecological problems involving its utilisation from the gaseous waste discharged into the atmosphere. The reactions involving the oxidation of C1-C7 hydrocarbons and C1-C2 alcohols by carbon dioxide, which have been investigated by the authors of this review, are examined in detail. Catalysts based on manganese oxides are most effective in these reactions. The bibliography includes 231 references.

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

Tunneling spectroscopy measurements on hydrogen-bonded supramolecular polymers.

PubMed

Vonau, François; Shokri, Roozbeh; Aubel, Dominique; Bouteiller, Laurent; Guskova, Olga; Sommer, Jens-Uwe; Reiter, Günter; Simon, Laurent

2014-07-21

We studied the formation of hydrogen-bonded supramolecular polymers of Ethyl Hexyl Urea Toluene (EHUT) on a gold (111) surface by low temperature scanning tunneling microscopy. Tunneling spectroscopy performed along an individual molecule embedded in a self-assembled layer revealed strong changes in the value of the HOMO-LUMO gap. A variation of the LUMO state is attributed to the effect of space charge accumulation resulting from anisotropic adhesion of the molecule. In addition, for specific tunneling conditions, changes induced through the formation of hydrogen bonds became visible in the differential conductance (dI/dV) maps; isolated molecules, hydrogen bonded dimers and supramolecular polymers of EHUT were distinguishable through their electronic properties.

Enhanced van der Waals epitaxy via electron transfer enabled interfacial dative bond formation

DOE PAGES

Xie, Weiyu; Lu, Toh -Ming; Wang, Gwo -Ching; ...

2017-11-14

Enhanced van der Waals (vdW) epitaxy of semiconductors on a layered vdW substrate is identified as the formation of dative bonds. For example, despite that NbSe 2 is a vdW layeredmaterial, first-principles calculations reveal that the bond strength at a CdTe-NbSe 2 interface is five times as large as that of vdW interactions at a CdTe-graphene interface. Finally, the unconventional chemistry here is enabled by an effective net electron transfer from Cd dangling-bond states at a CdTe surface to metallic nonbonding NbSe 2 states, which is a necessary condition to activate the Cd for enhanced binding with Se.

Tunneling spectroscopy measurements on hydrogen-bonded supramolecular polymers

NASA Astrophysics Data System (ADS)

Vonau, François; Shokri, Roozbeh; Aubel, Dominique; Bouteiller, Laurent; Guskova, Olga; Sommer, Jens-Uwe; Reiter, Günter; Simon, Laurent

2014-06-01

We studied the formation of hydrogen-bonded supramolecular polymers of Ethyl Hexyl Urea Toluene (EHUT) on a gold (111) surface by low temperature scanning tunneling microscopy. Tunneling spectroscopy performed along an individual molecule embedded in a self-assembled layer revealed strong changes in the value of the HOMO-LUMO gap. A variation of the LUMO state is attributed to the effect of space charge accumulation resulting from anisotropic adhesion of the molecule. In addition, for specific tunneling conditions, changes induced through the formation of hydrogen bonds became visible in the differential conductance (dI/dV) maps; isolated molecules, hydrogen bonded dimers and supramolecular polymers of EHUT were distinguishable through their electronic properties.

Enhanced van der Waals epitaxy via electron transfer enabled interfacial dative bond formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Weiyu; Lu, Toh -Ming; Wang, Gwo -Ching

Enhanced van der Waals (vdW) epitaxy of semiconductors on a layered vdW substrate is identified as the formation of dative bonds. For example, despite that NbSe 2 is a vdW layeredmaterial, first-principles calculations reveal that the bond strength at a CdTe-NbSe 2 interface is five times as large as that of vdW interactions at a CdTe-graphene interface. Finally, the unconventional chemistry here is enabled by an effective net electron transfer from Cd dangling-bond states at a CdTe surface to metallic nonbonding NbSe 2 states, which is a necessary condition to activate the Cd for enhanced binding with Se.

The transition state for formation of the peptide bond in the ribosome

PubMed Central

Gindulyte, Asta; Bashan, Anat; Agmon, Ilana; Massa, Lou; Yonath, Ada; Karle, Jerome

2006-01-01

Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3′ end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, Ea, is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be ≈18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2′ OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments. PMID:16938893

The adsorption of methyl, acetylide, chlorine and phosphorus trifluoride on zinc oxide: A quantum-chemical study

NASA Astrophysics Data System (ADS)

Rodriguez, JoséA.

1989-11-01

The chemisorptions of methyl (CH 3), acetylide (H-CC), chlorine (Cl) and phosphorus trifluoride (PF 3) on ZnO(0001) and of Cl on ZnO(101¯0) have been examined employing semi-em- pirical quantum-chemical calculations (INDO/S) and neutral clusters of limited size (Zn 13O 13). CH 3, H-CC and Cl appear as strong electron acceptors when adsorbed on Zn sites of ZnO. The chemisorption bonds of these molecules are almost pure σ-bonds and are largely localized on the adsorption site. An increase in the work function of ZnO surfaces upon adsorption of CH 3, H-CC and Cl is predicted. The PF 3 molecule is a very weak acceptor of electrons when adsorbed on a-top sites of ZnO(0001). The bonding mechanism of CH 3, H-CC, Cl and PF 3 on the ZnO(0001) surface involves primarily the HOMO and LUMO of the adsorbate and the Zn(4s,4p) orbitals of the substrate. The effects of chemisorption on the C-H bonds of CH 3 and H-CC, the C-C bond of H-CC, and the P-F bonds of PF 3 are examined. On the basis of these INDO/S results, the possible UPS spectra for CH 3, H-CC and PF 3 adsorbed on ZnO(0001) are discussed and compared with results for adsorption on transition-metal surfaces. A general picture of the chemisorption bond of alkyls, acetylides, alkoxides, carboxylates and halogens on a-top sites of ZnO(0001) is obtained by comparing our results for adsorption of CH 3, H-CC and Cl with those previously reported for adsorption of methoxy, OH and formate.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Hydrogen Bond Switching among Flavin and Amino Acid Side Chains in the BLUF Photoreceptor Observed by Ultrafast Infrared Spectroscopy

PubMed Central

Bonetti, Cosimo; Mathes, Tilo; van Stokkum, Ivo H. M.; Mullen, Katharine M.; Groot, Marie-Louise; van Grondelle, Rienk; Hegemann, Peter; Kennis, John T. M.

2008-01-01

BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD•− and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD•− to result in FADH• on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH• C=N stretch marker mode, with tyrosine as the likely proton donor. FADH• is reoxidized in 67 ps (180 ps in D2O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by ∼180° through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch. PMID:18708458

Orientation hydrogen-bonding effect on vibronic spectra of isoquinoline in water solvent: Franck-Condon simulation and interpretation

NASA Astrophysics Data System (ADS)

Liu, Yu-Hui; Wang, Shi-Ming; Wang, Chen-Wen; Zhu, Chaoyuan; Han, Ke-Li; Lin, Sheng-Hsien

2016-10-01

The excited-state orientation hydrogen-bonding dynamics, and vibronic spectra of isoquinoline (IQ) and its cationic form IQc in water have been investigated at the time-dependent density functional theory quantum chemistry level plus Franck-Condon simulation and interpretation. The excited-state orientation hydrogen bond strengthening has been found in IQ:H2O complex due to the charge redistribution upon excitation; this is interpreted by simulated 1:1 mixed absorption spectra of free IQ and IQ:H2O complex having best agreement with experimental results. Conversely, the orientation hydrogen bond in IQc:H2O complex would be strongly weakening in the S1 state and this is interpreted by simulated absorption spectra of free IQc having best agreement with experimental results. By performing Franck-Condon simulation, it reveals that several important vibrational normal modes with frequencies about 1250 cm-1 involving the wagging motion of the hydrogen atoms are very sensitive to the formation of the orientation hydrogen bond for the IQ/IQc:H2O complex and this is confirmed by damped Franck-Condon simulation with free IQ/IQc in water. However, the emission spectra of the IQ and IQc in water have been found differently. Upon the excitation, the simulated fluorescence of IQ in water is dominated by the IQ:H2O complex; thus hydrogen bond between IQ and H2O is much easier to form in the S1 state. While the weakened hydrogen bond in IQc:H2O complex is probably cleaved upon the laser pulse because the simulated emission spectrum of the free IQc is in better agreement with the experimental results.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Na; Su, Dian; Cort, John R.

Reversible disulfide oxidation between proximal cysteines in proteins represents a common regulatory control mechanism to modulate flux through metabolic pathways in response to changing environmental conditions. To enable in vivo measurements of cellular redox changes linked to disulfide bond formation, we have synthesized a cell-permeable monosubstituted cyanine dye derivatized with arsenic (i.e., TRAP_Cy3) to trap and visualize dithiols in cytosolic proteins. Alkylation of reactive thiols prior to displacement of the bound TRAP-Cy3 by ethanedithiol permits facile protein capture and mass spectrometric identification of proximal reduced dithiols to the exclusion of individual cysteines. Applying TRAP_Cy3 to evaluate cellular responses to increasesmore » in oxygen and light levels in the photosynthetic microbe Synechococcus sp. PCC 7002, we observe large decreases in the abundance of reduced dithiols in cellular proteins, which suggest redox-dependent mechanisms involving the oxidation of proximal disulfides. Under these same growth conditions that result in the oxidation of proximal thiols, there is a reduction in the abundance of post-translational oxidative modifications involving nitrotyrosine and methionine sulfoxide formation. These results suggest that the redox status of proximal cysteines respond to environmental conditions, acting to regulate metabolic flux and minimize the formation of reactive oxygen species to decrease oxidative protein damage.« less

Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.

PubMed

Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B

2016-05-13

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes. Copyright © 2016, American Association for the Advancement of Science.

Nanomanufacturing of silicon surface with a single atomic layer precision via mechanochemical reactions.

PubMed

Chen, Lei; Wen, Jialin; Zhang, Peng; Yu, Bingjun; Chen, Cheng; Ma, Tianbao; Lu, Xinchun; Kim, Seong H; Qian, Linmao

2018-04-18

Topographic nanomanufacturing with a depth precision down to atomic dimension is of importance for advancement of nanoelectronics with new functionalities. Here we demonstrate a mask-less and chemical-free nanolithography process for regio-specific removal of atomic layers on a single crystalline silicon surface via shear-induced mechanochemical reactions. Since chemical reactions involve only the topmost atomic layer exposed at the interface, the removal of a single atomic layer is possible and the crystalline lattice beneath the processed area remains intact without subsurface structural damages. Molecular dynamics simulations depict the atom-by-atom removal process, where the first atomic layer is removed preferentially through the formation and dissociation of interfacial bridge bonds. Based on the parametric thresholds needed for single atomic layer removal, the critical energy barrier for water-assisted mechanochemical dissociation of Si-Si bonds was determined. The mechanochemical nanolithography method demonstrated here could be extended to nanofabrication of other crystalline materials.

Adsorption properties of the molecule resveratrol on CNT(8,0-10) nanotube: Geometry optimization, molecular structure, spectroscopic (NMR, UV/Vis, excited state), FMO, MEP and HOMO-LUMO investigations

NASA Astrophysics Data System (ADS)

Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Hajikolaee, Fatemeh Haji; Balakhanava, Iryna; Alnajjar, Radwan

2018-05-01

In the present work the adsorption properties of the molecule Resveratrol (RSV) (trans-3,5,4‧-Trihydroxystilbene) on CNT(8,0-10) nanotube was investigated by Density Functional Theory (DFT) in the gaseous phase for the first time. The non-bonded interaction effects of compounds RSV and CNT(8,0-10) nanotube on the electronic properties, chemical shift tensors and natural charge were determined and discussed. The electronic spectra of the RSV and the complex CNT(8,0-10)/RSV in the gaseous phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for investigation of the maximum wavelength value of the RSV before and after the non-bonded interaction with the CNT(8,0-10) nanotube and molecular orbitals involved in the formation of absorption spectrum of the complex RSV at maximum wavelength.

Radicals and molecular products from the gas-phase pyrolysis of lignin model compounds. Cinnamyl alcohol

PubMed Central

Khachatryan, Lavrent; Xu, Meng-xia; Wu, Ang-jian; Pechagin, Mikhail; Asatryan, Rubik

2016-01-01

The experimental results on detection and identification of intermediate radicals and molecular products from gas-phase pyrolysis of cinnamyl alcohol (CnA), the simplest non-phenolic lignin model compound, over the temperature range of 400–800 °C are reported. The low temperature matrix isolation – electron paramagnetic resonance (LTMI-EPR) experiments along with the theoretical calculations, provided evidences on the generation of the intermediate carbon and oxygen centered as well as oxygen-linked, conjugated radicals. A mechanistic analysis is performed based on density functional theory to explain formation of the major products from CnA pyrolysis; cinnamaldehyde, indene, styrene, benzaldehyde, 1-propynyl benzene, and 2-propenyl benzene. The evaluated bond dissociation patterns and unimolecular decomposition pathways involve dehydrogenation, dehydration, 1,3-sigmatropic H-migration, 1,2-hydrogen shift, C—O and C—C bond cleavage processes. PMID:28344372

Synthesis, characterization, AIM and NBO analysis of HMX/DMI cocrystal explosive

NASA Astrophysics Data System (ADS)

Lin, He; Zhu, Shun-Guan; Li, Hong-Zhen; Peng, Xin-Hua

2013-09-01

1,3,5,7-Tetranitro-1,3,5,7-tetrazacyclooctane (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal explosive was synthesized and characterized by using X-ray single crystal diffraction. HMX/DMI cocrystal crystallizes in the monoclinic system (space group Cm), with cell parameters a = 7.231(2)Å, b = 14.739(2)Å, c = 7.552(1)Å, β = 96.66°. In addition, density functional theory, involving binding energy, natural bond orbital (NBO) analysis, atoms in molecule (AIM) analysis, band structure, and density of states, was adopted to investigate intermolecular interactions for the formation of HMX/DMI cocrystal. The results show that hydrogen bondings between methylene groups of HMX molecules and O atoms of DMI molecules are the main intermolecular interactions. This research provides the basis for further design of cocrystal explosives, which are composed of HMX and energetic materials.

True and masked three-coordinate T-shaped platinum(II) intermediates.

PubMed

Ortuño, Manuel A; Conejero, Salvador; Lledós, Agustí

2013-01-01

Although four-coordinate square-planar geometries, with a formally 16-electron counting, are absolutely dominant in isolated Pt(II) complexes, three-coordinate, 14-electron Pt(II) complexes are believed to be key intermediates in a number of platinum-mediated organometallic transformations. Although very few authenticated three-coordinate Pt(II) complexes have been characterized, a much larger number of complexes can be described as operationally three-coordinate in a kinetic sense. In these compounds, which we have called masked T-shaped complexes, the fourth position is occupied by a very weak ligand (agostic bond, solvent molecule or counteranion), which can be easily displaced. This review summarizes the structural features of the true and masked T-shaped Pt(II) complexes reported so far and describes synthetic strategies employed for their formation. Moreover, recent experimental and theoretical reports are analyzed, which suggest the involvement of such intermediates in reaction mechanisms, particularly C-H bond-activation processes.

Crystal and molecular structure of eight organic acid-base adducts from 2-methylquinoline and different acids

NASA Astrophysics Data System (ADS)

Zhang, Jing; Jin, Shouwen; Tao, Lin; Liu, Bin; Wang, Daqi

2014-08-01

Eight supramolecular complexes with 2-methylquinoline and acidic components as 4-aminobenzoic acid, 2-aminobenzoic acid, salicylic acid, 5-chlorosalicylic acid, 3,5-dinitrosalicylic acid, malic acid, sebacic acid, and 1,5-naphthalenedisulfonic acid were synthesized and characterized by X-ray crystallography, IR, mp, and elemental analysis. All of the complexes are organic salts except compound 2. All supramolecular architectures of 1-8 involve extensive classical hydrogen bonds as well as other noncovalent interactions. The results presented herein indicate that the strength and directionality of the classical hydrogen bonds (ionic or neutral) between acidic components and 2-methylquinoline are sufficient to bring about the formation of binary organic acid-base adducts. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, the complexes 1-8 displayed 2D-3D framework structure.

A classical but new kinetic equation for hydride transfer reactions.

PubMed

Zhu, Xiao-Qing; Deng, Fei-Huang; Yang, Jin-Dong; Li, Xiu-Tao; Chen, Qiang; Lei, Nan-Ping; Meng, Fan-Kun; Zhao, Xiao-Peng; Han, Su-Hui; Hao, Er-Jun; Mu, Yuan-Yuan

2013-09-28

A classical but new kinetic equation to estimate activation energies of various hydride transfer reactions was developed according to transition state theory using the Morse-type free energy curves of hydride donors to release a hydride anion and hydride acceptors to capture a hydride anion and by which the activation energies of 187 typical hydride self-exchange reactions and more than thirty thousand hydride cross transfer reactions in acetonitrile were safely estimated in this work. Since the development of the kinetic equation is only on the basis of the related chemical bond changes of the hydride transfer reactants, the kinetic equation should be also suitable for proton transfer reactions, hydrogen atom transfer reactions and all the other chemical reactions involved with breaking and formation of chemical bonds. One of the most important contributions of this work is to have achieved the perfect unity of the kinetic equation and thermodynamic equation for hydride transfer reactions.

Probing the Early Stages of Solvation of cis-Pinate Dianions by Water, Acetonitrile, and Methanol: A Photoelectron Spectroscopy and Theoretical Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Gao-Lei; Kong, Xiang-Tao; Valiev, Marat

2016-01-01

Cis-pinic acid is one of the most important oxidation products of α-pinene – a key monoterpene compound in biogenic emission processes affecting the atmosphere. Molecular level understanding of interactions involved in the cluster formations around cis-pinic acid is an important and necessary prerequisite toward ascertaining its role in the aerosol formation processes. In this work, we studied the structures and energetics of the solvated clusters of cis-pinate (cis-PA²⁻), the doubly deprotonated dicarboxylate of cis-pinic acid, with H₂O, CH₃OH, and CH₃CN by negative ion photoelectron spectroscopy and ab initio theoretical calculations. We found that cis-PA²⁻ prefers being solvated alternately on themore » two -CO₂⁻ groups with increase of solvent coverage, a well-known solvation pattern that has been observed in microhydrated linear dicarboxylate dianion (DC n²⁻) clusters. Experiments and calculations further reveal an intriguing feature for the existence of the asymmetric type isomers for cis-PA2–(H2O)2 and cis-PA²⁻(CH₃OH)₂, in which both solvent molecules interact with only one of the -CO²⁻ groups – a phenomena that has not been observed in DCn²⁻ water clusters and exhibits the subtle effect of the rigid four-membered carbon ring brought in on the cis-PA²⁻ solvation. The dominant interactions between cis-PA²⁻ and solvent molecules are forming bidentate O–···H–O H-bonds for H₂O, O–···H–O and O–···H–C H-bonds for CH₃OH, and tridentate O–···H–C H-bonds for CH₃CN. The formation of inter-solvent H-bonds between H₂O and CH₃CN is found to be favorable in mixed solvent clusters, distinctly different from that between H₂O and CH₃OH. These findings have important implications for understanding the mechanism of cluster growth and nucleation of atmospheric organic aerosols and the nature of structure-function relationship of proteins containing carboxylate groups under various solvent environments.« less

Surface pretreatments for medical application of adhesion

PubMed Central

Erli, Hans J; Marx, Rudolf; Paar, Othmar; Niethard, Fritz U; Weber, Michael; Wirtz, Dieter C

2003-01-01

Medical implants and prostheses (artificial hips, tendono- and ligament plasties) usually are multi-component systems that may be machined from one of three material classes: metals, plastics and ceramics. Typically, the body-sided bonding element is bone. The purpose of this contribution is to describe developments carried out to optimize the techniques , connecting prosthesis to bone, to be joined by an adhesive bone cement at their interface. Although bonding of organic polymers to inorganic or organic surfaces and to bone has a long history, there remains a serious obstacle in realizing long-term high-bonding strengths in the in vivo body environment of ever present high humidity. Therefore, different pretreatments, individually adapted to the actual combination of materials, are needed to assure long term adhesive strength and stability against hydrolysis. This pretreatment for metal alloys may be silica layering; for PE-plastics, a specific plasma activation; and for bone, amphiphilic layering systems such that the hydrophilic properties of bone become better adapted to the hydrophobic properties of the bone cement. Amphiphilic layering systems are related to those developed in dentistry for dentine bonding. Specific pretreatment can significantly increase bond strengths, particularly after long term immersion in water under conditions similar to those in the human body. The bond strength between bone and plastic for example can be increased by a factor approaching 50 (pealing work increasing from 30 N/m to 1500 N/m). This review article summarizes the multi-disciplined subject of adhesion and adhesives, considering the technology involved in the formation and mechanical performance of adhesives joints inside the human body. PMID:14561228

Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal-carbon bonding

NASA Astrophysics Data System (ADS)

Deng, Qingming; Heine, Thomas; Irle, Stephan; Popov, Alexey A.

2016-02-01

The endohedral metallofullerene (EMF) self-assembly process in Sc/carbon vapor in the presence and absence of an inert cooling gas (helium) is systematically investigated using quantum chemical molecular dynamics simulations. It is revealed that the presence of He atoms accelerates the formation of pentagons and hexagons and reduces the size of the self-assembled carbon cages in comparison with analogous He-free simulations. As a result, the Sc/C/He system simulations produce a larger number of successful trajectories (i.e. leading to Sc-EMFs) with more realistic cage-size distribution than simulations of the Sc/C system. The main Sc encapsulation mechanism involves nucleation of several hexagons and pentagons with Sc atoms already at the early stages of carbon vapor condensation. In such proto-cages, both Sc-C σ-bonds and coordination bonds between Sc atoms and the π-system of the carbon network are present. Sc atoms are thus rather labile and can move along the carbon network, but the overall bonding is sufficiently strong to prevent dissociation even at temperatures around 2000 kelvin. Further growth of the fullerene cage results in the encapsulation of one or two Sc atoms within the fullerene. In agreement with experimental studies, an extension of the simulations to Fe and Ti as the metal component showed that Fe-EMFs are not formed at all, whereas Ti is prone to form Ti-EMFs with small cage sizes, including Ti@C28-Td and Ti@C30-C2v(3).The endohedral metallofullerene (EMF) self-assembly process in Sc/carbon vapor in the presence and absence of an inert cooling gas (helium) is systematically investigated using quantum chemical molecular dynamics simulations. It is revealed that the presence of He atoms accelerates the formation of pentagons and hexagons and reduces the size of the self-assembled carbon cages in comparison with analogous He-free simulations. As a result, the Sc/C/He system simulations produce a larger number of successful trajectories (i.e. leading to Sc-EMFs) with more realistic cage-size distribution than simulations of the Sc/C system. The main Sc encapsulation mechanism involves nucleation of several hexagons and pentagons with Sc atoms already at the early stages of carbon vapor condensation. In such proto-cages, both Sc-C σ-bonds and coordination bonds between Sc atoms and the π-system of the carbon network are present. Sc atoms are thus rather labile and can move along the carbon network, but the overall bonding is sufficiently strong to prevent dissociation even at temperatures around 2000 kelvin. Further growth of the fullerene cage results in the encapsulation of one or two Sc atoms within the fullerene. In agreement with experimental studies, an extension of the simulations to Fe and Ti as the metal component showed that Fe-EMFs are not formed at all, whereas Ti is prone to form Ti-EMFs with small cage sizes, including Ti@C28-Td and Ti@C30-C2v(3). Electronic supplementary information (ESI) available: Additional information on metal-carbon bonding and MD simulations. See DOI: 10.1039/c5nr08645k

Synthesis, structure and reactivity of a terminal magnesium fluoride compound, [TpBut,Me]MgF: hydrogen bonding, halogen bonding and C-F bond formation.

PubMed

Rauch, Michael; Ruccolo, Serge; Mester, John Paul; Rong, Yi; Parkin, Gerard

2016-01-01

The bulky tris(3- tert -butyl-5-pyrazolyl)hydroborato ligand, [Tp Bu t ,Me ], has been employed to obtain the first structurally characterized example of a molecular magnesium compound that features a terminal fluoride ligand, namely [Tp Bu t ,Me ]MgF, via the reaction of [Tp Bu t ,Me ]MgMe with Me 3 SnF. The chloride, bromide and iodide complexes, [Tp Bu t ,Me ]MgX (X = Cl, Br, I), can also be obtained by an analogous method using Me 3 SnX. The molecular structures of the complete series of halide derivatives, [Tp Bu t ,Me ]MgX (X = F, Cl, Br, I) have been determined by X-ray diffraction. In each case, the Mg-X bond lengths are shorter than the sum of the covalent radii, thereby indicating that there is a significant ionic component to the bonding, in agreement with density functional theory calculations. The fluoride ligand of [Tp Bu t ,Me ]MgF undergoes halide exchange with Me 3 SiX (X = Cl, Br, I) to afford [Tp Bu t ,Me ]MgX and Me 3 SiF. The other halide derivatives [Tp Bu t ,Me ]MgX undergo similar exchange reactions, but the thermodynamic driving forces are much smaller than those involving fluoride transfer, a manifestation of the often discussed silaphilicity of fluorine. In accord with the highly polarized Mg-F bond, the fluoride ligand of [Tp Bu t ,Me ]MgF is capable of serving as a hydrogen bond and halogen bond acceptor, such that it forms adducts with indole and C 6 F 5 I. [Tp Bu t ,Me ]MgF also reacts with Ph 3 CCl to afford Ph 3 CF, thereby demonstrating that [Tp Bu t ,Me ]MgF may be used to form C-F bonds.

Spectroscopic investigation on cocrystal formation between adenine and fumaric acid based on infrared and Raman techniques

NASA Astrophysics Data System (ADS)

Du, Yong; Fang, Hong Xia; Zhang, Qi; Zhang, Hui Li; Hong, Zhi

2016-01-01

As an important component of double-stranded DNA, adenine has powerful hydrogen-bond capability, due to rich hydrogen bond donors and acceptors existing within its molecular structure. Therefore, it is easy to form cocrystal between adenine and other small molecules with intermolecular hydrogen-bond effect. In this work, cocrystal of adenine and fumaric acid has been characterized as model system by FT-IR and FT-Raman spectral techniques. The experimental results show that the cocrystal formed between adenine and fumaric acid possesses unique spectroscopical characteristic compared with that of starting materials. Density functional theory (DFT) calculation has been performed to optimize the molecular structures and simulate vibrational modes of adenine, fumaric acid and the corresponding cocrystal. Combining the theoretical and experimental vibrational results, the characteristic bands corresponding to bending and stretching vibrations of amino and carbonyl groups within cocrystal are shifted into lower frequencies upon cocrystal formation, and the corresponding bond lengths show some increase due to the effect of intermolecular hydrogen bonding. Different vibrational modes shown in the experimental spectra have been assigned based on the simulation DFT results. The study could provide experimental and theoretical benchmarks to characterize cocrystal formed between active ingredients and cocrystal formers and also the intermolecular hydrogen-bond effect within cocrystal formation process by vibrational spectroscopic techniques.

Synchrony and exertion during dance independently raise pain threshold and encourage social bonding

PubMed Central

Tarr, Bronwyn; Launay, Jacques; Cohen, Emma; Dunbar, Robin

2015-01-01

Group dancing is a ubiquitous human activity that involves exertive synchronized movement to music. It is hypothesized to play a role in social bonding, potentially via the release of endorphins, which are analgesic and reward-inducing, and have been implicated in primate social bonding. We used a 2 × 2 experimental design to examine effects of exertion and synchrony on bonding. Both demonstrated significant independent positive effects on pain threshold (a proxy for endorphin activation) and in-group bonding. This suggests that dance which involves both exertive and synchronized movement may be an effective group bonding activity. PMID:26510676

Chalcogen- and halogen-bonds involving SX2 (X = F, Cl, and Br) with formaldehyde.

PubMed

Mo, Lixin; Zeng, Yanli; Li, Xiaoyan; Zhang, Xueying; Meng, Lingpeng

2016-07-01

The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)-S bonds, and two σ-holes upon extension of S-Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F-S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX'2 (X = F, Cl, Br, and X' = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds. Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl2S···H2CO···SCl2 complex.

Nucleic acids, proteins, and chirality

NASA Technical Reports Server (NTRS)

Usher, D. A.; Profy, A. T.; Walstrum, S. A.; Needels, M. C.; Bulack, S. C.; Lo, K. M.

1984-01-01

The present investigation is concerned with experimental results related, in one case, to the chirality of nucleotides, and, in another case, to the possibility of a link between the chirality of nucleic acids, and that of peptides. It has been found that aminoacylation of the 'internal' hydroxyl group of a dinucleoside monophosphate can occur stereoselectively. However, this reaction has not yet been made a part of a working peptide synthesis scheme. The formation and cleavage of oligonucleotides is considered. In the event of the formation of a helical complex between the oligonucleotide and the polymer, 1-prime,5-prime-bonds in the oligomer are found to become more resistant towards cleavage. The conditions required for peptide bond formation are examined, taking into account the known structures of RNA and possible mechanisms for prebiotic peptide bond formation. The possibility is considered that the 2-prime,5-prime-internucleotide linkage could have played an important part in the early days of biological peptide synthesis.

Photosynthesis. Electronic structure of the oxygen-evolving complex in photosystem II prior to O-O bond formation.

PubMed

Cox, Nicholas; Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A; Boussac, Alain; Lubitz, Wolfgang

2014-08-15

The photosynthetic protein complex photosystem II oxidizes water to molecular oxygen at an embedded tetramanganese-calcium cluster. Resolving the geometric and electronic structure of this cluster in its highest metastable catalytic state (designated S3) is a prerequisite for understanding the mechanism of O-O bond formation. Here, multifrequency, multidimensional magnetic resonance spectroscopy reveals that all four manganese ions of the catalyst are structurally and electronically similar immediately before the final oxygen evolution step; they all exhibit a 4+ formal oxidation state and octahedral local geometry. Only one structural model derived from quantum chemical modeling is consistent with all magnetic resonance data; its formation requires the binding of an additional water molecule. O-O bond formation would then proceed by the coupling of two proximal manganese-bound oxygens in the transition state of the cofactor. Copyright © 2014, American Association for the Advancement of Science.

Pre-expression of a sulfhydryl oxidase significantly increases the yields of eukaryotic disulfide bond containing proteins expressed in the cytoplasm of E.coli.

PubMed

Nguyen, Van Dat; Hatahet, Feras; Salo, Kirsi E H; Enlund, Eveliina; Zhang, Chi; Ruddock, Lloyd W

2011-01-07

Disulfide bonds are one of the most common post-translational modifications found in proteins. The production of proteins that contain native disulfide bonds is challenging, especially on a large scale. Either the protein needs to be targeted to the endoplasmic reticulum in eukaryotes or to the prokaryotic periplasm. These compartments that are specialised for disulfide bond formation have an active catalyst for their formation, along with catalysts for isomerization to the native state. We have recently shown that it is possible to produce large amounts of prokaryotic disulfide bond containing proteins in the cytoplasm of wild-type bacteria such as E. coli by the introduction of catalysts for both of these processes. Here we show that the introduction of Erv1p, a sulfhydryl oxidase and a disulfide isomerase allows the efficient formation of natively folded eukaryotic proteins with multiple disulfide bonds in the cytoplasm of E. coli. The production of disulfide bonded proteins was also aided by the use of an appropriate fusion protein to keep the folding intermediates soluble and by choice of media. By combining the pre-expression of a sulfhydryl oxidase and a disulfide isomerase with these other factors, high level expression of even complex disulfide bonded eukaryotic proteins is possible Our results show that the production of eukaryotic proteins with multiple disulfide bonds in the cytoplasm of E. coli is possible. The required exogenous components can be put onto a single plasmid vector allowing facile transfer between different prokaryotic strains. These results open up new avenues for the use of E. coli as a microbial cell factory.

Pre-expression of a sulfhydryl oxidase significantly increases the yields of eukaryotic disulfide bond containing proteins expressed in the cytoplasm of E.coli

PubMed Central

2011-01-01

Background Disulfide bonds are one of the most common post-translational modifications found in proteins. The production of proteins that contain native disulfide bonds is challenging, especially on a large scale. Either the protein needs to be targeted to the endoplasmic reticulum in eukaryotes or to the prokaryotic periplasm. These compartments that are specialised for disulfide bond formation have an active catalyst for their formation, along with catalysts for isomerization to the native state. We have recently shown that it is possible to produce large amounts of prokaryotic disulfide bond containing proteins in the cytoplasm of wild-type bacteria such as E. coli by the introduction of catalysts for both of these processes. Results Here we show that the introduction of Erv1p, a sulfhydryl oxidase and a disulfide isomerase allows the efficient formation of natively folded eukaryotic proteins with multiple disulfide bonds in the cytoplasm of E. coli. The production of disulfide bonded proteins was also aided by the use of an appropriate fusion protein to keep the folding intermediates soluble and by choice of media. By combining the pre-expression of a sulfhydryl oxidase and a disulfide isomerase with these other factors, high level expression of even complex disulfide bonded eukaryotic proteins is possible Conclusions Our results show that the production of eukaryotic proteins with multiple disulfide bonds in the cytoplasm of E. coli is possible. The required exogenous components can be put onto a single plasmid vector allowing facile transfer between different prokaryotic strains. These results open up new avenues for the use of E. coli as a microbial cell factory. PMID:21211066

Unravelling the reaction mechanism of matrix metalloproteinase 3 using QM/MM calculations

NASA Astrophysics Data System (ADS)

Feliciano, Gustavo Troiano; da Silva, Antônio José Roque

2015-07-01

The matrix metalloproteinase family (MMP) constitutes a family of zinc (Zn) proteases that catalyze the breaking of peptide bonds in proteins. These enzymes are very promising drug targets, since they are involved in remodeling and degradation of the extracellular matrix, which is a key process required for cancer metastasis, and thus, their reaction mechanism has been an area of intensive research. Early proposal based on acid base catalyzed hydrolysis, suggested that a conserved zinc bound water molecule acted as the nucleophile attacking the peptide bond carbon, after being activated by essential glutamate. The possibility of a direct nucleophilic attack by the enzyme, performed by the glutamate was also suggested. These are the key yet unsolved issues about MMP reaction mechanism. In the present work, we used hybrid quantum/classical calculations to analyze the structure and energetics of different possible hydrolysis reaction paths. The results support a water mediated mechanism, where both the nucleophile water molecule and the carbonyl oxygen of the scissile peptide bond are coordinated to zinc in the reactive configuration, while the essential glutamate acts as the base accepting the proton from the nucleophilic water. Formation of the carbon-oxygen bond and breaking of carbon-nitrogen bond were found to be concerted events, with a computed barrier of 14.8 kcal/mol. Substrate polarization was found to be important for the observed reaction mechanism, and a substantial change in the metal coordination environment was observed, particularly, regarding the zinc-histidine coordination.

Bonding reactivity descriptor from conceptual density functional theory and its applications to elucidate bonding formation

NASA Astrophysics Data System (ADS)

Zhou, Pan-Pan; Liu, Shubin; Ayers, Paul W.; Zhang, Rui-Qin

2017-10-01

Condensed-to-atom Fukui functions which reflect the atomic reactivity like the tendency susceptible to either nucleophilic or electrophilic attack demonstrate the bonding trend of an atom in a molecule. Accordingly, Fukui functions based concepts, that is, bonding reactivity descriptors which reveal the bonding properties of molecules in the reaction were put forward and then applied to pericyclic and cluster reactions to confirm their effectiveness and reliability. In terms of the results from the bonding descriptors, a covalent bond can readily be predicted between two atoms with large Fukui functions (i.e., one governs nucleophilic attack while the other one governs electrophilic attack, or both of them govern radical attacks) for pericyclic reactions. For SinOm clusters' reactions, the clusters with a low O atom ratio readily form a bond between two Si atoms with big values of their Fukui functions in which they respectively govern nucleophilic and electrophilic attacks or both govern radical attacks. Also, our results from bonding descriptors show that Si—Si bonds can be formed via the radical mechanism between two Si atoms, and formations of Si—O and O—O bonds are possible when the O content is high. These results conform with experimental findings and can help experimentalists design appropriate clusters to synthesize Si nanowires with high yields. The approach established in this work could be generalized and applied to study reactivity properties for other systems.

19 CFR 210.68 - Complainant's temporary relief bond.

Code of Federal Regulations, 2010 CFR

2010-04-01

... bond is being posted, the amount of the bond, the effective date and duration of the bond (as... 19 Customs Duties 3 2010-04-01 2010-04-01 false Complainant's temporary relief bond. 210.68... relief bond. (a) In every investigation under this part involving a motion for temporary relief, the...

Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure on phosphodiester bond formation

NASA Technical Reports Server (NTRS)

Ferris, James P.; KAMALUDDIN

1989-01-01

The formation of oligomers from deoxynucleotides, catalyzed by Na(+)-montmorillonite, was investigated with special attention given to the effect of the monomer structure on the phosphodiester bond formation. It was found that adenine deoxynucleotides bind more strongly to montmorillonite than do the corresponding ribonucleotides and thymidine nucleotides. Tetramers of 2-prime-dpA were detected in the reaction of 2-prime-d-5-prime-AMP with a water-soluble carbodiimide EDAC in the presence of Na(+)-montmorillonite, illustrating the possible role of minerals in the formation of biopolymers on the primitive earth.

A single Watson-Crick G x C base pair in water: aqueous hydrogen bonds in hydrophobic cavities.

PubMed

Sawada, Tomohisa; Fujita, Makoto

2010-05-26

Hydrogen bond (H-bond) formation in water has been a challenging task because water molecules are constant competitors. In biological systems, however, stable H-bonds are formed by shielding the H-bonding sites from the competing water molecules within hydrophobic pockets. Inspired by the nature's elaborated way, we found that even mononucleotides (G and C) can form the minimal G x C Watson-Crick pair in water by simply providing a synthetic cavity that efficiently shields the Watson-Crick H-bonding sites. The minimal Watson-Crick structure in water was elucidated by NMR study and firmly characterized by crystallographic analysis. The crystal structure also displays that, within the cavity, coencapsulated anions and solvents efficiently mediate the minimal G x C Watson-Crick pair formation. Furthermore, the competition experiments with the other nucleobases clearly revealed the evident selectivity for the G x C base pairing in water. These results show the fact that a H-bonded nucleobase pair was effectively induced and stabilized in the local environment of an artificial hydrophobic cavity.

Multiple hydrogen bonds. Mass spectra of hydrogen bonded heterodimers. A comparison of ESI- and REMPI-ReTOF-MS.

PubMed

Taubitz, Jörg; Lüning, Ulrich; Grotemeyer, Jürgen

2004-11-07

Resonance enhanced multi-photon ionization-reflectron time of flight mass spectrometry is the analytical method of choice to observe hydrogen bonded supramolecules in the gas phase when protonation of basic centers competes with cluster formation.

C–H bond halogenation catalyzed or mediated by copper: an overview

PubMed Central

Hao, Wenyan

2015-01-01

Summary Carbon–halogen (C–X) bonds are amongst the most fundamental groups in organic synthesis, they are frequently and widely employed in the synthesis of numerous organic products. The generation of a C–X bond, therefore, constitutes an issue of universal interest. Herein, the research advances on the copper-catalyzed and mediated C–X (X = F, Cl, Br, I) bond formation via direct C–H bond transformation is reviewed. PMID:26664634

Catalytic RNA and synthesis of the peptide bond

NASA Technical Reports Server (NTRS)

Usher, D. A.; Kozlowski, M.; Zou, X.

1991-01-01

We are studying whether the L-19 IVS ribozyme from Tetrahymena thermophila can catalyze the formation of the peptide bond when it is supplied with synthetic aminoacyl oligonucleotides. If this reaction works, it could give us some insight into the mechanism of peptide bond formation and the origin of coded protein synthesis. Two short oligoribonucleotides, CCCCC and a protected form of CCCCU were prepared; the former was made by the controlled hydrolysis of Poly(C), and the later by multistep chemical synthesis from the protected monomers. The homopentamer was then aminocylated using C-14 labelled Boc-protected glycine imidazolide. This aminoacylated oligo-nucleotide has now been shown to enter the active site of the L-19 IVS, and aminoacyl transfer, and peptide bond formation reactions are being sought. Our synthesis of CCCCU made us aware of the inadequacy of many of the 2'- hydroxyl protecting groups that are in use today and we therefore designed a new 2'- protecting group that is presently being tested.

The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.

PubMed

Zarzycki, Jan; Kerfeld, Cheryl A

2013-11-09

Malyl-CoA lyase (MCL) is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related Coenzyme A (CoA) thioesters. This enzyme plays a crucial, multifunctional role in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus. A second, phylogenetically distinct MCL from Rhodobacter sphaeroides is involved in the ethylmalonyl-CoA pathway for acetate assimilation. Both MCLs belong to the large superfamily of CitE-like enzymes, which includes the name-giving β-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases). Here we report the first crystal structures of MCLs from two different phylogenetic subgroups in apo- and substrate-bound forms. Both the C. aurantiacus and the R. sphaeroides MCL contain elaborations on the canonical β8/α8 TIM barrel fold and form hexameric assemblies. Upon ligand binding, changes in the C-terminal domains of the MCLs result in closing of the active site, with the C-terminal domain of one monomer forming a lid over and contributing side chains to the active site of the adjacent monomer. The distinctive features of the two MCL subgroups were compared to known structures of other CitE-like superfamily enzymes and to malate synthases, providing insight into the structural subtleties that underlie the functional versatility of these enzymes. Although the C. aurantiacus and the R. sphaeroides MCLs have divergent primary structures (~37% identical), their tertiary and quaternary structures are very similar. It can be assumed that the C-C bond formation catalyzed by the MCLs occurs as proposed for malate synthases. However, a comparison of the two MCL structures with known malate synthases raised the question why the MCLs are not also able to hydrolyze CoA thioester bonds. Our results suggest the previously proposed reaction mechanism for malate synthases may be incomplete or not entirely correct. Further studies involving site-directed mutagenesis based on these structures may be required to solve this puzzling question.

Chemoselective Radical Dehalogenation and C-C Bond Formation on Aryl Halide Substrates Using Organic Photoredox Catalysts.

PubMed

Poelma, Saemi O; Burnett, G Leslie; Discekici, Emre H; Mattson, Kaila M; Treat, Nicolas J; Luo, Yingdong; Hudson, Zachary M; Shankel, Shelby L; Clark, Paul G; Kramer, John W; Hawker, Craig J; Read de Alaniz, Javier

2016-08-19

Despite the number of methods available for dehalogenation and carbon-carbon bond formation using aryl halides, strategies that provide chemoselectivity for systems bearing multiple carbon-halogen bonds are still needed. Herein, we report the ability to tune the reduction potential of metal-free phenothiazine-based photoredox catalysts and demonstrate the application of these catalysts for chemoselective carbon-halogen bond activation to achieve C-C cross-coupling reactions as well as reductive dehalogenations. This procedure works both for conjugated polyhalides as well as unconjugated substrates. We further illustrate the usefulness of this protocol by intramolecular cyclization of a pyrrole substrate, an advanced building block for a family of natural products known to exhibit biological activity.

Binding matter with antimatter: the covalent positron bond.

PubMed

Charry, Jorge Alfonso; Varella, Marcio T Do N; Reyes, Andrés

2018-05-16

We report sufficient theoretical evidence of the energy stability of the e⁺H₂²⁻ molecule, formed by two H⁻ anions and one positron. Analysis of the electronic and positronic densities of the latter compound undoubtedly points out the formation of a positronic covalent bond between the otherwise repelling hydride anions. The lower limit for the bonding energy of the e⁺H₂²⁻ molecule is 74 kJ/mol (0.77 eV), accounting for the zero-point vibrational correction. The formation of a non electronic covalent bond is fundamentally distinct from positron attachment to stable molecules, as the latter process is characterized by a positron affinity, analogous to the electron affinity. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, spectroscopic characterization and structural studies of a new proton transfer (H-bonded) complex of o-phenylenediamine with L-tartaric acid

NASA Astrophysics Data System (ADS)

Khan, Ishaat M.; Ahmad, Afaq

2013-10-01

A proton transfer or H-bonded (CT) complex of o-phenylenediamine (OPD) as donor with L-tartaric acid (TART) as acceptor was synthesized and characterized by spectral techniques such as FTIR, 1H NMR, elemental analysis, TGA-TDA, X-ray crystallography and spectrophotometric studies. The structural investigations exhibit that the cation [OPD+] and anion [TART-] are linked together through strong N+-H⋯O- type hydrogen bonds due to transfer of proton from acceptor to donor. Formed H-bonded complex exhibits well resolved proton transfer bands in the regions where neither donor nor acceptor has any absorption. The stoichiometry of the H-bonded complex (HBC) was found to be 1:1, determined by straight line methods. Spectrophotometric studies have been performed at room temperature and Benesi-Hildebrand equation was used to determine formation constant (KCT), molar extinction coefficient (ɛCT) and also transition energy (ECT) of the H-bonded complex. Spectrophotomeric and crystallographic studies have ascertained the formation of 1:1 H-bonded complex. Thermal analysis (TGA-DTA) was also used to confirm the thermal fragmentation and the stability of the synthesized H-bonded complex.

Chirality and protein biosynthesis.

PubMed

Banik, Sindrila Dutta; Nandi, Nilashis

2013-01-01

Chirality is present at all levels of structural hierarchy of protein and plays a significant role in protein biosynthesis. The macromolecules involved in protein biosynthesis such as aminoacyl tRNA synthetase and ribosome have chiral subunits. Despite the omnipresence of chirality in the biosynthetic pathway, its origin, role in current pathway, and importance is far from understood. In this review we first present an introduction to biochirality and its relevance to protein biosynthesis. Major propositions about the prebiotic origin of biomolecules are presented with particular reference to proteins and nucleic acids. The problem of the origin of homochirality is unresolved at present. The chiral discrimination by enzymes involved in protein synthesis is essential for keeping the life process going. However, questions remained pertaining to the mechanism of chiral discrimination and concomitant retention of biochirality. We discuss the experimental evidence which shows that it is virtually impossible to incorporate D-amino acids in protein structures in present biosynthetic pathways via any of the two major steps of protein synthesis, namely aminoacylation and peptide bond formation reactions. Molecular level explanations of the stringent chiral specificity in each step are extended based on computational analysis. A detailed account of the current state of understanding of the mechanism of chiral discrimination during aminoacylation in the active site of aminoacyl tRNA synthetase and peptide bond formation in ribosomal peptidyl transferase center is presented. Finally, it is pointed out that the understanding of the mechanism of retention of enantiopurity has implications in developing novel enzyme mimetic systems and biocatalysts and might be useful in chiral drug design.

Oxidation of p53 through DNA Charge Transport Involves a Network of Disulfides within the DNA-Binding Domain

PubMed Central

2016-01-01

Transcription factor p53 plays a critical role in the cellular response to stress stimuli. We have seen that p53 dissociates selectively from various promoter sites as a result of oxidation at long-range through DNA-mediated charge transport (CT). Here, we examine this chemical oxidation and determine the residues in p53 that are essential for oxidative dissociation, focusing on the network of cysteine residues adjacent to the DNA-binding site. Of the eight mutants studied, only the C275S mutation shows decreased affinity for the Gadd45 promoter site. However, both mutations C275S and C277S result in substantial attenuation of oxidative dissociation, with C275S causing the most severe attenuation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide-labeled, whereas oxidized cysteines participating in disulfide bonds were 13C2D2-iodoacetamide-labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed by mass spectrometry. A distinct shift in peptide labeling toward 13C2D2-iodoacetamide-labeled cysteines is observed in oxidized samples, confirming that chemical oxidation of p53 occurs at long range. All observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds among the cysteine network. On the basis of these data, it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA. PMID:25584637

Catalytic Activity of the Anaerobic Tyrosine Lyase Required for Thiamine Biosynthesis in Escherichia coli*

PubMed Central

Challand, Martin R.; Martins, Filipa T.; Roach, Peter L.

2010-01-01

Thiazole synthase in Escherichia coli is an αβ heterodimer of ThiG and ThiH. ThiH is a tyrosine lyase that cleaves the Cα–Cβ bond of tyrosine, generating p-cresol as a by-product, to form dehydroglycine. This reactive intermediate acts as one of three substrates for the thiazole cyclization reaction catalyzed by ThiG. ThiH is a radical S-adenosylmethionine (AdoMet) enzyme that utilizes a [4Fe-4S]+ cluster to reductively cleave AdoMet, forming methionine and a 5′-deoxyadenosyl radical. Analysis of the time-dependent formation of the reaction products 5′-deoxyadenosine (DOA) and p-cresol has demonstrated catalytic behavior of the tyrosine lyase. The kinetics of product formation showed a pre-steady state burst phase, and the involvement of DOA in product inhibition was identified by the addition of 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase to activity assays. This hydrolyzed the DOA and changed the rate-determining step but, in addition, substantially increased the uncoupled turnover of AdoMet. Addition of glyoxylate and ammonium inhibited the tyrosine cleavage reaction, but the reductive cleavage of AdoMet continued in an uncoupled manner. Tyrosine analogues were incubated with ThiGH, which showed a strong preference for phenolic substrates. 4-Hydroxyphenylpropionic acid analogues allowed uncoupled AdoMet cleavage but did not result in further reaction (Cα–Cβ bond cleavage). The results of the substrate analogue studies and the product inhibition can be explained by a mechanistic hypothesis involving two reaction pathways, a product-forming pathway and a futile cycle. PMID:19923213

The Role of zinc in the disulphide stress-regulated anti-sigma factor RsrA from Streptomyces coelicolor.

PubMed

Li, Wei; Bottrill, Andrew R; Bibb, Maureen J; Buttner, Mark J; Paget, Mark S B; Kleanthous, Colin

2003-10-17

The regulation of disulphide stress in actinomycetes such as Streptomyces coelicolor is known to involve the zinc-containing anti-sigma factor RsrA that binds and inactivates the redox-regulated sigma factor sigmaR. However, it is not known how RsrA senses disulphide stress nor what role the metal ion plays. Using in vitro assays, we show that while zinc is not required for sigmaR binding it is required for functional anti-sigma factor activity, and that it plays a critical role in modulating the reactivity of RsrA cysteine thiol groups towards oxidation. Apo-RsrA is easily oxidised and, while the Zn-bound form is relatively resistant, the metal ion is readily expelled when the protein is treated with strong oxidants such as diamide. We also show, using a combination of proteolysis and mass spectrometry, that the first critical disulphide to form in RsrA involves Cys11 and one of either Cys41 or Cys44, all previously implicated in metal binding. Circular dichroism spectroscopy was used to follow structural changes during oxidation of RsrA, which indicated that concomitant with formation of this critical disulphide bond is a major restructuring of the protein where its alpha-helical content increases. Our data demonstrate that RsrA can only bind sigmaR in the reduced state and that this state is stabilised by zinc. Redox stress induces disulphide bond formation amongst zinc-ligating residues, expelling the metal ion and stabilising a structure incapable of binding the sigma factor.

Emotional Experiences of Preservice Science Teachers in Online Learning: The Formation, Disruption and Maintenance of Social Bonds

ERIC Educational Resources Information Center

Bellocchi, Alberto; Mills, Kathy A.; Ritchie, Stephen M.

2016-01-01

The enactment of learning to become a science teacher in online mode is an emotionally charged experience. We attend to the formation, maintenance and disruption of social bonds experienced by online preservice science teachers as they shared their emotional online learning experiences through blogs, or e-motion diaries, in reaction to videos of…

Clumped isotope thermometry in deeply buried sedimentary carbonates: The effects of C-O bond reordering and recrystallization

NASA Astrophysics Data System (ADS)

Passey, B. H.; Shenton, B.; Grossman, E. L.; Henkes, G. A.; Laya, J. C.; Perez-Huerta, A.

2014-12-01

Constraining the thermal histories of sedimentary basins is fundamental to a range of geologic applications including tectonics, petroleum system analysis, and the genesis of ore deposits. Carbonate rocks can serve as archives of basin thermal histories through solid-state reordering of their 13C-18O, or 'clumped isotope', bonds at elevated burial temperatures. Here we present one of the first applied studies of carbonate clumped isotope reordering to explore the diagenetic and thermal histories of exhumed brachiopods, crinoids, cements, and host rock in the Permian Palmarito Formation, Venezuela and the Carboniferous Bird Spring Formation, Nevada, USA. Carbonate components in the Palmarito Formation, buried to ~4 km depth, yield statistically indistinguishable clumped isotope temperatures (T(Δ47)) ranging from 86 to 122 °C. Clumped isotope temperatures of components in the more deeply buried Bird Spring Formation (>5 km), range from ~100 to 165 °C and differ by component type, with brachiopods and pore-filling cements yielding the highest T(Δ47) (mean = 153 and 141 °C, respectively) and crinoids and host rock yielding significantly cooler T(Δ47) (mean = 103 and 114 °C). New high-resolution thermal histories are coupled with kinetic models to predict the extent of solid-state C-O bond reordering during burial and exhumation for both sites. Application of these models suggests that brachiopods in the Palmarito Formation experienced partial bond reordering without complete equilibration of clumped isotopes at maximum burial temperature. In contrast, clumped isotope bonds of brachiopods from the Bird Spring Formation appear to have completely equilibrated at maximum burial temperature, and now reflect blocking temperatures 'locked-in' during cooling. The 40-50 °C cooler clumped isotope temperatures measured in Bird Spring Formation crinoids and host rock can be explained by both recrystallization and cementation during shallow burial and a greater inherent resistance to solid-state reordering than brachiopods.

Late-Stage Functionalization of Arylacetic Acids by Photoredox-Catalyzed Decarboxylative Carbon-Heteroatom Bond Formation.

PubMed

Sakakibara, Yota; Ito, Eri; Fukushima, Tomohiro; Murakami, Kei; Itami, Kenichiro

2018-05-02

The rapid transformation of pharmaceuticals and agrochemicals enables access to unexplored chemical space and thus has accelerated the discovery of novel bioactive molecules. Because arylacetic acids are regarded as key structures in bioactive compounds, new transformations of these structures could contribute to drug/agrochemical discovery and chemical biology. This work reports carbon-nitrogen and carbon-oxygen bond formation through the photoredox-catalyzed decarboxylation of arylacetic acids. The reaction shows good functional group compatibility without pre-activation of the nitrogen- or oxygen-based coupling partners. Under similar reaction conditions, carbon-chlorine bond formation was also feasible. This efficient derivatization of arylacetic acids makes it possible to synthesize pharmaceutical analogues and bioconjugates of pharmaceuticals and natural products. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Positronium formation studies in solid molecular complexes: Triphenylphosphine oxide-triphenylmethanol

NASA Astrophysics Data System (ADS)

Oliveira, F. C.; Denadai, A. M. L.; Fulgêncio, F. H.; Magalhães, W. F.; Alcântara, A. F. C.; Windmöller, D.; Machado, J. C.

2012-06-01

Positronium formation in triphenylphosphine oxide (TPPO), triphenylmethanol (TPM), and systems [TPPO(1-X)ṡTPMX] has been studied. The low probability of positronium formation in complex [TPPO0.5ṡTPM0.5] was attributed to strong hydrogen bond and sixfold phenyl embrace interactions. These strong interactions in complex reduce the possibility of the n- and π-electrons to interact with positrons on the spur and consequently, the probability of positronium formation is lower. The τ3 parameter and free volume (correlated to τ3) were also sensitive to the formation of hydrogen bonds and sixfold phenyl embrace interactions within the complex. For physical mixture the positron annihilation parameters remained unchanged throughout the composition range.

Ratio of entropy to enthalpy in thermal transitions in biological tissues.

PubMed

Jacques, Steven L

2006-01-01

Thermal transitions in biological tissues that have been reported in the literature are summarized in terms of the apparent molar entropy (DeltaS) and molar enthalpy (DeltaH) involved in the transition. A plot of DeltaS versus DeltaH for all the data yields a straight line, consistent with the definition of free energy, DeltaG=DeltaH+TDeltaS. Various bonds may be involved in cooperative bond breakage during thermal transitions; however, for the sake of description, the equivalent number of cooperative hydrogen bonds can be cited. Most of the tissue data behave as if 10 to 20 hydrogen bonds are cooperatively broken during coagulation, with one transition, the expression of heat shock protein, involving 90 cooperative hydrogen bonds. The data are consistent with DeltaS=a+bDeltaH, where a=-327.5 J(mol K) and b=31.47 x 10(-4) K(-1). If each additional hydrogen bond adds 19 x 10(3) Jmol to DeltaH, then each additional bond adds 59.8 J(mol K) to DeltaS. Hence, the dynamics of irreversible thermal transitions can be described in terms of one free parameter, the apparent number of cooperative hydrogen bonds broken during the transition.

Reduction of unsaturated compounds under interstellar conditions: chemoselective reduction of C≡C and C=C bonds over C=O functional group

NASA Astrophysics Data System (ADS)

Jonusas, Mindaugas; Guillemin, Jean-Claude; Krim, Lahouari

2017-07-01

The knowledge of the H-addition reactions on unsaturated organic molecules bearing a triple or a double carbon-carbon bond such as propargyl or allyl alcohols and a CO functional group such as propynal, propenal or propanal may play an important role in the understanding of the chemical complexity of the interstellar medium. Why different aldehydes like methanal, ethanal, propynal and propanal are present in dense molecular clouds while the only alcohol detected in those cold regions is methanol? In addition, ethanol has only been detected in hot molecular cores. Are those saturated and unsaturated aldehyde and alcohol species chemically linked in molecular clouds through solid phase H-addition surface reactions or are they formed through different chemical routes? To answer such questions, we have investigated a hydrogenation study of saturated and unsaturated aldehydes and alcohols at 10 K. We prove through this experimental study that while pure unsaturated alcohol ices bombarded by H atoms lead to the formation of the corresponding fully or partially saturated alcohols, surface H-addition reactions on unsaturated aldehyde ices exclusively lead to the formation of fully saturated aldehyde. Such results show that in addition to a chemoselective reduction of C≡C and C=C bonds over the C=O group, there is no link between aldehydes and their corresponding alcohols in reactions involving H atoms in dense molecular clouds. Consequently, this could be one of the reasons why some aldehydes such as propanal are abundant in dense molecular clouds in contrast to the non-detection of alcohol species larger than methanol.

Let's stay together? Intrinsic and extrinsic factors involved in pair bond dissolution in a recolonizing wolf population.

PubMed

Milleret, Cyril; Wabakken, Petter; Liberg, Olof; Åkesson, Mikael; Flagstad, Øystein; Andreassen, Harry Peter; Sand, Håkan

2017-01-01

For socially monogamous species, breeder bond dissolution has important consequences for population dynamics, but the extent to which extrinsic or intrinsic population factors causes pair dissolution remain poorly understood, especially among carnivores. Using an extensive life-history data set, a survival analysis and competing risks framework, we examined the fate of 153 different wolf (Canis lupus) pairs in the recolonizing Scandinavian wolf population, during 14 winters of snow tracking and DNA monitoring. Wolf pair dissolution was generally linked to a mortality event and was strongly affected by extrinsic (i.e. anthropogenic) causes. No divorce was observed, and among the pair dissolution where causes have been identified, death of one or both wolves was always involved. Median time from pair formation to pair dissolution was three consecutive winters (i.e. approximately 2 years). Pair dissolution was mostly human-related, primarily caused by legal control actions (36·7%), verified poaching (9·2%) and traffic-related causes (2·1%). Intrinsic factors, such as disease and age, accounted for only 7·7% of pair dissolutions. The remaining 44·3% of dissolution events were from unknown causes, but we argue that a large portion could be explained by an additional source of human-caused mortality, cryptic poaching. Extrinsic population factors, such as variables describing the geographical location of the pair, had a stronger effect on risk of pair dissolution compared to anthropogenic landscape characteristics. Population intrinsic factors, such as the inbreeding coefficient of the male pair member, had a negative effect on pair bond duration. The mechanism behind this result remains unknown, but might be explained by lower survival of inbred males or more complex inbreeding effects mediated by behaviour. Our study provides quantitative estimates of breeder bond duration in a social carnivore and highlights the effect of extrinsic (i.e. anthropogenic) and intrinsic factors (i.e. inbreeding) involved in wolf pair bond duration. Unlike the effects of intrinsic and extrinsic factors that are commonly reported on individual survival or population growth, here we provide quantitative estimates of their potential effect on the social unit of the population, the wolf pair. © 2016 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Solution equilibrium behind the room-temperature synthesis of nanocrystalline titanium dioxide

NASA Astrophysics Data System (ADS)

Seisenbaeva, Gulaim A.; Daniel, Geoffrey; Nedelec, Jean-Marie; Kessler, Vadim G.

2013-03-01

Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions.Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions. Electronic supplementary information (ESI) available: Crystallographic data in cif and table format, detailed description of hydrogen bonding in (NH4)2[Ti(l-Lactate)3].3H2O, additional TEM images, DLS data on particle size in solutions and NanoSight data on particle size distribution, photos of produced TiO2 colloids, details of NMR experiments and a real-time movie demonstrating the equilibrium leading to TiO2 formation and re-dissolution in pH-neutral ammonium lactate solutions. CCDC 915222. For ESI and crystallographic data in CIF or other electronic format. see DOI: 10.1039/c3nr34068f

The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations.

PubMed

Becerra, Rosa; Cannady, J Pat; Dormer, Guy; Walsh, Robin

2009-07-14

Time-resolved kinetic studies of the reactions of silylene, SiH(2), and dideutero-silylene, SiD(2), generated by laser flash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH(3)C[triple bond, length as m-dash]CCH(3). The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF(6) bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(Infinity)/cm(3) molecule(-1) s(-1) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(1)/RTIn10log(k(D)(Infinity)/cm(3) molecule(-1) s(-1) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTIn10. Additionally, pressure-dependent rate coefficients for the reaction of SiH(2) with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC(4)H(8) reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH(2)C(CH(3))[double bond, length as m-dash]C(CH(3))-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH(3)CH[double bond, length as m-dash]C(CH(3))SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H-D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

New Approaches to Waterproofing of Space Shuttle Insulating Materials

NASA Technical Reports Server (NTRS)

Blum, Yigal D.; Johnson, Sylvia M.; Chen, Paul

1997-01-01

Future reusable space vehicles will be in service much more frequently than current space shuttles. Therefore, rapid reconditioning of spacecraft will be required. Currently, the waterproofing of space shuttles after each re-entry takes 72 hours and requires substantial labor. In addition, the currently used waterproofing reagent, DiMethylEthoxySilane (DMES), is considered toxic, and ethanol fumes are released during its hydrolytic activation. Consequently, a long time period, which is not acceptable for future operations, is needed to ensure that 0 the excess volatile compounds are removed before further maintenance of the space vehicle can be performed. The objective of this project was to assist NASA Ames in finding improved waterproofing systems by identifying suitable waterproofing agents that can be applied by vapor phase deposition and will be less toxic, bond more rapidly to the insulation material surface, and potentially have higher thermal stability than the DMES system. Several approaches to achieve faster waterproofing with less toxicity were assessed using the following alternatives: Reactive volatile compounds that are rapidly deposited by chemical bonding at the surface and leave no toxic volatiles. Reactive reagents that are the least toxic. Nonvolatile reagents that are very reactive and bond strongly to the insulating material surface. Three specific types of potential reagents were chosen for evaluation in this project: 1. Volatile reagents with Si-Cl functional groups for vapor deposition 2. Volatile reagents with Si-H functional groups for vapor deposition 3. Nonvolatile oligomeric or polymeric reactive siloxanes that are assumed to have higher thermal stability and/or strong bonding to the insulating material. The chemistry involved in the project was targeted at the generation of intermediates having reactive Si-OH bonds for the formation of either volatile species or polymeric species that bond rapidly to the surface and also cure rapidly. We focused on two chemical reactions@-hydrolysis of Si-Cl bonds and catalytic dehydrocoupling of Si-H bonds.

Dimerization of the keto tautomer of acetohydroxamic acid—infrared matrix isolation and theoretical study

NASA Astrophysics Data System (ADS)

Sałdyka, Magdalena; Mielke, Zofia

2005-05-01

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH 3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO···H sbnd ON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO···H sbnd N hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular N sbnd H···O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies ( ΔEZPECPI, II = -7.02, -6.34 kcal mol -1) being less stable than calculated structures III and IV ( ΔEZPECPIII, IV = -9.50, -8.87 kcal mol -1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO···H sbnd ON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA) 2 dimers in the studied matrixes indicates that the formation of (AHA) 2 is kinetically and not thermodynamically controlled.

Spectroscopic investigation on cocrystal formation between adenine and fumaric acid based on infrared and Raman techniques.

PubMed

Du, Yong; Fang, Hong Xia; Zhang, Qi; Zhang, Hui Li; Hong, Zhi

2016-01-15

As an important component of double-stranded DNA, adenine has powerful hydrogen-bond capability, due to rich hydrogen bond donors and acceptors existing within its molecular structure. Therefore, it is easy to form cocrystal between adenine and other small molecules with intermolecular hydrogen-bond effect. In this work, cocrystal of adenine and fumaric acid has been characterized as model system by FT-IR and FT-Raman spectral techniques. The experimental results show that the cocrystal formed between adenine and fumaric acid possesses unique spectroscopical characteristic compared with that of starting materials. Density functional theory (DFT) calculation has been performed to optimize the molecular structures and simulate vibrational modes of adenine, fumaric acid and the corresponding cocrystal. Combining the theoretical and experimental vibrational results, the characteristic bands corresponding to bending and stretching vibrations of amino and carbonyl groups within cocrystal are shifted into lower frequencies upon cocrystal formation, and the corresponding bond lengths show some increase due to the effect of intermolecular hydrogen bonding. Different vibrational modes shown in the experimental spectra have been assigned based on the simulation DFT results. The study could provide experimental and theoretical benchmarks to characterize cocrystal formed between active ingredients and cocrystal formers and also the intermolecular hydrogen-bond effect within cocrystal formation process by vibrational spectroscopic techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Why Combustions Are Always Exothermic, Yielding about 418 kJ per Mole of O[subscript 2

ERIC Educational Resources Information Center

Schmidt-Rohr, Klaus

2015-01-01

The strongly exothermic nature of reactions between molecular oxygen and all organic molecules as well as many other substances is explained in simple, general terms. The double bond in O[subscript 2] is much weaker than other double bonds or pairs of single bonds, and therefore the formation of the stronger bonds in CO[subscript 2] and…

Student Conceptions of Ionic Bonding: Patterns of Thinking across Three European Contexts

ERIC Educational Resources Information Center

Taber, Keith S.; Tsaparlis, Georgios; Nakiboglu, Canan

2012-01-01

Previous research has reported that students commonly develop alternative conceptions in the core topic of chemical bonding. Research in England has reported that students there commonly demonstrate an alternative "molecular" conceptual framework for thinking about ionic bonding: in terms of the formation of molecule-like ions pairs…

Bonds Between Metal Atoms: A New Mode of Transition Metal Chemistry.

ERIC Educational Resources Information Center

Cotton, F. Albert; Chisholm, Malcolm H.

1982-01-01

Discusses polynuclear metal clusters (containing two or more metal atoms bonded to one another as well as to nonmetallic elements), including their formation and applications. Studies of bonds between metal atoms reveal superconductors, organic-reaction catalysts, and photosensitive complexes that may play a role in solar energy. (JN)

Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member†

PubMed Central

Li, Huei-Jiun; Li, Xiaokai; Liu, Nina; Zhang, Huaning; Truglio, James J.; Mishra, Shambhavi; Kisker, Caroline; Garcia-Diaz, Miguel; Tonge, Peter J.

2014-01-01

MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 Å structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate α-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase, is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in α-proton acidity. PMID:21830810

Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member.

PubMed

Li, Huei-Jiun; Li, Xiaokai; Liu, Nina; Zhang, Huaning; Truglio, James J; Mishra, Shambhavi; Kisker, Caroline; Garcia-Diaz, Miguel; Tonge, Peter J

2011-11-08

MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 Å structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable, and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate α-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in α-proton acidity.

Molecular mechanism of gelation with ethylene glycol added to a solution of polyacrylonitrile in dimethylsulfoxide

NASA Astrophysics Data System (ADS)

Vettegren', V. I.; Machalaba, N. N.; Zharov, V. B.; Kulik, V. B.; Savitskii, A. V.

2011-06-01

The mechanism of solidifying a solution of polyacrylonitrile (PAN) in dimethylsulfoxide (DMSO) into which ethylene glycol is added is studied by the method of Raman spectroscopy. In the absence of ethylene glycol, DMSO molecules produce dipole-dipole bonds to PAN molecules. Upon adding ethylene glycol, DMSO molecules form hydrogen bonds with it and a line at 1000 cm-1 appears in the Raman spectrum, which is assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. After DMSO is removed, ethylene glycol molecules produce hydrogen bonds with two neighboring PAN molecules, giving rise to a band at 2264 cm-1, which is assigned to the valence vibrations of C≡N bonds involved in these hydrogen bonds. A high-viscosity gel consisting of PAN molecules arises in which these molecules are bonded to each other through ethylene glycol molecules.

Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies.

PubMed

Sutton, Kristin A; Black, Paul J; Mercer, Kermit R; Garman, Elspeth F; Owen, Robin L; Snell, Edward H; Bernhard, William A

2013-12-01

Electron paramagnetic resonance (EPR) and online UV-visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV-visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5-0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.

Eight supramolecular assemblies constructed from bis(benzimidazole) and organic acids through strong classical hydrogen bonding and weak noncovalent interactions

NASA Astrophysics Data System (ADS)

Jin, Shouwen; Wang, Daqi

2014-05-01

Eight crystalline organic acid-base adducts derived from alkane bridged bis(N-benzimidazole) and organic acids (2,4,6-trinitrophenol, p-nitrobenzoic acid, m-nitrobenzoic acid, 3,5-dinitrobenzoic acid, 5-sulfosalicylic acid and oxalic acid) were prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. Of the eight compounds five are organic salts (1, 4, 6, 7 and 8) and the other three (2, 3, and 5) are cocrystals. In all of the adducts except 1 and 8, the ratio of the acid and the base is 2:1. All eight supramolecular assemblies involve extensive intermolecular classical hydrogen bonds as well as other noncovalent interactions. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, all the complexes displayed 3D framework structure. The results presented herein indicate that the strength and directionality of the classical N+-H⋯O-, O-H⋯O, and O-H⋯N hydrogen bonds (ionic or neutral) and other nonbonding associations between acids and ditopic benzimidazoles are sufficient to bring about the formation of cocrystals or organic salts.

[Fe(F20 TPP)Cl]-catalyzed amination with arylamines and {[Fe(F20 TPP)(NAr)](PhI=NAr)} + . Intermediate assessed by high-resolution ESI-MS and DFT calculations.

PubMed

Liu, Yungen; Chen, Guo-Qiang; Tse, Chun-Wai; Guan, Xianguo; Xu, Zheng-Jiang; Huang, Jie-Sheng; Che, Chi-Ming

2015-01-01

Amination of CH bonds catalyzed by transition metal complexes via nitrene/imide insertion is an appealing strategy for CN bond formation, and the use of iminoiodinanes, or their in situ generated forms from 'PhI(OAc)2 +primary amides (such as sulfonamides, sulfamates, and carbamates)', as nitrogen sources for the amination reaction has been well documented. In this work, a 'metal catalyst+PhI(OAc)2 +primary arylamines' amination protocol has been developed using [Fe(F20 TPP)Cl] (H2 F20 TPP=meso-tetrakis(pentafluorophenyl)porphyrin) as a catalyst. This catalytic method is applicable for both intra- and intermolecular amination of sp(2) and sp(3) CH bonds (>27 examples), affording the amination products, including natural products such as rutaecarpine, in moderate-to-good yields. ESI-MS analysis and DFT calculations lend support for the involvement of {[Fe(F20 TPP)(NC6 H4 -p-NO2 )](PhI=NC6 H4 -p-NO2 )} + . intermediate in the catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de

2014-10-07

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H{sub 2}O{sub 2}−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry ofmore » the H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.« less

Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm

USDA-ARS?s Scientific Manuscript database

We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, HdeB and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALD...

Turn-Directed α-β Conformational Transition of α-syn12 Peptide at Different pH Revealed by Unbiased Molecular Dynamics Simulations

PubMed Central

Liu, Lei; Cao, Zanxia

2013-01-01

The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH. PMID:23708094

The effects of intramolecular H-bond formation on the stability constant and water exchange rate of the Gd(III)-diethylenetriamine-N'-(3-amino-1,1-propylenephosphonic)-N, N,N'',N''-tetraacetate complex.

PubMed

Baranyai, Zsolt; Gianolio, Eliana; Ramalingam, Kondareddiar; Swenson, Rolf; Ranganathan, Ramachandran; Brücher, E; Aime, Silvio

2007-01-01

The binding interaction of metal chelates to biological macromolecules, though driven by properly devoted recognition synthons, may cause dramatic changes in some property associated with the coordination cage such as the thermodynamic stability or the exchange rate of the metal coordinated water. Such changes are due to electrostatic and H-bonding interactions involving atoms of the coordination cage and atoms of the biological molecule at the binding site. To mimic this type of H-bonding interactions, lanthanide(III) complexes with a DTPA-monophosphonate ligand bearing a propylamino moiety (H6NP-DTPA) were synthesized. Their thermodynamic stabilities and the exchange lifetime of the coordinated water molecule (for the Gd-complex) were compared with those of the analog complexes with DTPA and the parent DTPA-monophosphonate derivative (H6P-DTPA). It was found that the intramolecular H-bond between the epsilon-amino group and the phosphonate moiety in NP-DTPA complexes causes displacements of electric charges in their coordination cage that are markedly pH dependent. In turn, this affects the characteristic properties of the coordination cage. In particular it results in a marked elongation of the exchange lifetime of the coordinated water molecule. (c) 2007 John Wiley & Sons, Ltd.

A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα–H hydrogen bonds

PubMed Central

Mueller, Benjamin K.; Subramaniam, Sabareesh; Senes, Alessandro

2014-01-01

Carbon hydrogen bonds between Cα–H donors and carbonyl acceptors are frequently observed between transmembrane helices (Cα–H···O=C). Networks of these interactions occur often at helix−helix interfaces mediated by GxxxG and similar patterns. Cα–H hydrogen bonds have been hypothesized to be important in membrane protein folding and association, but evidence that they are major determinants of helix association is still lacking. Here we present a comprehensive geometric analysis of homodimeric helices that demonstrates the existence of a single region in conformational space with high propensity for Cα–H···O=C hydrogen bond formation. This region corresponds to the most frequent motif for parallel dimers, GASright, whose best-known example is glycophorin A. The finding suggests a causal link between the high frequency of occurrence of GASright and its propensity for carbon hydrogen bond formation. Investigation of the sequence dependency of the motif determined that Gly residues are required at specific positions where only Gly can act as a donor with its “side chain” Hα. Gly also reduces the steric barrier for non-Gly amino acids at other positions to act as Cα donors, promoting the formation of cooperative hydrogen bonding networks. These findings offer a structural rationale for the occurrence of GxxxG patterns at the GASright interface. The analysis identified the conformational space and the sequence requirement of Cα–H···O=C mediated motifs; we took advantage of these results to develop a structural prediction method. The resulting program, CATM, predicts ab initio the known high-resolution structures of homodimeric GASright motifs at near-atomic level. PMID:24569864

A DFT investigation of a bulky biomimetic model catalyzing the 5'-outer ring deiodination of thyroxine.

PubMed

Fortino, Mariagrazia; Marino, Tiziana; Russo, Nino; Sicilia, Emilia

2016-12-01

This paper illustrates the outcomes of a density functional theory investigation aimed at unraveling mechanistic aspects of the 5'-outer ring deiodination process of thyroxine (T4) assisted by the sterically protected organoselenol compound BpqSeH. BpqSeH, which was previously synthesized and tested for its deiodinase activity, is able to afford the active hormone 3,5,3'-tetraiodothyronine (T3) by selective outer-ring deiodination of T4, and to protect the SeH moiety inside the nano-sized molecular cavity from further reactivity, allowing its isolation and characterization. Calculations were also performed including an imidazole ring that, mimicking a His residue in the active site of the original enzyme, plays an crucial role in deprotonating the selenol moiety. Both the suggested enol/keto tautomerization and the previously proven formation of an intermediate whose main characteristic is the presence of a Se⋯I⋯C halogen bond, were examined along the pathway leading to 5'-outer ring deiodination. The calculated potential energy surface showed that neither the pathway encompassing enol/keto tautomerism nor the formation of a halogen bond paving the way to C-I bond breaking and chalcogen-I bond forming is viable. The exergonic formation of the final selenenyl iodide product confirms the stabilization effect of the molecular cavity. Graphical Abstract Computed free energy profile describing the 5'-outer deiodination of thyroxine assisted by the steric hindered organoselenol BpqSH compound. The molecular electrostatic potential map reoported for the INT1 intermediate shows the non-covalent Se-I interaction, due to the attraction between charges of opposite sign, that weakens the C-I bond and prepares the formation of the new Se-I bond.

Anharmonic calculations of frequencies and intensities of Osbnd H stretching vibrations of (R)-1,3-butanediol conformers in the fundamentals and first overtones by density functional theory

NASA Astrophysics Data System (ADS)

Futami, Yoshisuke; Minamoto, Chihiro; Kudoh, Satoshi

2018-05-01

The frequencies and absorption intensities of the five kinds of conformers of 1,3-butanediol with the same carbon skeleton (GG‧) were calculated by anharmonic calculation for the fundamentals and first overtones of OH stretching vibrations. The four kinds of conformers form intramolecular hydrogen bonds and one conformer did not. Intramolecular hydrogen bond formation shifted the frequency of fundamental and first overtone of H-bonding OH stretching vibration to the lower frequency. The absorption intensities of the fundamentals as well as the vibrational anharmonicities increased upon hydrogen bond formation, while the intensities of first overtones decreased. The differences of conformers were clearly seen in the frequencies of the first overtones of free OH.

Disulphide bonds in casein micelle from milk.

PubMed

Bouguyon, Edwige; Beauvallet, Christian; Huet, Jean-Claude; Chanat, Eric

2006-05-05

Mammary epithelial cells synthesised and secreted caseins, the major milk proteins in most mammals, as large aggregates called micelles into the alveolar lumen they surround. We investigated the implication of the highly conserved cysteine(s) of kappa-casein in disulphide bond formation in casein micelles from several species. Dimers were found in all milks studied, confirming previous observation in ruminants. More importantly, the study of interchain disulphide bridges in mouse and rat casein micelles revealed that any casein possessing a cysteine is engaged in disulphide bond interchange; these species express four or five cysteine-containing caseins, respectively. We found that the main rodent caseins form both homo- and heterodimers. Additionally, disulphide bond formation among milk proteins was specific since the interaction of the caseins with cysteine-containing whey proteins was not observed in native casein micelles.

A pseudo MS3 approach for identification of disulfide-bonded proteins: uncommon product ions and database search.

PubMed

Chen, Jianzhong; Shiyanov, Pavel; Schlager, John J; Green, Kari B

2012-02-01

It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS(3) approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole time-of-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c(i-1) ions (the i(th) residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS(3) spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS(3) approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs. © American Society for Mass Spectrometry, 2011

The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak Csbnd H⋯Odbnd C hydrogen bonds

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Wójcik, Marek J.; Sato, Harumi; Nakajima, Takahito; Ozaki, Yukihiro

2017-06-01

In this letter we present results of study of weak Csbnd H⋯Odbnd C hydrogen bonds of crystalline poly-(R)-3-hydroxybutyrate (PHB) by using Born-Oppenheimer molecular dynamics. The polymeric structure and IR spectra of PHB result from the presence of the weak hydrogen bonds. We applied the post-molecular dynamics analysis to consider a Cdbnd O motion as indirectly involved in the hydrogen bonds. Quantization of the nuclear motion of the oxygens was done to perform detailed analysis of the strength and properties of the Cdbnd O bands involved in the weak hydrogen bonds. We have also shown the dynamic character of the weak hydrogen bond interactions.

Coordinated Analyses of Mineral-organic Matter Associations in Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Herzog, G. F.; Smith, T.; Keller, L. P.; Flynn, G. J.; Khodja, H.; Taylor, S.; Wirick, S.; Messenger, S.

2012-01-01

Little is known about the timing and processes involved in the incorporation of organic matter with inorganic materials in early Solar System bodies. Recently, X-ray absorption near-edge spectroscopy (XANES) studies showed carbon-rich rims surrounding individual mineral grains in anhydrous IDPs [1,2]. These carbonaceous rims are believed to have formed prior to parent body formation and likely served to bond mineral grains during accretion into larger aggregates. We are exploring the nature of these carbonaceous rims through coordinated analyses of their chemistry, mineralogy, spectroscopy and isotopic characteristics. Here we report our preliminary mineralogical observations.

Mini-Review: Ergothioneine and Ovothiol Biosyntheses, an Unprecedented Trans-Sulfur Strategy in Natural Product Biosynthesis.

PubMed

Naowarojna, Nathchar; Cheng, Ronghai; Chen, Li; Quill, Melissa; Xu, Meiling; Zhao, Changming; Liu, Pinghua

2018-06-19

As one of the most abundant elements on earth, sulfur is part of many small molecular metabolites and is key to their biological activities. Over the past few decades, some general strategies have been discovered for the incorporation of sulfur into natural products. In this review, we summarize recent efforts in elucidating the biosynthetic details for two sulfur-containing metabolites, ergothioneine and ovothiol. Their biosyntheses involve an unprecedented trans-sulfur strategy, a combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation reaction and a PLP enzyme-mediated C-S lyase reaction.

Copper(II)-catalyzed amidations of alkynyl bromides as a general synthesis of ynamides and Z-enamides. An intramolecular amidation for the synthesis of macrocyclic ynamides.

PubMed

Zhang, Xuejun; Zhang, Yanshi; Huang, Jian; Hsung, Richard P; Kurtz, Kimberly C M; Oppenheimer, Jossian; Petersen, Matthew E; Sagamanova, Irina K; Shen, Lichun; Tracey, Michael R

2006-05-26

A general and efficient method for the coupling of a wide range of amides with alkynyl bromides is described here. This novel amidation reaction involves a catalytic protocol using copper(II) sulfate-pentahydrate and 1,10-phenanthroline to direct the sp-C-N bond formation, leading to a structurally diverse array of ynamides including macrocyclic ynamides via an intramolecular amidation. Given the surging interest in ynamide chemistry, this atom economical synthesis of ynamides should invoke further attention from the synthetic organic community.

Surface-enhanced Raman scattering on molecular self-assembly in nanoparticle-hydrogel composite.

PubMed

Miljanić, Snezana; Frkanec, Leo; Biljan, Tomislav; Meić, Zlatko; Zinić, Mladen

2006-10-24

Surface-enhanced Raman scattering has been applied to study weak intermolecular interactions between small organic gelling molecules involved in the silver nanoparticle-hydrogel composite formation. Assembly and disassembly of the gelator molecules in close vicinity to embedded silver nanoparticles were followed by changes in Raman intensity of the amide II and carboxyl vibrational bands, whereas the strength of the bands related to benzene modes remained constant. This implied that the gelator molecules were strongly attached to the silver particles through the benzene units, while participating in gel structure organization by intermolecular hydrogen bonding between oxalyl amide and carboxyl groups.

Stereodivergent Synthesis of N-Heterocycles by Catalyst-Controlled, Activity-Directed Tandem Annulation of Diazo Compounds with Amino Alkynes.

PubMed

Liu, Kai; Zhu, Chenghao; Min, Junxiang; Peng, Shiyong; Xu, Guangyang; Sun, Jiangtao

2015-10-26

A stereodivergent synthesis of five-membered N-heterocycles, such as 2,3-dihydropyrroles, and 2-methylene and 3-methylene pyrrolidines, has been developed through a tandem annulation of amino alkynes with diazo compounds and involves the trapping of in situ formed intermediates. Mechanistic investigations indicate that the copper-catalyzed tandem annulations proceed by allenoate formation and subsequent intramolecular hydroamination. In contrast, the rhodium-catalyzed protocol features a carbenoid insertion into the NH bond and subsequent Conia-ene cyclization. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Central oxytocin receptors mediate mating-induced partner preferences and enhance correlated activation across forebrain nuclei in male prairie voles.

PubMed

Johnson, Zachary V; Walum, Hasse; Jamal, Yaseen A; Xiao, Yao; Keebaugh, Alaine C; Inoue, Kiyoshi; Young, Larry J

2016-03-01

Oxytocin (OT) is a deeply conserved nonapeptide that acts both peripherally and centrally to modulate reproductive physiology and sociosexual behavior across divergent taxa, including humans. In vertebrates, the distribution of the oxytocin receptor (OTR) in the brain is variable within and across species, and OTR signaling is critical for a variety of species-typical social and reproductive behaviors, including affiliative and pair bonding behaviors in multiple socially monogamous lineages of fishes, birds, and mammals. Early work in prairie voles suggested that the endogenous OT system modulates mating-induced partner preference formation in females but not males; however, there is significant evidence that central OTRs may modulate pair bonding behavior in both sexes. In addition, it remains unclear how transient windows of central OTR signaling during sociosexual interaction modulate neural activity to produce enduring shifts in sociobehavioral phenotypes, including the formation of selective social bonds. Here we re-examine the role of the central OT system in partner preference formation in male prairie voles using a selective OTR antagonist delivered intracranially. We then use the same antagonist to examine how central OTRs modulate behavior and immediate early gene (Fos) expression, a metric of neuronal activation, in males during brief sociosexual interaction with a female. Our results suggest that, as in females, OTR signaling is critical for partner preference formation in males and enhances correlated activation across sensory and reward processing brain areas during sociosexual interaction. These results are consistent with the hypothesis that central OTR signaling facilitates social bond formation by coordinating activity across a pair bonding neural network. Copyright © 2015 Elsevier Inc. All rights reserved.

Carbon-sulfur bond formation by reductive elimination of gold(iii) thiolates.

PubMed

Currie, Lucy; Rocchigiani, Luca; Hughes, David L; Bochmann, Manfred

2018-05-08

Whereas the reaction of the gold(iii) pincer complex (C^N^C)AuCl with 1-adamantyl thiol (AdSH) in the presence of base affords (C^N^C)AuSAd, the same reaction in the absence of base leads to formation of aryl thioethers as the products of reductive elimination of the Au-C and Au-S ligands (C^N^C = dianion of 2-6-diphenylpyridine or 2-6-diphenylpyrazine). Although high chemical stability is usually taken as a characteristic of pincer complexes, results show that thiols are capable of cleaving one of the pincer Au-C bonds. This reaction is not simply a function of S-H acidity, since no cleavage takes place with other more acidic X-H compounds, such as carbazole, amides, phenols and malonates. The reductive C-S elimination follows a second-order rate law, -d[1a]/dt = k[1a][AdSH]. Reductive elimination is enabled by displacement of the N-donor by thiol; this provides the conformational flexibility necessary for C-S bond formation to occur. Alternatively, reductive C-S bond formation can be induced by reaction of pre-formed thiolates (C^N^C)AuSR with a strong Brønsted acid, followed by addition of SMe2 as base. On the other hand, treatment of (C^N^C)AuR (R = Me, aryl, alkynyl) with thiols under similar conditions leads to selective C-C rather than C-S bond formation. The reaction of (C^N^C)AuSAd with H+ in the absence of a donor ligand affords the thiolato-bridged complex [{(C^N-CH)Au(μ-SAd)}2]2+ which was crystallographically characterised.

From CO2 to dimethyl carbonate with dialkyldimethoxystannanes: the key role of monomeric species.

PubMed

Kalhor, Mahboubeh Poor; Chermette, Henry; Chambrey, Stéphane; Ballivet-Tkatchenko, Danielle

2011-02-14

The formation of dimethyl carbonate (DMC) from CO(2) and methanol with the dimer [n-Bu(2)Sn(OCH(3))(2)](2) was investigated by experimental kinetics in support of DFT calculations. Under the reaction conditions (357-423 K, 10-20 MPa), identical initial rates are observed with three different reacting mixtures, CO(2)/toluene, supercritical CO(2), and CO(2)/methanol, and are consistent with the formation of monomeric di-n-butyltin(iv) species. An intramolecular mechanism is, therefore, proposed with an Arrhenius activation energy amounting to 104 ± 10 kJ mol(-1) for DMC synthesis. DFT calculations on the [(CH(3))(2)Sn(OCH(3))(2)](2)/CO(2) system show that the exothermic insertion of CO(2) into the Sn-OCH(3) bond occurs by a concerted Lewis acid-base interaction involving the tin center and the oxygen atom of the methoxy ligand. The Gibbs energy diagrams highlight that, under the reaction conditions, the dimer-monomer equilibrium is significantly shifted towards monomeric species, in agreement with the experimental kinetics. Importantly, the two Sn-OCH(3) bonds are prompt to insert CO(2). These results provide new insight into the reaction mechanism and catalyst design to enhance the turnover numbers.

Evidence for decoupled electron and proton transfer in the electrochemical oxidation of ammonia on Pt(100)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katsounaros, Ioannis; Chen, Ting; Gewirth, Andrew A.

The two traditional mechanisms of the electrochemical ammonia oxidation consider only concerted proton-electron transfer elementary steps and thus they predict that the rate–potential relationship is independent of the pH on the pH-corrected RHE potential scale. In this letter we show that this is not the case: the increase of the solution pH shifts the onset of the NH 3-to-N 2 oxidation on Pt(100) to lower potentials and also leads to higher surface concentration of formed N Oad before the latter is oxidized to nitrite. Therefore, we present a new mechanism for the ammonia oxidation which incorporates a deprotonation step occurringmore » prior to the electron transfer. The deprotonation step yields a negatively charged surface-adsorbed species which is discharged in a subsequent electron transfer step before the N–N bond formation. The negatively charged species is thus a precursor for the formation of N 2 and NO. The new mechanism should be a future guide for computational studies aiming at the identification of intermediates and corresponding activation barriers for the elementary steps. As a result, ammonia oxidation is a new example of a bond-forming reaction on (100) terraces which involves decoupled proton-electron transfer.« less

Evidence for decoupled electron and proton transfer in the electrochemical oxidation of ammonia on Pt(100)

DOE PAGES

Katsounaros, Ioannis; Chen, Ting; Gewirth, Andrew A.; ...

2016-01-12

The two traditional mechanisms of the electrochemical ammonia oxidation consider only concerted proton-electron transfer elementary steps and thus they predict that the rate–potential relationship is independent of the pH on the pH-corrected RHE potential scale. In this letter we show that this is not the case: the increase of the solution pH shifts the onset of the NH 3-to-N 2 oxidation on Pt(100) to lower potentials and also leads to higher surface concentration of formed N Oad before the latter is oxidized to nitrite. Therefore, we present a new mechanism for the ammonia oxidation which incorporates a deprotonation step occurringmore » prior to the electron transfer. The deprotonation step yields a negatively charged surface-adsorbed species which is discharged in a subsequent electron transfer step before the N–N bond formation. The negatively charged species is thus a precursor for the formation of N 2 and NO. The new mechanism should be a future guide for computational studies aiming at the identification of intermediates and corresponding activation barriers for the elementary steps. As a result, ammonia oxidation is a new example of a bond-forming reaction on (100) terraces which involves decoupled proton-electron transfer.« less

A comparative study of prebiotic and present day translational models

NASA Technical Reports Server (NTRS)

Rein, R.; Raghunathan, G.; Mcdonald, J.; Shibata, M.; Srinivasan, S.

1986-01-01

It is generally recognized that the understanding of the molecular basis of primitive translation is a fundamental step in developing a theory of the origin of life. However, even in modern molecular biology, the mechanism for the decoding of messenger RNA triplet codons into an amino acid sequence of a protein on the ribosome is understood incompletely. Most of the proposed models for prebiotic translation lack, not only experimental support, but also a careful theoretical scrutiny of their compatibility with well understood stereochemical and energetic principles of nucleic acid structure, molecular recognition principles, and the chemistry of peptide bond formation. Present studies are concerned with comparative structural modelling and mechanistic simulation of the decoding apparatus ranging from those proposed for prebiotic conditions to the ones involved in modern biology. Any primitive decoding machinery based on nucleic acids and proteins, and most likely the modern day system, has to satisfy certain geometrical constraints. The charged amino acyl and the peptidyl termini of successive adaptors have to be adjacent in space in order to satisfy the stereochemical requirements for amide bond formation. Simultaneously, the same adaptors have to recognize successive codons on the messenger. This translational complex has to be realized by components that obey nucleic acid conformational principles, stabilities, and specificities. This generalized condition greatly restricts the number of acceptable adaptor structures.

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.

Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

NASA Astrophysics Data System (ADS)

Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

2013-12-01

Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

Activation of C-O and C-C bonds and formation of novel HAlOH-ether complexes: an EPR study of the reaction of ground-state Al atoms with methylethyl ether and diethyl ether.

PubMed

Brunet, François D; Feola, Julie C; Joly, Helen A

2012-03-15

Reaction mixtures, containing Al atoms and methylethyl ether (MEE) or diethyl ether (DEE) in an adamantane matrix, were prepared with the aid of a metal-atom reactor known as a rotating cryostat. The EPR spectra of the resulting products were recorded from 77-260 K, at 10 K intervals. Al atoms were found to insert into methyl-O, ethyl-O, and C-C bonds to form CH(3)AlOCH(2)CH(3), CH(3)OAlCH(2)CH(3), and CH(3)OCH(2)AlCH(3), respectively, in the case of MEE while DEE produced CH(3)CH(2)AlOCH(2)CH(3) and CH(3)AlCH(2)OCH(2)CH(3), respectively. From the intensity of the transition lines attributed to the Al atom C-O insertion products of MEE, insertion into the methyl-O bond is preferred. The Al hyperfine interaction (hfi) extracted from the EPR spectra of the C-O insertion products was greater than that of the C-C insertion products, that is, 5.4% greater for the DEE system and 7% greater for the MEE system. The increase in Al hfi is thought to arise from the increased electron-withdrawing ability of the substituents bonded to Al. Besides HAlOH, resulting from the reaction of Al atoms with adventitious water, novel mixed HAlOH:MEE and HAlOH:DEE complexes were identified with the aid of isotopic studies involving H(2)(17)O and D(2)O. The Al and H hfi of HAlOH were found to decrease upon complex formation. These findings are consistent with the nuclear hfi calculated using a density functional theory (DFT) method with close agreement between theory and experiment occurring at the B3LYP level using a 6-311+G(2df,p) basis set.

[Energetics of complex formation of the DNA hairpin structure d(GCGAAGC) with aromatic ligands].

PubMed

Kostiukov, V V

2011-01-01

The energy contributions of various physical interactions to the total Gibbs energy of complex formation of the biologically important DNA hairpin d(GCGAAGC) with aromatic antitumor antibiotics daunomycin and novantron and the mutagens ethidium and proflavine have been calculated. It has been shown that the relatively small value of the total energy of binding of the ligands to the hairpin is the sum of components great in absolute value and different in sign. The contributions of van der Waals interactions and both intra- and intermolecular hydrogen bonds and bonds with aqueous environment have been studied. According to the calculations, the hydrophobic and van der Waals components are energetically favorable in complex formation of the ligands with the DNA pairpin d(GCGAAGC), whereas the electrostatic (with consideration of hydrogen bonds) and entropic components are unfavorable.

Bimetallic cooperative effect on O-O bond formation: copper polypyridyl complexes as water oxidation catalyst.

PubMed

Su, Xiao-Jun; Zheng, Chu; Hu, Qin-Qin; Du, Hao-Yi; Liao, Rong-Zhen; Zhang, Ming-Tian

2018-06-13

The performance of water oxidation catalysis by a Cu-based polypyridyl complex, [CuII(TPA)(OH2)]2+ (1H; TPA = tris-(pyridylmethyl)amine), has been investigated in neutral aqueous solution by electrochemical methods. Compared with our previously reported binuclear catalyst, [(BPMAN)(CuII)2(μ-OH)]3+ (2; BPMAN = 2,7-[bis(2-pyridylmethyl)aminomethyl]-1,8-naphthyridine), mononuclear catalyst 1 has a higher overpotential and lower catalytic activity toward water oxidation under the same conditions. Experimental results revealed that the O-O bond formation occurred via a water nucleophilic attack mechanism in which formal CuIV(O) is proposed as a key intermediate for the mononuclear catalyst 1H. In contrast, for the binuclear catalyst, O-O bond formation was facilitated by bimetallic cooperation between the two CuIII centers.

Using terahertz time-domain spectroscopical technique to monitor cocrystal formation between piracetam and 2,5-dihydroxybenzoic acid

NASA Astrophysics Data System (ADS)

Du, Yong; Xia, Yi; Zhang, Huili; Hong, Zhi

2013-07-01

Far-infrared vibrational absorption of cocrystal formation between 2,5-dihydroxybenzoic acid (2,5-DHBA) and piracetam compounds under solvent evaporation and grinding methods have been investigated using terahertz time-domain spectroscopy (THz-TDS) at room temperature. The experimental results show large difference among absorption spectra of the formed cocrystals and the involved individual parent molecules in 0.20-1.50 THz region, which probably originated from the intra-molecular and inter-molecular hydrogen bonds due to the presence of two hydroxyl groups in 2,5-DHBA and amide moieties in piracetam compound. The THz absorption spectra of two formed cocrystals with different methods are almost identical. With grinding method, the reaction process can be monitored directly from both time-domain and frequency-domain spectra using THz-TDS technique. The results indicate that THz-TDS technology can absolutely offer us a high potential method to identify and characterize the formed cocrystals, and also provide the rich information about their reaction dynamic process involving two or more molecular crystals in situ to better know the corresponding reaction mechanism in pharmaceutical fields.

Oxidative stress induced oligomerization inhibits the activity of the non-receptor tyrosine phosphatase STEP61

PubMed Central

Deb, Ishani; Poddar, Ranjana; Paul, Surojit

2011-01-01

The neuron-specific tyrosine phosphatase STEP (STriatal Enriched Phosphatase) is emerging as an important mediator of glutamatergic transmission in the brain. STEP is also thought to be involved in the etiology of neurodegenerative disorders that are linked to oxidative stress such as Alzheimer's disease and cerebral ischemia. However the mechanism by which oxidative stress can modulate STEP activity is still unclear. In the present study we have investigated whether dimerization may play a role in regulating the activity of STEP. Our findings show that STEP61, the membrane associated isoform, can undergo homodimerization under basal conditions in neurons. Dimerization of STEP61 involves intermolecular disulfide bond formation between two cysteine residues (Cys 65 and Cys 76 respectively) present in the hydrophobic region at the N-terminus specific to STEP61. Oxidative stress-induced by hydrogen peroxide leads to a significant increase in the formation of dimers and higher order oligomers of STEP61. Using two substrates, para-nitrophenylphosphate and ERK MAPK we further demonstrate that oligomerization leads to a significant reduction in its enzymatic activity. PMID:21198639

Formation and function of chromate conversion coating on aircraft aluminum alloy probed by vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Xia, Lin

2000-10-01

A Chromate Conversion Coating (CCC) is currently one of the most effective methods for protecting aluminum alloys from corrosion. Its unique "self-healing" property has been proved to be critical in corrosion prevention. During the formation process, CrVI, is "stored" in the CCC films. Under in-field conditions, most of the CrVI can leach out and diffuse to local defects, and stop corrosion. However, the involvement of highly toxic CrVI makes CCC system environmentally hazardous. In order to find less-toxic alternatives, the formation and protection mechanisms of CCC must be understood. Formation and function of CCC film are the focus of this study, and vibrational spectroscopy was chosen due to its superior structural sensitivity. First, the structure of CCC film was characterized. The structural similarity between CCC film and a synthetic Cr-mixed-oxide was found, and certain tests were conducted on the bulk synthetic powder which were not feasible on the thin film. All of the structural studies indicated that CCC film is mainly a CrIII-hydroxide gel layer, which adsorbs CrVI-oxy species through CrIII-O-Cr VI chemical bonds. Further analysis revealed the reversible Cr III-CrVI adsorption-desorption equilibrium, and a mathematical model ("Langmuir" model) was established to explain the Cr VI storage-release mechanism quantitatively. In addition, the function of Fe(CN)63-, an additive in the coating solution, was studied. The results indicate that Fe(CN)63- mediates the slow reaction between Al and CrVI, and the mediation mechanism can be illustrated as below: FeCN 3- 6+Al=FeCN 4-6+Al3+ ↑ FeCN 4- 6+CrVI=FeCN 3-6+CrIII In general, the formation of CCC is mediated by Fe(CN)63-, thus Al reduces CrVI quickly and generates CrIII-hydroxide on the alloy surface. The nascent CrIII-hydroxide is chemically active enough to form chemical bonds with CrVI from the solution, through Cr III-O-CrVI bonding. Such CrIII-O-Cr VI structure can form and break up reversibly according to the Langmuir model, providing mobile CrVI for in-field protection.

Bone bonding at natural and biomaterial surfaces.

PubMed

Davies, John E

2007-12-01

Bone bonding is occurring in each of us and all other terrestrial vertebrates throughout life at bony remodeling sites. The surface created by the bone-resorbing osteoclast provides a three-dimensionally complex surface with which the cement line, the first matrix elaborated during de novo bone formation, interdigitates and is interlocked. The structure and composition of this interfacial bony matrix has been conserved during evolution across species; and we have known for over a decade that this interfacial matrix can be recapitulated at a biomaterial surface implanted in bone, given appropriate healing conditions. No evidence has emerged to suggest that bone bonding to artificial materials is any different from this natural biological process. Given this understanding it is now possible to explain why bone-bonding biomaterials are not restricted to the calcium-phosphate-based bioactive materials as was once thought. Indeed, in the absence of surface porosity, calcium phosphate biomaterials are not bone bonding. On the contrary, non-bonding materials can be rendered bone bonding by modifying their surface topography. This paper argues that the driving force for bone bonding is bone formation by contact osteogenesis, but that this has to occur on a sufficiently stable recipient surface which has micron-scale surface topography with undercuts in the sub-micron scale-range.

Triggering the approach of an arene or heteroarene towards an aldehyde via Lewis acid-aldehyde communication.

PubMed

Pratihar, Sanjay

2016-03-14

The present work reports a combined experimental/computational study of the Lewis acid promoted hydroxyalkylation reaction involving aldehyde and arene/heteroarene and reveals a mechanism in which the rate determining aldehyde to alcohol formation via a four-member cyclic transition state (TS) involves a transfer of hydrogen from arene/heteroarene C-H to aldehyde oxygen with the breaking of the C-H bond and formation of C-C and O-H bonds. The effect of different Sn(iv) derivatives on the hydroxyalkylation reaction from different in situ NMR and computational studies reveals that although the exergonic formation of the intermediate and its gained electrophilicity at the carbonyl carbon drive the reaction in SnCl4 compared to other Sn(iv) derivatives, the overall reaction is low yielding because of its stable intermediate. With respect to different aldehydes, LA promoted hydroxylation was found to be more feasible for an electron withdrawing aldehyde compared to electron rich aldehyde because of lower stability, enhanced electrophilicity gained at the aldehyde center, and a lower activation barrier between its intermediate and TS in the former as compared to the latter. The relative stability of the LA-aldehyde adduct decreases in the order SnCl4 > AlCl3 > InCl3 > BF3 > ZnCl2 > TiCl4 > SiCl4, while the activation barrier (ΔG(#)) between intermediate and transition states increases in the order AlCl3 < SnCl4 < InCl3 < BF3 < TiCl4 < ZnCl2 < SiCl4. On the other hand, the activation barriers in the case of different arenes/heteroarenes are in the order of indole < furan < anisole < thiophene < toluene < benzene < chlorobenzene < cyanobenzene, which suggests a facile reaction in the case of indole and the most difficult reaction in the case of cyanobenzene. The ease of formation of the corresponding diaryl methyl carbocation from the alcohol-LA intermediate is responsible for the determination of the undesired product and is found to be more viable in the case of strong LAs like AlCl3, InCl3 and SnCl4 because they have negative free energy of formation (ΔG) for alcohol to the corresponding diaryl methyl carbocation.

Neurotensin and neuromedin N undergo distinct catabolic processes in murine astrocytes and primary cultured neurons.

PubMed

Vincent, B; Vincent, J P; Checler, F

1994-04-01

We examined the occurrence of various endopeptidases and exopeptidases and their subcellular partition within soluble and membrane-associated compartments of 15-day-old astrocytes and 4-day-old primary cultured neurons. Peptidases were monitored with chromogenic or fluorimetric substrates and identified by means of specific inhibitors. We assessed the contribution of these peptidases in the catabolism of two related neuropeptides, neurotensin and neuromedin N. Metabolites were separated by HPLC and the identity of the proteolytic activities involved in their formation was established using specific inhibitors. Neuromedin N and neurotensin undergo both quantitative and qualitative differential proteolysis. Initial maximal rates of neuromedin N degradation were higher than those of neurotensin in both cell types. Furthermore, the two peptides were inactivated much more rapidly by the soluble than by the membrane-associated fractions prepared from both cell cultures. Neuromedin N was rapidly broken down by an aminopeptidase M/leucine aminopeptidase attack, leading to the functionally silent Des-Lys1-neuromedin N metabolite. In the astrocytic membrane-associated fraction, neuromedin N underwent an additional minor endoproteolytic cleavage at the Pro3-Tyr4 bond elicited by endopeptidase 24.11, as suggested by the protective effect of its blocking agent phosphoramidon. Unlike neuromedin N, neurotensin totally resisted hydrolysis by aminopeptidases. Primary inactivating cleavages detected in both cell types appeared mainly located at the Arg8-Arg9 and Pro10-Tyr11 bonds, leading to the formations of neurotensin-(1-8) and neurotensin-(1-10) as the major biologically inactive neurotensin catabolites. Endopeptidase 24.15 appeared mainly responsible for neurotensin-(1-8) formation by the soluble fraction of neurons and astrocytes. In contrast, endopeptidase 24.16 was involved in neurotensin-(1-10) formation by both soluble and membrane-associated fractions of the two cell types. An additional cleavage leading to neurotensin-(1-11) formation and ascribed to endopeptidase 24.11 was detected mainly in the membrane-associated fraction from astrocytes. Finally, the secondary processing of neurotensin degradation products indicated that: (a) neurotensin-(1-11) was converted into neurotensin-(1-8) in the membrane fraction prepared from astrocytes; (b) neurotensin-(1-10) was transformed into neurotensin-(1-8) by an unidentified peptidase belonging to the class of metalloenzymes. The significance of distinct quantitative and qualitative catabolic fates of neuromedin N and neurotensin in cultured astrocytes and neurons is discussed.

Shake for Sigma, Pray for Pi: Classroom Orbital Overlap Analogies

ERIC Educational Resources Information Center

Dicks, Andrew P.

2011-01-01

An introductory organic classroom demonstration is discussed where analogies are made between common societal hand contact and covalent bond formation. A handshake signifies creation of a [sigma] bond ("head-on" orbital overlap), whereas the action of praying illustrates "sideways" overlap and generation of a [pi] bond. The nature of orbital and…

78 FR 37277 - CDFI Bond Guarantee Program; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-20

... the CDFI Fund in the following format: no more than 40 single-sided pages; double spaced; 12 font size... mail to the attention of Lisa Jones, Program Manager, CDFI Bond Guarantee Program, CDFI Fund, U.S... to the attention of Lisa Jones, Program Manager, CDFI Bond Guarantee Program, CDFI Fund, 1801-6215...

Laser photolysis studies of ω-bond dissociation in aromatic carbonyls with a C-C triple bond stimulated by triplet sensitization.

PubMed

Yamaji, Minoru; Horimoto, Ami; Marciniak, Bronislaw

2017-07-14

We have prepared three types of carbonyl compounds, benzoylethynylmethyl phenyl sulfide (2@SPh), (p-benzoyl)phenylethynylmethyl phenyl sulfide (3@SPh) and p-(benzoylethynyl)benzyl phenyl sulfide (4@SPh) with benzoyl and phenylthiylmethyl groups, which are interconnected with a C-C triple bond and a phenyl ring. Laser flash photolysis of 3@SPh and 4@SPh in acetonitrile provided the transient absorption spectra of the corresponding triplet states where no chemical reactions were recognized. Upon laser flash photolysis of 2@SPh, the absorption band due to the phenylthiyl radical (PTR) was obtained, indicating that the C-S bond cleaved in the excited state. Triplet sensitization of these carbonyl compounds using acetone and xanthone was conducted using laser photolysis techniques. The formation of triplet 3@SPh was seen in the transient absorption, whereas the PTR formation was observed for 2@SPh and 4@SPh, indicating that the triplet states were reactive for the C-S bond dissociation. The C-S bond dissociation mechanism for 4@SPh upon triplet sensitization is discussed in comparison with those for 2@SPh and 3@SPh.

Identification of hydrophilic group formation on polymer surface during Ar{sup +} ion irradiation in O{sub 2} environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, J.S.; Choi, W.K.; Jung, H.J.

1997-12-01

Ar{sup +} ion irradiation on low density polyethylene (LDPE), and polystyrene (PS) was performed in an O{sub 2} environment in order to improve wettability of polymers to water and to identify the formation of hydrophilic groups originated from chemical reactions on the surface of polymers. Doses of a broad Ar{sup +} ion beam of 1 keV energy were changed from 5 {times} 10{sup 15} to 1 {times} 10{sup 17}/cm{sup 2} and the rate of oxygen gas flowing near the sample surface was varied from 0 to 7 ml/min. The contact angle of polymers was not reduced much by Ar{sup +}more » ion irradiation without oxygen gas. However, it dropped largely to a minimum of 35{degree} and 26{degree} for Ar{sup +} ion irradiation in the presence of flowing oxygen gas on LDPE and PS, respectively. From x-ray photoelectron spectroscopy analysis, it was observed that hydrophilic groups were formed on the surface of polymers through an ion-assisted chemical reaction between the ion-induced unstable chains and oxygen. The newly formed hydrophilic group was identified as {single_bond}(C{double_bond}){single_bond} bond and {single_bond}(C{double_bond}O){single_bond}O{single_bond} bond. The contact angle of polymer was greatly dependent on the hydrophilic group formed on the surface.« less

Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques.

PubMed

Palombo, Francesca; Sassi, Paola; Paolantoni, Marco; Morresi, Assunta; Cataliotti, Rosario Sergio

2006-09-14

Liquid 1-octanol and 2-octanol have been investigated by infrared (IR), Raman, and Brillouin experiments in the 10-90 degrees C temperature range. Self-association properties of the neat liquids are described in terms of a three-state model in which OH oscillators differently implicated in the formation of H-bonds are considered. The results are in quantitative agreement with recent computational studies for 1-octanol. The H-bond probability is obtained by Raman data, and a stochastic model of H-bonded chains gives a consistent picture of the self-association characteristics. Average values of hydrogen bond enthalpy and entropy are evaluated. The H-bond formation enthalpy is ca. -22 kJ/mol and is slightly dependent on the structural isomerism. The different degree of self-association for the two octanols is attributed to entropic factors. The more shielded 2-isomer forms larger fractions of smaller, less cooperative, and more ordered clusters, likely corresponding to cyclic structures. Signatures of a different cluster organization are also evidenced by comparing the H-bond energy dispersion (HBED) of OH stretching IR bands. A limiting cooperative H-bond enthalpy value of 27 kJ/mol is found. It is also proposed that the different H-bonding capabilities may modulate the extent of interaggregate hydrocarbon interactions, which is important in explaining the differences in molar volume, compressibility, and vaporization enthalpy for the two isomers.

A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigments

PubMed Central

Rodrigo, María J.; Alquézar, Berta; Al-Babili, Salim

2013-01-01

Citrus is the first tree crop in terms of fruit production. The colour of Citrus fruit is one of the main quality attributes, caused by the accumulation of carotenoids and their derivative C30 apocarotenoids, mainly β-citraurin (3-hydroxy-β-apo-8′-carotenal), which provide an attractive orange-reddish tint to the peel of oranges and mandarins. Though carotenoid biosynthesis and its regulation have been extensively studied in Citrus fruits, little is known about the formation of C30 apocarotenoids. The aim of this study was to the identify carotenoid cleavage enzyme(s) [CCD(s)] involved in the peel-specific C30 apocarotenoids. In silico data mining revealed a new family of five CCD4-type genes in Citrus. One gene of this family, CCD4b1, was expressed in reproductive and vegetative tissues of different Citrus species in a pattern correlating with the accumulation of C30 apocarotenoids. Moreover, developmental processes and treatments which alter Citrus fruit peel pigmentation led to changes of β-citraurin content and CCD4b1 transcript levels. These results point to the involvement of CCD4b1 in β-citraurin formation and indicate that the accumulation of this compound is determined by the availability of the presumed precursors zeaxanthin and β-cryptoxanthin. Functional analysis of CCD4b1 by in vitro assays unequivocally demonstrated the asymmetric cleavage activity at the 7′,8′ double bond in zeaxanthin and β-cryptoxanthin, confirming its role in C30 apocarotenoid biosynthesis. Thus, a novel plant carotenoid cleavage activity targeting the 7′,8′ double bond of cyclic C40 carotenoids has been identified. These results suggest that the presented enzyme is responsible for the biosynthesis of C30 apocarotenoids in Citrus which are key pigments in fruit coloration. PMID:24006419

Bridge-bonded formate: active intermediate or spectator species in formic acid oxidation on a Pt film electrode?

PubMed

Chen, Y-X; Heinen, M; Jusys, Z; Behm, R J

2006-12-05

We present and discuss the results of an in situ IR study on the mechanism and kinetics of formic acid oxidation on a Pt film/Si electrode, performed in an attenuated total reflection (ATR) flow cell configuration under controlled mass transport conditions, which specifically aimed at elucidating the role of the adsorbed bridge-bonded formates in this reaction. Potentiodynamic measurements show a complex interplay between formation and desorption/oxidation of COad and formate species and the total Faradaic current. The notably faster increase of the Faradaic current compared to the coverage of bridge-bonded formate in transient measurements at constant potential, but with different formic acid concentrations, reveals that adsorbed formate decomposition is not rate-limiting in the dominant reaction pathway. If being reactive intermediate at all, the contribution of formate adsorption/decomposition to the reaction current decreases with increasing formic acid concentration, accounting for at most 15% for 0.2 M DCOOH at 0.7 VRHE. The rapid build-up/removal of the formate adlayer and its similarity with acetate or (bi-)sulfate adsorption/desorption indicate that the formate adlayer coverage is dominated by a fast dynamic adsorption-desorption equilibrium with the electrolyte, and that formate desorption is much faster than its decomposition. The results corroborate the proposal of a triple pathway reaction mechanism including an indirect pathway, a formate pathway, and a dominant direct pathway, as presented previously (Chen, Y. X.; et al. Angew. Chem. Int. Ed. 2006, 45, 981), in which adsorbed formates act as a site-blocking spectator in the dominant pathway rather than as an active intermediate.

Identification of non-heme diiron proteins that catalyze triple bond and epoxy group formation.

PubMed

Lee, M; Lenman, M; Banaś, A; Bafor, M; Singh, S; Schweizer, M; Nilsson, R; Liljenberg, C; Dahlqvist, A; Gummeson, P O; Sjödahl, S; Green, A; Stymne, S

1998-05-08

Acetylenic bonds are present in more than 600 naturally occurring compounds. Plant enzymes that catalyze the formation of the Delta12 acetylenic bond in 9-octadecen-12-ynoic acid and the Delta12 epoxy group in 12,13-epoxy-9-octadecenoic acid were characterized, and two genes, similar in sequence, were cloned. When these complementary DNAs were expressed in Arabidopsis thaliana, the content of acetylenic or epoxidated fatty acids in the seeds increased from 0 to 25 or 15 percent, respectively. Both enzymes have characteristics similar to the membrane proteins containing non-heme iron that have histidine-rich motifs.

Hydrogen-bond-driven electrophilic activation for selectivity control: scope and limitations of fluorous alcohol-promoted selective formation of 1,2-disubstituted benzimidazoles and mechanistic insight for rationale of selectivity.

PubMed

Chebolu, Rajesh; Kommi, Damodara N; Kumar, Dinesh; Bollineni, Narendra; Chakraborti, Asit K

2012-11-16

Hydrogen-bond-driven electrophilic activation for selectivity control during competitive formation of 1,2-disubstituted and 2-substituted benzimidazoles from o-phenylenediamine and aldehydes is reported. The fluorous alcohols trifluoroethanol and hexafluoro-2-propanol efficiently promote the cyclocondensation of o-phenylenediamine with aldehydes to afford selectively the 1,2-disubstituted benzimidazoles at rt in short times. A mechanistic insight is invoked by NMR, mass spectrometry, and chemical studies to rationalize the selectivity. The ability of the fluorous alcohols in promoting the reaction and controlling the selectivity can be envisaged from their better hydrogen bond donor (HBD) abilities compared to that of the other organic solvents as well as of water. Due to the better HBD values, the fluorous alcohols efficiently promote the initial bisimine formation by electrophilic activation of the aldehyde carbonyl. Subsequently the hydrogen-bond-mediated activation of the in situ-formed bisimine triggers the rearrangement via 1,3-hydride shift to form the 1,2-disubstituted benzimidazoles.

A PEG/copper(i) halide cluster as an eco-friendly catalytic system for C-N bond formation.

PubMed

Li, Cheng-An; Ji, Wei; Qu, Jian; Jing, Su; Gao, Fei; Zhu, Dun-Ru

2018-05-22

The catalytic activities of eight copper(i) halide clusters assembled from copper(i) halide and ferrocenyltelluroethers, 1-8, were investigated in C-N formation under various conditions. A catalytic procedure using poly(ethylene glycol) (PEG-400) as a greener alternative organic solvent has been developed. The PEG-400/5 system can achieve 99% targeted yield with a mild reaction temperature and short reaction time. After the isolation of the products by extraction with diethyl ether, this PEG-400/cluster system could be easily recycled. Spectroscopic studies elucidate a stepwise mechanism: firstly, proton-coupled electron transfer (PCET) involving the transfer of an electron from Cu+ and a proton from imidazole results in the formation of a labile penta-coordinated Cu2+ and aryl radical; the following effective electron transfer from the ferrocene unit reduces Cu2+ and forms the target product; finally, the ferrocenium unit is reduced by the I- anion. The merits of this eco-friendly synthesis are the efficient utilization of reagents and easy recyclability.

Sequential Diels–Alder/[3,3]-sigmatropic rearrangement reactions of β-nitrostyrene with 3-methyl-1,3-pentadiene

PubMed Central

Pipic, Alma; Zeller, Matthias; Tsetsakos, Panagiota

2013-01-01

Summary The tin(IV)-catalyzed reaction of β-nitrostyrene with (E)-3-methyl-1,3-pentadiene in toluene afforded two major nitronic ester cycloadducts in 27% and 29% yield that arise from the reaction at the less substituted diene double bond. Also present were four cycloadducts from the reaction at the higher substituted diene double bond, two of which were the formal cycloadducts of (Z)-3-methyl-1,3-pentadiene. A Friedel–Crafts alkylation product from the reaction of the diene, β-nitrostyrene, and toluene was also obtained in 10% yield. The tin(IV)-catalyzed reaction of β-nitrostyrene with (Z)-3-methyl-1,3-pentadiene in dichloromethane afforded four nitronic ester cycloadducts all derived from the reaction at the higher substituted double bond. One cycloadduct was isolated in 45% yield and two others are formal adducts of the E-isomer of the diene. The product formation in these reactions is consistent with a stepwise mechanism involving a zwitterionic intermediate. The initially isolated nitronic ester cycloadducts underwent tin(IV)-catalyzed interconversion, presumably via zwitterion intermediates. Cycloadducts derived from the reaction at the less substituted double bond of (E)-3-methyl-1,3-pentadiene underwent a [3,3]-sigmatropic rearrangement on heating to afford 4-nitrocyclohexenes. Cycloadducts derived from the reaction at the higher substituted diene double bond of either diene failed to undergo a thermal rearrangement. Rates and success of the rearrangement are consistent with a concerted mechanism possessing a dipolar transition state. An initial assessment of substituent effects on the rearrangement process is presented. PMID:24204426

Biochemical evidence that regulation of Ero1β activity in human cells does not involve the isoform-specific cysteine 262

PubMed Central

Hansen, Henning G.; Søltoft, Cecilie L.; Schmidt, Jonas D.; Birk, Julia; Appenzeller-Herzog, Christian; Ellgaard, Lars

2014-01-01

In the ER (endoplasmic reticulum) of human cells, disulfide bonds are predominantly generated by the two isoforms of Ero1 (ER oxidoreductin-1): Ero1α and Ero1β. The activity of Ero1α is tightly regulated through the formation of intramolecular disulfide bonds to help ensure balanced ER redox conditions. Ero1β is less tightly regulated, but the molecular details underlying control of activity are not as well characterized as for Ero1α. Ero1β contains an additional cysteine residue (Cys262), which has been suggested to engage in an isoform-specific regulatory disulfide bond with Cys100. However, we show that the two regulatory disulfide bonds in Ero1α are likely conserved in Ero1β (Cys90–Cys130 and Cys95–Cys100). Molecular modelling of the Ero1β structure predicted that the side chain of Cys262 is completely buried. Indeed, we found this cysteine to be reduced and partially protected from alkylation in the ER of living cells. Furthermore, mutation of Cys100–but not of Cys262–rendered Ero1β hyperactive in cells, as did mutation of Cys130. Ero1β hyperactivity induced the UPR (unfolded protein response) and resulted in oxidative perturbation of the ER redox state. We propose that features other than a distinct pattern of regulatory disulfide bonds determine the loose redox regulation of Ero1β relative to Ero1α. PMID:27919037

Self-etching adhesive on intact enamel, with and without pre-etching.

PubMed

Devarasa, G M; Subba Reddy, V V; Chaitra, N L; Swarna, Y M

2012-05-01

Bond strengths of composite resin to enamel using self-etch adhesive (SEA) Clearfil SE bond system on intact enamel and enamel pre-etched with phosphoric acid were compared. The objective was to determine if the pre-etching would increase the bond strengths of the SEA systems to intact enamel and to evaluate the effect of pre-etching on bond formation of self-etch adhesives on intact enamel. Labial surfaces of 40 caries free permanent upper central and lateral incisors were cleaned, sectioned of their roots. All specimens were mounted on acrylic block and divided randomly into four groups. In two groups the application of self-etch adhesive, Clearfil SE bond was carried as per manufacturer's instructions, composite cylinders were built, whereas in the other two groups, 37% phosphoric acid etching was done before the application of self-etching adhesives. Then the resin tags were analyzed using scanning electron microscope and shear bond strength was measured using Instron universal testing machine. When phosphoric acid was used, there was significant increase in the depth of penetration of resin tags and in the Shear Bond Strength of composite to enamel. The results indicate that out of both treatment groups, pre-etching the intact enamel with 37% phosphoric acid resulted in formation of longer resin tags and higher depth of penetration of resin tags of the Clearfil SE bond, and attaining higher bond strength of the Clearfil SE bond to intact enamel. Copyright © 2011 Wiley Periodicals, Inc.

The effect of nitrogen incorporation on the bonding structure of hydrogenated carbon nitride films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Camero, M.; Buijnsters, J. G.; Gomez-Aleixandre, C.

2007-03-15

This work describes the composition and bonding structure of hydrogenated carbon nitride (a-CN{sub x}:H) films synthesized by electron cyclotron resonance chemical vapor deposition using as precursor gases argon, methane, and nitrogen. The composition of the films was derived from Rutherford backscattering and elastic recoil detection analysis and the bonding structure was examined by infrared (IR) spectroscopy and x-ray absorption near edge spectroscopy (XANES). By varying the nitrogen to methane ratio in the applied gas mixture, polymeric a-CN{sub x}:H films with N/C contents varying from 0.06 to 0.49 were obtained. Remarkably, the H content of the films ({approx}40 at. %) wasmore » rather unaffected by the nitrogenation process. The different bonding states as detected in the measured XANES C(1s) and N(1s) spectra have been correlated with those of a large number of reference samples. The XANES and IR spectroscopy results indicate that N atoms are efficiently incorporated into the amorphous carbon network and can be found in different bonding environments, such as pyridinelike, graphitelike, nitrilelike, and amino groups. The nitrogenation of the films results in the formation of N-H bonding environments at the cost of C-H structures. Also, the insertion of N induces a higher fraction of double bonds in the structure at the expense of the linear polymerlike chains, hence resulting in a more cross-linked solid. The formation of double bonds takes place through complex C=N structures and not by formation of graphitic aromatic rings. Also, the mechanical and tribological properties (hardness, friction, and wear) of the films have been studied as a function of the nitrogen content. Despite the major modifications in the bonding structure with nitrogen uptake, no significant changes in these properties are observed.« less

A method for UV-bonding in the fabrication of glass electrophoretic microchips.

PubMed

Huang, Z; Sanders, J C; Dunsmor, C; Ahmadzadeh, H; Landers, J P

2001-10-01

This paper presents an approach for the development of methodologies amenable to simple and inexpensive microchip fabrication, potentially applicable to dissimilar materials bonding and chip integration. The method involves a UV-curable glue that can be used for glass microchip fabrication bonding at room temperature. This involves nothing more than fabrication of glue "guide channels" into the microchip architecture that upon exposure to the appropriate UV light source, bonds the etched plate and cover plate together. The microchip performance was verified by capillary zone electrophoresis (CZE) of small fluorescent molecules with no microchannel surface modification carried out, as well as with a DNA fragment separation following surface modification. The performance of these UV-bonded electrophoretic microchips indicates that this method may provide an alternative to high temperature bonding.

Depupylase Dop Requires Inorganic Phosphate in the Active Site for Catalysis.

PubMed

Bolten, Marcel; Vahlensieck, Christian; Lipp, Colette; Leibundgut, Marc; Ban, Nenad; Weber-Ban, Eilika

2017-03-10

Analogous to eukaryotic ubiquitination, proteins in actinobacteria can be post-translationally modified in a process referred to as pupylation, the covalent attachment of prokaryotic ubiquitin-like protein Pup to lysine side chains of the target protein via an isopeptide bond. As in eukaryotes, an opposing activity counteracts the modification by specific cleavage of the isopeptide bond formed with Pup. However, the enzymes involved in pupylation and depupylation have evolved independently of ubiquitination and are related to the family of ATP-binding and hydrolyzing carboxylate-amine ligases of the glutamine synthetase type. Furthermore, the Pup ligase PafA and the depupylase Dop share close structural and sequence homology and have a common evolutionary history despite catalyzing opposing reactions. Here, we investigate the role played by the nucleotide in the active site of the depupylase Dop using a combination of biochemical experiments and X-ray crystallographic studies. We show that, although Dop does not turn over ATP stoichiometrically with substrate, the active site nucleotide species in Dop is ADP and inorganic phosphate rather than ATP, and that non-hydrolyzable analogs of ATP cannot support the enzymatic reaction. This finding suggests that the catalytic mechanism is more similar to the mechanism of the ligase PafA than previously thought and likely involves the transient formation of a phosphorylated Pup-intermediate. Evidence is presented for a mechanism where the inorganic phosphate acts as the nucleophilic species in amide bond cleavage and implications for Dop function are discussed. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Ambient Mechanochemical Solid-State Reactions of Carbon Nanotubes and Their Reactions via Covalent Coordinate Bond in Solution

NASA Astrophysics Data System (ADS)

Kabbani, Mohamad A.

In its first part, this thesis deals with ambient mechanochemical solid-state reactions of differently functionalized multiple walled carbon nanotubes (MWCNTs) while in its second part it investigates the cross-linking reactions of CNTs in solution via covalent coordinate bonds with transitions metals and carboxylate groups decorating their surfaces. In the first part a series of mechanochemical reactions involving different reactive functionalities on the CNTs such as COOH/OH, COOH/NH2 and COCl/OH were performed. The solid-state unzipping of CNTs leading to graphene formation was confirmed using spectroscopic, thermal and electron microscopy techniques. The non-grapheme products were established using in-situ quadruple mass spectroscopy. The experimental results were confirmed by theoretical simulation calculations using the 'hot spots' protocol. The kinetics of the reaction between MWCNT-COOH and MWCNT-OH was monitored using variable temperature Raman spectroscopy. The low activation energy was discussed in terms of hydrogen bond mediated proton transfer mechanism. The second part involves the reaction of MWCNTII COOH with Zn (II) and Cu (II) to form CNT metal-organic frame (MOFs) products that were tested for their effective use as counter-electrodes in dyes sensitized solar cells (DSSC). The thesis concludes by the study of the room temperature reaction between the functionalized graphenes, GOH and G'-COOH followed by the application of compressive loads. The 3D solid graphene pellet product ( 0.6gm/cc) is conductive and reflective with a 35MPa ultimate strength as compared to 10MPa strength of graphite electrode ( 2.2gm/cc).

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.

PubMed

Harris, Michael E; Piccirilli, Joseph A; York, Darrin M

2015-11-01

The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

Iterative reactions of transient boronic acids enable sequential C-C bond formation

NASA Astrophysics Data System (ADS)

Battilocchio, Claudio; Feist, Florian; Hafner, Andreas; Simon, Meike; Tran, Duc N.; Allwood, Daniel M.; Blakemore, David C.; Ley, Steven V.

2016-04-01

The ability to form multiple carbon-carbon bonds in a controlled sequence and thus rapidly build molecular complexity in an iterative fashion is an important goal in modern chemical synthesis. In recent times, transition-metal-catalysed coupling reactions have dominated in the development of C-C bond forming processes. A desire to reduce the reliance on precious metals and a need to obtain products with very low levels of metal impurities has brought a renewed focus on metal-free coupling processes. Here, we report the in situ preparation of reactive allylic and benzylic boronic acids, obtained by reacting flow-generated diazo compounds with boronic acids, and their application in controlled iterative C-C bond forming reactions is described. Thus far we have shown the formation of up to three C-C bonds in a sequence including the final trapping of a reactive boronic acid species with an aldehyde to generate a range of new chemical structures.

Formation of unprecedented actinidecarbon triple bonds in uranium methylidyne molecules

PubMed Central

Lyon, Jonathan T.; Hu, Han-Shi; Andrews, Lester; Li, Jun

2007-01-01

Chemistry of the actinide elements represents a challenging yet vital scientific frontier. Development of actinide chemistry requires fundamental understanding of the relative roles of actinide valence-region orbitals and the nature of their chemical bonding. We report here an experimental and theoretical investigation of the uranium methylidyne molecules X3UCH (X = F, Cl, Br), F2ClUCH, and F3UCF formed through reactions of laser-ablated uranium atoms and trihalomethanes or carbon tetrafluoride in excess argon. By using matrix infrared spectroscopy and relativistic quantum chemistry calculations, we have shown that these actinide complexes possess relatively strong UC triple bonds between the U 6d-5f hybrid orbitals and carbon 2s-2p orbitals. Electron-withdrawing ligands are critical in stabilizing the U(VI) oxidation state and sustaining the formation of uranium multiple bonds. These unique UC-bearing molecules are examples of the long-sought actinide-alkylidynes. This discovery opens the door to the rational synthesis of triple-bonded actinidecarbon compounds. PMID:18024591

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jankowski, A.F.; Hayes, J.P.; Kanna, R.L.

The formation of high energy density, storage devices is achievable using composite material systems. Alternate layering of carbon aerogel wafers and Ni foils with rnicroporous separators is a prospective composite for capacitor applications. An inherent problem exists to form a physical bond between Ni and the porous carbon wafer. The bonding process must be limited to temperatures less than 1000{degrees}C, at which point the aerogel begins to degrade. The advantage of a low temperature eutectic in the Ni-Ti alloy system solves this problem. Ti, a carbide former, is readily adherent as a sputter deposited thin film onto the carbon wafer.more » A vacuum bonding process is then used to join the Ni foil and Ti coating through eutectic phase formation. The parameters required for successfld bonding are described along with a structural characterization of the Ni foil-carbon aerogel wafer interface.« less

[Cleavage time for a hydrogen bond under a load].

PubMed

Bespalov, S V; Tolpygo, K B

1993-01-01

Statistics of the hydrogen bond formation and break in a bundle of actin and myosin filaments realizing the attractive force in the sarcomere of a muscle is studied. Purely mechanical problem of the attractive-force formation and motion of myosin heads and action globules under their action is supplemented by accounting for the irreversible processes: 1. Thermal de-excitation of the latter in the chain of hydrogen bond during the elementary act of the ATP energy use resulting in fixing the extended actin filament. 2. Break of the hydrogen bonds, realizing this fixing, due to thermal fluctuations for the time tau. The average life-time turns out to be the order of time necessary for the movement of z-membrane sarcomere for the value of action filament extension delta 1, which is necessary for the process of muscle contraction to be continued.

Alkali metal mediated C-C bond coupling reaction

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto

2015-02-01

Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2]- was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

Energy efficient synthesis of boranes

DOEpatents

Thorn, David L [Los Alamos, NM; Tumas, William [Los Alamos, NM; Schwarz, Daniel E [Los Alamos, NM; Burrell, Anthony K [Los Alamos, NM

2012-01-24

The reaction of halo-boron compounds (B--X compounds, compounds having one or more boron-halogen bonds) with silanes provides boranes (B--H compounds, compounds having one or more B--H bonds) and halosilanes. Inorganic hydrides, such as surface-bound silane hydrides (Si--H) react with B--X compounds to form B--H compounds and surface-bound halosilanes. The surface bound halosilanes are converted back to surface-bound silanes electrochemically. Halo-boron compounds react with stannanes (tin compounds having a Sn--H bond) to form boranes and halostannanes (tin compounds having a Sn--X bond). The halostannanes are converted back to stannanes electrochemically or by the thermolysis of Sn-formate compounds. When the halo-boron compound is BCl.sub.3, the B--H compound is B.sub.2H.sub.6, and where the reducing potential is provided electrochemically or by the thermolysis of formate.

Energy efficient synthesis of boranes

DOEpatents

Thorn, David L.; Tumas, William; Schwarz, Daniel E.; Burrell, Anthony K.

2010-11-23

The reaction of halo-boron compounds (B--X compounds, compounds having one or more boron-halogen bonds) with silanes provides boranes (B--H compounds, compounds having one or more B--H bonds) and halosilanes. Inorganic hydrides, such as surface-bound silane hydrides (Si--H) react with B--X compounds to form B--H compounds and surface-bound halosilanes. The surface bound halosilanes are converted back to surface-bound silanes electrochemically. Halo-boron compounds react with stannanes (tin compounds having a Sn--H bond) to form boranes and halostannanes (tin compounds having a Sn--X bond). The halostannanes are converted back to stannanes electrochemically or by the thermolysis of Sn-formate compounds. When the halo-boron compound is BCl.sub.3, the B--H compound is B.sub.2H.sub.6, and where the reducing potential is provided electrochemically or by the thermolysis of formate.

Microstructural Evolution of Ni-Sn Transient Liquid Phase Sintering Bond during High-Temperature Aging

NASA Astrophysics Data System (ADS)

Feng, Hongliang; Huang, Jihua; Peng, Xianwen; Lv, Zhiwei; Wang, Yue; Yang, Jian; Chen, Shuhai; Zhao, Xingke

2018-05-01

For high-temperature-resistant packaging of new generation power chip, a chip packaging simulation structure of Ni/Ni-Sn/Ni was bonded by a transient liquid-phase sintering process. High-temperature aging experiments were carried out to investigate joint heat stability. The microstructural evolution and mechanism during aging, and mechanical properties after aging were analyzed. The results show that the 30Ni-70Sn bonding layer as-bonded at 340°C for 240 min is mainly composed of Ni3Sn4 and residual Ni particles. When aged at 350°C, because of the difficulty of nucleation for Ni3Sn and quite slow growth of Ni3Sn2, the bonding layer is stable and the strength of that doesn't change obviously with aging time. When aging temperature increased to 500°C, however, the residual Ni particles were gradually dissolved and the bonding layer formed a stable structure with dominated Ni3Sn2 after 36 h. Meanwhile, due to the volume shrinkage (4.43%) from Ni3Sn2 formation, a number of voids were formed. The shear strength shows an increase, resulting from Ni3Sn2 formation, but then it decreases slightly caused by voids. After aging at 500°C for 100 h, shear strength is still maintained at 29.6 MPa. In addition, the mechanism of void formation was analyzed and microstructural evolution model was also established.

Protonation switching to the least-basic heteroatom of carbamate through cationic hydrogen bonding promotes the formation of isocyanate cations.

PubMed

Kurouchi, Hiroaki; Sumita, Akinari; Otani, Yuko; Ohwada, Tomohiko

2014-07-07

We found that phenethylcarbamates that bear ortho-salicylate as an ether group (carbamoyl salicylates) dramatically accelerate OC bond dissociation in strong acid to facilitate generation of isocyanate cation (N-protonated isocyanates), which undergo subsequent intramolecular aromatic electrophilic cyclization to give dihydroisoquinolones. To generate isocyanate cations from carbamates in acidic media as electrophiles for aromatic substitution, protonation at the ether oxygen, the least basic heteroatom, is essential to promote CO bond cleavage. However, the carbonyl oxygen of carbamates, the most basic site, is protonated exclusively in strong acids. We found that the protonation site can be shifted to an alternative basic atom by linking methyl salicylate to the ether oxygen of carbamate. The methyl ester oxygen ortho to the phenolic (ether) oxygen of salicylate is as basic as the carbamate carbonyl oxygen, and we found that monoprotonation at the methyl ester oxygen in strong acid resulted in the formation of an intramolecular cationic hydrogen bond (>CO(+) H⋅⋅⋅O<) with the phenolic ether oxygen. This facilitates OC bond dissociation of phenethylcarbamates, thereby promoting isocyanate cation formation. In contrast, superacid-mediated diprotonation at the methyl ester oxygen of the salicylate and the carbonyl oxygen of the carbamate afforded a rather stable dication, which did not readily undergo CO bond dissociation. This is an unprecedented and unknown case in which the monocation has greater reactivity than the dication. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Copper-catalyzed transformation of ketones to amides via C(CO)-C(alkyl) bond cleavage directed by picolinamide.

PubMed

Ma, Haojie; Zhou, Xiaoqiang; Zhan, Zhenzhen; Wei, Daidong; Shi, Chong; Liu, Xingxing; Huang, Guosheng

2017-09-13

Copper catalyzed chemoselective cleavage of the C(CO)-C(alkyl) bond leading to C-N bond formation with chelation assistance of N-containing directing groups is described. Inexpensive Cu(ii)-acetate serves as a convenient catalyst for this transformation. This method highlights the emerging strategy to transform unactivated alkyl ketones into amides in organic synthesis and provides a new strategy for C-C bond cleavage.

Renewable Formate from C-H Bond Formation with CO2: Using Iron Carbonyl Clusters as Electrocatalysts.

PubMed

Loewen, Natalia D; Neelakantan, Taruna V; Berben, Louise A

2017-09-19

As a society, we are heavily dependent on nonrenewable petroleum-derived fuels and chemical feedstocks. Rapid depletion of these resources and the increasingly evident negative effects of excess atmospheric CO 2 drive our efforts to discover ways of converting excess CO 2 into energy dense chemical fuels through selective C-H bond formation and using renewable energy sources to supply electrons. In this way, a carbon-neutral fuel economy might be realized. To develop a molecular or heterogeneous catalyst for C-H bond formation with CO 2 requires a fundamental understanding of how to generate metal hydrides that selectively donate H - to CO 2 , rather than recombining with H + to liberate H 2 . Our work with a unique series of water-soluble and -stable, low-valent iron electrocatalysts offers mechanistic and thermochemical insights into formate production from CO 2 . Of particular interest are the nitride- and carbide-containing clusters: [Fe 4 N(CO) 12 ] - and its derivatives and [Fe 4 C(CO) 12 ] 2- . In both aqueous and mixed solvent conditions, [Fe 4 N(CO) 12 ] - forms a reduced hydride intermediate, [H-Fe 4 N(CO) 12 ] - , through stepwise electron and proton transfers. This hydride selectively reacts with CO 2 and generates formate with >95% efficiency. The mechanism for this transformation is supported by crystallographic, cyclic voltammetry, and spectroelectrochemical (SEC) evidence. Furthermore, installation of a proton shuttle onto [Fe 4 N(CO) 12 ] - facilitates proton transfer to the active site, successfully intercepting the hydride intermediate before it reacts with CO 2 ; only H 2 is observed in this case. In contrast, isoelectronic [Fe 4 C(CO) 12 ] 2- features a concerted proton-electron transfer mechanism to form [H-Fe 4 C(CO) 12 ] 2- , which is selective for H 2 production even in the presence of CO 2 , in both aqueous and mixed solvent systems. Higher nuclearity clusters were also studied, and all are proton reduction electrocatalysts, but none promote C-H bond formation. Thermochemical insights into the disparate reactivities of these clusters were achieved through hydricity measurements using SEC. We found that only [H-Fe 4 N(CO) 12 ] - and its derivative [H-Fe 4 N(CO) 11 (PPh 3 )] - have hydricities modest enough to avoid H 2 production but strong enough to make formate. [H-Fe 4 C(CO) 12 ] 2- is a stronger hydride donor, theoretically capable of making formate, but due to an overwhelming thermodynamic driving force and the increased electrostatic attraction between the more negative cluster and H + , only H 2 is observed experimentally. This illustrates the fundamental importance of controlling thermochemistry when designing new catalysts selective for C-H bond formation and establishes a hydricity range of 15.5-24.1 or 44-49 kcal mol -1 where C-H bond formation may be favored in water or MeCN, respectively.

Experimental evidence for the participation of deep eutectic solvents in silver chloride crystal formation at low temperature

NASA Astrophysics Data System (ADS)

Bhatt, Jitkumar; Mondal, Dibyendu; Prasad, Kamalesh

2016-05-01

Deep eutectic solvents (DESs) obtained by the complexation of choline chloride (ChoCl) as hydrogen bond acceptor and hydrogen bond donors such as ethylene glycol (ChoCl-EG 1:2) and glycerol (ChoCl-Gly 1:2) were used as media for the formation of AgCl crystals. Although formation of AgCl crystals was observed in both the solvents but the rate of formation of crystals was faster in ChoCl-EG 1:2 at low temperature (4-5 °C). In the crystals, cholinium cations were found to be present with chloride ions bridged with Ag ions resulting generation of 1D network of AgCl2 anions.

Peptide bonds affect the formation of haloacetamides, an emerging class of N-DBPs in drinking water: free amino acids versus oligopeptides

PubMed Central

Chu, Wenhai; Li, Xin; Gao, Naiyun; Deng, Yang; Yin, Daqiang; Li, Dongmei; Chu, Tengfei

2015-01-01

Haloacetamides (HAcAms), an emerging class of nitrogenous disinfection by-products (N-DBPs) of health concern, have been frequently identified in drinking waters. It has long been appreciated that free amino acids (AAs), accounting for a small fraction of the dissolved organic nitrogen (DON) pool, can form dichloroacetamide (DCAcAm) during chlorination. However, the information regarding the impacts of combined AAs, which contribute to the greatest identifiable DON portion in natural waters, is limited. In this study, we compared the formation of HAcAms from free AAs (tyrosine [Tyr] and alanine [Ala]) and combined AAs (Tyr-Ala, Ala-Tyr, Tyr-Tyr-Tyr, Ala-Ala-Ala), and found that HAcAm formation from the chlorination of AAs in combined forms (oligopeptides) significantly exhibited a different pattern with HAcAm formation from free AAs. Due to the presence of peptide bonds in tripeptides, Tyr-Tyr-Tyr and Ala-Ala-Ala produced trichloroacetamide (TCAcAm) in which free AAs was unable to form TCAcAm during chlorination. Moreover, peptide bond in tripeptides formed more tri-HAcAms than di-HAcAms in the presence of bromide. Therefore, the peptide bond may be an important indicator to predict the formation of specific N-DBPs in chlorination. The increased use of algal- and wastewater-impacted water as drinking water sources will increase health concerns over exposure to HAcAms in drinking water. PMID:26394759

Peptide bonds affect the formation of haloacetamides, an emerging class of N-DBPs in drinking water: free amino acids versus oligopeptides

NASA Astrophysics Data System (ADS)

Chu, Wenhai; Li, Xin; Gao, Naiyun; Deng, Yang; Yin, Daqiang; Li, Dongmei; Chu, Tengfei

2015-09-01

Haloacetamides (HAcAms), an emerging class of nitrogenous disinfection by-products (N-DBPs) of health concern, have been frequently identified in drinking waters. It has long been appreciated that free amino acids (AAs), accounting for a small fraction of the dissolved organic nitrogen (DON) pool, can form dichloroacetamide (DCAcAm) during chlorination. However, the information regarding the impacts of combined AAs, which contribute to the greatest identifiable DON portion in natural waters, is limited. In this study, we compared the formation of HAcAms from free AAs (tyrosine [Tyr] and alanine [Ala]) and combined AAs (Tyr-Ala, Ala-Tyr, Tyr-Tyr-Tyr, Ala-Ala-Ala), and found that HAcAm formation from the chlorination of AAs in combined forms (oligopeptides) significantly exhibited a different pattern with HAcAm formation from free AAs. Due to the presence of peptide bonds in tripeptides, Tyr-Tyr-Tyr and Ala-Ala-Ala produced trichloroacetamide (TCAcAm) in which free AAs was unable to form TCAcAm during chlorination. Moreover, peptide bond in tripeptides formed more tri-HAcAms than di-HAcAms in the presence of bromide. Therefore, the peptide bond may be an important indicator to predict the formation of specific N-DBPs in chlorination. The increased use of algal- and wastewater-impacted water as drinking water sources will increase health concerns over exposure to HAcAms in drinking water.

Peptide bonds affect the formation of haloacetamides, an emerging class of N-DBPs in drinking water: free amino acids versus oligopeptides.

PubMed

Chu, Wenhai; Li, Xin; Gao, Naiyun; Deng, Yang; Yin, Daqiang; Li, Dongmei; Chu, Tengfei

2015-09-23

Haloacetamides (HAcAms), an emerging class of nitrogenous disinfection by-products (N-DBPs) of health concern, have been frequently identified in drinking waters. It has long been appreciated that free amino acids (AAs), accounting for a small fraction of the dissolved organic nitrogen (DON) pool, can form dichloroacetamide (DCAcAm) during chlorination. However, the information regarding the impacts of combined AAs, which contribute to the greatest identifiable DON portion in natural waters, is limited. In this study, we compared the formation of HAcAms from free AAs (tyrosine [Tyr] and alanine [Ala]) and combined AAs (Tyr-Ala, Ala-Tyr, Tyr-Tyr-Tyr, Ala-Ala-Ala), and found that HAcAm formation from the chlorination of AAs in combined forms (oligopeptides) significantly exhibited a different pattern with HAcAm formation from free AAs. Due to the presence of peptide bonds in tripeptides, Tyr-Tyr-Tyr and Ala-Ala-Ala produced trichloroacetamide (TCAcAm) in which free AAs was unable to form TCAcAm during chlorination. Moreover, peptide bond in tripeptides formed more tri-HAcAms than di-HAcAms in the presence of bromide. Therefore, the peptide bond may be an important indicator to predict the formation of specific N-DBPs in chlorination. The increased use of algal- and wastewater-impacted water as drinking water sources will increase health concerns over exposure to HAcAms in drinking water.

The PDI genes of wheat and their syntenic relationship to the esp2 locus of rice.

PubMed

Johnson, Joshua C; Appels, Rudi; Bhave, Mrinal

2006-04-01

The storage protein polymers in the endosperm, stabilised by disulphide bonds, determine a number of processing qualities of wheat dough. The enzyme protein disulphide isomerase (PDI), involved in the formation of disulphide bonds, is strongly suggested to play a role in the formation of wheat storage protein bodies. Reports of the rice mutant esp2 exhibiting aberrant storage protein deposition in conjunction with a lack of PDI expression provided strong indications of a direct role for PDI in storage protein deposition. The potential significance of wheat PDI prompted the present studies into exploring any orthology between wheat PDI genes and rice PDI and esp2 loci. By designing allele-specific (AS)-polymerase chain reaction (PCR) markers, two of the three wheat PDI genes could be genetically mapped to group 4 chromosomes and showed close association with GERMIN genes. Physical mapping led to localisation of wheat PDI genes to chromosomal "bins" on the proximal section of chromosome 4AL and distal sections of 4BS and 4DS. Identification of the putative PDI gene of rice and its comparison to the esp2 locus revealed that they were present at similar positions on the short arm of chromosome 11. Analysis of a large section of the PDI-containing section of rice chromosome 11S revealed a number of putative orthologues from The Institute for Genomic Research Triticum aestivum Gene Index database, of which five had been mapped, each localising to group 4 chromosomes, many in good agreement with our mapping results. The results strongly suggest a close linkage between the esp2 marker and the PDI gene of rice and an orthology between the PDI loci of rice and wheat and predict quantitative-trait loci involved in storage protein deposition at the PDI loci.

Mononuclear ruthenium polypyridine complexes that catalyze water oxidation

DOE PAGES

Tong, Lianpeng; Thummel, Randolph P.

2016-08-05

Over the past decade, significant advances have been made in the development of molecular water oxidation catalysts (WOCs) in the context of developing a system that would accomplish artificial photosynthesis. Mononuclear ruthenium complexes with polypyridine ligands have drawn considerable attention in this regard, due to their high catalytic activity and relatively simple structure. In this perspective review, we will discuss mononuclear Ru polypyridine WOCs by organizing them into four groups according to their ligand environments. Each group will be discussed with regard to three fundamental questions: first, how does the catalyst initiate O–O bond formation? Second, which step in themore » catalytic cycle is rate-determining? Third, how efficient is the catalyst according to the specific descriptors such as turnover frequency? All discussion is based on the high-valent ruthenium intermediates that are proposed in the catalytic cycle according to experimental observation and theoretical simulation. Two fundamental mechanisms are set forth. An acid–base mechanism that involves the attack of a water molecule on the oxo of a high valent Ru=O species to form the O–O bond. Subsequent steps lead to dissociation of O 2 and rehydration of the metal center. A second mechanism involves the formation of a Ru–O˙ radical species, two of which then couple to form a Ru–O–O–Ru species that can release O 2 afterwards. The acid–base mechanism appears to be more common and mechanistic differences could result from variation directly related to polypyridine ligand structures. Thus, understanding how electronic, steric, and conformational properties can effect catalyst performance will lead to the rational design of more effective WOCs with not only ruthenium but also other transition metals.« less

Visible Light Driven Nanosecond Bromide Oxidation by a Ru Complex with Subsequent Br-Br Bond Formation.

PubMed

Li, Guocan; Ward, William M; Meyer, Gerald J

2015-07-08

Visible light excitation of [Ru(deeb)(bpz)2](2+) (deeb = 4,4'-diethylester-2,2'-bipyridine; bpz = 2,2'-bipyrazine), in Br(-) acetone solutions, led to the formation of Br-Br bonds in the form of dibromide, Br2(•-). This light reactivity stores ∼1.65 eV of free energy for milliseconds. Combined (1)H NMR, UV-vis and photoluminescence measurements revealed two distinct mechanisms. The first involves diffusional quenching of the excited state by Br(-) with a rate constant of (8.1 ± 0.1) × 10(10) M(-1) s(-1). At high Br(-) concentrations, an inner-sphere pathway is dominant that involves the association of Br(-), most likely with the 3,3'-H atoms of a bpz ligand, before electron transfer from Br(-) to the excited state, ket = (2.5 ± 0.3) × 10(7) s(-1). In both mechanisms, the direct photoproduct Br(•) subsequently reacts with Br(-) to yield dibromide, Br(•) + Br(-) → Br2(•-). Under pseudo-first-order conditions, this occurs with a rate constant of (1.1 ± 0.4) × 10(10) M(-1) s(-1) that was, within experimental error, the same as that measured when Br(•) were generated with ultraviolet light. Application of Marcus theory to the sensitized reaction provided an estimate of the Br(•) formal reduction potential E(Br(•)/Br(-)) = 1.22 V vs SCE in acetone, which is about 460 mV less positive than the accepted value in H2O. The results demonstrate that Br(-) oxidation by molecular excited states can be rapid and useful for solar energy conversion.

Synthesis and characterization of crystalline structures based on phenylboronate ligands bound to alkaline earth cations.

PubMed

Reinholdt, Marc; Croissant, Jonas; Di Carlo, Lidia; Granier, Dominique; Gaveau, Philippe; Bégu, Sylvie; Devoisselle, Jean-Marie; Mutin, P Hubert; Smith, Mark E; Bonhomme, Christian; Gervais, Christel; van der Lee, Arie; Laurencin, Danielle

2011-08-15

We describe the preparation of the first crystalline compounds based on arylboronate ligands PhB(OH)(3)(-) coordinated to metal cations: [Ca(PhB(OH)(3))(2)], [Sr(PhB(OH)(3))(2)]·H(2)O, and [Ba(PhB(OH)(3))(2)]. The calcium and strontium structures were solved using powder and single-crystal X-ray diffraction, respectively. In both cases, the structures are composed of chains of cations connected through phenylboronate ligands, which interact one with each other to form a 2D lamellar structure. The temperature and pH conditions necessary for the formation of phase-pure compounds were investigated: changes in temperature were found to mainly affect the morphology of the crystallites, whereas strong variations in pH were found to affect the formation of pure phases. All three compounds were characterized using a wide range of analytical techniques (TGA, IR, Raman, XRD, and high resolution (1)H, (11)B, and (13)C solid-state NMR), and the different coordination modes of phenylboronate ligands were analyzed. Two different kinds of hydroxyl groups were identified in the structures: those involved in hydrogen bonds, and those that are effectively "free" and not involved in hydrogen bonds of any significant strength. To position precisely the OH protons within the structures, an NMR-crystallography approach was used: the comparison of experimental and calculated NMR parameters (determined using the Gauge Including Projector Augmented Wave method, GIPAW) allowed the most accurate positions to be identified. In the case of the calcium compound, it was found that it is the (43)Ca NMR data that are critical to help identify the best model of the structure. © 2011 American Chemical Society

Thioredoxin-dependent Redox Regulation of Chloroplastic Phosphoglycerate Kinase from Chlamydomonas reinhardtii*

PubMed Central

Morisse, Samuel; Michelet, Laure; Bedhomme, Mariette; Marchand, Christophe H.; Calvaresi, Matteo; Trost, Paolo; Fermani, Simona; Zaffagnini, Mirko; Lemaire, Stéphane D.

2014-01-01

In photosynthetic organisms, thioredoxin-dependent redox regulation is a well established mechanism involved in the control of a large number of cellular processes, including the Calvin-Benson cycle. Indeed, 4 of 11 enzymes of this cycle are activated in the light through dithiol/disulfide interchanges controlled by chloroplastic thioredoxin. Recently, several proteomics-based approaches suggested that not only four but all enzymes of the Calvin-Benson cycle may withstand redox regulation. Here, we characterized the redox features of the Calvin-Benson enzyme phosphoglycerate kinase (PGK1) from the eukaryotic green alga Chlamydomonas reinhardtii, and we show that C. reinhardtii PGK1 (CrPGK1) activity is inhibited by the formation of a single regulatory disulfide bond with a low midpoint redox potential (−335 mV at pH 7.9). CrPGK1 oxidation was found to affect the turnover number without altering the affinity for substrates, whereas the enzyme activation appeared to be specifically controlled by f-type thioredoxin. Using a combination of site-directed mutagenesis, thiol titration, mass spectrometry analyses, and three-dimensional modeling, the regulatory disulfide bond was shown to involve the not strictly conserved Cys227 and Cys361. Based on molecular mechanics calculation, the formation of the disulfide is proposed to impose structural constraints in the C-terminal domain of the enzyme that may lower its catalytic efficiency. It is therefore concluded that CrPGK1 might constitute an additional light-modulated Calvin-Benson cycle enzyme with a low activity in the dark and a TRX-dependent activation in the light. These results are also discussed from an evolutionary point of view. PMID:25202015

Enthalpy Costs of Making and Breaking Bonds: A Game of Generating Molecules with Proper Lewis Structures

ERIC Educational Resources Information Center

Bell, Peter T.; Adkins, Alyssa D.; Gamble, Rex J.; Schultz, Linda D.

2009-01-01

"Enthalpy Costs" is a simple card game created to assist students in developing proper Lewis structure drawing skills. Score keeping is accomplished by tracking the enthalpy changes associated with bond-making and bond-breaking processes during formation of molecules represented by proper Lewis structures. Playing the game requires the student to…

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)

Copper(I)-Catalyzed Chemoselective Coupling of Cyclopropanols with Diazoesters: Ring-Opening C-C Bond Formations.

PubMed

Zhang, Hang; Wu, Guojiao; Yi, Heng; Sun, Tong; Wang, Bo; Zhang, Yan; Dong, Guangbin; Wang, Jianbo

2017-03-27

Reported herein is an exceptional chemoselective ring-opening/C(sp 3 )-C(sp 3 ) bond formation in the copper(I)-catalyzed reaction of cyclopropanols with diazo esters. The conventional O-H insertion product is essentially suppressed by judicious choice of reaction conditions. DFT calculations provide insights into the reaction mechanism and the rationale for this unusual chemoselectivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Out-of-water constitutional self-organization of chitosan-cinnamaldehyde dynagels.

PubMed

Marin, Luminita; Moraru, Simona; Popescu, Maria-Cristina; Nicolescu, Alina; Zgardan, Cristina; Simionescu, Bogdan C; Barboiu, Mihail

2014-04-14

An investigation of the constitutional adaptive gelation process of chitosan/cinnamaldehyde (C/Cy) dynagels is reported. These gels generate timely variant macroscopic organization across extended scales. In the first stage, imine-bond formation takes place "in-water" and generates low-ordered hydrogels. The progressive formation of imine bonds further induces "out-of-water" increased reactivity within interdigitated hydrophobic self-assembled layers of Cy, with a protecting environmental effect against hydrolysis and that leads to the stabilization of the imine bonds. The hydrophobic swelling due to Cy layers at the interfaces reaches a critical step when lamellar self-organized hybrids are generated (24 hours). This induces an important restructuration of the hydrogels on the micrometric scale, thus resulting in the formation of highly ordered microporous xerogel morphologies of high potential interest for chemical separations, drug delivery, and sensors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-Assembly of Molecular Threads into Reversible Gels

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Stupp, Samuel I.

2001-03-01

Reversible gels formed by low concentrations of molecular gelators that self-assemble into fibers with molecular width and extremely long length have been studied via Monte Carlo simulations. The gelators of interest have two kinds of interactions, one governs self-assembly into fibers and the other provides inter-fiber connectivity to drive the formation of a network. The off-lattice Monte Carlo simulation presented here is based on a point particle representation of gelators. In this model each particle can form only two strong bonds, that enable linear fiber formation, but a variable number of weak bonds which provide inter-fiber connectivity. The gel formation has been studied as a function of concentration of monomers, the strength of interactions, number of bonding sites per particle for weak interactions, and the stiffness of the fibers. The simulation results are compared with two experimental systems synthesized in our group in order to understand gelation mechanisms.

Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules.

PubMed

Ayoub, Ahmed T; Craddock, Travis J A; Klobukowski, Mariusz; Tuszynski, Jack

2014-08-05

Microtubules are key structural elements that, among numerous biological functions, maintain the cytoskeleton of the cell and have a major role in cell division, which makes them important cancer chemotherapy targets. Understanding the energy balance that brings tubulin dimers, the building blocks of microtubules, together to form a microtubule is especially important for revealing the mechanism of their dynamic instability. Several studies have been conducted to estimate various contributions to the free energy of microtubule formation. However, the hydrogen-bond contribution was not studied before as a separate component. In this work, we use concepts such as the quantum theory of atoms in molecules to estimate the per-residue strength of hydrogen bonds contributing to the overall stability that brings subunits together in pair of tubulin heterodimers, across both the longitudinal and lateral interfaces. Our study shows that hydrogen bonding plays a major role in the stability of tubulin systems. Several residues that are crucial to the binding of vinca alkaloids are shown to be strongly involved in longitudinal microtubule stabilization. This indicates a direct relation between the binding of these agents and the effect on the interfacial hydrogen-bonding network, and explains the mechanism of their action. Lateral contacts showed much higher stability than longitudinal ones (-462 ± 70 vs. -392 ± 59 kJ/mol), which suggests a dramatic lateral stabilization effect of the GTP cap in the β-subunit. The role of the M-loop in lateral stability in absence of taxol was shown to be minor. The B-lattice lateral hydrogen bonds are shown to be comparable in strength to the A-lattice ones (-462 ± 70 vs. -472 ± 46 kJ/mol). These findings establish the importance of hydrogen bonds to the stability of tubulin systems. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Crystal structure of 2α-(1,1-di­phenyl­eth­yl)-4-methyl-4α,5α-diphenyl-1,3-dioxolane: the result of a non-acid pinacol rearrangement

PubMed Central

Kirchner, Richard M.; Corfield, Peter W. R.; Annabi, Michelle; Regan, John; Speina, Kevin; DiProperzio, Anthony; Ciaccio, James A.; Capitani, Joseph F.

2015-01-01

The title compound, C30H28O2, was obtained during recrystallization of (±)-1,2-diphenyl-1,2-propane­diol in 1-butanol, from an unexpected non-acid-catalyzed pinacol rearrangement followed by acetal formation of the newly formed aldehyde with the diol. The tri-substituted dioxolane ring has a twist conformation on the C—O bond opposite the methyl-substituted C atom. There is an intra­molecular C—H⋯π inter­action present involving one of the di­phenyl­ethyl rings and an H atom of the phenyl ring in position 4 of the dioxolane ring. In the crystal, mol­ecules are linked by weak C—H⋯O hydrogen bonds, forming chains along [001]. The chains are linked by a second C—H⋯π inter­action, forming sheets parallel to the bc plane. PMID:26594491

Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism.

PubMed

Irani, Seema; Naowarojna, Nathchar; Tang, Yang; Kathuria, Karan R; Wang, Shu; Dhembi, Anxhela; Lee, Norman; Yan, Wupeng; Lyu, Huijue; Costello, Catherine E; Liu, Pinghua; Zhang, Yan Jessie

2018-05-17

Sulfur incorporation in the biosynthesis of ergothioneine, a histidine thiol derivative, differs from other well-characterized transsulfurations. A combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation and a subsequent pyridoxal 5'-phosphate (PLP)-mediated C-S lyase reaction leads to the net transfer of a sulfur atom from a cysteine to a histidine. In this study, we structurally and mechanistically characterized a PLP-dependent C-S lyase Egt2, which mediates the sulfoxide C-S bond cleavage in ergothioneine biosynthesis. A cation-π interaction between substrate and enzyme accounts for Egt2's preference of sulfoxide over thioether as a substrate. Using mutagenesis and structural biology, we captured three distinct states of the Egt2 C-S lyase reaction cycle, including a labile sulfenic intermediate captured in Egt2 crystals. Chemical trapping and high-resolution mass spectrometry were used to confirm the involvement of the sulfenic acid intermediate in Egt2 catalysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Principles of Chemical Bonding and Band Gap Engineering in Hybrid Organic-Inorganic Halide Perovskites.

PubMed

Walsh, Aron

2015-03-19

The performance of solar cells based on hybrid halide perovskites has seen an unparalleled rate of progress, while our understanding of the underlying physical chemistry of these materials trails behind. Superficially, CH 3 NH 3 PbI 3 is similar to other thin-film photovoltaic materials: a semiconductor with an optical band gap in the optimal region of the electromagnetic spectrum. Microscopically, the material is more unconventional. Progress in our understanding of the local and long-range chemical bonding of hybrid perovskites is discussed here, drawing from a series of computational studies involving electronic structure, molecular dynamics, and Monte Carlo simulation techniques. The orientational freedom of the dipolar methylammonium ion gives rise to temperature-dependent dielectric screening and the possibility for the formation of polar (ferroelectric) domains. The ability to independently substitute on the A, B, and X lattice sites provides the means to tune the optoelectronic properties. Finally, ten critical challenges and opportunities for physical chemists are highlighted.

Molecular structures of five adducts assembled from p-dimethylaminobenzaldehyde and organic acids

NASA Astrophysics Data System (ADS)

Jin, Shouwen; Wang, Lanqing; Liu, Hui; Liu, Li; Zhang, Huan; Wang, Daqi; Li, Minghui; Guo, Jianzhong; Guo, Ming

2016-07-01

Five adducts 1-5 derived from p-dimethylaminobenzaldehyde have been prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. Of the five adducts two are organic salts (1, and 2) and the other three (3-5) are cocrystals. In salts 1, and 2, the L molecules are protonated. The supramolecular architectures of the adducts 1-5 involve extensive intermolecular N-H⋯O, O-H⋯O, O-H⋯S, and C-H⋯O hydrogen bonds as well as other non-covalent interactions. The role of weak and strong non-covalent interactions in the crystal packing is ascertained. The complexes displayed 2D/3D framework structure for the synergistic effect of the various non-covalent interactions. The results presented herein tell that the strength and directionality of the N-H⋯O, O-H⋯O, and O-H⋯S hydrogen bonds between organic acids and p-dimethylaminobenzaldehyde are sufficient to bring about the formation of binary cocrystals or organic salts.

Competition between inter- and intra-molecular hydrogen bonding: An infrared spectroscopic study of jet-cooled amino-ethanol and its dimer

NASA Astrophysics Data System (ADS)

Asselin, Pierre; Madebène, Bruno; Soulard, Pascale; Georges, Robert; Goubet, Manuel; Huet, Thérèse R.; Pirali, Olivier; Zehnacker-Rentien, Anne

2016-12-01

The Fourier transform IR vibrational spectra of amino-ethanol (AE) and its dimer have been recorded at room temperature and under jet-cooled conditions over the far and mid infrared ranges (50-4000 cm-1) using the White-type cell and the supersonic jet of the Jet-AILES apparatus at the synchrotron facility SOLEIL. Assignment of the monomer experimental frequencies has been derived from anharmonic frequencies calculated at a hybrid CCSD(T)-F12/MP2 level. Various thermodynamical effects in the supersonic expansion conditions including molar dilution of AE and nature of carrier gas have been used to promote or not the formation of dimers. Four vibrational modes of the observed dimer have been unambiguously assigned using mode-specific scaling factors deduced from the ratio between experimental and computed frequencies for the monomer. The most stable g'Gg' monomer undergoes strong deformation upon dimerization, leading to a homochiral head to head dimer involving two strong hydrogen bonds.

Principles of Chemical Bonding and Band Gap Engineering in Hybrid Organic–Inorganic Halide Perovskites

PubMed Central

2015-01-01

The performance of solar cells based on hybrid halide perovskites has seen an unparalleled rate of progress, while our understanding of the underlying physical chemistry of these materials trails behind. Superficially, CH3NH3PbI3 is similar to other thin-film photovoltaic materials: a semiconductor with an optical band gap in the optimal region of the electromagnetic spectrum. Microscopically, the material is more unconventional. Progress in our understanding of the local and long-range chemical bonding of hybrid perovskites is discussed here, drawing from a series of computational studies involving electronic structure, molecular dynamics, and Monte Carlo simulation techniques. The orientational freedom of the dipolar methylammonium ion gives rise to temperature-dependent dielectric screening and the possibility for the formation of polar (ferroelectric) domains. The ability to independently substitute on the A, B, and X lattice sites provides the means to tune the optoelectronic properties. Finally, ten critical challenges and opportunities for physical chemists are highlighted. PMID:25838846

An Isozyme-specific Redox Switch in Human Brain Glycogen Phosphorylase Modulates Its Allosteric Activation by AMP.

PubMed

Mathieu, Cécile; Duval, Romain; Cocaign, Angélique; Petit, Emile; Bui, Linh-Chi; Haddad, Iman; Vinh, Joelle; Etchebest, Catherine; Dupret, Jean-Marie; Rodrigues-Lima, Fernando

2016-11-11

Brain glycogen and its metabolism are increasingly recognized as major players in brain functions. Moreover, alteration of glycogen metabolism in the brain contributes to neurodegenerative processes. In the brain, both muscle and brain glycogen phosphorylase isozymes regulate glycogen mobilization. However, given their distinct regulatory features, these two isozymes could confer distinct metabolic functions of glycogen in brain. Interestingly, recent proteomics studies have identified isozyme-specific reactive cysteine residues in brain glycogen phosphorylase (bGP). In this study, we show that the activity of human bGP is redox-regulated through the formation of a disulfide bond involving a highly reactive cysteine unique to the bGP isozyme. We found that this disulfide bond acts as a redox switch that precludes the allosteric activation of the enzyme by AMP without affecting its activation by phosphorylation. This unique regulatory feature of bGP sheds new light on the isoform-specific regulation of glycogen phosphorylase and glycogen metabolism. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Carbon-carbon bond activation of 2,2,6,6-tetramethyl-piperidine-1-oxyl by a Rh(II) metalloradical: a combined experimental and theoretical study.

PubMed

Chan, Kin Shing; Li, Xin Zhu; Dzik, Wojciech I; de Bruin, Bas

2008-02-13

Competitive major carbon-carbon bond activation (CCA) and minor carbon-hydrogen bond activation (CHA) channels are identified in the reaction between rhodium(II) meso-tetramesitylporphyrin [Rh(II)(tmp)] (1) and 2,2,6,6-tetramethyl-piperidine-1-oxyl (TEMPO) (2). The CCA and CHA pathways lead to formation of [Rh(III)(tmp)Me] (3) and [Rh(III)(tmp)H] (5), respectively. In the presence of excess TEMPO, [Rh(II)(tmp)] is regenerated from [Rh(III)(tmp)H] with formation of 2,2,6,6-tetramethyl-piperidine-1-ol (TEMPOH) (4) via a subsequent hydrogen atom abstraction pathway. The yield of the CCA product [Rh(III)(tmp)Me] increased with higher temperature at the cost of the CHA product TEMPOH in the temperature range 50-80 degrees C. Both the CCA and CHA pathways follow second-order kinetics. The mechanism of the TEMPO carbon-carbon bond activation was studied by means of kinetic investigations and DFT calculations. Broken symmetry, unrestricted b3-lyp calculations along the open-shell singlet surface reveal a low-energy transition state (TS1) for direct TEMPO methyl radical abstraction by the Rh(II) radical (SH2 type mechanism). An alternative ionic pathway, with a somewhat higher barrier, was identified along the closed-shell singlet surface. This ionic pathway proceeds in two sequential steps: Electron transfer from TEMPO to [Rh(II)(por)] producing the [TEMPO]+ [RhI(por)]- cation-anion pair, followed by net CH3+ transfer from TEMPO+ to Rh(I) with formation of [Rh(III)(por)Me] and (DMPO-like) 2,2,6-trimethyl-2,3,4,5-tetrahydro-1-pyridiniumolate. The transition state for this process (TS2) is best described as an SN2-like nucleophilic substitution involving attack of the d(z)2 orbital of [Rh(I)(por)]- at one of the C(Me)-C(ring) sigma* orbitals of [TEMPO]+. Although the calculated barrier of the open-shell radical pathway is somewhat lower than the barrier for the ionic pathway, R-DFT and U-DFT are not likely comparatively accurate enough to reliably distinguish between these possible pathways. Both the radical (SH2) and the ionic (SN2) pathway have barriers which are low enough to explain the experimental kinetic data.

Gold-based electrical interconnections for microelectronic devices

DOEpatents

Peterson, Kenneth A.; Garrett, Stephen E.; Reber, Cathleen A.; Watson, Robert D.

2002-01-01

A method of making an electrical interconnection from a microelectronic device to a package, comprising ball or wedge compression bonding a gold-based conductor directly to a silicon surface, such as a polysilicon bonding pad in a MEMS or IMEMS device, without using layers of aluminum or titanium disposed in-between the conductor and the silicon surface. After compression bonding, optional heating of the bond above 363 C. allows formation of a liquid gold-silicon eutectic phase containing approximately 3% (by weight) silicon, which significantly improves the bond strength by reforming and enhancing the initial compression bond. The same process can be used for improving the bond strength of Au--Ge bonds by forming a liquid Au-12Ge eutectic phase.

Vapor-Gas Bubble Evolution and Growth in Extremely Viscous Fluids Under Vacuum

NASA Technical Reports Server (NTRS)

Kizito, John; Balasubramaniam, R.; Nahra, Henry; Agui, Juan; Truong, Duc

2008-01-01

Formation of vapor and gas bubbles and voids is normal and expected in flow processes involving extremely viscous fluids in normal gravity. Practical examples of extremely viscous fluids are epoxy-like filler materials before the epoxy fluids cure to their permanent form to create a mechanical bond between two substrates. When these fluids flow with a free liquid interface exposed to vacuum, rapid bubble expansion process may ensue. Bubble expansion might compromise the mechanical bond strength. The potential sources for the origin of the gases might be incomplete out-gassing process prior to filler application; regasification due to seal leakage in the filler applicator; and/or volatiles evolved from cure reaction products formed in the hardening process. We embarked on a study that involved conducting laboratory experiments with imaging diagnostics in order to deduce the seriousness of bubbling caused by entrained air and volatile fluids under space vacuum and low gravity environment. We used clear fluids with the similar physical properties as the epoxy-like filler material to mimic the dynamics of bubbles. Another aspect of the present study was to determine the likelihood of bubbling resulting from dissolved gases nucleating from solution. These experimental studies of the bubble expansion are compared with predictions using a modified Rayleigh- Plesset equation, which models the bubble expansion.

The Nature of the Intramolecular Charge Transfer State in Peridinin

PubMed Central

Wagner, Nicole L.; Greco, Jordan A.; Enriquez, Miriam M.; Frank, Harry A.; Birge, Robert R.

2013-01-01

Experimental and theoretical evidence is presented that supports the theory that the intramolecular charge transfer (ICT) state of peridinin is an evolved state formed via excited-state bond-order reversal and solvent reorganization in polar media. The ICT state evolves in <100 fs and is characterized by a large dipole moment (∼35 D). The charge transfer character involves a shift of electron density within the polyene chain, and it does not involve participation of molecular orbitals localized in either of the β-rings. Charge is moved from the allenic side of the polyene into the furanic ring region and is accompanied by bond-order reversal in the central portion of the polyene chain. The electronic properties of the ICT state are generated via mixing of the “11Bu+” ionic state and the lowest-lying “21Ag–” covalent state. The resulting ICT state is primarily 1Bu+-like in character and exhibits not only a large oscillator strength but an unusually large doubly excited character. In most solvents, two populations exist in equilibrium, one with a lowest-lying ICT ionic state and a second with a lowest-lying “21Ag–” covalent state. The two populations are separated by a small barrier associated with solvent relaxation and cavity formation. PMID:23528091

Unexpected Trimerization of Pyrazine in the Coordination Sphere of Low-Valent Titanocene Fragments.

PubMed

Jung, Thomas; Beckhaus, Rüdiger; Klüner, Thorsten; Höfener, Sebastian; Klopper, Wim

2009-08-11

The titanium mediated trimerization of pyrazine leads to the formation of a tris-chelate complex employing a 4a,4b,8a,8b,12a,12b-hexahydrodiyprazino[2,3-f:2',3'-h]quinoxaline ligand (HATH6, 3). The driving force in the formation of the (Cp*2Ti)3(HATH6) complex 2 is attributed to the formation of six Ti-N bonds. We show that density functional theory (DFT) fails to predict quantitatively correct results. Therefore, post-Hartree-Fock methods, such as second-order Møller-Plesset perturbation theory (MP2), in combination with coupled-cluster (CC) methods must be used. Both MP2 and CCSD(T) levels of theory provide endothermic trimerization energies, showing that the plain pyrazine trimer is not stable with respect to decomposition into its monomers. Complete basis set (CBS) results for the MP2 level of theory were computed using explicitly correlated wave functions. With these, we estimate the CCSD(T) CBS limit of the hypothetical trimerization energy to be +0.78 eV. Thus, the trimerization is facilitated by the formation of six Ti-N bonds with a calculated formation energy of -1.32 eV per bond.

Oxidative cleavage of the octyl side chain of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045) in rat and dog liver preparations.

PubMed

Umehara, K; Kudo, S; Hirao, Y; Morita, S; Uchida, M; Odomi, M; Miyamoto, G

2000-08-01

The metabolism of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045), a new potent biguanide antiseptic, was investigated using rat and dog liver preparations to elucidate the mechanism of OPB-2045 metabolite formation, in which the octyl side chain is reduced to four, five, or six carbon atoms. Chemical structures of metabolites were characterized by 1H NMR, fast atom bombardment/mass spectrometry, and liquid chromatography/electrospray ionization-tandem mass spectrometry. Three main metabolites were observed during incubation of OPB-2045 with rat liver S9: 2-octanol (M-1), 3-octanol (M-2), and 4-octanol (M-3). In the incubation of OPB-2045 with dog liver S9, eight metabolites were observed, seven of which being M-1, M-2, M-3, 2-octanone (M-4), threo-2,3-octandiol (M-5), erythro-2,3-octandiol (M-6), and 1,2-octandiol (M-7). M-5 and M-6 were further biotransformed to a ketol derivative and C-C bond cleavage metabolite (hexanoic acid derivative), an in vivo end product, in the incubation with dog liver microsomes. The reactions required NADPH as a cofactor and were significantly inhibited by the various inhibitors of cytochrome P450 (i.e., CO, n-octylamine, SKF 525-A, metyrapone, and alpha-naphthoflavone). The results indicate that the degraded products of OPB-2045 are produced by C-C bond cleavage after monohydroxylation, dihydroxylation, and ketol formation at the site of the octyl side chain with possible involvement of cytochrome P450 systems. This aliphatic C-C bond cleavage by sequential oxidative reactions may play an important role in the metabolism of other drugs or endogenous compounds that possess aliphatic chains.

Targeting allosteric disulphide bonds in cancer.

PubMed

Hogg, Philip J

2013-06-01

Protein action in nature is generally controlled by the amount of protein produced and by chemical modification of the protein, and both are often perturbed in cancer. The amino acid side chains and the peptide and disulphide bonds that bind the polypeptide backbone can be post-translationally modified. Post-translational cleavage or the formation of disulphide bonds are now being identified in cancer-related proteins and it is timely to consider how these allosteric bonds could be targeted for new therapies.

Asymmetrical bonding in cold spraying of dissimilar materials

NASA Astrophysics Data System (ADS)

Nikbakht, R.; Seyedein, S. H.; Kheirandish, S.; Assadi, H.; Jodoin, B.

2018-06-01

Characteristics of particle bonding, especially for dissimilar materials, remains a key question in cold spray deposition. There are limited reports in direct correlation to particle/substrate bonding and peripheral shear zones. Cold spraying experiments and numerical simulations are conducted to characterise and analyse the correlation between bonding and peripheral shear zones for asymmetric particle/substrate pairs of intermetallic-forming elements of nickel and titanium. The correlation between metallic bonding and highly strained areas is explored in view of the growth of the intermetallic phase at the particle/substrate interface during subsequent heat treatments. Characterisation of the as-sprayed samples reveal that for the Ni(particle)/Ti(substrate) pair, plastic deformation of the particle is dominating over substrate deformation. However, for the Ti(particle)/Ni(substrate) pair, it is observed that the substrate and particle deform to similar extents. Characterisation of the samples after a brief heat treatment at 700 °C indicate that intermetallic formation, and hence metallurgical bonding of the pairs is more likely to occur at the particle peripheries where the interface areas are highly strained, and rarely achieved at the particle base. Results also reveal that bonding extends from peripheries toward the central part of the interfaces with increasing the impact velocity. The kinetics of interfacial intermetallic formation at peripheral areas and its correlation to particle bonding is discussed in view of deformation-enhanced interdiffusion.

Brittle-to-ductile transition of lithiated silicon electrodes: Crazing to stable nanopore growth.

PubMed

Wang, Haoran; Wang, Xueju; Xia, Shuman; Chew, Huck Beng

2015-09-14

Using first principle calculations, we uncover the underlying mechanisms explaining the brittle-to-ductile transition of LixSi electrodes in lithium ion batteries with increasing Li content. We show that plasticity initiates at x = ∼ 0.5 with the formation of a craze-like network of nanopores separated by Si-Si bonds, while subsequent failure is still brittle-like with the breaking of Si-Si bonds. Transition to ductile behavior occurs at x ⩾ 1 due to the increased density of highly stretchable Li-Li bonds, which delays nanopore formation and stabilizes nanopore growth. Collapse of the nanopores during unloading of the LixSi alloys leads to significant strain recovery.

Formation of Si{sup 1+} in the early stages of the oxidation of the Si[001] 2 × 1 surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herrera-Gomez, Alberto, E-mail: aherrerag@cinvestav.mx; Aguirre-Tostado, Francisco-Servando; Pianetta, Piero

2016-03-15

The early stages of the oxidation of the Si[001] 2 × 1 surface were studied with synchrotron radiation photoelectron spectroscopy. The analysis was based on the block approach, which is a refinement of spectra-subtraction that accounts for changes on the background signal and for band-bending shifts. By this method, it was possible to robustly show that the formation of Si{sup 1+} is due to oxygen bonding to the upper dimer atoms. Our results contrast with ab initio calculation, which indicates that the most favorable bonding site is the back-bond of the down-dimer.

Nanometre-scale 3D defects in Cr2AlC thin films.

PubMed

Chen, Y T; Music, D; Shang, L; Mayer, J; Schneider, J M

2017-04-20

MAX-phase Cr 2 AlC containing thin films were synthesized by magnetron sputtering in an industrial system. Nanometre-scale 3D defects are observed near the boundary between regions of Cr 2 AlC and of the disordered solid solution (CrAl) x C y . Shrinkage of the Cr-Cr interplanar distance and elongation of the Cr-Al distance in the vicinity of the defects are detected using transmission electron microscopy. The here observed deformation surrounding the defects was described using density functional theory by comparing the DOS of bulk Cr 2 AlC with the DOS of a strained and unstrained Cr 2 AlC(0001) surface. From the partial density of states analysis, it can be learned that Cr-C bonds are stronger than Cr-Al bonds in bulk Cr 2 AlC. Upon Cr 2 AlC(0001) surface formation, both bonds are weakened. While the Cr-C bonds recover their bulk strength as Cr 2 AlC(0001) is strained, the Cr-Al bonds experience only a partial recovery, still being weaker than their bulk counterparts. Hence, the strain induced bond strengthening in Cr 2 AlC(0001) is larger for Cr d - C p bonds than for Cr d - Al p bonds. The here observed changes in bonding due to the formation of a strained surface are consistent with the experimentally observed elongation of the Cr-Al distance in the vicinity of nm-scale 3D defects in Cr 2 AlC thin films.

Studies of carbon incorporation on the diamond [100] surface during chemical vapor deposition using density functional theory.

PubMed

Cheesman, Andrew; Harvey, Jeremy N; Ashfold, Michael N R

2008-11-13

Accurate potential energy surface calculations are presented for many of the key steps involved in diamond chemical vapor deposition on the [100] surface (in its 2 x 1 reconstructed and hydrogenated form). The growing diamond surface was described by using a large (approximately 1500 atoms) cluster model, with the key atoms involved in chemical steps being described by using a quantum mechanical (QM, density functional theory, DFT) method and the bulk of the atoms being described by molecular mechanics (MM). The resulting hybrid QM/MM calculations are more systematic and/or at a higher level of theory than previous work on this growth process. The dominant process for carbon addition, in the form of methyl radicals, is predicted to be addition to a surface radical site, opening of the adjacent C-C dimer bond, insertion, and ultimate ring closure. Other steps such as insertion across the trough between rows of dimer bonds or addition to a neighboring dimer leading to formation of a reconstruction on the next layer may also contribute. Etching of carbon can also occur; the most likely mechanism involves loss of a two-carbon moiety in the form of ethene. The present higher-level calculations confirm that migration of inserted carbon along both dimer rows and chains should be relatively facile, with barriers of approximately 150 kJ mol (-1) when starting from suitable diradical species, and that this step should play an important role in establishing growth of smooth surfaces.

Dynamics of micelle formation from temperature-jump Monte Carlo simulations.

PubMed

Heinzelmann, G; Seide, P; Figueiredo, W

2015-11-01

In the present work we perform temperature jumps in a surfactant solution by means of Monte Carlo simulations, investigating the dynamics of micelle formation. We use a lattice model that allows orientational freedom and hydrogen bonding for solvent molecules, which can make a connection between the different time scales of hydrogen bond formation and amphiphilic aggregation. When we perform a large jump between a high-temperature nonmicellized state and a micellized state, there is strong hysteresis between the heating and cooling processes, the latter showing the formation of premicelles that act as nucleation centers for the assembly of larger aggregates and the former is a drive for dissociation of the existing aggregates. Hysteresis is not seen when we perform a small jump between two states that can be both micellized or nonmicellized. Looking for a more detailed analysis of the hydrophobic effect that drives aggregation, we compare the time evolution of the solvent hydrogen bonds in our system close and far from micelles and how that is affected by the formation of large clusters at low temperatures. We find a strong connection between them, with the total number of hydrogen bonds in the system always increasing when micelles are formed. To gain insights into the mechanism of premicellar formation and growth, we measure the lifetime of micellized amphiphiles as a function of the aggregate size and the stage of the aggregation process. Our results indicate that the premicelles are always unstable, quickly exchanging amphiphiles with the solution due to their low probabilty in equilibrium. Furthermore, we find that the stability of individual surfactants in micelles increases with the aggregate size, with the lifetime of amphiphiles in large micelles being as much as 35 times longer than in the case of the unstable premicellar region.

The Au/Si eutectic bonding compatibility with KOH etching for 3D devices fabrication

NASA Astrophysics Data System (ADS)

Liang, Hengmao; Liu, Mifeng; Liu, Song; Xu, Dehui; Xiong, Bin

2018-01-01

KOH etching and Au/Si eutectic bonding are cost-efficient technologies for 3D device fabrication. Aimed at investigating the process compatibility of KOH etching and Au/Si bonding, KOH etching tests have been carried out for Au/bulk Si and Au/amorphous Si (a-Si) bonding wafers in this paper. For the Au/bulk Si bonding wafer, a serious underetch phenomenon occurring on the damage layer in KOH etching definitely results in packaging failure. In the microstructure analysis, it is found that the formation of the damage layer between the bonded layer and bulk Si is attributed to the destruction of crystal Si lattices in Au/bulk Si eutectic reaction. Considering the occurrence of underetch for Au/Si bonding must meet two requirements: the superfluous Si and the defective layer near the bonded layer, the Au/a-Si bonding by regulating the a-Si/Au thickness ratio is presented in this study. Only when the a-Si/Au thickness ratio is relatively low are there not underetch phenomena, of which the reason is the full reaction of the a-Si layer avoiding the formation of the damage layer for easy underetch. Obviously, the Au/a-Si bonding via choosing a moderate a-Si/Au thickness ratio (⩽1.5:1 is suggested) could be reliably compatible with KOH etching, which provides an available and low-cost approach for 3D device fabrication. More importantly, the theory of the damage layer proposed in this study can be naturally applied to relevant analyses on the eutectic reaction of other metals and single crystal materials.

Concentration-dependent multiple chirality transition in halogen-bond-driven 2D self-assembly process

NASA Astrophysics Data System (ADS)

Miao, Xinrui; Li, Jinxing; Zha, Bao; Miao, Kai; Dong, Meiqiu; Wu, Juntian; Deng, Wenli

2018-03-01

The concentration-dependent self-assembly of iodine substituted thienophenanthrene derivative (5,10-DITD) is investigated at the 1-octanic acid/graphite interface using scanning tunneling microscopy. Three kinds of chiral arrangement and transition of 2D molecular assembly mainly driven by halogen bonding is clearly revealed. At high concentration the molecules self-assembled into a honeycomb-like chiral network. Except for the interchain van der Waals forces, this pattern is stabilized by intermolecular continuous Cdbnd O⋯I⋯S halogen bonds in each zigzag line. At moderate concentration, a chiral kite-like nanoarchitecture are observed, in which the Cdbnd O⋯I⋯S and I⋯Odbnd C halogen bonds, along with the molecule-solvent Cdbnd O⋯I⋯H halogen bonds are the dominated forces to determine the structural formation. At low concentration, the molecules form a chiral cyclic network resulting from the solvent coadsorption mainly by molecule-molecule Cdbnd O⋯I⋯S halogen bonds and molecule-solvent Cdbnd O⋯I⋯H halogen bonds. The density of molecular packing becomes lower with the decreasing of the solution concentration. The solution-concentration dependent self-assembly of thienophenanthrene derivative with iodine and ester chain moieties reveals that the type of intermolecular halogen bond and the number of the co-adsorbing 1-octanic acids by molecule-solvent Cdbnd O⋯I⋯H halogen bonds determine the formation and transformation of chirality. This research emphasizes the role of different types of halogen (I) bonds in the controllable supramolecular structures and provides an approach for the fabrication of chirality.

Studying physical properties of deformed intact and fractured rocks by micro-scale hydro-mechanical-seismicity model

NASA Astrophysics Data System (ADS)

Raziperchikolaee, Samin

The pore pressure variation in an underground formation during hydraulic stimulation of low permeability formations or CO2 sequestration into saline aquifers can induce microseismicity due to fracture generation or pre-existing fracture activation. While the analysis of microseismic data mainly focuses on mapping the location of fractures, the seismic waves generated by the microseismic events also contain information for understanding of fracture mechanisms based on microseismic source analysis. We developed a micro-scale geomechanics, fluid-flow and seismic model that can predict transport and seismic source behavior during rock failure. This model features the incorporation of microseismic source analysis in fractured and intact rock transport properties during possible rock damage and failure. The modeling method considers comprehensive grains and cements interaction through a bonded-particle-model. As a result of grain deformation and microcrack development in the rock sample, forces and displacements in the grains involved in the bond breakage are measured to determine seismic moment tensor. In addition, geometric description of the complex pore structure is regenerated to predict fluid flow behavior of fractured samples. Numerical experiments are conducted for different intact and fractured digital rock samples, representing various mechanical behaviors of rocks and fracture surface properties, to consider their roles on seismic and transport properties of rocks during deformation. Studying rock deformation in detail provides an opportunity to understand the relationship between source mechanism of microseismic events and transport properties of damaged rocks to have a better characterizing of fluid flow behavior in subsurface formations.

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

Kinetics and Mechanism of the Reaction of a Ruthenium(VI) Nitrido Complex with HSO3 (-) and SO3 (2-) in Aqueous Solution.

PubMed

Wang, Qian; Zhao, Hong Yan; Man, Wai-Lun; Lam, William W Y; Lau, Kai-Chung; Lau, Tai-Chu

2016-07-25

The kinetics and mechanism of the reaction of S(IV) (SO3 (2-) +HSO3 (-) ) with a ruthenium(VI) nitrido complex, [(L)Ru(VI) (N)(OH2 )](+) (Ru(VI) N, L=N,N'-bis(salicylidene)-o-cyclohexyldiamine dianion), in aqueous acidic solutions are reported. The kinetic results are consistent with parallel pathways involving oxidation of HSO3 (-) and SO3 (2-) by Ru(VI) N. A deuterium isotope effect of 4.7 is observed in the HSO3 (-) pathway. Based on experimental results and DFT calculations the proposed mechanism involves concerted N-S bond formation (partial N-atom transfer) between Ru(VI) N and HSO3 (-) and H(+) transfer from HSO3 (-) to a H2 O molecule. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxygen plasma etching of graphene: A first-principles dynamical inspection of the reaction mechanisms and related activation barriers

NASA Astrophysics Data System (ADS)

Koizumi, Kenichi; Boero, Mauro; Shigeta, Yasuteru; Oshiyama, Atsushi; Dept. of Applied Physics Team; Institute of Physics and Chemistry of Strasbourg (IPCMS) Collaboration; Department Of Materials Engineering Science Collaboration

2013-03-01

Oxygen plasma etching is a crucial step in the fabrication of electronic circuits and has recently received a renovated interest in view of the realization of carbon-based nanodevices. In an attempt at unraveling the atomic-scale details and to provide guidelines for the control of the etching processes mechanisms, we inspected the possible reaction pathways via reactive first principles simulations. These processes involve breaking and formation of several chemical bonds and are characterized by different free-energy barriers. Free-energy sampling techniques (metadynamics and blue moon), used to enhance the standard Car-Parrinello molecular dynamics, provide us a detailed microscopic picture of the etching of graphene surfaces and a comprehensive scenario of the activation barriers involved in the various steps. MEXT, Japan - contract N. 22104005

Anomalously enhanced hydration of aqueous electrolyte solution in hydrophobic carbon nanotubes to maintain stability.

PubMed

Ohba, Tomonori

2014-02-24

An understanding of the structure and behavior of electrolyte solutions in nanoenvironements is crucial not only for a wide variety of applications, but also for the development of physical, chemical, and biological processes. We demonstrate the structure and stability of electrolyte in carbon nanotubes using hybrid reverse Monte Carlo simulations of X-ray diffraction patterns. Hydrogen bonds between water are adequately formed in carbon nanotubes, although some hydrogen bonds are restricted by the interfaces of carbon nanotubes. The hydrogen bonding network of water in electrolyte in the carbon nanotubes is further weakened. On the other hand, formation of the ion hydration shell is significantly enhanced in the electrolyte in the carbon nanotubes in comparison to ion hydration in bulk electrolyte. The significant hydrogen bond and hydration shell formation are a result of gaining stability in the hydrophobic nanoenvironment. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

PubMed Central

Serganov, Alexander; Keiper, Sonja; Malinina, Lucy; Tereshko, Valentina; Skripkin, Eugene; Höbartner, Claudia; Polonskaia, Anna; Phan, Anh Tuân; Wombacher, Richard; Micura, Ronald; Dauter, Zbigniew; Jäschke, Andres; Patel, Dinshaw J

2015-01-01

The majority of structural efforts addressing RNA’s catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions. PMID:15723077