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Sample records for amide bond rotation

  1. Acceleration of Amide Bond Rotation by Encapsulation in the Hydrophobic Interior of a Water-Soluble Supramolecular Assembly

    SciTech Connect

    Pluth, Michael D.; Bergman, Robert G.; Raymond, Kenneth N.

    2008-04-08

    The hydrophobic interior cavity of a self-assembled supramolecular assembly exploits the hydrophobic effect for the encapsulation of tertiary amides. Variable temperature 1H NMR experiments reveal that the free energy barrier for rotation around the C-N amide bond is lowered by up to 3.6 kcal/mol upon encapsulation. The hydrophobic cavity of the assembly is able to stabilize the less polar transition state of the amide rotation process. Carbon-13 labeling studies showed that the {sup 13}C NMR carbonyl resonance increases with temperature for the encapsulated amides which suggests that the assembly is able to favor a twisted for of the amide.

  2. Investigation of the energy barrier to the rotation of amide CN bonds in ACE inhibitors by NMR, dynamic HPLC and DFT.

    PubMed

    Bouabdallah, S; Ben Dhia, M T; Driss, M R; Touil, S

    2016-09-01

    The isomerizations of Enalapril, Perindopril, Enalaprilat and Lisinopril have been investigated using NMR spectroscopic, dynamic chromatographic, unified equation and DFT theoretical calculations. The thermodynamic parameters (ΔH, ΔS and ΔG) were determined by varying the temperature in the NMR experiments. At the coalescence temperature, we can evaluate the isomerization barrier to the rotation (ΔG(≠)) around the amide bond. Using dynamics chromatography and an unified equation introduced by Trap, we can determine isomerization rate constants and Gibbs activation energies. Molecular mechanics calculations also provided evidence for the presence of low energy conformers for the ACE due to restricted amide rotation. With the value of barriers (ΔE) between them of the order of (20kJmol(-1)), which is in agreement with the dynamic NMR results and DFT calculations. PMID:27344631

  3. Modulations in restricted amide rotation by steric induced conformational trapping

    NASA Astrophysics Data System (ADS)

    Krishnan, V. V.; Thompson, William B.; Goto, Joy J.; Maitra, Kalyani; Maitra, Santanu

    2012-01-01

    The rotation around the amide bond in N,N-diethyl-m-toluamide (m-DEET) has been studied extensively and often used in laboratory instructions to demonstrate the phenomenon of chemical exchange. Herein, we show that a simple modification to N,N-diethyl-o-toluamide (o-DEET) significantly alters the dynamics of the restricted rotation around the amide bond due to steric interactions between the ring methyl group and the two N-ethyl groups. This alters the classic two-site exchange due to restricted rotation around the amide bond, to a three-site exchange, with the third conformation trapped at a higher-energy state compared to the other two. This often overlooked phenomenon is elucidated using variable-temperature NMR, two-dimensional exchange spectroscopy and molecular modeling studies.

  4. An Efficient Computational Model to Predict Protonation at the Amide Nitrogen and Reactivity along the C–N Rotational Pathway

    PubMed Central

    Szostak, Roman; Aubé, Jeffrey

    2015-01-01

    N-protonation of amides is critical in numerous biological processes, including amide bonds proteolysis and protein folding, as well as in organic synthesis as a method to activate amide bonds towards unconventional reactivity. A computational model enabling prediction of protonation at the amide bond nitrogen atom along the C–N rotational pathway is reported. Notably, this study provides a blueprint for the rational design and application of amides with a controlled degree of rotation in synthetic chemistry and biology. PMID:25766378

  5. Conformation analysis and computation of energy barrier to rotation about Csbnd N bond in para-methylphenyl carbamate and its solvent dependence in comparison with tertiary carbamates and tertiary amides

    NASA Astrophysics Data System (ADS)

    Modarresi-Alam, Ali Reza; Nowroozi, Alireza; Najafi, Parisa; Movahedifar, Fahimeh; Hajiabadi, Hossein

    2014-11-01

    Barrier to rotation about conjugated Csbnd N bond in p-Methyl phenyl carbamate (PMPC) was computed 14-16 kcal/mol at three levels of HF, B3LYP and MP2 using 6-311++G∗∗ basis set. The solvent effect and energy barriers about Csbnd N bond in PMPC were compared to the case of tertiary carbamates and tertiary amides. Moreover, it is shown that in primary carbamates such as PMPC and tertiary amides isomerisation process passes through TS2 and TS1 respectively, while in tertiary carbamates goes through a combination of both TSs. Furthermore, X-ray analysis which is reported for the first time for primary aryl carbamates demonstrated that the inclusive plane of carbamate functional group is perpendicular to the plane of phenyl ring. The results of computations are completely in agreement with the X-ray data.

  6. Intramolecular amide bonds stabilize pili on the surface of bacilli

    SciTech Connect

    Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.; Whitelegge, Julian P.; He, Chuan; Schneewind, Olaf

    2010-01-12

    Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili. We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.

  7. Amide bond formation through iron-catalyzed oxidative amidation of tertiary amines with anhydrides.

    PubMed

    Li, Yuanming; Ma, Lina; Jia, Fan; Li, Zhiping

    2013-06-01

    A general and efficient method for amide bond synthesis has been developed. The method allows for synthesis of tertiary amides from readily available tertiary amines and anhydrides in the presence of FeCl2 as catalyst and tert-butyl hydroperoxide in water (T-Hydro) as oxidant. Mechanistic studies indicated that the in situ-generated α-amino peroxide of tertiary amine and iminium ion act as key intermediates in this oxidative transformation. PMID:23668222

  8. T. thermophila group I introns that cleave amide bonds

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor)

    1997-01-01

    The present invention relates to nucleic acid enzymes or enzymatic RNA molecules that are capable of cleaving a variety of bonds, including phosphodiester bonds and amide bonds, in a variety of substrates. Thus, the disclosed enzymatic RNA molecules are capable of functioning as nucleases and/or peptidases. The present invention also relates to compositions containing the disclosed enzymatic RNA molecule and to methods of making, selecting, and using such enzymes and compositions.

  9. Universal mechanism for breaking amide bonds by ionizing radiation

    NASA Astrophysics Data System (ADS)

    Johnson, Phillip S.; Cook, Peter L.; Liu, Xiaosong; Yang, Wanli; Bai, Yiqun; Abbott, Nicholas L.; Himpsel, F. J.

    2011-07-01

    The photodissociation of the amide bond by UV light and soft x-rays is investigated by x-ray absorption spectroscopy at the C, N, and O 1s edges. Irradiation leaves a clear and universal signature for a wide variety of amides, ranging from oligopeptides to large proteins and synthetic polyamides, such as nylon. As the π* peak of the amide bond shrinks, two new π* peaks appear at the N 1s edge with a characteristic splitting of 1.1 eV. An additional characteristic is the overall intensity reduction of both the π* and σ* features at the O 1s edge, which indicates loss of oxygen. The spectroscopic results are consistent with the release of the O atom from the amide bond, followed by the migration of the H atom from the N to one of its two C neighbors. Migration to the carbonyl C leads to an imine, and migration to the Cα of the amino acid residue leads to a nitrile. Imine and nitrile produce the two characteristic π* transitions at the N 1s edge. A variety of other models is considered and tested against the N 1s spectra of reference compounds.

  10. Conversion of amides to esters by the nickel-catalysed activation of amide C-N bonds

    NASA Astrophysics Data System (ADS)

    Hie, Liana; Fine Nathel, Noah F.; Shah, Tejas K.; Baker, Emma L.; Hong, Xin; Yang, Yun-Fang; Liu, Peng; Houk, K. N.; Garg, Neil K.

    2015-08-01

    Amides are common functional groups that have been studied for more than a century. They are the key building blocks of proteins and are present in a broad range of other natural and synthetic compounds. Amides are known to be poor electrophiles, which is typically attributed to the resonance stability of the amide bond. Although amides can readily be cleaved by enzymes such as proteases, it is difficult to selectively break the carbon-nitrogen bond of an amide using synthetic chemistry. Here we demonstrate that amide carbon-nitrogen bonds can be activated and cleaved using nickel catalysts. We use this methodology to convert amides to esters, which is a challenging and underdeveloped transformation. The reaction methodology proceeds under exceptionally mild reaction conditions, and avoids the use of a large excess of an alcohol nucleophile. Density functional theory calculations provide insight into the thermodynamics and catalytic cycle of the amide-to-ester transformation. Our results provide a way to harness amide functional groups as synthetic building blocks and are expected to lead to the further use of amides in the construction of carbon-heteroatom or carbon-carbon bonds using non-precious-metal catalysis.

  11. Conversion of Amides to Esters by the Nickel-Catalyzed Activation of Amide C–N Bonds

    PubMed Central

    Hie, Liana; Fine Nathel, Noah F.; Shah, Tejas K.; Baker, Emma L.; Hong, Xin; Yang, Yun-Fang; Liu, Peng; Houk, K. N.; Garg, Neil K.

    2015-01-01

    Amides are common functional groups that have been well studied for more than a century.1 They serve as the key building blocks of proteins and are present in an broad range of other natural and synthetic compounds. Amides are known to be poor electrophiles, which is typically attributed to resonance stability of the amide bond.1,2 Whereas Nature can easily cleave amides through the action of enzymes, such as proteases,3 the ability to selectively break the C–N bond of an amide using synthetic chemistry is quite difficult. In this manuscript, we demonstrate that amide C–N bonds can be activated and cleaved using nickel catalysts. We have used this methodology to convert amides to esters, which is a challenging and underdeveloped transformation. The reaction methodology proceeds under exceptionally mild reaction conditions, and avoids the use of a large excess of an alcohol nucleophile. Density functional theory (DFT) calculations provide insight into the thermodynamics and catalytic cycle of this unusual transformation. Our results provide a new strategy to harness amide functional groups as synthons and are expected fuel the further use of amides for the construction of carbon–heteroatom or carbon–carbon bonds using non-precious metal catalysis. PMID:26200342

  12. Amide and Peptide Bond Formation in Water at Room Temperature.

    PubMed

    Gabriel, Christopher M; Keener, Megan; Gallou, Fabrice; Lipshutz, Bruce H

    2015-08-21

    A general and environmentally responsible method for the formation of amide/peptide bonds in an aqueous micellar medium is described. Use of uronium salt (1-cyano-2-ethoxy-2-oxoethylidenaminooxy)dimethylaminomorpholinocarbenium hexafluorophosphate (COMU) as a coupling reagent, 2,6-lutidine, and TPGS-750-M represents mild conditions associated with these valuable types of couplings. The aqueous reaction medium is recyclable leading to low E Factors. PMID:26251952

  13. Cleavage of an amide bond by a ribozyme

    NASA Technical Reports Server (NTRS)

    Dai, X.; De Mesmaeker, A.; Joyce, G. F.; Miller, S. L. (Principal Investigator)

    1995-01-01

    A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

  14. Binding of Fatty Acid Amide Amphiphiles to Bovine Serum Albumin: Role of Amide Hydrogen Bonding.

    PubMed

    Ghosh, Subhajit; Dey, Joykrishna

    2015-06-25

    The study of protein-surfactant interactions is important because of the widespread use of surfactants in industry, medicine, and pharmaceutical fields. Sodium N-lauroylsarcosinate (SL-Sar) is a widely used surfactant in cosmetics, shampoos. In this paper, we studied the interactions of bovine serum albumin (BSA) with SL-Sar and sodium N-lauroylglycinate (SL-Gly) by use of a number of techniques, including fluorescence and circular dichroism spectroscopy and isothermal titration calorimetry. The binding strength of SL-Sar is stronger than that of structurally similar SL-Gly, which differs only by the absence of a methyl group in the amide nitrogen atom. Also, these two surfactants exhibit different binding patterns with the BSA protein. The role of the amide bond and hence the surfactant headgroup in the binding mechanism is discussed in this paper. It was observed that while SL-Sar destabilized, SL-Gly stabilized the protein structure, even at concentrations less than the critical micelle concentration (cmc) value. The thermodynamics of surfactant binding to BSA was studied by use of ITC. From the ITC results, it is concluded that three molecules of SL-Sar in contrast to only one molecule of SL-Gly bind to BSA in one set of binding sites at room temperature. However, on increasing temperature four molecules of SL-Gly bind to the BSA through H-bonding and van der Waals interactions, due to loosening of the BSA structure. In contrast, with SL-Sar the binding process is enthalpy driven, and very little structural change of BSA was observed at higher temperature. PMID:26023820

  15. Recent advances in copper-catalyzed C-H bond amidation.

    PubMed

    Wan, Jie-Ping; Jing, Yanfeng

    2015-01-01

    Copper catalysis has been known as a powerful tool for its ubiquitous application in organic synthesis. One of the fundamental utilities of copper catalysis is in the C-N bond formation by using carbon sources and nitrogen functional groups such as amides. In this review, the recent progress in the amidation reactions employing copper-catalyzed C-H amidation is summarized. PMID:26664644

  16. Recent advances in copper-catalyzed C–H bond amidation

    PubMed Central

    Jing, Yanfeng

    2015-01-01

    Summary Copper catalysis has been known as a powerful tool for its ubiquitous application in organic synthesis. One of the fundamental utilities of copper catalysis is in the C–N bond formation by using carbon sources and nitrogen functional groups such as amides. In this review, the recent progress in the amidation reactions employing copper-catalyzed C–H amidation is summarized. PMID:26664644

  17. Collective vibrational effects in hydrogen bonded liquid amides and proteins studied by isotopic substitution

    NASA Astrophysics Data System (ADS)

    Nielsen, O. F.; Johansson, C.; Christensen, D. H.; Hvidt, S.; Flink, J.; Høime Hansen, S.; Poulsen, F.

    2000-09-01

    Raman spectroscopy is used to study the fast dynamics of simple liquid amides and proteins. Raman spectra in the visible region of liquid amides are obtained with a triple additive scanning monochromator, whereas FT-Raman technique is used in the near-IR region in order to avoid fluorescence from impurities in the proteins. Raman spectra are shown in the amide-I region of HCONHCH 3 ( N-methylformamide with all isotopes in their natural abundance), H 13CONHCH 3, HC 18ONHCH 3, human growth hormone, frog tropomyosin and chymotrypsin inhibitor 2 including C-13 and N-15 enriched samples of the latter. Resonance energy transfer (RET) between amide molecules gives rise to a non-coincidence effect of the anisotropic and the isotropic components of the amide-I band. This effect influences the band position in mixtures of liquid amide isotopomers. A further spectral feature caused by collective vibrational modes in the hydrogen bonded liquid amides is named coalescence of bands in mixtures of isotopomers (CBMI). The result of this effect is that only one band is found in mixtures of isotopomers where bands at different frequencies are observed for each of the isotopomers. A similar effect may account for the observation of protein amide-I bands with frequencies dependent only on the secondary structure of the protein and not on the amino acid residues. RET and CBMI are due to a collectivity of vibrational modes in different amide molecules. This collectivity may be related to a cooperativity of hydrogen bonds. A low-frequency band around 100 cm -1 is observed in hydrogen bonded liquid amides and proteins. Isotopic substitution shows that the mode corresponding to this band involves displacements of atoms in hydrogen bonds. This mode may drive a breaking of the hydrogen bond.

  18. Water templated hydrogen-bonded network of pyridine amide appended carbamate in solid state

    NASA Astrophysics Data System (ADS)

    Ghosh, Kumaresh; Adhikari, Suman; Fröhlich, Roland

    2006-03-01

    The pyridine amide appended carbamates 1 and 2 have been synthesized and their hydrogen-bonded self-assemblies in solid state have been described. The self-association pattern is dependent on the nature the anchored group of the carbamate moiety and influenced by water inclusion. Inclusion of water molecule gives a ladder type hydrogen bonded assemblies with cavities.

  19. Cp*Co(III) -Catalyzed C(sp(3) )-H Bond Amidation of 8-Methylquinoline.

    PubMed

    Barsu, Nagaraju; Rahman, Md Atiur; Sen, Malay; Sundararaju, Basker

    2016-06-27

    An efficient and external oxidant-free, Cp*Co(III) -catalyzed C(sp(3) )-H bond amidation of 8-methylquinoline, using oxazolone as an efficient amidating agent, is reported for the first time under mild conditions. The reaction is selective and tolerates a variety of functional groups. Based on previous reports and experimental results, the deprotonation pathway proceeds through an external base-assisted concerted metalation and deprotonation process. PMID:27168249

  20. Synthesis of Glycosyl Amides Using Selenocarboxylates as Traceless Reagents for Amide Bond Formation.

    PubMed

    Silva, Luana; Affeldt, Ricardo F; Lüdtke, Diogo S

    2016-07-01

    Carbohydrate-derived amides were successfully prepared in good yields from a broad range of substrates, including furanosyl and pyranosyl derivatives. The methodology successfully relied on the in situ generation of lithium selenocarboxylates from Se/LiEt3BH and acyl chlorides or carboxylic acids and their reaction with sugar azides. A key aspect of the present protocol is that we start from elemental selenium; isolation and handling of all reactive and sensitive selenium-containing intermediates is avoided, therefore providing the selenocarboxylate the status of a traceless reagent. PMID:27275515

  1. Nickel-Catalyzed Decarbonylative Borylation of Amides: Evidence for Acyl C-N Bond Activation.

    PubMed

    Hu, Jiefeng; Zhao, Yue; Liu, Jingjing; Zhang, Yemin; Shi, Zhuangzhi

    2016-07-18

    A nickel/N-heterocyclic carbene catalytic system has been established for decarbonylative borylation of amides with B2 nep2 by C-N bond activation. This transformation shows good functional-group compatibility and can serve as a powerful synthetic tool for late-stage borylation of amide groups in complex compounds. More importantly, as a key intermediate, the structure of an acyl nickel complex was first confirmed by X-ray analysis. Furthermore, the decarbonylative process was also observed. These findings confirm the key mechanistic features of the acyl C-N bond activation process. PMID:27258597

  2. H-localized mode in chains of hydrogen-bonded amide groups

    NASA Astrophysics Data System (ADS)

    Barthes, Mariette; Kellouai, Hassan; Page, Gabriel; Moret, Jacques; Johnson, Susanna W.; Eckert, Juergen

    1993-09-01

    New infrared measurements of the anomalous amide modes in acetanilide and its derivatives are presented. Preliminary results of structural data obtained by neutron diffraction at low temperature are also described. Besides the well-known anomalous amide-1 mode (1650 cm -1), it is shown that the NH out-of-plane bend (770 cm -1) and the “H-bond strain” (at about 105 cm -1) exhibit an anomalous increase of intensity proportional to the law exp(- T2/ Θ2), suggesting that the amide proton bears a significant electronic distribution as formerly observed for H - localized modes. Structural data, moreover, show that the thermal ellips of the amide proton has an increasing anisotropy at 15 K. Considering these new results, the theoretical model of a self-trapped “polaronic” state seems to be the most consistent with the whole set of observed anomalies in this family of crystals.

  3. Investigation hydrogen-bonding capabilities of modified amide groups using calculated nuclear quadruple coupling constants

    NASA Astrophysics Data System (ADS)

    Elmi, F.; Hadipour, N. L.; Safinezhad, F.

    2003-07-01

    Nuclear quadrupole coupling constants, χs, for 17 chemical species are calculated. These are retroamide, N-hydroxamide, N-amino amide, thioamide, methylamine and complexes which amide generates with retroamide and other modified amides. The charge distributions around quadrupolar nuclei are most affected upon intermolecular hydrogen bond formations. χs of these nuclei are computed using ab initio calculations. Some of our findings for average values of χs of 2H, 14N and 17O in hydrogen bonds are 200.00 kHz, 4.40 MHz and 10.50 MHz, respectively. There is a fairly linear dependency between RO⋯H and the logarithm of 2H χs. This correlation is approximately linear for 17O and 14N nuclei.

  4. Cobalt(III)-Catalyzed C–H Bond Amidation with Isocyanates

    PubMed Central

    Hummel, Joshua R.; Ellman, Jonathan A.

    2015-01-01

    The first examples of cobalt(III)-catalyzed C–H bond addition to isocyanates are described, providing a convergent strategy for arene and heteroarene amidation. Using a robust air- and moisture-stable catalyst, this transformation demonstrates broad isocyanate scope, good functional-group compatibility and has been performed on gram scale. PMID:25945401

  5. The effect of intermolecular hydrogen bonding on the planarity of amides.

    PubMed

    Platts, James A; Maarof, Hasmerya; Harris, Kenneth D M; Lim, Gin Keat; Willock, David J

    2012-09-14

    Ab initio and density functional theory (DFT) calculations on some model systems are presented to assess the extent to which intermolecular hydrogen bonding can affect the planarity of amide groups. Formamide and urea are examined as archetypes of planar and non-planar amides, respectively. DFT optimisations suggest that appropriately disposed hydrogen-bond donor or acceptor molecules can induce non-planarity in formamide, with OCNH dihedral angles deviating by up to ca. 20° from planarity. Ab initio energy calculations demonstrate that the energy required to deform an amide molecule from the preferred geometry of the isolated molecule is more than compensated by the stabilisation due to hydrogen bonding. Similarly, the NH(2) group in urea can be made effectively planar by the presence of appropriately positioned hydrogen-bond acceptors, whereas hydrogen-bond donors increase the non-planarity of the NH(2) group. Small clusters (a dimer, two trimers and a pentamer) extracted from the crystal structure of urea indicate that the crystal field acts to force planarity of the urea molecule; however, the interaction with nearest neighbours alone is insufficient to induce the molecule to become completely planar, and longer-range effects are required. Finally, the potential for intermolecular hydrogen bonding to induce non-planarity in a model of a peptide is explored. Inter alia, the insights obtained in the present work on the extent to which the geometry of amide groups may be deformed under the influence of intermolecular hydrogen bonding provide structural guidelines that can assist the interpretation of the geometries of such groups in structure determination from powder X-ray diffraction data. PMID:22847473

  6. New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

    PubMed Central

    Klare, Helge; Neudörfl, Jörg M

    2014-01-01

    Summary Ten novel hydrogen-bonding catalysts based on open-chain PV-amides of BINOL and chinchona alkaloids as well as three catalysts based on rigid cis-PV-cyclodiphosphazane amides of N 1,N 1-dimethylcyclohexane-1,2-diamine have been developed. Employed in the asymmetric Michael addition of 2-hydroxynaphthoquinone to β-nitrostyrene, the open-chain 9-epi-aminochinchona-based phosphorus amides show a high catalytic activity with almost quantitative yields of up to 98% and enantiomeric excesses of up to 51%. The cyclodiphosphazane catalysts show the same high activity and give improved enantiomeric excesses of up to 75%, thus representing the first successful application of a cyclodiphosphazane in enantioselective organocatalysis. DFT computations reveal high hydrogen-bonding strengths of cyclodiphosphazane PV-amides compared to urea-based catalysts. Experimental results and computations on the enantiodetermining step with cis-cyclodiphosphazane 14a suggest a strong bidentate H-bond activation of the nitrostyrene substrate by the catalyst. PMID:24605142

  7. Core ionization energies of amides as a probe of structure and bonding

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; Moore, David T.

    1997-09-01

    Core orbital energies are computed for planar ground-state and rotational transition-state structures for formamide and N,N-dimethylacetamide using ab initio molecular orbital calculations at the 6-31G∗ level. Distortion of the amide linkage decreases the core ionization energy of nitrogen and increases the core ionization energies of oxygen and the carbonyl carbon. Similar trends are observed for bridgehead bicyclic lactams and are corroborated by the limited experimental data available. A simple interpretation can be made in the language of resonance theories through reference to contributions of three canonical structures ( 1A-1C) and in particular, the reduced contribution of 1B in distorted amides.

  8. Palladium-catalyzed Suzuki-Miyaura coupling of amides by carbon-nitrogen cleavage: general strategy for amide N-C bond activation.

    PubMed

    Meng, Guangrong; Szostak, Michal

    2016-06-15

    The first palladium-catalyzed Suzuki-Miyaura cross-coupling of amides with boronic acids for the synthesis of ketones by sterically-controlled N-C bond activation is reported. The transformation is characterized by operational simplicity using bench-stable, commercial reagents and catalysts, and a broad substrate scope, including substrates with electron-donating and withdrawing groups on both coupling partners, steric-hindrance, heterocycles, halides, esters and ketones. The scope and limitations are presented in the synthesis of >60 functionalized ketones. Mechanistic studies provide insight into the catalytic cycle of the cross-coupling, including the first experimental evidence for Pd insertion into the amide N-C bond. The synthetic utility is showcased by a gram-scale cross-coupling and cross-coupling at room temperature. Most importantly, this process provides a blueprint for the development of a plethora of metal catalyzed reactions of typically inert amide bonds via acyl-metal intermediates. A unified strategy for amide bond activation to enable metal insertion into N-C amide bond is outlined (). PMID:26864384

  9. Substituent effects on hydrogen bonding of aromatic amide-carboxylate.

    PubMed

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

    N-(p-benzoyl)-anthranilic acid (BAA) derivatives have been synthesized with different substituents (X: Br, Cl, OCH3, CH3), and their crystal structures have been analyzed in order to understand the variations in their molecular geometries with respect to the substituents by using (1)H NMR, (13)C NMR, IR and X-ray single-crystal diffraction. The carboxylic acid group forms classic OH⋯O hydrogen bonded dimers in a centrosymmetric R2(2)(8) ring motifs for BAA-Br and BAA-Cl. However, no carboxylic acid group forms classic OH⋯O hydrogen bonded dimers in BAA-OCH3 and BAA-CH3. The asymmetric unit consists of two crystallographically independent molecules in BAA-OCH3. DFT computations show that the interaction energies between monomer and dimer are in the range of 0.5-3.8kcal/mol with the B3LYP/6-31+G*, B3LYP/6-31++G*, B3LYP/6-31++G**, and B3LYP/AUG-cc-pVDZ levels of theory. The presence of different hydrogen bond patterns is also governed by the substrate. For monomeric compounds studied herein, theoretical calculations lead to two low-energy conformers; trans (a) and cis (b). Former one is more stable than latter by about 4kcal/mol. PMID:27239947

  10. Synthesis of Biaryls through Nickel-Catalyzed Suzuki-Miyaura Coupling of Amides by Carbon-Nitrogen Bond Cleavage.

    PubMed

    Shi, Shicheng; Meng, Guangrong; Szostak, Michal

    2016-06-01

    The first Ni-catalyzed Suzuki-Miyaura coupling of amides for the synthesis of widely occurring biaryl compounds through N-C amide bond activation is reported. The reaction tolerates a wide range of electron-withdrawing, electron-neutral, and electron-donating substituents on both coupling partners. The reaction constitutes the first example of the Ni-catalyzed generation of aryl electrophiles from bench-stable amides with potential applications for a broad range of organometallic reactions. PMID:27101428

  11. Reversible Alkene Insertion into the Pd–N Bond of Pd(II)-Sulfonamidates and Implications for Catalytic Amidation Reactions

    PubMed Central

    White, Paul B.; Stahl, Shannon S.

    2011-01-01

    Alkene insertion into Pd–N bonds is a key step in Pd-catalyzed oxidative amidation of alkenes. A series of well-defined Pd(II)-sulfonamidate complexes have been prepared and shown to react via insertion of a tethered alkene. The Pd–amidate and resulting Pd–alkyl species have been crystallographically characterized. The alkene insertion reaction is found to be reversible, but complete conversion to oxidative amination products is observed in the presence of O2. Electronic-effect studies reveal that alkene insertion into the Pd–N bond is favored kinetically and thermodynamically with electron-rich amidates. PMID:22007610

  12. Cu-Catalyzed Intramolecular Amidation of Unactivated C(sp(3) )-H Bonds To Synthesize N-Substituted Indolines.

    PubMed

    Pan, Fei; Wu, Bin; Shi, Zhang-Jie

    2016-05-01

    A copper-catalyzed intramolecular amidation of unactivated C(sp(3) )-H bonds to construct indoline derivatives has been developed. Such an amidation proceeded well at primary C-H bonds preferred to secondary C-H bonds. The transformation owned a broad substrate scope. The corresponding indolines were obtained in good to excellent yields. N-Formal and other carbonyl groups were suitable and were easily deprotected and transformed into methyl or long-chained alkyl groups. Preliminary mechanistic studies suggested a radical pathway. PMID:26945702

  13. Facile amine formation by intermolecular catalytic amidation of carbon-hydrogen bonds.

    PubMed

    Fructos, Manuel R; Trofimenko, Swiatoslaw; Díaz-Requejo, M Mar; Pérez, Pedro J

    2006-09-13

    A simple copper-based catalytic system has been developed for the carbon-hydrogen amidation reaction. The copper-homoscorpionate complex Tp(Br3)Cu(NCMe) catalyzes the transfer of the nitrene unit NTs (Ts = p-toluenesulfonyl) and its subsequent insertion into the sp(3) C-H bonds of alkyl aromatic and cyclic ethers or the sp(2) C-H bonds of benzene using PhI=NTs as the nitrene source, affording the corresponding trisubstitued NR(1)HTs amines in moderate to high yields. The use of the environmentally friendly chloramine-T has also proven effective, with the advantage that sodium chloride is formed as the only byproduct. A tandem, one-pot consecutive nitrene-carbene insertion system has been developed to yield amino acid derivatives. PMID:16953617

  14. Amide bond cleavage initiated by coordination with transition metal ions and tuned by an auxiliary ligand.

    PubMed

    Yang, Yongpo; Lu, Chunxin; Wang, Hailong; Liu, Xiaoming

    2016-06-21

    The reaction of ligand , N,N-bis(pyridin-2-ylmethyl)acetamide, with five transition metal salts, FeCl3·6H2O, CuCl2·2H2O, Cu(ClO4)2·6H2O, ZnCl2 and K2PtCl4/KI, produced five metal complexes, [(μ-O)(FeClL')(FeCl3)] (), [CuLCl2] (), [CuBPA(ClO4)(CHCN)] ClO4 (), [ZnLCl2] () and [PtLI2] (), where = 1-(2,4,5-tri(pyridin-2-yl)-3-(pyridin-2-ylmethyl)imidazolidin-1-yl)ethanone which formed in situ, and BPA = bis(pyridin-2-ylmethyl)amine. The ligand and complexes were characterized by a variety of spectroscopic techniques including X-ray single crystal diffraction where applicable. Depending on the metal ion and auxiliary ligand of the complex, the acetyl group of the ligand could be either intact or cleaved. When ferric chloride hexahydrate was used, the deacetylation proceeded even further and a novel heterocyclic compound () was formed in situ. A possible mechanism was proposed for the formation of the heterocyclic compound found in complex . Our results indicate that to cleave effectively an amide bond, it is essential for a metal centre to bind to the amide bond and the metal centre is of sufficient Lewis acidity. PMID:27241864

  15. The contamination mechanism and behavior of amide bond containing organic contaminant on PEMFC

    SciTech Connect

    Cho, Hyun -Seok; Das, Mayukhee; Wang, Heli; Dinh, Huyen N.; Van Zee, J. W.

    2015-02-03

    In this paper, a study is presented of the effects of an organic contaminant containing an amide bond (-CONH-), ε-caprolactam, on polymer electrolyte membrane fuel cells (PEMFCs). The ε-caprolactam has been detected in leachates from polyphthalamide materials that are being considered for use as balance-of-plant structural materials for PEMFCs. Contamination effects from ε-caprolactam in Nafion membranes are shown to be controlled by temperature. A possible explanation of the temperature effect is the endothermic ring-opening reaction of the amide bond (-NHCO-) of the cyclic ε-caprolactam. UV-vis and ATR-IR spectroscopy studies confirmed the presence of open ring structure of ε-caprolactam in membranes. The ECSA and kinetic current for the ORR of the Pt/C catalyst were also investigated and were observed to decrease upon contamination by the ε-caprolactam. By comparison of the CVs of ammonia and acetic acid, we confirmed the adsorption of carboxylic acid (-COOH) or carboxylate anion (-COO-) onto the surface of the Pt. In conclusion, a comparison of in situ voltage losses at 80°C and 50°C also revealed temperature effects, especially in the membrane, as a result of the dramatic increase in the HFR.

  16. The contamination mechanism and behavior of amide bond containing organic contaminant on PEMFC

    DOE PAGESBeta

    Cho, Hyun -Seok; Das, Mayukhee; Wang, Heli; Dinh, Huyen N.; Van Zee, J. W.

    2015-02-03

    In this paper, a study is presented of the effects of an organic contaminant containing an amide bond (-CONH-), ε-caprolactam, on polymer electrolyte membrane fuel cells (PEMFCs). The ε-caprolactam has been detected in leachates from polyphthalamide materials that are being considered for use as balance-of-plant structural materials for PEMFCs. Contamination effects from ε-caprolactam in Nafion membranes are shown to be controlled by temperature. A possible explanation of the temperature effect is the endothermic ring-opening reaction of the amide bond (-NHCO-) of the cyclic ε-caprolactam. UV-vis and ATR-IR spectroscopy studies confirmed the presence of open ring structure of ε-caprolactam in membranes.more » The ECSA and kinetic current for the ORR of the Pt/C catalyst were also investigated and were observed to decrease upon contamination by the ε-caprolactam. By comparison of the CVs of ammonia and acetic acid, we confirmed the adsorption of carboxylic acid (-COOH) or carboxylate anion (-COO-) onto the surface of the Pt. In conclusion, a comparison of in situ voltage losses at 80°C and 50°C also revealed temperature effects, especially in the membrane, as a result of the dramatic increase in the HFR.« less

  17. Improvement of the Thermal Stability of TEMPO-Oxidized Cellulose Nanofibrils by Heat-Induced Conversion of Ionic Bonds to Amide Bonds.

    PubMed

    Lavoine, Nathalie; Bras, Julien; Saito, Tsuguyuki; Isogai, Akira

    2016-07-01

    Improving thermal stability of TEMPO-oxidized cellulose nanofibrils (TOCNs) is a major challenge for the development and preparation of new nanocomposites. However, thermal degradation of TOCNs occurs at 220 °C. The present study reports a simple way to improve thermal stability of TOCNs by the heat-induced conversion of ionic bonds to amide bonds. Coupling amine-terminated polyethylene glycol to the TOCNs is performed through ionic bond formation. Films are produced from the dispersions by the casting method. Infrared spectroscopy and thermogravimetric analysis confirm conversion of ionic bonds to amide bonds for the modified TOCN samples after heating. As a result, improvement of TOCNs' thermal stability by up to 90 °C is successfully achieved. PMID:27184669

  18. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  19. Influence of intermolecular amide hydrogen bonding on the geometry, atomic charges, and spectral modes of acetanilide: An ab initio study

    NASA Astrophysics Data System (ADS)

    Binoy, J.; Prathima, N. B.; Murali Krishna, C.; Santhosh, C.; Hubert Joe, I.; Jayakumar, V. S.

    2006-08-01

    Acetanilide, a compound of pharmaceutical importance possessing pain-relieving properties due to its blocking the pulse dissipating along the nerve fiber, is subjected to vibrational spectral investigation using NIR FT Raman, FT-IR, and SERS. The geometry, Mulliken charges, and vibrational spectrum of acetanilide have been computed using the Hartree-Fock theory and density functional theory employing the 6-31G (d) basis set. To investigate the influence of intermolecular amide hydrogen bonding, the geometry, charge distribution, and vibrational spectrum of the acetanilide dimer have been computed at the HF/6-31G (d) level. The computed geometries reveal that the acetanilide molecule is planar, while twisting of the secondary amide group with respect to the phenyl ring is found upon hydrogen bonding. The trans isomerism and “amido” form of the secondary amide, hyperconjugation of the C=O group with the adjacent C-C bond, and donor-acceptor interaction have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of the phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation, and hyperconjugation. A decrease in the NH and C=O bond orders and increase in the C-N bond orders due to donor-acceptor interaction can be observed in the vibrational spectra. The SERS spectral analysis reveals that the flat orientation of the molecule on the adsorption plane is preferred.

  20. Infrared and nuclear magnetic resonance spectroscopic study of secondary amide hydrogen bonding in benzoyl PABA derivatives (retinoids).

    PubMed

    Dalterio, Richard; Huang, Xiaohua Stella; Yu, Kuo-Long

    2007-06-01

    Attenuated total reflection (ATR) Fourier transform infrared (FT-IR) and nuclear magnetic resonance (NMR) data are used to characterize the hydrogen bonding of the secondary amide N-H group of several structurally similar benzoyl derivatives of p-aminobenzoic acid esters (retinoids) in chloroform solution. The amide N-H can form intermolecular hydrogen bonds to several proton acceptors in these molecules or it can form an intramolecular hydrogen bond to a fluorine or oxygen atom in some of the molecules. The concentration dependence of the solution N-H infrared absorption bands is used to determine the formation of intramolecular and/or intermolecular H-bonds. Proton NMR spectra were obtained from deuterated chloroform solutions and the sec-amide N-H resonance was assigned for each compound. The downfield shift in the N-H resonance is correlated to intramolecular H-bond formation. Also, the NMR spectra of fluorine-containing compounds provide J(F-H) through-space coupling values. Using infrared and NMR data, the relative intramolecular hydrogen bond strengths (N-H...F or N-H...O) of the compounds are approximately ranked. PMID:17650370

  1. Oxidatively Triggered Carbon-Carbon Bond Formation in Ene-amide Complexes.

    PubMed

    Jacobs, Brian P; Wolczanski, Peter T; Lobkovsky, Emil B

    2016-05-01

    Ene-amides have been explored as ligands and substrates for oxidative coupling. Treatment of CrCl2, Cl2Fe(PMe3)2, and Cl2Copy4 with 2 equiv of {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}Li afforded pseudosquare planar {η(3)-C,C,N-(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}2Cr (1-Cr, 78%), trigonal {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}2Fe(PMe3) (2-Fe, 80%), and tetrahedral {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}2Co(py)2 (3-Co, 91%) in very good yields. The addition of CrCl3 to 1-Cr, and FeCl3 to 2-Fe, afforded oxidatively triggered C-C bond formation as rac-2,2'-di(2,6-(i)Pr2C6H3N═)2dicyclohexane (EA2) was produced in modest yields. Various lithium ene-amides were similarly coupled, and the mechanism was assessed via stoichiometric reactions. Some ferrous compounds (e.g., 2-Fe, FeCl2) were shown to catalyze C-arylation of {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}Li with PhBr, but the reaction was variable. Structural characterizations of 1-Cr, 2-Fe, and 3-Co are reported. PMID:27064509

  2. 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

  3. Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis.

    PubMed

    Park, In-Hee; Venable, John D; Steckler, Caitlin; Cellitti, Susan E; Lesley, Scott A; Spraggon, Glen; Brock, Ansgar

    2015-09-28

    Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure, and dynamics. More recently, hydrogen exchange mass spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from molecular dynamics (MD) simulation snapshots is used to determine partitioning over bonded and nonbonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of

  4. Dicumyl Peroxide as a Methylating Reagent in the Ni-Catalyzed Methylation of Ortho C-H Bonds in Aromatic Amides.

    PubMed

    Kubo, Teruhiko; Chatani, Naoto

    2016-04-01

    The direct methylation of ortho C-H bonds in aromatic amides with dicumyl peroxide (DCP) using a nickel complex as the catalyst is reported. The reaction shows a high functional group tolerance and is inhibited by radical scavengers. In reactions of meta-substituted aromatic amides, the reaction proceeds in a highly selective manner at the less hindered C-H bonds. PMID:26991045

  5. Kinetic and thermodynamic characterization of C-N bond rotation by N-methylacetohydroxamic acid in aqueous media.

    PubMed

    Sippl, Stefanie P; White, Paul B; Fry, Charles G; Volk, Sarah E; Ye, Lingxiao; Schenck, Heather L

    2016-01-01

    Hydroxamic acids (HAs) perform tasks in medicine and industry that require bidentate metal binding. The two favored conformations of HAs are related by rotation around the C(=O)-N bond. The conformations are unequal in stability. Recently, we reported that the most stable conformation of a small secondary HA in water places the oxygen atoms anti to one another. The barrier to C-N bond rotation may therefore modulate metal binding by secondary HAs in aqueous media. We have now determined the activation barrier to C-N rotation from major to minor conformation of a small secondary HA in D2O to be 67.3 kJ/mol. The HA rotational barrier scales with solvent polarity, as is observed in amides, although the HA barrier is less than that of a comparable tertiary amide in aqueous solution. Successful design of new secondary HAs to perform specific tasks requires solid understanding of rules governing HA structural behavior. Results from this work provide a more complete foundation for HA design efforts. PMID:26477862

  6. Rotational Spectra of Hydrogen Bonded Networks of Amino Alcohols

    NASA Astrophysics Data System (ADS)

    Zhang, Di; Zwier, Timothy S.

    2014-06-01

    The rotational spectra of several different amino alcohols including D/L-allo-threoninol, 2-amino-1,3-propanediol and 1,3-diamino-2-propanol over the 6.5-18.5 GHz range have been investigated under jet-cooled conditions using chirped-pulsed Fourier transform microwave spectroscopy. Despite the small size of these molecules, a great variety of conformations have been observed in the molecular expansion. While the NH2 group is typically thought of as a H-bond acceptor, it often acts both as acceptor and donor in forming H-bonded networks. With three adjacent H-bonding substituents (a combination of OH and NH2 groups), many different hydrogen bonding patterns are possible, including H-bonded chains and H-bonded cycles. Since many of these structures differ primarily by the relative orientation of the H-atoms, the analysis of these rotational spectra are challenging. Only through an exhaustive conformational search and the comparison with the experimental rotational constants, nuclear quadrupolar splittings, and line strengths are we able to understand the complex nature of these interactions. The ways in which the presence and number of NH2 groups affects the relative energies, and distorts the structures will be explored.

  7. One-Pot Amide Bond Formation from Aldehydes and Amines via a Photoorganocatalytic Activation of Aldehydes.

    PubMed

    Papadopoulos, Giorgos N; Kokotos, Christoforos G

    2016-08-19

    A mild, one-pot, and environmentally friendly synthesis of amides from aldehydes and amines is described. Initially, a photoorganocatalytic reaction of aldehydes with di-isopropyl azodicarboxylate leads to an intermediate carbonyl imide, which can react with a variety of amines to afford the desired amides. The initial visible light-mediated activation of a variety of monosubstituted or disubstituted aldehydes is usually fast, occurring in a few hours. Following the photocatalytic reaction, addition of the primary amine at room temperature or the secondary amine at elevated temperatures leads to the corresponding amide from moderate to excellent yields without epimerization. This methodology was applied in the synthesis of Moclobemide, a drug against depression and social anxiety. PMID:27227271

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  9. Effect of Amide Hydrogen Bonding Interaction on Supramolecular Self-Assembly of Naphthalene Diimide Amphiphiles with Aggregation Induced Emission.

    PubMed

    Ghule, Namdev V; La, Duong Duc; Bhosale, Rajesh S; Al Kobaisi, Mohammad; Raynor, Aaron M; Bhosale, Sheshanath V; Bhosale, Sidhanath V

    2016-04-01

    In the present work, two new naphthalene diimide (NDI) amphiphiles, NDI-N and NDI-NA, were successfully synthesized and employed to investigate their self-assembly and optical properties. For NDI-NA, which contains an amide group, aggregation-induced emission enhancement (AIEE) was demonstrated in the presence of various ratios of methylcyclohexane (MCH) in chloroform, which led to the visual color changes. This new amide-containing NDI-NA amphiphile formed nanobelt structures in chloroform/MCH (10:90, v/v) and microcup-like morphologies in chloroform/MCH (5:95, v/v). The closure of these microcups led to the formation of vesicles and microcapsules. The structural morphologies gained from the solvophobic control of NDI-NA were confirmed by various complementary techniques such as infrared spectroscopy, X-ray diffraction, and scanning and transmission electron microscopy. In the absence of the amide moiety in NDI-N, no self-assembly was observed, indicating the fundamental role of H-bonding in the self-association process. PMID:27308233

  10. Toward quantification of protein backbone–backbone hydrogen bonding energies: An energetic analysis of an amide-to-ester mutation in an α-helix within a protein

    PubMed Central

    Gao, Jianmin; Kelly, Jeffery W.

    2008-01-01

    Amide-to-ester backbone mutagenesis enables a specific backbone–backbone hydrogen bond (H-bond) in a protein to be eliminated in order to quantify its energetic contribution to protein folding. To extract a H-bonding free energy from an amide-to-ester perturbation free energy (ΔG folding,wt − ΔG folding,mut), it is necessary to correct for the putative introduction of a lone pair–lone pair electrostatic repulsion, as well as for the transfer free energy differences that may arise between the all amide sequence and the predominantly amide sequence harboring an ester bond. Mutation of the 9–10 amide bond within the V9F variant of the predominantly helical villin headpiece subdomain (HP35) to an ester or an E-olefin backbone bond results in a less stable but defined wild-type fold, an attribute required for this study. Comparing the folding free energies of the ester and E-olefin mutants, with correction for the desolvation free energy differences (ester and E-olefin) and the loss of an n-to-π* interaction (E-olefin), yields an experimentally based estimate of +0.4 kcal/mol for the O–O repulsion energy in an α-helical context, analogous to our previous experimentally based estimate of the O–O repulsion free energy in the context of a β-sheet. The small O–O repulsion energy indicates that amide-to-ester perturbation free energies can largely be attributed to the deletion of the backbone H-bonds after correction for desolvation differences. Quantitative evaluation of H-bonding in an α-helix should now be possible, an important step toward deciphering the balance of forces that enable spontaneous protein folding. PMID:18434500

  11. Pd-Catalyzed Coupling of γ-C(sp(3))-H Bonds of Oxalyl Amide-Protected Amino Acids with Heteroaryl and Aryl Iodides.

    PubMed

    Han, Jian; Zheng, Yongxiang; Wang, Chao; Zhu, Yan; Huang, Zhi-Bin; Shi, Da-Qing; Zeng, Runsheng; Zhao, Yingsheng

    2016-07-01

    Pd-catalyzed regioselective coupling of γ-C(sp(3))-H bonds of oxalyl amide-protected amino acids with heteroaryl and aryl iodides is reported. A wide variety of iodides are tolerated, giving the corresponding products in moderate to good yields. Various oxalyl amide-protected amino acids were compatible in this C-H transformation, thus representing a practical method for constructing non-natural amino acid derivatives. PMID:27286881

  12. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth.

    PubMed

    Forsythe, Jay G; Yu, Sheng-Sheng; Mamajanov, Irena; Grover, Martha A; Krishnamurthy, Ramanarayanan; Fernández, Facundo M; Hud, Nicholas V

    2015-08-17

    Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides-oligomers with a combination of ester and amide linkages-in model prebiotic reactions that are driven by wet-cool/dry-hot cycles. Through a combination of ester-amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors. PMID:26201989

  13. Ab initio study of β-lactam antibiotics. I. Potential energy surface for the amidic CN bond breaking in the β-lactam + OH - reaction

    NASA Astrophysics Data System (ADS)

    Petrongolo, Carlo; Ranghino, Graziella; Scordamaglia, Raimondo

    1980-01-01

    The potential energy surface of the β-lactam + OH - reaction, related to the mode of action of β-lactam antibiotics, was investigated using the ab initio Hartree—Fock method with the STO-3G basis set. Three possible reaction paths for the B A C2 breaking of the amidic CN bond were obtained and discussed. The minimum-energy reaction path is characterized by the following processes: (1) the formation of a tetrahedral intermediate, ≈ 121 kcal mol -1 more stable than the reagents; (2) a barrier, ≈ 15 kcal mol -1 above the intermediate, which is mainly due to the partial breaking of the amidic bond; (3) the complete breaking of the amidic bond concerted with a proton transfer till the formation of the final product, ≈ 34 kcal mol -1 more stable than the intermediate. The evolution of some molecular orbitals and of the electron population along the reaction path was also discussed.

  14. Ester-Mediated Amide Bond Formation Driven by Wet–Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth**

    PubMed Central

    Forsythe, Jay G; Yu, Sheng-Sheng; Mamajanov, Irena; Grover, Martha A; Krishnamurthy, Ramanarayanan; Fernández, Facundo M; Hud, Nicholas V

    2015-01-01

    Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors. PMID:26201989

  15. Analog of small Holstein polaron in hydrogen-bonded amide systems

    NASA Astrophysics Data System (ADS)

    Alexander, D. M.

    1985-01-01

    A class of amide-I (C = O stretch) related excitations and their contribution to the spectral function for infrared absorption is determined by use of the Davydov Hamiltonian. The treatment is a fully quantum, finite-temperature one. A consistent picture and a quantitative fit to the absorption data for crystalline acetanilide confirms that the model adequately explains the anomalous behavior cited by Careri et al. The localized excitation responsible for this behavior is the vibronic analog of the small Holstein polaron. The possible extension to other modes and biological relevance is examined.

  16. Effect of Amide Hydrogen Bonding Interaction on Supramolecular Self‐Assembly of Naphthalene Diimide Amphiphiles with Aggregation Induced Emission

    PubMed Central

    Ghule, Namdev V.; La, Duong Duc; Bhosale, Rajesh S.; Al Kobaisi, Mohammad; Raynor, Aaron M.

    2016-01-01

    Abstract In the present work, two new naphthalene diimide (NDI) amphiphiles, NDI‐N and NDI‐NA, were successfully synthesized and employed to investigate their self‐assembly and optical properties. For NDI‐NA, which contains an amide group, aggregation‐induced emission enhancement (AIEE) was demonstrated in the presence of various ratios of methylcyclohexane (MCH) in chloroform, which led to the visual color changes. This new amide‐containing NDI‐NA amphiphile formed nanobelt structures in chloroform/MCH (10:90, v/v) and microcup‐like morphologies in chloroform/MCH (5:95, v/v). The closure of these microcups led to the formation of vesicles and microcapsules. The structural morphologies gained from the solvophobic control of NDI‐NA were confirmed by various complementary techniques such as infrared spectroscopy, X‐ray diffraction, and scanning and transmission electron microscopy. In the absence of the amide moiety in NDI‐N, no self‐assembly was observed, indicating the fundamental role of H‐bonding in the self‐association process. PMID:27308233

  17. Oxygen activation and intramolecular C-H bond activation by an amidate-bridged diiron(II) complex.

    PubMed

    Jones, Matthew B; Hardcastle, Kenneth I; Hagen, Karl S; MacBeth, Cora E

    2011-07-18

    A diiron(II) complex containing two μ-1,3-(κN:κO)-amidate linkages has been synthesized using the 2,2',2''-tris(isobutyrylamido)triphenylamine (H(3)L(iPr)) ligand. The resulting diiron complex, 1, reacts with dioxygen (or iodosylbenzene) to effect intramolecular C-H bond activation at the methine position of the ligand isopropyl group. The ligand-activated product, 2, has been isolated and characterized by a variety of methods including X-ray crystallography. Electrospray ionization mass spectroscopy of 2 prepared from(18)O(2) was used to confirm that the oxygen atom incorporated into the ligand framework is derived from molecular oxygen. PMID:21667986

  18. The Shono-type electroorganic oxidation of unfunctionalised amides. Carbon–carbon bond formation via electrogenerated N-acyliminium ions

    PubMed Central

    2014-01-01

    Summary N-acyliminium ions are useful reactive synthetic intermediates in a variety of important carbon–carbon bond forming and cyclisation strategies in organic chemistry. The advent of an electrochemical anodic oxidation of unfunctionalised amides, more commonly known as the Shono oxidation, has provided a complementary route to the C–H activation of low reactivity intermediates. In this article, containing over 100 references, we highlight the development of the Shono-type oxidations from the original direct electrolysis methods, to the use of electroauxiliaries before arriving at indirect electrolysis methodologies. We also highlight new technologies and techniques applied to this area of electrosynthesis. We conclude with the use of this electrosynthetic approach to challenging syntheses of natural products and other complex structures for biological evaluation discussing recent technological developments in electroorganic techniques and future directions. PMID:25670975

  19. The Shono-type electroorganic oxidation of unfunctionalised amides. Carbon-carbon bond formation via electrogenerated N-acyliminium ions.

    PubMed

    Jones, Alan M; Banks, Craig E

    2014-01-01

    N-acyliminium ions are useful reactive synthetic intermediates in a variety of important carbon-carbon bond forming and cyclisation strategies in organic chemistry. The advent of an electrochemical anodic oxidation of unfunctionalised amides, more commonly known as the Shono oxidation, has provided a complementary route to the C-H activation of low reactivity intermediates. In this article, containing over 100 references, we highlight the development of the Shono-type oxidations from the original direct electrolysis methods, to the use of electroauxiliaries before arriving at indirect electrolysis methodologies. We also highlight new technologies and techniques applied to this area of electrosynthesis. We conclude with the use of this electrosynthetic approach to challenging syntheses of natural products and other complex structures for biological evaluation discussing recent technological developments in electroorganic techniques and future directions. PMID:25670975

  20. Electron Transfer Dissociation Reveals Changes in the Cleavage Frequencies of Backbone Bonds Distant to Amide-to-Ester Substitutions in Polypeptides

    NASA Astrophysics Data System (ADS)

    Hansen, Thomas A.; Jung, Hye R.; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization.

  1. Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.

    PubMed Central

    Shimoni, L.; Glusker, J. P.

    1995-01-01

    The modes of hydrogen bonding of arginine, asparagine, and glutamine side chains and of urea have been examined in small-molecule crystal structures in the Cambridge Structural Database and in crystal structures of protein-nucleic acid and protein-protein complexes. Analysis of the hydrogen bonding patterns of each by graph-set theory shows three patterns of rings (R) with one or two hydrogen bond acceptors and two donors and with eight, nine, or six atoms in the ring, designated R2(2)(8), R2(2)(9), and R1(2)(6). These three patterns are found for arginine-like groups and for urea, whereas only the first two patterns R2(2)(8) and R2(2)(9) are found for asparagine- and glutamine-like groups. In each case, the entire system is planar within 0.7 A or less. On the other hand, in macromolecular crystal structures, the hydrogen bonding patterns in protein-nucleic acid complexes between the nucleic acid base and the protein are all R2(2)(9), whereas hydrogen bonding between Watson-Crick-like pairs of nucleic acid bases is R2(2)(8). These two hydrogen bonding arrangements [R2(2)(9)] and R2(2)(8)] are predetermined by the nature of the groups available for hydrogen bonding. The third motif identified, R1(2)(6), involves hydrogen bonds that are less linear than in the other two motifs and is found in proteins. PMID:7773178

  2. Key role of intramolecular metal chelation and hydrogen bonding in the cobalt-mediated radical polymerization of N-vinyl amides.

    PubMed

    Debuigne, Antoine; Morin, Aurélie N; Kermagoret, Anthony; Piette, Yasmine; Detrembleur, Christophe; Jérôme, Christine; Poli, Rinaldo

    2012-10-01

    This work reveals the preponderance of an intramolecular metal chelation phenomenon in a controlled radical polymerization system involving the reversible trapping of the radical chains by a cobalt complex bis(acetylacetonato)cobalt(II). The cobalt-mediated radical polymerization (CMRP) of a series of N-vinyl amides was considered with the aim of studying the effect of the cobalt chelation by the amide moiety of the last monomer unit of the chain. The latter reinforces the cobalt-polymer bond in the order N-vinylpyrrolidonebond and a dative bond, is unique in the field of controlled radical polymerization and represents a powerful opportunity to fine tune the equilibrium between latent and free radicals. Possible hydrogen bond formation is also taken into account in the case of N-vinyl acetamide and N-vinyl formamide. These results are essential for understanding the factors influencing Co-C bond strength in general, and the CMRP mechanism in particular, but also for developing a powerful platform for the synthesis of new precision poly(N-vinyl amide) materials, which are an important class of polymers that sustain numerous applications today. PMID:22907863

  3. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

    PubMed Central

    Desai, Bijoy J.; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A.; Almo, Steven C.; Gao, Jiali; Suga, Hiroaki; Gerlt, John A.

    2014-01-01

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5′-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide–substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼1017) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with l-glycerate (HOS) was used to generate the ester backbone substitution (S127HOS). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼102) to the 1017 rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations. PMID:25275007

  4. Palladium-catalyzed C–N and C–O bond formation of N-substituted 4-bromo-7-azaindoles with amides, amines, amino acid esters and phenols

    PubMed Central

    Surasani, Rajendra; Rao, A V Dhanunjaya; Chandrasekhar, K B

    2012-01-01

    Summary Simple and efficient procedures for palladium-catalyzed cross-coupling reactions of N-substituted 4-bromo-7-azaindole (1H-pyrrole[2,3-b]pyridine), with amides, amines, amino acid esters and phenols through C–N and C–O bond formation have been developed. The C–N cross-coupling reaction of amides, amines and amino acid esters takes place rapidly by using the combination of Xantphos, Cs2CO3, dioxane and palladium catalyst precursors Pd(OAc)2/Pd2(dba)3. The combination of Pd(OAc)2, Xantphos, K2CO3 and dioxane was found to be crucial for the C–O cross-coupling reaction. This is the first report on coupling of amides, amino acid esters and phenols with N-protected 4-bromo-7-azaindole derivatives. PMID:23209536

  5. Diacetoxyiodobenzene assisted C-O bond formation via sequential acylation and deacylation process: synthesis of benzoxazole amides and their mechanistic study by DFT.

    PubMed

    Nahakpam, Lokendrajit; Chipem, Francis A S; Chingakham, Brajakishor S; Laitonjam, Warjeet S

    2016-08-10

    An efficient method for the transformation of N-substituted-N'-benzoylthioureas to substituted N-benzoxazol-2-yl-amides using diacetoxyiodobenzene (DIB) is described in this work. The transformation follows the C-O bond formation leading to the benzoxazole derivative, due to oxidative dehydrogenation by DIB, instead of the expected C-S bond formation of the benzothiazole moiety. The C-O bond formation leading to benzoxazole is due to consecutive acylation and deacylation in conjunction with the reduction of two moles of DIB. A plausible mechanism was proposed for the reaction and density functional calculations were also performed to study the reaction mechanism. PMID:27461562

  6. Efficient Amide Bond Formation through a Rapid and Strong Activation of Carboxylic Acids in a Microflow Reactor**

    PubMed Central

    Fuse, Shinichiro; Mifune, Yuto; Takahashi, Takashi

    2014-01-01

    The development of highly efficient amide bond forming methods which are devoid of side reactions, including epimerization, is important, and such a method is described herein and is based on the concept of rapid and strong activation of carboxylic acids. Various carboxylic acids are rapidly (0.5 s) converted into highly active species, derived from the inexpensive and less-toxic solid triphosgene, and then rapidly (4.3 s) reacted with various amines to afford the desired peptides in high yields (74 %–quant.) without significant epimerization (≤3 %). Our process can be carried out at ambient temperature, and only CO2 and HCl salts of diisopropylethyl amine are generated. In the long history of peptide synthesis, a significant number of active coupling reagents have been abandoned because the highly active electrophilic species generated are usually susceptible to side reactions such as epimerization. The concept presented herein should renew interest in the use of these reagents. PMID:24402801

  7. Chromatographically separable rotamers of an unhindered amide

    PubMed Central

    Geffe, Mario; Andernach, Lars; Trapp, Oliver

    2014-01-01

    Summary Surprisingly stable formamide rotamers were encountered in the tetrahydroisoquinoline and morphinan series of alkaloids. We investigated the hindered rotation around the amide bond by dynamic high-performance liquid chromatography (DHPLC) and kinetic measurements of the interconversion of the rotamers which can readily be separated by HPLC as well as TLC. The experimental results of the different methods were compared to each other as well as to results obtained by DFT calculations. PMID:24778722

  8. A Dynamic Pathway for Stone-Wales Bond Rotation on Carbon Nanotubes through Diamond-Like Bonds

    NASA Technical Reports Server (NTRS)

    Wei, Chen-Yu; Srivastava, Deepak; Cho, Kyeong-Jae; Menon, Madhu

    2003-01-01

    A new lower energy barrier with a two-step pathway of Stone-Wales (SW) ,ond rotation on carbon nanotubes (CNTs) is found through molecular dynamics (MD) simulations of CNTs under tension. The first step involves going over to a stable sp3-like metastable configuration with half rotated and partially tilted C-C bond. The second step involves going over to the fully rotated C-C bond with the formation of a SW defect in the nanotube. The energy barrier for this two-step dynamic pathway is significantly lower than the previously known static barrier for in-plane rotation of the C-C bond on a tensile strained (> 4%) CNT.

  9. 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).

  10. Electron transfer dissociation reveals changes in the cleavage frequencies of backbone bonds distant to amide-to-ester substitutions in polypeptides.

    PubMed

    Hansen, Thomas A; Jung, Hye R; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization. PMID:21952783

  11. Conformation-Specific IR and UV Spectroscopy of the Amino Acid Glutamine: Amide-Stacking and Hydrogen Bonding in AN Important Residue in Neurodegenerative Diseases

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; Dean, Jacob C.; Zwier, Timothy S.

    2014-06-01

    Glutamine plays an important role in several neurodegenerative diseases including Huntington's disease (HD) and Alzheimer's disease (AD). An intriguing aspect of the structure of glutamine is its incorporation of an amide group in its side chain, thereby opening up the possibility of forming amide-amide H-bonds between the peptide backbone and side chain. In this study the conformational preferences of two capped gluatamines Z(carboxybenzyl)-Glutamine-X (X=OH, NHMe) are studied under jet-cooled conditions in the gas phase in order to unlock the intrinsic structural motifs that are favored by this flexible sidechain. Conformational assignments are made by comparing the hydride stretch ( 3100-3700 cm-1) and amide I and II ( 1400-1800 cm-1) resonant ion-dip infrared spectra with predictions from harmonic frequency calculations. Assigned structures will be compared to previously published results on both natural and unnatural residues. Particular emphasis will be placed on the comparison between glutamine and unconstrained γ-peptides due to the similar three-carbon spacing between backbone and side chain in glutamine to the backbone spacing in γ-peptides. The ability of the glutamine side-chain to form amide stacked conformations will be a main focus, along with the prevalence of extended backbone type structures. W. H. James, III, C W. Müller, E. G. Buchanan, M. G. D. Nix, L. Guo, L. Roskop, M. S. Gordon, L. V. Slipchenko, S. H. Gellman, and T. S. Zwier, J. Am. Chem. Soc., 2009, 131(40), 14243-14245.

  12. 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.

  13. Studies on the translational and rotational motions of ionic liquids composed of N-methyl-N-propyl-pyrrolidinium (P13) cation and bis(trifluoromethanesulfonyl)amide and bis(fluorosulfonyl)amide anions and their binary systems including lithium salts

    NASA Astrophysics Data System (ADS)

    Hayamizu, Kikuko; Tsuzuki, Seiji; Seki, Shiro; Fujii, Kenta; Suenaga, Masahiko; Umebayashi, Yasuhiro

    2010-11-01

    Room-temperature ionic liquids (RTIL, IL) are stable liquids composed of anions and cations. N-methyl-N-propyl-pyrrolidinium (P13, Py13, PYR13, or mppy) is an important cation and produces stable ILs with various anions. In this study two amide-type anions, bis(trifluoromethanesulfonyl)amide [N(SO2CF3)2, TFSA, TFSI, NTf2, or Tf2N] and bis(fluorosulfonyl)amide [N(SO2F)2, FSA, or FSI], were investigated. In addition to P13-TFSA and P13-FSA, lithium salt doped samples were prepared (P13-TFSA-Li and P13-FSA-Li). The individual ion diffusion coefficients (D) and spin-lattice relaxation times (T1) were measured by H1, F19, and L7i NMR. At the same time, the ionic conductivity (σ), viscosity (η), and density (ρ) were measured over a wide temperature range. The van der Waals volumes of P13, TFSA, FSA, Li(TFSA)2, and Li(FSA)3 were estimated by molecular orbital calculations. The experimental values obtained in this study were analyzed by the classical Stokes-Einstein, Nernst-Einstein (NE), and Stokes-Einstein-Debye equations and Walden plots were also made for the neat and binary ILs to clarify physical and mobile properties of individual ions. From the temperature-dependent velocity correlation coefficients for neat P13-TFSA and P13-FSA, the NE parameter 1-ξ was evaluated. The ionicity (electrochemical molar conductivity divided by the NE conductivity from NMR) and the 1-ξ had exactly the same values. The rotational and translational motions of P13 and jump of a lithium ion are also discussed.

  14. Understanding Rotation about a C=C Double Bond

    ERIC Educational Resources Information Center

    Barrows, Susan E.; Eberlein, Thomas H.

    2005-01-01

    The study focuses on the process and energetic cost of twisting around a C=C double bond and provides instructors with a simple vehicle for rectifying the common misrepresentation of C=C double bonds as rigid and inflexible. Discussions of cis and trans isomers of cycloalkenes are a good entry point for introducing students to the idea of a…

  15. Role of the delta 8 double bond of agroclavine in lysergic acid amide biosynthesis by Claviceps purpurea.

    PubMed

    Willingale, J; Manzarpour, A; Mantle, P G

    1985-08-15

    Agroclavine, given to actively-growing sclerotial tissue of a strain of Claviceps purpurea which can not normally elaborate ergot alkaloids, was transformed by this tissue into lysergic acid amide with overall efficiency of approximately 40%. By contrast, festuclavine (8,9-dihydro-agroclavine) was not transformed, indicating specificity in the mechanism of lysergyl biosynthesis. PMID:4018228

  16. Efficient Synthesis of Diaryl Ketones by Nickel-Catalyzed Negishi Cross-Coupling of Amides by Carbon-Nitrogen Bond Cleavage at Room Temperature Accelerated by a Solvent Effect.

    PubMed

    Shi, Shicheng; Szostak, Michal

    2016-07-18

    The first Negishi cross-coupling of amides for the synthesis of versatile diaryl ketones by selective C-N bond activation under exceedingly mild conditions is reported. The cross-coupling was accomplished with bench-stable, inexpensive precatalyst [Ni(PPh3 )2 Cl2 ] that shows high functional-group tolerance and enables the synthesis of highly functionalized diaryl ketone motifs. The coupling occurred with excellent chemoselectivity favoring the ketone (cf. biaryl) products. Notably, this process represents the mildest conditions for amide N-C bond activation accomplished to date (room temperature, <10 min). Considering the versatile role of polyfunctional biaryl ketone linchpins in modern organic synthesis, availability, and excellent functional-group tolerance of organozinc reagents, this strategy provides a new platform for amide N-C bond/organozinc cross-coupling under mild conditions. PMID:27304392

  17. Amide bond hydrolysis in peptides and cyclic peptides catalyzed by a dimeric Zr(IV)-substituted Keggin type polyoxometalate.

    PubMed

    Ly, Hong Giang T; Absillis, Gregory; Parac-Vogt, Tatjana N

    2013-08-14

    Detailed kinetic studies on the hydrolysis of glycylserine (Gly-Ser) and glycylglycine (Gly-Gly) in the presence of the dimeric zirconium(IV)-substituted Keggin type polyoxometalate (Et2NH2)8[{α-PW11O39Zr(μ-OH)(H2O)}2]·7H2O (1) were performed by a combination of (1)H, (13)C and (31)P NMR spectroscopy. The observed rate constants for the hydrolysis of Gly-Ser and Gly-Gly at pD 5.4 and 60 °C were 63.3 × 10(-7) s(-1) and 4.44 × 10(-7) s(-1) respectively, representing a significant acceleration as compared to the uncatalyzed reactions. The pD dependence of the rate constant for both reactions exhibited a bell-shaped profile with the fastest hydrolysis observed in the pD range of 5.5-6.0. Interaction of 1 with Gly-Ser and Gly-Gly via their amine nitrogen and amide oxygen was proven by (13)C NMR spectroscopy. The effective hydrolysis of Gly-Ser in the presence of 1 is most likely a combination of the polarization of the amide oxygen due to its binding to the Zr(IV) ion in 1 and the intramolecular attack of the Ser hydroxyl group on the amide carbonyl carbon. The effect of temperature, inhibitors, and ionic strength on the hydrolysis rate constant was also examined. The solution structure of 1 was investigated by means of (31)P NMR spectroscopy, revealing that its stability is highly dependent on pH, concentration and temperature. A 2.0 mM solution of 1 was found to be fully stable under hydrolytic conditions (pD 5.4 and 60 °C) both in the presence and in the absence of the dipeptides. PMID:23787813

  18. Accurate rotational constant and bond lengths of hexafluorobenzene by femtosecond rotational Raman coherence spectroscopy and ab initio calculations

    SciTech Connect

    Den, Takuya S.; Frey, Hans-Martin; Leutwyler, Samuel

    2014-11-21

    The gas-phase rotational motion of hexafluorobenzene has been measured in real time using femtosecond (fs) time-resolved rotational Raman coherence spectroscopy (RR-RCS) at T = 100 and 295 K. This four-wave mixing method allows to probe the rotation of non-polar gas-phase molecules with fs time resolution over times up to ∼5 ns. The ground state rotational constant of hexafluorobenzene is determined as B{sub 0} = 1029.740(28) MHz (2σ uncertainty) from RR-RCS transients measured in a pulsed seeded supersonic jet, where essentially only the v = 0 state is populated. Using this B{sub 0} value, RR-RCS measurements in a room temperature gas cell give the rotational constants B{sub v} of the five lowest-lying thermally populated vibrationally excited states ν{sub 7/8}, ν{sub 9}, ν{sub 11/12}, ν{sub 13}, and ν{sub 14/15}. Their B{sub v} constants differ from B{sub 0} by between −1.02 MHz and +2.23 MHz. Combining the B{sub 0} with the results of all-electron coupled-cluster CCSD(T) calculations of Demaison et al. [Mol. Phys. 111, 1539 (2013)] and of our own allow to determine the C-C and C-F semi-experimental equilibrium bond lengths r{sub e}(C-C) = 1.3866(3) Å and r{sub e}(C-F) = 1.3244(4) Å. These agree with the CCSD(T)/wCVQZ r{sub e} bond lengths calculated by Demaison et al. within ±0.0005 Å. We also calculate the semi-experimental thermally averaged bond lengths r{sub g}(C-C)=1.3907(3) Å and r{sub g}(C-F)=1.3250(4) Å. These are at least ten times more accurate than two sets of experimental gas-phase electron diffraction r{sub g} bond lengths measured in the 1960s.

  19. Competing hydrogen bonding in methoxyphenols: The rotational spectrum of o-vanillin

    NASA Astrophysics Data System (ADS)

    Cocinero, Emilio J.; Lesarri, Alberto; Écija, Patricia; Basterretxea, Francisco; Fernández, José A.; Castaño, Fernando

    2011-05-01

    The conformational preferences of o-vanillin have been investigated in a supersonic jet expansion using Fourier transform microwave (FT-MW) spectroscopy. Three molecular conformations were derived from the rotational spectrum. The two most stable structures are characterized by a moderate O sbnd H···O dbnd C hydrogen bond between the aldehyde and the hydroxyl groups, with the methoxy side chain either in plane (global minimum a- cis-trans) or out of plane (a- cis-gauche) with respect to the aromatic ring. In the third conformer the aldehyde group is rotated by ca. 180°, forming a O sbnd H···O hydrogen bond between the methoxy and hydroxyl groups (s- trans-trans). Rotational parameters and relative populations are provided for the three conformations, which are compared with the results of ab initio (MP2) and density-functional (B3LYP, M05-2X) theoretical predictions.

  20. On the Involvement of Single-Bond Rotation in the Primary Photochemistry of Photoactive Yellow Protein

    PubMed Central

    Stahl, Andreas D.; Hospes, Marijke; Singhal, Kushagra; van Stokkum, Ivo; van Grondelle, Rienk; Groot, Marie Louise; Hellingwerf, Klaas J.

    2011-01-01

    Prior experimental observations, as well as theoretical considerations, have led to the proposal that C4-C7 single-bond rotation may play an important role in the primary photochemistry of photoactive yellow protein (PYP). We therefore synthesized an analog of this protein's 4-hydroxy-cinnamic acid chromophore, (5-hydroxy indan-(1E)-ylidene)acetic acid, in which rotation across the C4-C7 single bond has been locked with an ethane bridge, and we reconstituted the apo form of the wild-type protein and its R52A derivative with this chromophore analog. In PYP reconstituted with the rotation-locked chromophore, 1), absorption spectra of ground and intermediate states are slightly blue-shifted; 2), the quantum yield of photochemistry is ∼60% reduced; 3), the excited-state dynamics of the chromophore are accelerated; and 4), dynamics of the thermal recovery reaction of the protein are accelerated. A significant finding was that the yield of the transient ground-state intermediate in the early phase of the photocycle was considerably higher in the rotation-locked samples than in the corresponding samples reconstituted with p-coumaric acid. In contrast to theoretical predictions, the initial photocycle dynamics of PYP were observed to be not affected by the charge of the amino acid residue at position 52, which was varied by 1), varying the pH of the sample between 5 and 10; and 2), site-directed mutagenesis to construct R52A. These results imply that C4-C7 single-bond rotation in PYP is not an alternative to C7=C8 double-bond rotation, in case the nearby positive charge of R52 is absent, but rather facilitates, presumably with a compensatory movement, the physiological Z/E isomerization of the blue-light-absorbing chromophore. PMID:21889456

  1. Amide bond direction modulates G-quadruplex recognition and telomerase inhibition by 2,6 and 2,7 bis-substituted anthracenedione derivatives.

    PubMed

    Zagotto, Giuseppe; Sissi, Claudia; Moro, Stefano; Dal Ben, Diego; Parkinson, Gary N; Fox, Keith R; Neidle, Stephen; Palumbo, Manlio

    2008-01-01

    G-quadruplex structures of DNA represent a potentially useful target for anticancer drugs. Stabilisation of this arrangement at the ends of chromosomes may inhibit the action of telomerase, an enzyme involved in immortalization of cancer cells. Appropriately substituted amido anthracenediones are effective G-quadruplex stabilizers, but no information is available as yet on the possible modulation of G-quadruplex recognition and telomerase inhibition produced by the direction of the amide bond. To understand the basis of amido anthracenedione selectivity, we have synthesized a number of derivatives bearing the -CO-NH- or -NH-CO- group linked to the planar anthraquinone (AQ) moiety at 2,6 and 2,7 positions. The various isomers were tested in terms of telomerase inhibition, determined by the TRAP assay, G-quadruplex stabilisation measured by the increase in melting temperature of the appropriately folded oligonucleotide using FRET, and conformational and G4 binding properties examined by molecular modelling techniques. In all cases, enzymatic inhibition and G-quadruplex stabilization were directly related, which strongly supports the proposed molecular mechanism of telomerase interference. Interestingly, the AQ-NH-CO- arrangement performs invariantly better than the AQ-CO-NH- arrangement, showing a clear preference among isomeric derivatives. Theoretical calculations suggest that the former amide arrangement is co-planar with the aromatic system, whereas the latter is tilted by about 30 degrees when considering the most stable conformation. A more extended planar surface would allow more efficient stacking interactions with the quadruplex structure, hence more effective telomerase inhibition. PMID:17936629

  2. On the ClC halogen bond: a rotational study of CF3Cl-CO.

    PubMed

    Caminati, Walther; Evangelisti, Luca; Feng, Gang; Giuliano, Barbara M; Gou, Qian; Melandri, Sonia; Grabow, Jens-Uwe

    2016-07-21

    The rotational spectra of two isotopologues (CF3(35)Cl-CO and CF3(37)Cl-CO) of the CF3Cl-CO adduct have been investigated and analyzed using supersonic-jet Fourier transform microwave spectroscopy, and found to have the features of a symmetric top. Rotational, centrifugal distortion, and nuclear quadrupole ((35)Cl and (37)Cl) coupling constants have been precisely obtained from high-resolution measurements. The two subunits of the complex are held together via a ClC halogen bond interaction. Information on the internal dynamics and the dissociation energy of the complex is provided. PMID:27049637

  3. A rotating-disk study on Teflon-bonded porous zinc electrodes

    NASA Astrophysics Data System (ADS)

    Duffield, A.; Mitchell, P. J.; Hampson, N. A.; Kumar, N.; Shield, D. W.

    1985-07-01

    Microcomputer-controlled, rotating-disk experiments have been carried out on Teflon-bonded porous electrodes fabricated from a 5 percent PTFE suspension + ZnO. The effect of using 1 percent mercuric oxide as an additive on this type of electrode has been examined. Plots of i exp -1 vs omega exp -1/2 on electrodes containing mercuric oxide show intercepts through the origin for low overpotentials, implying that quasi-reversible kinetics prevail.

  4. 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

  5. Rotational spectra and gas phase structure of the maleimide - Formic acid doubly hydrogen bonded dimer

    NASA Astrophysics Data System (ADS)

    Pejlovas, Aaron M.; Kukolich, Stephen G.

    2016-03-01

    Rotational transitions were measured for the maleimide - formic acid doubly hydrogen bonded dimer using a Flygare-Balle type pulsed-beam Fourier transform microwave spectrometer. No splittings caused by possible concerted double proton tunneling motion were observed. Experimental rotational constants (MHz), quadrupole coupling constants (MHz), and centrifugal distortion constants (kHz) were determined for the parent and three deuterium substituted isotopologues. The values for the parent are A = 2415.0297(10), B = 784.37494(38), C = 592.44190(33), DJ = 0.0616(64), DJK = -0.118(35), DK = -1.38(15), 1.5χaa = 2.083(14), and 0.25(χbb-χcc) = 1.1565(29). The hydrogen bond lengths were determined using a nonlinear least squares structure fitting program. Rotational constants for this complex are consistent with a planar structure, with an inertial defect of Δ = -0.528 amu Å2. The B3LYP calculation yielded rotational constants within 0.1% of the experimental values.

  6. Amide I bands of terminally blocked alanine in solutions investigated by infrared spectroscopy and density functional theory calculation: hydrogen-bonding interactions and solvent effects.

    PubMed

    Lee, Maeng-Eun; Lee, So Yeong; Joo, Sang-Woo; Cho, Kwang-Hwi

    2009-05-14

    Structural aspects of terminally blocked alanine trans-N-acetyl-L-alanyl-trans-N'-methylamide (Ac-Ala-NHMe) in several different solvents were compared by attenuated total reflection infrared (ATR-IR) spectroscopy and density functional theory (DFT) calculations. The amide I bands between 1600 and 1700 cm(-1) appeared to change depending on media, indicating dissimilar hydrogen-bonding interactions among the peptides and solvent molecules. The minimum energy geometry in the isolated gas phase and aqueous environments were calculated at the B3LYP/6-311++G** theoretical level. In the solid state, Ac-Ala-NHMe is assumed to have an extended beta-stranded structure (C5), whereas it is assumed to have a cyclic structure (C7eq or alphaL) in a nonpolar tetrahydrofuran (THF) solvent. The optimized backbone dihedral angles (Phi, Psi) of Ac-Ala-NHMe plus four explicit water molecules were estimated to be -94 degrees and +133 degrees, respectively, indicating the polyproline II structure (PII). The energy differences between the most stable conformers were predicted to be larger for Ac-Ala-NHMe, which implies that more conformational ensemble structures should coexist for the gas phase than for the aqueous medium with explicit water molecules. PMID:19374358

  7. Highly Chemoselective Synthesis of Indolizidine Lactams by SmI2 -Induced Umpolung of the Amide Bond via Aminoketyl Radicals: Efficient Entry to Alkaloid Scaffolds.

    PubMed

    Shi, Shicheng; Lalancette, Roger; Szostak, Roman; Szostak, Michal

    2016-08-16

    Samarium(II) iodide enables a wide range of highly chemoselective umpolung radical transformations proceeding by electron transfer to carbonyl groups; however, cyclizations of important nitrogen-containing precursors have proven limited due to their prohibitive redox potential. Herein, we report the first reductive cyclizations of unactivated cyclic imides onto N-tethered olefins using SmI2 /H2 O. This new umpolung protocol leads to the rapid synthesis of nitrogen-containing heterocycles that are of particular significance as precursors to pharmaceutical pharmacophores and numerous classes of alkaloids. The reaction conditions tolerate a wide range of functional groups. Excellent chemoselectivity is observed in the cyclization over amide and ester functional groups. Such unconventional reactivity has important implications for the design and optimization of new bond-forming reactions by umpolung radical processes. The reaction advances the SmI2 cyclization platform to the challenging unactivated N-tethered acyl-type radical precursors to access nitrogen-containing architectures. PMID:27418326

  8. Amide coordination effects in organolithiums

    SciTech Connect

    Bachrach, S.M.; Ritchie, J.P. )

    1989-04-26

    Organolithiums containing the amide group are examined by ab initio molecular orbital calculations with the 3-21G basis set. Amide coordination with the metal cation results in a large thermodynamic stabilization of the ion pair. Basis set superposition errors at 3-21G are estimated to favor the complex by 10-15 kcal mol{sup {minus}1}; nevertheless, qualitative trends at this level are believed to be reliable. The calculations stabilization energy due to the amide drops off depending upon whether lithiation occurs {alpha}, {beta}, or {gamma} to the amide - provided the cation is accessible to the amide oxygen. Without correction for basis set superposition error, stabilization energies at 3-21G (in kcal mol{sup {minus}1}) are 45 in acetamide, 40 in benzamide, and 38 in syn-bicyclo(1.1.1)-pentane-2-carboxamide. Amide coordination effects in lithiocubanes are also estimated and found to be large. Thus, thermodynamics plays an important role in amide-assisted metalations. In addition, formation of an acetamide-methyllithium complex is found to be 37.5 kcal mol{sup {minus}1} exothermic relative to separated molecules, suggesting that formation of this complex lies along the metalation reaction pathways. This complexation facilitates the reaction kinetically. Analysis of electron density distributions and electrostatic potentials shows that the carbanion-lithium and the amide-lithium interactions are primarily closed-shell ones, being essentially ionic bonds.

  9. Hydrogen Bond Network Isomers of the Water Nonamer and Decamer Observed by Broadband Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Perez, Cristobal; Zaleski, Daniel P.; Seifert, Nathan A.; Pate, Brooks H.; Kisiel, Zbigniew; Temelso, Berhane; Shields, George C.

    2013-06-01

    After our previous study of the rotational spectrum of water clusters in the 6-18 GHz region, in order to study clusters of larger size (>8 water molecules), a chirped-pulse Fourier transform microwave spectrometer in the 2-8 GHz frequency range has been used to obtain the broadband rotational spectra of five water nonamer isomers and four water decamer isomers in a pulsed molecular beam. The oxygen atom framework geometries for three nonamers and two decamers have also been unambiguously identified from isotopic labeling measurements using an H_{2}^{18}O enriched sample. Three of the four observed water decamer show tunneling effect associated with the internal dynamics of hydrogen-bond network in a similar fashion as the prism water hexamer. These tunneling paths are quenched upon a single incorporation of a H_{2}^{18}O molecule in the cluster. Due the large amount of closely-spaced rotational transitions in the H_{2}^{18}O spectrum, automated fitting tools were employed to extract the corresponding rotational spectra, which will be also briefly described. C. Perez, M. T. Muckle, D. P. Zaleski, N. A. Seifert, B. Temelso, G. C. Shields, Z. Kisiel, and B. H. Pate, Science 336, 897 (2012).

  10. A link between structure, diffusion and rotations of hydrogen bonding tracers in ionic liquids.

    PubMed

    Araque, Juan C; Daly, Ryan P; Margulis, Claudio J

    2016-05-28

    When solutes are small compared to the size of the ions in an ionic liquid, energetic heterogeneities associated with charge enhanced (stiff) and charge depleted (soft) nanoenvironments are sampled. In a recent article [J. C. Araque et al., J. Phys. Chem. B 119(23), 7015-7029 (2015)], we explored large deviations from Stokes-Einstein translational diffusion caused by such a heterogeneity. The current article is set to explore the effect of soft and stiff solvent environments (i.e., structure) on OH-bond rotations in the case of water and small alcohols in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (Im1,2 (+)NTf2 (-)). Is solute rotational dynamics heterogeneous? If so, are solute rotations and translations coupled in the sense that stiff and soft solvent environments hinder or speed up both types of dynamics? For the systems studied here, there appears to be a clear connection between translations, rotations, and stiff/soft solvent environments. We also discuss interesting asymmetries of the correlation between solutes with anions and cations. PMID:27250313

  11. A link between structure, diffusion and rotations of hydrogen bonding tracers in ionic liquids

    NASA Astrophysics Data System (ADS)

    Araque, Juan C.; Daly, Ryan P.; Margulis, Claudio J.

    2016-05-01

    When solutes are small compared to the size of the ions in an ionic liquid, energetic heterogeneities associated with charge enhanced (stiff) and charge depleted (soft) nanoenvironments are sampled. In a recent article [J. C. Araque et al., J. Phys. Chem. B 119(23), 7015-7029 (2015)], we explored large deviations from Stokes-Einstein translational diffusion caused by such a heterogeneity. The current article is set to explore the effect of soft and stiff solvent environments (i.e., structure) on OH-bond rotations in the case of water and small alcohols in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([" separators="Im1,2 + ][" separators="NTf2- ]). Is solute rotational dynamics heterogeneous? If so, are solute rotations and translations coupled in the sense that stiff and soft solvent environments hinder or speed up both types of dynamics? For the systems studied here, there appears to be a clear connection between translations, rotations, and stiff/soft solvent environments. We also discuss interesting asymmetries of the correlation between solutes with anions and cations.

  12. Fluorine Scan of Inhibitors of the Cysteine Protease Human Cathepsin L: Dipolar and Quadrupolar Effects in the π-Stacking of Fluorinated Phenyl Rings on Peptide Amide Bonds.

    PubMed

    Giroud, Maude; Harder, Michael; Kuhn, Bernd; Haap, Wolfgang; Trapp, Nils; Schweizer, W Bernd; Schirmeister, Tanja; Diederich, François

    2016-05-19

    The π-stacking of fluorinated benzene rings on protein backbone amide groups was investigated, using a dual approach comprising enzyme-ligand binding studies complemented by high-level quantum chemical calculations. In the experimental study, the phenyl substituent of triazine nitrile inhibitors of human cathepsin L (hCatL), which stacks onto the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket, was systematically fluorinated, and differences in inhibitory potency were measured in a fluorimetric assay. Binding affinity is influenced by lipophilicity (clog P), the dipole and quadrupole moments of the fluorinated rings, but also by additional interactions of the introduced fluorine atoms with the local environment of the pocket. Generally, the higher the degree of fluorination, the better the binding affinities. Gas phase calculations strongly support the contributions of the molecular quadrupole moments of the fluorinated phenyl rings to the π-stacking interaction with the peptide bond. These findings provide useful guidelines for enhancing π-stacking on protein amide fragments. PMID:27095165

  13. Oligomers Based on a Weak Hydrogen Bond Network: the Rotational Spectrum of the Tetramer of Difluoromethane

    NASA Astrophysics Data System (ADS)

    Feng, Gang; Evangelisti, Luca; Caminati, Walther; Cacelli, Ivo; Carbonaro, Laura; Prampolini, Giacomo

    2013-06-01

    Following the investigation of the rotational spectra of three conformers (so-called ``book'', ``prism'' and ``cage'') of the water hexamer, and of some other water oligomers, we report here the rotational spectrum of the tetramer of a freon molecule. The pulse jet Fourier transform microwave (pj-FTMW) spectrum of an isomer of the difluoromethane tetramer has been assigned. This molecular system is made of units of a relatively heavy asymmetric rotor, held together by a network of weak hydrogen bonds. The search of the rotational spectrum has been based on a high-level reference method, the CCSD(T)/CBS protocol. It is interesting to outline that the rotational spectrum of the water tetramer was not observed, probably because the minimum energy structures of this oligomer is effectively nonpolar in its ground states, or because of high energy tunnelling splittings. The rotational spectra of the monomer, dimer, trimer and tetramer of difluoromethane have been assigned in 1952, 1999, 2007, and 2013 (present work), with a decreasing time spacing between the various steps, looking then promising for a continuous and rapid extension of the size limits of molecular systems accessible to MW spectroscopy. C. Pérez, M. T. Muckle, D. P. Zaleski, N. A. Seifert, B. Temelso, G. C. Shields, Z. Kisiel, B. H. Pate, Science {336} (2012) 897. D. R. Lide, Jr., J. Am. Chem. Soc. {74} (1952) 3548. W. Caminati, S. Melandri, P. Moreschini, P. G. Favero, Angew. Chem. Int. Ed. {38} (1999) 2924. S. Blanco, S. Melandri, P. Ottaviani, W. Caminati, J. Am. Chem. Soc. {129} (2007) 2700.

  14. An eclipsed Csp3-CH3 bond? An ab initio investigation of an atypical rotation barrier

    NASA Astrophysics Data System (ADS)

    Vacek, George

    In 1987, Seiler et al. (1987, Angew. Chem. Int. Edn Engl., 26, 1175) reported the observation of an eclipsed Csp3-CH3 bond in the low-temperature X-ray analysis of a crystalline trihydrate tricyclic orthoamide. This contrasts with the observed staggered conformation in an anhydrous crystal of the tricyclic orthoamide. Modest quantum chemical calculations estimated that a 5.5 kcal-mol-1 energy difference between the eclipsed form and the expected staggered form could be accounted for by unprecedented hydrogen bonding interaction strengths due to cooperative effects. In 1993, Novoa et al. (1993, Angew. Chem. Int. Edn Engl, 32, 588) showed that the earlier calculations were in error since they did not correct for basis set superposition error (BSSE). The BSSE corrected results of Novoa et al. could not account for the necessary 5.5 kcal mol-1 and this led them to question the original X-ray analysis of Seiler et al. Both sets of calculations suffered from the use of insufficiently accurate levels of theory and an inappropriate choice of model system. A current best estimate for the barrier to rotation is 1.4 kcal mol-1, far below that of the earlier studies. The stabilization of the eclipsed geometry due to hydrogen bonding after correction for BSSE is enough to match this small barrier. At today's best level of theory, the experimentally observed structure is 0.2 kcal mol-1 more stable than the staggered geometry.

  15. The amide C-N bond of isatins as the directing group and the internal oxidant in Ru-catalyzed C-H activation and annulation reactions: access to 8-amido isocoumarins.

    PubMed

    Kaishap, Partha Pratim; Sarma, Bipul; Gogoi, Sanjib

    2016-07-28

    The N-O, N-N and O-O bonds are the frequently used internally oxidative directing groups used in various redox-neutral coupling reactions. The sole use of the C-N bond as the oxidizing directing group was reported recently by Li X. and co-workers for the Rh(iii)-catalyzed C-H activation of phenacyl ammonium salts. Herein, we report the use of the amide C-N bond of isatins as the oxidizing directing group for the Ru(ii)-catalyzed redox-neutral C-H activation and annulation reactions with alkynes which afford 8-amido isocoumarins. The reaction also features excellent regioselectivity with alkyl aryl substituted alkynes. PMID:27417438

  16. Nuclear magnetic resonance studies on the rotational and translational motions of ionic liquids composed of 1-ethyl-3-methylimidazolium cation and bis(trifluoromethanesulfonyl)amide and bis(fluorosulfonyl)amide anions and their binary systems including lithium salts

    NASA Astrophysics Data System (ADS)

    Hayamizu, Kikuko; Tsuzuki, Seiji; Seki, Shiro; Umebayashi, Yasuhiro

    2011-08-01

    Room temperature ionic liquids (ILs) are stable liquids composed of anions and cations. 1-ethyl-3-methyl-imidazolium (EMIm, EMI) is a popular and important cation that produces thermally stable ILs with various anions. In this study two amide-type anions, bis(trifluoro-methanesulfonyl)amide [N(SO2CF3)2, TFSA, TFSI, NTf2, or Tf2N] and bis(fluorosulfonyl)amide [(N(SO2F)2, FSA, or FSI] were investigated by multinuclear NMR spectroscopy. In addition to EMIm-TFSA and EMIm-FSA, lithium-salt-doped binary systems were prepared (EMIm-TFSA-Li and EMIm-FSA-Li). The spin-lattice relaxation times (T1) were measured by 1H, 19F, and 7Li NMR spectroscopy and the correlation times of 1H NMR, τc(EMIm) (8 × 10-10 to 3 × 10-11 s) for the librational molecular motion of EMIm and those of 7Li NMR, τc(Li) (5 × 10-9 to 2 × 10-10 s) for a lithium jump were evaluated in the temperature range between 253 and 353 K. We found that the bulk viscosity (η) versus τc(EMIm) and cation diffusion coefficient DEMIm versus the rate 1/τc(EMIm) have good relationships. Similarly, linear relations were obtained for the η versus τc(Li) and the lithium diffusion coefficient DLi versus the rate 1/τc(Li). The mean one-jump distances of Li were calculated from τc(Li) and DLi. The experimental values for the diffusion coefficients, ionic conductivity, viscosity, and density in our previous paper were analyzed by the Stokes-Einstein, Nernst-Einstein, and Stokes-Einstein-Debye equations for the neat and binary ILs to clarify the physicochemical properties and mobility of individual ions. The deviations from the classical equations are discussed.

  17. Dissecting Hofmeister Effects: Direct Anion-Amide Interactions Are Weaker than Cation-Amide Binding.

    PubMed

    Balos, Vasileios; Kim, Heejae; Bonn, Mischa; Hunger, Johannes

    2016-07-01

    Whereas there is increasing evidence for ion-induced protein destabilization through direct ion-protein interactions, the strength of the binding of anions to proteins relative to cation-protein binding has remained elusive. In this work, the rotational mobility of a model amide in aqueous solution was used as a reporter for the interactions of different anions with the amide group. Protein-stabilizing salts such as KCl and KNO3 do not affect the rotational mobility of the amide. Conversely, protein denaturants such as KSCN and KI markedly reduce the orientational freedom of the amide group. Thus these results provide evidence for a direct denaturation mechanism through ion-protein interactions. Comparing the present findings with results for cations shows that in contrast to common belief, anion-amide binding is weaker than cation-amide binding. PMID:27237055

  18. Iodine-Catalyzed Oxidative Functionalization of Azaarenes with Benzylic C(sp(3))-H Bonds via N-Alkylation/Amidation Cascade: Two-Step Synthesis of Isoindolo[2,1-b]isoquinolin-7(5H)-one.

    PubMed

    Luo, Wen-Kun; Shi, Xin; Zhou, Wang; Yang, Luo

    2016-05-01

    An efficient and practical iodine-catalyzed oxidative functionalization of azaarenes with benzylic C-H bonds via an N-alkylation and amidation cascade is developed to provide isoquinolin-1(2H)-ones. This method utilizes readily available unfunctionalized azaarenes and methylarenes as starting materials and proceeds under metal-free conditions with good to excellent yields, avoiding the use of expensive noble metal catalysts and generation of halide and metal wastes. The synthetic utility of this reaction is exemplified by the concise, two-step synthesis of isoindolo[2,1-b]isoquinolin-7(5H)-one. PMID:27123751

  19. Raman analysis of bond conformations in the rotator state and premelting of normal alkanes.

    PubMed

    Kotula, Anthony P; Walker, Angela R Hight; Migler, Kalman B

    2016-06-14

    We perform Raman spectroscopic measurements on normal alkanes (CnH2n+2) to quantify the n dependence of the conformational disorder that occurs below the melt temperature. We employ a three-state spectral analysis method originally developed for semi-crystalline polyethylene that posits crystalline, amorphous, and non-crystalline consecutive trans (NCCT) conformations to extract their respective mass fractions. For the alkanes studied that melt via a rotator phase (21 ≤n≤ 37), we find that conformational disorder can be quantified by the loss of NCCT mass fraction, which systematically decreases with increasing chain length. For those that melt directly via the crystal phase (n≥ 40), we observe NCCT conformational mass fractions that are independent of chain length but whose disordered mass fraction increases with length. These complement prior IR measurements which measure disorder via gauche conformations, but have not been able to measure the mass fraction of this disorder as a function of n. An interesting feature of the three-state analysis when applied to alkanes is that the measured fraction of disordered chain conformations in the rotator phase of (10 to 30)% greatly exceeds the mass fraction of gauche bonds (1 to 7)% as measured from IR; we reconcile this difference through DFT calculations. PMID:27174157

  20. Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

    SciTech Connect

    Mani, Devendra; Arunan, E.

    2014-10-28

    Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer [A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and “Atoms in Molecules” analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O–H⋯O, O–H⋯π, and C–H⋯π. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact.

  1. Ru(II)-Catalyzed C-H Activation: Amide-Directed 1,4-Addition of the Ortho C-H Bond to Maleimides.

    PubMed

    Keshri, Puspam; Bettadapur, Kiran R; Lanke, Veeranjaneyulu; Prabhu, Kandikere Ramaiah

    2016-07-15

    Maleimide has been used as a selective coupling partner to generate conjugate addition products exclusively. The typical Heck-type oxidative coupling that occurs when alkenes are used is avoided by choosing maleimide as an alkene, which cannot undergo β-hydride elimination due to the unavailability of a syn-periplanar β-hydrogen atom. The amide nitrogen, which is notorious for undergoing tandem reactions to generate spirocyclic or annulation products under cross-coupling conditions, remains innocent in this report. Along with the substrate scope, a robustness screen has been performed to analyze the performance of amide as a directing group in the presence of other directing groups and also to examine the tolerance of the reaction conditions for other frequently encountered functional groups. PMID:27314834

  2. A one-pot copper catalyzed biomimetic route to N-heterocyclic amides from methyl ketones via oxidative C-C bond cleavage.

    PubMed

    Subramanian, Parthasarathi; Indu, Satrajit; Kaliappan, Krishna P

    2014-12-01

    A direct one-pot Cu-catalyzed biomimetic oxidation of methyl ketones to pharmaceutically important N-heterocyclic amides is reported. The scope of the method is broad, scalable, and mild, and the reaction is tolerant with various acid, base sensitive functionalities with multiple heteroatoms and aryl halides. The extensive mechanistic studies suggest that this reaction follows the Luciferin-Luciferase-like pathway. PMID:25409417

  3. Synthesis and characterization of bridged bis(amidato) rare earth metal amides and their applications in C-N bond formation reactions.

    PubMed

    Zhao, Bei; Xiao, Yang; Yuan, Dan; Lu, Chengrong; Yao, Yingming

    2016-03-01

    Based on three bisamide proligands H2Ln (n = 1–3) (H2L1 = [(Me3C6H2CONHCH2)2CH2], H2L2 = [(Me3C6H2CONHCH2)2C(CH3)2], H2L3 = [Me3C6H2CONH(CH2)2]2NCH3), eight bis(amidato) trivalent rare-earth metal amides {LnRE[N(TMS)2]}2 (n = 1, RE = La (1), Sm (2), Nd (3), Y (4); n = 2, RE = La (5), Nd (6);n = 3, RE = La (7), Nd (8); TMS = SiMe3) were successfully synthesized by treatment of H2Ln with RE[N(TMS)2]3 in a 1 : 1 molar ratio. Complexes 3, and 5–8 were characterized by single-crystal X-ray diffraction, and NMR characterization was carried out for the La complexes 1, 5, 7 and the Y complex 4. These complexes exhibited high catalytic activities in both the direct amidation of aldehydes and the addition of amines with carbodiimine. It was found that the bis(amidato) rare earth metal amides bearing different linkers have different effects on the transformations and lanthanum and neodymium complexes performed better than others. PMID:26906617

  4. A Molecular orbital study of the rotation about the CC bond in styrene

    NASA Astrophysics Data System (ADS)

    Bock, Charles W.; Trachtman, Mendel; George, Philip

    1985-03-01

    The geometry and energy of styrene have been calculated using the 6-31G basis set as a function of the C βC 2C 1C 2 dihedral angle-Φ = 0°(cis), 15°, 30°, 60° and 90° — assuming that the vinyl and phenyl groups remain planar, but otherwise with full geometry optimization. Similar calculations have been carried out for 1,3-butadiene and 3-methylene-1,4-pentadiene (MPD) where rotation about 180° generates a different and not the same conformer. The torsional potential energy curve for styrene has a very flat minimum Φ = 0, i.e. the cis structure is the most stable, whereas butadiene and MPD have minima in the region Φ = 37° to 40°, indicative of more stable gauche structures. For styrene the barrier height Φ = 90° is 131.1 KJ mol -1. These results provide strong support for the potential function obtained by Hollas and Ridley from single level vibronic fluorescence and other spectroscopic data. The distortion of the benzene ring brought about the vinyl group substitution is discussed, also the variation of the C/C and H/C bond lenghts with Φ and the change in charge on the vinyl group and the polarity of the various bonds in the conversion of the cis into the 90° gauche conformer. The stabilization energy for styrene relative to that for benzene has been evaluated according to various criteria, and, in addition, the energy associated with the distortion of the ring.

  5. Creating a single twin boundary between two CdTe (111) wafers with controlled rotation angle by wafer bonding

    SciTech Connect

    Sun, Ce; Lu, Ning; Wang, Jinguo; Lee, Jihyung; Peng, Xin; Kim, Moon J.; Klie, Robert F.

    2013-12-16

    The single twin boundary with crystallographic orientation relationship (1{sup ¯}1{sup ¯}1{sup ¯})//(111) [01{sup ¯}1]//[011{sup ¯}] was created by wafer bonding. Electron diffraction patterns and high-resolution transmission electron microscopy images demonstrated the well control of the rotation angle between the bonded pair. At the twin boundary, one unit of wurtzite structure was found between two zinc-blende matrices. High-angle annular dark-field scanning transmission electron microscopy images showed Cd- and Te-terminated for the two bonded portions, respectively. The I-V curve across the twin boundary showed increasingly nonlinear behavior, indicating a potential barrier at the bonded twin boundary.

  6. High-Resolution Rotational Spectroscopy Study of the Smallest Sugar Dimer: Interplay of Hydrogen Bonds in the Glycolaldehyde Dimer.

    PubMed

    Zinn, Sabrina; Medcraft, Chris; Betz, Thomas; Schnell, Melanie

    2016-05-10

    Molecular recognition of carbohydrates plays an important role in nature. The aggregation of the smallest sugar, glycolaldehyde, was studied in a conformer-selective manner using high-resolution rotational spectroscopy. Two different dimer structures were observed. The most stable conformer reveals C2 -symmetry by forming two intermolecular hydrogen bonds, giving up the strong intramolecular hydrogen bonds of the monomers and thus showing high hydrogen bond selectivity. By analyzing the spectra of the (13) C and (18) O isotopologues of the dimer in natural abundance, we could precisely determine the heavy backbone structure of the dimer. Comparison to the monomer structure and the complex with water provides insight into intermolecular interactions. Despite hydrogen bonding being the dominant interaction, precise predictions from quantum-chemical calculations highly rely on the consideration of dispersion. PMID:27060475

  7. cis–trans-Amide isomerism of the 3,4-dehydroproline residue, the ‘unpuckered’ proline

    PubMed Central

    2016-01-01

    Summary Proline (Pro) is an outstanding amino acid in various biochemical and physicochemical perspectives, especially when considering the cis–trans isomerism of the peptidyl-Pro amide bond. Elucidation of the roles of Pro in chemical or biological systems and engineering of its features can be addressed with various Pro analogues. Here we report an experimental work investigating the basic physicochemical properties of two Pro analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans/cis ratios compared to that of Pro and 4-trifluoromethylproline derivatives. Finally we demonstrate that the 3,4-double bond in the investigated structures leads to an increase of the amide rotational barriers, presumably due to an interplay with the transition state. PMID:27340450

  8. Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability.

    PubMed

    Wu, R R; Rodgers, M T

    2016-06-21

    Our previous gas-phase infrared multiple photon dissociation action spectroscopy study of protonated 2'-deoxyadenosine and adenosine, [dAdo+H](+) and [Ado+H](+), found that both N3 and N1 protonated conformers are populated with the N3 protonated ground-state conformers predominant in the experiments. Therefore, N-glycosidic bond dissociation mechanisms of N3 and N1 protonated [dAdo+H](+) and [Ado+H](+) and the associated quantitative thermochemical values are investigated here using both experimental and theoretical approaches. Threshold collision-induced dissociation (TCID) of [dAdo+H](+) and [Ado+H](+) with Xe is studied using guided ion beam tandem mass spectrometry techniques. For both systems, N-glycosidic bond cleavage reactions are observed as the major dissociation pathways resulting in production of protonated adenine or elimination of neutral adenine. Electronic structure calculations are performed at the B3LYP/6-311+G(d,p) level of theory to probe the potential energy surfaces (PESs) for N-glycosidic bond cleavage of [dAdo+H](+) and [Ado+H](+). Relative energetics of the reactants, transition states, intermediates and products along the PESs for N-glycosidic bond cleavage are determined at the B3LYP/6-311+G(2d,2p), B3LYP-GD3BJ/6-311+G(2d,2p), and MP2(full)/6-311+G(2d,2p) levels of theory. The predicted N-glycosidic bond dissociation mechanisms for the N3 and N1 protonated species differ. Base rotation of the adenine residue enables formation of a strong N3H(+)O5' hydrogen-bonding interaction that stabilizes the N3 protonated species and its glycosidic bond. Comparison between experiment and theory indicates that the N3 protonated species determine the threshold energies, as excellent agreement between the measured and B3LYP computed activation energies (AEs) and reaction enthalpies (ΔHrxns) for N-glycosidic bond cleavage of the N3 protonated species is found. PMID:27240654

  9. Salt forms of the pharmaceutical amide dihydrocarbamazepine.

    PubMed

    Buist, Amanda R; Kennedy, Alan R

    2016-02-01

    Carbamazepine (CBZ) is well known as a model active pharmaceutical ingredient used in the study of polymorphism and the generation and comparison of cocrystal forms. The pharmaceutical amide dihydrocarbamazepine (DCBZ) is a less well known material and is largely of interest here as a structural congener of CBZ. Reaction of DCBZ with strong acids results in protonation of the amide functionality at the O atom and gives the salt forms dihydrocarbamazepine hydrochloride {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium chloride, C15H15N2O(+)·Cl(-)}, dihydrocarbamazepine hydrochloride monohydrate {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium chloride monohydrate, C15H15N2O(+)·Cl(-)·H2O} and dihydrocarbamazepine hydrobromide monohydrate {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium bromide monohydrate, C15H15N2O(+)·Br(-)·H2O}. The anhydrous hydrochloride has a structure with two crystallographically independent ion pairs (Z' = 2), wherein both cations adopt syn conformations, whilst the two hydrated species are mutually isostructural and have cations with anti conformations. Compared to neutral dihydrocarbamazepine structures, protonation of the amide group is shown to cause changes to both the molecular (C=O bond lengthening and C-N bond shortening) and the supramolecular structures. The amide-to-amide and dimeric hydrogen-bonding motifs seen for neutral polymorphs and cocrystalline species are replaced here by one-dimensional polymeric constructs with no direct amide-to-amide bonds. The structures are also compared with, and shown to be closely related to, those of the salt forms of the structurally similar pharmaceutical carbamazepine. PMID:26846502

  10. Amide-Substituted Titanocenes in Hydrogen-Atom Transfer Catalysis.

    PubMed

    Zhang, Yong-Qiang; Jakoby, Verena; Stainer, Katharina; Schmer, Alexander; Klare, Sven; Bauer, Mirko; Grimme, Stefan; Cuerva, Juan Manuel; Gansäuer, Andreas

    2016-01-22

    Two new catalytic systems for hydrogen-atom transfer (HAT) catalysis involving the N-H bonds of titanocene(III) complexes with pendant amide ligands are reported. In a monometallic system, a bifunctional catalyst for radical generation and reduction through HAT catalysis depending on the coordination of the amide ligand is employed. The pendant amide ligand is used to activate Crabtree's catalyst to yield an efficient bimetallic system for radical generation and HAT catalysis. PMID:26636435

  11. Conformational features of secondary N-cyclopropyl amides.

    PubMed

    González-de-Castro, Ángela; Broughton, Howard; Martínez-Pérez, José A; Espinosa, Juan F

    2015-04-17

    NMR studies in conjunction with ab initio calculations revealed unexpected conformational behavior of N-cyclopropylacetamide (1). This secondary amide displays 16-19% E-rotamer (cis) around the carbonyl-nitrogen bond in apolar solvents, in contrast to other aliphatic secondary acetamides in which significant E-rotamer populations are rare due to steric contacts between the substituents on the amide bond. In addition, 1 adopts an ortho conformation around the N-cPr bond instead of the anti conformation generally preferred by secondary acetamides. This distinct conformational behavior was also observed for other secondary N-cyclopropyl amides. PMID:25803271

  12. Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. Observation of a thermally accessible triplet state resulting from rotation around a main-group π bond.

    PubMed

    Kostenko, Arseni; Tumanskii, Boris; Karni, Miriam; Inoue, Shigeyoshi; Ichinohe, Masaaki; Sekiguchi, Akira; Apeloig, Yitzhak

    2015-10-01

    We report the first direct spectroscopic observation by electron paramagnetic resonance (EPR) spectroscopy of a triplet diradical that is formed in a thermally induced rotation around a main-group π bond, that is, the SiSi double bond of tetrakis(di-tert-butylmethylsilyl)disilene (1). The highly twisted ground-state geometry of singlet 1 allows access to the perpendicular triplet diradical 2 at moderate temperatures of 350-410 K. DFT-calculated zero-field splitting (ZFS) parameters of 2 accurately reproduce the experimentally observed half-field transition. Experiment and theory suggest a thermal equilibrium between 1 and 2 with a very low singlet-triplet energy gap of only 7.3 kcal mol(-1) . PMID:26297814

  14. Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling

    NASA Astrophysics Data System (ADS)

    Buchanan, Evan G.; James, William H.; Choi, Soo Hyuk; Guo, Li; Gellman, Samuel H.; Müller, Christian W.; Zwier, Timothy S.

    2012-09-01

    Single-conformation infrared spectra in the amide I and amide II regions have been recorded for a total of 34 conformations of three α-peptides, three β-peptides, four α/β-peptides, and one γ-peptide using resonant ion-dip infrared spectroscopy of the jet-cooled, isolated molecules. Assignments based on the amide NH stretch region were in hand, with the amide I/II data providing additional evidence in favor of the assignments. A set of 21 conformations that represent the full range of H-bonded structures were chosen to characterize the conformational dependence of the vibrational frequencies and infrared intensities of the local amide I and amide II modes and their amide I/I and amide II/II coupling constants. Scaled, harmonic calculations at the DFT M05-2X/6-31+G(d) level of theory accurately reproduce the experimental frequencies and infrared intensities in both the amide I and amide II regions. In the amide I region, Hessian reconstruction was used to extract local mode frequencies and amide I/I coupling constants for each conformation. These local amide I frequencies are in excellent agreement with those predicted by DFT calculations on the corresponding 13C = 18O isotopologues. In the amide II region, potential energy distribution analysis was combined with the Hessian reconstruction scheme to extract local amide II frequencies and amide II/II coupling constants. The agreement between these local amide II frequencies and those obtained from DFT calculations on the N-D isotopologues is slightly worse than for the corresponding comparison in the amide I region. The local mode frequencies in both regions are dictated by a combination of the direct H-bonding environment and indirect, "backside" H-bonds to the same amide group. More importantly, the sign and magnitude of the inter-amide coupling constants in both the amide I and amide II regions is shown to be characteristic of the size of the H-bonded ring linking the two amide groups. These amide I/I and

  15. Ground-State Distortion in N-Acyl-tert-butyl-carbamates (Boc) and N-Acyl-tosylamides (Ts): Twisted Amides of Relevance to Amide N-C Cross-Coupling.

    PubMed

    Szostak, Roman; Shi, Shicheng; Meng, Guangrong; Lalancette, Roger; Szostak, Michal

    2016-09-01

    Amide N-C(O) bonds are generally unreactive in cross-coupling reactions employing low-valent transition metals due to nN → π*C═O resonance. Herein we demonstrate that N-acyl-tert-butyl-carbamates (Boc) and N-acyl-tosylamides (Ts), two classes of acyclic amides that have recently enabled the development of elusive amide bond N-C cross-coupling reactions with organometallic reagents, are intrinsically twisted around the N-C(O) axis. The data have important implications for the design of new amide cross-coupling reactions with the N-C(O) amide bond cleavage as a key step. PMID:27480938

  16. Nickel-catalysed Suzuki-Miyaura coupling of amides

    NASA Astrophysics Data System (ADS)

    Weires, Nicholas A.; Baker, Emma L.; Garg, Neil K.

    2016-01-01

    The Suzuki-Miyaura coupling has become one of the most important and prevalent methods for the construction of C-C bonds. Although palladium catalysis has historically dominated the field, the use of nickel catalysis has become increasingly widespread because of its unique ability to cleave carbon-heteroatom bonds that are unreactive towards other transition metals. We report the first nickel-catalysed Suzuki-Miyaura coupling of amides, which proceeds by an uncommon cleavage of the amide C-N bond after N-tert-butoxycarbonyl activation. The methodology is mild, functional-group tolerant and can be strategically employed in sequential transition-metal-catalysed cross-coupling sequences to unite heterocyclic fragments. These studies demonstrate that amides, despite classically considered inert substrates, can be harnessed as synthons for use in reactions that form C-C bonds through cleavage of the C-N bond using non-precious metal catalysis.

  17. Copper-catalyzed direct amidation of heterocycles with N-fluorobenzenesulfonimide.

    PubMed

    Wang, Sichang; Ni, Zhangqin; Huang, Xin; Wang, Jichao; Pan, Yuanjiang

    2014-11-01

    A highly efficient amidation reaction of heterocycles with N-fluorobenzenesulfonimide (NFSI) has been developed, presumably proceeding via C-H bond activation. Cuprous iodide was employed as the catalyst, and various α-amidated heterocycle derivatives have been generated in good to excellent yields. This chemistry endowed an economic method of synthesis of valuable amidated heterocycles through a direct C-N bond-coupling processes. PMID:25310043

  18. Cytotoxic Amides from Fruits of Kawakawa, Macropiper excelsum.

    PubMed

    Lei, Jeremy; Burgess, Elaine J; Richardson, Alistair T B; Hawkins, Bill C; Baird, Sarah K; Smallfield, Bruce M; van Klink, John W; Perry, Nigel B

    2015-08-01

    Cytotoxic amides have been isolated from the fruits of the endemic New Zealand medicinal plant kawakawa, Macropiper excelsum (Piperaceae). The main amide was piperchabamide A and this is the first report of this rare compound outside the genus Piper. Eleven other amides were purified including two new compounds with the unusual 3,4-dihydro-1(2H)-pyridinyl group. The new compounds were fully characterized by 2D NMR spectroscopy, which showed a slow exchange between two rotamers about the amide bond, and they were chemically synthesized. In view of the antitumor activity of the related piperlongumine, all of these amides plus four synthetic analogs were tested for cytotoxicity. The most active was the piperine homolog piperdardine, with an IC50 of 14 µM against HT 29 colon cancer cells. PMID:26039266

  19. Energetics of hydrogen bonding in proteins: a model compound study.

    PubMed Central

    Habermann, S. M.; Murphy, K. P.

    1996-01-01

    Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-amide hydrogen bond is about twice that of the amide-hydroxyl. Additionally, the interaction of the hydroxyl group with water is seen most readily in its contributions to entropy and heat capacity changes. Surprisingly, the hydroxyl group shows weakly hydrophobic behavior in terms of these contributions. These results can be used to understand the effects of mutations on the stability of globular proteins. PMID:8819156

  20. Variable temperature 1H and 13C NMR study of restricted rotation in N,N-bis(2-hydroxyethyl)acetamide

    NASA Astrophysics Data System (ADS)

    Aitken, R. Alan; Smith, Melanja H.; Wilson, Heather S.

    2016-06-01

    N,N-bis(2-hydroxyethyl)acetamide shows restricted rotation about the amide bond in both 1H and 13C NMR spectra rendering the two hydroxyethyl groups non-equivalent. A variable temperature study in CD3SOCD3 allowed estimation of the free energy barrier to rotation as 75.6 ± 0.2 kJ mol-1. Previously published data in CDCl3 appears to be erroneous.

  1. The halogen bond between ethene and a simple perfluoroiodoalkane: C2H4\\ctdot ICF3 identified by broadband rotational spectroscopy

    NASA Astrophysics Data System (ADS)

    Stephens, Susanna L.; Mizukami, Wataru; Tew, David P.; Walker, Nicholas R.; Legon, Anthony C.

    2012-10-01

    An isolated complex of C2H4 and ICF3 has been generated in the gas phase and studied by chirped-pulse, Fourier transform microwave (CP-FTMW) spectroscopy. Ab initio calculations at the CCSD(T)(F12*)/VTZ level support the experimental work and further establish the dissociation energy, De, and dipole moment, μ, of the complex. Rotational constants, B0 and C0, the centrifugal distortion constant, ΔJ, nuclear quadrupole coupling constants, χaa (I) and (χbb(I)-χcc(I)) and the nuclear spin-rotation coupling constant Cbb(I) of the complex are determined from the experimental data. The iodine atom interacts with π-electrons on C2H4 resulting in the formation of a linear (∠(Csbnd I⋯*)) halogen bond (where * indicates the centre of the Cdbnd C bond) and a complex of Cs symmetry. The measured rotational constants allow the length of the halogen bond to be determined as 3.434(2) Å in the r0 geometry. The complex is formally an asymmetric top but with a very low barrier to internal rotation of C2H4 about the C3 axis defined by the CF3I sub-unit. Adopting an approach also used in a recent study of H2O⋯ICF3, other transitions are assigned using the Hamiltonian of a symmetric top molecule.

  2. Dynamic Behavior of N-Heterocyclic Carbene Boranes: Boron-Carbene Bonds in B,B-Disubstituted N,N-Dimethylimidazol-2-ylidene Boranes Have Substantial Rotation Barriers.

    PubMed

    Damodaran, Krishnan; Li, Xiben; Pan, Xiangcheng; Curran, Dennis P

    2015-05-01

    Dynamic NMR spectroscopy has been used to measure rotation barriers in five B,B-disubstituted 1,3-dimethylimidazol-2-ylidene boranes. The barriers are attributed to the sp(2)-sp(3) bond between C(1) of the N-heterocyclic carbene ring and the boron atom. Bonds to boron atoms bearing a thexyl (1,1,2-trimethylpropyl) group show especially high barriers, ranging from 75-86 kJ mol(-1). 2-Isopropyl-1,3,5-trimethylbenzene is used as a comparable to help understand the nature and magnitude of the barriers. PMID:25843519

  3. Atom-economic catalytic amide synthesis from amines and carboxylic acids activated in situ with acetylenes.

    PubMed

    Krause, Thilo; Baader, Sabrina; Erb, Benjamin; Gooßen, Lukas J

    2016-01-01

    Amide bond-forming reactions are of tremendous significance in synthetic chemistry. Methodological research has, in the past, focused on efficiency and selectivity, and these have reached impressive levels. However, the unacceptable amounts of waste produced have led the ACS GCI Roundtable to label 'amide bond formation avoiding poor atom economy' as the most pressing target for sustainable synthetic method development. In response to this acute demand, we herein disclose an efficient one-pot amide coupling protocol that is based on simple alkynes as coupling reagents: in the presence of a dichloro[(2,6,10-dodecatriene)-1,12-diyl]ruthenium catalyst, carboxylate salts of primary or secondary amines react with acetylene or ethoxyacetylene to vinyl ester intermediates, which undergo aminolysis to give the corresponding amides along only with volatile acetaldehyde or ethyl acetate, respectively. The new amide synthesis is broadly applicable to the synthesis of structurally diverse amides, including dipeptides. PMID:27282773

  4. Atom-economic catalytic amide synthesis from amines and carboxylic acids activated in situ with acetylenes

    PubMed Central

    Krause, Thilo; Baader, Sabrina; Erb, Benjamin; Gooßen, Lukas J.

    2016-01-01

    Amide bond-forming reactions are of tremendous significance in synthetic chemistry. Methodological research has, in the past, focused on efficiency and selectivity, and these have reached impressive levels. However, the unacceptable amounts of waste produced have led the ACS GCI Roundtable to label ‘amide bond formation avoiding poor atom economy' as the most pressing target for sustainable synthetic method development. In response to this acute demand, we herein disclose an efficient one-pot amide coupling protocol that is based on simple alkynes as coupling reagents: in the presence of a dichloro[(2,6,10-dodecatriene)-1,12-diyl]ruthenium catalyst, carboxylate salts of primary or secondary amines react with acetylene or ethoxyacetylene to vinyl ester intermediates, which undergo aminolysis to give the corresponding amides along only with volatile acetaldehyde or ethyl acetate, respectively. The new amide synthesis is broadly applicable to the synthesis of structurally diverse amides, including dipeptides. PMID:27282773

  5. Rotational isomerism about the 17(20)-bond of steroids and euphoids as shown by the crystal structures of euphol and tirucallol.

    PubMed Central

    Nes, W D; Wong, R Y; Benson, M; Landrey, J R; Nes, W R

    1984-01-01

    The influence of configuration at C-20 on rotation about the 17(20)-bond in steroids and euphoids was examined by x-ray crystallographic studies of the C-20 epimers euphol and tirucallol. The H atom on C-20 was in back next to C-18 in the crystal structures of both of the compounds, and C-22 was found to be cis-oriented ("left-handed") to C-13 in euphol and trans-oriented to it ("right-handed") in tirucallol. The results, which are consistent with the known left-handed crystal structure of 24(25)-dihydroeuphol and right-handed crystal structure of cholesterol and other natural sterols, lend further credence to the earlier suggestion that rotational isomerism at the 17(20)-bond can arise in C-20 epimers and that there is preference for an arrangement with the 20-H atom adjacent to C-18. PMID:6592593

  6. Rotational isomerism about the 17(20)-bond of steroids and euphoids as shown by the crystal structures of euphol and tirucallol.

    PubMed

    Nes, W D; Wong, R Y; Benson, M; Landrey, J R; Nes, W R

    1984-09-01

    The influence of configuration at C-20 on rotation about the 17(20)-bond in steroids and euphoids was examined by x-ray crystallographic studies of the C-20 epimers euphol and tirucallol. The H atom on C-20 was in back next to C-18 in the crystal structures of both of the compounds, and C-22 was found to be cis-oriented ("left-handed") to C-13 in euphol and trans-oriented to it ("right-handed") in tirucallol. The results, which are consistent with the known left-handed crystal structure of 24(25)-dihydroeuphol and right-handed crystal structure of cholesterol and other natural sterols, lend further credence to the earlier suggestion that rotational isomerism at the 17(20)-bond can arise in C-20 epimers and that there is preference for an arrangement with the 20-H atom adjacent to C-18. PMID:6592593

  7. Isotopic studies of trans- and cis-HOCO using rotational spectroscopy: Formation, chemical bonding, and molecular structures

    NASA Astrophysics Data System (ADS)

    McCarthy, Michael C.; Martinez, Oscar; McGuire, Brett A.; Crabtree, Kyle N.; Martin-Drumel, Marie-Aline; Stanton, John F.

    2016-03-01

    HOCO is an important intermediate in combustion and atmospheric processes because the OH + CO → H + CO2 reaction represents the final step for the production of CO2 in hydrocarbon oxidation, and theoretical studies predict that this reaction proceeds via various intermediates, the most important being this radical. Isotopic investigations of trans- and cis-HOCO have been undertaken using Fourier transform microwave spectroscopy and millimeter-wave double resonance techniques in combination with a supersonic molecular beam discharge source to better understand the formation, chemical bonding, and molecular structures of this radical pair. We find that trans-HOCO can be produced almost equally well from either OH + CO or H + CO2 in our discharge source, but cis-HOCO appears to be roughly two times more abundant when starting from H + CO2. Using isotopically labelled precursors, the OH + C18O reaction predominately yields HOC18O for both isomers, but H18OCO is observed as well, typically at the level of 10%-20% that of HOC18O; the opposite propensity is found for the 18OH + CO reaction. DO + C18O yields similar ratios between DOC18O and D18OCO as those found for OH + C18O, suggesting that some fraction of HOCO (or DOCO) may be formed from the back-reaction H + CO2, which, at the high pressure of our gas expansion, can readily occur. The large 13C Fermi-contact term (aF) for trans- and cis-HO13CO implicates significant unpaired electronic density in a σ-type orbital at the carbon atom, in good agreement with theoretical predictions. By correcting the experimental rotational constants for zero-point vibration motion calculated theoretically using second-order vibrational perturbation theory, precise geometrical structures have been derived for both isomers.

  8. Isotopic studies of trans- and cis-HOCO using rotational spectroscopy: Formation, chemical bonding, and molecular structures.

    PubMed

    McCarthy, Michael C; Martinez, Oscar; McGuire, Brett A; Crabtree, Kyle N; Martin-Drumel, Marie-Aline; Stanton, John F

    2016-03-28

    HOCO is an important intermediate in combustion and atmospheric processes because the OH + CO → H + CO2 reaction represents the final step for the production of CO2 in hydrocarbon oxidation, and theoretical studies predict that this reaction proceeds via various intermediates, the most important being this radical. Isotopic investigations of trans- and cis-HOCO have been undertaken using Fourier transform microwave spectroscopy and millimeter-wave double resonance techniques in combination with a supersonic molecular beam discharge source to better understand the formation, chemical bonding, and molecular structures of this radical pair. We find that trans-HOCO can be produced almost equally well from either OH + CO or H + CO2 in our discharge source, but cis-HOCO appears to be roughly two times more abundant when starting from H + CO2. Using isotopically labelled precursors, the OH + C(18)O reaction predominately yields HOC(18)O for both isomers, but H(18)OCO is observed as well, typically at the level of 10%-20% that of HOC(18)O; the opposite propensity is found for the (18)OH + CO reaction. DO + C(18)O yields similar ratios between DOC(18)O and D(18)OCO as those found for OH + C(18)O, suggesting that some fraction of HOCO (or DOCO) may be formed from the back-reaction H + CO2, which, at the high pressure of our gas expansion, can readily occur. The large (13)C Fermi-contact term (aF) for trans- and cis-HO(13)CO implicates significant unpaired electronic density in a σ-type orbital at the carbon atom, in good agreement with theoretical predictions. By correcting the experimental rotational constants for zero-point vibration motion calculated theoretically using second-order vibrational perturbation theory, precise geometrical structures have been derived for both isomers. PMID:27036445

  9. Amide N-oxides: an ab initio molecular orbital study

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; DuBois, Thomas D.

    2001-06-01

    There are no known examples of amide N-oxides. The present study employs ab initio molecular orbital calculations at the 6-3G ∗ level to explore potential target molecules in this class. Bridgehead bicyclic lactams appear to be attractive targets for oxidation to form the corresponding N-oxides because they have reduced (or zero) amide resonance energy. The amide N-oxide linkage is predicted to have a ca. 9-10 kcal/mol rotational barrier due to eclipsing of nonbonded oxygen atoms in the transition state. The linkage has a nearly flat conformational ( ΦON-CO) profile in the range 120-240° and this suggests that a very sterically hindered acyclic amide N-oxide may be a practical synthetic target. The oxidation of strained amides is calculated to be highly exothermic if dimethyldioxirane is employed. This reagent is predicted to react appreciably exothermically with normal, stable amides such as N, N-dimethylacetamide, thus offering the potential for generating and studying such relatively unstable amide N-oxides at low temperatures.

  10. Reaction of arynes with vinylogous amides: nucleophilic addition to the ortho-quinodimethide intermediate.

    PubMed

    Li, Ran; Wang, Xuemei; Wei, Zhibin; Wu, Chunrui; Shi, Feng

    2013-09-01

    The reaction of arynes with vinylogous amides containing no free N-H bonds proceeds in a [2 + 2] cycloaddition fashion at ambient temperature. The electronic properties of the vinylogous amides allow for the cycloadducts undergoing a facile ring-opening process, leading to electronically biased ortho-quinodimethide intermediates. Subsequent nucleophilic addition with alcohols affords 2-substituted benzaldehydes or ketones. PMID:23957502

  11. On the unconventional amide I band in acetanilide

    NASA Astrophysics Data System (ADS)

    Tenenbaum, Alexander; Campa, Alessandro; Giansanti, Andrea

    1987-04-01

    We developed a new model to study the molecular dynamics of the acetanilide (ACN) crystal by computer simulation. Low-frequency oscillations of the molecules as a whole were considered with high-frequency vibrations of the amidic degrees of freedom involved in hydrogen bonding. The low-temperature power spectrum has two peaks, shifted by 15 cm -1, in the region of the amide I band: one of them corresponds to the so-called anomalous amide I band in the IR and Raman spectra of ACN. We found that this peak is due to the coupling of the low-frequency motion in the chain of molecules with the motion of the hydrogen-bonded protons, at variance with current suggestions.

  12. Evaluation of the Ser-His Dipeptide, a Putative Catalyst of Amide and Ester Hydrolysis.

    PubMed

    MacDonald, Melissa J; Lavis, Luke D; Hilvert, Donald; Gellman, Samuel H

    2016-08-01

    Efficient hydrolysis of amide bonds has long been a reaction of interest for organic chemists. The rate constants of proteases are unmatched by those of any synthetic catalyst. It has been proposed that a dipeptide containing serine and histidine is an effective catalyst of amide hydrolysis, based on an apparent ability to degrade a protein. The capacity of the Ser-His dipeptide to catalyze the hydrolysis of several discrete ester and amide substrates is investigated using previously described conditions. This dipeptide does not catalyze the hydrolysis of amide or unactivated ester groups in any of the substrates under the conditions evaluated. PMID:27400366

  13. Polymer Amide as an Early Topology

    PubMed Central

    McGeoch, Julie E. M.; McGeoch, Malcolm W.

    2014-01-01

    Hydrophobic polymer amide (HPA) could have been one of the first normal density materials to accrete in space. We present ab initio calculations of the energetics of amino acid polymerization via gas phase collisions. The initial hydrogen-bonded di-peptide is sufficiently stable to proceed in many cases via a transition state into a di-peptide with an associated bound water molecule of condensation. The energetics of polymerization are only favorable when the water remains bound. Further polymerization leads to a hydrophobic surface that is phase-separated from, but hydrogen bonded to, a small bulk water complex. The kinetics of the collision and subsequent polymerization are discussed for the low-density conditions of a molecular cloud. This polymer in the gas phase has the properties to make a topology, viz. hydrophobicity allowing phase separation from bulk water, capability to withstand large temperature ranges, versatility of form and charge separation. Its flexible tetrahedral carbon atoms that alternate with more rigid amide groups allow it to deform and reform in hazardous conditions and its density of hydrogen bonds provides adhesion that would support accretion to it of silicon and metal elements to form a stellar dust material. PMID:25048204

  14. Structural measurements of hydrogen-bonded van der Waals dimers and trimers by rotational coherence spectroscopy: 2,5-diphenyloxadiazole with argon, methane, water, and alcohols

    NASA Astrophysics Data System (ADS)

    Troxler, Thomas; Smith, Philip G.; Stratton, John R.; Topp, Michael R.

    1994-01-01

    Picosecond time-resolved polarized fluorescence experiments involving time-correlated single-photon counting have studied rotational coherence phenomena of hydrogen-bonded and other molecular aggregates in their lowest excited singlet states. The experiments are supported by detailed simulations. Using the molecule 2,5-diphenyl-1,3,4-oxadiazole (PPD) as a host species, experiments have compared van der Waals aggregates with Ar1,2, (CH4)1,2, (H2O)1,2, (CH3OH)1,2, (C2H5OH)1, and (1-C3H7OH)1. Bare PPD, and the argon and methane aggregates all exhibit prominent J-type recurrences. The resulting sums of rotational constants (B+C) are consistent with center-of-mass-bound, three-dimensional structures, having out-of-plane distances for the attached species of 3.3-3.5 Å. The 1:2 aggregates involving argon and methane exhibit additive spectral shifts and nearly additive rotational recurrence times. This shows that the sites for addition of consecutive species are equivalent. Calculations of rotational constants confirm these findings. All except the Ar 1:2 cluster exist close to the prolate symmetric top limit. On the other hand, the excitation spectra of complexes involving hydrogen-bonding species all show small complexation shifts at the 1:1 level and disproportionately larger shifts at the 1:2 level. Similar nonadditive behavior is seen for the rotational recurrence transients. Hydrogen-bonded species differ from the nonpolar cases, since they show both prominent C-type and J-type transients. This shows that these species all differ significantly from prolate symmetric tops. Detailed simulations reveal that all of the hydrogen-bonding species produce aggregates that involve a single hydrogen bond to one of the PPD nitrogen atoms. This imposes a planar type of structure on the 1:1 water and methanol complexes. On the other hand, the aggregates methanol 1:2, ethanol 1:1, and propanol 1:1 all involve a distinct out-of-plane twist, consistent with the increasing influence

  15. n→π* Interactions Are Competitive with Hydrogen Bonds.

    PubMed

    Newberry, Robert W; Orke, Samuel J; Raines, Ronald T

    2016-08-01

    Because carbonyl groups can participate in both hydrogen bonds and n→π* interactions, these two interactions likely affect one another. Herein, enhancement of an amidic n→π* interaction is shown to reduce the ability of β-keto amides to tautomerize to the enol, indicating decreased hydrogen-bonding capacity of the amide carbonyl group. Thus, an n→π* interaction can have a significant effect on the strength of a hydrogen bond to the same carbonyl group. PMID:27409515

  16. Encapsulation of Protonated Diamines in a Water-Soluble Chiral, Supramolecular Assembly Allows for Measurement of Hydrogen-Bond Breaking Followed by Nitrogen Inversion/Rotation (NIR)

    SciTech Connect

    Meux, Susan C.; Pluth, Michael D.; Bergman, Robert G.; Raymond, Kenneth N.

    2007-09-19

    Amine nitrogen inversion, difficult to observe in aqueous solution, is followed in a chiral, supramolecular host molecule with purely-rotational T-symmetry that reduces the local symmetry of encapsulated monoprotonated diamines and enables the observation and quantification of {Delta}G{double_dagger} for the combined hydrogen-bond breaking and nitrogen inversion rotation (NIR) process. Free energies of activation for the combined hydrogen-bond breaking and NIR process inside of the chiral assembly were determined by the NMR coalescence method. Activation parameters for ejection of the protonated amines from the assembly confirm that the NIR process responsible for the coalescence behavior occurs inside of the assembly rather than by a guest ejection/NIR/re-encapsulation mechanism. For one of the diamines, N,N,N{prime},N{prime}-tetramethylethylenediamine (TMEDA), the relative energy barriers for the hydrogen-bond breaking and NIR process were calculated at the G3(MP2)//B3LYP/6-31++G(d,p) level of theory, and these agreed well with the experimental data.

  17. MS/MS Digital Readout: Analysis of Binary Information Encoded in the Monomer Sequences of Poly(triazole amide)s.

    PubMed

    Amalian, Jean-Arthur; Trinh, Thanh Tam; Lutz, Jean-François; Charles, Laurence

    2016-04-01

    Tandem mass spectrometry was evaluated as a reliable sequencing methodology to read codes encrypted in monodisperse sequence-coded oligo(triazole amide)s. The studied oligomers were composed of monomers containing a triazole ring, a short ethylene oxide segment, and an amide group as well as a short alkyl chain (propyl or isobutyl) which defined the 0/1 molecular binary code. Using electrospray ionization, oligo(triazole amide)s were best ionized as protonated molecules and were observed to adopt a single charge state, suggesting that adducted protons were located on every other monomer unit. Upon collisional activation, cleavages of the amide bond and of one ether bond were observed to proceed in each monomer, yielding two sets of complementary product ions. Distribution of protons over the precursor structure was found to remain unchanged upon activation, allowing charge state to be anticipated for product ions in the four series and hence facilitating their assignment for a straightforward characterization of any encoded oligo(triazole amide)s. PMID:26950162

  18. Synthesis, spectroscopic and structural perspective of new ferrocenyl amides

    NASA Astrophysics Data System (ADS)

    Etter, Martin; Nigar, Asifa; Ali, Naveed Zafar; Akhter, Zareen; Dinnebier, Robert E.

    2016-05-01

    Two new ferrocene derivatives with amide linkages were synthesized by the condensation of 4-ferrocenylaniline with n-alkyl acid chloride derivatives as pristine orange solids in good yields. FTIR and 1H/13C NMR studies have confirmed the basic structure of the molecules with the involvement of intermolecular H-bonding, which together with the ferrocene-like packing ensures the stability of the crystal structure. Crystal structures for both compounds were solved by Rietveld refinements of high resolution X-ray powder diffraction data. The XRD results show that both compounds crystallize in the monoclinic space group P21/c. The primary feature of the crystal structure is a double layer of ferrocenyl groups stretched out in the b-c -plane perpendicular to the a-axis, with packing of the ferrocenyl groups occurring in a manner similar to that of pure ferrocene. Despite the close structural similarity, both compounds differ in the optimized geometry of respective Ferrocene conformers. The Cp rings are eclipsed for one Ferrocene conformer and close to staggered for the other, owing to the low energy barrier for the rotation of a cyclopentadienyl ring relative to the rest of the molecule.

  19. Vibrational lifetimes of protein amide modes

    SciTech Connect

    Peterson, K.A.; Rella, C.A.

    1995-12-31

    Measurement of the lifetimes of vibrational modes in proteins has been achieved with a single frequency infrared pump-probe technique using the Stanford Picosecond Free-electron Laser, These are the first direct measurements of vibrational dynamics in the polyamide structure of proteins. In this study, modes associated with the protein backbone are investigated. Results for the amide I band, which consists mainly of the stretching motion of the carbonyl unit of the amide linkage, show that relaxation from the first vibrational excited level (v=1) to the vibrational ground state (v=0) occurs within 1.5 picoseconds with apparent first order kinetics. Comparison of lifetimes for myoglobin and azurin, which have differing secondary structures, show a small but significant difference. The lifetime for the amide I band of myoglobin is 300 femtoseconds shorter than for azurin. Further measurements are in progress on other backbone vibrational modes and on the temperature dependence of the lifetimes. Comparison of vibrational dynamics for proteins with differing secondary structure and for different vibrational modes within a protein will lead to a greater understanding of energy transfer and dissipation in biological systems. In addition, these results have relevance to tissue ablation studies which have been conducted with pulsed infrared lasers. Vibrational lifetimes are necessary for calculating the rate at which the energy from absorbed infrared photons is converted to equilibrium thermal energy within the irradiated volume. The very fast vibrational lifetimes measured here indicate that mechanisms which involve direct vibrational up-pumping of the amide modes with consecutive laser pulses, leading to bond breakage or weakening, are not valid.

  20. Intramolecular hydrogen bonds: ab initio Car Parrinello simulations of arylamide torsions

    NASA Astrophysics Data System (ADS)

    Doerksen, Robert J.; Chen, Bin; Klein, Michael L.

    2003-10-01

    Gas-phase, room temperature Car-Parrinello molecular dynamics simulations using the HCTH density functional are reported for the arylamides acetanilide ( 1) and ortho-methylthioacetanilide ( 2). The simulations show that in 1, rotation around the ring-amide bond is relatively unrestricted. By contrast, in 2 the methylthio side chain encourages the amide to be directed with N-H pointing toward S, not to flip by 360°, and furthermore to remain close to coplanar with the benzene ring. Because of an intramolecular N-H⋯S hydrogen bond, the N-H stretch frequency of 2 is red-shifted by ˜78 cm -1 compared to that of 1.

  1. The temperature dependent amide I band of crystalline acetanilide

    NASA Astrophysics Data System (ADS)

    Cruzeiro, Leonor; Freedman, Holly

    2013-10-01

    The temperature dependent anomalous peak in the amide I band of crystalline acetanilide is thought to be due to self-trapped states. On the contrary, according to the present model, the anomalous peak comes from the fraction of ACN molecules strongly hydrogen-bonded to a neighboring ACN molecule, and its intensity decreases because, on average, this fraction decreases as temperature increases. This model provides, for the first time, an integrated and theoretically consistent view of the temperature dependence of the full amide I band and a qualitative explanation of some of the features of nonlinear pump-probe experiments.

  2. Copper-Catalyzed Carbonylative Coupling of Cycloalkanes and Amides.

    PubMed

    Li, Yahui; Dong, Kaiwu; Zhu, Fengxiang; Wang, Zechao; Wu, Xiao-Feng

    2016-06-13

    Carbonylation reactions are a most powerful method for the synthesis of carbonyl-containing compounds. However, most known carbonylation procedures still require noble-metal catalysts and the use of activated compounds and good nucleophiles as substrates. Herein, we developed a copper-catalyzed carbonylative transformation of cycloalkanes and amides. Imides were prepared in good yields by carbonylation of a C(sp(3) )-H bond of the cycloalkane with the amides acting as weak nucleophiles. Notably, this is the first report of copper-catalyzed carbonylative C-H activation. PMID:27167881

  3. Determination of the bond-angle distribution in vitreous B{sub 2}O{sub 3} by {sup 11}B double rotation (DOR) NMR spectroscopy

    SciTech Connect

    Hung, I.; Howes, A.P.; Parkinson, B.G.; Anupold, T.; Samoson, A.; Brown, S.P.; Harrison, P.F.; Holland, D.; Dupree, R.

    2009-09-15

    The B-O-B bond angle distributions for both ring and non-ring boron sites in vitreous B{sub 2}O{sub 3} have been determined by {sup 11}B double rotation (DOR) NMR and multiple-quantum (MQ) DOR NMR. The [B{sub 3}O{sub 6}] boroxol rings are observed to have a mean internal B-O-B angle of 120.0+-0.7 deg. with a small standard deviation, sigma{sub R}=3.2+-0.4 deg., indicating that the rings are near-perfect planar, hexagonal structures. The rings are linked predominantly by non-ring [BO{sub 3}] units, which share oxygens with the boroxol ring, with a mean B{sub ring}-O-B{sub non-ring} angle of 135.1+-0.6 deg. and sigma{sub NR}=6.7+-0.4 deg. In addition, the fraction of boron atoms, f, which reside in the boroxol rings has been measured for this sample as f=0.73+-0.01. - Graphical abstract: Connectivities and B-O-B bond angle distributions of ring and non-ring boron atoms in v-B{sub 2}O{sub 3} have been determined by {sup 11}B double rotation (DOR) NMR, multiple-quantum (MQ) DOR NMR and spin-diffusion DOR. Near-perfect planar, hexagonal [B{sub 3}O{sub 6}] boroxol rings are shown to be present. Display Omitted

  4. Kinetic isotope effects support the twisted amide mechanism of Pin1 peptidyl-prolyl isomerase.

    PubMed

    Mercedes-Camacho, Ana Y; Mullins, Ashley B; Mason, Matthew D; Xu, Guoyan G; Mahoney, Brendan J; Wang, Xingsheng; Peng, Jeffrey W; Etzkorn, Felicia A

    2013-11-01

    The Pin1 peptidyl-prolyl isomerase catalyzes isomerization of pSer/pThr-Pro motifs in regulating the cell cycle. Peptide substrates, Ac-Phe-Phe-phosphoSer-Pro-Arg-p-nitroaniline, were synthesized in unlabeled form, and with deuterium-labeled Ser-d3 and Pro-d7 amino acids. Kinetic data were collected as a function of Pin1 concentration to measure kinetic isotope effects (KIEs) on catalytic efficiency (kcat/Km). The normal secondary (2°) KIE value measured for the Ser-d3 substrate (kH/kD = 1.6 ± 0.2) indicates that the serine carbonyl does not rehybridize from sp(2) to sp(3) in the rate-determining step, ruling out a nucleophilic addition mechanism. The normal 2° KIE can be explained by hyperconjugation between Ser α-C-H/D and C═O and release of steric strain upon rotation of the amide bond from cis to syn-exo. The inverse 2° KIE value (kH/kD = 0.86 ± 0.08) measured for the Pro-d7 substrate indicates rehybridization of the prolyl nitrogen from sp(2) to sp(3) during the rate-limiting step of isomerization. No solvent kinetic isotope was measured by NMR exchange spectroscopy (kH2O/kD2O = 0.92 ± 0.12), indicating little or no involvement of exchangeable protons in the mechanism. These results support the formation of a simple twisted amide transition state as the mechanism for peptidyl prolyl isomerization catalyzed by Pin1. A model of the reaction mechanism is presented using crystal structures of Pin1 with ground state analogues and an inhibitor that resembles a twisted amide transition state. PMID:24116866

  5. Kinetic Isotope Effects Support the Twisted Amide Mechanism of Pin1 Peptidyl-Prolyl Isomerase

    PubMed Central

    Mercedes-Camacho, Ana Y.; Mullins, Ashley B.; Mason, Matthew D.; Xu, Guoyan G.; Mahoney, Brendan J.; Wang, Xingsheng; Peng, Jeffrey W.; Etzkorn, Felicia A.

    2013-01-01

    The Pin1 peptidyl-prolyl isomerase (PPIase) catalyzes isomerization of pSer/pThr-Pro motifs in regulating the cell cycle. Peptide substrates, Ac–Phe–Phe–phosphoSer–Pro–Arg–p-nitroaniline, were synthesized in unlabeled form, and with deuterium labeled Ser-d3 and Pro-d7 amino acids. Kinetic data was collected as a function of Pin1 concentration to measure kinetic isotope effects (KIE) on catalytic efficiency (kcat/Km). The normal secondary (2°) KIE value measured for the Ser-d3 substrate (kH/kD = 1.6 ± 0.2) indicates that the serine carbonyl does not rehybridize from sp2 to sp3 in the rate-determining step, ruling out a nucleophilic addition mechanism. The normal 2° KIE can be explained by hyperconjugation between Ser α-C–H/D and C=O, and release of steric strain upon rotation of the amide bond from cis to syn-exo. The inverse 2° KIE value (kH/kD = 0.86 ± 0.08) measured for the Pro-d7 substrate indicates rehybridization of the prolyl nitrogen from sp2 to sp3 during the rate-limiting step of isomerization. No solvent kinetic isotope was measured by NMR exchange spectroscopy (EXSY) (kH2O/kD2O = 0.92 ± 0.12), indicating little or no involvement of exchangeable protons in the mechanism. These results support the formation of a simple twisted-amide transition state as the mechanism for peptidyl prolyl isomerization catalyzed by Pin1. A model of the reaction mechanism is presented using crystal structures of Pin1 with ground state analogues and an inhibitor that resembles a twisted amide transition state. PMID:24116866

  6. Mechanistic Insights into Carbonyl-Directed Rhodium-Catalyzed Hydroboration: ab Initio Study of a Cyclic γ,δ-Unsaturated Amide.

    PubMed

    Yang, Zhao-Di; Pal, Rhitankar; Hoang, Gia L; Zeng, Xiao Cheng; Takacs, James M

    2014-03-01

    A two-point binding mechanism for the cationic rhodium(I)-catalyzed carbonyl-directed catalytic asymmetric hydroboration of a cyclic γ,δ-unsaturated amide is investigated using density functional theory. Geometry optimizations and harmonic frequency calculations for the model reaction are carried out using the basis set 6-31+G** for C, O, P, B, N, and H and LANL2DZ for Rh atoms. The Gibbs free energy of each species in THF solvent is obtained based on the single-point energy computed using the PCM model at the ECP28MWB/6-311+G(d,p) level plus the thermal correction to Gibbs free energy by deducting translational entropy contribution. The Rh-catalyzed reaction cycle involves the following sequence of events: (1) chelation of the cyclic γ,δ-unsaturated amide via alkene and carbonyl complexation in a model active catalytic species, [Rh(L2)2S2](+), (2) oxidative addition of pinacol borane (pinBH), (3) migratory insertion of the alkene double bond into Rh-H (preferred pathway) or Rh-B bond, (4) isomerization of the resulting intermediate, and finally, (5) reductive elimination to form the B-C or H-C bond with regeneration of the catalyst. Free energy profiles for potential pathways leading to the major γ-borylated product are computed and discussed in detail. The potential pathways considered include (1) pathways proceeding via migratory insertion into the Rh-H bond (pathways I, I-1, and I-2), (2) a potential pathway proceeding via migratory insertion into the Rh-B bond (pathway II), and two potential competing routes to a β-borylated byproduct (pathway III). The results find that the Rh-H migratory insertion pathway I-2, followed in sequence by an unanticipated isomerization via amide rotation and reductive elimination, is the most favorable reaction pathway. A secondary consequence of amide rotation is access to a competing β-hydride elimination pathway. The pathways computed in this study are supported by and help explain related experimental results. PMID

  7. The interplay of hydrogen bonding and dispersion in phenol dimer and trimer: structures from broadband rotational spectroscopy.

    PubMed

    Seifert, Nathan A; Steber, Amanda L; Neill, Justin L; Pérez, Cristóbal; Zaleski, Daniel P; Pate, Brooks H; Lesarri, Alberto

    2013-07-21

    The structures of the phenol dimer and phenol trimer complexes in the gas phase have been determined using chirped-pulse Fourier transform microwave spectroscopy in the 2-8 GHz band. All fourteen (13)C and (18)O phenol dimer isotopologues were assigned in natural abundance. A full heavy atom experimental substitution structure was determined, and a least-squares fit ground state r0 structure was determined by proper constraint of the M06-2X/6-311++g(d,p) ab initio structure. The structure of phenol dimer features a water dimer-like hydrogen bond, as well as a cooperative contribution from inter-ring dispersion. Comparisons between the experimental structure and previously determined experimental structures, as well as ab initio structures from various levels of theory, are discussed. For phenol trimer, a C3 symmetric barrel-like structure is found, and an experimental substitution structure was determined via measurement of the six unique (13)C isotopologues. The least-squares fit rm((1)) structure reveals a similar interplay between hydrogen bonding and dispersion in the trimer, with water trimer-like hydrogen bonding and C-H···π interactions. PMID:23749053

  8. Synthesis of amide-functionalized cellulose esters by olefin cross-metathesis.

    PubMed

    Meng, Xiangtao; Edgar, Kevin J

    2015-11-01

    Cellulose esters with amide functionalities were synthesized by cross-metathesis (CM) reaction of terminally olefinic esters with different acrylamides, catalyzed by Hoveyda-Grubbs 2nd generation catalyst. Chelation by amides of the catalyst ruthenium center caused low conversions using conventional solvents. The effects of both solvent and structure of acrylamide on reaction conversion were investigated. While the inherent tendency of acrylamides to chelate Ru is governed by the acrylamide N-substituents, employing acetic acid as a solvent significantly improved the conversion of certain acrylamides, from 50% to up to 99%. Homogeneous hydrogenation using p-toluenesulfonyl hydrazide successfully eliminated the α,β-unsaturation of the CM products to give stable amide-functionalized cellulose esters. The amide-functionalized product showed higher Tg than its starting terminally olefinic counterpart, which may have resulted from strong hydrogen bonding interactions of the amide functional groups. PMID:26256383

  9. Preparation and Evaluation at the Delta Opioid Receptor of a Series of Linear Leu-Enkephalin Analogues Obtained by Systematic Replacement of the Amides

    PubMed Central

    2013-01-01

    Leu-enkephalin analogues, in which the amide bonds were sequentially and systematically replaced either by ester or N-methyl amide bonds, were prepared using classical organic chemistry as well as solid phase peptide synthesis (SPPS). The peptidomimetics were characterized using competition binding, ERK1/2 phosphorylation, receptor internalization, and contractility assays to evaluate their pharmacological profile over the delta opioid receptor (DOPr). The lipophilicity (LogD7.4) and plasma stability of the active analogues were also measured. Our results revealed that the last amide bond can be successfully replaced by either an ester or an N-methyl amide bond without significantly decreasing the biological activity of the corresponding analogues when compared to Leu-enkephalin. The peptidomimetics with an N-methyl amide function between residues Phe and Leu were found to be more lipophilic and more stable than Leu-enkephalin. Findings from the present study further revealed that the hydrogen-bond donor properties of the fourth amide of Leu-enkephalin are not important for its biological activity on DOPr. Our results show that the systematic replacement of amide bonds by isosteric functions represents an efficient way to design and synthesize novel peptide analogues with enhanced stability. Our findings further suggest that such a strategy can also be useful to study the biological roles of amide bonds. PMID:23650868

  10. Sterically-controlled intermolecular Friedel-Crafts acylation with twisted amides via selective N-C cleavage under mild conditions.

    PubMed

    Liu, Yongmei; Meng, Guangrong; Liu, Ruzhang; Szostak, Michal

    2016-05-21

    Highly chemoselective Friedel-Crafts acylation with twisted amides under mild conditions is reported for the first time. The reaction shows high functional group tolerance, obviating the need for preformed sensitive organometallic reagents and expensive transition metal catalysts. The high reactivity of amides is switched on by ground-state steric distortion to disrupt the amide bond nN→πCO* resonance as a critical design feature. Conceptually, this new acid-promoted mechanism of twisted amides provides direct access to bench-stable acylating reagents under mild, metal-free conditions. PMID:27139813

  11. Bifunctional Brønsted Base Catalyzes Direct Asymmetric Aldol Reaction of α-Keto Amides.

    PubMed

    Echave, Haizea; López, Rosa; Palomo, Claudio

    2016-03-01

    The first enantioselective direct cross-aldol reaction of α-keto amides with aldehydes, mediated by a bifunctional ureidopeptide-based Brønsted base catalyst, is described. The appropriate combination of a tertiary amine base and an aminal, and urea hydrogen-bond donor groups in the catalyst structure promoted the exclusive generation of the α-keto amide enolate which reacted with either non-enolizable or enolizable aldehydes to produce highly enantioenriched polyoxygenated aldol adducts without side-products resulting from dehydration, α-keto amide self-condensation, aldehyde enolization, and isotetronic acid formation. PMID:26835655

  12. Stereoselective Arene-Forming Aldol Condensation: Synthesis of Axially Chiral Aromatic Amides.

    PubMed

    Fäseke, Vincent C; Sparr, Christof

    2016-06-13

    The increasing awareness of the importance of amide atropisomers prompts the development of novel strategies for their selective preparation. Described herein is a method for the enantioselective synthesis of atropisomeric aromatic amides by an amine-catalyzed arene-forming aldol condensation. The high reactivity of the glyoxylic amide substrates enables a remarkably efficient construction of a new aromatic ring, which proceeds within minutes at ambient temperature to afford products with excellent stereoselectivity. The high rotational barriers of the reduced products highlight the utility of this stable, spatially organized chiral scaffold. PMID:27166995

  13. A molecular orbital study of pyridine and the rotation about the CC bond in 4-vinylpyridine

    NASA Astrophysics Data System (ADS)

    Bock, Charles W.; Trachtman, Mendel; George, Philip

    1986-06-01

    The geometry and energy of pyridine and the planar conformer of 4-vinylpyridine have been calculated using the 6-31G basis set. The distortion of the pyridyl ring brought about by the vinyl substitution is compared to the distortion of the phenyl ring in styrene. Δ ET for the exchange reaction, 4-vinylpyridine + benzene → pyridine + styrene, is very small, 1.73 kJ mol -1, showing that such additional stabilization as there may be in the two vinyl derivatives relative to that in the parent molecules is almost identical. The geometry and energy of 4-vinyl-pyridine have also been calculated as a function of the C βC αC 4C 5 dihedral angle (φ = 0°, 30°, and 90°) assuming that the vinyl group and pyridyl group remain planar but otherwise with full geometry optimization. The torsional potential energy curve is almost identical to that calculated for styrene (Bock, Trachtman and George, 1985), which, in turn, was found to follow closely the experimental curve derived from single vibronic level fluorescence and other spectroscopic data. The curve has a very flat minimum at φ = 0° with a barrier height of 12.7 kJ mol -1. The changes in key geometrical parameters as the planar conformer is converted into the 90°-gauche conformer are likewise very similar to those in styrene, as are the changes in total atomic charge throughout the molecule, despite the profound differences in charge distribution in the two ring systems. Utilizing the increments between the calculated and experimental bond lengths for pyridine and trans-1,3-butadiene an experimental geometry is predicted for 4-vinylpyridine; and the "superimposition hypothesis", proposed by Domenicano and Murray-Rust (1979) for para-disubstituted benzene derivatives, is tested using the 6-31G optimized geometries for pyridine and styrene.

  14. Solvent-induced Mn(II)/Zn(II)/Co(II) organopolymolybdate compounds constructed by bis-pyridyl-bis-amide ligands through the Mo-N bond: synthesis, structures and properties.

    PubMed

    Xu, Na; Zhang, Ju-Wen; Wang, Xiu-Li; Liu, Guo-Cheng; Li, Tian-Jiao

    2016-01-14

    Three transition metal organopolymolybdate hybrid compounds, namely, H2[Mn(H2O)4L3(γ-Mo8O26)] 8H2O (), H[M2(CH3O)(H2O)6L3(γ-Mo8O26)] [M = Zn () and Co ()] [L = 1,4-bis(3-pyridinecarboxamido)benzene] have been synthesized under solvothermal conditions and characterized by IR spectroscopy, TG analysis, powder XRD and single-crystal X-ray diffraction. Compounds were obtained by the one-pot method, and the mixture of methanol and water with different ratios was used as the solvent. In compound , the γ-Mo8 anions were connected with pyridine groups of ligand L by the Mo-N bond, forming an uncommon 1D γ-Mo8-L chain. The adjacent chains were connected by [MnL2(H2O)4](2+) moieties through hydrogen bonding interaction to construct a 2D supramolecular network. Compounds and are isostructural, which show a 3D 2,4,6-connected {4(4)·6(2)}{4(4)·6(6)·8(4)·10}{6} framework. The γ-Mo8 anions were connected by [M(H2O)2(CH3O)](+) [M = Zn () and Co ()] subunits forming 1D M-Mo8 chains, which were connected by [ML2(H2O)4](2+) moieties to construct a 2D layer. In compounds and , there also exist the same 1D γ-Mo8-L chains as in , which extended the 2D networks to 3D frameworks. The Mo-N bond with pyridyl groups was formed under the solvothermal conditions, which is scarcely reported to our knowledge. The effect of the solvent on the assembly of the title compounds and the formation of the Mo-N bond, as well as the role of metal-organic moieties on the construction of diverse organopolymolybdate compounds have been discussed in detail. Furthermore, the electrochemical and photocatalytic properties of have been investigated. PMID:26631431

  15. Diaminopimelic Acid Amidation in Corynebacteriales

    PubMed Central

    Levefaudes, Marjorie; Patin, Delphine; de Sousa-d'Auria, Célia; Chami, Mohamed; Blanot, Didier; Hervé, Mireille; Arthur, Michel; Houssin, Christine; Mengin-Lecreulx, Dominique

    2015-01-01

    A gene named ltsA was earlier identified in Rhodococcus and Corynebacterium species while screening for mutations leading to increased cell susceptibility to lysozyme. The encoded protein belonged to a huge family of glutamine amidotransferases whose members catalyze amide nitrogen transfer from glutamine to various specific acceptor substrates. We here describe detailed physiological and biochemical investigations demonstrating the specific role of LtsA protein from Corynebacterium glutamicum (LtsACg) in the modification by amidation of cell wall peptidoglycan diaminopimelic acid (DAP) residues. A morphologically altered but viable ΔltsA mutant was generated, which displays a high susceptibility to lysozyme and β-lactam antibiotics. Analysis of its peptidoglycan structure revealed a total loss of DAP amidation, a modification that was found in 80% of DAP residues in the wild-type polymer. The cell peptidoglycan content and cross-linking were otherwise not modified in the mutant. Heterologous expression of LtsACg in Escherichia coli yielded a massive and toxic incorporation of amidated DAP into the peptidoglycan that ultimately led to cell lysis. In vitro assays confirmed the amidotransferase activity of LtsACg and showed that this enzyme used the peptidoglycan lipid intermediates I and II but not, or only marginally, the UDP-MurNAc pentapeptide nucleotide precursor as acceptor substrates. As is generally the case for glutamine amidotransferases, either glutamine or NH4+ could serve as the donor substrate for LtsACg. The enzyme did not amidate tripeptide- and tetrapeptide-truncated versions of lipid I, indicating a strict specificity for a pentapeptide chain length. PMID:25847251

  16. An investigation of the structure and bond rotational potential of some fluorinated ethanes by NMR spectroscopy of solutions in nematic liquid crystalline solvents.

    PubMed

    Emsley, J W; Longeri, M; Merlet, D; Pileio, G; Suryaprakash, N

    2006-06-01

    NMR spectra of 1,2-dibromo-1,1-difluoroethane and 1-bromo-2-iodo-tetrafluoroethane dissolved in nematic liquid crystalline solvents have been analysed to yield the magnitudes and signs of the scalar couplings, J(ij), and total anisotropic couplings, T(ij), between all the (1)H, (19)F, and (13)C nuclei, except for those between two (13)C nuclei. The values obtained for T(ij) in principle contain a contribution from J(ij)(aniso), the component along the static applied magnetic field of the anisotropic part of the electron-mediated spin-spin coupling. Neglecting this contribution allows partially averaged dipolar couplings, D(ij), to be extracted from the T(ij), and these were used to determine the structure, orientational order, and the conformational distribution generated by rotation about the C-C bond. The values obtained are compared with the results of calculations by ab initio and density functional methods. The differences found are no greater than those obtained for similar compounds which do not contain fluorine, so that there is no definitive evidence for significant contributions from J(CF)(aniso) or J(FF)(aniso) in the two compounds studied. PMID:16554180

  17. An investigation of the structure and bond rotational potential of some fluorinated ethanes by NMR spectroscopy of solutions in nematic liquid crystalline solvents

    NASA Astrophysics Data System (ADS)

    Emsley, J. W.; Longeri, M.; Merlet, D.; Pileio, G.; Suryaprakash, N.

    2006-06-01

    NMR spectra of 1,2-dibromo-1,1-difluoroethane and 1-bromo-2-iodo-tetrafluoroethane dissolved in nematic liquid crystalline solvents have been analysed to yield the magnitudes and signs of the scalar couplings, Jij, and total anisotropic couplings, Tij, between all the 1H, 19F, and 13C nuclei, except for those between two 13C nuclei. The values obtained for Tij in principle contain a contribution from Jijaniso, the component along the static applied magnetic field of the anisotropic part of the electron-mediated spin-spin coupling. Neglecting this contribution allows partially averaged dipolar couplings, Dij, to be extracted from the Tij, and these were used to determine the structure, orientational order, and the conformational distribution generated by rotation about the C-C bond. The values obtained are compared with the results of calculations by ab initio and density functional methods. The differences found are no greater than those obtained for similar compounds which do not contain fluorine, so that there is no definitive evidence for significant contributions from JCFaniso or JFFaniso in the two compounds studied.

  18. Isotope-enriched protein standards for computational amide I spectroscopy

    SciTech Connect

    Reppert, Mike; Roy, Anish R.; Tokmakoff, Andrei

    2015-03-28

    We present a systematic isotope labeling study of the protein G mutant NuG2b as a step toward the production of reliable, structurally stable, experimental standards for amide I infrared spectroscopic simulations. By introducing isotope enriched amino acids into a minimal growth medium during bacterial expression, we induce uniform labeling of the amide bonds following specific amino acids, avoiding the need for chemical peptide synthesis. We use experimental data to test several common amide I frequency maps and explore the influence of various factors on map performance. Comparison of the predicted absorption frequencies for the four maps tested with empirical assignments to our experimental spectra yields a root-mean-square error of 6-12 cm{sup −1}, with outliers of at least 12 cm{sup −1} in all models. This means that the predictions may be useful for predicting general trends such as changes in hydrogen bonding configuration; however, for finer structural constraints or absolute frequency assignments, the models are unreliable. The results indicate the need for careful testing of existing literature maps and shed light on possible next steps for the development of quantitative spectral maps.

  19. Computational Amide I Spectroscopy for Refinement of Disordered Peptide Ensembles: Maximum Entropy and Related Approaches

    NASA Astrophysics Data System (ADS)

    Reppert, Michael; Tokmakoff, Andrei

    The structural characterization of intrinsically disordered peptides (IDPs) presents a challenging biophysical problem. Extreme heterogeneity and rapid conformational interconversion make traditional methods difficult to interpret. Due to its ultrafast (ps) shutter speed, Amide I vibrational spectroscopy has received considerable interest as a novel technique to probe IDP structure and dynamics. Historically, Amide I spectroscopy has been limited to delivering global secondary structural information. More recently, however, the method has been adapted to study structure at the local level through incorporation of isotope labels into the protein backbone at specific amide bonds. Thanks to the acute sensitivity of Amide I frequencies to local electrostatic interactions-particularly hydrogen bonds-spectroscopic data on isotope labeled residues directly reports on local peptide conformation. Quantitative information can be extracted using electrostatic frequency maps which translate molecular dynamics trajectories into Amide I spectra for comparison with experiment. Here we present our recent efforts in the development of a rigorous approach to incorporating Amide I spectroscopic restraints into refined molecular dynamics structural ensembles using maximum entropy and related approaches. By combining force field predictions with experimental spectroscopic data, we construct refined structural ensembles for a family of short, strongly disordered, elastin-like peptides in aqueous solution.

  20. Characteristic conformation of Mosher's amide elucidated using the cambridge structural database.

    PubMed

    Ichikawa, Akio; Ono, Hiroshi; Mikata, Yuji

    2015-01-01

    Conformations of the crystalline 3,3,3-trifluoro-2-methoxy-2-phenylpropanamide derivatives (MTPA amides) deposited in the Cambridge Structural Database (CSD) were examined statistically as Racid-enantiomers. The majority of dihedral angles (48/58, ca. 83%) of the amide carbonyl groups and the trifluoromethyl groups ranged from -30° to 0° with an average angle θ1 of -13°. The other conformational properties were also clarified: (1) one of the fluorine atoms was antiperiplanar (ap) to the amide carbonyl group, forming a staggered conformation; (2) the MTPA amides prepared from primary amines showed a Z form in amide moieties; (3) in the case of the MTPA amide prepared from a primary amine possessing secondary alkyl groups (i.e., Mosher-type MTPA amide), the dihedral angles between the methine groups and the carbonyl groups were syn and indicative of a moderate conformational flexibility; (4) the phenyl plane was inclined from the O-Cchiral bond of the methoxy moiety with an average dihedral angle θ2 of +21°; (5) the methyl group of the methoxy moiety was ap to the ipso-carbon atom of the phenyl group. PMID:26193245

  1. Binding of the Respiratory Chain Inhibitor Antimycin to theMitochondrial bc1 Complex: A New Crystal Structure Reveals an AlteredIntramolecular Hydrogen-Bonding Pattern

    SciTech Connect

    Huang, Li-shar; Cobessi, David; Tung, Eric Y.; Berry, Edward A.

    2005-05-10

    Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex.Structure-activity-relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28Angstrom resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cyt b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alpha-A helix.

  2. Experimental studies of peptide bonds: Identification of the C7eq conformation of the alanine dipeptide analog N-acetyl-alanine N'-methylamide from torsion-rotation interactions

    NASA Astrophysics Data System (ADS)

    Lavrich, R. J.; Plusquellic, D. F.; Suenram, R. D.; Fraser, G. T.; Walker, A. R. Hight; Tubergen, M. J.

    2003-01-01

    Rotational spectra of the biomimetic molecule, alanine dipeptide and the double 15N(15N2) isotopomer have been observed using a pulsed-molecular-beam Fourier transform microwave spectrometer. The spectra reveal tunneling splittings from the torsional mode structure of two of its three methyl rotors. The torsional states assigned include one AA-state and two AE-states (i.e., AE and EA) for each isotopomer. The AA-states are well-fit to A-reduction asymmetricrotor Hamiltonians. The "infinite-barrier-limit" rotational constants of the 14N2 isotopomer are A=1710.97(8) MHz, B=991.89(9) MHz, and C=716.12(6) MHz. The AE-states are analyzed independently using "high-barrier" torsion-rotation Hamiltonians, yielding observedminus-calculated standard deviations of <400 kHz. The fits improve substantially (>100-fold for the 15N2 isotopomer) when analyzed in a ρ-axis frame where ρb=ρc=0. The best-fit torsion-rotation parameters provide accurate V3 barriers and C3 rotor axis angles for both methyl groups. The observed angles are shown to uniquely correlate with those calculated for the acetyl and amide methyl groups in the C7eq conformational form. The V3 barriers of the amide and acetyl methyl groups are 84.0(3) cm-1 and 98.4(2) cm-1 for the 14N2 and 84.1(1) cm-1 and 98.65(8) cm-1 for the 15N2 isotopomers, respectively. These results are in good agreement with prior geometry optimizations and with current V3 barrier calculations which predict the C7eq conformation as the lowest energy form in the gas phase. Under certain conditions, the spectrum is dominated by transitions from a thermal decomposition product formed by dehydration of alanine dipeptide. This molecule is tentatively identified as 3,5-dihydro-2,3,5-trimethyl-(9CI) 4H imidazole-4-one (CAS registry #32023-93-1).

  3. Crystal structure of the high-energy-density material guanylurea dipicryl­amide

    PubMed Central

    Deblitz, Raik; Hrib, Cristian G.; Hilfert, Liane; Edelmann, Frank T.

    2014-01-01

    The title compound, 1-carbamoylguanidinium bis­(2,4,6-tri­nitro­phen­yl)amide [H2NC(=O)NHC(NH2)2]+[N{C6H2(NO2)3-2,4,6}2]− (= guanylurea dipicryl­amide), was prepared as dark-red block-like crystals in 70% yield by salt-metathesis reaction between guanylurea sulfate and sodium dipicryl­amide. In the solid state, the new compound builds up an array of mutually linked guanylurea cations and dipicryl­amide anions. The crystal packing is dominated by an extensive network of N—H⋯O hydrogen bonds, resulting in a high density of 1.795 Mg m−3, which makes the title compound a potential secondary explosive. PMID:25249869

  4. In situ azimuthal rotation device for linear dichroism measurements in scanning transmission x-ray microscopy

    NASA Astrophysics Data System (ADS)

    Hernández-Cruz, D.; Hitchcock, A. P.; Tyliszczak, T.; Rousseau, M.-E.; Pézolet, M.

    2007-03-01

    A novel miniature rotation device used in conjunction with a scanning transmission x-ray microscope is described. It provides convenient in situ sample rotation to enable measurements of linear dichroism at high spatial resolution. The design, fabrication, and mechanical characterization are presented. This device has been used to generate quantitative maps of the spatial distribution of the orientation of proteins in several different spider and silkworm silks. Specifically, quantitative maps of the dichroic signal at the C 1s→π*amide transition in longitudinal sections of the silk fibers give information about the spatial orientation, degree of alignment, and spatial distribution of protein peptide bonds. A new approach for analyzing the dichroic signal to extract orientation distributions, in addition to magnitudes of aligned components, is presented and illustrated with results from Nephila clavipes dragline spider silk measured using the in situ rotation device.

  5. Hydrogen-Bond Cooperativity in Formamide2 -Water: A Model for Water-Mediated Interactions.

    PubMed

    Blanco, Susana; Pinacho, Pablo; López, Juan Carlos

    2016-08-01

    The rotational spectrum of formamide2 -H2 O formed in a supersonic jet has been characterized by Fourier-transform microwave spectroscopy. This adduct provides a simple model of water-mediated interaction involving the amide linkages, as occur in protein folding or amide-association processes, showing the interplay between self-association and solvation. Mono-substituted (13) C, (15) N, (18) O, and (2) H isotopologues have been observed and their data used to investigate the structure. The adduct forms an almost planar three-body sequential cycle. The two formamide molecules link on one side through an N-H⋅⋅⋅O hydrogen bond and on the other side through a water-mediated interaction with the formation of C=O⋅⋅⋅H-O and O⋅⋅⋅H-N hydrogen bonds. The analysis of the quadrupole coupling effects of two (14) N-nuclei reveals the subtle inductive forces associated to cooperative hydrogen bonding. These forces are involved in the changes in the C=O and C-N bond lengths with respect to pure formamide. PMID:27351296

  6. Breaking the low barrier hydrogen bond in a serine protease.

    PubMed Central

    Kidd, R. D.; Sears, P.; Huang, D. H.; Witte, K.; Wong, C. H.; Farber, G. K.

    1999-01-01

    The serine protease subtilisin BPN' is a useful catalyst for peptide synthesis when dissolved in high concentrations of a water-miscible organic co-solvent such as N,N-dimethylformamide (DMF). However, in 50% DMF, the k(cat) for amide hydrolysis is two orders of magnitude lower than in aqueous solution. Surprisingly, the k(cat) for ester hydrolysis is unchanged in 50% DMF. To explain this alteration in activity, the structure of subtilisin 8397+1 was determined in 20, 35, and 50% (v/v) DMF to 1.8 A resolution. In 50% DMF, the imidazole ring of His64, the central residue of the catalytic triad, has rotated approximately 180 degrees around the Cbeta-Cgamma bond. Two new water molecules in the active site stabilize the rotated conformation. This rotation places His64 in an unfavorable geometry to interact with the other members of the catalytic triad, Ser221 and Asp32. NMR experiments confirm that the characteristic resonance due to the low barrier hydrogen bond between the His64 and Asp32 is absent in 50% DMF. These experiments provide a clear structural basis for the change in activity of serine proteases in organic co-solvents. PMID:10048334

  7. Novel endogenous N-acyl amides activate TRPV1-4 receptors, BV-2 microglia, and are regulated in brain in an acute model of inflammation

    PubMed Central

    Raboune, Siham; Stuart, Jordyn M.; Leishman, Emma; Takacs, Sara M.; Rhodes, Brandon; Basnet, Arjun; Jameyfield, Evan; McHugh, Douglas; Widlanski, Theodore; Bradshaw, Heather B.

    2014-01-01

    A family of endogenous lipids, structurally analogous to the endogenous cannabinoid, N-arachidonoyl ethanolamine (Anandamide), and called N-acyl amides have emerged as a family of biologically active compounds at TRP receptors. N-acyl amides are constructed from an acyl group and an amine via an amide bond. This same structure can be modified by changing either the fatty acid or the amide to form potentially hundreds of lipids. More than 70 N-acyl amides have been identified in nature. We have ongoing studies aimed at isolating and characterizing additional members of the family of N-acyl amides in both central and peripheral tissues in mammalian systems. Here, using a unique in-house library of over 70 N-acyl amides we tested the following three hypotheses: (1) Additional N-acyl amides will have activity at TRPV1-4, (2) Acute peripheral injury will drive changes in CNS levels of N-acyl amides, and (3) N-acyl amides will regulate calcium in CNS-derived microglia. Through these studies, we have identified 20 novel N-acyl amides that collectively activate (stimulating or inhibiting) TRPV1-4. Using lipid extraction and HPLC coupled to tandem mass spectrometry we showed that levels of at least 10 of these N-acyl amides that activate TRPVs are regulated in brain after intraplantar carrageenan injection. We then screened the BV2 microglial cell line for activity with this N-acyl amide library and found overlap with TRPV receptor activity as well as additional activators of calcium mobilization from these lipids. Together these data provide new insight into the family of N-acyl amides and their roles as signaling molecules at ion channels, in microglia, and in the brain in the context of inflammation. PMID:25136293

  8. Characterization of fatty amides produced by lipase-catalyzed amidation of multihydroxylated fatty acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Novel multi-hydroxylated primary fatty amides produced by direct amidation of 7,10-dihydroxy-8(E)-octadecenoic acid (DOD) and 7,10,12-trihydroxy-8(E)-octadecenoic acid (TOD) were characterized by GC-MS and NMR. The amidation reactions were catalyzed by immobilized Pseudozyma (Candida) antarctica li...

  9. Synthesis, structural, conformational and pharmacological study of some amides derived from 3 -methyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9α-amine

    NASA Astrophysics Data System (ADS)

    Iriepa, I.; Bellanato, J.; Gálvez, E.; Gil-Alberdi, B.

    2010-07-01

    Some mono-substituted amides ( 2- 5) derived from 3-methyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9α-amine were synthesized and studied by IR, 1H and 13C NMR spectroscopy. The crystal structure of 3-methyl-2,4-diphenyl-9α-(3,5-dichlorobenzamido)-3-azabicyclo[3.3.1]nonane ( 3) was determined by X-ray diffraction. NMR data showed that all compounds adopt in CDCl 3 a preferred flattened chair-chair conformation with the N-CH 3 group in equatorial disposition. X-ray data agreed with this conformation in the case of compound 3. IR data revealed that compounds 2 and 3 present a C dbnd O⋯HN intermolecular bond in the solid state. This conclusion was also confirmed by X-ray data of compound 3. In the case of compound 5, IR results suggested intermolecular NH⋯N-heterocyclic bonding. On the contrary, in the pyrazine derivative ( 4), IR, 1H and 13C NMR data showed the presence of an intramolecular NH⋯N1″-heterocyclic hydrogen bond in the solid state and solution. Moreover, NMR and IR data showed a preferred trans disposition for the NH-C dbnd O group. NMR also revealed free rotation of the -NH-CO-R group around C9-NH bond. Pharmacological assays on mice were drawn to evaluate analgesic activity.

  10. Synthesis and characterization of ester and amide derivatives of titanium(IV) carboxymethylphosphonate

    SciTech Connect

    Melánová, Klára; Beneš, Ludvík; Trchová, Miroslava; Svoboda, Jan; Zima, Vítězslav

    2013-06-15

    A set of layered ester and amide derivatives of titanium(IV) carboxymethylphosphonate was prepared by solvothermal treatment of amorphous titanium(IV) carboxymethylphosphonate with corresponding 1-alkanols, 1,ω-alkanediols, 1-aminoalkanes, 1,ω-diaminoalkanes and 1,ω-amino alcohols and characterized by powder X-ray diffraction, IR spectroscopy and thermogravimetric analysis. Whereas alkyl chains with one functional group form bilayers tilted to the layers, 1,ω-diaminoalkanes and most of 1,ω-alkanediols form bridges connecting the adjacent layers. In the case of amino alcohols, the alkyl chains form bilayer and either hydroxyl or amino group is used for bonding. This simple method for the synthesis of ester and amide derivatives does not require preparation of acid chloride derivative as a precursor or pre-intercalation with alkylamines and can be used also for the preparation of ester and amide derivatives of titanium carboxyethylphosphonate and zirconium carboxymethylphosphonate. - Graphical abstract: Ester and amide derivatives of layered titanium carboxymethylphosphonate were prepared by solvothermal treatment of amorphous solid with alkanol or alkylamine. - Highlights: • Ester and amide derivatives of titanium carboxymethylphosphonate. • Solvothermal treatment of amorphous solid with alkanol or alkylamine. • Ester and amide formation confirmed by IR spectroscopy.

  11. Cloning of a Novel Arylamidase Gene from Paracoccus sp. Strain FLN-7 That Hydrolyzes Amide Pesticides

    PubMed Central

    Zhang, Jun; Yin, Jin-Gang; Hang, Bao-Jian; Cai, Shu; Li, Shun-Peng

    2012-01-01

    The bacterial isolate Paracoccus sp. strain FLN-7 hydrolyzes amide pesticides such as diflubenzuron, propanil, chlorpropham, and dimethoate through amide bond cleavage. A gene, ampA, encoding a novel arylamidase that catalyzes the amide bond cleavage in the amide pesticides was cloned from the strain. ampA contains a 1,395-bp open reading frame that encodes a 465-amino-acid protein. AmpA was expressed in Escherichia coli BL21 and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. AmpA is a homodimer with an isoelectric point of 5.4. AmpA displays maximum enzymatic activity at 40°C and a pH of between 7.5 and 8.0, and it is very stable at pHs ranging from 5.5 to 10.0 and at temperatures up to 50°C. AmpA efficiently hydrolyzes a variety of secondary amine compounds such as propanil, 4-acetaminophenol, propham, chlorpropham, dimethoate, and omethoate. The most suitable substrate is propanil, with Km and kcat values of 29.5 μM and 49.2 s−1, respectively. The benzoylurea insecticides (diflubenzuron and hexaflumuron) are also hydrolyzed but at low efficiencies. No cofactor is needed for the hydrolysis activity. AmpA shares low identities with reported arylamidases (less than 23%), forms a distinct lineage from closely related arylamidases in the phylogenetic tree, and has different biochemical characteristics and catalytic kinetics with related arylamidases. The results in the present study suggest that AmpA is a good candidate for the study of the mechanism for amide pesticide hydrolysis, genetic engineering of amide herbicide-resistant crops, and bioremediation of amide pesticide-contaminated environments. PMID:22544249

  12. Cloning of a novel arylamidase gene from Paracoccus sp. strain FLN-7 that hydrolyzes amide pesticides.

    PubMed

    Zhang, Jun; Yin, Jin-Gang; Hang, Bao-Jian; Cai, Shu; He, Jian; Zhou, Shun-Gui; Li, Shun-Peng

    2012-07-01

    The bacterial isolate Paracoccus sp. strain FLN-7 hydrolyzes amide pesticides such as diflubenzuron, propanil, chlorpropham, and dimethoate through amide bond cleavage. A gene, ampA, encoding a novel arylamidase that catalyzes the amide bond cleavage in the amide pesticides was cloned from the strain. ampA contains a 1,395-bp open reading frame that encodes a 465-amino-acid protein. AmpA was expressed in Escherichia coli BL21 and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. AmpA is a homodimer with an isoelectric point of 5.4. AmpA displays maximum enzymatic activity at 40°C and a pH of between 7.5 and 8.0, and it is very stable at pHs ranging from 5.5 to 10.0 and at temperatures up to 50°C. AmpA efficiently hydrolyzes a variety of secondary amine compounds such as propanil, 4-acetaminophenol, propham, chlorpropham, dimethoate, and omethoate. The most suitable substrate is propanil, with K(m) and k(cat) values of 29.5 μM and 49.2 s(-1), respectively. The benzoylurea insecticides (diflubenzuron and hexaflumuron) are also hydrolyzed but at low efficiencies. No cofactor is needed for the hydrolysis activity. AmpA shares low identities with reported arylamidases (less than 23%), forms a distinct lineage from closely related arylamidases in the phylogenetic tree, and has different biochemical characteristics and catalytic kinetics with related arylamidases. The results in the present study suggest that AmpA is a good candidate for the study of the mechanism for amide pesticide hydrolysis, genetic engineering of amide herbicide-resistant crops, and bioremediation of amide pesticide-contaminated environments. PMID:22544249

  13. Iron-catalyzed N-alkylation of azoles via cleavage of an sp3 C-H bond adjacent to a nitrogen atom.

    PubMed

    Xia, Qinqin; Chen, Wanzhi

    2012-10-19

    Iron-catalyzed direct C-N bond formation between azoles and amides is described. The oxidative coupling reactions of sp(3) C-H bonds adjacent to a nitrogen atom in amides and sulfonamides with the N-H bond in azoles proceeded smoothly in the presence of FeCl(2) and di-tert-butyl peroxide (DTBP). PMID:23025235

  14. Diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams

    PubMed Central

    2015-01-01

    Summary The conjugate addition reaction has been a useful tool in the formation of carbon–carbon bonds. The utility of this reaction has been demonstrated in the synthesis of many natural products, materials, and pharmacological agents. In the last three decades, there has been a significant increase in the development of asymmetric variants of this reaction. Unfortunately, conjugate addition reactions using α,β-unsaturated amides and lactams remain underdeveloped due to their inherently low reactivity. This review highlights the work that has been done on both diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams. PMID:25977728

  15. Hydrogen bonding in bulk heterojunction solar cells: A case study

    PubMed Central

    Xiao, Zeyun; Sun, Kuan; Subbiah, Jegadesan; Ji, Shaomin; Jones, David J.; Wong, Wallace W. H.

    2014-01-01

    Small molecules with dithieno[3,2-b;2′,3′-d]thiophene as central building block and octyl cyanoacetate and octyl cyanoacetamide as different terminal building blocks have been designed and synthesized. The amide containing small molecule can form intermolecular hydrogen bonding between N-H…O = C of the amide group. The photovoltaic properties and active layer morphologies of the two molecules in bulk heterojunction solar cells are compared to study the influence of hydrogen bonding on the active layer morphology. New methanofullerene compound containing amide group has also been synthesized and compared with conventional fullerene electron acceptors. PMID:25027678

  16. Mapping Buried Hydrogen-Bonding Networks.

    PubMed

    Thomas, John C; Goronzy, Dominic P; Dragomiretskiy, Konstantin; Zosso, Dominique; Gilles, Jérôme; Osher, Stanley J; Bertozzi, Andrea L; Weiss, Paul S

    2016-05-24

    We map buried hydrogen-bonding networks within self-assembled monolayers of 3-mercapto-N-nonylpropionamide on Au{111}. The contributing interactions include the buried S-Au bonds at the substrate surface and the buried plane of linear networks of hydrogen bonds. Both are simultaneously mapped with submolecular resolution, in addition to the exposed interface, to determine the orientations of molecular segments and directional bonding. Two-dimensional mode-decomposition techniques are used to elucidate the directionality of these networks. We find that amide-based hydrogen bonds cross molecular domain boundaries and areas of local disorder. PMID:27096290

  17. Crystal structures of (E)-3-(furan-2-yl)-2-phenyl-N-tosyl-acryl-amide and (E)-3-phenyl-2-(m-tol-yl)-N-tosyl-acryl-amide.

    PubMed

    Cheng, Dong; Meng, Xiangzhen; Sheng, Zeyuan; Wang, Shuangming; Duan, Yuanyuan; Li, Ziqian

    2016-06-01

    In the title N-tosyl-acryl-amide compounds, C20H17NO4S, (I), and C23H21NO3S, (II), the conformation about the C=C bond is E. The acryl-amide groups, [-NH-C(=O)-C=C-], are almost planar, with the N-C-C=C torsion angle being -170.18 (14)° in (I) and -168.01 (17)° in (II). In (I), the furan, phenyl and 4-methyl-benzene rings are inclined to the acryl-amide mean plane by 26.47 (11), 69.01 (8) and 82.49 (9)°, respectively. In (II), the phenyl, 3-methyl-benzene and 4-methyl-benzene rings are inclined to the acryl-amide mean plane by 11.61 (10), 78.44 (10) and 78.24 (10)°, respectively. There is an intra-molecular C-H⋯π inter-action present in compound (II). In the crystals of both compounds, mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(8) ring motif. In (I), the dimers are reinforced by C-H⋯O hydrogen bonds and linked by C-H⋯π inter-actions, forming chains along [011]. In the crystal of (II), the dimers are linked via C-H⋯O hydrogen bonds, forming chains along [100]. The chains are further linked by C-H⋯π inter-actions, forming layers parallel to (010). PMID:27308045

  18. Metal-Free C–H Alkyliminylation and Acylation of Alkenes with Secondary Amides

    PubMed Central

    Huang, Pei-Qiang; Huang, Ying-Hong; Geng, Hui; Ye, Jian-Liang

    2016-01-01

    Carbon–carbon bond formation by metal-free cross-coupling of two reactants with low reactivity represents a challenge in organic synthesis. Secondary amides and alkenes are two classes of bench-stable compounds. The low electrophilicity of the former and low nucleophilicity of the latter make the direct coupling of these two partners challenging yet highly desirable. We report herein an unprecedented intermolecular reaction of secondary amides with alkenes to afford α,β-unsaturated ketimines or enones, which are versatile intermediates for organic synthesis and are prevalent in bioactive compounds and functional materials. Our strategy relies on the chemoselective activation of the secondary amide with trifluoromethanesulfonic anhydride (Tf2O)/2-fluoropyridine to generate a highly reactive nitrilium intermediate, which reacts efficiently with alkenes. This metal-free synthesis is characterized by its mild reaction conditions, excellent functional group tolerance and chemoselectivity, allowing the preparation of multi-functionalized compounds without using protecting groups. PMID:27356173

  19. Metal-Free C-H Alkyliminylation and Acylation of Alkenes with Secondary Amides.

    PubMed

    Huang, Pei-Qiang; Huang, Ying-Hong; Geng, Hui; Ye, Jian-Liang

    2016-01-01

    Carbon-carbon bond formation by metal-free cross-coupling of two reactants with low reactivity represents a challenge in organic synthesis. Secondary amides and alkenes are two classes of bench-stable compounds. The low electrophilicity of the former and low nucleophilicity of the latter make the direct coupling of these two partners challenging yet highly desirable. We report herein an unprecedented intermolecular reaction of secondary amides with alkenes to afford α,β-unsaturated ketimines or enones, which are versatile intermediates for organic synthesis and are prevalent in bioactive compounds and functional materials. Our strategy relies on the chemoselective activation of the secondary amide with trifluoromethanesulfonic anhydride (Tf2O)/2-fluoropyridine to generate a highly reactive nitrilium intermediate, which reacts efficiently with alkenes. This metal-free synthesis is characterized by its mild reaction conditions, excellent functional group tolerance and chemoselectivity, allowing the preparation of multi-functionalized compounds without using protecting groups. PMID:27356173

  20. Assessing Spectral Simulation Protocols for the Amide I Band of Proteins.

    PubMed

    Cunha, Ana V; Bondarenko, Anna S; Jansen, Thomas L C

    2016-08-01

    We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure-function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins. PMID:27348022

  1. Chemoselective Reduction of Tertiary Amides under Thermal Control: Formation of either Aldehydes or Amines.

    PubMed

    Tinnis, Fredrik; Volkov, Alexey; Slagbrand, Tove; Adolfsson, Hans

    2016-03-24

    The chemoselective reduction of amides in the presence of other more reactive reducible functional groups is a highly challenging transformation, and successful examples thereof are most valuable in synthetic organic chemistry. Only a limited number of systems have demonstrated the chemoselective reduction of amides over ketones. Until now, the aldehyde functionality has not been shown to be compatible in any catalytic reduction protocol. Described herein is a [Mo(CO)6 ]-catalyzed protocol with an unprecedented chemoselectivity and allows for the reduction of amides in the presence of aldehydes and imines. Furthermore, the system proved to be tunable by variation of the temperature, which enabled for either C-O or C-N bond cleavage that ultimately led to the isolation of both amines and aldehydes, respectively, in high chemical yields. PMID:26934055

  2. Design and Conformational Analysis of Peptoids Containing N-Hydroxy Amides Reveals a Unique Sheet-Like Secondary Structure

    PubMed Central

    Crapster, J. Aaron; Stringer, Joseph R.; Guzei, Ilia A.; Blackwell, Helen E.

    2011-01-01

    N-hydroxy amides can be found in many naturally occurring and synthetic compounds and are known to act as both strong proton donors and chelators of metal cations. We have initiated studies of peptoids, or N-substituted glycines, that contain N-hydroxy amide side chains to investigate the potential effects of these functional groups on peptoid backbone amide rotamer equilibria and local conformations. We reasoned that the propensity of these functional groups to participate in hydrogen bonding could be exploited to enforce intramolecular or intermolecular interactions that yield new peptoid structures. Here, we report the design, synthesis, and detailed conformational analysis of a series of model N-hydroxy peptoids. These peptoids were readily synthesized, and their structures were analyzed in solution by 1D and 2D NMR and in the solid-state by X-ray crystallography. The N-hydroxy amides were found to strongly favor trans conformations with respect to the peptoid backbone in chloroform. More notably, unique sheet-like structures held together via intermolecular hydrogen bonds were observed in the X-ray crystal structures of an N-hydroxy amide peptoid dimer, which to our knowledge represent the first structure of this type reported for peptoids. These results suggest that the N-hydroxy amide can be utilized to control both local backbone geometries and longer-range intermolecular interactions in peptoids, and represents a new functional group in the peptoid design toolbox. PMID:22180908

  3. The formation of lipid hydroperoxide-derived amide-type lysine adducts on proteins: a review of current knowledge.

    PubMed

    Kato, Yoji

    2014-01-01

    Lipid peroxidation is an important biological reaction. In particular, polyunsaturated fatty acid (PUFA) can be oxidized easily. Peroxidized lipids often react with other amines accompanied by the formation of various covalent adducts. Novel amide-type lipid-lysine adducts have been identified from an in vitro reaction mixture of lipid hydroperoxide with a protein, biological tissues exposed to conditions of oxidative stress and human urine from a healthy person. In this chapter, the current knowledge of amide type adducts is reviewed with a focus on the evaluation of functional foods and diseases with a history of discovery of hexanoyl-lysine (HEL). Although there is extensive research on HEL and other amide-type adducts, the mechanism of generation of the amide bond remains unclear. We have found that the decomposed aldehyde plus peroxide combined with a lysine moiety does not fully explain the formation of the amide-type lipid-lysine adduct that is generated by lipid hydroperoxide. Singlet oxygen or an excited state of the ketone generated from the lipid hydroperoxide may also contribute to the formation of the amide linkage. The amide-adducts may prove useful not only for the detection of oxidative stress induced by disease but also for the estimation of damage caused by an excess intake of PUFA. PMID:24374915

  4. Gas-Phase Amidation of Carboxylic Acids with Woodward's Reagent K Ions

    NASA Astrophysics Data System (ADS)

    Peng, Zhou; Pilo, Alice L.; Luongo, Carl A.; McLuckey, Scott A.

    2015-06-01

    Gas-phase amidation of carboxylic acids in multiply-charged peptides is demonstrated via ion/ion reactions with Woodward's reagent K (wrk) in both positive and negative mode. Woodward's reagent K, N-ethyl-3-phenylisoxazolium-3'-sulfonate, is a commonly used reagent that activates carboxylates to form amide bonds with amines in solution. Here, we demonstrate that the analogous gas-phase chemistry occurs upon reaction of the wrk ions and doubly protonated (or doubly deprotonated) peptide ions containing the carboxylic acid functionality. The reaction involves the formation of the enol ester intermediate in the electrostatic complex. Upon collisional activation, the ethyl amine on the reagent is transferred to the activated carbonyl carbon on the peptide, resulting in the formation of an ethyl amide (addition of 27 Da to the peptide) with loss of a neutral ketene derivative. Further collision-induced dissociation (CID) of the products and comparison with solution-phase amidation product confirms the structure of the ethyl amide.

  5. Quantum entanglement between amide-I and amide-site in Davydov-Scott model

    NASA Astrophysics Data System (ADS)

    Liang, Xian-Ting; Fan, Heng

    2014-01-01

    In this paper, we firstly derive non-Markovian operator Langevin equations of the Davydov monomer in its environment. Next, we replace the equations with the c-number quantum general Langevin equations (QGLEs) by calculating statistical and quantum averages of the operator Langevin equations. Then, by using the c-number QGLEs we investigate the evolutions of the subsystems amide-I and amide-site. The evolution of a parameter θ describing quantum entanglement of the coupling subsystems with continuous variable Hamiltonian has also been investigated. It is shown that there is certain entanglement between the amide-I and amide-site in the Davydov-Scott monomer.

  6. Interaction of a pseudo-π C-C bond with cuprous and argentous chlorides: Cyclopropane⋯CuCl and cyclopropane⋯AgCl investigated by rotational spectroscopy and ab initio calculations.

    PubMed

    Zaleski, Daniel P; Mullaney, John C; Bittner, Dror M; Tew, David P; Walker, Nicholas R; Legon, Anthony C

    2015-10-28

    Strongly bound complexes (CH2)3⋯MCl (M = Cu or Ag), formed by non-covalent interaction of cyclopropane and either cuprous chloride or argentous chloride, have been generated in the gas phase by means of the laser ablation of either copper or silver metal in the presence of supersonically expanded pulses of a gas mixture containing small amounts of cyclopropane and carbon tetrachloride in a large excess of argon. The rotational spectra of the complexes so formed were detected with a chirped-pulse, Fourier transform microwave spectrometer and analysed to give rotational constants and Cu and Cl nuclear quadrupole coupling constants for eight isotopologues of each of (CH2)3⋯CuCl and (CH2)3⋯AgCl. The geometry of each of these complexes was established unambiguously to have C(2v) symmetry, with the three C atoms coplanar, and with the MCl molecule lying along a median of the cyclopropane C3 triangle. This median coincides with the principal inertia axis a in each of the two complexes (CH2)3⋯MCl. The M atom interacts with the pseudo-π bond linking the pair of equivalent carbon atoms (F)C (F = front) nearest to it, so that M forms a non-covalent bond to one C-C edge of the cyclopropane molecule. The (CH2)3⋯MCl complexes have similar angular geometries to those of the hydrogen- and halogen-bonded analogues (CH2)3⋯HCl and (CH2)3⋯ClF, respectively. Quantitative details of the geometries were determined by interpretation of the observed rotational constants and gave results in good agreement with those from ab initio calculations carried out at the CCSD(T)(F12*)/aug-cc-pVTZ-F12 level of theory. Interesting geometrical features are the lengthening of the (F)C-(F)C bond and the shrinkage of the two equivalent (B)C-(F)C (B = back) bonds relative to the C-C bond in cyclopropane itself. The expansions of the (F)C-(F)C bond are 0.1024(9) Å and 0.0727(17) Å in (CH2)3⋯CuCl and (CH2)3⋯AgCl, respectively, according to the determined r0 geometries. The C-C bond

  7. Interaction of a pseudo-π C—C bond with cuprous and argentous chlorides: Cyclopropane⋯CuCl and cyclopropane⋯AgCl investigated by rotational spectroscopy and ab initio calculations

    SciTech Connect

    Zaleski, Daniel P.; Mullaney, John C.; Bittner, Dror M.; Walker, Nicholas R. E-mail: nick.walker@newcastle.ac.uk; Tew, David P.; Legon, Anthony C. E-mail: nick.walker@newcastle.ac.uk

    2015-10-28

    Strongly bound complexes (CH{sub 2}){sub 3}⋯MCl (M = Cu or Ag), formed by non-covalent interaction of cyclopropane and either cuprous chloride or argentous chloride, have been generated in the gas phase by means of the laser ablation of either copper or silver metal in the presence of supersonically expanded pulses of a gas mixture containing small amounts of cyclopropane and carbon tetrachloride in a large excess of argon. The rotational spectra of the complexes so formed were detected with a chirped-pulse, Fourier transform microwave spectrometer and analysed to give rotational constants and Cu and Cl nuclear quadrupole coupling constants for eight isotopologues of each of (CH{sub 2}){sub 3}⋯CuCl and (CH{sub 2}){sub 3}⋯AgCl. The geometry of each of these complexes was established unambiguously to have C{sub 2v} symmetry, with the three C atoms coplanar, and with the MCl molecule lying along a median of the cyclopropane C{sub 3} triangle. This median coincides with the principal inertia axis a in each of the two complexes (CH{sub 2}){sub 3}⋯MCl. The M atom interacts with the pseudo-π bond linking the pair of equivalent carbon atoms {sup F}C (F = front) nearest to it, so that M forms a non-covalent bond to one C—C edge of the cyclopropane molecule. The (CH{sub 2}){sub 3}⋯MCl complexes have similar angular geometries to those of the hydrogen- and halogen-bonded analogues (CH{sub 2}){sub 3}⋯HCl and (CH{sub 2}){sub 3}⋯ClF, respectively. Quantitative details of the geometries were determined by interpretation of the observed rotational constants and gave results in good agreement with those from ab initio calculations carried out at the CCSD(T)(F12*)/aug-cc-pVTZ-F12 level of theory. Interesting geometrical features are the lengthening of the {sup F}C—{sup F}C bond and the shrinkage of the two equivalent {sup B}C—{sup F}C (B = back) bonds relative to the C—C bond in cyclopropane itself. The expansions of the {sup F}C—{sup F}C bond are 0

  8. Interaction of a pseudo-π C—C bond with cuprous and argentous chlorides: Cyclopropane⋯CuCl and cyclopropane⋯AgCl investigated by rotational spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Zaleski, Daniel P.; Mullaney, John C.; Bittner, Dror M.; Tew, David P.; Walker, Nicholas R.; Legon, Anthony C.

    2015-10-01

    Strongly bound complexes (CH2)3⋯MCl (M = Cu or Ag), formed by non-covalent interaction of cyclopropane and either cuprous chloride or argentous chloride, have been generated in the gas phase by means of the laser ablation of either copper or silver metal in the presence of supersonically expanded pulses of a gas mixture containing small amounts of cyclopropane and carbon tetrachloride in a large excess of argon. The rotational spectra of the complexes so formed were detected with a chirped-pulse, Fourier transform microwave spectrometer and analysed to give rotational constants and Cu and Cl nuclear quadrupole coupling constants for eight isotopologues of each of (CH2)3⋯CuCl and (CH2)3⋯AgCl. The geometry of each of these complexes was established unambiguously to have C2v symmetry, with the three C atoms coplanar, and with the MCl molecule lying along a median of the cyclopropane C3 triangle. This median coincides with the principal inertia axis a in each of the two complexes (CH2)3⋯MCl. The M atom interacts with the pseudo-π bond linking the pair of equivalent carbon atoms FC (F = front) nearest to it, so that M forms a non-covalent bond to one C—C edge of the cyclopropane molecule. The (CH2)3⋯MCl complexes have similar angular geometries to those of the hydrogen- and halogen-bonded analogues (CH2)3⋯HCl and (CH2)3⋯ClF, respectively. Quantitative details of the geometries were determined by interpretation of the observed rotational constants and gave results in good agreement with those from ab initio calculations carried out at the CCSD(T)(F12*)/aug-cc-pVTZ-F12 level of theory. Interesting geometrical features are the lengthening of the FC—FC bond and the shrinkage of the two equivalent BC—FC (B = back) bonds relative to the C—C bond in cyclopropane itself. The expansions of the FC—FC bond are 0.1024(9) Å and 0.0727(17) Å in (CH2)3⋯CuCl and (CH2)3⋯AgCl, respectively, according to the determined r0

  9. Characterization of FdmV as an Amide Synthetase for Fredericamycin A Biosynthesis in Streptomyces griseus ATCC 43944*

    PubMed Central

    Chen, Yihua; Wendt-Pienkowski, Evelyn; Ju, Jianhua; Lin, Shuangjun; Rajski, Scott R.; Shen, Ben

    2010-01-01

    Fredericamycin (FDM) A is a pentadecaketide natural product that features an amide linkage. Analysis of the fdm cluster from Streptomyces griseus ATCC 43944, however, failed to reveal genes encoding the types of amide synthetases commonly seen in natural product biosynthesis. Here, we report in vivo and in vitro characterizations of FdmV, an asparagine synthetase (AS) B-like protein, as an amide synthetase that catalyzes the amide bond formation in FDM A biosynthesis. This is supported by the findings that (i) inactivation of fdmV in vivo afforded the ΔfdmV mutant strain SB4027 that abolished FDM A and FDM E production but accumulated FDM C, a biosynthetic intermediate devoid of the characteristic amide linkage; (ii) FdmV in vitro catalyzes conversion of FDM C to FDM B, a known intermediate for FDM A biosynthesis (apparent Km = 162 ± 67 μm and kcat = 0.11 ± 0.02 min−1); and (iii) FdmV also catalyzes the amidation of FDM M-3, a structural analog of FDM C, to afford amide FDM M-6 in vitro, albeit at significantly reduced efficiency. Preliminary enzymatic studies revealed that, in addition to the common nitrogen sources (l-Gln and free amine) of class II glutamine amidotransferases (to which AS B belongs), FdmV can also utilize l-Asn as a nitrogen donor. The amide bond formation in FDM A biosynthesis is proposed to occur after C-8 hydroxylation but before the carbaspirocycle formation. PMID:20926388

  10. Electronic structure of lithium amide

    NASA Astrophysics Data System (ADS)

    Kamakura, N.; Takeda, Y.; Saitoh, Y.; Yamagami, H.; Tsubota, M.; Paik, B.; Ichikawa, T.; Kojima, Y.; Muro, T.; Kato, Y.; Kinoshita, T.

    2011-01-01

    The electronic structure of the insulator lithium amide (LiNH2), which is a lightweight complex hydride being considered as a high-capacity hydrogen storage material, is investigated by N 1s soft x-ray emission spectroscopy (XES) and absorption spectroscopy (XAS). The XES and XAS spectra show a band gap between the valence and conduction bands. The valence band in the XES spectrum consists of three peaks, which extend up to ~-8 eV from the valence band top. The band calculation within the local-density approximation (LDA) for LiNH2shows energetically separated three peaks in the occupied N 2p partial density of states (pDOS) and the band gap. The energy distribution of three peaks in the XES spectrum agrees with that in the calculated pDOS except for the peak at the highest binding energy, which is attributed to the strongly hybridized state between N 2p and H 1s. The XES experiment has clarified that the strongly hybridized state with H 1s in LiNH2is located at binding energy higher than that of the LDA calculation, while the overall feature of the electronic structure of LiNH2experimentally obtained by XES and XAS is consistent with the calculated result.

  11. How amide hydrogens exchange in native proteins

    PubMed Central

    Persson, Filip; Halle, Bertil

    2015-01-01

    Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N–H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N–H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion. PMID:26195754

  12. How amide hydrogens exchange in native proteins.

    PubMed

    Persson, Filip; Halle, Bertil

    2015-08-18

    Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion. PMID:26195754

  13. Isomer selective infrared spectroscopy of supersonically cooled cis- and trans-N-phenylamides in the region from the amide band to NH stretching vibration.

    PubMed

    Miyazaki, Mitsuhiko; Saikawa, Jiro; Ishizuki, Hideki; Taira, Takunori; Fujii, Masaaki

    2009-08-01

    We measured the infrared (IR) spectra of supersonically cooled N-phenylformamide (formanilide) and N-phenylacetamide (acetanilide) in the amide band and X-H stretch vibration regions by using IR-UV depletion spectroscopy combined with a newly developed mid-IR light source based on difference frequency generation in ZnGeP(2). The two rotational isomers, cis- and trans- of the amide group were separately monitored to record the IR spectra. Both of the conformers showed similar features in the amide I and II regions, while major differences of the isomers appeared in the amide III vibration region. The IR spectrum of trans-acetanilide closely resembles that of trans-formanilide, except for vibrations of the methyl group; that is, substitution of the formyl hydrogen to a methyl group has only a minor effect on the amide vibrations. PMID:19606319

  14. Combined ESR and thermodynamic studies of the superoxide adduct of 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO): hindered rotation around the O-O bond evidenced by two-dimensional simulation of temperature-dependent spectra.

    PubMed

    Rockenbauer, Antal; Clément, Jean-Louis; Culcasi, Marcel; Mercier, Anne; Tordo, Paul; Pietri, Sylvia

    2007-06-14

    Experiments were performed to elucidate the origin of the superhyperfine structure and line width alternation (LWA) seen in the ESR spectrum of the major diastereoisomer (1) of DEPMPO-OOH, the remarkably persistent superoxide adduct of 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO). Using selectively deuterated DEPMPO derivatives, we demonstrated that the superhyperfine pattern can be unambiguously attributed to long-range couplings. The recording in pyridine of highly resolved spectra in a wide temperature range, combined with two-dimensional simulation, allowed us to characterize an inverted LWA in 1 and revealed a uniform line broadening in the spectrum of the minor DEPMPO-OOH diastereoisomer (2), with both effects originating from a chemical exchange between conformers. When the individual spectra of 1 presenting LWA in the fast-exchange regime were simulated, four equally good fits were obtained and this ambiguity could be resolved by using a two-dimensional simulation technique. The thermodynamic and kinetic constants of this exchange were consistent with a rotation around the O-O bond. We propose that line broadening effects in 1 and 2 result from this O-O rotation concerted with the pseudo-rotation of the pyrrolidine ring. PMID:17518450

  15. N-Acylsaccharins: Stable Electrophilic Amide-Based Acyl Transfer Reagents in Pd-Catalyzed Suzuki-Miyaura Coupling via N-C Cleavage.

    PubMed

    Liu, Chengwei; Meng, Guangrong; Liu, Yongmei; Liu, Ruzhang; Lalancette, Roger; Szostak, Roman; Szostak, Michal

    2016-09-01

    The development of efficient catalytic methods for N-C bond cleavage in amides remains an important synthetic challenge. The first Pd-catalyzed Suzuki-Miyaura cross-coupling of N-acylsaccharins with boronic acids by selective N-C bond activation is reported. The reaction enables preparation of a variety of functionalized diaryl and alkyl-aryl ketones with broad functional group tolerance and in good to excellent yields. Of general interest, N-acylsaccharins serve as new, highly reactive, bench-stable, economical, amide-based, electrophilic acyl transfer reagents via acyl-metal intermediates. Mechanistic studies strongly support the amide N-C(O) bond twist as the enabling feature of N-acylsaccharins in the N-C bond cleavage. PMID:27513821

  16. Convergent synthesis of digitally-encoded poly(alkoxyamine amide)s.

    PubMed

    Roy, Raj Kumar; Laure, Chloé; Fischer-Krauser, Diane; Charles, Laurence; Lutz, Jean-François

    2015-11-01

    Binary-encoded poly(alkoxyamine amide)s were prepared by oligomer ligation. These polymers contain digital sequences based on two monomers defined as 0 and 1 bits. A library of oligomers containing all possible dyads 00, 01, 10 and 11 was prepared and used to construct long coded sequences. PMID:26359908

  17. Renaissance for low shrinking resins: all-in-one solution by bi-functional vinylcyclopropane-amides.

    PubMed

    Pineda Contreras, Paul; Kuttner, Christian; Fery, Andreas; Stahlschmidt, Ullrich; Jérôme, Valérie; Freitag, Ruth; Agarwal, Seema

    2015-07-28

    A low volume shrinking vinylcyclopropane (VCP) monomer, showing both a high reactivity and a low viscosity, was obtained by applying a sterically hindered and isomeric spacer element, incorporating intermolecular amide hydrogen bonds. The resulting properties locate this VCP system in a pronounced range that so far no other efficient and radical polymerizable resin could enter. PMID:26111896

  18. Direct enantioselective conjugate addition of carboxylic acids with chiral lithium amides as traceless auxiliaries.

    PubMed

    Lu, Ping; Jackson, Jeffrey J; Eickhoff, John A; Zakarian, Armen

    2015-01-21

    Michael addition is a premier synthetic method for carbon-carbon and carbon-heteroatom bond formation. Using chiral dilithium amides as traceless auxiliaries, we report the direct enantioselective Michael addition of carboxylic acids. A free carboxyl group in the product provides versatility for further functionalization, and the chiral reagent can be readily recovered by extraction with aqueous acid. The method has been applied in the enantioselective total synthesis of the purported structure of pulveraven B. PMID:25562717

  19. Ni-Catalyzed Dehydrogenative Cross-Coupling: Direct Transformation of Aldehydes to Esters and Amides

    PubMed Central

    Whittaker, Aaron M.; Dong, Vy M.

    2015-01-01

    By exploring a new mode of Ni-catalyzed cross-coupling, we have developed a protocol to transform both aromatic and aliphatic aldehydes into either esters or amides directly. The success of this oxidative coupling depends on the appropriate choice of catalyst and organic oxidant, including the use of either α,α,α-trifluoroacetophenone or excess aldehyde. We present mechanistic data that supports a catalytic cycle involving oxidative addition into the aldehyde C–H bond. PMID:25424967

  20. Nickel-catalyzed dehydrogenative cross-coupling: direct transformation of aldehydes into esters and amides.

    PubMed

    Whittaker, Aaron M; Dong, Vy M

    2015-01-19

    By exploring a new mode of nickel-catalyzed cross-coupling, a method to directly transform both aromatic and aliphatic aldehydes into either esters or amides has been developed. The success of this oxidative coupling depends on the appropriate choice of catalyst and organic oxidant, including the use of either α,α,α-trifluoroacetophenone or excess aldehyde. Mechanistic data that supports a catalytic cycle involving oxidative addition into the aldehyde C-H bond is also presented. PMID:25424967

  1. Vibrational characterization of the peptide bond

    NASA Astrophysics Data System (ADS)

    Herrebout, W.; Clou, K.; Desseyn, H. O.; Blaton, N.

    2003-01-01

    This article describes the complete vibrational analysis of N, N'-dimethyloxamide, CH 3HNCOCONHCH 3, on basis of the infrared and Raman spectra of four isotopes (H, D, CH 3, CD 3). Force field calculations on the monomers and multimers ( n=5) combined with solid state spectra in the -196 to +100 °C temperature range have been used to obtain a better understanding of the influence of hydrogen bonding on the typical amide fundamentals. The cooperative effect in de series monomer→multimers→solid state at decreasing temperatures has been demonstrated. Nine typical so-called 'amide bands' have been further characterized and special attention has been given to the Amide IV mode. The influence of the CH and CD vibrations on the amide fundamentals, has been studied by comparison with the calculated and experimental fundamentals and P.E.D. values of the CH 3 and CD 3 isotopes. The most important amide bands have further been assigned in X-CONHCH 3 molecules where X=methyl, amide, thioamide, ester, salt, cyanide and acid functional groups.

  2. Vibrational characterization of the peptide bond.

    PubMed

    Herrebout, W; Clou, K; Desseyn, H O; Blaton, N

    2003-01-01

    This article describes the complete vibrational analysis of N,N'-dimethyloxamide, CH3HNCOCONHCH3, on basis of the infrared and Raman spectra of four isotopes (H, D, CH3, CD3). Force field calculations on the monomers and multimers (n = 5) combined with solid state spectra in the -196 to +100 degrees C temperature range have been used to obtain a better understanding of the influence of hydrogen bonding on the typical amide fundamentals. The cooperative effect in de series monomer --> multimers --> solid state at decreasing temperatures has been demonstrated. Nine typical so-called 'amide bands' have been further characterized and special attention has been given to the Amide IV mode. The influence of the CH and CD vibrations on the amide fundamentals, has been studied by comparison with the calculated and experimental fundamentals and P.E.D. values of the CH3 and CD3 isotopes. The most important amide bands have further been assigned in X-CONHCH3 molecules where X = methyl, amide, thioamide, ester, salt, cyanide and acid functional groups. PMID:12509146

  3. Nature of Amide Carbonyl−Carbonyl Interactions in Proteins

    PubMed Central

    2010-01-01

    Noncovalent interactions define and modulate biomolecular structure, function, and dynamics. In many protein secondary structures, an intimate interaction exists between adjacent carbonyl groups of the main-chain amide bonds. As this short contact contributes to the energetics of protein conformational stability as well as protein−ligand interactions, understanding its nature is crucial. The intimacy of the carbonyl groups could arise from a charge−charge or dipole−dipole interaction, or n→π * electronic delocalization. This last putative origin, which is reminiscent of the Bürgi−Dunitz trajectory, involves delocalization of the lone pairs (n) of the oxygen (Oi−1) of a peptide bond over the antibonding orbital (π*) of the carbonyl group (Ci=Oi) of the subsequent peptide bond. By installing isosteric chemical substituents in a peptidic model system and using NMR spectroscopy, X-ray diffraction analysis, and ab initio calculations to analyze the consequences, the intimate interaction between adjacent carbonyl groups is shown to arise primarily from n→π* electronic delocalization. This finding has implications for organic, biological, and medicinal chemistry. PMID:19469574

  4. Rotational spectra and properties of complexes B⋯ICF3 (B = Kr or CO) and a comparison of the efficacy of ICl and ICF3 as iodine donors in halogen bond formation

    NASA Astrophysics Data System (ADS)

    Stephens, Susanna L.; Walker, Nicholas R.; Legon, Anthony C.

    2011-12-01

    The ground-state rotational spectra of two weakly bound complexes B⋯ICF3 (B = Kr or CO) formed by trifluoroiodomethane have been observed in pulsed jets by using two types of Fourier-transform microwave spectroscopy (chirped-pulse and Fabry-Perot cavity). Both complexes exhibit symmetric-top type spectra, thus indicating that the Kr atom in Kr⋯ICF3 and both the C and O atoms in OC⋯ICF3 lie along the C3 axis of ICF3. The rotational constant B0, the centrifugal distortion constants DJ and DJK, and the iodine nuclear quadrupole coupling constant χaa(I) were determined for each of the isotopologues 84Kr⋯ICF3, 86Kr⋯ICF3, 16O12C⋯ICF3, 16O13C⋯ICF3, and 18O12C⋯ICF3. Interpretation of the spectroscopic constants reveals that the carbon atom of CO is adjacent to I and participates in the weak bond in OC⋯ICF3. Simple models based on unperturbed component geometries lead to the distances r(Kr⋯I) = 3.830(1) Å and r(C⋯I) = 3.428(1) Å in Kr⋯ICF3 and OC⋯ICF3, respectively, and to the quadratic force constants for stretching of the weak bond kσ = 2.80 N m-1 and 3.96 N m-1, respectively. The distances r(Z⋯I) (Z is the acceptor atom in B), the kσ values, and the angular geometries of the pair of complexes B⋯ICF3 and B⋯ICl for a given B are compared when B = Kr, CO, H2O, H2S, or NH3. The comparison reveals that the iodine bond in B⋯ICF3 is systematically longer and weaker than that of B⋯ICl, while the angular geometry of the B⋯I moiety is isomorphic in B⋯ICF3 and B⋯ICl for a given B. It is concluded that -CF3 is less effective than -Cl as an electron-withdrawing group when attached to an I atom and that the angular geometries of the B⋯ICF3 can be predicted by means of a simple rule that holds for many hydrogen- and halogen-bonded complexes.

  5. Durability of amide N-chloramine biocides to ethylene oxide sterilization.

    PubMed

    Zhao, Nan; Logsetty, Sarvesh; Liu, Song

    2012-01-01

    The objective of this work is to study the stability of three novel topical antimicrobial dressings consisting of amide N-chloramine structures against ethylene oxide sterilization. Cotton gauze samples bonded with one of three amide N-chloramine structures were subjected to standard ethylene oxide (EtO) sterilization. The amounts of amide N-chloramine structures before and after the sterilization were quantified to indicate the stabilities of these amide N-chloramine structures to the sterilization. The samples after sterilization were challenged with a clinical isolate of healthcare-associated multidrug-resistant Escherichia coli. N-Chloramine structure converted from polymethacrylamide (dressing 2) had the highest durability (89.7% retained active chlorine) toward EtO sterilization; that from hydantoin (dressing 3; 86.3% retained active chlorine) followed; and poly(N-chloroacrylamide) (dressing 1) had the lowest (64.0% retained active chlorine). After EtO sterilization, all the samples still reduced E. coli presence at 5 minutes of contact, with dressing 2 retaining a log 6 reduction. The three tested amide N-chloramine structures could all survive EtO sterilization while retaining percentages of active chlorine ranging from 64.0 to 89.7%. Dressing 2 showed the best durability, whereas dressing 1 had the poorest durability. With the remaining amounts of amide N-chloramine structures after EtO sterilization, all the dressings could still reduce E. coli numbers within 5 minutes of contact, and dressing 2 resulted in a log 6 reduction in colony count. PMID:22157019

  6. A novel reaction mediated by human aldehyde oxidase: amide hydrolysis of GDC-0834.

    PubMed

    Sodhi, Jasleen K; Wong, Susan; Kirkpatrick, Donald S; Liu, Lichuan; Khojasteh, S Cyrus; Hop, Cornelis E C A; Barr, John T; Jones, Jeffrey P; Halladay, Jason S

    2015-06-01

    GDC-0834, a Bruton's tyrosine kinase inhibitor investigated as a potential treatment of rheumatoid arthritis, was previously reported to be extensively metabolized by amide hydrolysis such that no measurable levels of this compound were detected in human circulation after oral administration. In vitro studies in human liver cytosol determined that GDC-0834 (R)-N-(3-(6-(4-(1,4-dimethyl-3-oxopiperazin-2-yl)phenylamino)-4-methyl-5-oxo- 4,5-dihydropyrazin-2-yl)-2-methylphenyl)-4,5,6,7-tetrahydrobenzo[b] thiophene-2-carboxamide) was rapidly hydrolyzed with a CLint of 0.511 ml/min per milligram of protein. Aldehyde oxidase (AO) and carboxylesterase (CES) were putatively identified as the enzymes responsible after cytosolic fractionation and mass spectrometry-proteomics analysis of the enzymatically active fractions. Results were confirmed by a series of kinetic experiments with inhibitors of AO, CES, and xanthine oxidase (XO), which implicated AO and CES, but not XO, as mediating GDC-0834 amide hydrolysis. Further supporting the interaction between GDC-0834 and AO, GDC-0834 was shown to be a potent reversible inhibitor of six known AO substrates with IC50 values ranging from 0.86 to 1.87 μM. Additionally, in silico modeling studies suggest that GDC-0834 is capable of binding in the active site of AO with the amide bond of GDC-0834 near the molybdenum cofactor (MoCo), orientated in such a way to enable potential nucleophilic attack on the carbonyl of the amide bond by the hydroxyl of MoCo. Together, the in vitro and in silico results suggest the involvement of AO in the amide hydrolysis of GDC-0834. PMID:25845827

  7. Polyimides Containing Amide And Perfluoroisopropyl Links

    NASA Technical Reports Server (NTRS)

    Dezem, James F.

    1993-01-01

    New polyimides synthesized from reactions of aromatic hexafluoroisopropyl dianhydrides with asymmetric amide diamines. Soluble to extent of at least 10 percent by weight at temperature of about 25 degrees C in common amide solvents such as N-methylpyrrolidone, N,N-dimethylacetamide, and N,N-dimethylformamide. Polyimides form tough, flexible films, coatings, and moldings. Glass-transition temperatures ranged from 300 to 365 degrees C, and crystalline melting temperatures observed between 543 and 603 degrees C. Display excellent physical, chemical, and electrical properties. Useful as adhesives, laminating resins, fibers, coatings for electrical and decorative purposes, films, wire enamels, and molding compounds.

  8. Friedel-Crafts Acylation with Amides

    PubMed Central

    Raja, Erum K.; DeSchepper, Daniel J.; Nilsson Lill, Sten O.; Klumpp, Douglas A.

    2012-01-01

    Friedel-Crafts acylation has been known since the 1870s and it is an important organic synthetic reaction leading to aromatic ketone products. Friedel-Crafts acylation is usually done with carboxylic acid chlorides or anhydrides while amides are generally not useful substrates in these reactions. Despite being the least reactive carboxylic acid derivative, we have found a series of amides capable of providing aromatic ketones in good yields (55–96%, 17 examples). We propose a mechanism involving diminished C-N resonance through superelectrophilic activation and subsequent cleavage to acyl cations. PMID:22690740

  9. Copper-Catalyzed Intermolecular Amidation and Imidation of Unactivated Alkanes

    PubMed Central

    2015-01-01

    We report a set of rare copper-catalyzed reactions of alkanes with simple amides, sulfonamides, and imides (i.e., benzamides, tosylamides, carbamates, and phthalimide) to form the corresponding N-alkyl products. The reactions lead to functionalization at secondary C–H bonds over tertiary C–H bonds and even occur at primary C–H bonds. [(phen)Cu(phth)] (1-phth) and [(phen)Cu(phth)2] (1-phth2), which are potential intermediates in the reaction, have been isolated and fully characterized. The stoichiometric reactions of 1-phth and 1-phth2 with alkanes, alkyl radicals, and radical probes were investigated to elucidate the mechanism of the amidation. The catalytic and stoichiometric reactions require both copper and tBuOOtBu for the generation of N-alkyl product. Neither 1-phth nor 1-phth2 reacted with excess cyclohexane at 100 °C without tBuOOtBu. However, the reactions of 1-phth and 1-phth2 with tBuOOtBu afforded N-cyclohexylphthalimide (Cy-phth), N-methylphthalimide, and tert-butoxycyclohexane (Cy-OtBu) in approximate ratios of 70:20:30, respectively. Reactions with radical traps support the intermediacy of a tert-butoxy radical, which forms an alkyl radical intermediate. The intermediacy of an alkyl radical was evidenced by the catalytic reaction of cyclohexane with benzamide in the presence of CBr4, which formed exclusively bromocyclohexane. Furthermore, stoichiometric reactions of [(phen)Cu(phth)2] with tBuOOtBu and (Ph(Me)2CO)2 at 100 °C without cyclohexane afforded N-methylphthalimide (Me-phth) from β-Me scission of the alkoxy radicals to form a methyl radical. Separate reactions of cyclohexane and d12-cyclohexane with benzamide showed that the turnover-limiting step in the catalytic reaction is the C–H cleavage of cyclohexane by a tert-butoxy radical. These mechanistic data imply that the tert-butoxy radical reacts with the C–H bonds of alkanes, and the subsequent alkyl radical combines with 1-phth2 to form the corresponding N-alkyl imide product

  10. Bent Bonds and Multiple Bonds.

    ERIC Educational Resources Information Center

    Robinson, Edward A.; Gillespie, Ronald J.

    1980-01-01

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

  11. Enantioselective synthesis of α-oxy amides via Umpolung amide synthesis.

    PubMed

    Leighty, Matthew W; Shen, Bo; Johnston, Jeffrey N

    2012-09-19

    α-Oxy amides are prepared through enantioselective synthesis using a sequence beginning with a Henry addition of bromonitromethane to aldehydes and finishing with Umpolung Amide Synthesis (UmAS). Key to high enantioselection is the finding that ortho-iodo benzoic acid salts of the chiral copper(II) bis(oxazoline) catalyst deliver both diastereomers of the Henry adduct with high enantiomeric excess, homochiral at the oxygen-bearing carbon. Overall, this approach to α-oxy amides provides an innovative complement to alternatives that focus almost entirely on the enantioselective synthesis of α-oxy carboxylic acids. PMID:22967461

  12. Rotational-vibration analysis of the n=0, nν6+ν1-nν6 subband in the hydrogen-bonded system 16O 12C ṡṡṡ 1H 19F

    NASA Astrophysics Data System (ADS)

    Kyrö, E. K.; Shoja-Chaghervand, P.; McMillan, K.; Eliades, M.; Danzeiser, D.; Bevan, J. W.

    1983-07-01

    Thirty-three P(J) branch and 15 R(J) branch transitions associated with the n=0, nν6+ν1-nν6 vibration in 16O 12C ṡṡṡ 1H 19F have been assigned. Rotational constants B, centrifugal distortion constants DJ, rotational-vibrational interaction constant α1, and the frequency of the band origin ν0, have been determined as: B″=0.102 148(14)cm-1; B'=0.104 196(14) cm-1; D″J=3.6(1.8)×10-7 cm-1; D″J=3.8 (1.8)×10-7 cm-1; α1=-61.4(5) MHz; ν0=3844.0294 (50) cm-1. The spectrum is consistent with a linear complex having a hydrogen bond ν6 bending frequency of 75±12 cm-1 and excited state r(CṡṡṡF) distance of 3.012 Å. A lower limit to the excited state lifetime is set at ≥2.8×10-10 s.

  13. Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics

    PubMed Central

    Kim, Yung Sam; Hochstrasser, Robin M.

    2010-01-01

    Following a survey of 2D IR principles this Feature Article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils. PMID:19351162

  14. Chlorination-Promoted Skeletal-Cage Transformations of C88 Fullerene by C2 Losses and a C-C Bond Rotation.

    PubMed

    Yang, Shangfeng; Wei, Tao; Scheurell, Kerstin; Kemnitz, Erhard; Troyanov, Sergey I

    2015-10-19

    High-temperature chlorination of fullerene C88 (isomer 33) with VCl4 gives rise to skeletal transformations affording several nonclassical (NC) fullerene chlorides, C86 (NC1)Cl24/26 and C84 (NC2)Cl26 , with one and two heptagons, respectively, in the carbon cages. The branched skeletal transformation including C2 losses as well as a Stone-Wales rearrangement has been comprehensively characterized by the structure determination of two intermediates and three final chlorination products. Quantum-chemical calculations demonstrate that the average energy of the C-Cl bond is significantly increased in chlorides of nonclassical fullerenes with a large number of chlorinated sites of pentagon-pentagon adjacency. PMID:26332709

  15. Multidrug resistance-selective antiproliferative activity of Piper amide alkaloids and synthetic analogues

    PubMed Central

    Wang, Yue-Hu; Goto, Masuo; Wang, Li-Ting; Hsieh, Kan-Yen; Morris-Natschke, Susan L.; Tang, Gui-Hua; Long, Chun-Lin; Lee, Kuo-Hsiung

    2015-01-01

    Twenty-five amide alkaloids (1–25) from Piper boehmeriifolium and 10 synthetic amide alkaloid derivatives (39–48) were evaluated for antiproliferative activity against eight human tumor cell lines, including chemosensitive and multidrug-resistant (MDR) cell lines. The results suggested tumor type-selectivity. 1-[7-(3,4,5-Trimethoxyphenyl)heptanoyl]piperidine (46) exhibited the best inhibitory activity (IC50 = 4.94 µM) against the P-glycoprotein (P-gp)-overexpressing KBvin MDR sub-line, while it and all other tested compounds, except 9, were inactive (IC50 >40 µM) against MDA-MB-231 and SK-BR-3. Structure-activity relationships (SARs) indicated that (i) 3,4,5-trimethoxy phenyl substitution is critical for selectivity against KBvin, (ii) the 4-methoxy group in this pattern is crucial for antiproliferative activity, (iii) double bonds in the side chain are not needed for activity, and (iv), in arylalkenylacyl amide alkaloids, replacement of an isobutylamino group with pyrrolidin-1-yl or piperidin-1-yl significantly improved activity. Further study on Piper amides is warranted, particularly whether side chain length affects the ability to overcome the MDR cancer phenotype. PMID:25241925

  16. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy.

    PubMed

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-14

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2-3 cm(-1). This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance. PMID:26277120

  17. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics.

    PubMed

    Reppert, Mike; Tokmakoff, Andrei

    2016-05-27

    Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl stretching vibration of the protein backbone, provides information on secondary structures as a result of vibrational couplings and on hydrogen-bonding contacts when isotope labeling is used to isolate specific sites. In parallel with experiments, computational models of amide I spectra that use atomistic structures from molecular dynamics simulations have evolved to calculate experimental spectra. Mixed quantum-classical models use spectroscopic maps to translate the structural information into a quantum-mechanical Hamiltonian for the spectroscopically observed vibrations. This allows one to model the spectroscopy of large proteins, disordered states, and protein conformational dynamics. With improvements in amide I models, quantitative modeling of time-dependent structural ensembles and of direct feedback between experiments and simulations is possible. We review the advances in developing these models, their theoretical basis, and current and future applications. PMID:27023758

  18. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2016-05-01

    Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl stretching vibration of the protein backbone, provides information on secondary structures as a result of vibrational couplings and on hydrogen-bonding contacts when isotope labeling is used to isolate specific sites. In parallel with experiments, computational models of amide I spectra that use atomistic structures from molecular dynamics simulations have evolved to calculate experimental spectra. Mixed quantum-classical models use spectroscopic maps to translate the structural information into a quantum-mechanical Hamiltonian for the spectroscopically observed vibrations. This allows one to model the spectroscopy of large proteins, disordered states, and protein conformational dynamics. With improvements in amide I models, quantitative modeling of time-dependent structural ensembles and of direct feedback between experiments and simulations is possible. We review the advances in developing these models, their theoretical basis, and current and future applications.

  19. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-01

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2-3 cm-1. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

  20. Synthesis and structural characterisation of amides from picolinic acid and pyridine-2,6-dicarboxylic acid

    PubMed Central

    Devi, Prarthana; Barry, Sarah M.; Houlihan, Kate M.; Murphy, Michael J.; Turner, Peter; Jensen, Paul; Rutledge, Peter J.

    2015-01-01

    Coupling picolinic acid (pyridine-2-carboxylic acid) and pyridine-2,6-dicarboxylic acid with N-alkylanilines affords a range of mono- and bis-amides in good to moderate yields. These amides are of interest for potential applications in catalysis, coordination chemistry and molecular devices. The reaction of picolinic acid with thionyl chloride to generate the acid chloride in situ leads not only to the N-alkyl-N-phenylpicolinamides as expected but also the corresponding 4-chloro-N-alkyl-N-phenylpicolinamides in the one pot. The two products are readily separated by column chromatography. Chlorinated products are not observed from the corresponding reactions of pyridine-2,6-dicarboxylic acid. X-Ray crystal structures for six of these compounds are described. These structures reveal a general preference for cis amide geometry in which the aromatic groups (N-phenyl and pyridyl) are cis to each other and the pyridine nitrogen anti to the carbonyl oxygen. Variable temperature 1H NMR experiments provide a window on amide bond isomerisation in solution. PMID:25954918

  1. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

    SciTech Connect

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-14

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2–3 cm{sup −1}. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

  2. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zahn, Dirk

    2004-05-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C⋯O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate.

  3. Single-Point Remote Control of Flapping Motion in Clothespin-Shaped Bimetallic Palladium Complexes Based on the N(sp(2) )-N(sp(3) ) Interconversion in Amide Functionalities.

    PubMed

    Inoue, Ryo; Kawamorita, Soichiro; Naota, Takeshi

    2016-04-11

    The synthesis, structure, and flapping motion of clothespin-shaped binuclear trans-bis(salicylaldiminato)palladium(II) complexes (anti-1) with 4-azaheptamethylene linkers bearing amide (a-g), urethane (h), or urea (i) functionalities are described in this report. Various 2D (1) H NMR experiments and XRD analyses indicate that the amide- and urethane-linked anti-1 a,b,d-h complexes exist as equilibrated mixtures of major and minor conformers I and II in CDCl3 , whereas the complexes anti-1 c and i were observed as a single species. The mapping of NOESY cross-peaks between conformers I and II revealed that the equilibration of the major and minor conformers of anti-1 a,b,d-h proceeds by two pathways, namely a nonrotatory flapping motion of the coordinated blades and a nonflapping rotation of C-N bonds, whereas the equilibration of anti-1 c proceeds by simultaneous flapping and rotation motions. Kinetic studies carried out by means of (1) H-(1) H EXSY experiments revealed that 1) the ΔG(≠) 298K values for the flapping motion are controlled remotely by the steric and electronic effects of the RCON functionalities and 2) the activation parameters for the nonrotatory flapping process are identical to those for the nonflapping peptide rotation in the complexes anti-1 a,b,d-h, which indicates that the present multistep conformational transformation induced by the flapping motion is controlled by the rate-determining pyramidalization/depyramidalization (i.e., sp(2) /sp(3) interconversion) of the nitrogen atoms of the functionalities. The static and controllable molecular mobility of anti-1 bearing peptide linkers has been discussed by comparison with the dynamic behavior of its analogues anti-2-4 with flexible polymethylene linkers. PMID:26934178

  4. PLANT FATTY ACID (ETHANOL) AMIDE HYDROLASES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fatty acid amide hydrolase (FAAH) plays a central role in modulating endogenous N-acylethanolamine (NAE) levels in vertebrates, and, in part, constitutes an “endocannabinoid” signaling pathway that regulates diverse physiological and behavioral processes in animals. Recently, an Arabidopsis FAAH hom...

  5. 40 CFR 721.10320 - Fatty acid amide (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Fatty acid amide (generic). 721.10320... Substances § 721.10320 Fatty acid amide (generic). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as fatty acid amide (PMN P-03-186) is...

  6. 40 CFR 721.10463 - Fatty acid amides (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Fatty acid amides (generic). 721.10463... Substances § 721.10463 Fatty acid amides (generic). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as fatty acid amides (PMN...

  7. Hydroalumination of Ketenimines and Subsequent Reactions with Heterocumulenes: Synthesis of Unsaturated Amide Derivatives and 1,3-Diimines.

    PubMed

    Jin, Xing; Willeke, Matthias; Lucchesi, Ralph; Daniliuc, Constantin-Gabriel; Fröhlich, Roland; Wibbeling, Birgit; Uhl, Werner; Würthwein, Ernst-Ulrich

    2015-06-19

    The series of differently substituted ketenimines 1 was hydroluminated using di-iso-butyl aluminum hydride. For the sterically congested ketenimine 1a, preferred hydroalumination of the C═N-bond was proven by X-ray crystallography (compound 5a). In situ treatment of the hydroaluminated ketenimines 5 with various heterocumulenes like carbodiimides, isocycanates, isothiocyanates and ketenimines as electrophiles and subsequent hydrolytic workup resulted in novel enamine derived amide species in case of N-attack (sterically less hindered ketenimines) under formation of a new C-N-bond or in 1,3-diimines by C-C-bond-formation in case of bulky substituents at the ketenimine-nitrogen atom. Furthermore, domino reactions with more than 1 equiv of the electrophile or by subsequent addition of two different electrophiles are possible and lead to polyfunctional amide derivatives of the biuret type which are otherwise not easily accessible. PMID:26031425

  8. Linear poly(ethylene oxide)-based polyurethane hydrogels: polyurethane-ureas and polyurethane-amides.

    PubMed

    Petrini, P; Tanzi, M C; Moran, C R; Graham, N B

    1999-01-01

    Over the last 30 years, water-swellable and water-insoluble hydrogels have been extensively investigated and developed, leading to a large family of materials which have found uses in a wide range of biomedical applications. While hydrogels usually present a crosslinked structure, linear polyurethane-ureas (PUUs) based on poly(ethylene oxide) have been shown to be able to absorb and swell with aqueous media without dissolving. This behavior is due to the phase separated domain morphology, where hydrogen bonded urethane/urea hard segment domains are dispersed in a PEO soft segment domain. This work investigates the possibility of obtaining linear poly(ethylene oxide)-based polyurethane-amide (PUA) hydrogels using two amide diols as chain extenders, a mono amide diol (AD) and a diamide diol (DD), and a dicarboxylic acid (maleic acid, MA). Poly(ethylene oxide) based PUAs were obtained using a "one-shot" bulk polymerization technique. The chemicophysical characterization and water-solubility tests showed that these materials, while having molecular weights similar to the PUUs, do not possess sufficient phase separation, hydrogen bonding and hydrophobicity of the hard segment domains to exhibit hydrogel behavior. Crosslinked PUAs using maleic acid as chain extender show interesting hydrogel properties. PMID:15347978

  9. Theory and experiment in concert: templated synthesis of amide rotaxanes, catenanes, and knots.

    PubMed

    Schalley, Christoph A; Reckien, Werner; Peyerimhoff, Sigrid; Baytekin, Bilge; Vögtle, Fritz

    2004-10-01

    The synthesis of amide rotaxanes, amide catenanes, and trefoil amide knots is based on template effects mediated by hydrogen bonds. While a large body of experimental data is available, in-depth theoretical studies of these template syntheses are virtually unavailable, although they would provide a more profound insight into the exact details of the hydrogen-bonding patterns involved in the formation of these mechanically interlocked species. In this article we present a density functional study of the conformational properties of tetralactam macrocycles and the threading mechanism that produces the immediate precursor for rotaxane and catenane formation. Predictions of the geometries and relative energies made on the basis of semi-empirical AM1 calculations are compared with these results in order to judge the reliability of the simpler approach. Since these calculations yield good agreement with the structural features, they have been used to extend the calculations in order to understand the mechanism of formation of a trefoil dodecaamide knot that has recently been synthesized. The inherent topological chirality of the knot is reflected in the intermediates generated during its formation; these involve helical loops. These loops parallel the rotaxane and catenane wheels with respect to the arrangement of the functional groups that mediate the template effect and may well serve as wheel analogues through which one of the precursor molecules can be threaded. This threading step finally results in the knotted structure. Good agreement between the results of the calculations presented here and experimental findings is achieved. PMID:15372695

  10. Systematic evaluation of amide bioisosteres leading to the discovery of novel and potent thiazolylimidazolidinone inhibitors of SCD1 for the treatment of metabolic diseases.

    PubMed

    Sun, Shaoyi; Zhang, Zaihui; Kodumuru, Vishnumurthy; Pokrovskaia, Natalia; Fonarev, Julia; Jia, Qi; Leung, Po-Yee; Tran, Jennifer; Ratkay, Leslie G; McLaren, David G; Radomski, Chris; Chowdhury, Sultan; Fu, Jianmin; Hubbard, Brian; Winther, Michael D; Dales, Natalie A

    2014-01-15

    Several five- and six-membered heterocycles were introduced to replace the C2-position amide bond of the original 2-aminothiazole-based hit compound 5. Specifically, replacement of the amide bond with an imidazolidinone moiety yielded a novel and potent thiazolylimidazolidinone series of SCD1 inhibitors. XEN723 (compound 22) was identified after optimization of the thiazolylimidazolidinone series. This compound demonstrated a 560-fold improvement in in vitro potency and reduced plasma desaturation indices in a dose dependent manner, with an EC50 of 4.5 mg/kg. PMID:24374272

  11. Rotational Spectrum, Conformational Composition, Intramolecular Hydrogen Bonding, and Quantum Chemical Calculations of Mercaptoacetonitrile (HSCH2C≡N), a Compound of Potential Astrochemical Interest.

    PubMed

    Møllendal, Harald; Samdal, Svein; Guillemin, Jean-Claude

    2016-03-31

    The microwave spectra of mercaptoacetonitrile (HSCH2C≡N) and one deuterated species (DSCH2C≡N) were investigated in the 7.5-124 GHz spectral interval. The spectra of two conformers denoted SC and AP were assigned. The H-S-C-C chain of atoms is synclinal in SC and anti-periplanar in AP. The ground state of SC is split into two substates separated by a comparatively small energy difference resulting in closely spaced transitions with equal intensities. Several transitions of the parent species of SC deviate from Watson's Hamiltonian. Only slight improvements were obtained using a Hamiltonian that takes coupling between the two substates into account. Deviations from Watson's Hamiltonian were also observed for the parent species of AP. However, the spectrum of the deuterated species, which was investigated only for the SC conformer, fits satisfactorily to Watson's Hamiltonian. Relative intensity measurements found SC to be lower in energy than AP by 3.8(3) kJ/mol. The strength of the intramolecular hydrogen bond between the thiol and cyano groups was estimated to be ∼2.1 kJ/mol. The microwave work was augmented by quantum chemical calculations at CCSD and MP2 levels using basis sets of minimum triple-ζ quality. Mercaptoacetonitrile has astrochemical interest, and the spectra presented herein should be useful for a potential identification of this compound in the interstellar medium. Three different ways of generating mercaptoacetonitrile from compounds already found in the interstellar medium were explored by quantum chemical calculations. PMID:26974178

  12. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    NASA Astrophysics Data System (ADS)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

  13. Design, Synthesis, and Fungicidal Activities of Novel 5-Methyl-1H-1,2,3- trizole-4-carboxyl Amide Analogues.

    PubMed

    Wang, Zhen-Jun; Yang, Hui-Hui; Tian, Lei; Zhao, Wei-Guang

    2016-01-01

    Succinate dehydrogenase inhibitors (SDHIs) are fungicides with an amide bond widely used to control plant diseases caused by phytopathogenic fungi. Because of broad spectrum activity of new SDHIs, they have attracted wide attention from the research community. A series of structurally novel SDHIs with a bioactive 1,2,3-triazole moiety were designed and synthesized. Bioactivity screening showed that some of designed N-phenethyl-1,2,3-trizole-4-carboxyl amide analogues exhibited good fungicidal activities toward Sclerotinia sclerotiorum and Botrytis cinerea, while some of Nbenzyl- 1,2,3-trizole-4-carboxyl amide analogues exhibited good fungicidal activities toward Phytophthora capsici and Cercospora arachidicola. EC50 value of compound 5d against Cercospora arachidicola (6.6 µg/mL) was lower than that of chlorothalonil (12.3 µg/mL). PMID:26558376

  14. Structures of Plutonium(IV) and Uranium(VI) with N,N-Dialkyl Amides from Crystallography, X-ray Absorption Spectra, and Theoretical Calculations.

    PubMed

    Acher, Eléonor; Hacene Cherkaski, Yanis; Dumas, Thomas; Tamain, Christelle; Guillaumont, Dominique; Boubals, Nathalie; Javierre, Guilhem; Hennig, Christoph; Solari, Pier Lorenzo; Charbonnel, Marie-Christine

    2016-06-01

    The structures of plutonium(IV) and uranium(VI) ions with a series of N,N-dialkyl amides ligands with linear and branched alkyl chains were elucidated from single-crystal X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS), and theoretical calculations. In the field of nuclear fuel reprocessing, N,N-dialkyl amides are alternative organic ligands to achieve the separation of uranium(VI) and plutonium(IV) from highly concentrated nitric acid solution. EXAFS analysis combined with XRD shows that the coordination structure of U(VI) is identical in the solution and in the solid state and is independent of the alkyl chain: two amide ligands and four bidentate nitrate ions coordinate the uranyl ion. With linear alkyl chain amides, Pu(IV) also adopt identical structures in the solid state and in solution with two amides and four bidentate nitrate ions. With branched alkyl chain amides, the coordination structure of Pu(IV) was more difficult to establish unambiguously from EXAFS. Density functional theory (DFT) calculations were consequently performed on a series of structures with different coordination modes. Structural parameters and Debye-Waller factors derived from the DFT calculations were used to compute EXAFS spectra without using fitting parameters. By using this methodology, it was possible to show that the branched alkyl chain amides form partly outer-sphere complexes with protonated ligands hydrogen bonded to nitrate ions. PMID:27171842

  15. NMe amide as a synthetic surrogate for the thioester moiety in thiocoraline.

    PubMed

    Tulla-Puche, Judit; Marcucci, Eleonora; Prats-Alfonso, Elisabet; Bayó-Puxan, Núria; Albericio, Fernando

    2009-02-12

    Bridged N-methyl amides are used as isosteres for depsi and thiodepsi bonds in thiocoraline. The introduction of NMe-amides in bridges mimics the thioester bonds without imposing steric hindrance and allows conservation of the hydrogen bonding map of the natural product. NMe-azathiocoraline was constructed by solid-phase N-methylation of the side chain of diaminopropionic acid (Dap). The three consecutive N-methyl amino acids could be coupled in good yields by using HATU/HOAt/DIEA in DMF, and the final octapeptide was also obtained on solid phase following a 4 + 4 fragment coupling approach. NMe-azathiocoraline (NMA) displayed nanomolar activity in the same order as the natural product and the same mode of action. In fact, modeling of NMe-azathiocoraline bonded to a TCGA sequence showed how the methyl groups remained further away from the DNA strand without changing the recognition pattern of thiocoraline. Moreover, NMe-azathiocoraline displayed an increased stability in human serum as compared to the parent natural product. This approach could be used in other depsipeptides and side chain to side chain cyclic peptides. PMID:19193161

  16. Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families.

    PubMed

    Defelipe, Lucas A; Lanzarotti, Esteban; Gauto, Diego; Marti, Marcelo A; Turjanski, Adrián G

    2015-03-01

    Cysteine residues have a rich chemistry and play a critical role in the catalytic activity of a plethora of enzymes. However, cysteines are susceptible to oxidation by Reactive Oxygen and Nitrogen Species, leading to a loss of their catalytic function. Therefore, cysteine oxidation is emerging as a relevant physiological regulatory mechanism. Formation of a cyclic sulfenyl amide residue at the active site of redox-regulated proteins has been proposed as a protection mechanism against irreversible oxidation as the sulfenyl amide intermediate has been identified in several proteins. However, how and why only some specific cysteine residues in particular proteins react to form this intermediate is still unknown. In the present work using in-silico based tools, we have identified a constrained conformation that accelerates sulfenyl amide formation. By means of combined MD and QM/MM calculation we show that this conformation positions the NH backbone towards the sulfenic acid and promotes the reaction to yield the sulfenyl amide intermediate, in one step with the concomitant release of a water molecule. Moreover, in a large subset of the proteins we found a conserved beta sheet-loop-helix motif, which is present across different protein folds, that is key for sulfenyl amide production as it promotes the previous formation of sulfenic acid. For catalytic activity, in several cases, proteins need the Cysteine to be in the cysteinate form, i.e. a low pKa Cys. We found that the conserved motif stabilizes the cysteinate by hydrogen bonding to several NH backbone moieties. As cysteinate is also more reactive toward ROS we propose that the sheet-loop-helix motif and the constraint conformation have been selected by evolution for proteins that need a reactive Cys protected from irreversible oxidation. Our results also highlight how fold conservation can be correlated to redox chemistry regulation of protein function. PMID:25741692

  17. Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families

    PubMed Central

    Defelipe, Lucas A.; Lanzarotti, Esteban; Gauto, Diego; Marti, Marcelo A.; Turjanski, Adrián G.

    2015-01-01

    Cysteine residues have a rich chemistry and play a critical role in the catalytic activity of a plethora of enzymes. However, cysteines are susceptible to oxidation by Reactive Oxygen and Nitrogen Species, leading to a loss of their catalytic function. Therefore, cysteine oxidation is emerging as a relevant physiological regulatory mechanism. Formation of a cyclic sulfenyl amide residue at the active site of redox-regulated proteins has been proposed as a protection mechanism against irreversible oxidation as the sulfenyl amide intermediate has been identified in several proteins. However, how and why only some specific cysteine residues in particular proteins react to form this intermediate is still unknown. In the present work using in-silico based tools, we have identified a constrained conformation that accelerates sulfenyl amide formation. By means of combined MD and QM/MM calculation we show that this conformation positions the NH backbone towards the sulfenic acid and promotes the reaction to yield the sulfenyl amide intermediate, in one step with the concomitant release of a water molecule. Moreover, in a large subset of the proteins we found a conserved beta sheet-loop-helix motif, which is present across different protein folds, that is key for sulfenyl amide production as it promotes the previous formation of sulfenic acid. For catalytic activity, in several cases, proteins need the Cysteine to be in the cysteinate form, i.e. a low pKa Cys. We found that the conserved motif stabilizes the cysteinate by hydrogen bonding to several NH backbone moieties. As cysteinate is also more reactive toward ROS we propose that the sheet-loop-helix motif and the constraint conformation have been selected by evolution for proteins that need a reactive Cys protected from irreversible oxidation. Our results also highlight how fold conservation can be correlated to redox chemistry regulation of protein function. PMID:25741692

  18. Thorium Mono- and Bis(imido) Complexes Made by Reprotonation of cyclo-Metalated Amides.

    PubMed

    Bell, Nicola L; Maron, Laurent; Arnold, Polly L

    2015-08-26

    Molecules containing actinide-nitrogen multiple bonds are of current interest as simple models for new actinide nitride nuclear fuels, and for their potential for the catalytic activation of inert hydrocarbon C-H bonds. Complexes with up to three uranium-nitrogen double bonds are now being widely studied, yet those with one thorium-nitrogen double bond are rare, and those with two are unknown. A new, simple mono(imido) thorium complex and the first bis(imido) thorium complex, K[Th(═NAr)N″3] and K2[Th(═NAr)2N″2], are readily made from insertion reactions (Ar = aryl, N″ = N(SiMe3)2) into the Th-C bond of the cyclometalated thorium amides [ThN″2(N(SiMe3)(SiMe2CH2))] and K[ThN″(N(SiMe3)(SiMe2CH2))2]. X-ray and computational structural analyses show a "transition-metal-like" cis-bis(imido) geometry and polarized Th═N bonds with twice the Wiberg bond order of the formally single Th-N bond in the same molecule. PMID:26244991

  19. Palladium-Catalyzed Deaminative Phenanthridinone Synthesis from Aniline via C-H Bond Activation.

    PubMed

    Yedage, Subhash L; Bhanage, Bhalchandra M

    2016-05-20

    This work reports palladium-catalyzed phenanthridinone synthesis using the coupling of aniline and amide by formation of C-C and C-N bonds in a one-pot fashion via dual C-H bond activation. It involves simultaneous cleavage of four bonds and the formation of two new bonds. The present protocol is ligand-free, takes place under mild reaction conditions, and is environmentally benign as nitrogen gas and water are the only side products. This transformation demonstrates a broad range of aniline and amide substrates with different functional groups and has been scaled up to gram level. PMID:27088815

  20. [Amides of creatine: perspectives of neuroprotection].

    PubMed

    Vlasov, T D; Chefu, S G; Baĭsa, A E; Leko, M V; Burov, S V; Veselkina, O S

    2011-07-01

    We evaluated the efficacy of derivatives of creatine and amino acids (CrAA) for decreasing cerebral injury in rats with transient middle cerebral artery occlusion (MCAO). Neuroprotective effects of amides of creatine and glycine (CrGlyOEt), phenylalanine (CrPheNH2), thyrosine (CrTyrNH2), and GABA (CrGABAOEt) were investigated. Brain injury was evaluated on day 2 after transient MCAO using a TTC staining of brain slices. Compared with the MCAO control group, all the CrAms showed decreased cerebral injury (p < 0.05). However CrPheNH2, CrTyrNH2, and CrGABAOEt were toxic after intravenous administration and investigated only after intraperitoneal injection. CrGlyOEt did not show any toxicity at dose of 1 mmol/kg. These data evidenced that creatinyl amides can represent promising candidates for the development of new drugs useful in brain ischemia treatment. PMID:21961295

  1. The Influence of the Amide Linkage in the Fe(III) -Binding Properties of Catechol-Modified Rosamine Derivatives.

    PubMed

    Queirós, Carla; Leite, Andreia; G M Couto, Maria; Cunha-Silva, Luís; Barone, Giampaolo; de Castro, Baltazar; Rangel, Maria; M N Silva, André; M G Silva, Ana

    2015-10-26

    The two new fluorescent ligands RosCat1 and RosCat2 contain catechol receptors connected to rosamine platforms through an amide linkage and were synthesized by using microwave-assisted coupling reactions of carboxyl- or amine-substituted rosamines with the corresponding catechol units and subsequent deprotection. RosCat1 possesses a reverse amide, whereas RosCat2 has the usual oriented amide bond (HNCO vs. CONH, respectively). The ligands were characterized by means of NMR spectroscopy, mass-spectrometry, and DFT calculations and X-ray crystallography studies for RosCat1. The influence of the amide linkage on the photophysical properties of the fluorescent ligands was assessed in different solvents and showed a higher fluorescence quantum yield for RosCat1. The coordination chemistry of these ligands with a Fe(III) center has been rationalized by mass-spectrometric analysis and semiempirical calculations. Octahedral Fe(III) complexes were obtained by the chelation of three RosCat1 or RosCat2 ligands. Interestingly, the unconventional amide connectivity in RosCat1 imposes the formation of an eight-membered ring on the chelate complex through a "salicylate-type" mode of coordination. PMID:26493881

  2. Studies of indium amides and nitrides

    SciTech Connect

    Purdy, A.P.; Berry, A.D.

    1993-12-31

    A reaction between InI{sub 3} and 3 eq. of KNH{sub 2} in liquid NH{sub 3} forms indium(III) amide (In(NH{sub 2}){sub 3}) a white, nearly insoluble compound. Indium(III) amide readily combines with KNH{sub 2} in liquid NH{sub 3} to form the mixed metal amide K{sub 2}In(NH{sub 2}){sub 5}. Other potassium and sodium derivatives MxIn(NH{sub 2}){sub 3+x} derivatives were prepared in a similar manner, but not all were obtained pure in the solid state. An impure tri-lithium derivative (Li{sub 3}In(NH{sub 2}){sub 6}) was obtained by adding a KNH{sub 2} solution (6 eq) to a solution of InI{sub 3} and 3 eq of LiI. Pyrolysis (in vacuo 25-300{degrees}C, under N{sub 2} 300-400{degrees}C) of In(NH{sub 2}){sub 3} or MxIn(NH{sub 2}){sub x+3} (M = Na, K) to 400{degrees}C results in the formation of InN, but indium metal is also formed from some of the mixed metal amides. The product from thermal decomposition of Li{sub 3}In(NH{sub 2}){sub 6} under vacuum was tentatively identified as the ternary nitride Li{sub 3}InN{sub 2}. Products were characterized by elemental analysis, IR spectroscopy, and powder x-ray diffraction experiments.

  3. Polyimides containing amide and perfluoroisopropylidene connecting groups

    NASA Technical Reports Server (NTRS)

    Dezern, James F. (Inventor)

    1993-01-01

    New, thermooxidatively stable polyimides were prepared from the reaction of aromatic dianhydrides containing isopropylidene bridging groups with aromatic diamines containing amide connecting groups between the rings. Several of these polyimides were shown to be semi-crystalline as evidenced by wide angle x ray scattering and differential scanning calorimetry. Most of the polyimides form tough, flexible films with high tensile properties. These polyimide films exhibit enhanced solubility in organic solvents.

  4. Cooling rate effects on the microstructure, solid content, and rheological properties of organogels of amides derived from stearic and (R)-12-hydroxystearic acid in vegetable oil.

    PubMed

    Toro-Vazquez, Jorge F; Morales-Rueda, Juan; Torres-Martínez, Adriana; Charó-Alonso, Miriam A; Mallia, V Ajay; Weiss, Richard G

    2013-06-25

    Using safflower oil as the liquid phase, we investigated the organogelation properties of stearic acid (SA), (R)-12-hydroxystearic acid (HSA), and different primary and secondary amides synthesized from SA and HSA. The objective was to establish the relationship between the gelator's molecular structure, solid content, and gels' microstructure that determines the rheological properties of organogels developed at two cooling rates, 1 and 20 °C/min. The results showed that the presence of a 12-OH group in the gelator molecule makes its crystallization kinetics cooling rate dependent and modifies its crystallization behavior. Thus, SA crystallizes as large platelets, while HSA crystallizes as fibers forming gels with higher solid content, particularly at 20 °C/min. The addition to HSA of a primary or a secondary amide bonded with an alkyl group resulted in gelator molecules that crystallized as fibrillar spherulites at both cooling rates. Independent of the cooling rate, gels of HSA and its amide derivatives showed thixotropic behavior. The rheological properties of the amide's organogels depend on a balance between hydrogen-bonding sites and the alkyl chain length bonded to the amide group. However, it might also be associated with the effect that the gelators' molecular weight has on crystal growth and its consequence on fiber interpenetration among vicinal spherulites. These results were compared with those obtained with candelilla wax (CW), a well-known edible gelling additive used by the food industry. CW organogels had higher elasticity than HSA gels but lower than the gels formed by amides. Additionally, CW gels showed similar or even higher thixotropic behavior than HSA and the amide's gels. These remarkable rheological properties resulted from the microstructural organization of CW organogels. We concluded that microstructure has a more important role determining the organogels' rheology than the solid content. The fitting models developed to describe the

  5. Thioamide Hydroxypyrothiones Supersede Amide Hydroxypyrothiones in Potency Against Anthrax Lethal Factor

    PubMed Central

    Agrawal, Arpita; de Oliveira, César Augusto F.; Cheng, Yuhui; Jacobsen, Jennifer A.; McCammon, J. Andrew; Cohen, Seth M.

    2009-01-01

    Anthrax lethal factor (LF) is a critical virulence factor in the pathogenesis of anthrax. A structure-activity relationship (SAR) of potential lethal factor inhibitors (LFi) is presented in which the zinc-binding group (ZBG), linker, and backbone moieties for a series of hydroxypyrone-based compounds were systematically varied. It was found that hydroxypyrothione ZBGs generate more potent inhibitors than hydroxypyrone ZBGs. Furthermore, coupling the hydroxypyrothione to a backbone group via a thioamide bond improves potency when compared to an amide linker. QM/MM studies show that the thioamide bond in these inhibitors allows for the formation of two additional hydrogen bonds with the protein active site. In both types of hydroxypyrothione compounds, ligand efficiencies of 0.29-0.54 kcal mol-1 per heavy atom were achieved. The results highlight the need for a better understanding to optimize the interplay between the ZBG, linker, and backbone to get improved LFi. PMID:19170530

  6. New Umami Amides: Structure-Taste Relationship Studies of Cinnamic Acid Derived Amides and the Natural Occurrence of an Intense Umami Amide in Zanthoxylum piperitum.

    PubMed

    Frerot, Eric; Neirynck, Nathalie; Cayeux, Isabelle; Yuan, Yoyo Hui-Juan; Yuan, Yong-Ming

    2015-08-19

    A series of aromatic amides were synthesized from various acids and amines selected from naturally occurring structural frameworks. These synthetic amides were evaluated for umami taste in comparison with monosodium glutamate. The effect of the substitution pattern of both the acid and the amine parts on umami taste was investigated. The only intensely umami-tasting amides were those made from 3,4-dimethoxycinnamic acid. The amine part was more tolerant to structural changes. Amides bearing an alkyl- or alkoxy-substituted phenylethylamine residue displayed a clean umami taste as 20 ppm solutions in water. Ultraperformance liquid chromatography coupled with a high quadrupole-Orbitrap mass spectrometer (UPLC/MS) was subsequently used to show the natural occurrence of these amides. (E)-3-(3,4-Dimethoxyphenyl)-N-(4-methoxyphenethyl)acrylamide was shown to occur in the roots and stems of Zanthoxylum piperitum, a plant of the family Rutaceae growing in Korea, Japan, and China. PMID:26230212

  7. (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

  8. Crystal structures of (E)-3-(furan-2-yl)-2-phenyl-N-tosyl­acryl­amide and (E)-3-phenyl-2-(m-tol­yl)-N-tosyl­acryl­amide

    PubMed Central

    Cheng, Dong; Meng, Xiangzhen; Sheng, Zeyuan; Wang, Shuangming; Duan, Yuanyuan; Li, Ziqian

    2016-01-01

    In the title N-tosyl­acryl­amide compounds, C20H17NO4S, (I), and C23H21NO3S, (II), the conformation about the C=C bond is E. The acryl­amide groups, [–NH—C(=O)—C=C–], are almost planar, with the N—C—C=C torsion angle being −170.18 (14)° in (I) and −168.01 (17)° in (II). In (I), the furan, phenyl and 4-methyl­benzene rings are inclined to the acryl­amide mean plane by 26.47 (11), 69.01 (8) and 82.49 (9)°, respectively. In (II), the phenyl, 3-methyl­benzene and 4-methyl­benzene rings are inclined to the acryl­amide mean plane by 11.61 (10), 78.44 (10) and 78.24 (10)°, respectively. There is an intra­molecular C—H⋯π inter­action present in compound (II). In the crystals of both compounds, mol­ecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with an R 2 2(8) ring motif. In (I), the dimers are reinforced by C—H⋯O hydrogen bonds and linked by C—H⋯π inter­actions, forming chains along [011]. In the crystal of (II), the dimers are linked via C—H⋯O hydrogen bonds, forming chains along [100]. The chains are further linked by C—H⋯π inter­actions, forming layers parallel to (010). PMID:27308045

  9. Lewis Acid Catalyzed Regiospecific Cross-Dehydrative Coupling Reaction of 2-Furylcarbinols with β-Keto Amides or 4-Hydroxycoumarins: A Route to Furyl Enols.

    PubMed

    Miao, Maozhong; Luo, Yi; Li, Hongli; Xu, Xin; Chen, Zhengkai; Xu, Jianfeng; Ren, Hongjun

    2016-06-17

    Lewis acid catalyzed directly dehydrative carbon-carbon bond formation reaction of 2-furylcarbinols with β-keto amides provides a straightforward method for regioselective synthesis of (Z)-furyl enols. Moreover, this Lewis acid catalyzed cross-coupling reaction can be extended to an interesting heterocyclic version featuring a functionalized 3-furyl-4-hydroxycoumarin synthesis. PMID:27224045

  10. Electrochemical reduction of nitrate in the presence of an amide

    DOEpatents

    Dziewinski, Jacek J.; Marczak, Stanislaw

    2002-01-01

    The electrochemical reduction of nitrates in aqueous solutions thereof in the presence of amides to gaseous nitrogen (N.sub.2) is described. Generally, electrochemical reduction of NO.sub.3 proceeds stepwise, from NO.sub.3 to N.sub.2, and subsequently in several consecutive steps to ammonia (NH.sub.3) as a final product. Addition of at least one amide to the solution being electrolyzed suppresses ammonia generation, since suitable amides react with NO.sub.2 to generate N.sub.2. This permits nitrate reduction to gaseous nitrogen to proceed by electrolysis. Suitable amides include urea, sulfamic acid, formamide, and acetamide.

  11. Synthesis of Nitriles via Palladium-Catalyzed Water Shuffling from Amides to Acetonitrile

    PubMed Central

    Zhang, Wandi; Haskins, Christopher W.; Yang, Yang; Dai, Mingji

    2014-01-01

    Palladium-catalyzed synthesis of nitriles from amides has been described. Two similar, but complementary reaction conditions have been identified to convert various amides including α,β,γ,δ-unsaturated amides, cinnamides, aromatic amides and alkyl amides to the corresponding nitriles in good to excellent yield. PMID:25316145

  12. Palladium-Catalyzed Carbonylation of β-Arylethylamide Directed by Oxalyl Amide in the Presence of Carbon Monoxide.

    PubMed

    Zhang, Li; Wang, Chao; Han, Jian; Huang, Zhi-Bin; Zhao, Yingsheng

    2016-06-17

    Pd-catalyzed regioselective coupling of β-C(sp(2))-H bonds in aromatic amines protected by oxalyl amide with carbon monoxide is reported. The reaction could tolerate various functional groups and could afford good to excellent yields of the corresponding 3,4-dihydroisoquinolinone derivatives. Remarkably, it could also tolerate β-arylethylamino acid and thiopheneethylamine derivatives, thus showing their potential for producing several important units for bioactive compound synthesis. PMID:27213988

  13. Aerobic palladium(II)-catalyzed dehydrogenation of cyclohexene-1-carbonyl indole amides: an indole-directed aromatization.

    PubMed

    Kandukuri, Sandeep R; Oestreich, Martin

    2012-10-01

    A palladium(II)-catalyzed oxidative dehydrogenation of cyclohexene-1-carbonyl indole amides yielding the corresponding benzoylindoles is reported. The new aromatization is also applied to functionalized indoles such as tryptamine and tryptophan. The tethered indole is likely acting as a directing group for allylic C-H bond activation, and there is evidence for a mechanism proceeding through 1,3-diene formation followed by aromatization. PMID:22950832

  14. Enantioselective Synthesis of α-Hydroxy Amides and β-Amino Alcohols from α-Keto Amides.

    PubMed

    Mamillapalli, N Chary; Sekar, Govindasamy

    2015-12-14

    Synthesis of enantiomerically enriched α-hydroxy amides and β-amino alcohols has been accomplished by enantioselective reduction of α-keto amides with hydrosilanes. A series of α-keto amides were reduced in the presence of chiral Cu(II)/(S)-DTBM-SEGPHOS catalyst to give the corresponding optically active α-hydroxy amides with excellent enantioselectivities by using (EtO)3SiH as a reducing agent. Furthermore, a one-pot complete reduction of both ketone and amide groups of α-keto amides has been achieved using the same chiral copper catalyst followed by tetra-n-butylammonium fluoride (TBAF) catalyst in presence of (EtO)3SiH to afford the corresponding chiral β-amino alcohol derivatives. PMID:26503887

  15. Copper-catalyzed oxidative amidation of aldehydes with amine salts: synthesis of primary, secondary, and tertiary amides.

    PubMed

    Ghosh, Subhash Chandra; Ngiam, Joyce S Y; Seayad, Abdul M; Tuan, Dang Thanh; Chai, Christina L L; Chen, Anqi

    2012-09-21

    A practical method for the amidation of aldehydes with economic ammonium chloride or amine hydrochloride salts has been developed for the synthesis of a wide variety of amides by using inexpensive copper sulfate or copper(I) oxide as a catalyst and aqueous tert-butyl hydroperoxide as an oxidant. This amidation reaction is operationally straightforward and provides primary, secondary, and tertiary amides in good to excellent yields for most cases utilizing inexpensive and readily available reagents under mild conditions. In situ formation of amine salts from free amines extends the substrate scope of the reaction. Chiral amides are also synthesized from their corresponding chiral amines without detectable racemization. The practicality of this amide formation reaction has been demonstrated in an efficient synthesis of the antiarrhythmic drug N-acetylprocainamide. PMID:22894712

  16. The Importance of Hydrogen Bonding and Aromatic Stacking to the Affinity and Efficacy of Cannabinoid Receptor CB2 Antagonist, 5-(4-Chloro-3-methyl-phenyl)-1-(4-methyl-benzyl)-1H-pyrazole-3-carboxylic acid (1,3,3-trimethyl-bicyclo[2.2.1]hept-2-yl)-amide (SR144528)

    PubMed Central

    Kotsikorou, Evangelia; Navas, Frank; Roche, Michael J.; Gilliam, Anne F.; Thomas, Brian; Seltzman, Herbert H.; Kumar, Pritesh; Song, Zhao-Hui; Hurst, Dow P.; Lynch, Diane L.; Reggio, Patricia H.

    2013-01-01

    Despite the therapeutic promise of the sub-nanomolar affinity cannabinoid CB2 antagonist, N-[(1S)-endo-1,3,3-trimethylbicyclo[2.2.1]heptan2-yl]-5-(4-chloro-3-methylphenyl)-1-[(4-methylphenyl)methyl]-1H-pyrazole-3-carboxamide (SR144528, 1), little is known about its binding site interactions and no primary interaction site for 1 at CB2 has been identified. We report here the results of Glide docking studies in our cannabinoid CB2 inactive state model that were then tested via compound synthesis, binding and functional assays. Our results show that the amide functional group of 1 is critical to its CB2 affinity and efficacy and that aromatic stacking interactions in the TMH5/6 aromatic cluster of CB2 are also important. Molecular modifications that increased the positive electrostatic potential in the region between the fenchyl and aromatic rings led to more efficacious compounds. This result is consistent with the EC-3 loop negatively charged amino acid, D275 (identified via Glide docking studies) acting as the primary interaction site for 1 and its analogs. PMID:23855811

  17. Photoinduced hydrogen-bonding dynamics.

    PubMed

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

    Hydrogen bonding dynamics has received extensive research attention in recent years due to the significant advances in femtolaser spectroscopy experiments and quantum chemistry calculations. Usually, photoexcitation would cause changes in the hydrogen bonding formed through the interaction between hydrogen donor and acceptor molecules on their ground electronic states, and such transient strengthening or weakening of hydrogen bonding could be crucial for the photophysical transformations and the subsequent photochemical reactions that occurred on a time scale from tens of femtosecond to a few nanoseconds. In this article, we review the combined experimental and theoretical studies focusing on the ultrafast electronic and vibrational hydrogen bonding dynamics. Through these studies, new mechanisms and proposals and common rules have been put forward to advance our understanding of the hydrogen bondings dynamics in a variety of important photoinduced phenomena like photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer processes, chemosensor fluorescence sensing, rearrangements of the hydrogen-bond network including forming and breaking hydrogen bond in water. Graphical Abstract We review the recent advances on exploring the photoinduced hydrogen bonding dynamics in solutions through a joint approach of laser spectroscopy and theoretical calculation. The reviewed studies have put forward a new mechanism, new proposal, and new rule for a variety of photoinduced phenomena such as photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer, chemosensor fluorescence sensing, and rearrangements of the hydrogen-bond network in water. PMID:27491849

  18. Bond Issues.

    ERIC Educational Resources Information Center

    Pollack, Rachel H.

    2000-01-01

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

  19. Role of native defects in the Li amide/Li imide hydrogen storage reaction

    NASA Astrophysics Data System (ADS)

    Hoang, Khang; van de Walle, Chris G.

    2010-03-01

    Reversible reaction involving Li amide/Li imide (LiNH2 + LiH <-> Li2NH + H2) has been shown to be a potential mechanism for hydrogen storage [1]. Recent synchrotron x-ray diffraction refinement suggests that the transformation between LiNH2 and Li2NH is a bulk reaction that occurs through non-stoichiometric processes [2]. To build a deeper understanding of these processes, we have carried out first-principles studies based on density functional theory of native point defects and defect complexes in LiNH2 and Li2NH. Among the native defects, we find that positively and negatively charged Li and H interstitials and vacancies have the lowest formation energies. Some of the Li-related defects are found to be very mobile, and should be the dominant migratory species in the systems. Our first-principles results suggest specific mechanisms for the role of native defects in the Li amide/Li imide reaction. [1] P. Chen et al., Nature 420, 302 (2002). [2] W. I. F. David et al., J. Am. Chem. Soc. 129, 1594 (2007).

  20. General and Mild Cobalt-Catalyzed C-Alkylation of Unactivated Amides and Esters with Alcohols.

    PubMed

    Deibl, Nicklas; Kempe, Rhett

    2016-08-31

    The borrowing hydrogen or hydrogen autotransfer methodology is an elegant and sustainable or green concept to construct carbon-carbon bonds. In this concept, alcohols, which can be obtained from barely used and indigestible biomass, such as lignocellulose, are employed as alkylating reagents. An especially challenging alkylation is that of unactivated esters and amides. Only noble metal catalysts based on iridium and ruthenium have been used to accomplish these reactions. Herein, we report on the first base metal-catalyzed α-alkylation of unactivated amides and esters by alcohols. Cobalt complexes stabilized with pincer ligands, recently developed in our laboratory, catalyze these reactions very efficiently. The precatalysts can be synthesized easily from commercially available starting materials on a multigram scale and are self-activating under the basic reaction conditions. This Co catalyst class is also able to mediate alkylation reactions of both esters and amides. In addition, we apply the methodology to synthesize ketones and to convert alcohols into aldehydes elongated by two carbon atoms. PMID:27490682

  1. Reduction of N-allylamides by LiAlH4: unexpected attack of the double bond with mechanistic studies of product and byproduct formation.

    PubMed

    Thiedemann, Birk; Schmitz, Christin M L; Staubitz, Anne

    2014-11-01

    The reduction of secondary allyl amides with LiAlH4 can lead to a concomitant reduction of the double bond. Previously, an excess of LiAlH4 in hazardous solvents was used for the reduction. This work discusses optimized reaction conditions in tBuOMe as a safe solvent, with only a 1.5-fold excess of LiAlH4, without reduction of the double bond in most cases. (1)H and (2)D NMR spectroscopic studies give evidence for the mechanism of the reduction of the amide as well as the double bond: Amide reduction generally precedes double bond reduction. Sterically hindered allylamides are an exception. They are reduced considerably more slowly at higher temperatures, and double bond reduction is observed before amide reduction has gone to completion. PMID:25347383

  2. Biodegradable gadolinium-chelated cationic poly(urethane amide) copolymers for gene transfection and magnetic resonance imaging.

    PubMed

    Gao, Xiaolong; Wang, Gangmin; Shi, Ting; Shao, Zhihong; Zhao, Peng; Shi, Donglu; Ren, Jie; Lin, Chao; Wang, Peijun

    2016-08-01

    Theranostic nano-polyplexes containing gene and imaging agents hold a great promise for tumor diagnosis and therapy. In this work, we develop a group of new gadolinium (Gd)-chelated cationic poly(urethane amide)s for gene delivery and T1-weighted magnetic resonance (MR) imaging. Cationic poly(urethane amide)s (denoted as CPUAs) having multiple disulfide bonds, urethane and amide linkages were synthesized by stepwise polycondensation reaction between 1,4-bis(3-aminopropyl)piperazine and a mixture of di(4-nitrophenyl)-2, 2'-dithiodiethanocarbonate (DTDE-PNC) and diethylenetriaminepentaacetic acid (DTPA) dianhydride at varied molar ratios. Then, Gd-chelated CPUAs (denoted as GdCPUAs) were produced by chelating Gd(III) ions with DTPA residues of CPUAs. These GdCPUAs could condense gene into nanosized and positively-charged polyplexes in a physiological condition and, however, liberated gene in an intracellular reductive environment. In vitro transfection experiments revealed that the GdCPUA at a DTDE-PNC/DTPA residue molar ratio of 85/15 induced the highest transfection efficiency in different cancer cells. This efficiency was higher than that yielded with 25kDa branched polyethylenimine as a positive control. GdCPUAs and their polyplexes exhibited low cytotoxicity when an optimal transfection activity was detected. Moreover, GdCPUAs may serve as contrast agents for T1-weighted magnetic resonance imaging. The results of this work indicate that biodegradable Gd-chelated cationic poly(urethane amide) copolymers have high potential for tumor theranostics. PMID:27157741

  3. Amide Link Scission in the Polyamide Active Layers of Thin-Film Composite Membranes upon Exposure to Free Chlorine: Kinetics and Mechanisms.

    PubMed

    Powell, Joshua; Luh, Jeanne; Coronell, Orlando

    2015-10-20

    The volume-averaged amide link scission in the aromatic polyamide active layer of a reverse osmosis membrane upon exposure to free chlorine was quantified at a variety of free chlorine exposure times, concentrations, and pH and rinsing conditions. The results showed that (i) hydroxyl ions are needed for scission to occur, (ii) hydroxide-induced amide link scission is a strong function of exposure to hypochlorous acid, (iii) the ratio between amide links broken and chlorine atoms taken up increased with the chlorination pH and reached a maximum of ∼25%, (iv) polyamide disintegration occurs when high free chlorine concentrations, alkaline conditions, and high exposure times are combined, (v) amide link scission promotes further chlorine uptake, and (vi) scission at the membrane surface is unrepresentative of volume-averaged scission in the active layer. Our observations are consistent with previously proposed mechanisms describing amide link scission as a result of the hydrolysis of the N-chlorinated amidic N-C bond due to nucleophilic attack by hydroxyl ions. This study increases the understanding of the physicochemical changes that could occur for membranes in treatment plants using chlorine as an upstream disinfectant and the extent and rate at which those changes would occur. PMID:26394532

  4. Reactions of HC triple bond CCMe sub 2 NHCOR alkynes with M sub 3 (CO) sub 12 carbonyls (M = Ru, R = C sub 6 H sub 9 , Ph; M = Os, R = C sub 6 H sub 9 ). Synthesis and crystal structure of Ru sub 4 (CO) sub 11 (HC triple bond CCMe sub 2 NHCOC sub 6 H sub 9 ), a butterfly cluster showing an interaction between a wingtip metal and the amide CO

    SciTech Connect

    Predieri, G.; Tiripicchio, A.; Camellini, M.T.; Costa, M. ); Sappa, E. )

    1990-06-01

    The alkynes HC{triple bond}CCMe{sub 2}NHCOR react with M{sub 3}(CO){sub 12} (M = Ru or Os) giving, upon oxidative addition, the expected hydrides ({mu}-H)M{sub 3}(CO){sub 9}({mu}{sub 3}-{eta}{sup 2}-C{triple bond}CCMe{sub 2}NHCOR) and the unprecedented butterfly clusters M{sub 4}(CO){sub 11}({mu}{sub 4}-{eta}{sup 2}-HC{triple bond}CCME{sub 2}NHCOR). These complexes have been characterized by spectroscopic studies; the structure of the ruthenium butterfly cluster with R = C{sub 6}H{sub 9} has been determined by X-ray diffraction methods. Crystals, containing CHCl{sub 3} as solvation molecules, are triclinic with Z = 2 in a unit cell of dimensions a = 13.521 (6), b = 14.617 (6), c = 9.049 (5) {angstrom}, {alpha} = 79.28 (2), {beta} = 108.79 (2), {gamma} = 111.85 (2){degree}.

  5. Platinum-catalyzed reduction of amides with hydrosilanes bearing dual Si-H groups: a theoretical study of the reaction mechanism.

    PubMed

    Nakatani, Naoki; Hasegawa, Jun-ya; Sunada, Yusuke; Nagashima, Hideo

    2015-11-28

    A platinum-catalyzed amide reduction through hydrosilylation with 1,2-bis(dimethylsilyl)benzene (BDSB) was investigated on a theoretical basis. While the platinum-catalyzed hydrosilylation of alkenes is well known, that of carbonyl groups rarely occurs. The only exception involves the use of bifunctional hydrosilanes having dual, closely located Si-H groups, which accelerate the hydrosilylation of carbonyl groups, leading to successful reduction of amides to amines under mild conditions. In the present study, we determined through density functional theory calculations that the platinum-catalyzed hydrosilylation of the C=O bond proceeds via a Pt(IV)-disilyl-dihydride intermediate with an associated activation energy of 29.6 kcal mol(-1). Although it was believed that the hydrosilylation of carbonyl groups does not occur via the classical Chalk-Harrod cycle, the computational results support a mechanism involving the insertion of the amide C=O bond into a Pt-H bond. This insertion readily occurs because a Pt-H bond in the Pt(IV)-disilyl-dihydride intermediate is highly activated due to the strong σ-donating interaction of the silyl groups. The modified Chalk-Harrod mechanism that occurs preferentially in rhodium-catalyzed hydrosilylation as well as the ionic outer sphere mechanism associated with iridium-catalyzed amide reduction were both safely ruled out as mechanisms for this platinum-catalyzed amide reduction, because of the unexpectedly large activation barrier (>40 kcal mol(-1)) for the Si-O bond formation. PMID:26497866

  6. Cesium Carboxylate-Promoted Iridium Catalyzed C-H Amidation/Cyclization with 2,2,2-Trichloroethoxycarbonyl Azide.

    PubMed

    Zhang, Tao; Wang, Zhen; Hu, Xuejiao; Yu, Meng; Deng, Tianning; Li, Guigen; Lu, Hongjian

    2016-06-01

    An Ir(III)-catalyzed direct C-H amidation/cyclization of benzamides using 2,2,2-trichloroethoxycarbonyl azide (TrocN3) as the aminocarbonyl source is reported. With the aid of cesium carboxylate, the reactions proceed efficiently and with high regioselectivity, producing various functionalized quinazoline-2,4(1H,3H)-diones, which are important building blocks and key synthetic intermediates for biologically and medicinally important compounds. During the reactions, two new C-N bonds were formed by breaking C-H and N-H bonds sequence. PMID:27164005

  7. Phenyltrimethylammonium Salts as Methylation Reagents in the Nickel-Catalyzed Methylation of C-H Bonds.

    PubMed

    Uemura, Takeshi; Yamaguchi, Mao; Chatani, Naoto

    2016-02-24

    Methylation of C(sp(2))-H bonds was achieved through the Ni(II)-catalyzed reaction of benzamides with phenyltrimethylammonium bromide or iodide as the source of the methyl group. The reaction has a broad scope and shows high functional-group compatibility. The reaction is also applicable to the methylation of C(sp(3))-H bonds in aliphatic amides. PMID:26821872

  8. Rotational spectrum of tryptophan

    SciTech Connect

    Sanz, M. Eugenia Cabezas, Carlos Mata, Santiago Alonso, Josè L.

    2014-05-28

    The rotational spectrum of the natural amino acid tryptophan has been observed for the first time using a combination of laser ablation, molecular beams, and Fourier transform microwave spectroscopy. Independent analysis of the rotational spectra of individual conformers has conducted to a definitive identification of two different conformers of tryptophan, with one of the observed conformers never reported before. The analysis of the {sup 14}N nuclear quadrupole coupling constants is of particular significance since it allows discrimination between structures, thus providing structural information on the orientation of the amino group. Both observed conformers are stabilized by an O–H···N hydrogen bond in the side chain and a N–H···π interaction forming a chain that reinforce the strength of hydrogen bonds through cooperative effects.

  9. Exocyclic push-pull conjugated compounds. Part 3. An experimental NMR and theoretical MO ab initio study of the structure, the electronic properties and barriers to rotation about the exocyclic partial double bond in 2- exo-methylene- and 2-cyanoimino-quinazolines and -benzodiazepines

    NASA Astrophysics Data System (ADS)

    Benassi, R.; Bertarini, C.; Hilfert, L.; Kempter, G.; Kleinpeter, E.; Spindler, J.; Taddei, F.; Thomas, S.

    2000-03-01

    The structure of a number of 2- exo-methylene substituted quinazolines and benzodiazepines, respectively, 1, 3a, b, 4( X=-CN, -COOEt ) and their 2-cyanoimino substituted analogues 2, 3c, d( X=-CN, -SO 2C 6H 4-Me (p) was completely assigned by the whole arsenal of 1D and 2D NMR spectroscopic methods. The E/ Z isomerism at the exo-cyclic double bond was determined by both NMR spectroscopy and confirmed by ab initio quantum chemical calculations; the Z isomer is the preferred one, its amount proved dependent on steric hindrance. Due to the push-pull effect in this part of the molecules the restricted rotation about the partial C 2,C 11 and C 2,N 11 double bonds, could also be studied and the barrier to rotation measured by dynamic NMR spectroscopy. The free energies of activation of this dynamic process proved very similar along the compounds studied but being dependent on the polarity of the solvent. Quantum chemical calculations at the ab initio level were employed to prove the stereochemistry at the exo-cyclic partial double bonds of 1- 4, to calculate the barriers to rotation but also to discuss in detail both the ground and the transition state of the latter dynamic process in order to better understand electronic, inter- and intramolecular effects on the barrier to rotation which could be determined experimentally. In the cyanoimino substituted compounds 2, 3c, d, the MO ab initio calculations evidence the isomer interconversion to be better described by the internal rotation process than by the lateral shift mechanism.

  10. Nickel-Catalyzed Reductive Amidation of Unactivated Alkyl Bromides.

    PubMed

    Serrano, Eloisa; Martin, Ruben

    2016-09-01

    A user-friendly, nickel-catalyzed reductive amidation of unactivated primary, secondary, and tertiary alkyl bromides with isocyanates is described. This catalytic strategy offers an efficient synthesis of a wide range of aliphatic amides under mild conditions and with an excellent chemoselectivity profile while avoiding the use of stoichiometric and sensitive organometallic reagents. PMID:27357076

  11. Fatty acid amides from freshwater green alga Rhizoclonium hieroglyphicum.

    PubMed

    Dembitsky, V M; Shkrob, I; Rozentsvet, O A

    2000-08-01

    Freshwater green algae Rhizoclonium hieroglyphicum growing in the Ural Mountains were examined for their fatty acid amides using capillary gas chromatography-mass spectrometry (GC-MS). Eight fatty acid amides were identified by GC-MS. (Z)-9-octadecenamide was found to be the major component (2.26%). PMID:11014298

  12. Rotational moulding.

    PubMed

    Crawford, R J; Kearns, M P

    2003-10-01

    Rotational moulding promises designers attractive economics and a low-pressure process. The benefits of rotational moulding are compared here with other manufacturing methods such as injection and blow moulding. PMID:14603714

  13. Rotating Vesta

    NASA Video Gallery

    Astronomers combined 146 exposures taken by NASA's Hubble SpaceTelescope to make this 73-frame movie of the asteroid Vesta's rotation.Vesta completes a rotation every 5.34 hours.› Asteroid and...

  14. 1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

    PubMed

    Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

    2014-07-01

    The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). PMID:24824670

  15. The amide linker in nonpeptide neurotensin receptor ligands plays a key role in calcium signaling at the neurotensin receptor type 2.

    PubMed

    Thomas, James B; Giddings, Angela M; Olepu, Srinivas; Wiethe, Robert W; Warner, Keith R; Sarret, Philippe; Longpre, Jean-Michel; Runyon, Scott P; Gilmour, Brian P

    2015-01-01

    Compounds acting via the GPCR neurotensin receptor type 2 (NTS2) display analgesia in relevant preclinical models. The amide bond in nonpeptide NTS1 antagonists plays a central role in receptor recognition and molecular conformation. Using NTS2 FLIPR and binding assays, we found that it is also a key molecular structure for binding and calcium mobilization at NTS2. We found that reversed amides display a shift from agonist to antagonist activity and provided examples of the first competitive nonpeptide antagonists observed in the NTS2 FLIPR assay. These compounds will be valuable tools for determining the role of calcium signaling in vitro to NTS2 mediated analgesia. PMID:25881832

  16. Catalyst-Free Three-Component Tandem CDC Cyclization: Convenient Access to Isoindolinones from Aromatic Acid, Amides, and DMSO by a Pummerer-Type Rearrangement.

    PubMed

    Wang, Peng-Min; Pu, Fan; Liu, Ke-Yan; Li, Chao-Jun; Liu, Zhong-Wen; Shi, Xian-Ying; Fan, Juan; Yang, Ming-Yu; Wei, Jun-Fa

    2016-04-25

    A catalyst-free multicomponent CDC reaction is rarely reported, especially for the intermolecular tandem CDC cyclization, which represents an important strategy for constructing cyclic compounds. Herein, a three-component tandem CDC cyclization by a Pummerer-type rearrangement to afford biologically relevant isoindolinones from aromatic acids, amides, and DMSO, is described. This intermolecular tandem reaction undergoes a C(sp(2) )-H/C(sp(3) )-H cross-dehydrogenative coupling, C-N bond formation, and intramolecular amidation. A notable feature of this novel protocol is avoiding a catalyst and additive (apart from oxidant). PMID:26998754

  17. NMR Study on Ion Dynamics and Phase Behavior of a Piperidinium-Based Room-Temperature Ionic Liquid: 1-Butyl-1-methylpiperidinium Bis(fluorosulfonyl)amide.

    PubMed

    Shimizu, Yuichi; Wachi, Yuto; Fujii, Kozo; Imanari, Mamoru; Nishikawa, Keiko

    2016-06-30

    By use of pulse NMR methods, the temperature dependences of the longitudinal and transverse relaxation times for (1)H and (19)F were measured for the three phases of 1-butyl-1-methylpiperidinium bis(fluorosulfonyl)amide ([Pip1,4][FSA]), i.e., liquid or supercooled liquid, Cryst-α, and Cryst-β, to investigate the ion dynamics and phase behavior related to the dynamics. Since the cations and anions in the room-temperature ionic liquid have (1)H and (19)F nuclei, respectively, the dynamics of the [Pip1,4] cation and [FSA] anion can be independently observed and the relation between them can be evaluated. The relevant local motions of the ions are fluctuational motion around the chair form of the piperidinium ring, libration or rotation of the alkyl groups, and libration or rotation of the SO2F groups around the N-S axes. Each phase preferentially exhibits these motions. In the Cryst-β phase, it is thought that O atoms in the SO2F groups form strong hydrogen bonds with the H atoms in the piperidinium ring. As a result, the motions of the SO2F groups and the piperidinium ring are restricted. In the liquid or supercooled liquid states and Cryst-α phase, the motion of the anion is more significant than that of the cation and the former works as a trigger for phase changes. Particularly, the motion of the SO2F groups in the Cryst-α phase becomes very significant with rising temperature and is directly related to the melting phase transition. PMID:27281062

  18. Structure-based Mechanistic Insights into Terminal Amide Synthase in Nosiheptide-Represented Thiopeptides Biosynthesis

    PubMed Central

    Liu, Shanshan; Guo, Heng; Zhang, Tianlong; Han, Li; Yao, Pengfei; Zhang, Yan; Rong, Naiyan; Yu, Yi; Lan, Wenxian; Wang, Chunxi; Ding, Jianping; Wang, Renxiao; Liu, Wen; Cao, Chunyang

    2015-01-01

    Nosiheptide is a parent compound of thiopeptide family that exhibit potent activities against various bacterial pathogens. Its C-terminal amide formation is catalyzed by NosA, which is an unusual strategy for maturating certain thiopeptides by processing their precursor peptides featuring a serine extension. We here report the crystal structure of truncated NosA1-111 variant, revealing three key elements, including basic lysine 49 (K49), acidic glutamic acid 101 (E101) and flexible C-terminal loop NosA112-151, are crucial to the catalytic terminal amide formation in nosiheptide biosynthesis. The side-chain of residue K49 and the C-terminal loop fasten the substrate through hydrogen bonds and hydrophobic interactions. The side-chain of residue E101 enhances nucleophilic attack of H2O to the methyl imine intermediate, leading to Cα-N bond cleavage and nosiheptide maturation. The sequence alignment of NosA and its homologs NocA, PbtH, TpdK and BerI, and the enzymatic assay suggest that the mechanistic studies on NosA present an intriguing paradigm about how NosA family members function during thiopeptide biosynthesis. PMID:26244829

  19. Probing the Backbone Function of Tumor Targeting Peptides by an Amide-to-Triazole Substitution Strategy.

    PubMed

    Valverde, Ibai E; Vomstein, Sandra; Fischer, Christiane A; Mascarin, Alba; Mindt, Thomas L

    2015-09-24

    Novel backbone-modified radiolabeled analogs based on the tumor targeting peptide bombesin were synthesized and fully evaluated in vitro and in vivo. We have recently introduced the use of 1,4-disubstituted 1,2,3-triazoles as metabolically stable trans-amide bond surrogates in radiolabeled peptides in order to improve their tumor targeting. As an extension of our approach, we now report several backbone-modified analogs of the studied bombesin peptide bearing multiple triazole substitutions. We investigated the effect of the modifications on several biological parameters including the internalization of the radiopeptidomimetics into tumor cells, their affinity toward the gastrin releasing peptide receptor (GRPr), metabolic stability in blood plasma, and biodistribution in mice bearing GRPr-expressing xenografts. The backbone-modified radiotracers exhibited a significantly increased resistance to proteolytic degradation. In addition, some of the radiopeptidomimetics retained a nanomolar affinity toward GRPr, resulting in an up to 2-fold increased tumor uptake in vivo in comparison to a (all amide bond) reference compound. PMID:26309061

  20. Poly(amide-graft-acrylate) interfacial compounds

    NASA Astrophysics Data System (ADS)

    Zamora, Michael Perez

    Graft copolymers with segments of dissimilar chemistries have been shown to be useful in a variety of applications as surfactants, compatibilizers, impact modifiers, and surface modifiers. The most common route to well defined graft copolymers is through the use of macromonomers, polymers containing a reactive functionality and thus capable of further polymerization. However, the majority of the studies thus far have focused on the synthesis of macromonomers capable of reacting with vinyl monomers to form graft copolymers. This study focused on the synthesis of macromonomers capable of participating in condensation polymerizations. A chain transfer functionalization method was utilized. Cysteine was evaluated as a chain transfer agent for the synthesis of amino acid functionalized poly(acrylate) and poly(methacrylate) macromonomers. Low molar mass, functionalized macromonomers were produced. These macromonomers were proven to be capable of reacting with amide precursors to form poly(amide-g-acrylate) graft copolymers. Macromonomers and graft copolymers were characterized by gel permeation chromatography (GPC), Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR) spectroscopy, elemental analysis (EA), inductively coupled plasma (ICP), and differential scanning calorimetry (DSC). The second part of this research involved poly(dimethacrylate) dental restorative materials. Volumetric shrinkage during the cure of these resins results in a poor interface between the resin and the remaining tooth structure, limiting the lifetime of these materials. Cyclic anhydrides were incorporated into common monomer compositions used in dental applications. Volume expansion from the ring opening hydrolysis of these anhydrides was shown to be feasible. The modified dental resins were characterized by swelling, extraction and ultraviolet spectroscopy (UV), and density measurements. Linear poLymers designed to model the crosslinked dental resins were

  1. Amidation of Bioactive Peptides: The Structure of the Lyase Domain of the Amidating Enzyme

    SciTech Connect

    Chufan, E.; De, M; Eipper, B; Mains, R; Amzel, L

    2009-01-01

    Many neuropeptides and peptide hormones require amidation of their carboxy terminal for full biological activity. The enzyme peptidyl-{alpha}-hydroxyglycine {alpha}-amidating lyase (PAL; EC 4.3.2.5) catalyzes the second and last step of this reaction, N-dealkylation of the peptidyl-{alpha}-hydroxyglycine to generate the {alpha}-amidated peptide and glyoxylate. Here we report the X-ray crystal structure of the PAL catalytic core (PALcc) alone and in complex with the nonpeptidic substrate {alpha}-hydroxyhippuric acid. The structures show that PAL folds as a six-bladed {Beta}-propeller. The active site is formed by a Zn(II) ion coordinated by three histidine residues; the substrate binds to this site with its {alpha}-hydroxyl group coordinated to the Zn(II) ion. The structures also reveal a tyrosine residue (Tyr{sup 654}) at the active site as the catalytic base for hydroxyl deprotonation, an unusual role for tyrosine. A reaction mechanism is proposed based on this structural data and validated by biochemical analysis of site-directed PALcc mutants.

  2. Institutional Bonding.

    ERIC Educational Resources Information Center

    Allard, M. June

    Institutional bonding was examined at a public, urban commuter college with exceptionally high attrition and visibly low morale. Changes in bonding and attrition were measured 6 years after a 2-year effort to develop school identity and student feelings of membership. It was found that a simple index of campus morale is provided by level of…

  3. Chemical attributes of some clouds amid a forest ecosystem's trees

    USGS Publications Warehouse

    DeFelice, Thomas P.

    2002-01-01

    Simultaneous physical and chemical characteristics of clouds amid and above the trees of a montane forest, located about 3.3 km southwest of Mt. Mitchell, NC, were collected between 13 and 22 June 1993. This paper summarizes the chemical characteristics of the cloud droplets amid the trees. The ionic composition and pH of the analyzed amid-canopy cloud water samples are generally consistent with those of previous above-canopy cloud water samples obtained at this site. Magnesium, sodium, and calcium are highly correlated to each other amid the canopy as compared to above the canopy. Above-canopy and amid-canopy cloud-only episodes, with concurrent event-averaged cloud water pH values at or below 3.1, generally contain more magnesium, sodium, and calcium in the amid-canopy cloud water samples compared to concurrent above-canopy cloud water samples. The observed chemical differences between the amid-canopy cloud and the above- canopy cloud suggest an unhealthier environment for the tree canopy when the cloud water traversing this site has a pH value at or below 3.1. The predominant ion deposition fluxes were calculated to provide preliminary data for studies designed to explicitly quantify how the chemical composition of cloud water affects tree health. ?? 2002 Elsevier Science B.V. All rights reserved.

  4. Gas Phase Chemistry of Li+ with Amides: the Observation of LiOH Loss in Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Guo, Cheng; Zhou, Yuping; Liu, Pengyuan; Chai, Yunfeng; Pan, Yuanjiang

    2012-07-01

    Collision-induced dissociation (CID) of Li+ adducts of three sets of compounds that contains an amide bond, including 2-(4, 6-dimethoxypyrimidin-2-ylsulfanyl)- N-phenylbenzamide, its derivatives and simpler structures was investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Observed fragment ions include those that reflect loss of LiOH. Other product ions result from the Smiles rearrangement and direct C-S bond cleavage. MS/MS of H/D exchange products demonstrated occurrence of a 1,3-H shift from the amide nitrogen atom to the phenyl ring of these compounds. The LiOH loss from Li+ adducts of amides was further examined by CID of [M + Li]+ ions of N-phenylbenzamide and N-phenylcinnamide. Loss of LiOH was essentially the sole fragmentation reaction observed for the former. For the latter, both losses of LiOH and H2O were discovered. The presence of electron-donating substituents of the phenyl ring of these compounds was found to facilitate elimination of LiOH, while that loss was retarded by electron-withdrawing substituents. Proposed fragment ion structures were supported by elemental compositions deduced from ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS) m/z value determinations. Density functional theory-based (DFT) calculations were performed to evaluate potential mechanisms for these reactions.

  5. Quantum Chemical Calculations of Amide-15N Chemical Shift Anisotropy Tensors for a Membrane-Bound Cytochrome b5

    PubMed Central

    Pandey, Manoj Kumar; Ramamoorthy, Ayyalusamy

    2013-01-01

    There is considerable interest in determining amide-15N chemical shift anisotropy (CSA) tensors from biomolecules and understanding their variation for structural and dynamics studies using solution and solid-state NMR spectroscopy and also by quantum chemical calculations. Due to the difficulties associated with the measurement of CSA tensors from membrane proteins, NMR-based structural studies heavily relied on the CSA tensors determined from model systems, typically single crystals of model peptides. In the present study, the principal components of backbone amide-15N CSA tensor have been determined using density functional theory for a 16.7-kDa membrane-bound paramagnetic heme containing protein, cytochrome b5 (cytb5). All the calculations were performed by taking residues within 5Å distance from the backbone amide-15N nucleus of interest. The calculated amide-15N CSA spans agree less well with our solution NMR data determined for an effective internuclear distance rN-H = 1.023 Å and a constant angle β = 18° that the least shielded component (δ11) makes with the N-H bond. The variation of amide-15N CSA span obtained using quantum chemical calculations is found to be smaller than that obtained from solution NMR measurements, whereas the trends of the variations are found to be in close agreement. We believe that the results reported in this study will be useful in studying the structure and dynamics of membrane proteins and heme-containing proteins, and also membrane-bound protein-protein complexes such as cytochromes-b5-P450. PMID:23268659

  6. Influence of chain length and polymer concentration on the gelation of (amidated) low-methoxyl pectin induced by calcium.

    PubMed

    Capel, François; Nicolai, Taco; Durand, Dominique; Boulenguer, Patrick; Langendorff, Virginie

    2005-01-01

    The gelation of low-methoxyl pectin (LMP) induced by addition of Ca2+ was studied by measuring the storage modulus as a function of temperature during cooling. Samples with different molar masses were prepared by mechanical degradation. The effect of the molar mass and the pectin concentration on the gelation properties was investigated. The effect of partial amidation was studied by comparing LMP and partially amidated LMP with the same molar mass and degree of methylation. The results are compared to those from a model developed for Ca2+-induced pectin gelation, and good agreement is found except at low concentrations and low molar masses where the gels are weaker than predicted. At low concentrations intrachain bonding weakens the gel, while the presence of small pectin chains weakens the gel because it neutralizes binding sites on larger chains. PMID:16283714

  7. Amide proton exchange rates of a bound pepsin inhibitor determined by isotope-edited proton NMR experiments

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Stein, H.H.; BaMaung, N.

    1987-09-30

    From a series of isotope-edited proton NMR spectra, amide proton exchange rates were measured at 20 C, 30 C, and 40/sup 0/C for a tightly bound /sup 15/N-labeled tripeptide inhibitor of porcine pepsin (IC50 = 1.7 X 10(-) M). Markedly different NH exchange rates were observed for the three amide protons of the bound inhibitor. The P1 NH exchanged much more slowly than the P2 NH and P3 NH. These results are discussed in terms of the relative solvent accessibility in the active site and the role of the NH protons of the inhibitor for hydrogen bonding to the enzyme. In this study a useful approach is demonstrated for obtaining NH exchange rates on ligands bound to biomacromolecules, the knowledge of which could be of potential utility in the design of therapeutically useful nonpeptide enzyme inhibitors from peptide leads.

  8. Anion-directed self-assembly of a 2,6-bis(2-anilinoethynyl)pyridine bis(amide) scaffold

    PubMed Central

    Tresca, Blakely W.; Berryman, Orion B.; Zakharov, Lev N.; Johnson, Darren W.; Haley, Michael M.

    2015-01-01

    Bis(sulfonamide) receptors based on the 2,6-bis(2-anilinoethynyl)pyridine scaffold form persistent dimers with water and halides in solution and in the solid-state. The structurally related bis(amide) receptor derived from 3,5-dinitrobenzoyl chloride is a dimer in the solid-state with two HCl molecules directing the self-assembly. The 2+2 dimer, with a twisted “S”-shaped backbone, is held together by six hydrogen bonds. Dissolution of the (H2+·Cl−)2 adduct in CHCl3 results, however, in a monomeric structure. DOSY and 1H NMR experiments were used to identify the dominance of monomer in solution for both 2 and H2+·Cl−. The ‘OFF-ON’ fluorescence response of 2, 6-bis(2-anilinoethynyl)pyridine is retained with amide arms. PMID:27110083

  9. Improved 1H amide resonance line narrowing in oriented sample solid-state NMR of membrane proteins in phospholipid bilayers

    NASA Astrophysics Data System (ADS)

    Lu, George J.; Park, Sang Ho; Opella, Stanley J.

    2012-07-01

    We demonstrate 1H amide resonance line widths <300 Hz in 1H/15N heteronuclear correlation (HETCOR) spectra of membrane proteins in aligned phospholipid bilayers. This represents a substantial improvement over typically observed line widths of ˜1 kHz. Furthermore, in a proton detected local field (PDLF) version of the experiment that measures heteronuclear dipolar couplings, line widths <130 Hz are observed. This dramatic line narrowing of 1H amide resonances enables many more individual signals to be resolved and assigned from uniformly 15N labeled membrane proteins in phospholipid bilayers under physiological conditions of temperature and pH. Finding that the decrease in line widths occurs only for membrane proteins that undergo fast rotational diffusion around the bilayer normal, but not immobile molecules, such as peptide single crystals, identifies a potential new direction for pulse sequence development that includes overall molecular dynamics in their design.

  10. MICROBIAL DEGRADATION OF SEVEN AMIDES BY SUSPENDED BACTERIAL POPULATIONS

    EPA Science Inventory

    Microbial transformation rate constants were determined for seven amides in natural pond water. A second-order mathematical rate expression served as the model for describing the microbial transformation. Also investigated was the relationship between the infrared spectra and the...

  11. Silver-catalyzed synthesis of amides from amines and aldehydes

    DOEpatents

    Madix, Robert J; Zhou, Ling; Xu, Bingjun; Friend, Cynthia M; Freyschlag, Cassandra G

    2014-11-18

    The invention provides a method for producing amides via the reaction of aldehydes and amines with oxygen adsorbed on a metallic silver or silver alloy catalyst. An exemplary reaction is shown in Scheme 1: (I), (II), (III). ##STR00001##

  12. Synthesis, HPLC measurement and bioavailability of the phenolic amide amkamide

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Amkamide, oretamide, becatamide, enferamide and veskamide are phenolic amides whose analogues are found in plants. Recently, becatamide was reported to have very potent mitochondria protective activity. In this study, becatamide and analogues (amkamide, oretamide, enferamide and veskamide) were chem...

  13. A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin.

    PubMed

    Anderson, Janet S; Hernández, Griselda; Lemaster, David M

    2008-06-10

    The exchange rates of the static solvent-accessible amide hydrogens of Pyrococcus furiosus rubredoxin range from near the diffusion-limited rate to a billion-fold slower for the non-hydrogen-bonded Val 38 (eubacterial numbering). Hydrogen exchange directly monitors the kinetic acidity of the peptide nitrogen. Electrostatic solvation free energies were calculated by Poisson-Boltzmann methods for the individual peptide anions that form during the hydroxide-catalyzed exchange reaction to examine how well the predicted thermodynamic acidities match the experimentally determined kinetic acidities. With the exception of the Ile 12 amide, the differential exchange rate constant for each solvent-exposed amide proton that is not hydrogen bonded to a backbone carbonyl can be predicted within a factor of 6 (10 (0.78)) root-mean-square deviation (rmsd) using the CHARMM22 electrostatic parameter set and an internal dielectric value of 3. Under equivalent conditions, the PARSE parameter set yields a larger rmsd value of 1.28 pH units, while the AMBER parm99 parameter set resulted in a considerably poorer correlation. Either increasing the internal dielectric value to 4 or reducing it to a value of 2 significantly degrades the quality of the prediction. Assigning the excess charge of the peptide anion equally between the peptide nitrogen and the carbonyl oxygen also reduces the correlation to the experimental data. These continuum electrostatic calculations were further analyzed to characterize the specific structural elements that appear to be responsible for the wide range of peptide acidities observed for these solvent-exposed amides. The striking heterogeneity in the potential at sites along the protein-solvent interface should prove germane to the ongoing challenge of quantifying the contribution that electrostatic interactions make to the catalytic acceleration achieved by enzymes. PMID:18479148

  14. Rotating Wavepackets

    ERIC Educational Resources Information Center

    Lekner, John

    2008-01-01

    Any free-particle wavepacket solution of Schrodinger's equation can be converted by differentiations to wavepackets rotating about the original direction of motion. The angular momentum component along the motion associated with this rotation is an integral multiple of [h-bar]. It is an "intrinsic" angular momentum: independent of origin and…

  15. Crystal structure of catena-poly[[[bis­(pyridine-4-carbo­thio­amide-κN 1)cadmium]-di-μ-thio­cyanato-κ2 N:S;κ2 S:N] methanol disolvate

    PubMed Central

    Neumann, Tristan; Jess, Inke; Näther, Christian

    2016-01-01

    The asymmetric unit of the polymeric title compound, {[Cd(NCS)2(C6H6N2S)]·2CH3OH}n, consists of one cadmium(II) cation that is located on a centre of inversion as well as one thio­cyanate anion, one pyridine-4-carbo­thio­amide ligand and one methanol mol­ecule in general positions. The CdII cations are octa­hedrally coordinated by the pyridine N atom of two pyridine-4-carbo­thio­amide ligands and by the S and N atoms of four thio­cyanate anions and are linked into chains along [010] by pairs of anionic ligands. These chains are further linked into layers extending along (201) by inter­molecular N—H⋯O and O—H⋯S hydrogen bonds. One of the amino H atoms of the pyridine-4-carbo­thio­amide ligand is hydrogen-bonded to the O atom of a methanol mol­ecule, and a symmetry-related methanol mol­ecule is the donor group to the S atom of another pyridine-4-carbo­thio­amide ligand whereby each of the pyridine-4-carbo­thio­amide ligands forms two pairs of centrosymmetric N—H⋯S and O—H⋯S hydrogen bonds. The methanol mol­ecules are equally disordered over two orientations. PMID:27006810

  16. Crystal structure of catena-poly[[[bis-(pyridine-4-carbo-thio-amide-κN (1))cadmium]-di-μ-thio-cyanato-κ(2) N:S;κ(2) S:N] methanol disolvate].

    PubMed

    Neumann, Tristan; Jess, Inke; Näther, Christian

    2016-03-01

    The asymmetric unit of the polymeric title compound, {[Cd(NCS)2(C6H6N2S)]·2CH3OH} n , consists of one cadmium(II) cation that is located on a centre of inversion as well as one thio-cyanate anion, one pyridine-4-carbo-thio-amide ligand and one methanol mol-ecule in general positions. The Cd(II) cations are octa-hedrally coordinated by the pyridine N atom of two pyridine-4-carbo-thio-amide ligands and by the S and N atoms of four thio-cyanate anions and are linked into chains along [010] by pairs of anionic ligands. These chains are further linked into layers extending along (201) by inter-molecular N-H⋯O and O-H⋯S hydrogen bonds. One of the amino H atoms of the pyridine-4-carbo-thio-amide ligand is hydrogen-bonded to the O atom of a methanol mol-ecule, and a symmetry-related methanol mol-ecule is the donor group to the S atom of another pyridine-4-carbo-thio-amide ligand whereby each of the pyridine-4-carbo-thio-amide ligands forms two pairs of centrosymmetric N-H⋯S and O-H⋯S hydrogen bonds. The methanol mol-ecules are equally disordered over two orientations. PMID:27006810

  17. A Simple and Versatile Amide Directing Group for C-H Functionalizations.

    PubMed

    Zhu, Ru-Yi; Farmer, Marcus E; Chen, Yan-Qiao; Yu, Jin-Quan

    2016-08-26

    Achieving selective C-H activation at a single and strategic site in the presence of multiple C-H bonds can provide a powerful and generally useful retrosynthetic disconnection. In this context, a directing group serves as a compass to guide the transition metal to C-H bonds by using distance and geometry as powerful recognition parameters to distinguish between proximal and distal C-H bonds. However, the installation and removal of directing groups is a practical drawback. To improve the utility of this approach, one can seek solutions in three directions: 1) Simplifying the directing group, 2) using common functional groups or protecting groups as directing groups, and 3) attaching the directing group to substrates via a transient covalent bond to render the directing group catalytic. This Review describes the rational development of an extremely simple and yet broadly applicable directing group for Pd(II) , Rh(III) , and Ru(II) catalysts, namely the N-methoxy amide (CONHOMe) moiety. Through collective efforts in the community, a wide range of C-H activation transformations using this type of simple directing group have been developed. PMID:27479708

  18. Herringbone array of hydrogen-bonded ribbons in 2-ethoxybenzamide from high-resolution X-ray powder diffraction.

    PubMed

    Pagola, Silvina; Stephens, Peter W

    2009-11-01

    In 2-ethoxybenzamide, C(9)H(11)NO(2), the amide substituents are linked into centrosymmetric head-to-head hydrogen-bonded dimers. Additional hydrogen bonds between adjacent dimers give rise to ribbon-like packing motifs, which extend along the c axis and possess a third dimension caused by twisting of the 2-ethoxyphenyl substituent with respect to the hydrogen-bonded amide groups. The ribbons are arranged in a T-shaped herringbone pattern and cohesion between them is achieved by van der Waals forces. PMID:19893241

  19. Synthetic polyspermine imidazole-4, 5-amide as an efficient and cytotoxicity-free gene delivery system

    PubMed Central

    Duan, Shi-Yue; Ge, Xue-Mei; Lu, Nan; Wu, Fei; Yuan, Weien; Jin, Tuo

    2012-01-01

    A chemically dynamic spermine-based polymer: polyspermine imidazole-4, 5-amide (PSIA, Mw > 7 kDa) was designed, synthesized, and evaluated in terms of its ability to deliver nucleic acids. This polymer was made from an endogenous monomer professionally condensing genes in sperms, spermine, and a known safety drug metabolite, imidazole-4, 5-dicarboxylic acid, through a bis-amide bond conjugated with the imidazole ring. This polymer can condense pDNA at a W/W ratio above 10 to form polyplexes (100–200 nm in diameter), which is consistent with the observation by transmission electron microscopy (TEM), and the zeta potential was in the range of 10–20 mV. The pDNA packaged polymer was stable in phosphate buffer solution (PBS) at pH 7.4 (simulated body fluid) while the polyplexes were releasing pDNA into the solution at pH 5.8 (simulated endo-lysosomes) due to the degradation of the bis-amide linkages in response to changes in pH values. PSIA-polyplexes were able to achieve efficient cellular uptake and luciferase gene silencing by co-transfection of pDNA and siRNA in COS-7 cells and HepG2 cells with negligible cytotoxicity. Biodistribution of Rhodamine B-labeled PSIA-polyplexes after being systemically injected in BALB/c nude-mice showed that the polyplexes circulated throughout the body, accumulated mainly in the kidney at 4 hours of sample administration, and moved to the liver and spleen after 24 hours. All the results suggested that PSIA offered a promising example to balance the transfection efficiency and toxicity of a synthetic carrier system for the delivery of therapeutic nucleic acids. PMID:22888236

  20. Polyfluorinated amides as a historical PFCA source by electrochemical fluorination of alkyl sulfonyl fluorides.

    PubMed

    Jackson, Derek A; Mabury, Scott A

    2013-01-01

    Polyfluorinated amides (PFAMs) are a class of compounds produced as byproducts of polyfluorinated sulfonamide synthesis by electrochemical fluorination (ECF). We measured four PFAM derivatives of perfluorooctanoic acid (PFOA) in a wide range of compounds, experimental materials, and commercial products synthesized by ECF. Initial screening was performed using headspace solid phase microextraction gas chromatography mass spectrometry (SPME-GC-MS), and quantification using in-house synthesized standards was accomplished with GC-MS using positive chemical ionization. Two monosubstituted PFAMs, N-methylperfluorooctanamide (MeFOA) and N-ethylperfluorooctanamide (EtFOA), were detected in the majority of materials that were analyzed. Two disubstituted PFAMs, N-methyl-N-(2-hydroxyethyl)perfluorooctanamide (MeFOAE) and N-ethyl-N-(2-hydroxyethyl)perfluorooctanamide (EtFOAE), were not detected in any sample, likely because they were never synthesized. The concentrations of PFAMs in the sulfonamide compounds under study ranged from 12 to 6736 μg/g, suggesting their historical importance as PFCA precursors. In each case, branched isomers for PFAMs were detected, providing further support for their link to an ECF source. A hydrolysis study performed at pH 8.5 showed no degradation of EtFOA to PFOA after 8 days due to the stability of the amide bond. The environmental fate of PFAMs is suggested to be volatilization to the atmosphere followed by oxidation by hydroxyl radical with a predicted lifetime of 3-20 days. Subsequent PFAM exposure to biota will likely lead to enzymatic hydrolysis of the amide linkage to give a PFCA. Human exposure to PFAMs may have contributed to the presence of branched PFOA isomers in blood by serving as an indirect source. The decline in PFOA concentrations in human blood is consistent with a significant drop in PFAM production concurrent with the POSF phase-out in 2000-2001. PMID:23205559

  1. Amide Proton Solvent Protection in Amylin Fibrils Probed by Quenched Hydrogen Exchange NMR

    PubMed Central

    Alexandrescu, Andrei T.

    2013-01-01

    Amylin is an endocrine hormone that accumulates in amyloid plaques in patients with advanced type 2 diabetes. The amyloid plaques have been implicated in the destruction of pancreatic β-cells, which synthesize amylin and insulin. To better characterize the secondary structure of amylin in amyloid fibrils we assigned the NMR spectrum of the unfolded state in 95% DMSO and used a quenched hydrogen-deuterium exchange technique to look at amide proton solvent protection in the fibrils. In this technique, partially exchanged fibrils are dissolved in 95% DMSO and information about amide proton occupancy in the fibrils is determined from DMSO-denatured monomers. Hydrogen exchange lifetimes at pH 7.6 and 37°C vary between ∼5 h for the unstructured N-terminus to 600 h for amide protons in the two β-strands that form inter-molecular hydrogen bonds between amylin monomers along the length of the fibril. Based on the protection data we conclude that residues A8-H18 and I26-Y37 comprise the two β-strands in amylin fibrils. There is variation in protection within the β-strands, particularly for strand β1 where only residues F15-H18 are strongly protected. Differences in protection appear to be due to restrictions on backbone dynamics imposed by the packing of two-layers of C2-symmetry-related β-hairpins in the protofilament structure, with strand β1 positioned on the surface and β2 in the interior. PMID:23457571

  2. Synthesis of imides via palladium-catalyzed decarboxylative amidation of α-oxocarboxylic acids with secondary amides.

    PubMed

    Xu, Ning; Liu, Jie; Li, Dengke; Wang, Lei

    2016-05-18

    An efficient synthesis of imides has been developed through a Pd-catalyzed decarboxylative amidation of α-oxocarboxylic acids with secondary amides. The reactions of N-substituted N-heteroarene-2-carboxamides with 2-oxo-2-arylacetic acids proceeded smoothly to generate the corresponding products in good yields in the presence of Pd(OAc)2 and K2S2O8. PMID:27143171

  3. Amide-Directed Formation of Five-Coordinate Osmium Alkylidenes from Alkynes

    PubMed Central

    2015-01-01

    The amide-directed synthesis of five-coordinate osmium alkylidene derivatives from alkynes is reported. These types of complexes, which have been elusive until now because of the tendency of osmium to give hydride alkylidyne species, are prepared by reaction of the dihydride OsH2Cl2(PiPr3)2 (1) with terminal alkynes containing a distal amide group. Complex 1 reacts with N-phenylhex-5-ynamide and N-phenylhepta-6-ynamide to give OsCl2{=C(CH3)(CH2)nNH(CO)Ph}(PiPr3)2 (n = 3 (2), 4 (3)). The relative position of carbonyl and NH groups in the organic substrates has no influence on the reaction. Thus, treatment of 1 with N-(pent-4-yn-1-yl)benzamide leads to OsCl2{=C(CH3)(CH2)3NHC(O)Ph}(PiPr3)2 (4). The new compounds are intermediate species in the cleavage of the C–C triple bond of the alkynes. Under mild conditions, they undergo the rupture of the Cα–CH3 bond of the alkylidene, which comes from the alkyne triple bond, to afford six-coordinate hydride–alkylidyne derivatives. In dichloromethane, complex 2 gives a 10:7 mixture of OsHCl2{≡C(CH2)3C(O)NHPh}(PiPr3)2 (5) and OsHCl2{≡CCH(CH3)(CH2)2C(O)NHPh}(PiPr3)2 (6). The first complex contains a linear separation between the alkylidyne Cα atom and the amide group, whereas the spacer is branched in the second complex. In contrast to the case for 2, complex 4 selectively affords OsHCl2{≡C(CH2)3NHC(O)Ph}(PiPr3)2 (7). In spite of their instability, these compounds give the alkylidene–allene metathesis, being a useful entry to five-coordinate vinylidene complexes, including the dicarbon-disubstituted OsCl2(=C=CMe2)(PiPr3)2 (8) and the monosubstituted OsCl2(=C=CHCy)(PiPr3)2 (9). PMID:26877575

  4. Biodegradable and injectable paclitaxel-loaded poly(ester amide)s microspheres: fabrication and characterization.

    PubMed

    Guo, Kai; Chu, C C

    2009-05-01

    Novel biodegradable submicron microspheres of amino acid based poly(ester amide)s (PEAs) were fabricated by an oil-in-water (O/W) emulsion/solvent evaporation technique and their morphology and drug loading efficiency were examined. PEAs microspheres of mean diameter <1 microm with very narrow size distribution were obtained at a fair yield about 80%. The effects of PEA polymer concentration, polyvinyl alcohol emulsifier concentration, and the homogenizer speed on the size and morphology of final PEA microspheres were examined by analyzing their SEM images. It is found that a low PEA concentration, a high PVA concentration, and a high homogenizer speed are the optimal conditions for obtaining smaller microspheres. The biodegradation behaviors of these PEA microspheres at 37 degrees C were investigated as a function of enzyme (alpha-chymotrypsin) concentration and incubation time. The data showed similar surface erosion degradation mechanism as PEA polymers reported previously. Paclitaxel loaded PEA microspheres with high encapsulation efficiency were obtained without significantly affecting their size and surface morphology. The high drug loading efficiency close to 100% suggested that PEA microspheres may have the potential for the injection administration of highly hydrophobic anticancer drugs. PMID:18937264

  5. Synthesis and Characterization of Group 4 Amide Chloride and Amide Imide Complexes

    SciTech Connect

    Yu, Xianghua; Cheng, Shu-Jian; Wang, Xiaoping; Chen, Xue-Tai; Xue, Zi-Ling

    2009-01-01

    Group 4 amide chloride complexes (Me2N)(2)Ht[N(SiMe3)(2)]Cl (1b), [(Me3Si)(2)N](2)MCl2Li(THF)(3)Cl (M = Zr, 2a; Hf, 2b), and [(Me3Si)(2)MCl2MCl2(THF) (M = Zr, 3a; Hf, 3b) and their X-ray crystal structures are reported. An improved synthesis of {[(Me3Si)(2)N]Ti(mu-NSiMe3)Cl}(2) (4) and its use to prepare amide imide {[(Me3Si)(2)N]Ti(mu-NSiMe3)(NMe2}(2) (5) are also presented. X-ray crystal structures of 5 and previously reported complexes (Me2N)(2)Zr[N(SiMe3)(2)]Cl (1a), [(Me3Si)(2)N](2)TiCl2 (6), and [(Me3Si)(2)N]ZrCl3(THF)(2) (7) have been determined. Both 1a and 1b are dimers {[(Me3Si)(2)N](2)TiCl2 (M = Zr, Hf) in the solid state.

  6. Supergranulation rotation

    NASA Astrophysics Data System (ADS)

    Schou, Jesper; Beck, John G.

    2001-01-01

    Simple convection models estimate the depth of supergranulation at approximately 15,000 km which suggests that supergranules should rotate at the rate of the plasma in the outer 2% of the Sun by radius. Previous measurements (Snodgrass & Ulrich, 1990; Beck & Schou, 2000) found that supergranules rotate significantly faster than this, with a size-dependent rotation rate. We expand on previous work and show that the torsional oscillation signal seen in the supergranules tracks that obtained for normal modes. We also find that the amplitudes and lifetimes of the supergranulation are size dependent.

  7. Distinguishing Bonds.

    PubMed

    Rahm, Martin; Hoffmann, Roald

    2016-03-23

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

  8. Halogen bonds in biological molecules

    PubMed Central

    Auffinger, Pascal; Hays, Franklin A.; Westhof, Eric; Ho, P. Shing

    2004-01-01

    Short oxygen–halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short CX···OY interaction (CX is a carbon-bonded chlorine, bromine, or iodine, and OY is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X···O distance is less than or equal to the sums of the respective van der Waals radii (3.27 Å for Cl···O, 3.37Å for Br···O, and 3.50 Å for I···O) and can conform to the geometry seen in small molecules, with the CX···O angle ≈165° (consistent with a strong directional polarization of the halogen) and the X···OY angle ≈120°. Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized π -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology. PMID:15557000

  9. Halogen bonds in biological molecules.

    PubMed

    Auffinger, Pascal; Hays, Franklin A; Westhof, Eric; Ho, P Shing

    2004-11-30

    Short oxygen-halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short C-X...O-Y interaction (C-X is a carbon-bonded chlorine, bromine, or iodine, and O-Y is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X...O distance is less than or equal to the sums of the respective van der Waals radii (3.27 A for Cl...O, 3.37 A for Br...O, and 3.50 A for I...O) and can conform to the geometry seen in small molecules, with the C-X...O angle approximately 165 degrees (consistent with a strong directional polarization of the halogen) and the X...O-Y angle approximately 120 degrees . Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized pi -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology. PMID:15557000

  10. "Amide resonance" in the catalysis of 1,2-α-L-fucosidase from Bifidobacterium bifidum.

    PubMed

    Liu, Jingli; Zheng, Min; Zhang, Chunchun; Xu, Dingguo

    2013-09-01

    Bifidobacterium is a genus of Gram-positive bacteria, which is important in the absorption of nourishment from the human milk oligosaccharides (HMO). We present here the detailed simulation of the enzymatic hydrolysis of 2'-fucosyllactose catalyzed by 1,2-α-L-fucosidase from Bifidobacterium bifidum using the combined quantum mechanical and molecular mechanical approach. Molecular dynamics simulations and free energy profiles support that the overall reaction is a stepwise mechanism. The first step is the proton transfer from N423 to D766, and the second step involves the hydrolysis reaction via the inversion mechanism catalyzed by the amide group of N423. Assisted by D766, N423 serves as the general base to activate the water molecule to attack the anomeric carbon center. E566 is the general acid to facilitate the cleavage of glycosidic bond between L-fucose and galactose units. The intrinsic resonance structure for the side chain amide group of the asparagine residue is shown to be the origin to the catalytic activity, which is also confirmed by the mutagenesis simulation of N423G. PMID:23952813

  11. Association of chlorophyll with amides on plasticized polyethylene particles. II. The isomeric N-(pyridyl)myristamides

    SciTech Connect

    Kusumoto, Y.; Seely, G.R.; Senthilathipan, V.

    1982-01-01

    When chlorophyll, together with certain other amphiphilic substances, is adsorbed to particles of polyethylene plasticized by incorporation of tetradecane, it is maintained in monomeric or oligomeric forms with characteristic absorption and fluorescence spectra. The present work describes the properties of chlorophyll a on such particles in the presence of the three isomeric N-(pyridyl)myristamides, and of the similarly shaped but not basic compound myristanilide, in an effort to ascertain the structural factors governing associations of these species. Absorption and fluorescence spectra at room temperature are resolved into minimal sets of Gaussian components, and relations between the component sets are proposed. The positions of the component bands and their relative abundance are characteristic of the amide used. The 3- and 4-pyridyl isomers bind more strongly to chlorophyll, probably by ligation of the pyridine nitrogen to Mg of the pigment. The 2-pyridyl isomer and myristanilide bind more weakly, probably through the amide carbonyl group. The association of chlorophyll into species with characteristic absorption and fluorescence bands is promoted more strongly by the 3- and 4-isomers than by the 2-isomer and myristanilide, and probably involves hydrogen bonding to chlorophyll carbonyl groups. A possible manner of association of chlorophyll in the presence of N,N-dimethylmyristamide is also presented. By way of comparison, chlorophyll adsorbed with dodecylpyridinium bromide, which lacks a nucleophilic function, is mainly in the microcrystalline hydrate form absorbing near 740 nm.

  12. Cinnamic acid amides from Tribulus terrestris displaying uncompetitive α-glucosidase inhibition.

    PubMed

    Song, Yeong Hun; Kim, Dae Wook; Curtis-Long, Marcus J; Park, Chanin; Son, Minky; Kim, Jeong Yoon; Yuk, Heung Joo; Lee, Keun Woo; Park, Ki Hun

    2016-05-23

    The α-glucosidase inhibitory potential of Tribulus terrestris extracts has been reported but as yet the active ingredients are unknown. This study attempted to isolate the responsible metabolites and elucidate their inhibition mechanism of α-glucosidase. By fractionating T. terristris extracts, three cinnamic acid amide derivatives (1-3) were ascertained to be active components against α-glucosidase. The lead structure, N-trans-coumaroyltyramine 1, showed significant inhibition of α-glucosidase (IC50 = 0.42 μM). Moreover, all active compounds displayed uncompetitive inhibition mechanisms that have rarely been reported for α-glucosidase inhibitors. This kinetic behavior was fully demonstrated by showing a decrease of both Km and Vmax, and Kik/Kiv ratio ranging between 1.029 and 1.053. We progressed to study how chemical modifications to the lead structure 1 may impact inhibition. An α, β-unsaturation carbonyl group and hydroxyl group in A-ring of cinnamic acid amide emerged to be critical functionalities for α-glucosidase inhibition. The molecular modeling study revealed that the inhibitory activities are tightly related to π-π interaction as well as hydrogen bond interaction between enzyme and inhibitors. PMID:26974386

  13. A backbone amide protecting group for overcoming difficult sequences and suppressing aspartimide formation.

    PubMed

    Abdel-Aal, Abu-Baker M; Papageorgiou, George; Raz, Richard; Quibell, Martin; Burlina, Fabienne; Offer, John

    2016-05-01

    A backbone amide bond protecting group, 2-hydroxy-4-methoxy-5-nitrobenzyl (Hmnb), improved the synthesis of aggregation and aspartimide-prone peptides. Introduction of Hmnb is automated and carried out during peptide assembly by addition of 4-methoxy-5-nitrosalicylaldehyde to the peptidyl-resin and on-resin reduction to the secondary amine. Acylation of the hindered secondary amine is aided by the formation of an internal nitrophenol ester that undergoes a favourable O,N intramolecular acyl transfer. This activated ester participates in the coupling and generally gives complete reaction with standard coupling conditions. Hmnb is easily available in a single preparative step from commercially available material. Different methods for removing the amide protecting group were explored. The protecting group is labile to acidolysis, following reduction of the nitro group to the aniline. The two main uses of backbone protection of preventing aspartimide formation and of overcoming difficult sequences are demonstrated, first with the synthesis of a challenging aspartimide-prone test sequence and then with the classic difficult sequence ACP (65-74) and a 23-mer homopolymer of polyalanine. PMID:27086749

  14. Synthesis, characterization and biological evaluation of novel α, β unsaturated amides.

    PubMed

    Esmailzadeh, K; Housaindokht, M R; Moradi, A; Esmaeili, A A; Sharifi, Z

    2016-05-15

    Three derivatives of α,β unsaturated amides have been successfully synthesized via Ugi-four component (U-4CR) reaction. The interactions of the amides with calf thymus deoxyribonucleic acid (ct-DNA) have been investigated in the Tris-HCl buffer (pH=7.4) using viscometric, spectroscopic, thermal denaturation studies, and also molecular docking. By UV-Vis absorption spectroscopy studies, adding CT-DNA to the compound solution caused the hypochromism indicates that there are interactions between the compounds and DNA base pairs. In competitive fluorescence with methylene blue as an intercalator probe, adding compounds to DNA-MB solution caused an increase in emission spectra of the complex. This could be because of compound replacing, with similar binding mode of MB, between the DNA base pairs due to release of bonded MB molecules from DNA-MB complex. Thermal denaturation studies and viscometric experiments also indicated that all three investigated compounds bind to CT-DNA by non-classical intercalation mode. Additionally, molecular docking technique predicted partial intercalation binding mode for the compounds. Also, the highest binding energy was obtained for compound 5a. These results are in agreement with results obtained by empirical methods. PMID:26971027

  15. Predicting autoxidation stability of ether- and amide-based electrolyte solvents for Li-air batteries.

    PubMed

    Bryantsev, Vyacheslav S; Faglioni, Francesco

    2012-07-01

    Finding suitable solvents remains one of the most elusive challenges in rechargeable, nonaqueous Li-air battery technology. Although ether and amides are identified as stable classes of aprotic solvents against nucleophilic attack by superoxide, many of them are prone to autoxidation under oxygen atmosphere. In this work, we use density functional theory calculations coupled with an implicit solvent model to investigate the autoxidative stability of ether- and N,N-dialkylamide-based solvents. The change in the activation free energy for the C-H bond cleavage by O(2) is consistent with the extent of peroxide production for each class of solvent. Conversely, the thermodynamic stability alone is not sufficient to account for the observed variation in solvent reactivity toward O(2). A detailed understanding of the factors influencing the autoxidative stability provides several strategies for designing molecules with enhanced air/O(2) stability, comparable or superior to that of structurally related hydrocarbons. The mechanism of superoxide-mediated oxidation of hydroperoxides derived from ethers and amides is presented. The degradation mechanism accounts for the primary decomposition products (esters and carboxylates) observed in the Li-air battery with ether-based electrolytes. The identification of solvents having resistance to autoxidation is critical for the development of rechargeable Li-air batteries with long cycle life. PMID:22681046

  16. Synthesis, characterization and biological evaluation of novel α, β unsaturated amides

    NASA Astrophysics Data System (ADS)

    Esmailzadeh, K.; Housaindokht, M. R.; Moradi, A.; esmaeili, A. A.; Sharifi, Z.

    2016-05-01

    Three derivatives of α,β unsaturated amides have been successfully synthesized via Ugi-four component (U-4CR) reaction. The interactions of the amides with calf thymus deoxyribonucleic acid (ct-DNA) have been investigated in the Tris-HCl buffer (pH = 7.4) using viscometric, spectroscopic, thermal denaturation studies, and also molecular docking. By UV-Vis absorption spectroscopy studies, adding CT-DNA to the compound solution caused the hypochromism indicates that there are interactions between the compounds and DNA base pairs. In competitive fluorescence with methylene blue as an intercalator probe, adding compounds to DNA-MB solution caused an increase in emission spectra of the complex. This could be because of compound replacing, with similar binding mode of MB, between the DNA base pairs due to release of bonded MB molecules from DNA-MB complex. Thermal denaturation studies and viscometric experiments also indicated that all three investigated compounds bind to CT-DNA by non-classical intercalation mode. Additionally, molecular docking technique predicted partial intercalation binding mode for the compounds. Also, the highest binding energy was obtained for compound 5a. These results are in agreement with results obtained by empirical methods.

  17. Amide proton exchange rates of oxidized and reduced Saccharomyces cerevisiae iso-1-cytochrome c.

    PubMed Central

    Marmorino, J. L.; Auld, D. S.; Betz, S. F.; Doyle, D. F.; Young, G. B.; Pielak, G. J.

    1993-01-01

    Proton NMR spectroscopy was used to determine the rate constant, kobs, for exchange of labile protons in both oxidized (Fe(III)) and reduced (Fe(II)) iso-1-cytochrome c. We find that slowly exchanging backbone amide protons tend to lack solvent-accessible surface area, possess backbone hydrogen bonds, and are present in regions of regular secondary structure as well as in omega-loops. Furthermore, there is no correlation between kobs and the distance from a backbone amide nitrogen to the nearest solvent-accessible atom. These observations are consistent with the local unfolding model. Comparisons of the free energy change for denaturation, delta Gd, at 298 K to the free energy change for local unfolding, delta Gop, at 298 K for the oxidized protein suggest that certain conformations possessing higher free energy than the denatured state are detected at equilibrium. Reduction of the protein results in a general increase in delta Gop. Comparisons of delta Gd to delta Gop for the reduced protein show that the most open states of the reduced protein possess more structure than its chemically denatured form. This persistent structure in high-energy conformations of the reduced form appears to involve the axially coordinated heme. PMID:8268806

  18. Solar rotation.

    NASA Astrophysics Data System (ADS)

    Dziembowski, W.

    Sunspot observations made by Johannes Hevelius in 1642 - 1644 are the first ones providing significant information about the solar differential rotation. In modern astronomy the determination of the rotation rate is done in a routine way by measuring positions of various structures on the solar surface as well as by studying the Doppler shifts of spectral lines. In recent years a progress in helioseismology enabled determination of the rotation rate in the layers inaccessible for direct observations. There are still uncertainties concerning, especially, the temporal variations of the rotation rate and its behaviour in the radiative interior. We are far from understanding the observations. Theoretical works have not yet resulted in a satisfactory model for the angular momentum transport in the convective zone.

  19. Rotational aerophones

    NASA Astrophysics Data System (ADS)

    Fletcher, N. H.; Tarnopolsky, A. Z.; Lai, J. C. S.

    2002-03-01

    Free rotational aerophones such as the bullroarer, which consists of a wooden slat whirled around on the end of a string, and which emits a loud pulsating roar, have been used in many ancient and traditional societies for ceremonial purposes. This article presents an experimental and theoretical investigation of this instrument. The aerodynamics of rotational behavior is elucidated, and relates slat rotation frequency to slat width and velocity through the air. Analysis shows that sound production is due to generation of an oscillating-rotating dipole across the slat, the role of the vortices shed by the slat being relatively minor. Apparent discrepancies between the behavior of a bullroarer slat and a slat mounted on an axle in a wind tunnel are shown to be due to viscous friction in the bearings of the wind-tunnel experiment.

  20. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis

    PubMed Central

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; Stevenson, David M.

    2015-01-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  1. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis.

    PubMed

    Pisithkul, Tippapha; Jacobson, Tyler B; O'Brien, Thomas J; Stevenson, David M; Amador-Noguez, Daniel

    2015-09-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using (13)C-labeled sugars and [(15)N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  2. Crystal structure and Hirshfeld-surface analysis of (benzene-carbo-thio-amide-κS)bromido-bis-(tri-phenylphosphane-κP)silver(I).

    PubMed

    Ruangwut, Wattana; Saithong, Saowanit; Pakawatchai, Chaveng

    2016-07-01

    The title complex, [AgBr(C7H7NS)(C18H15P)2], was obtained from the reaction of silver(I) bromide with benzene-carbo-thio-amide (C7H7NS) and tri-phenyl-phosphane (C18H15P) in the mixed solvent of aceto-nitrile and ethanol. The mononuclear complex exhibits a distorted tetra-hedral coordination geometry about the metal atom, arising from one S atom of a benzene-carbo-thio-amide ligand, two P atoms of two tri-phenyl-phosphane mol-ecules and one bromide ion. An intra-molecular N-H⋯Br hydrogen bond is observed and in the crystal structure, inversion dimers linked by pairs of N-H⋯Br and C-H⋯Br hydrogen bonds are observed. In addition, C-H⋯π inter-actions occur, leading to [101] chains. Hirshfeld-surface analyses are presented and discussed. PMID:27555946

  3. Yankee bonds

    SciTech Connect

    Delaney, P. )

    1993-10-01

    Yankee and Euromarket bonds may soon find their way into the financing of power projects in Latin America. For developers seeking long-term commitments under build, own, operate, and transfer (BOOT) power projects in Latin America, the benefits are substantial.

  4. Self-trapping of the amide I band in a peptide model crystal

    NASA Astrophysics Data System (ADS)

    Edler, J.; Hamm, P.

    2002-08-01

    A femtosecond pump-probe study of the peculiar amide I band of acetanilide, a molecular crystal with hydrogen bonded chains of peptide units, is presented. The almost perfect harmonicity of the 1666 cm-1 subpeak is related to significant delocalization of this state at low enough temperatures (93 K). The "anomalous" peak (1650 cm-1), on the other hand, is strongly anharmonic, and hence assigned to a self-trapped state. This assignment is in agreement with a more indirect previous work. With increasing temperature, thermal disorder localizes the 1666 cm-1 band (Anderson localization) and at the same time destroys the self-trapping mechanism. Both the self-trapped state and the delocalized state decay on a 2 ps time scale into states outside the spectral window of this study. The excitation energy reappears on a much slower 35 ps time scale in the form of an increased lattice temperature.

  5. Rapid ligations with equimolar reactants in water with the potassium acyltrifluoroborate (KAT) amide formation.

    PubMed

    Noda, Hidetoshi; Erős, Gábor; Bode, Jeffrey W

    2014-04-16

    The identification of fast, chemoselective bond-forming reactions is one of the major contemporary challenges in chemistry. We show that chemoselective amide-forming ligations of potassium acyltrifluoroborates (KATs) and O-carbamoylhydroxylamines proceed in the presence of all unprotected functional groups with a second-order rate constant of 20 M(-1) s(-1). PEG chains, lipids, biotin, and dyes were introduced onto an unprotected 31-mer peptide (a GLP-1 analogue) with equimolar ratios of reactants within minutes at 1 mM and within 1 h at 100 μM, even with Mw 20,000 PEG. This conjugation reaction provides a new approach to the synthesis of molecules such as protein-protein and protein-polymer conjugates. PMID:24684235

  6. Mechanism of Oxidative Amidation of Nitroalkanes with Oxygen and Amine Nucleophiles by Using Electrophilic Iodine.

    PubMed

    Li, Jing; Lear, Martin J; Kwon, Eunsang; Hayashi, Yujiro

    2016-04-11

    Recently, we developed a direct method to oxidatively convert primary nitroalkanes into amides that entailed mixing an iodonium source with an amine, base, and oxygen. Herein, we systematically investigated the mechanism and likely intermediates of such methods. We conclude that an amine-iodonium complex first forms through N-halogen bonding. This complex reacts with aci-nitronates to give both α-iodo- and α,α-diiodonitroalkanes, which can act as alternative sources of electrophilic iodine and also generate an extra equimolar amount of I(+) under O2. In particular, evidence supports α,α-diiodonitroalkane intermediates reacting with molecular oxygen to form a peroxy adduct; alternatively, these tetrahedral intermediates rearrange anaerobically to form a cleavable nitrite ester. In either case, activated esters are proposed to form that eventually reacts with nucleophilic amines in a traditional fashion. PMID:26938791

  7. Biocatalytic amidation of carboxylic acids and their antinemic activity.

    PubMed

    Bose, Abinesh; Shakil, Najam Akhtar; Pankaj; Kumar, Jitendra; Singh, Manish K

    2010-04-01

    A series of novel N-alkyl substituted amides, synthesized by enzyme catalysis, were evaluated against root-knot nematode, Meloidogyne incognita and found to have potential antinemic activity. The corresponding amides were prepared by the condensation of equimolar amounts of carboxylic acids with different alkyl amines in the presence of Candida antarctica lipase at 60-90 degrees C in 16-20 h. The reactions were carried out in a non - solvent system without the use of any activating agents. All the products were obtained in appreciable amounts and the yields for different compounds varied between 77.4-82.3%. The synthesized compounds were characterized using spectroscopy techniques namely Infra Red (IR) and Nuclear Magnetic Resonance (NMR) ((1)H and (13)C). Nematicidal activity of synthesized amides was evaluated against J(2)s of Meloidogyne incognita at 500, 250, 125 and 62.5 ppm concentrations after 24 h, 48 h and 72 h of exposure. Among all the tested compounds, N-propyl-butyramide, N-propyl-pentanamide and N-propyl-hexanamide were found to possess significant activity with LC(50) values of 67.46, 83.49 and 96.53 respectively. N-propyl-butyramide with LC(50) value of 67.46 ppm was found to be most active amide against J(2)s of Meloidogyne incognita. The bioactivity study showed that an increase in alkyl chain significantly decreased the activity of amides against root-knot nematode. PMID:20390959

  8. Synthesis and structural studies of amino amide salts derived from 2-(aminomethyl)benzimidazole and α-amino acids

    NASA Astrophysics Data System (ADS)

    Avila-Montiel, Concepción; Tapia-Benavides, Antonio R.; Falcón-León, Martha; Ariza-Castolo, Armando; Tlahuext, Hugo; Tlahuextl, Margarita

    2015-11-01

    2-{[(Ammoniumacetyl)amino]methyl}-1H-benzimidazol-3-ium dichloride 4, 2-{[(2-ammoniumpropanoyl)amino]methyl}-1H-benzimidazol-3-ium dichloride 5, and 2-{[(2-ammonium-3-phenylpropanoyl)amino]methyl}-1H-benzimidazol-3-ium dichloride 6 amino amides were synthesized via condensation of 2AMBZ dihydrochloride with the corresponding amino acid. Compounds 7-12 were obtained by replacing chloride ions (in salts 4-6) with nitrate or tetrachlorozincate ions. The results of X-ray diffraction crystallographic studies indicated that the geometries, charges and sizes of the anions are essential for the formation of the strong hydrogen bond interactions of compounds 4, 5, 9-12. Moreover, in most cases, the presence of water and solvent molecules stabilizes the supramolecular structures of these compounds. Nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy indicated that the presence of chloride or tetrachlorozincate anions increases the acidity of the benzimidazolic and amide groups more significantly than the presence of nitrate anions. However, Quantum Theory of Atoms in Molecules (QTAIM) computations of the crystal structures demonstrate that amino amides interact more strongly with NO3- than with Cl- and ZnCl42- anions; this difference explains the spectroscopic results.

  9. Protonolysis and amide exchange reactions of a three-coordinate cobalt amide complex supported by an N-heterocyclic carbene ligand.

    PubMed

    Hansen, Christopher B; Jordan, Richard F; Hillhouse, Gregory L

    2015-05-18

    A three-coordinate cobalt species, IPrCoCl{N(SiMe3)2} [1; IPr = 1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene], was synthesized by the reaction of {IPrCoCl2}2 with NaN(SiMe3)2. Compound 1 is a useful starting material for low-coordinate (IPr)Co species. 1 reacts with 2,6-di-tert-butyl-4-methylphenol (BHT-H) via aminolysis of the Co-N bond to generate a three-coordinate phenoxide complex, IPrCoCl(O-2,6-(t)Bu2-4-MeC6H2) (2). The reaction of 1 with 2,6-diisopropylaniline (NH2DIPP) generates IPrCoCl(NHDIPP) (4), which undergoes disproportionation to form a mixture of 4, {IPrCoCl2}2, and IPrCo(NHDIPP)2 (3). The same product mixture is formed by the reaction of 1 with Li[NH(DIPP)], which unexpectedly proceeds by amide exchange. Compound 3 was synthesized independently by the reaction of {IPrCoCl2}2 with 4 equiv of Li[NH(DIPP)]. The reaction of 1 with the bulkier lithium 2,6-dimesitylanilide (LiNHDMP) also proceeds by amide exchange to generate IPrCoCl(NHDMP) (5), which is stable toward disproportionation. Compounds 1 and 2 exhibit trigonal-planar geometries at cobalt in the solid state. The solid-state structure of 3 also contains a trigonal-planar cobalt center and exhibits close Co---H contacts involving the methine hydrogen atoms of the NH(DIPP) groups in the axial positions. The solid-state structure of 5 features an interaction between cobalt and a flanking aryl group of the anilide ligand, resulting in pyramidalization of the cobalt center. PMID:25938547

  10. Direct amidation of carboxylic acids catalyzed by ortho-iodo arylboronic acids: catalyst optimization, scope, and preliminary mechanistic study supporting a peculiar halogen acceleration effect.

    PubMed

    Gernigon, Nicolas; Al-Zoubi, Raed M; Hall, Dennis G

    2012-10-01

    The importance of amides as a component of biomolecules and synthetic products motivates the development of catalytic, direct amidation methods employing free carboxylic acids and amines that circumvent the need for stoichiometric activation or coupling reagents. ortho-Iodophenylboronic acid 4a has recently been shown to catalyze direct amidation reactions at room temperature in the presence of 4A molecular sieves as dehydrating agent. Herein, the arene core of ortho-iodoarylboronic acid catalysts has been optimized with regards to the electronic effects of ring substitution. Contrary to the expectation, it was found that electron-donating substituents are preferable, in particular, an alkoxy substituent positioned para to the iodide. The optimal new catalyst, 5-methoxy-2-iodophenylboronic acid (MIBA, 4f), was demonstrated to be kinetically more active than the parent des-methoxy catalyst 4a, providing higher yields of amide products in shorter reaction times under mild conditions at ambient temperature. Catalyst 4f is recyclable and promotes the formation of amides from aliphatic carboxylic acids and amines, and from heteroaromatic carboxylic acids and other functionalized substrates containing moieties like a free phenol, indole and pyridine. Mechanistic studies demonstrated the essential role of molecular sieves in this complex amidation process. The effect of substrate stoichiometry, concentration, and measurement of the catalyst order led to a possible catalytic cycle based on the presumed formation of an acylborate intermediate. The need for an electronically enriched ortho-iodo substituent in catalyst 4f supports a recent theoretical study (Marcelli, T. Angew. Chem. Int. Ed.2010, 49, 6840-6843) with a purported role for the iodide as a hydrogen-bond acceptor in the orthoaminal transition state. PMID:23013456

  11. Quantifying the Sigma and Pi interactions between U(V) f orbitals and halide, alkyl, alkoxide, amide and ketimide ligands

    SciTech Connect

    University of California, Berkeley; Lukens, Wayne W.; Edelstein, Norman M.; Magnani, Nicola; Hayton, Trevor W.; Fortier, Skye; Seaman, Lani A.

    2013-06-20

    f Orbital bonding in actinide and lanthanide complexes is critical to their behavior in a variety of areas from separations to magnetic properties. Octahedral f1 hexahalide complexes have been extensively used to study f orbital bonding due to their simple electronic structure and extensive spectroscopic characterization. The recent expansion of this family to include alkyl, alkoxide, amide, and ketimide ligands presents the opportunity to extend this study to a wider variety of ligands. To better understand f orbital bonding in these complexes, the existing molecular orbital (MO) model was refined to include the effect of covalency on spin orbit coupling in addition to its effect on orbital angular momentum (orbital reduction). The new MO model as well as the existing MO model and the crystal field (CF) model were applied to the octahedral f1 complexes to determine the covalency and strengths of the ? and ? bonds formed by the f orbitals. When covalency is significant, MO models more precisely determined the strengths of the bonds derived from the f orbitals; however, when covalency was small, the CF model was better than either MO model. The covalency determined using the new MO model is in better agreement with both experiment and theory than that predicted by the existing MO model. The results emphasize the role played by the orbital energy in determining the strength and covalency of bonds formed by the f orbitals.

  12. In vitro evaluation of N-methyl amide tripeptidomimetics as substrates for the human intestinal di-/tri-peptide transporter hPEPT1.

    PubMed

    Andersen, Rikke; Nielsen, Carsten Uhd; Begtrup, Mikael; Jørgensen, Flemming Steen; Brodin, Birger; Frokjaer, Sven; Steffansen, Bente

    2006-07-01

    Oral absorption of tripeptides is generally mediated by the human intestinal di-/tri-peptide transporter, hPEPT1. However, the bioavailability of tripeptides is often limited due to degradation in the GI-tract by various peptidases. The aim of the present study was to evaluate the general application of N-methyl amide bioisosteres as peptide bond replacements in tripeptides in order to decrease degradation by peptidases and yet retain affinity for and transport via hPEPT1. Seven structurally diverse N-methyl amide tripeptidomimetics were selected based on a principal component analysis of structural properties of 6859 N-methyl amide tripeptidomimetics. In vitro extracellular degradation of the selected tripeptidomimetics as well as affinity for and transepithelial transport via hPEPT1 were investigated in Caco-2 cells. Decreased apparent degradation was observed for all tripeptidomimetics compared to the corresponding natural tripeptides. However, affinity for and transepithelial transport via hPEPT1 were only seen for Gly-Sar-Sar, AsnPsi[CONCH(3)]PhePsi[CONCH(3)]Trp, and Gly-Sar-Leu. This implies that tripeptidomimetics originating from tripeptides with neutral side chains are more likely to be substrates for hPEPT1 than tripeptidomimetics with charged side chains. The results of the present study indicate that the N-methyl amide peptide bond replacement approach for increasing bioavailability of tripeptidomimetic drug candidates is not generally applicable to all tripeptides. Nevertheless, retained affinity for and transport via hPEPT1 were shown for three of the evaluated N-methyl amide tripeptidomimetics. PMID:16713701

  13. First synthesis of etidronate partial amides starting from PCl3.

    PubMed

    Turhanen, Petri A; Niemi, Riku; Peräkylä, Mikael; Järvinen, Tomi; Vepsäläinen, Jouko J

    2003-09-21

    Methods for the preparation of mixed tetra-amide esters 1 and 2, the partial amide ester 3, and tri- and P,P-diamides 4 and 5 from monophosphorus spieces 12, 8 and 9, respectively, were developed. Compounds 8 and 9 were obtained from phosphorus trichloride via MeOPCl2, which was treated with 2 eq. and 4 eq. of piperidine, followed by water or acetyl chloride, respectively. Tetrasubstituted amide bisphosphonates 1 and 2 were selectively dealkylated with lithium or silyl halide to achieve target compounds 3-5. Piperidine was found to be a good desilylation reagent. Quantum mechanical calculations illustrate why derivative 2 was produced in low yield. The usefulness of compounds 1, 3 and 4 as prodrugs of etidronate was determined in aqueous buffer and human serum. PMID:14527155

  14. Earth Rotation

    NASA Technical Reports Server (NTRS)

    Dickey, Jean O.

    1995-01-01

    The study of the Earth's rotation in space (encompassing Universal Time (UT1), length of day, polar motion, and the phenomena of precession and nutation) addresses the complex nature of Earth orientation changes, the mechanisms of excitation of these changes and their geophysical implications in a broad variety of areas. In the absence of internal sources of energy or interactions with astronomical objects, the Earth would move as a rigid body with its various parts (the crust, mantle, inner and outer cores, atmosphere and oceans) rotating together at a constant fixed rate. In reality, the world is considerably more complicated, as is schematically illustrated. The rotation rate of the Earth's crust is not constant, but exhibits complicated fluctuations in speed amounting to several parts in 10(exp 8) [corresponding to a variation of several milliseconds (ms) in the Length Of the Day (LOD) and about one part in 10(exp 6) in the orientation of the rotation axis relative to the solid Earth's axis of figure (polar motion). These changes occur over a broad spectrum of time scales, ranging from hours to centuries and longer, reflecting the fact that they are produced by a wide variety of geophysical and astronomical processes. Geodetic observations of Earth rotation changes thus provide insights into the geophysical processes illustrated, which are often difficult to obtain by other means. In addition, these measurements are required for engineering purposes. Theoretical studies of Earth rotation variations are based on the application of Euler's dynamical equations to the problem of finding the response of slightly deformable solid Earth to variety of surface and internal stresses.

  15. Rotation Measurement

    NASA Technical Reports Server (NTRS)

    1979-01-01

    In aircraft turbine engine research, certain investigations require extremely precise measurement of the position of a rotating part, such as the rotor, a disc-like part of the engine's compressor which revolves around a shaft at extremely high speeds. For example, in studies of airflow velocity within a compressor, researchers need to know-for data correlation the instantaneous position of a given spot on the rotor each time a velocity measurement is made. Earlier methods of measuring rotor shaft angle required a physical connection to the shaft, which limited the velocity of the rotating object.

  16. Diffusion bonding

    DOEpatents

    Anderson, Robert C.

    1976-06-22

    1. A method for joining beryllium to beryllium by diffusion bonding, comprising the steps of coating at least one surface portion of at least two beryllium pieces with nickel, positioning a coated surface portion in a contiguous relationship with an other surface portion, subjecting the contiguously disposed surface portions to an environment having an atmosphere at a pressure lower than ambient pressure, applying a force upon the beryllium pieces for causing the contiguous surface portions to abut against each other, heating the contiguous surface portions to a maximum temperature less than the melting temperature of the beryllium, substantially uniformly decreasing the applied force while increasing the temperature after attaining a temperature substantially above room temperature, and maintaining a portion of the applied force at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions.

  17. Direct Reaction of Amides with Nitric Oxide To Form Diazeniumdiolates

    PubMed Central

    2015-01-01

    We report the apparently unprecedented direct reaction of nitric oxide (NO) with amides to generate ions of structure R(C=O)NH–N(O)=NO–, with examples including R = Me (1a) or 3-pyridyl (1b). The sodium salts of both released NO in pH 7.4 buffer, with 37 °C half-lives of 1–3 min. As NO-releasing drug candidates, diazeniumdiolated amides would have the advantage of generating only 1 equiv of base on hydrolyzing exhaustively to NO, in contrast to their amine counterparts, which generate 2 equiv of base. PMID:25210948

  18. Decomposition of lithium amide and imide films on nickel

    NASA Astrophysics Data System (ADS)

    Engbæk, Jakob; Nielsen, Gunver; Nielsen, Jane H.; Chorkendorff, Ib

    2007-02-01

    Thin films of lithium hydride, lithium amide and lithium imide were grown from lithium and ammonia under controlled conditions in an ultra high vacuum chamber. By making thin films instead of bulk or powder samples, it was possible to study the stability and the release of hydrogen without influence of transport phenomena. Surprisingly, lithium amide and lithium imide were seen to decompose at higher temperatures than lithium hydride. Furthermore, it was seen that hydrogen reversibly could be removed by heat treatment and subsequently refilled.

  19. A Direct and Stereoretentive Synthesis of Amides from Cyclic Alcohols

    PubMed Central

    Mondal, Deboprosad; Bellucci, Luca

    2013-01-01

    Chlorosulfites prepared in situ using thionyl chloride react with nitrile complexes of titanium (IV) fluoride to give a one-pot conversion of alcohols into amides. For the first time, amides are obtained from cyclic alcohols with stereoretention. Critical to the design of these new Ti(IV) reactions has been the use of little explored Ti(IV) nitrile complexes which are thought to chelate chlorosulfites in the transition state to create a carbocation that is rapidly captured by the nitrile nucleophile via a front-side attack mechanism. PMID:24273447

  20. Iodine-Catalyzed Decarboxylative Amidation of β,γ-Unsaturated Carboxylic Acids with Chloramine Salts Leading to Allylic Amides.

    PubMed

    Kiyokawa, Kensuke; Kojima, Takumi; Hishikawa, Yusuke; Minakata, Satoshi

    2015-10-26

    The iodine-catalyzed decarboxylative amidation of β,γ-unsaturated carboxylic acids with chloramine salts is described. This method enables the regioselective synthesis of allylic amides from various types of β,γ-unsaturated carboxylic acids containing substituents at the α- and β-positions. In the reaction, N-iodo-N-chloroamides, generated by the reaction of a chloramine salt with I2 , function as a key active species. The reaction provides an attractive alternative to existing methods for the synthesis of useful secondary allylic amine derivatives. PMID:26493878

  1. Nonlinear Spectroscopy Study of Vibrational Self-Trapping in Hydrogen Bonded Crystals

    NASA Astrophysics Data System (ADS)

    Edler, Julian; Hamm, Peter

    Femtosecond pump probe spectroscopy proves that self-trapping occurs in the NH and amide I band of crystalline acetanilide (ACN). The phonon modes that mediate the self-trapping are identified. Comparison between ACN and N-methylacetamide, both model systems for proteins, shows that self-trapping is a common feature in hydrogen bonded systems.

  2. Three component assemblies by orthogonal H-bonding and donor-acceptor charge-transfer interaction.

    PubMed

    Kar, Haridas; Ghosh, Suhrit

    2014-02-01

    Three component supramolecular assemblies from a mixture of an aromatic donor (D), acceptor (A) and external structure directing agent (ESDA) are achieved by orthogonal noncovalent interactions involving two different types of H-bonding and alternate D-A stacking. An ESDA containing amide or urea produces a charge-transfer gel and sol, respectively, owing to their contrasting morphology. PMID:24309620

  3. Pi Bond Orders and Bond Lengths

    ERIC Educational Resources Information Center

    Herndon, William C.; Parkanyi, Cyril

    1976-01-01

    Discusses three methods of correlating bond orders and bond lengths in unsaturated hydrocarbons: the Pauling theory, the Huckel molecular orbital technique, and self-consistent-field techniques. (MLH)

  4. Synthesis of P-stereogenic diarylphosphinic amides by directed lithiation: transformation into tertiary phosphine oxides via methanolysis, aryne chemistry and complexation behaviour toward zinc(ii).

    PubMed

    del Águila-Sánchez, Miguel A; Navarro, Yolanda; García López, Jesús; Guedes, Guilherme P; López Ortiz, Fernando

    2016-02-01

    The highly diastereoselective synthesis of P-stereogenic phosphinic amides via directed ortho lithiation (DoLi) of (SC)-P,P-diphenylphosphinic amides with t-BuLi followed by electrophilic quench reactions is described. Functionalised derivatives containing a wide variety of ortho substituents (Cl, Br, I, OH, N3, SiMe3, SnMe3, P(O)Ph2, Me, allyl, (t)BuOCO) have been prepared in high yields with diastereomeric ratios up to 98 : 2. The X-ray diffraction structure of the ortho-stannylated and ortho-iodo compounds showed that the pro-S P-phenyl ring was stereoselectively ortho-deprotonated by the organolithium base. The usefulness of the method is supported by two key transformations, the synthesis of P-stereogenic methyl phosphinates through replacement of the chiral auxiliary by a methoxy group and the first example of the insertion of benzyne into the P-N bond of a P-stereogenic phosphinic amide. A DFT study of this reaction showed that the insertion proceeds through a [2 + 2] cycloaddition and a subsequent ring-opening with retention of the P-configuration. Explorative coordination chemistry of the new P-stereogenic ligands provided access to a chiral phosphinic amide-phosphine oxide Zn(ii) complex, the crystal structure of which is reported. PMID:26370566

  5. Ultrasound-assisted direct oxidative amidation of benzyl alcohols catalyzed by graphite oxide.

    PubMed

    Mirza-Aghayan, Maryam; Ganjbakhsh, Nahid; Molaee Tavana, Mahdieh; Boukherroub, Rabah

    2016-09-01

    Ultrasound irradiation was successfully applied for the direct oxidative amidation of benzyl alcohols with amines into the corresponding amides using graphite oxide (GO) as an oxidative and reusable solid acid catalyst in acetonitrile as solvent at 50°C under air atmosphere. The direct oxidative amidation of benzyl alcohols takes place under mild conditions yielding the corresponding amides in good to high yields (69-95%) and short reaction times under metal-free conditions. PMID:27150743

  6. Amidation of esters with amino alcohols using organobase catalysis.

    PubMed

    Caldwell, Nicola; Campbell, Peter S; Jamieson, Craig; Potjewyd, Frances; Simpson, Iain; Watson, Allan J B

    2014-10-01

    A catalytic protocol for the base-mediated amidation of unactivated esters with amino alcohol derivatives is reported. Investigations into mechanistic aspects of the process indicate that the reaction involves an initial transesterification, followed by an intramolecular rearrangement. The reaction is highly general in nature and can be extended to include the synthesis of oxazolidinone systems through use of dimethyl carbonate. PMID:25226088

  7. Insecticidal, repellent and fungicidal properties of novel trifluoromethylphenyl amides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twenty trifluoromethylphenyl amides were synthesized and evaluated as fungicides and as mosquito toxicants and repellents. Against Aedes aegypti larvae, (trifluoromethyl)phenyl)-3,5-dinitrobenzamide (1e) was the most toxic compound (24 h LC50 1940 nM), while against adults (trifluoromethyl)phenyl)-...

  8. Adsorption of sulfur(IV) oxide by amide sorbents

    SciTech Connect

    Nikandrov, I.S.; Kogtev, S.E.; Kazimirov, O.E.; Pavlova, I.V.

    1994-04-10

    Adsorption of sulfur(IV) oxide by industrial amide plastics has been studied. Sorption capacity of the sorbents studied has been determined under static and dynamic conditions. Physical and chemical interaction has been demonstrated to take place between sulfur(IV) oxide and the sorbent studied.

  9. Amides and Hydrazides from Amine and Hydrazine Hydrochlorides.

    ERIC Educational Resources Information Center

    Shama, Sami A.; Tran, Thuan L.

    1978-01-01

    This safe and efficient procedure for the synthesis of N-substituted amides and hydrazides is a modification of the Schotten-Bausmann procedure in which the amine or hydrazide is replaced by the corresponding hydrochloride salt, and the use of alkali is eliminated. (Author/BB)

  10. Use of triphenyl phosphate as risk mitigant for metal amide hydrogen storage materials

    DOEpatents

    Cortes-Concepcion, Jose A.; Anton, Donald L.

    2016-04-26

    A process in a resulting product of the process in which a hydrogen storage metal amide is modified by a ball milling process using an additive of TPP. The resulting product provides for a hydrogen storage metal amide having a coating that renders the hydrogen storage metal amide resistant to air, ambient moisture, and liquid water while improving useful hydrogen storage and release kinetics.

  11. 40 CFR 721.10176 - Amides, peanut-oil, N-[3-(dimethylamino)propyl].

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Amides, peanut-oil, N- . 721.10176... Substances § 721.10176 Amides, peanut-oil, N- . (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, peanut-oil, N- (PMN P-04-144; CAS No....

  12. 40 CFR 721.10176 - Amides, peanut-oil, N-[3-(dimethylamino)propyl].

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Amides, peanut-oil, N- . 721.10176... Substances § 721.10176 Amides, peanut-oil, N- . (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, peanut-oil, N- (PMN P-04-144; CAS No....

  13. 40 CFR 721.10176 - Amides, peanut-oil, N-[3-(dimethylamino)propyl].

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Amides, peanut-oil, N- . 721.10176... Substances § 721.10176 Amides, peanut-oil, N- . (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, peanut-oil, N- (PMN P-04-144; CAS No....

  14. 40 CFR 721.10176 - Amides, peanut-oil, N-[3-(dimethylamino)propyl].

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Amides, peanut-oil, N- . 721.10176... Substances § 721.10176 Amides, peanut-oil, N- . (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, peanut-oil, N- (PMN P-04-144; CAS No....

  15. 40 CFR 721.10176 - Amides, peanut-oil, N-[3-(dimethylamino)propyl].

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Amides, peanut-oil, N- . 721.10176... Substances § 721.10176 Amides, peanut-oil, N- . (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, peanut-oil, N- (PMN P-04-144; CAS No....

  16. 40 CFR 721.10191 - Amides, coco, N-[3-(dibutylamino)propyl].

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Amides, coco, N- . 721.10191 Section... Substances § 721.10191 Amides, coco, N- . (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, coco, N- (PMN P-06-262; CAS No. 851544-20-2)...

  17. 40 CFR 721.10192 - Amides, coco, N-[3-(dibutylamino)propyl], acrylates.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Amides, coco, N- , acrylates. 721... Substances § 721.10192 Amides, coco, N- , acrylates. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, coco, N- , acrylates (PMN...

  18. 40 CFR 721.10192 - Amides, coco, N-[3-(dibutylamino)propyl], acrylates.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Amides, coco, N- , acrylates. 721... Substances § 721.10192 Amides, coco, N- , acrylates. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, coco, N- , acrylates (PMN...

  19. 40 CFR 721.10191 - Amides, coco, N-[3-(dibutylamino)propyl].

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Amides, coco, N- . 721.10191 Section... Substances § 721.10191 Amides, coco, N- . (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as amides, coco, N- (PMN P-06-262; CAS No. 851544-20-2)...

  20. 40 CFR 721.10512 - Fatty acid maleic acid amides (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Fatty acid maleic acid amides (generic... Specific Chemical Substances § 721.10512 Fatty acid maleic acid amides (generic). (a) Chemical substance... fatty acid maleic acid amides (PMNs P-07-563 and P-07-564) are subject to reporting under this...

  1. 40 CFR 721.10512 - Fatty acid maleic acid amides (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Fatty acid maleic acid amides (generic... Specific Chemical Substances § 721.10512 Fatty acid maleic acid amides (generic). (a) Chemical substance... fatty acid maleic acid amides (PMNs P-07-563 and P-07-564) are subject to reporting under this...

  2. The synthesis of a pyridine-N-oxide isophthalamide rotaxane utilizing supplementary amide hydrogen bond interactions.

    PubMed

    Evans, Nicholas H; Gell, Charles E; Peach, Michael J G

    2016-08-16

    The synthesis of a pyridine-N-oxide containing rotaxane, not requiring an additional ionic template, has been achieved in 32% yield. Successful rotaxane formation is dependent upon the structure of the isophthalamide macrocycle used, an observation which has been rationalised by a combination of NMR spectroscopy, X-ray crystallography and computational modelling. PMID:27494803

  3. Multiple Noncovalent Bonding in Halogen Complexes with Oxygen Organics. I. Tertiary Amides.

    PubMed

    Suponitsky, Kyrill Yu; Burakov, N I; Kanibolotsky, Alexander L; Mikhailov, Vasilii A

    2016-06-23

    The present work describes the structure and binding of adducts of N,N'-diacetylpiperazine with halogens and interhalogens based on combination of different experimental methods and quantum chemical calculations. On the basis of conductometric and spectro-photometric experimental results, behavior of complexes in the acetonitrile solution was described. The iodine adduct with N,N'-diacetylpiperazine fully degrades into components. Adducts of interhalogens I-X (X = Cl or Br) with N,N'-diacetylpiperazine in acetonitrile partially dissociate to anionic [X-I-X](-) and cationic species. In the solid state, molecules are connected via C═O···I, C-H···I, and Cl···Cl attractive interactions. N,N'-diacetylpiperazine···dihalogen complex is stabilized by simultaneous C═O···I and C-H···I interactions. Such binding mode allows to explain the problems of the direct halogenation of acetyl-containing compounds with molecular halogens as reagents. We believe that the observed binding pattern can be used as prototypical for future design of halogeno complexes. PMID:27228362

  4. Insecticidal, repellent and fungicidal properties of novel trifluoromethylphenyl amides.

    PubMed

    Tsikolia, Maia; Bernier, Ulrich R; Coy, Monique R; Chalaire, Katelyn C; Becnel, James J; Agramonte, Natasha M; Tabanca, Nurhayat; Wedge, David E; Clark, Gary G; Linthicum, Kenneth J; Swale, Daniel R; Bloomquist, Jeffrey R

    2013-09-01

    Twenty trifluoromethylphenyl amides were synthesized and evaluated as fungicides and as mosquito toxicants and repellents. Against Aedes aegypti larvae, N-(2,6-dichloro-4-(trifluoromethyl)phenyl)-3,5-dinitrobenzamide (1e) was the most toxic compound (24 h LC50 1940 nM), while against adults N-(2,6-dichloro-4-(trifluoromethyl)phenyl)-2,2,2-trifluoroacetamide (1c) was most active (24 h LD50 19.182 nM, 0.5 μL/insect). However, the 24 h LC50 and LD50 values of fipronil against Ae. aegypti larvae and adults were significantly lower: 13.55 nM and 0.787 × 10(-4) nM, respectively. Compound 1c was also active against Drosophila melanogaster adults with 24 h LC50 values of 5.6 and 4.9 μg/cm(2) for the Oregon-R and 1675 strains, respectively. Fipronil had LC50 values of 0.004 and 0.017 μg/cm(2) against the two strains of D. melanogaster, respectively. In repellency bioassays against female Ae. aegypti, 2,2,2-trifluoro-N-(2-(trifluoromethyl)phenyl)acetamide (4c) had the highest repellent potency with a minimum effective dosage (MED) of 0.039 μmol/cm(2) compared to DEET (MED of 0.091 μmol/cm(2)). Compound N-(2-(trifluoromethyl)phenyl)hexanamide (4a) had an MED of 0.091 μmol/cm(2) which was comparable to DEET. Compound 4c was the most potent fungicide against Phomopsis obscurans. Several trends were discerned between the structural configuration of these molecules and the effect of structural changes on toxicity and repellency. Para- or meta- trifluoromethylphenyl amides with an aromatic ring attached to the carbonyl carbon showed higher toxicity against Ae. aegypti larvae, than ortho- trifluoromethylphenyl amides. Ortho- trifluoromethylphenyl amides with trifluoromethyl or alkyl group attached to the carbonyl carbon produced higher repellent activity against female Ae. aegypti and Anopheles albimanus than meta- or para- trifluoromethylphenyl amides. The presence of 2,6-dichloro- substitution on the phenyl ring of the amide had an influence on larvicidal and repellent

  5. Bonded Lubricants

    NASA Technical Reports Server (NTRS)

    1977-01-01

    Another spinoff to the food processing industry involves a dry lubricant developed by General Magnaplate Corp. of Linden, N.J. Used in such spacecraft as Apollo, Skylab and Viking, the lubricant is a coating bonded to metal surfaces providing permanent lubrication and corrosion resistance. The coating lengthens equipment life and permits machinery to be operated at greater speed, thus increasing productivity and reducing costs. Bonded lubricants are used in scores of commercia1 applications. They have proved particularly valuable to food processing firms because, while increasing production efficiency, they also help meet the stringent USDA sanitation codes for food-handling equipment. For example, a cookie manufacturer plagued production interruptions because sticky batter was clogging the cookie molds had the brass molds coated to solve the problem. Similarly, a pasta producer faced USDA action on a sanitation violation because dough was clinging to an automatic ravioli-forming machine; use of the anti-stick coating on the steel forming plates solved the dual problem of sanitation deficiency and production line downtime.

  6. Basics of Fidelity Bonding.

    ERIC Educational Resources Information Center

    Kahn, Steven P.

    Fidelity bonds are important for an agency to hold to protect itself against any financial loss that can result from dishonest acts by its employees. Three types of fidelity bonds are available to an agency: (1) public official bonds; (2) dishonesty bonds; and (3) faithful performance bonds. Public official bonds are required by state law to be…

  7. Crystal structure of glycidamide: the mutagenic and genotoxic metabolite of acryl­amide

    PubMed Central

    Hemgesberg, Melanie N.; Bonck, Thorsten; Merz, Karl-Heinz; Sun, Yu; Schrenk, Dieter

    2016-01-01

    The title compound, glycidamide (systematic name: oxirane-2-carboxamide), C3H5NO2, is the mutagenic and genotoxic metabolite of acryl­amide, a food contaminant and industrial chemical that has been classified as being probably carcinogenic to humans. Synthesized via the reaction of acrylo­nitrile and hydrogen peroxide, it crystallizes with both enanti­omers occurring as two crystallographically independent mol­ecules (A and B) in the asymmetric unit. They have similar conformations with an r.m.s. deviation of 0.0809 Å for mol­ecule B inverted on mol­ecule A. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, which lead to the formation of β-sheet structures enclosing R 2 2(8) and R 4 2(8) loops. The β-sheets are linked by weaker C—H⋯O hydrogen bonds, forming a supra­molecular three-dimensional structure. PMID:27536408

  8. Crystal structure of glycidamide: the mutagenic and genotoxic metabolite of acryl-amide.

    PubMed

    Hemgesberg, Melanie N; Bonck, Thorsten; Merz, Karl-Heinz; Sun, Yu; Schrenk, Dieter

    2016-08-01

    The title compound, glycidamide (systematic name: oxirane-2-carboxamide), C3H5NO2, is the mutagenic and genotoxic metabolite of acryl-amide, a food contaminant and industrial chemical that has been classified as being probably carcinogenic to humans. Synthesized via the reaction of acrylo-nitrile and hydrogen peroxide, it crystallizes with both enanti-omers occurring as two crystallographically independent mol-ecules (A and B) in the asymmetric unit. They have similar conformations with an r.m.s. deviation of 0.0809 Å for mol-ecule B inverted on mol-ecule A. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds, which lead to the formation of β-sheet structures enclosing R 2 (2)(8) and R 4 (2)(8) loops. The β-sheets are linked by weaker C-H⋯O hydrogen bonds, forming a supra-molecular three-dimensional structure. PMID:27536408

  9. Hydrogen bonded and stacked geometries of the temozolomide dimer.

    PubMed

    Kasende, Okuma Emile; Muya, Jules Tshishimbi; de Paul N Nziko, Vincent; Scheiner, Steve

    2016-04-01

    Dispersion-corrected density functional theory (DFT) and MP2 quantum chemical methods are used to examine homodimers of temozolomide (TMZ). Of the 12 dimer configurations found to be minima, the antarafacial stacked dimer is the most favored, it is lower in energy than coplanar dimers which are stabilized by H-bonds. The comparison between B3LYP and B3LYP-D binding energies points to dispersion as a primary factor in stabilizing the stacked geometries. CO(π) → CO(π*) charge transfers between amide groups in the global minimum are identified by NBO, as well as a pair of weak CH∙∙N H-bonds. AIM analysis of the electron density provides an alternative description which includes N∙∙O, N∙∙N, and C∙∙C noncovalent bonds. Graphical Abstract Hydrogen bonded and stacked geometries of the temozolomide dimerᅟ. PMID:26971506

  10. Nine of 16 stereoisomeric polyhydroxylated proline amides are potent β-N-acetylhexosaminidase inhibitors.

    PubMed

    Ayers, Benjamin J; Glawar, Andreas F G; Martínez, R Fernando; Ngo, Nigel; Liu, Zilei; Fleet, George W J; Butters, Terry D; Nash, Robert J; Yu, Chu-Yi; Wormald, Mark R; Nakagawa, Shinpei; Adachi, Isao; Kato, Atsushi; Jenkinson, Sarah F

    2014-04-18

    All 16 stereoisomeric N-methyl 5-(hydroxymethyl)-3,4-dihydroxyproline amides have been synthesized from lactones accessible from the enantiomers of glucuronolactone. Nine stereoisomers, including all eight with a (3R)-hydroxyl configuration, are low to submicromolar inhibitors of β-N-acetylhexosaminidases. A structural correlation between the proline amides is found with the ADMDP-acetamide analogues bearing an acetamidomethylpyrrolidine motif. The proline amides are generally more potent than their ADMDP-acetamide equivalents. β-N-Acetylhexosaminidase inhibition by an azetidine ADMDP-acetamide analogue is compared to an azetidine carboxylic acid amide. None of the amides are good α-N-acetylgalactosaminidase inhibitors. PMID:24641544

  11. Polaronlike vibrational bands of molecular crystals with one-dimensional hydrogen-bond chains: N-methylacetamide

    NASA Astrophysics Data System (ADS)

    Araki, Gako; Suzuki, Kazuaki; Nakayama, Hideyuki; Ishii, Kikujiro

    1991-05-01

    N-methylacetamide (NMA) crystal forms one-dimensional hydrogen-bond chains, which are similar to those in an acetanilide (ACN) crystal for which an unconventional vibrational band accompanying the amide-I band has been observed. Infrared spectra of NMA crystals show an additional band on the small-wave-number side of the amide-II band as the temperature is lowered. There is a close resemblance between this band and the band of ACN. It is likely that these bands appear by the same mechanism. The polaron model, which has been employed to explain the band of ACN, was found to be applicable also to the case of NMA, although the main vibrational mode is amide I in ACN and amide II in NMA.

  12. Experimental and theoretical understanding of the gas phase oxidation of atmospheric amides with OH radicals: kinetics, products, and mechanisms.

    PubMed

    Borduas, Nadine; da Silva, Gabriel; Murphy, Jennifer G; Abbatt, Jonathan P D

    2015-05-14

    Atmospheric amides have primary and secondary sources and are present in ambient air at low pptv levels. To better assess the fate of amides in the atmosphere, the room temperature (298 ± 3 K) rate coefficients of five different amides with OH radicals were determined in a 1 m(3) smog chamber using online proton-transfer-reaction mass spectrometry (PTR-MS). Formamide, the simplest amide, has a rate coefficient of (4.44 ± 0.46) × 10(-12) cm(3) molec(-1) s(-1) against OH, translating to an atmospheric lifetime of ∼1 day. N-methylformamide, N-methylacetamide and propanamide, alkyl versions of formamide, have rate coefficients of (10.1 ± 0.6) × 10(-12), (5.42 ± 0.19) × 10(-12), and (1.78 ± 0.43) × 10(-12) cm(3) molec(-1) s(-1), respectively. Acetamide was also investigated, but due to its slow oxidation kinetics, we report a range of (0.4-1.1) × 10(-12) cm(3) molec(-1) s(-1) for its rate coefficient with OH radicals. Oxidation products were monitored and quantified and their time traces were fitted using a simple kinetic box model. To further probe the mechanism, ab initio calculations are used to identify the initial radical products of the amide reactions with OH. Our results indicate that N-H abstractions are negligible in all cases, in contrast to what is predicted by structure-activity relationships. Instead, the reactions proceed via C-H abstraction from alkyl groups and from formyl C(O)-H bonds when available. The latter process leads to radicals that can readily react with O2 to form isocyanates, explaining the detection of toxic compounds such as isocyanic acid (HNCO) and methyl isocyanate (CH3NCO). These contaminants of significant interest are primary oxidation products in the photochemical oxidation of formamide and N-methylformamide, respectively. PMID:25019427

  13. Mechanisms for the decomposition and dehydrogenation of Li amide/imide

    NASA Astrophysics Data System (ADS)

    Hoang, Khang; Janotti, Anderson; van de Walle, Chris G.

    2012-02-01

    Reversible reaction involving Li amide (LiNH2) and Li imide (Li2NH) is a potential mechanism for hydrogen storage. Recent synchrotron x-ray diffraction experiments [W. I. David , J. Am. Chem. Soc.JACSAT0002-786310.1021/ja066016s 129, 1594 (2007)] suggest that the transformation between LiNH2 and Li2NH is a bulk reaction that occurs through nonstoichiometric processes and involves the migration of Li+ and H+ ions. In order to understand the atomistic mechanisms behind these processes, we carry out comprehensive first-principles studies of native point defects and defect complexes in the two compounds. We find that both LiNH2 and Li2NH are prone to Frenkel disorder on the Li sublattice. Lithium interstitials and vacancies have low formation energies and are highly mobile, and therefore play an important role in mass transport and ionic conduction. Hydrogen interstitials and vacancies, on the other hand, are responsible for forming and breaking N-H bonds, which is essential in the Li amide/imide reaction. Based on the structure, energetics, and migration of hydrogen-, lithium-, and nitrogen-related defects, we propose that LiNH2 decomposes into Li2NH and NH3 according to two competing mechanisms with different activation energies: one mechanism involves the formation of native defects in the interior of the material, the other at the surface. As a result, the prevailing mechanism and hence the effective activation energy for decomposition depend on the surface-to-volume ratio or the specific surface area, which changes with particle size during ball milling. These mechanisms also provide an explanation for the dehydrogenation of LiNH2 + LiH mixtures.

  14. Proposal of an Amide-Directed Carbocupration Mechanism for Copper-Catalyzed meta-Selective C—H Arylation of Acetanilides by Diaryliodonium Salts

    NASA Astrophysics Data System (ADS)

    Zhang, Song-lin; Ding, Yu-qiang

    2011-12-01

    We examined the puzzling mechanism for Cu-catalyzed meta-C—H arylation reaction of anilides by diaryliodonium salts through systematic theoretical analysis. The previously proposed anti-oxy-cupration mechanism featuring anti-1,2- or anti-1,4-addition of cuprate and oxygen to the phenyl ring generating a meta-cuprated intermediate was excluded due to the large activation barriers. Alternatively, a new amide-directed carbocupration mechanism was proposed which involves a critical rate- and regio-determining step of amide-directed addition of the Cu(III)-aryl bond across the phenyl C2=C3 double bond to form an ortho-cuprated, meta-arylated intermediate. This mechanism is kinetically the most favored among several possible mechanisms such as ortho- or para-cupration/migration mechanism, direct meta C—H bond cleavage mediated by Cu(III) or Cu(I), and Cu(III)-catalyzed ortho-directed C—H bond activation mechanism. Furthermore, the predicted regioselectivity based on this mechanism has been shown to favor the meta-arylation that is consistent with the experimental observations.

  15. Two-dimensional vibrational spectroscopy of the amide I band of crystalline acetanilide: Fermi resonance, conformational substates, or vibrational self-trapping?

    NASA Astrophysics Data System (ADS)

    Edler, J.; Hamm, P.

    2003-08-01

    Two-dimensional infrared (2D-IR) spectroscopy is applied to investigate acetanilide, a molecular crystal consisting of quasi-one-dimensional hydrogen bonded peptide units. The amide-I band exhibits a double peak structure, which has been attributed to different mechanisms including vibrational self-trapping, a Fermi resonance, or the existence of two conformational substates. The 2D-IR spectrum of crystalline acetanilide is compared with that of two different molecular systems: (i) benzoylchloride, which exhibits a strong symmetric Fermi resonance and (ii) N-methylacetamide dissolved in methanol which occurs in two spectroscopically distinguishable conformations. Both 2D-IR spectra differ significantly from that of crystalline acetanilide, proving that these two alternative mechanisms cannot account for the anomalous spectroscopy of crystalline acetanilide. On the other hand, vibrational self-trapping of the amide-I band can naturally explain the 2D-IR response.

  16. Simple Amides of Oleanolic Acid as Effective Penetration Enhancers

    PubMed Central

    Bednarczyk-Cwynar, Barbara; Partyka, Danuta; Zaprutko, Lucjusz

    2015-01-01

    Transdermal transport is now becoming one of the most convenient and safe pathways for drug delivery. In some cases it is necessary to use skin penetration enhancers in order to allow for the transdermal transport of drugs that are otherwise insufficiently skin-permeable. A series of oleanolic acid amides as potential transdermal penetration enhancers was formed by multistep synthesis and the synthesis of all newly prepared compounds is presented. The synthetized amides of oleanolic acid were tested for their in vitro penetration promoter activity. The above activity was evaluated by means of using the Fürst method. The relationships between the chemical structure of the studied compounds and penetration activity are presented. PMID:26010090

  17. Fine structure of the amide i band in acetanilide

    NASA Astrophysics Data System (ADS)

    Careri, G.; Gratton, E.; Shyamsunder, E.

    1988-05-01

    Their absorption spectrum of both single crystals and powdered samples of acetanilide (a model system for proteins) has been studied in the amide i region, where a narrow band has been identified as a highly trapped soliton state. The powder-sample spectra have been decomposed using four Lorentzian bands. A strong temperature dependence has been found for the intensity of two of the subbands, which also show a complementary behavior. Polarization studies performed on thin crystals have shown that the subbands have the same polarization. Low-temperature spectra of partially deuterated samples show the presence of the subbands at the same absorption frequencies found using the fitting procedure in the spectra of nondeuterated samples. The soliton model currently proposed to explain the origin of the anomalous amide i component at 1650 cm-1 still holds, but some modification of the model is required to account for the new features revealed by this study.

  18. New substituted amides and hydrazides of pectic acid

    SciTech Connect

    Lapenko, V.L.; Potapova, L.B.; Slivkin, A.I.; Razumnaya, Z.A.

    1988-05-10

    Structural variants of pectin amides and hydrazides are of practical value as flocculants in water treatment. The purpose of this work was to further investigate the synthesis of substituted amides and hydrazides of pectic acid and to study their activity as flocculants. They used pectin, methylation products of pectin, pectic acid, and methyl pectates. The synthesized analogs of pectinic materials containing nitrogen are essentially copolymers of hydrazido (amido) and carboxyl (methoxyl) derivatives of D-galacturonic acid. The flocculant activity of the new polymers was monitored with simulated drainage water containing kaolin or abrasive powder (for glass manufacture) in the presence of polyvalent metal ions. The use of the new ampholytic flocculants in the purification of water from suspended impurities permits a high degree of clarification with a sharp decrease in reagent consumption.

  19. Amino alcohol-based degradable poly(ester amide) elastomers

    PubMed Central

    Bettinger, Christopher J.; Bruggeman, Joost P.; Borenstein, Jeffrey T.; Langer, Robert S.

    2009-01-01

    Currently available synthetic biodegradable elastomers are primarily composed of crosslinked aliphatic polyesters, which suffer from deficiencies including (1) high crosslink densities, which results in exceedingly high stiffness, (2) rapid degradation upon implantation, or (3) limited chemical moieties for chemical modification. Herein, we have developed poly(1,3-diamino-2-hydroxypropane-co-polyol sebacate)s, a new class of synthetic, biodegradable elastomeric poly(ester amide)s composed of crosslinked networks based on an amino alcohol. These crosslinked networks feature tensile Young’s modulus on the order of 1 MPa and reversable elongations up to 92%. These polymers exhibit in vitro and in vivo biocompatibility. These polymers have projected degradation half-lives up to 20 months in vivo. PMID:18295329

  20. Communication: Creation of molecular vibrational motions via the rotation-vibration coupling

    SciTech Connect

    Shu, Chuan-Cun; Henriksen, Niels E.

    2015-06-14

    Building on recent advances in the rotational excitation of molecules, we show how the effect of rotation-vibration coupling can be switched on in a controlled manner and how this coupling unfolds in real time after a pure rotational excitation. We present the first examination of the vibrational motions which can be induced via the rotation-vibration coupling after a pulsed rotational excitation. A time-dependent quantum wave packet calculation for the HF molecule shows how a slow (compared to the vibrational period) rotational excitation leads to a smooth increase in the average bond length whereas a fast rotational excitation leads to a non-stationary vibrational motion. As a result, under field-free postpulse conditions, either a stretched stationary bond or a vibrating bond can be created due to the coupling between the rotational and vibrational degrees of freedom. The latter corresponds to a laser-induced breakdown of the adiabatic approximation for rotation-vibration coupling.

  1. Total chemical synthesis of lassomycin and lassomycin-amide.

    PubMed

    Lear, S; Munshi, T; Hudson, A S; Hatton, C; Clardy, J; Mosely, J A; Bull, T J; Sit, C S; Cobb, S L

    2016-05-11

    Herein we report a practical synthetic route to the lasso peptide lassomycin () and C-terminal variant lassomycin-amide (). The biological evaluation of peptides and against Mycobacterium tuberculosis revealed that neither had any activity against this bacterium. This lack of biological activity has led us to propose that naturally occurring lassomycin may actually exhibit a standard lasso peptide threaded conformation rather than the previously reported unthreaded structure. PMID:27101411

  2. Rapid Access to 3-Aminoindazoles from Tertiary Amides.

    PubMed

    Cyr, Patrick; Régnier, Sophie; Bechara, William S; Charette, André B

    2015-07-17

    A two-step synthesis of structurally diverse 3-aminoindazoles from readily available starting materials was developed. This sequence includes a one-pot synthesis of aminohydrazones through chemoselective Tf2O-mediated activation of tertiary amides and subsequent addition of nucleophilic hydrazides. These precursors then participate in an intramolecular ligand-free Pd-catalyzed C-H amination reaction. The azaheterocycles synthesized via this approach were further diversified through subsequent deprotection/functionalization reactions. PMID:26154712

  3. Toxocara canis: Larvicidal activity of fatty acid amides.

    PubMed

    Mata-Santos, Taís; D'Oca, Caroline da Ros Montes; Mata-Santos, Hílton Antônio; Fenalti, Juliana; Pinto, Nitza; Coelho, Tatiane; Berne, Maria Elisabeth; da Silva, Pedro Eduardo Almeida; D'Oca, Marcelo Gonçalves Montes; Scaini, Carlos James

    2016-02-01

    Considering the therapeutic potential of fatty acid amides, the present study aimed to evaluate their in vitro activity against Toxocara canis larvae and their cytotoxicity for the first time. Linoleylpyrrolidilamide was the most potent, with a minimal larvicidal concentration (MLC) of 0.05 mg/mL and 27% cytotoxicity against murine peritoneal macrophages C57BL/6 mice, as assessed by the MTT assay. PMID:26783180

  4. Structural characterization of synthetic poly(ester amide) from sebacic acid and 4-amino-1-butanol by matrix-assisted laser desorption ionization time-of-flight/time-of-flight tandem mass spectrometry.

    PubMed

    Rizzarelli, Paola; Puglisi, Concetto

    2008-01-01

    Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS) was employed to analyze a poly(ester amide) sample (PEA-Bu) from the melt condensation of sebacic acid and 4-amino-1-butanol. In particular, we investigated the fragmentation pathways, the ester/amide bond sequences and the structure of species derived from side reactions during the synthesis. MALDI-TOF/TOF-MS/MS analysis was performed on cyclic species and linear oligomers terminated by dicarboxyl groups, carboxyl and hydroxyl groups and diamino alcohol groups. The sodium adducts of these oligomers were selected as precursor ions. Different end groups do not influence the fragmentation of sodiated poly(ester amide) oligomers and similar series of product ions were observed in the MALDI-TOF/TOF-MS/MS spectra. According to the structures of the most abundant product ions identified, the main cleavages proceed through a beta-hydrogen-transfer rearrangement, leading to the selective scission of the --O--CH2-- bonds. Abundant product ions originating from --CH2--CH2-- (beta-gamma) bond cleavage in the sebacate moiety were also detected. Their formation should be promoted by the presence of an alpha,beta-unsaturated ester or amide end group. MALDI-TOF/TOF-MS/MS provided structural information concerning the ester/amide sequences in the polymer chains. In the MALDI-TOF/TOF-MS/MS spectra acquired, using argon as the collision gas, of cyclic species and linear oligomers terminated by diamino alcohol groups, product ions in the low-mass range, undetected in the mass spectra acquired using air as the collision gas, proved to be diagnostic and made it possible to establish the presence of random sequences of ester and amide bonds in the poly(ester amide) sample. Furthermore, MALDI-TOF/TOF-MS/MS provided useful information to clarify the structures of precursor ions derived from side reactions during the synthesis. PMID:18278818

  5. Mild Metal-Free Hydrosilylation of Secondary Amides to Amines.

    PubMed

    Huang, Pei-Qiang; Lang, Qi-Wei; Wang, Yan-Rong

    2016-05-20

    The combination of amide activation by Tf2O with B(C6F5)3-catalyzed hydrosilylation with TMDS constitutes a method for the one-pot reduction of secondary amides to amines under mild conditions. The method displays a broad applicability for the reduction of many types of substrates, and shows good compatibility and excellent chemoselectivity for many sensitive functional groups. Reductions of a multifunctionalized α,β-unsaturated amide obtained from another synthetic methodology, and a C-H functionalization product produced the corresponding amines in good to excellent yield. Chemoselective reduction of enantiomeric pure (ee >99%) tetrahydro-5-oxo-2-furaneamides yielded 5-(aminomethyl)dihydrofuran-2(3H)-ones in a racemization-free manner. The latter were converted in one pot to N-protected 5-hydroxypiperidin-2-ones, which are building blocks for the synthesis of many natural products. Further elaboration of an intermediate led to a concise four-step synthesis of (-)-epi-pseudoconhydrine. PMID:27100232

  6. MATE Transporter-Dependent Export of Hydroxycinnamic Acid Amides.

    PubMed

    Dobritzsch, Melanie; Lübken, Tilo; Eschen-Lippold, Lennart; Gorzolka, Karin; Blum, Elke; Matern, Andreas; Marillonnet, Sylvestre; Böttcher, Christoph; Dräger, Birgit; Rosahl, Sabine

    2016-02-01

    The ability of Arabidopsis thaliana to successfully prevent colonization by Phytophthora infestans, the causal agent of late blight disease of potato (Solanum tuberosum), depends on multilayered defense responses. To address the role of surface-localized secondary metabolites for entry control, droplets of a P. infestans zoospore suspension, incubated on Arabidopsis leaves, were subjected to untargeted metabolite profiling. The hydroxycinnamic acid amide coumaroylagmatine was among the metabolites secreted into the inoculum. In vitro assays revealed an inhibitory activity of coumaroylagmatine on P. infestans spore germination. Mutant analyses suggested a requirement of the p-coumaroyl-CoA:agmatine N4-p-coumaroyl transferase ACT for the biosynthesis and of the MATE transporter DTX18 for the extracellular accumulation of coumaroylagmatine. The host plant potato is not able to efficiently secrete coumaroylagmatine. This inability is overcome in transgenic potato plants expressing the two Arabidopsis genes ACT and DTX18. These plants secrete agmatine and putrescine conjugates to high levels, indicating that DTX18 is a hydroxycinnamic acid amide transporter with a distinct specificity. The export of hydroxycinnamic acid amides correlates with a decreased ability of P. infestans spores to germinate, suggesting a contribution of secreted antimicrobial compounds to pathogen defense at the leaf surface. PMID:26744218

  7. First synthesis and anticancer activity of novel naphthoquinone amides.

    PubMed

    Pradidphol, Narathip; Kongkathip, Ngampong; Sittikul, Pichamon; Boonyalai, Nonlawat; Kongkathip, Boonsong

    2012-03-01

    Sixteen novel naphthoquinone aromatic amides were synthesized by a new route starting from 1-hydroxy-2-naphthoic acid in nine or ten steps with good to excellent yield. Amide formation reaction was carried out by using 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM) as an efficient condensing agent leading to carboxamides in high yield. The key step for converting naphthol to 3-hydroxynaphthoquinone was the Fremy's salt oxidation followed by hydroxylation with tert-butyl hydroperoxide and triton B. Anticancer activity of these new naphthoquinone amides were evaluated and benzamide 22 showed potent inhibition against NCI-H187 cell lines while naphthamides 23 and 43 were the most potent inhibition against KB cells. The decatenation assay revealed that compounds 24 and 43 at 20 μM can inhibit hTopoIIα activity while three other compounds, namely compounds 22, 23, and 45, exhibited hTopoIIα inhibitory activity at final concentration of 50 μM. Docking experiment revealed the same trend as the cytotoxicity and decatenation assay. Therefore, naphthamides 24 and 43 can be promising target molecules for anticancer drug development. PMID:22280818

  8. Rotating Bioreactor

    NASA Technical Reports Server (NTRS)

    1988-01-01

    The NASA Bioreactor provides a low turbulence culture environment which promotes the formation of large, three-dimensional cell clusters. Due to their high level of cellular organization and specialization, samples constructed in the bioreactor more closely resemble the original tumor or tissue found in the body. NASA-sponsored bioreactor research has been instrumental in helping scientists to better understand normal and cancerous tissue development. In cooperation with the medical community, the bioreactor design is being used to prepare better models of human colon, prostate, breast and ovarian tumors. Cartilage, bone marrow, heart muscle, skeletal muscle, pancreatic islet cells, liver and kidney are just a few of the normal tissues currently being cultured in rotating bioreactors by investigators.

  9. Aromaticity effects on the profiles of the lowest triplet-state potential-energy surfaces for rotation about the C=C bonds of olefins with five-membered ring substituents: an example of the impact of Baird's rule.

    PubMed

    Zhu, Jun; Fogarty, Heather A; Möllerstedt, Helene; Brink, Maria; Ottosson, Henrik

    2013-08-01

    A density functional theory study on olefins with five-membered monocyclic 4n and 4n+2 π-electron substituents (C4H3X; X=CH(+), SiH(+), BH, AlH, CH2, SiH2, O, S, NH, and CH(-)) was performed to assess the connection between the degree of substituent (anti)aromaticity and the profile of the lowest triplet-state (T1) potential-energy surface (PES) for twisting about olefinic C=C bonds. It exploited both Hückel's rule on aromaticity in the closed-shell singlet ground state (S0) and Baird's rule on aromaticity in the lowest ππ* excited triplet state. The compounds CH2=CH(C4H3X) were categorized as set A and set B olefins depending on which carbon atom (C2 or C3) of the C4H3X ring is bonded to the olefin. The degree of substituent (anti)aromaticity goes from strongly S0 -antiaromatic/T1 -aromatic (C5H4 (+)) to strongly S0 -aromatic/T1- antiaromatic (C5H4(-)). Our hypothesis is that the shapes of the T1 PESs, as given by the energy differences between planar and perpendicularly twisted olefin structures in T1 [ΔE(T1)], smoothly follow the changes in substituent (anti)aromaticity. Indeed, correlations between ΔE(T1) and the (anti)aromaticity changes of the C4 H3 X groups, as measured by the zz-tensor component of the nucleus-independent chemical shift ΔNICS(T1;1)zz , are found both for sets A and B separately (linear fits; r(2) =0.949 and 0.851, respectively) and for the two sets combined (linear fit; r(2) =0.851). For sets A and B combined, strong correlations are also found between ΔE(T1) and the degree of S0 (anti)aromaticity as determined by NICS(S0,1)zz (sigmoidal fit; r(2) =0.963), as well as between the T1 energies of the planar olefins and NICS(S0,1)zz (linear fit; r(2) =0.939). Thus, careful tuning of substituent (anti)aromaticity allows for design of small olefins with T1 PESs suitable for adiabatic Z/E photoisomerization. PMID:23794153

  10. Synergistic effects of three Piper amides on generalist and specialist herbivores.

    PubMed

    Dyer, L A; Dodson, C D; Stireman, J O; Tobler, M A; Smilanich, A M; Fincher, R M; Letourneau, D K

    2003-11-01

    The tropical rainforest shrub Piper cenocladum, which is normally defended against herbivores by a mutualistic ant, contains three amides that have various defensive functions. While the ants are effective primarily against specialist herbivores, we hypothesized that these secondary compounds would be effective against a wider range of insects, thus providing a broad array of defenses against herbivores. We also tested whether a mixture of amides would be more effective against herbivores than individual amides. Diets spiked with amides were offered to five herbivores: a naïve generalist caterpillar (Spodoptera frugiperda), two caterpillar species that are monophagous on P. cenocladum (Eois spp.), leaf-cutting ants (Atta cephalotes), and an omnivorous ant (Paraponera clavata). Amides had negative effects on all insects, whether they were naïve, experienced, generalized, or specialized feeders. For Spodoptera, amide mixtures caused decreased pupal weights and survivorship and increased development times. Eois pupal weights, larval mass gain, and development times were affected by additions of individual amides, but increased parasitism and lower survivorship were caused only by the amide mixture. Amide mixtures also deterred feeding by the two ant species, and crude plant extracts were strongly deterrent to P. clavata. The mixture of all three amides had the most dramatic deterrent and toxic effects across experiments, with the effects usually surpassing expected additive responses, indicating that these compounds can act synergistically against a wide array of herbivores. PMID:14682530

  11. Halochromism, ionochromism, solvatochromism and density functional study of a synthesized copper(II) complex containing hemilabile amide derivative ligand

    NASA Astrophysics Data System (ADS)

    Golchoubian, Hamid; Moayyedi, Golasa; Reisi, Neda

    2015-03-01

    This study investigates chromotropism of newly synthesized 3,3‧-(ethane-1,2-diylbis(benzylazanediyl))dipropanamide copper(II) perchlorate complex. The compound was structurally characterized by physico-chemical and spectroscopic methods. X-ray crystallography of the complex showed that the copper atom achieved a distorted square pyramidal environment through coordination of two amine N atoms and two O atoms of the amide moieties. The pH effect on the visible absorption spectrum of the complex was studied which functions as pH-induced "off-on-off" switches through protonation and deprotonation of amide moieties along with the Cusbnd O to Cusbnd N bond rearrangement at room temperature. The complex was also observed to show solvatochromism and ionochromism. The distinct solution color changes mainly associated with hemilability of the amide groups. The solvatochromism of the complex was investigated with different solvent parameter models using stepwise multiple linear regression method. The results suggested that the basicity power of the solvent has a dominant contribution to the shift of the d-d absorption band of the complex. Density functional theory, DFT calculations were performed in order to study the electronic structure of the complex, the relative stabilities of the Cusbnd N/Cusbnd O isomers, and to understand the nature of the halochromism processes taking place. DFT computational results buttressed the experimental observations indicating that in the natural pH (5.8) the Cusbnd O isomer is more stable than its linkage isomer and conversely in alkaline aqueous solution.

  12. Chemical Bonds II

    ERIC Educational Resources Information Center

    Sanderson, R. T.

    1972-01-01

    The continuation of a paper discussing chemical bonding from a bond energy viewpoint, with a number of examples of single and multiple bonds. (Part I appeared in volume 1 number 3, pages 16-23, February 1972.) (AL)

  13. What Determines Bond Costs. Municipal Bonds Series.

    ERIC Educational Resources Information Center

    Young, Douglas; And Others

    Public officials in small towns who participate infrequently in the bond market need information about bond financing. This publication, one in a series of booklets published by the Western Rural Development Center using research gathered between 1967-77, discusses factors influencing the marketability and cost of bond financing for towns and…

  14. Electronic transitions in liquid amides studied by using attenuated total reflection far-ultraviolet spectroscopy and quantum chemical calculations.

    PubMed

    Morisawa, Yusuke; Yasunaga, Manaka; Fukuda, Ryoichi; Ehara, Masahiro; Ozaki, Yukihiro

    2013-10-21

    Attenuated total reflection far-ultraviolet (ATR-FUV) spectra in the 140-260 nm region were measured for several types of liquid amides (formamide, FA; N-methylformamide, NMF; N-methylacetamide, NMA; N,N-dimethylformamide, NdMF; and N,N-dimethylacetamide, NdMA) to investigate their electronic transitions in the FUV region. The spectra were compared with the corresponding gas-phase spectra to examine the shift in the major absorption band in the 180-200 nm region going from the gas phase to the liquid phase, and it was found that the peak shift was dependent on the particular amide. FA and NMF, which exhibit intermolecular C=O[ellipsis...H-N hydrogen bonding, show a large shift of ~0.60 eV to lower energy; however, NMA, which also exhibits hydrogen bonding, shows only a small shift. In NdMF and NdMA, C=O groups seem to be coupled, which results in a small peak shift. Two types of quantum chemical calculations, time-dependent density functional theory (TD-DFT) and symmetry-adapted-cluster configuration interaction (SAC-CI) method, were performed to elucidate the origin of the shifts and the band assignments. The shift estimated by the monomer and dimer models with TD-DFT reproduced well the observed shift from the gas phase to the liquid phase. This suggests that the intermolecular hydrogen-bonding interaction significantly affects the magnitude of the shift. The many-body effects were also considered using the larger cluster models (trimer to pentamer). The energy shift calculated using SAC-CI with the monomer and the state-specific polarizable continuum model was also accurate, indicating that the nonlinear polarization effect appears to be important. As for the band assignments, it was found that though the major band can be mainly attributed to the π-π* transition, several types of Rydberg transitions also exist in its vicinity and mixing of orbitals with the same symmetry occurs. The number and type of Rydberg transitions in the spectra depend upon the type of

  15. Electronic transitions in liquid amides studied by using attenuated total reflection far-ultraviolet spectroscopy and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Morisawa, Yusuke; Yasunaga, Manaka; Fukuda, Ryoichi; Ehara, Masahiro; Ozaki, Yukihiro

    2013-10-01

    Attenuated total reflection far-ultraviolet (ATR-FUV) spectra in the 140-260 nm region were measured for several types of liquid amides (formamide, FA; N-methylformamide, NMF; N-methylacetamide, NMA; N,N-dimethylformamide, NdMF; and N,N-dimethylacetamide, NdMA) to investigate their electronic transitions in the FUV region. The spectra were compared with the corresponding gas-phase spectra to examine the shift in the major absorption band in the 180-200 nm region going from the gas phase to the liquid phase, and it was found that the peak shift was dependent on the particular amide. FA and NMF, which exhibit intermolecular C=O…H-N hydrogen bonding, show a large shift of ˜0.60 eV to lower energy; however, NMA, which also exhibits hydrogen bonding, shows only a small shift. In NdMF and NdMA, C=O groups seem to be coupled, which results in a small peak shift. Two types of quantum chemical calculations, time-dependent density functional theory (TD-DFT) and symmetry-adapted-cluster configuration interaction (SAC-CI) method, were performed to elucidate the origin of the shifts and the band assignments. The shift estimated by the monomer and dimer models with TD-DFT reproduced well the observed shift from the gas phase to the liquid phase. This suggests that the intermolecular hydrogen-bonding interaction significantly affects the magnitude of the shift. The many-body effects were also considered using the larger cluster models (trimer to pentamer). The energy shift calculated using SAC-CI with the monomer and the state-specific polarizable continuum model was also accurate, indicating that the nonlinear polarization effect appears to be important. As for the band assignments, it was found that though the major band can be mainly attributed to the π-π* transition, several types of Rydberg transitions also exist in its vicinity and mixing of orbitals with the same symmetry occurs. The number and type of Rydberg transitions in the spectra depend upon the type of amide

  16. Clocking Surface Reaction by In-Plane Product Rotation.

    PubMed

    Anggara, Kelvin; Huang, Kai; Leung, Lydie; Chatterjee, Avisek; Cheng, Fang; Polanyi, John C

    2016-06-15

    Electron-induced reaction of physisorbed meta-diiodobenzene (mDIB) on Cu(110) at 4.6 K was studied by Scanning Tunneling Microscopy and molecular dynamics theory. Single-electron dissociation of the first C-I bond led to in-plane rotation of an iodophenyl (IPh) intermediate, whose motion could be treated as a "clock" of the reaction dynamics. Alternative reaction mechanisms, successive and concerted, were observed giving different product distributions. In the successive mechanism, two electrons successively broke single C-I bonds; the first C-I bond breaking yielded IPh that rotated directionally by three different angles, with the second C-I bond breaking giving chemisorbed I atoms (#2) at three preferred locations corresponding to the C-I bond alignments in the prior rotated IPh configurations. In the concerted mechanism a single electron broke two C-I bonds, giving two chemisorbed I atoms; significantly these were found at angles corresponding to the C-I bond direction for unrotated mDIB. Molecular dynamics accounted for the difference in reaction outcomes between the successive and the concerted mechanisms in terms of the time required for the IPh to rotate in-plane; in successive reaction the time delay between first and second C-I bond-breaking events allowed the IPh to rotate, whereas in concerted reaction the computed delay between excitation and reaction (∼1 ps) was too short for molecular rotation before the second C-I bond broke. The dependence of the extent of motion at a surface on the delay between first and second bond breaking suggested a novel means to "clock" sub-picosecond dynamics by imaging the products arising from varying time delays between impacting pairs of electrons. PMID:27191189

  17. The molecular structure, conformation, potential to internal rotation and force field of 2,2,2-trifluoroacetamide as studied by gas electron diffraction and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Gundersen, Snefrid; Samdal, Svein; Seip, Ragnhild; Shorokhov, Dmitry J.; Strand, Tor G.

    1998-04-01

    2,2,2-Trifluoroacetamide (TFA) has been studied by electron diffraction (ED), ab initio Hartree-Fock (HF), density functional theory (DFT), and MP2 calculations. The calculations give one conformation with one of the CF bonds anti to the CO bond and a planar NH 2 group, except for MP2/6-311 + + G∗∗, which predicts a slightly pyramidale NH 2 group. A molecular force field has been determined, and the fundamental frequencies have tentatively been assigned. The refined structural parameters were determined using constrained ED, i.e. ab initio results are included as constraints in the analysis. The structural parameters are: rg(N-H 4) = 1.040(4), rg(CO) = 1.211(2), rg(C-N) = 1.362(4), rg = 1.562(1), rg(C-F 7) = 1.347(1), ∠ αOCN = 126.5(2), ∠ αCCN = 116.3(4), ∠ αCCF 7 = 111.9(1), and ∠ αCNH 4 = 118.5(11). Bond distances are in Å and bond angles in degrees. Uncertainties are one standard deviation from least squares refinement using a diagonal weight matrix and inclusion of the uncertainty in the electron wavelength. The structural parameters have been compared with related amides. The Fourier coefficients V3 and V6 in the potential to internal rotation of the CF 3 group, V(α) = 1/2∗V 3∗(1 - cos(3∗α)) + 1/2∗V 6∗(1 - cos(6∗α)) , are determined to be 2.7(4) and - 0.7(3) kJ/mol, respectively. The syn barrier is experimentally determined to be 2.6(4) kJ/mol, which is in good agreeent with theoretical calculations.

  18. Highly Enantioselective Fluorescent Recognition of Both Unfunctionalized and Functionalized Chiral Amines by a Facile Amide Formation from a Perfluoroalkyl Ketone.

    PubMed

    Wang, Chao; Anbaei, Parastoo; Pu, Lin

    2016-05-17

    The H8 BINOL-based perfluoroalkyl ketone (S)-2 is found to exhibit highly enantioselective fluorescent enhancements toward both unfunctionalized and functionalized chiral amines. It greatly expands the substrate scope of the corresponding BINOL-based sensor. A dramatic solvent effect was observed for the reaction of the amines with compound (S)-2. In DMF, cleavage of the perfluoroalkyl group of compound (S)-2 to form amides was observed but not in other solvents, such as methylene chloride, chloroform, THF, hexane, and perfluorohexane. Thus, the addition of another solvent, such as THF, can effectively quench the reaction of compound (S)-2 with amines in DMF to allow stable fluorescent measurement. This is the first example that the formation of strong amide bonds under very mild conditions is used for the enantioselective recognition of chiral amines. The mechanism of the reaction of compound (S)-2 with chiral amines is investigated by using various analytical methods including mass spectrometry as well as NMR and UV/Vis absorption spectroscopy. PMID:27061205

  19. Transition Metals Catalyzed Element-Cyano Bonds Activations

    PubMed Central

    Wang, Rui; Falck, John R.

    2014-01-01

    Cyano group as a versatile functionalized intermediate has been explored for several decades, as it readily transfers to many useful functionalization groups such as amine, amide, acid, etc., which make it possess high popularization and use value in organic synthesis. Reactions involved with element-cyano bond cleavage can provide not only a new cyano group but also a freshly functionalized skeleton in one-pot, consequently making it of high importance. The highlights reviewed herein include H-CN, Si-CN, C-CN, B-CN, Sn-CN, Ge-CN, S-CN, Halo-CN, N-CN, and O-CN bonds cleavages and will summarize progress in such an important research area. This review article will focus on transition metal catalyzed reactions involving element-cyano bond activation. PMID:25558119

  20. Interfacial characterization of Al-Al thermocompression bonds

    NASA Astrophysics Data System (ADS)

    Malik, N.; Carvalho, P. A.; Poppe, E.; Finstad, T. G.

    2016-05-01

    Interfaces formed by Al-Al thermocompression bonding were studied by the transmission electron microscopy. Si wafer pairs having patterned bonding frames were bonded using Al films deposited on Si or SiO2 as intermediate bonding media. A bond force of 36 or 60 kN at bonding temperatures ranging from 400-550 °C was applied for a duration of 60 min. Differences in the bonded interfaces of 200 μm wide sealing frames were investigated. It was observed that the interface had voids for bonding with 36 kN at 400 °C for Al deposited both on Si and on SiO2. However, the dicing yield was 33% for Al on Si and 98% for Al on SiO2, attesting for the higher quality of the latter bonds. Both a bond force of 60 kN applied at 400 °C and a bond force of 36 kN applied at 550 °C resulted in completely bonded frames with dicing yields of, respectively, 100% and 96%. A high density of long dislocations in the Al grains was observed for the 60 kN case, while the higher temperature resulted in grain boundary rotation away from the original Al-Al interface towards more stable configurations. Possible bonding mechanisms and reasons for the large difference in bonding quality of the Al films deposited on Si or SiO2 are discussed.

  1. Iridium-Catalyzed Enantioselective Hydroalkynylation of Enamides for the Synthesis of Homopropargyl Amides.

    PubMed

    Bai, Xiao-Yan; Wang, Zi-Xuan; Li, Bi-Jie

    2016-07-25

    Reported is an iridium-catalyzed asymmetric hydroalkynylation of enamides with terminal alkynes. The reaction occurs regioselectively at the β-position of an enamide to produce homopropargyl amides. Good to high enantioselectivity was observed with an iridium complex ligated by a chiral bis(phosphine) ligand. This method provides a straightforward route to synthesize chiral homopropargyl amides with a stereocenter β to the amide. PMID:27111577

  2. Synthesis of Imidates: TFA-Mediated Regioselective Amide Alkylation Using Meerwein's Reagent.

    PubMed

    Popov, Kirill; Somfai, Peter

    2016-04-15

    Regioselective O-alkylation of an amide to form the corresponding imidate is a common synthetic problem, often resulting in varying amounts of N-alkylation. Screening existing methods for converting amides to imidates gave inconsistent or irreproducible results, sometimes affording N-alkylamide as the major product. A simple and reliable protocol for amide O-alkylation with complete regioselectivity has been designed, and its scope and efficiency demonstrated on a number of substrates. PMID:27019206

  3. Does Electron Capture Dissociation Cleave Protein Disulfide Bonds?

    PubMed Central

    Ganisl, Barbara; Breuker, Kathrin

    2012-01-01

    Peptide and protein characterization by mass spectrometry (MS) relies on their dissociation in the gas phase into specific fragments whose mass values can be aligned as ‘mass ladders’ to provide sequence information and to localize possible posttranslational modifications. The most common dissociation method involves slow heating of even-electron (M+n H)n+ ions from electrospray ionization by energetic collisions with inert gas, and cleavage of amide backbone bonds. More recently, dissociation methods based on electron capture or transfer were found to provide far more extensive sequence coverage through unselective cleavage of backbone N–Cα bonds. As another important feature of electron capture dissociation (ECD) and electron transfer dissociation (ETD), their unique unimolecular radical ion chemistry generally preserves labile posttranslational modifications such as glycosylation and phosphorylation. Moreover, it was postulated that disulfide bond cleavage is preferred over backbone cleavage, and that capture of a single electron can break both a backbone and a disulfide bond, or even two disulfide bonds between two peptide chains. However, the proposal of preferential disulfide bond cleavage in ECD or ETD has recently been debated. The experimental data presented here reveal that the mechanism of protein disulfide bond cleavage is much more intricate than previously anticipated. PMID:24363980

  4. High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

    PubMed Central

    Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole

  5. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

    PubMed

    Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from

  6. Copper-Catalyzed Reductive N-Alkylation of Amides with N-Tosylhydrazones Derived from Ketones.

    PubMed

    Xu, Peng; Qi, Fu-Ling; Han, Fu-She; Wang, Yan-Hua

    2016-07-20

    A CuI-catalyzed reductive coupling of ketone-derived N-tosylhydrazones with amides is presented. Under the optimized conditions, an array of N-tosylhydrazones derived from aryl-alkyl and diaryl ketones could couple effectively with a wide variety of (hetero)aryl as well as aliphatic amides to afford the N-alkylated amides in high yields. The method represents the very few examples for reliably accessing secondary and tertiary amides through a reductive N-alkylation protocol. PMID:27346856

  7. Formation of Amides from Imines via Cyanide-Mediated Metal-Free Aerobic Oxidation.

    PubMed

    Seo, Hong-Ahn; Cho, Yeon-Ho; Lee, Ye-Sol; Cheon, Cheol-Hong

    2015-12-18

    A new protocol for the direct formation of amides from imines derived from aromatic aldehydes via metal-free aerobic oxidation in the presence of cyanide is described. This protocol was applicable to various aldimines, and the desired amides were obtained in moderate to good yields. Mechanistic studies suggested that this aerobic oxidative amidation might proceed via the addition of cyanide to imines followed by proton transfer from carbon to nitrogen in the original imines, leading to carbanions of α-amino nitriles, which undergo subsequent oxidation with molecular oxygen in air to provide the desired amide compounds. PMID:26580330

  8. BODIPY catalyzed amide synthesis promoted by BHT and air under visible light.

    PubMed

    Wang, Xiao-Fei; Yu, Shu-Sheng; Wang, Chao; Xue, Dong; Xiao, Jianliang

    2016-08-01

    A novel and efficient protocol for the synthesis of amides is reported which employs a BODIPY catalyzed oxidative amidation reaction between aromatic aldehydes and amines under visible light. Compared with the known Ru or Ir molecular catalysts and other organic dyes, the BODIPY catalyst showed higher reactivity toward this reaction. Mechanistic studies reveal that dioxygen could be activated through an ET and a SET pathway, forming active peroxides in situ, which are vital for the key step of the reaction, i.e. the oxidation of hemiaminal to amide. The broad substrate scope and mild reaction conditions make this reaction practically useful and environmentally friendly for the synthesis of amide compounds. PMID:27363514

  9. Rotator Cuff Tears

    MedlinePlus

    ... doctors because of a rotator cuff problem. A torn rotator cuff will weaken your shoulder. This means ... or more of the rotator cuff tendons is torn, the tendon no longer fully attaches to the ...

  10. Rotator Cuff Injuries

    MedlinePlus

    ... others can be very painful. Treatment for a torn rotator cuff depends on age, health, how severe ... is, and how long you've had the torn rotator cuff. Treatment for torn rotator cuff includes: ...

  11. Rotator cuff problems

    MedlinePlus

    ... days, such as in painting and carpentry Poor posture over many years Aging Rotator cuff tears TEARS ... also help prevent rotator cuff problems. Practice good posture to keep your rotator cuff tendons and muscles ...

  12. Design and Synthesis of Peptide YY Analogues with C-terminal Backbone Amide-to-Ester Modifications

    PubMed Central

    2013-01-01

    Peptide YY (PYY) is a gut hormone that activates the G protein-coupled neuropeptide Y (NPY) receptors, and because of its appetite reducing actions, it is evaluated as an antiobesity drug candidate. The C-terminal tail of PYY is crucial for activation of the NPY receptors. Here, we describe the design and preparation of a series of PYY(3–36) depsipeptide analogues, in which backbone amide-to-ester modifications were systematically introduced in the C-terminal. Functional NPY receptor assays and circular dichroism revealed that the ψ(CONH) bonds at positions 30–31 and 33–34 are particularly important for receptor interaction and that the latter is implicated in Y2 receptor selectivity. PMID:24900634

  13. Conjugation of insulin onto the sidewalls of single-walled carbon nanotubes through functionalization and diimide-activated amidation

    PubMed Central

    Ng, Chee Meng; Loh, Hwei-San; Muthoosamy, Kasturi; Sridewi, Nanthini; Manickam, Sivakumar

    2016-01-01

    Purpose The high aspect ratio of carbon nanotubes (CNTs) allows the attachment of compounds that enhance the functionality of the drug vehicle. Considering this, use of CNTs as a multifunctional insulin carrier may be an interesting prospect to explore. Materials and methods The carboxylic acid groups were functionalized on the sidewalls of single-walled CNTs (SWCNTs) followed by diimidation to form amide bonds with the amine groups of the insulin. Results Scanning transmission electron microscopy and transmission electron microscopy establish clear conjugation of insulin onto the surface of nanotube sidewalls. The incorporation of insulin further increased the solubility of SWCNTs in biological solution for the tested period of 5 months. Bicinchoninic acid assay confirms that 0.42 mg of insulin could be attached to every 1 mg of carboxylated SWCNTs. Conclusion With the successful conjugation of insulin to SWCNTs, it opens up the potential use of SWCNTs as an insulin carrier which in need of further biological studies. PMID:27143882

  14. Theoretical analysis of x-ray absorption spectra of Ti compounds used as catalysts in lithium amide/imide reactions

    NASA Astrophysics Data System (ADS)

    Tsumuraya, Takao; Shishidou, Tatsuya; Oguchi, Tamio

    2008-06-01

    We present a theoretical analysis and interpretation of the x-ray absorption near-edge structure of x-ray absorption spectroscopy (XAS) at the titanium K -edge of several Ti compounds for understanding catalysis mechanism in lithium amide LiNH2 and imide Li2NH systems for hydrogen storage. Our theoretical approach is based on first-principles calculations using all-electron full-potential linear augmented plane-wave method. Chemical bonding and local geometry of catalytically-active Ti states in the hydrogen desorption reaction LiNH2+LiH→Li2NH+H2 are investigated. It is found that XAS spectra of some compounds consisting of elements Li, N, H, and Ti are quite similar to measured ones of catalytically-active Ti compounds. We conclude that Ti ions may occupy the Li sites in LiNH2 during the reaction.

  15. Efficient Synthesis of the Disialylated Tetrasaccharide Motif in N-Glycans through an Amide-Protection Strategy.

    PubMed

    Zhou, Jiazhou; Manabe, Yoshiyuki; Tanaka, Katsunori; Fukase, Koichi

    2016-05-01

    A disialylated tetrasaccharide, Neu5Ac(α2,3)Gal(β1,3)[Neu5Ac(α2,6)]GlcNAc (1), which is found at the termini of some N-glycans, has been synthesized. Compound 1 was obtained through an α-sialylation reaction between a sialic acid donor and a trisaccharide that was synthesized from the glycosylation of a sialylated disaccharide with a glucosaminyl donor. This synthetic route enabled the synthesis of the as-described disialylated structure. A more-convergent route based on the glycosylation of two sialylated disaccharides was also established to scale up the synthesis. Protection of the amide groups in the sialic acid residues significantly increased the yield of the glycosylation reaction between the two sialylated disaccharides, thus suggesting that the presence of hydrogen bonds on the sialic acid residues diminished their reactivity. PMID:26929048

  16. In vitro apoptotic effect of cassaine-type diterpene amides from Erythrophleum fordii on PC-3 prostate cancer cells.

    PubMed

    Hung, Tran Manh; Cuong, To Dao; Kim, Jeong Ah; Lee, Jeong Hyung; Woo, Mi Hee; Min, Byung Sun

    2014-11-01

    Cytotoxic activity-guided fractionation of Erythrophleum fordii led to the isolation of two new cassaine diterpenoid-diterpenoid amide dimers, erythrophlesins H-I (1, 2). Spectral data indicated that they consist of asymmetrical dimeric structure via an ester bond between two cassaine diterpenoids. MTT assay confirmed that compound 1, erythrophlesin H, had the strongest cytotoxic effect toward the human prostate cancer cell line, PC-3. The molecular mechanism by which this compound induced apoptosis cell in prostate cancer remains unknown. Erythrophlesin H induced apoptosis in a dose-dependent manner. Acridine orange and annexin V-FITC/PI double staining confirmed that erythrophlesin H effectively induces apoptosis in PC-3 cells. PMID:25278231

  17. An efficient phase-selective gelator for aromatic solvents recovery based on a cyanostilbene amide derivative.

    PubMed

    Zhang, Yuping; Ma, Yao; Deng, Mengyu; Shang, Hongxing; Liang, Chunshuang; Jiang, Shimei

    2015-07-01

    Two novel low molecular weight organogelators (LMOGs) 1 and 2 composed of a cholesteryl group, an amide group and various terminal cyanostilbene moieties were synthesized. They could form stable gels in p-xylene. In particular, 2 with more extended π-conjugation length showed remarkable gelation ability in many aromatic solvents, chloroform and chloroform-containing mixed solvents at a relatively low concentration. FT-IR and XRD spectra indicated that the difference between 1 and 2 in the gelation properties may result from the deviation of the intermolecular hydrogen bonding and π–π stacking as driving forces for the formation of the gels. Significantly, 2 can function as an efficient room-temperature phase-selective gelator (PSG) for potential application in the separation and recovery of various aromatic solvents from its mixture with water. Meanwhile, the gelator can be easily recovered and reused several times. Furthermore, the phase-selective gelation properties of 2 can provide a simple and feasible approach for the removal of the rhodamine B (RhB) dye from water. PMID:26035825

  18. Direct Catalytic Asymmetric Mannich-Type Reaction of α- and β-Fluorinated Amides.

    PubMed

    Brewitz, Lennart; Arteaga, Fernando Arteaga; Yin, Liang; Alagiri, Kaliyamoorthy; Kumagai, Naoya; Shibasaki, Masakatsu

    2015-12-23

    The last two decades have witnessed the emergence of direct enolization protocols providing atom-economical and operationally simple methods to use enolates for stereoselective C-C bond-forming reactions, eliminating the inherent drawback of the preformation of enolates using stoichiometric amounts of reagents. In its infancy, direct enolization relied heavily on the intrinsic acidity of the latent enolates, and the reaction scope was limited to readily enolizable ketones and aldehydes. Recent advances in this field enabled the exploitation of carboxylic acid derivatives for direct enolization, offering expeditious access to synthetically versatile chiral building blocks. Despite the growing demand for enantioenriched fluorine-containing small molecules, α- and β-fluorinated carbonyl compounds have been neglected in direct enolization chemistry because of the competing and dominating defluorination pathway. Herein we present a comprehensive study on direct and highly stereoselective Mannich-type reactions of α- and β-fluorine-functionalized 7-azaindoline amides that rely on a soft Lewis acid/hard Brønsted base cooperative catalytic system to guarantee an efficient enolization while suppressing undesired defluorination. This protocol contributes to provide a series of fluorinated analogs of enantioenriched β-amino acids for medicinal chemistry. PMID:26652911

  19. Amide I band and photoinduced disassembly of a peptide hydrogel

    NASA Astrophysics Data System (ADS)

    Measey, Thomas J.; Markiewicz, Beatrice N.; Gai, Feng

    2013-08-01

    Peptide hydrogels are promising candidates for a wide range of medical and biotechnological applications. To further expand the potential utility of peptide hydrogels, herein we demonstrate a simple yet effective strategy to render peptide hydrogels photodegradable, making controlled disassembly of the gel structure of interest feasible. In addition, we find that the high-frequency amide I' component (i.e., the peak at ˜1685 cm-1) of the photodegradable peptide hydrogel studied shows an unusually large enhancement, in comparison to that of other peptide fibrils consisting of antiparallel β-sheets, making it a good model system for further study of the coupling-structure relationship.

  20. Dapdiamides, Tripeptide Antibiotics Formed by Unconventional Amide Ligases†

    PubMed Central

    2009-01-01

    Construction of a genomic DNA library from Pantoea agglomerans strain CU0119 and screening against the plant pathogen Erwinia amylovora yielded a new family of antibiotics, dapdiamides A−E (1−5). The structures were established through 2D-NMR experiments and mass spectrometry, as well as the synthesis of dapdiamide A (1). Transposon mutagenesis of the active cosmid allowed identification of the biosynthetic gene cluster. The dapdiamide family’s promiscuous biosynthetic pathway contains two unconventional amide ligases that are predicted to couple its constituent monomers. PMID:20041689

  1. Antiproliferative activity of synthetic fatty acid amides from renewable resources.

    PubMed

    dos Santos, Daiane S; Piovesan, Luciana A; D'Oca, Caroline R Montes; Hack, Carolina R Lopes; Treptow, Tamara G M; Rodrigues, Marieli O; Vendramini-Costa, Débora B; Ruiz, Ana Lucia T G; de Carvalho, João Ernesto; D'Oca, Marcelo G Montes

    2015-01-15

    In the work, the in vitro antiproliferative activity of a series of synthetic fatty acid amides were investigated in seven cancer cell lines. The study revealed that most of the compounds showed antiproliferative activity against tested tumor cell lines, mainly on human glioma cells (U251) and human ovarian cancer cells with a multiple drug-resistant phenotype (NCI-ADR/RES). In addition, the fatty methyl benzylamide derived from ricinoleic acid (with the fatty acid obtained from castor oil, a renewable resource) showed a high selectivity with potent growth inhibition and cell death for the glioma cell line-the most aggressive CNS cancer. PMID:25510639

  2. Isolation and identification of fatty acid amides from Shengli coal

    SciTech Connect

    Ming-Jie Ding; Zhi-Min Zong; Ying Zong; Xiao-Dong Ou-Yang; Yao-Guo Huang; Lei Zhou; Feng Wang; Jiang-Pei Cao; Xian-Yong Wei

    2008-07-15

    Shengli coal, a Chinese brown coal, was extracted with carbon disulfide and the extract was gradiently eluted with n-hexane and ethyl acetate (EA)/n-hexane mixed solvents with different concentrations of EA in a silica gel-filled column. A series of fatty acid amides, including fourteen alkanamides (C{sub 15}-C{sub 28}) and three alkenamides (C{sub 18} and C{sub 22}), were isolated from the coal by this method and analyzed with a gas chromatography/mass spectrometry. 26 refs., 2 figs., 2 tabs.

  3. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N-H···O=C and C-H···O=C hydrogen-bonded complexes.

    PubMed

    Li, Shu-Shi; Huang, Cui-Ying; Hao, Jiao-Jiao; Wang, Chang-Sheng

    2014-03-01

    In this article, a polarizable dipole-dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen-bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N-H, C=O, and C-H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole-dipole interaction model to a series of hydrogen-bonded complexes containing the N-H···O=C and C-H···O=C hydrogen bonds, such as simple amide-amide dimers, base-base dimers, peptide-base dimers, and β-sheet models. We find that a simple two-term function, only containing the permanent dipole-dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6-31G(d) method, whereas the high-quality counterpoise-corrected (CP-corrected) MP2/aug-cc-pVTZ interaction energies for the hydrogen-bonded complexes can be well-reproduced by a four-term function which involves the permanent dipole-dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole-dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen-bonded complexes are further discussed. PMID:24497309

  4. Using Multiple Bonding Strategies.

    PubMed

    Larson, Thomas D

    2015-01-01

    There are many ways to bond to tooth structure, some micro-mechanical some chemical, some a combination. Different dentin bonding materials have different bonding strengths to differently prepared surfaces, and because of differences in their nature, different areas of tooth structure present peculiar bonding challenges. This paper will review a variety of material types, elucidating their particular bonding strengths and commenting on improved bonding strategies to increase durability, strength, and favorable pulpal response. In this discussion, resin dentin bonding systems, glass ionomers, Gluma, resin cements, and newer combined products will br reviewed. PMID:26485903

  5. Are azobenzenophanes rotation-restricted?

    PubMed

    Ciminelli, Cosimo; Granucci, Giovanni; Persico, Maurizio

    2005-11-01

    We simulated the photoisomerization dynamics of an azobenzenophane with a semiclassical surface hopping approach and a semiempirical reparametrized quantum mechanics/molecular mechanics Hamiltonian. Only one of the two azobenzene chromophores in the molecule is taken into account quantum mechanically: the other one is treated by molecular mechanics. Both n-->pi* and pi-->pi* excitations are considered. Our results show that the photoisomerization reaction mainly involves the rotation around the N=N double bond. The excited state relaxation features are in qualitative agreement with experimental time-resolved fluorescence results. PMID:16375538

  6. Are azobenzenophanes rotation-restricted?

    NASA Astrophysics Data System (ADS)

    Ciminelli, Cosimo; Granucci, Giovanni; Persico, Maurizio

    2005-11-01

    We simulated the photoisomerization dynamics of an azobenzenophane with a semiclassical surface hopping approach and a semiempirical reparametrized quantum mechanics/molecular mechanics Hamiltonian. Only one of the two azobenzene chromophores in the molecule is taken into account quantum mechanically: the other one is treated by molecular mechanics. Both n →π* and π →π* excitations are considered. Our results show that the photoisomerization reaction mainly involves the rotation around the N N double bond. The excited state relaxation features are in qualitative agreement with experimental time-resolved fluorescence results.

  7. Are azobenzenophanes rotation-restricted?

    SciTech Connect

    Ciminelli, Cosimo; Granucci, Giovanni; Persico, Maurizio

    2005-11-01

    We simulated the photoisomerization dynamics of an azobenzenophane with a semiclassical surface hopping approach and a semiempirical reparametrized quantum mechanics/molecular mechanics Hamiltonian. Only one of the two azobenzene chromophores in the molecule is taken into account quantum mechanically: the other one is treated by molecular mechanics. Both n{yields}{pi}* and {pi}{yields}{pi}* excitations are considered. Our results show that the photoisomerization reaction mainly involves the rotation around the N=N double bond. The excited state relaxation features are in qualitative agreement with experimental time-resolved fluorescence results.

  8. Rotation and inversion in nitrosamines

    NASA Astrophysics Data System (ADS)

    Kirste, Karl; Rademacher, Paul

    1981-04-01

    Geometry optimizations of the ground states as well as of the transition states for internal rotation and inversion have been performed by the semiempirical MNDO method for dimethyl nitrosamine (1), perfluordimethyl nitrosamine (2), N-nitroso aziridine (3), and N-nitroso azetidine (4). It was found that the potential barrier to internal rotation about the N-N bond is always of lower energy than that to inversion on the nitroso nitrogen. While the ground states tend to adopt structures which enable mesomerism, the lowest transition state is characterized by a pyramidal sp3-hybridized amino nitrogen. In accordance with experimental results the low barriers to rotation of 2 (7.96 kcal mol -1), 3 (3.38 kcal mol -1) and 4 (9.97 kcal mol -1) in comparison with 1 (12.54 kcal mol -1) indicate that in donor-acceptor molecules the transfer of charge can be limited by electronic and stereochemical effects. In particular, the equivalence of the α-methylene hydrogens which was observed in the NMR-spectrum of 3 is due to unhindered rotation and ring inveirsion.

  9. Intramolecular Hydrogen Bonding in Benzoxazines: When Structural Design Becomes Functional.

    PubMed

    Froimowicz, Pablo; Zhang, Kan; Ishida, Hatsuo

    2016-02-18

    The future evolution of benzoxazines and polybenzoxazines as advanced molecular, structural, functional, engineering, and newly commercial materials depends to a great extent on a deeper and more fundamental understanding at the molecular level. In this contribution, the field of benzoxazines is briefly introduced along with a more detailed review of ortho-amide-functional benzoxazines, which are the main subjects of this article. Provided in this article are the detailed and solid scientific evidences of intramolecular five-membered-ring hydrogen bonding, which is supposed to be responsible for the unique and characteristic features exhibited by this ever-growing family of ortho-functionalized benzoxazines. One-dimensional (1D) (1)H NMR spectroscopy was used to study various concentrations of benzoxazines in various solvents with different hydrogen-bonding capability and at various temperatures to investigate in detail the nature of hydrogen bonding in both ortho-amide-functionalized benzoxazine and its para counterpart. These materials were further investigated by two-dimensional (2D) (1)H-(1)H nuclear Overhauser effect spectroscopy (NOESY) to verify and support the conclusions derived during the 1D (1)H NMR experiments. Only highly purified single-crystal benzoxazine samples have been used for this study to avoid additional interactions caused by any impurities. PMID:26797690

  10. A 2:1 co-crystal of p-nitro­benzoic acid and N,N′-bis­(pyridin-3-ylmeth­yl)ethanedi­amide: crystal structure and Hirshfeld surface analysis

    PubMed Central

    Syed, Sabrina; Halim, Siti Nadiah Abdul; Jotani, Mukesh M.; Tiekink, Edward R. T.

    2016-01-01

    The title 2:1 co-crystal, 2C7H5NO4·C14H14N4O2, in which the complete di­amide mol­ecule is generated by crystallographic inversion symmetry, features a three-mol­ecule aggregate sustained by hydroxyl-O—H⋯N(pyrid­yl) hydrogen bonds. The p-nitro­benzoic acid mol­ecule is non-planar, exhibiting twists of both the carb­oxy­lic acid and nitro groups, which form dihedral angles of 10.16 (9) and 4.24 (4)°, respectively, with the benzene ring. The di­amide mol­ecule has a conformation approximating to a Z shape, with the pyridyl rings lying to either side of the central, almost planar di­amide residue (r.m.s. deviation of the eight atoms being 0.025 Å), and forming dihedral angles of 77.22 (6)° with it. In the crystal, three-mol­ecule aggregates are linked into a linear supra­molecular ladder sustained by amide-N—H⋯O(nitro) hydrogen bonds and orientated along [10-4]. The ladders are connected into a double layer via pyridyl- and benzene-C—H⋯O(amide) inter­actions, which, in turn, are connected into a three-dimensional architecture via π–π stacking inter­actions between pyridyl and benzene rings [inter-centroid distance = 3.6947 (8) Å]. An evaluation of the Hirshfeld surfaces confirm the importance of inter­molecular inter­actions involving oxygen atoms as well as the π–π inter­actions. PMID:26870591

  11. A 2:1 co-crystal of p-nitro-benzoic acid and N,N'-bis-(pyridin-3-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

    PubMed

    Syed, Sabrina; Halim, Siti Nadiah Abdul; Jotani, Mukesh M; Tiekink, Edward R T

    2016-01-01

    The title 2:1 co-crystal, 2C7H5NO4·C14H14N4O2, in which the complete di-amide mol-ecule is generated by crystallographic inversion symmetry, features a three-mol-ecule aggregate sustained by hydroxyl-O-H⋯N(pyrid-yl) hydrogen bonds. The p-nitro-benzoic acid mol-ecule is non-planar, exhibiting twists of both the carb-oxy-lic acid and nitro groups, which form dihedral angles of 10.16 (9) and 4.24 (4)°, respectively, with the benzene ring. The di-amide mol-ecule has a conformation approximating to a Z shape, with the pyridyl rings lying to either side of the central, almost planar di-amide residue (r.m.s. deviation of the eight atoms being 0.025 Å), and forming dihedral angles of 77.22 (6)° with it. In the crystal, three-mol-ecule aggregates are linked into a linear supra-molecular ladder sustained by amide-N-H⋯O(nitro) hydrogen bonds and orientated along [10-4]. The ladders are connected into a double layer via pyridyl- and benzene-C-H⋯O(amide) inter-actions, which, in turn, are connected into a three-dimensional architecture via π-π stacking inter-actions between pyridyl and benzene rings [inter-centroid distance = 3.6947 (8) Å]. An evaluation of the Hirshfeld surfaces confirm the importance of inter-molecular inter-actions involving oxygen atoms as well as the π-π inter-actions. PMID:26870591

  12. [Activated Sludge Bacteria Transforming Cyanopyridines and Amides of Pyridinecarboxylic Acids].

    PubMed

    Demakov, V A; Vasil'ev, D M; Maksimova, Yu G; Pavlova, Yu A; Ovechkina, G V; Maksimov, A Yu

    2015-01-01

    Species diversity of bacteria from the activated sludge of Perm biological waste treatment facilities capable of transformation of cyanopyridines and amides of pyridinecarboxylic acids was investigated. Enrichment cultures in mineral media with 3-cyanopyridine as the sole carbon and nitrogen source were used to obtain 32 clones of gram-negative heterotrophic bacteria exhibiting moderate growth on solid and liquid media with 3- and 4-cyanopyridine. Sequencing of the 16S rRNA gene fragments revealed that the clones with homology of at least 99% belonged to the genera Acinetobacte, Alcaligenes, Delftia, Ochrobactrum, Pseudomonas, Stenotrophomonas, and Xanthobacter. PCR analysis showed that 13 out of 32 isolates contained the sequences (-1070 bp) homologous to the nitrilase genes reported previously in Alcaligenes faecalis JM3 (GenBank, D13419.1). Nine clones were capable of nitrile and amide transformation in minimal salt medium. Acinetobacter sp. 11 h and Alcaligenes sp. osv transformed 3-cyanopyridine to nicotinamide, while most of the clones possessed amidase activity (0.5 to 46.3 mmol/(g h) for acetamide and 0.1 to 5.6 mmol/(g h) for nicotinamide). Nicotinamide utilization by strain A. faecalis 2 was shown to result in excretion of a secondary metabolite, which was identified as dodecyl acrylate at 91% probability. PMID:26263697

  13. Complexation of di-amides of dipicolinic acid with neodymium

    SciTech Connect

    Lapka, J.L.; Paulenova, A.

    2013-07-01

    Di-amides have undergone significant studies as possible ligands for use in the partitioning of trivalent minor actinides and lanthanides. The binding affinities of three isomeric ligands with neodymium in acetonitrile solution have been investigated. The stability constants of the metal-ligand complexes formed between different isomers of N,N'-diethyl-N,N'- ditolyl-di-picolinamide (EtTDPA) and trivalent neodymium in acetonitrile have been determined by spectrophotometric and calorimetric methods. Each isomer of EtTDPA has been found to be capable of forming three complexes with trivalent neodymium, Nd(EtTDPA), Nd(EtTDPA){sub 2}, and Nd(EtTDPA){sub 3}. Values from spectrophotometric and calorimetric titrations are within reasonable agreement with each other. The order of stability constants for each metal:ligand complex decreases in the order Et(m)TDPA > Et(p)TDPA > Et(o)TDPA. The obtained values are comparable to other di-amidic ligands obtained under similar system conditions and mirror previously obtained solvent extraction data for EtTDPA at low ionic strengths. (authors.

  14. Interaction of thioamides, selenoamides, and amides with diiodine.

    PubMed

    Hadjikakou, Sotiris K; Hadjiliadis, Nick

    2006-01-01

    We review the results of our work on the iodine interaction with thioamides, selenoamides, and amides. Complexes with (i) "spoke" or "extended spoke" structures, D . I(2) and D . I(2) . I(2), respectively, (D is the ligand donor) (ii) iodonium salts of {[D(2) - I](+)[I(n)](-)} (n = 3, 7) and {[D(2) - I](+)[FeCl(4)](-)} formulae and (iii) disulfides of the categories (a) [D - D], (b) {[D - DH](+)[I(3)](-)} have been isolated and characterized. A compound of formula {[D(2) - I](+)[I(3)](-)[D . I(2)]} containing both types of complexes (i) and (ii) was also isolated. The interaction of diiodine with selenium analogs of the antithyroid drug 6-n-propyl-2-thiouracil (PTU), of formulae RSeU (6-alkyl-2-Selenouracil) results in the formation of complexes with formulae [(RSeU)I(2)]. All these results are correlated with the mechanism of action of antithyroid drugs. Finally, we review here our work on the diiodine interaction with the amides (LO). PMID:17497011

  15. Collagen and component polypeptides: Low frequency and amide vibrations

    NASA Astrophysics Data System (ADS)

    Fontaine-Vive, F.; Merzel, F.; Johnson, M. R.; Kearley, G. J.

    2009-01-01

    Collagen is a fibrous protein, which exists widely in the human body. The biomechanical properties of collagen depend on its triple helix structure and the corresponding low frequency vibrations. We use first-principles, density functional theory methods and analytical force fields to investigate the molecular vibrations of a model collagen compound, the results being validated by comparison with published, inelastic neutron scattering data. The results from these atomistic simulations are used at higher frequency to study the Amide I and V vibrations and therefore the vibrational signature of secondary and tertiary structure formation. In addition to collagen, its component homopolymers, poly-glycine and poly-proline are also studied. The Amide V vibration of glycine is strongly modified in going from the single helix of poly-glycine II to the triple helix of collagen. The collagen models are hydrated and this work allows us to discuss the relative merits of density functional theory and force field methods when tackling complex, partially crystalline systems.

  16. Extraction and spectrophotometric determination of molybdenum with thiocyanate and amides

    SciTech Connect

    Patel, K.S.; Khatri, H.; Mishra, K.

    1983-09-01

    The organic solution of commonly available amides (HAL), such as N-phenylacetamide, N-(methylphenyl) acetamide, N-(dimethylphenyl)acetamide, N-(diethylphenyl)acetamide, N-phenylpropionamide, N-phenylbutramide, and benzamide, is capable of extracting Mo(V) from SCN/sup -/ solutions. Mo(VI) was reduced to Mo(V) with mild reducing agents and allowed to react with SCN/sup -/ in strongly acidic media. The species formed was extracted with a benzene solution of amide dimers as a mixed-ligand complex. The special advantage of the method is that the HAL has good chemical stability with a very simple method of preparation. Moreover, it eliminates most of the drawbacks of established methods, such as interference from metal ions, variation of color intensity of the complex with respect to amounts of reagents, or prolonged extraction of the metal. The effect of various acids in the extraction of the metal was studied, as well as the effect of diverse ions in the determination of Mo. The ions and their tolerated amounts causing an error <2% are reported. The present method was accurately applied to ore, alloy steels, and synthetic matrices. 19 references, 3 figures, 2 tables.

  17. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Use of existing bonds, separate bonds and additional..., separate bonds and additional bonding. (a) Additional bonding. Section 13 neither prevents additional... or separate bond. (b) Use of existing bonds. Insofar as a bond currently in use is adequate to...

  18. Hydroxide-catalyzed bonding

    NASA Technical Reports Server (NTRS)

    Gwo, Dz-Hung (Inventor)

    2003-01-01

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

  19. 40 CFR 721.10063 - Halo substituted hydroxy nitrophenyl amide (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Halo substituted hydroxy nitrophenyl... Specific Chemical Substances § 721.10063 Halo substituted hydroxy nitrophenyl amide (generic). (a) Chemical... as halo substituted hydroxy nitrophenyl amide (PMN P-04-792) is subject to reporting under...

  20. 40 CFR 721.10063 - Halo substituted hydroxy nitrophenyl amide (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Halo substituted hydroxy nitrophenyl... Specific Chemical Substances § 721.10063 Halo substituted hydroxy nitrophenyl amide (generic). (a) Chemical... as halo substituted hydroxy nitrophenyl amide (PMN P-04-792) is subject to reporting under...

  1. 40 CFR 721.10063 - Halo substituted hydroxy nitrophenyl amide (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Halo substituted hydroxy nitrophenyl... Specific Chemical Substances § 721.10063 Halo substituted hydroxy nitrophenyl amide (generic). (a) Chemical... as halo substituted hydroxy nitrophenyl amide (PMN P-04-792) is subject to reporting under...

  2. 40 CFR 721.10063 - Halo substituted hydroxy nitrophenyl amide (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Halo substituted hydroxy nitrophenyl... Specific Chemical Substances § 721.10063 Halo substituted hydroxy nitrophenyl amide (generic). (a) Chemical... as halo substituted hydroxy nitrophenyl amide (PMN P-04-792) is subject to reporting under...

  3. 40 CFR 721.10063 - Halo substituted hydroxy nitrophenyl amide (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Halo substituted hydroxy nitrophenyl... Specific Chemical Substances § 721.10063 Halo substituted hydroxy nitrophenyl amide (generic). (a) Chemical... as halo substituted hydroxy nitrophenyl amide (PMN P-04-792) is subject to reporting under...

  4. Synthesis and evaluation of backbone/amide-modified analogs of leualacin.

    PubMed

    Hu, M K; Yang, F C; Chou, C C; Yen, M H

    1999-02-22

    Leualacin (1), a cyclic depsi-pentapeptide, and its backbone/amide-modified analogs 2-4 were synthesized. Amide analogue 3 exhibited stronger vasodilatory effects. It also strongly inhibited collagen- and arachidonic acid (AA)-induced platelet aggregations with IC50s of 0.6 microM and 2.0 microM, respectively. PMID:10098664

  5. Biosynthesis of peptide neurotransmitters: studies on the formation of peptide amides.

    PubMed

    Bradbury, A F; Smyth, D G

    1988-01-01

    A high proportion of peptide transmitters and peptide hormones terminate their peptide chain in a C-terminal amide group which is essential for their biological activity. The specificity of an enzyme that catalyses the formation of the amide was investigated with the aid of synthetic peptide substrates. With peptides containing l-amino acids the enzyme exhibited an essential requirement for glycine in the C-terminal position; amidation did not take place with peptides that had leucine, alanine, glutamic acid, lysine or N-methylglycine at the C-terminus and a peptide extended by the attachment of lysine to the C-terminal glycine did not act as a substrate. Amidation did occur with a peptide containing C-terminal D-alanine but no reaction was detected with peptides having C-terminal, D-serine or D-leucine. In tripeptides with a neutral amino acid in the penultimate position, amidation, took place readily but the reaction was slower when this position was occupied by an acidic or a basic residue. A series of overlapping peptides with C-terminal glycine, based on partial sequences of calcitonin, underwent amidation at similar rates, indicating that the amidating enzyme recognizes only a limited sequence at the C-terminus of its substrates. The results provide evidence that the amidating enzyme has a highly compact substrate binding site. PMID:2906151

  6. 40 CFR 721.720 - Alkoxylated fatty acid amide, alkylsulfate salt.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., alkylsulfate salt. 721.720 Section 721.720 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Specific Chemical Substances § 721.720 Alkoxylated fatty acid amide, alkylsulfate salt. (a) Chemical... as an alkoxylated fatty acid amide, alkylsulfate salt (PMN P-97-136) is subject to reporting...

  7. 40 CFR 721.720 - Alkoxylated fatty acid amide, alkylsulfate salt.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., alkylsulfate salt. 721.720 Section 721.720 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Specific Chemical Substances § 721.720 Alkoxylated fatty acid amide, alkylsulfate salt. (a) Chemical... as an alkoxylated fatty acid amide, alkylsulfate salt (PMN P-97-136) is subject to reporting...

  8. 40 CFR 721.720 - Alkoxylated fatty acid amide, alkylsulfate salt.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., alkylsulfate salt. 721.720 Section 721.720 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Specific Chemical Substances § 721.720 Alkoxylated fatty acid amide, alkylsulfate salt. (a) Chemical... as an alkoxylated fatty acid amide, alkylsulfate salt (PMN P-97-136) is subject to reporting...

  9. 40 CFR 721.720 - Alkoxylated fatty acid amide, alkylsulfate salt.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ..., alkylsulfate salt. 721.720 Section 721.720 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Specific Chemical Substances § 721.720 Alkoxylated fatty acid amide, alkylsulfate salt. (a) Chemical... as an alkoxylated fatty acid amide, alkylsulfate salt (PMN P-97-136) is subject to reporting...

  10. 40 CFR 721.720 - Alkoxylated fatty acid amide, alkylsulfate salt.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ..., alkylsulfate salt. 721.720 Section 721.720 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Specific Chemical Substances § 721.720 Alkoxylated fatty acid amide, alkylsulfate salt. (a) Chemical... as an alkoxylated fatty acid amide, alkylsulfate salt (PMN P-97-136) is subject to reporting...

  11. Langmuir films of an amide extracted from Piperaceae and its interaction with phospholipids

    NASA Astrophysics Data System (ADS)

    Antunes, P. A.; Oliveira, O. N.; Aroca, R. F.; Chierice, G. O.; Constantino, C. J. L.

    2005-06-01

    In this work, we investigate Langmuir monolayers from an amide extracted from dried roots of Ottonia propinqua, a native Brazilian plant believed to exhibit anesthetic and hallucinogen activities. In addition to producing monolayers from the amide itself, we probe the molecular-level action of the amide on phospholipids employed as simple membrane models. The surface pressure-molecular area ( π- A) isotherms for the amide were little affected by a number of subphase conditions. Almost no changes were observed upon varying the compression speed, spreading volume onto the surface, ions in the subphase, ionic strength and the solution solvent. However, stronger effects occurred when the subphase temperature and pH were altered, as the isotherms were shifted to larger areas with increasing temperatures and decreasing pHs. These results are discussed in terms of the molecular packing adopted by the amide at the air-water interface. In the mixed films with arachidic acid, the area per molecule varied linearly with the concentration of amide, probably due to phase separation. On the other hand, in the mixed films with dipalmitoyl phosphatidyl choline (DPPC), small amounts of the amide were sufficient to change the π- A isotherms significantly. This points to a strong molecular-level interaction, probably between the phosphate group in the zwitterion of DPPC and the nitrogen from the amidic group.

  12. Dynamics of molecules in extreme rotational states

    PubMed Central

    Yuan, Liwei; Teitelbaum, Samuel W.; Robinson, Allison; Mullin, Amy S.

    2011-01-01

    We have constructed an optical centrifuge with a pulse energy that is more than 2 orders of magnitude larger than previously reported instruments. This high pulse energy enables us to create large enough number densities of molecules in extreme rotational states to perform high-resolution state-resolved transient IR absorption measurements. Here we report the first studies of energy transfer dynamics involving molecules in extreme rotational states. In these studies, the optical centrifuge drives CO2 molecules into states with J ∼ 220 and we use transient IR probing to monitor the subsequent rotational, translational, and vibrational energy flow dynamics. The results reported here provide the first molecular insights into the relaxation of molecules with rotational energy that is comparable to that of a chemical bond.

  13. Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds.

    PubMed

    García, Angel E; Sanbonmatsu, Kevin Y

    2002-03-01

    We study atomic models of the thermodynamics of the structural transition of peptides that form alpha-helices. The effect of sequence variation on alpha-helix formation for alanine-rich peptides, Ac-Ala21-methyl amide (A21) and Ac-A5 (AAARA)3A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds. This desolvation can be directly correlated with a higher probability of hydrogen bond formation. We find that Fs has higher helical content than A21 at all temperatures. A small modification in the amber force field reproduces the experimental helical content and helix-coil transition temperatures for the Fs peptide. PMID:11867710

  14. Bifurcate localization modes of excess electron in aqueous Ca(2+)amide solution revealed by ab initio molecular dynamics simulation: towards hydrated electron versus hydrated amide anion.

    PubMed

    Zhang, Ru; Bu, Yuxiang

    2016-07-28

    In this work, we conduct ab initio molecular dynamics simulations on the localization dynamics of an excess electron (EE) in acetamide/Ca(2+) aqueous solutions with three different interaction modes of Ca(2+) with acetamide: tight contact, solvent-shared state, and separated interaction. The simulated results reveal that an EE could exhibit two different localization behaviors in these acetamide/Ca(2+) aqueous solutions depending on different amideCa(2+) interactions featuring different contact distances. For the tight contact and solvent-shared state of amideCa(2+) solutions, vertically injected diffuse EEs follow different mechanisms with different dynamics, forming a cavity-shaped hydrated electron or a hydrated amide anion, respectively. Meanwhile, for the separated state, only one localization pattern of a vertically injected diffuse EE towards the formation of hydrated amide anion is observed. The hindrance of hydrated Ca(2+) and the attraction of the hydrated amide group originating from its polarity and low energy π* orbital are the main driving forces. Additionally, different EE localization modes have different effects on the interaction between the amide group and Ca(2+) in turn. This work provides an important basis for further understanding the mechanisms and dynamics of localizations/transfers of radiation-produced EEs and associated EE-induced lesions and damage to biological species in real biological environments or other aqueous solutions. PMID:27351489

  15. Amide enolate additions to acylsilanes: in situ generation of unusual and stereoselective homoenolate equivalents.

    PubMed

    Lettan, Robert B; Galliford, Chris V; Woodward, Chase C; Scheidt, Karl A

    2009-07-01

    The synthesis of beta-hydroxy carbonyl compounds is an important goal due to their prevalence in bioactive molecules. A novel approach to construct these structural motifs involves the multicomponent reaction of acylsilanes, amides, and electrophiles. The addition of amide enolates to acylsilanes generates beta-silyloxy homoenolate reactivity by undergoing a 1,2-Brook rearrangement. These unique nucleophiles formed in situ can then undergo addition to alkyl halides, aldehydes, ketones, and imines. The gamma-amino-beta-hydroxy amide products derived from the addition of these homoenolates to N-diphenylphosphinyl imines are generated with excellent diastereoselectivity (> or = 20:1) and can be efficiently converted to highly valuable gamma-lactams. Finally, the use of optically active amide enolates delivers beta-hydroxy amide products with high levels of diastereoselectivity (> or = 10:1). PMID:19505076

  16. Formation, Reactivity, and Properties of Nondative Late Transition Metal–Oxygen and–Nitrogen Bonds

    PubMed Central

    FULTON, J. ROBIN; HOLLAND, ANDREW W.; FOX, DANIEL J.; BERGMAN*, ROBERT G.

    2005-01-01

    Complexes containing bonds between heteroatoms such as nitrogen and oxygen and “late” transition metals (i.e., those located on the right side of the transition series) have been implicated as reactive intermediates in numerous important catalytic systems. Despite this, our understanding of such M–X linkages still lags behind that of their M–H and M–C analogues. New synthetic strategies have now made possible the isolation and study of a variety of monomeric late-metal alkoxide, aryloxide, and amide complexes, including parent hydroxide and amide species. The heteroatoms in these materials form surprisingly strong bonds to their metal centers, and their bond energies do not necessarily correlate with the energies of the corresponding H–X bonds. The M–X complexes typically exhibit nucleophilic reactivity, in some cases form strong hydrogen bonds to proton donors, and even deprotonate relatively weak acids. These observations, as well as thermodynamic investigations, suggest that late metal–heteroatom bonds are strongly polarized and possess significant ionic character, properties that play an important role in their interactions with organic compounds. PMID:11790088

  17. C-H bond activation with actinides: The first example of intramolecular ring bite of a pentamethylcyclopentadienyl methyl group

    SciTech Connect

    Peters, R.G.; Warner, B.P.; Scott, B.L.; Burns, C.J.

    1999-07-05

    Thermolysis of (C{sub 5}Me{sub 5}){sub 2}U({double_bond}NAd){sub 2}, 1 (Ad = 1-adamantyl), in benzene or hexane results in the intramolecular C-H bond activation of a methyl group on a pentamethylcyclopentadienyl ligand across the two imido functional groups. The product of this reaction has been spectroscopically and structurally characterized. The activation product is a reduced U(IV) metallocene bis(amide) complex with an N-bound methylene unit derived from the methyl group attached to one amide group. The activation parameters for this process have been determined; the results are consistent with a simple unimolecular process. This is the first example of intramolecular activation of a (C{sub 5}Me{sub 5}) methyl C-H bond in an actinide complex.

  18. Structure–Activity Relationships Comparing N-(6-Methylpyridin-yl)-Substituted Aryl Amides to 2-Methyl-6-(substituted-arylethynyl)pyridines or 2-Methyl-4-(substituted-arylethynyl)thiazoles as Novel Metabotropic Glutamate Receptor Subtype 5 Antagonists†

    PubMed Central

    Kulkarni, Santosh S.; Zou, Mu-Fa; Cao, Jianjing; Deschamps, Jeffrey R.; Rodriguez, Alice L.; Conn, P. Jeffrey; Newman, Amy Hauck

    2010-01-01

    The metabotropic glutamate receptor subtype 5 (mGluR5) has been implicated in anxiety, depression, pain, mental retardation, and addiction. The potent and selective noncompetitive mGluR5 antagonist 2-methyl-6-(phenylethynyl)pyridine (MPEP, 1) has been a critically important tool used to further elucidate the role of mGluR5 in these CNS disorders. In an effort to provide novel and structurally diverse selective mGluR5 antagonists, we previously described a set of analogues with moderate activity wherein the alkyne bond was replaced with an amide group. In the present report, extended series of both amide and alkyne-based ligands were synthesized. MGluR5 binding and functional data were obtained that identified (1) several novel alkynes with comparable affinities to 1 at mGluR5 (e.g., 10 and 20–23), but (2) most structural variations to the amide template were not well tolerated, although a few potent amides were discovered (e.g., 55 and 56). Several of these novel analogues show drug-like physical properties (e.g., cLogP range) 2–5) that support their use for in vivo investigation into the role of mGluR5 in CNS disorders. PMID:19445453

  19. Synthetic, structural, NMR and catalytic studies of phosphinic amide-phosphoryl chalcogenides (chalcogen = O, S, Se) as mixed-donor bidentate ligands in zinc chemistry.

    PubMed

    del Águila-Sánchez, Miguel A; Santos-Bastos, Neidemar M; Ramalho-Freitas, Maria C; García López, Jesús; Costa de Souza, Marcos; Camargos-Resende, Jackson A L; Casimiro, María; Alves-Romeiro, Gilberto; Iglesias, María José; López Ortiz, Fernando

    2014-10-01

    ortho Substituted (diphenylphosphoryl)-, (diphenylphosphorothioyl)- and (diphenylphosphoroselenoyl)-phosphinic amides o-C6H4(P(X)Ph2)(P(O)N(i)Pr2) (X = O (20a), S (20b), Se (20c)) were synthesized by ortho directed lithiation of N,N-diisopropyl-P,P-diphenylphosphinic amide (Ph2P(O)N(i)Pr2) followed by trapping with Ph2PCl and subsequent oxidation of the o-(diphenylphosphine)phosphinic amide (19) with H2O2, S8 and Se. The reaction of the new mixed-donor bidentate ligands with zinc dichloride afforded the corresponding complexes [ZnCl2(P(X)Ph2)o-C6H4(P(O)N(i)Pr2)] (21a-c). The new compounds were structurally characterized in solution by nuclear magnetic resonance spectroscopy and in the solid-state by X-ray diffraction analysis of the ligand (20b) and the three complexes (21a-c). The X-ray crystal structure of 20b suggests the existence of a P[double bond, length as m-dash]O→P(S)-C intramolecular nonbonded interaction. The natural bond orbital (NBO) analysis using DFT methods showed that the stabilization effect provided by a nO→σ*P-C orbital interaction was negligible. The molecular structure of the complexes consisted of seven-membered chelates formed by O,X-coordination of the ligands to the zinc cation. The metal is four-coordinated by binding to the two chlorine atoms showing a distorted tetrahedral geometry. Applications in catalysis revealed that hemilabile ligands 20a-c act as significant promoters of the addition of diethylzinc to aldehydes, with 20a showing the highest activity. Chelation of Et2Zn with 20a was evidenced by NMR spectroscopy. PMID:25121963

  20. Reactivity of functionalized indoles with rare-earth metal amides. Synthesis, characterization and catalytic activity of rare-earth metal complexes incorporating indolyl ligands.

    PubMed

    Feng, Zhijun; Wei, Yun; Zhou, Shuangliu; Zhang, Guangchao; Zhu, Xiancui; Guo, Liping; Wang, Shaowu; Mu, Xiaolong

    2015-12-21

    The reactivity of several functionalized indoles 2-(RNHCH2)C8H5NH (R = C6H5 (1), (t)Bu (2), 2,6-(i)Pr2C6H3 (3)) with rare-earth metal amides is described. Reactions of 1 or 2 with [(Me3Si)2N]3RE(μ-Cl)Li(THF)3 (RE = Eu, Yb) respectively produced the europium complexes [2-(C6H5N[double bond, length as m-dash]CH)C8H5N]2Eu[N(SiMe3)2] (4) and [2-((t)BuN[double bond, length as m-dash]CH)C8H5N]Eu[N(SiMe3)2]2 (5), and the ytterbium complex [2-((t)BuN[double bond, length as m-dash]CH)C8H5N]2Yb[N(SiMe3)2] (6), containing bidentate anionic indolyl ligands via dehydrogenation of the amine to the imine. In contrast, reactions of the more sterically bulky indole 3 with [(Me3Si)2N]3RE(μ-Cl)Li(THF)3 afforded complexes [2-(2,6-(i)Pr2C6H3NCH2)C8H5N]RE[N(SiMe3)2](THF)2 (RE = Yb (7), Y (8), Er (9), Dy (10)) with the deprotonated indolyl ligand. While reactions of 3 with yttrium and ytterbium amides in refluxing toluene respectively gave the complexes [2-(2,6-(i)Pr2C6H3N[double bond, length as m-dash]CH)C8H5N]3Y (11) and [2-(2,6-(i)Pr2C6H3N[double bond, length as m-dash]CH)C8H5N]2Yb(II)(THF)2 (12), along with transformation of the amino group to the imino group, and also with a reduction of Yb(3+) to Yb(2+) in the formation of 12. Reactions of 3 with samarium and neodymium amides provided novel dinuclear complexes {[μ-η(5):η(1):η(1)-2-(2,6-(i)Pr2C6H3NCH2)C8H5N]RE[N(SiMe3)2]}2 (RE = Sm (13), Nd (14)) having indolyl ligands in μ-η(5):η(1):η(1) hapticities. The pathway for the transformation of the amino group to the imino group is proposed on the basis of the experimental results. The new complexes displayed excellent activity in the intramolecular hydroamination of aminoalkenes. PMID:26548974

  1. Conversion of a Benzofuran Ester to an Amide through an Enamine Lactone Pathway: Synthesis of HCV Polymerase Inhibitor GSK852A.

    PubMed

    Bowman, Roy K; Bullock, Kae M; Copley, Royston C B; Deschamps, Nicole M; McClure, Michael S; Powers, Jeremiah D; Wolters, Andy M; Wu, Lianming; Xie, Shiping

    2015-10-01

    HCV NS5B polymerase inhibitor GSK852A (1) was synthesized in only five steps from ethyl 4-fluorobenzoylacetate (3) in 46% overall yield. Key to the efficient route was the synthesis of the highly functionalized benzofuran core 15 from the β-keto ester in one pot and the efficient conversion of ester 6 to amide 19 via enamine lactone 22. Serendipitous events led to identification of the isolable enamine lactone intermediate 22. Single crystal X-ray diffraction and NMR studies supported the intramolecular hydrogen bond shown in enamine lactone 22. The hydrogen bond was considered an enabler in the proposed pathway from ester 6 to enamine lactone 22 and its rearrangement to amide 19. GSK852A (1) was obtained after reductive amination and mesylation with conditions amenable to the presence of the boronic acid moiety which was considered important for the desirable pharmacokinetics of 1. The overall yield of 46% in five steps was a significant improvement to the previous synthesis from the same β-keto ester in 5% yield over 13 steps. PMID:26355847

  2. Chemical shift and electric field gradient tensors for the amide and carboxyl hydrogens in the model peptide N-acetyl-D,L-valine. Single-crystal deuterium NMR study.

    SciTech Connect

    Gerald, R. E., II; Bernhard, T.; Haeberlen, U.; Rendell, J.; Opella, S.; Chemical Engineering

    1993-01-01

    Solid-state NMR spectroscopy is well established as a method for describing molecular structure with resolution on the atomic scale. Many of the NMR observables result from anisotropic interactions between the nuclear spin and its environment. These observables can be described by second-rank tensors. For example, the eigenvalues of the traceless symmetric part of the hydrogen chemical shift (CS) tensor provide information about the strength of inter- or intramolecular hydrogen bonding. On the other hand, the eigenvectors of the deuterium electric field gradient (EFG) tensor give deuteron/proton bond directions with an accuracy rivalled only by neutron diffraction. In this paper the authors report structural information of this type for the amide and carboxyl hydrogen sites in a single crystal of the model peptide N-acetyl-D,L-valine (NAV). They use deuterium NMR to infer both the EFG and CS tensors at the amide and carboxyl hydrogen sites in NAV. Advantages of this technique over multiple-pulse proton NMR are that it works in the presence of {sup 14}N spins which are very hard to decouple from protons and that additional information in form of the EFG tensors can be derived. The change in the CS and EFG tensors upon exchange of a deuteron for a proton (the isotope effect) is anticipated to be very small; the effect on the CS tensors is certainly smaller than the experimental errors. NAV has served as a model peptide before in a variety of NMR studies, including those concerned with developing solid-state NMR spectroscopy as a method for determining the structure of proteins. NMR experiments on peptide or protein samples which are oriented in at least one dimension can provide important information about the three-dimensional structure of the peptide or the protein. In order to interpret the NMR data in terms of the structure of the polypeptide, the relationship of the CS and EFG tensors to the local symmetry elements of an amino acide, e.g., the peptide plane, is

  3. Diffusion bonding aeroengine components

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, G. A.; Broughton, T.

    1988-10-01

    The use of diffusion bonding processes at Rolls-Royce for the manufacture of titanium-alloy aircraft engine components and structures is described. A liquid-phase diffusion bonding process called activated diffusion bonding has been developed for the manufacture of the hollow titanium wide chord fan blade. In addition, solid-state diffusion bonding is being used in the manufacture of hollow vane/blade airfoil constructions mainly in conjunction with superplastic forming and hot forming techniques.

  4. (2E)-2-(5-Bromo-2-hy­droxy-3-meth­oxy­benzyl­idene)-N-cyclo­hexyl­hydrazine­carbothio­amide

    PubMed Central

    Jacob, Jinsa Mary; Kurup, M. R. Prathapachandra

    2012-01-01

    The title compound, C15H20BrN3O2S, crystallizes in the thio­amide form and adopts an E,E conformation with respect to the azomethine and hydrazinic bonds, respectively. The mol­ecules are paired through N—H⋯O and O—H⋯S hydrogen bonds, leading to the formation of centrosymmetric dimers in the crystal. These dimers are stacked along the a axis and are inter­connected through N—H⋯S hydrogen bonds to generate polymeric chains. The structure also features C—H⋯π interactions. An intra­molecular O—H⋯O bond is also present. PMID:22412698

  5. Uranium complexes with amide, alkoxide and thiolate ligands

    NASA Astrophysics Data System (ADS)

    Ephritikhine, Michel

    1994-10-01

    Alkoxide, hydroxide and mu-oxo complexes of U(IV) have been synthesized by (a) the reaction of alcohols, ketones and water with hydride or borohydride derivatives, (b) the coupling reaction of ketones with UCl4 in the presence of sodium amalgam; (c) the reduction of CO2 by (U(C5H4SiMe3)3) or (U(C5H4SiMe3)3H); (d) the deoxygenation of CO by (U(C5H5)3R) complexes; and (e) condensation reactions of alkoxide and hydroxide compounds. Thiolate complexes were made by the treatment of uranium borohydride or hydride compounds with thiols. The reaction of UCl4 with NaSR reagents afforded the homoleptic thiolate complexes ((THF)3Na(mu-SR)3U(mu-SR)3Na(THF)3). Amide compounds, including U(V) derivatives, were prepared from U(NEt 2)4.

  6. Small Antimicrobial Agents Based on Acylated Reduced Amide Scaffold.

    PubMed

    Teng, Peng; Huo, Da; Nimmagadda, Alekhya; Wu, Jianfeng; She, Fengyu; Su, Ma; Lin, Xiaoyang; Yan, Jiyu; Cao, Annie; Xi, Chuanwu; Hu, Yong; Cai, Jianfeng

    2016-09-01

    Prevalence of drug-resistant bacteria has emerged to be one of the greatest threats in the 21st century. Herein, we report the development of a series of small molecular antibacterial agents that are based on the acylated reduced amide scaffold. These molecules display good potency against a panel of multidrug-resistant Gram-positive and Gram-negative bacterial strains. Meanwhile, they also effectively inhibit the biofilm formation. Mechanistic studies suggest that these compounds kill bacteria by compromising bacterial membranes, a mechanism analogous to that of host-defense peptides (HDPs). The mechanism is further supported by the fact that the lead compounds do not induce resistance in MRSA bacteria even after 14 passages. Lastly, we also demonstrate that these molecules have therapeutic potential by preventing inflammation caused by MRSA induced pneumonia in a rat model. This class of compounds could lead to an appealing class of antibiotic agents combating drug-resistant bacterial strains. PMID:27526720

  7. Lead Optimization Studies of Cinnamic Amide EP2 Antagonists

    PubMed Central

    2015-01-01

    Prostanoid receptor EP2 can play a proinflammatory role, exacerbating disease pathology in a variety of central nervous system and peripheral diseases. A highly selective EP2 antagonist could be useful as a drug to mitigate the inflammatory consequences of EP2 activation. We recently identified a cinnamic amide class of EP2 antagonists. The lead compound in this class (5d) displays anti-inflammatory and neuroprotective actions. However, this compound exhibited moderate selectivity to EP2 over the DP1 prostanoid receptor (∼10-fold) and low aqueous solubility. We now report compounds that display up to 180-fold selectivity against DP1 and up to 9-fold higher aqueous solubility than our previous lead. The newly developed compounds also display higher selectivity against EP4 and IP receptors and a comparable plasma pharmacokinetics. Thus, these compounds are useful for proof of concept studies in a variety of models where EP2 activation is playing a deleterious role. PMID:24773616

  8. Sulfonyl fluoride inhibitors of fatty acid amide hydrolase.

    PubMed

    Alapafuja, Shakiru O; Nikas, Spyros P; Bharathan, Indu T; Shukla, Vidyanand G; Nasr, Mahmoud L; Bowman, Anna L; Zvonok, Nikolai; Li, Jing; Shi, Xiaomeng; Engen, John R; Makriyannis, Alexandros

    2012-11-26

    Sulfonyl fluorides are known to inhibit esterases. Early work from our laboratory has identified hexadecyl sulfonylfluoride (AM374) as a potent in vitro and in vivo inhibitor of fatty acid amide hydrolase (FAAH). We now report on later generation sulfonyl fluoride analogs that exhibit potent and selective inhibition of FAAH. Using recombinant rat and human FAAH, we show that 5-(4-hydroxyphenyl)pentanesulfonyl fluoride (AM3506) has similar inhibitory activity for both the rat and the human enzyme, while rapid dilution assays and mass spectrometry analysis suggest that the compound is a covalent modifier for FAAH and inhibits its action in an irreversible manner. Our SAR results are highlighted by molecular docking of key analogs. PMID:23083016

  9. Lead optimization studies of cinnamic amide EP2 antagonists.

    PubMed

    Ganesh, Thota; Jiang, Jianxiong; Yang, Myung-Soon; Dingledine, Ray

    2014-05-22

    Prostanoid receptor EP2 can play a proinflammatory role, exacerbating disease pathology in a variety of central nervous system and peripheral diseases. A highly selective EP2 antagonist could be useful as a drug to mitigate the inflammatory consequences of EP2 activation. We recently identified a cinnamic amide class of EP2 antagonists. The lead compound in this class (5d) displays anti-inflammatory and neuroprotective actions. However, this compound exhibited moderate selectivity to EP2 over the DP1 prostanoid receptor (∼10-fold) and low aqueous solubility. We now report compounds that display up to 180-fold selectivity against DP1 and up to 9-fold higher aqueous solubility than our previous lead. The newly developed compounds also display higher selectivity against EP4 and IP receptors and a comparable plasma pharmacokinetics. Thus, these compounds are useful for proof of concept studies in a variety of models where EP2 activation is playing a deleterious role. PMID:24773616

  10. Catalysis of a Flavoenzyme-Mediated Amide Hydrolysis

    SciTech Connect

    Mukherjee, Tathagata; Zhang, Yang; Abdelwahed, Sameh; Ealick, Steven E.; Begley, Tadhg P.

    2010-09-13

    A new pyrimidine catabolic pathway (the Rut pathway) was recently discovered in Escherichia coli K12. In this pathway, uracil is converted to 3-hydroxypropionate, ammonia, and carbon dioxide. The seven-gene Rut operon is required for this conversion. Here we demonstrate that the flavoenzyme RutA catalyzes the initial uracil ring-opening reaction to give 3-ureidoacrylate. This reaction, while formally a hydrolysis reaction, proceeds by an oxidative mechanism initiated by the addition of a flavin hydroperoxide to the C4 carbonyl. While peroxide-catalyzed amide hydrolysis has chemical precedent, we are not aware of a prior example of analogous chemistry catalyzed by flavin hydroperoxides. This study further illustrates the extraordinary catalytic versatility of the flavin cofactor.

  11. Polymer amide in the Allende and Murchison meteorites

    NASA Astrophysics Data System (ADS)

    McGeoch, Julie E. M.; McGeoch, Malcolm W.

    2015-11-01

    It has been proposed that exothermic gas phase polymerization of amino acids can occur in the conditions of a warm dense molecular cloud to form hydrophobic polymer amide (HPA) (McGeoch and McGeoch 2014). In a search for evidence of this presolar chemistry Allende and Murchison meteorites and a volcano control were diamond burr-etched and Folch extracted for potential HPA yielding 85 unique peaks in the meteorite samples via matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI TOF/MS). The amino acids after acid hydrolysis in Allende were below the level of detection but many of the Allende peaks via the more sensitive MALDI/TOF analysis could be fitted to a polymer combination of glycine, alanine, and alpha-hydroxyglycine with high statistical significance. A similar significant fit using these three amino acids could not be applied to the Murchison data indicating more complex polymer chemistry.

  12. Amides and neolignans from the aerial parts of Piper bonii.

    PubMed

    Ding, Duo-Duo; Wang, Yue-Hu; Chen, Ya-Hui; Mei, Ren-Qiang; Yang, Jun; Luo, Ji-Feng; Li, Yan; Long, Chun-Lin; Kong, Yi

    2016-09-01

    Six amides, piperbonamides A-F, three neolignans piperbonins A-C, and 11 known compounds were isolated from the aerial parts of Piper bonii (Piperaceae). The structures of piperbonamides A-F and piperbonins A-C were elucidated based on the analysis of 1D and 2D NMR and MS data. Piperbonin A, (+)-trans-acuminatin, (+)-cis-acuminatin, (+)-kadsurenone, and pipernonaline showed weak activity against platelet aggregation with IC50 values of 118.2, 108.5, 90.02, 107.3, and 116.3 μM, respectively, as compared with the positive control, tirofiban, with an IC50 value of 5.24 μM. Piperbonamides A-F were inactive against five tumor cell lines at concentrations up to 40 μM. PMID:27452451

  13. Rapid adhesive bonding concepts

    NASA Technical Reports Server (NTRS)

    Stein, B. A.; Tyeryar, J. R.; Hodges, W. T.

    1984-01-01

    Adhesive bonding in the aerospace industry typically utilizes autoclaves or presses which have considerable thermal mass. As a consequence, the rates of heatup and cooldown of the bonded parts are limited and the total time and cost of the bonding process is often relatively high. Many of the adhesives themselves do not inherently require long processing times. Bonding could be performed rapidly if the heat was concentrated in the bond lines or at least in the adherends. Rapid adhesive bonding concepts were developed to utilize induction heating techniques to provide heat directly to the bond line and/or adherends without heating the entire structure, supports, and fixtures of a bonding assembly. Bonding times for specimens are cut by a factor of 10 to 100 compared to standard press bonding. The development of rapid adhesive bonding for lap shear specimens (per ASTM D1003 and D3163), for aerospace panel bonding, and for field repair needs of metallic and advanced fiber reinforced polymeric matrix composite structures are reviewed.

  14. Rotational preference in gymnastics.

    PubMed

    Heinen, Thomas; Jeraj, Damian; Vinken, Pia M; Velentzas, Konstantinos

    2012-06-01

    In gymnastics, most skills incorporate rotations about one or more body axes. At present, the question remains open if factors such as lateral preference and/or vestibulo-spinal asymmetry are related to gymnast's rotational preference. Therefore, we sought to explore relationships in gymnast's rotation direction between different gymnastic skills. Furthermore, we sought to explore relationships between rotational preference, lateral preference, and vestibulo-spinal asymmetry. In the experiment n = 30 non-experts, n = 30 near-experts and n = 30 experts completed a rotational preference questionnaire, a lateral preference inventory, and the Unterberger-Fukuda Stepping Test. The results revealed, that near-experts and experts more often rotate rightward in the straight jump with a full turn when rotating leftward in the round-off and vice versa. The same relationship was found for experts when relating the rotation preference in the handstand with a full turn to the rotation preference in the straight jump with a full turn. Lateral preference was positively related to rotational preference in non-expert gymnasts, and vestibulo-spinal asymmetry was positively related to rotational preference in experts. We suggest, that gymnasts should explore their individual rotational preference by systematically practicing different skills with a different rotation direction, bearing in mind that a clearly developed structure in rotational preference between different skills may be appropriate to develop more complex skills in gymnastics. PMID:23486362

  15. Rotational Preference in Gymnastics

    PubMed Central

    Heinen, Thomas; Jeraj, Damian; Vinken, Pia M.; Velentzas, Konstantinos

    2012-01-01

    In gymnastics, most skills incorporate rotations about one or more body axes. At present, the question remains open if factors such as lateral preference and/or vestibulo-spinal asymmetry are related to gymnast’s rotational preference. Therefore, we sought to explore relationships in gymnast’s rotation direction between different gymnastic skills. Furthermore, we sought to explore relationships between rotational preference, lateral preference, and vestibulo-spinal asymmetry. In the experiment n = 30 non-experts, n = 30 near-experts and n = 30 experts completed a rotational preference questionnaire, a lateral preference inventory, and the Unterberger-Fukuda Stepping Test. The results revealed, that near-experts and experts more often rotate rightward in the straight jump with a full turn when rotating leftward in the round-off and vice versa. The same relationship was found for experts when relating the rotation preference in the handstand with a full turn to the rotation preference in the straight jump with a full turn. Lateral preference was positively related to rotational preference in non-expert gymnasts, and vestibulo-spinal asymmetry was positively related to rotational preference in experts. We suggest, that gymnasts should explore their individual rotational preference by systematically practicing different skills with a different rotation direction, bearing in mind that a clearly developed structure in rotational preference between different skills may be appropriate to develop more complex skills in gymnastics. PMID:23486362

  16. Construction of hybrid material with double chemical bond from functional bridge ligand: Molecular modification, lotus root-like micromorphology and strong luminescence

    NASA Astrophysics Data System (ADS)

    Yan, Bing; Sui, Yu-Long

    2006-07-01

    Modifying benzoic acid with a cross-linking molecule (3-aminopropyl)triethoxysilane (abbreviated as APES), a fictional molecular bridge with double reactivity was achieved by the amidation reaction between them. Then the modified functional molecule, which behaving as a bridge, both coordinate with terbium ion through amide's oxygen atom and form the Si-O chemical bond in an in situ sol-gel process with matrix precursor (tetraethoxysilane, TEOS). As a result, a novel molecular hybrid material (Tb-BA-APES) with double chemical bond (Tb-O coordination bond and Si-O covalent bond) was constructed. The strong luminescence of Tb 3+ substantiates optimum energy couple and effective intramolecular energy transfer between the triplet state energy of modified ligand bridge and emissive energy level of Tb 3+. Especially SEM of the molecular hybrid material exhibits unexpected microlotus root-like pore morphology.

  17. Bonding thermoplastic polymers

    DOEpatents

    Wallow, Thomas I.; Hunter, Marion C.; Krafcik, Karen Lee; Morales, Alfredo M.; Simmons, Blake A.; Domeier, Linda A.

    2008-06-24

    We demonstrate a new method for joining patterned thermoplastic parts into layered structures. The method takes advantage of case-II permeant diffusion to generate dimensionally controlled, activated bonding layers at the surfaces being joined. It is capable of producing bonds characterized by cohesive failure while preserving the fidelity of patterned features in the bonding surfaces. This approach is uniquely suited to production of microfluidic multilayer structures, as it allows the bond-forming interface between plastic parts to be precisely manipulated at micrometer length scales. The bond enhancing procedure is easily integrated in standard process flows and requires no specialized equipment.

  18. Prospective bonding applications

    NASA Astrophysics Data System (ADS)

    Ancenay, H.; Benazet, D.

    1981-07-01

    Adhesive bonding in industry and in the laboratory is surveyed and prospects for its wider utilization are assessed. The economic impact of bonding technology on industry is discussed. Research is reviewed, centering on the development of nondestructive testing and inspection techniques. Traditional (wood) as well as new materials susceptible to bonding are considered. Applications in construction and civil engineering, in aeronautics, and in the automobile industry are covered. The use of glues in mechanical constructions, in assembling cylindrical parts, and in metal-metal bonding are examined. Hybrid assembling and bonding of composite materials are included.

  19. Carbon–heteroatom bond formation catalysed by organometallic complexes

    PubMed Central

    Hartwig, John F.

    2010-01-01

    At one time the synthetic chemist’s last resort, reactions catalysed by transition metals are now the preferred method for synthesizing many types of organic molecule. A recent success in this type of catalysis is the discovery of reactions that form bonds between carbon and heteroatoms (such as nitrogen, oxygen, sulphur, silicon and boron) via complexes of transition metals with amides, alkoxides, thiolates, silyl groups or boryl groups. The development of these catalytic processes has been supported by the discovery of new elementary reactions that occur at metal–heteroatom bonds and by the identification of factors that control these reactions. Together, these findings have led to new synthetic processes that are in daily use and have formed a foundation for the development of processes that are likely to be central to synthetic chemistry in the future. PMID:18800130

  20. New synthesis route for ternary transition metal amides as well as ultrafast amide-hydride hydrogen storage materials.

    PubMed

    Cao, Hujun; Santoru, Antonio; Pistidda, Claudio; Richter, Theresia M M; Chaudhary, Anna-Lisa; Gizer, Gökhan; Niewa, Rainer; Chen, Ping; Klassen, Thomas; Dornheim, Martin

    2016-04-14

    K2[Mn(NH2)4] and K2[Zn(NH2)4] were successfully synthesized via a mechanochemical method. The mixture of K2[Mn(NH2)4] and LiH showed excellent rehydrogenation properties. In fact, after dehydrogenation K2[Mn(NH2)4]-8LiH fully rehydrogenates within 60 seconds at ca. 230 °C and 5 MPa of H2. This is one of the fastest rehydrogenation rates in amide-hydride systems known to date. This work also shows a strategy for the synthesis of transition metal nitrides by decomposition of the mixtures of M[M'(NH2)n] (where M is an alkali or alkaline earth metal and M' is a transition metal) and metal hydrides. PMID:26936831

  1. AMID Mediates Adenosine-Induced Caspase-Independent HuH-7 Cell Apoptosis

    PubMed Central

    Yang, Dongqin; Yaguchi, Takahiro; Nagata, Tetsu; Gotoh, Akinobu; Dovat, Sinisa; Song, Chunhua; Nishizaki, Tomoyuki

    2011-01-01

    Background/Aims: The mechanism underlying extracellular adenosine-induced caspase-independent apoptosis in HuH-7 human hepatoma cells is not fully understood. The present study investigated the role for apoptosis-inducing factor (AIF)-homologous mitochondrion-associated inducer of death (AMID) in the pathway. Methods: To see the implication of AMID in adenosine-induced HuH-7 cell apoptosis, real-time reverse transcription-polymerase chain reaction (RT-PCR), immunofluorescent cytochemistry, time-laps GFP monitoring, cell cycle analysis, flow cytometry, Western blotting, cell viability assay, and TUNEL staining were carried out. Results: Adenosine upregulated AMID expression in HuH-7 cells, and translocated AMID from the cytosol into the nucleus. Adenosine induced HuH-7 cell apoptosis, and the effect was further enhanced by overexpressing AMID. Adenosine-induced HuH-7 cell apoptosis, alternatively, was inhibited by knocking-down AMID. Conclusion: The results of the present study provide evidence for AMID as a critical factor for adenosine-induced caspase-independent HuH-7 cell apoptosis. PMID:21325820

  2. Recent developments in the electronic spectroscopy of amides and alpha-helical polypeptides.

    PubMed

    Woody, Robert W; Koslowski, Axel

    2002-12-10

    Recent experimental and theoretical advances in understanding the electronic excited states of simple amides are reviewed. Polarized reflection spectroscopy of single crystals of N-acetylglycine shows that the direction of the first pipi* (NV(1)) transition dipole moment of a secondary amide differs by approximately 15 degrees from that of a primary amide. Ab initio calculations on simple amides support this conclusion. Ab initio studies of di- and tri-amides demonstrate that several inter-amide charge-transfer (CT) transitions occur in the 150-175-nm region, between the NV(1) and NV(2) transitions. When the correct dipole transition moment direction for peptides is used in calculations of the circular dichroism of the alpha-helix, the results are much improved over those from earlier calculations that used the direction for primary amides. Studies that consider the mixing of the NV(1) transition with CT transitions are reviewed. These indicate that such mixing is likely to have a significant effect on the absorption and CD spectra of the alpha-helix and other types of peptide conformation. Nevertheless, the independent systems model gives a reasonable first approximation to the absorption and CD spectra of the alpha-helix. PMID:12488025

  3. Synthesis of novel naphthoquinone aliphatic amides and esters and their anticancer evaluation.

    PubMed

    Kongkathip, Boonsong; Akkarasamiyo, Sunisa; Hasitapan, Komkrit; Sittikul, Pichamon; Boonyalai, Nonlawat; Kongkathip, Ngampong

    2013-02-01

    Fourteen new naphthoquinone aliphatic amides and seventeen naphthoquinone aliphatic esters were synthesized in nine to ten steps from 1-hydroxy-2-naphthoic acid with 9-25% overall yield for the amides, and 16-21% overall yield for the esters. The key step of the amide synthesis is a coupling reaction between amine and various aliphatic acids using 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM) as a coupling agent while for the ester synthesis, DCC/DMAP or CDI was used as the coupling reagent between aliphatic acids and naphthoquinone alcohol. Both naphthoquinone amides and esters were evaluated for their anticancer activity against KB cells. It was found that naphthoquinone aliphatic amides showed stronger anticancer activity than those of the esters when the chains are longer than 7-carbon atoms. The optimum chain of amides is expected to be 16-carbon atoms. In addition, naphthoquinone aliphatic esters with α-methyl on the ester moiety possessed much stronger anticancer activity than the straight chains. Decatenation assay revealed that naphthoquinone amide with 16-carbon atoms chain at 15 μM and 20 μM can completely inhibit hTopoIIα activity while at 10 μM the enzyme activity was moderately inhibited. Molecular docking result also showed the same trend as the cytotoxicity and decatenation assay. PMID:23313636

  4. Microbial Transformation of Nitriles to High-Value Acids or Amides

    NASA Astrophysics Data System (ADS)

    Chen, Jing; Zheng, Ren-Chao; Zheng, Yu-Guo; Shen, Yin-Chu

    Biotransformation of nitriles mediated by nitrile-amide converting enzymes has attracted considerable attention and developed tremendously in the recent years in China since it offers a valuable alternative to traditional chemical reaction which requires harsh conditions. As a result, an upsurge of these promising enzymes (including nitrile hydratase, nitrilase and amidase) has been taking place. This review aims at describing these enzymes in detail. A variety of microorganisms harboring nitrile-amide converting activities have been isolated and identified in China, some of which have already applied with moderate success. Currently, a wide range of high-value compounds such as aliphatic, alicyclic, aromatic and heterocyclic amides and their corresponding acids were provided by these nitrile-amide degra-ding organisms. Simultaneously, with the increasing demand of chiral substances, the enantioselectivity of the nitrilase superfamily is widely investigated and exploited in China, especially the bioconversion of optically active α-substituted phenylacetamides, acids and 2,2-dimethylcyclopropanecarboxamide and 2,2-dimethylcyclopropanecarboxylic acid by means of the catalysts exhibiting excellent stereoselectivity. Besides their synthetic value, the nitrile-amide converting enzymes also play an important role in environmental protection. In this context, cloning of the genes and expression of these enzymes are presented. In the near future in China, an increasing number of novel nitrile-amide converting organisms will be screened and their potential in the synthesis of useful acids and amides will be further exploited.

  5. Empirical Maps For The Calculation of Amide I Vibrational Spectra of Proteins From Classical Molecular Dynamics Simulations

    PubMed Central

    2015-01-01

    New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obtained from standard all-atom molecular simulations without any additional constraints on the system. Six proteins representing a wide range of sizes and secondary structure complexity were chosen as a test set. Spectra calculated for these proteins reproduce experimental data both qualitatively and quantitatively. The proposed maps lead to spectra that capture the weak second peak observed in proteins containing β-sheets, allowing for clear distinction between α-helical and β-sheet proteins. While the parametrization is specific to the CHARMM force field, the methodology presented can be readily applied to any empirical force field. PMID:24654732

  6. Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations.

    PubMed

    Małolepsza, Edyta; Straub, John E

    2014-07-17

    New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obtained from standard all-atom molecular simulations without any additional constraints on the system. Six proteins representing a wide range of sizes and secondary structure complexity were chosen as a test set. Spectra calculated for these proteins reproduce experimental data both qualitatively and quantitatively. The proposed maps lead to spectra that capture the weak second peak observed in proteins containing β-sheets, allowing for clear distinction between α-helical and β-sheet proteins. While the parametrization is specific to the CHARMM force field, the methodology presented can be readily applied to any empirical force field. PMID:24654732

  7. Simple Bond Cleavage

    SciTech Connect

    Gary S. Groenewold

    2005-08-01

    Simple bond cleavage is a class of fragmentation reactions in which a single bond is broken, without formation of new bonds between previously unconnected atoms. Because no bond making is involved, simple bond cleavages are endothermic, and activation energies are generally higher than for rearrangement eliminations. The rate of simple bond cleavage reactions is a strong function of the internal energy of the molecular ion, which reflects a loose transition state that resembles reaction products, and has a high density of accessible states. For this reason, simple bond cleavages tend to dominate fragmentation reactions for highly energized molecular ions. Simple bond cleavages have negligible reverse activation energy, and hence they are used as valuable probes of ion thermochemistry, since the energy dependence of the reactions can be related to the bond energy. In organic mass spectrometry, simple bond cleavages of odd electron ions can be either homolytic or heterolytic, depending on whether the fragmentation is driven by the radical site or the charge site. Simple bond cleavages of even electron ions tend to be heterolytic, producing even electron product ions and neutrals.

  8. The Utilization of Amide Groups To Expand and Functionalize Metal-Organic Frameworks Simultaneously.

    PubMed

    Lu, Zhiyong; Bai, Junfeng; Hang, Cheng; Meng, Fei; Liu, Wenlong; Pan, Yi; You, Xiaozeng

    2016-04-25

    A new stepwise ligand-elongation strategy by amide spacers is utilized to prepare isoreticularly high-porous metal-organic frameworks (MOFs), namely, quasi-mesoporous [Cu2 (PDBAD)(H2 O)]n (H4 PDBAD=5,5'-((4,4'-((pyridine-3,5-dicarbonyl)bis(azanediyl))bis(benzoyl))bis(azanediyl))diisophthalic acid; NJU-Bai22: NJU-Bai for Nanjing University Bai's group), and mesoporous [Cu2 (PABAD)(H2 O)]n (H4 PABAD=5,5'-((4,4'-((4,4'-((pyridine-3,5-dicarbonyl)bis(azanediyl))bis(benzoyl))bis (azanediyl))bis(benzoyl))bis(azanediyl))diisophthalic acid; NJU-Bai23). Compared with the prototypical MOF of [Cu2 (PDAD)(H2 O)]n (H4 PDAD=5,5'-(pyridine-3,5-dicarbonyl)bis(azanediyl)diisophthalic acid; NJU-Bai21, also termed as PCN-124), both MOFs exhibit almost the same CO2 adsorption enthalpy and CO2 selectivity values, and better capacity for CO2 storage under high pressure; these results make them promising candidate materials for CO2 capture and sequestration. Interestingly, this new method, in comparison with traditional strategies of using phenyl or triple-bond spacers, is easier and cheaper, resulting in a better ability to retain high CO2 affinity and selectivity in MOFs with large pores and high CO2 storage capacity. Additionally, it may lead to the high thermal stability of the MOFs and also their tolerance to water, which is related to the balance between the density of functional groups and pore sizes. Therefore, this strategy could provide new opportunities to explore more functionalized mesoporous MOFs with high performance. PMID:27031809

  9. Specificity and formation of unusual amino acids of an amide ligation strategy for unprotected peptides.

    PubMed

    Tam, J P; Rao, C; Liu, C F; Shao, J

    1995-03-01

    An important step in the recently developed ligation strategy known as domain ligation strategy to link unprotected peptide segments without activation is the ring formation between the C-terminal ester aldehyde and the N-terminal amino acid bearing a beta-thiol or beta-hydroxide. A new method was developed to define the specificity of this reaction using a dye-labeled alanyl ester aldehyde to react with libraries of 400 dipeptides which contained all dipeptide combinations of the 20 genetically coded amino acids. Three different ester aldehydes of the dye-labeled alanine: alpha-formylmethyl (FM), beta-formylethyl (FE), and beta,beta,beta-dimethyl and formylethyl esters (DFE), were examined. The DFE ester was overly hindered and reacted with N-terminal Cys dipeptides (Cys-X). Interestingly, it also reacted slowly with the sequences of X-Gly where Gly was the second amino acid and the X-Gly amide bond participated in the ring formation. Although the FE ester reacted similarly as the FM ester in the ring formation, the subsequent O,N-acyl transfer was at least 30-fold slower than those of the FM-ester. The FM alpha-formyl methyl ester was the most suitable ester and was reactive with dipeptides of six N-terminal amino acids: Cys, Thr, Trp, Ser, His and Asn. The order and extent of their reactivity were highly dependent on pH, solvent and neighboring participation by the adjacent amino acid. In general, they could be divided into three categories. (1) N-Terminal Cys and Thr were the most reactive.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7775013

  10. Power Harvesting from Rotation?

    ERIC Educational Resources Information Center

    Chicone, Carmen; Feng, Z. C.

    2008-01-01

    We show the impossibility of harvesting power from rotational motions by devices attached to the rotating object. The presentation is suitable for students who have studied Lagrangian mechanics. (Contains 2 figures.)

  11. Chemo- and Stereoselective Transition-Metal-Free Amination of Amides with Azides

    PubMed Central

    2016-01-01

    The synthesis of α-amino carbonyl/carboxyl compounds is a contemporary challenge in organic synthesis. Herein, we present a stereoselective α-amination of amides employing simple azides that proceeds under mild conditions with release of nitrogen gas. The amide is used as the limiting reagent, and through simple variation of the azide pattern, various differently substituted aminated products can be obtained. The reaction is fully chemoselective for amides even in the presence of esters or ketones and lends itself to preparation of optically enriched products. PMID:27350334

  12. Exendin-4 agonist and exendin(9-39)amide antagonist of the GLP-1(7-36)amide effects in liver and muscle.

    PubMed

    Alcántara, A I; Morales, M; Delgado, E; López-Delgado, M I; Clemente, F; Luque, M A; Malaisse, W J; Valverde, I; Villanueva-Peñacarrillo, M L

    1997-05-01

    The GLP-1 structurally related peptides exendin-4 and exendin(9-39)amide were found to act, in rat liver and skeletal muscle, as agonist and antagonist, respectively, of the GLP-1(7-36)amide effects on glucose metabolism. Thus, like GLP-1(7-36)amide, exendin-4 increased glycogen synthase a activity and glucose incorporation into glycogen in both tissues and also stimulated exogenous D-glucose utilization and oxidation in muscle. These effects of GLP-1(7-36)amide and exendin-4 were inhibited by exendin(9-39)amide. Our findings provide further support to the proposed use of GLP-1, or exendin-4, as a tool in the treatment of diabetes mellitus. Thus, in addition to the well-known insulinotropic action of the peptides, they act both in liver and in muscle in a manner most suitable for restoration of glucose homeostasis, with emphasis on their positive effects upon glycogen synthesis in the two tissues and on the stimulation of exogenous glucose catabolism in muscle. PMID:9143346

  13. The role of C-terminal amidation in the membrane interactions of the anionic antimicrobial peptide, maximin H5.

    PubMed

    Dennison, Sarah R; Mura, Manuela; Harris, Frederick; Morton, Leslie H G; Zvelindovsky, Andrei; Phoenix, David A

    2015-05-01

    Maximin H5 is an anionic antimicrobial peptide from amphibians, which carries a C-terminal amide moiety, and was found to be moderately haemolytic (20%). The α-helicity of the peptide was 42% in the presence of lipid mimics of erythrocyte membranes and was found able to penetrate (10.8 mN m(-1)) and lyse these model membranes (64 %). In contrast, the deaminated peptide exhibited lower levels of haemolysis (12%) and α-helicity (16%) along with a reduced ability to penetrate (7.8 m Nm(-1)) and lyse (55%) lipid mimics of erythrocyte membranes. Taken with molecular dynamic simulations and theoretical analysis, these data suggest that native maximin H5 primarily exerts its haemolytic action via the formation of an oblique orientated α-helical structure and tilted membrane insertion. However, the C-terminal deamination of maximin H5 induces a loss of tilted α-helical structure, which abolishes the ability of the peptide's N-terminal and C-terminal regions to H-bond and leads to a loss in haemolytic ability. Taken in combination, these observations strongly suggest that the C-terminal amide moiety carried by maximin H5 is required to stabilise the adoption of membrane interactive tilted structure by the peptide. Consistent with previous reports, these data show that the efficacy of interaction and specificity of maximin H5 for membranes can be attenuated by sequence modification and may assist in the development of variants of the peptide with the potential to serve as anti-infectives. PMID:25640709

  14. Rotations with Rodrigues' Vector

    ERIC Educational Resources Information Center

    Pina, E.

    2011-01-01

    The rotational dynamics was studied from the point of view of Rodrigues' vector. This vector is defined here by its connection with other forms of parametrization of the rotation matrix. The rotation matrix was expressed in terms of this vector. The angular velocity was computed using the components of Rodrigues' vector as coordinates. It appears…

  15. Mechanism of rotational relaxation.

    NASA Technical Reports Server (NTRS)

    Polanyi, J. C.; Woodall, K. B.

    1972-01-01

    A model is presented which describes the characteristic pattern of relaxation of a nonthermal rotational distribution of hydrogen halide, peaked initially at high rotational quantum number J, to a thermal distribution without generating a peak at intermediate J. A method for correcting infrared chemiluminiscence data for modest rotational relaxation is also suggested.

  16. Weak bond screening system

    NASA Astrophysics Data System (ADS)

    Chuang, S. Y.; Chang, F. H.; Bell, J. R.

    Consideration is given to the development of a weak bond screening system which is based on the utilization of a high power ultrasonic (HPU) technique. The instrumentation of the prototype bond strength screening system is described, and the adhesively bonded specimens used in the system developmental effort are detailed. Test results obtained from these specimens are presented in terms of bond strength and level of high power ultrasound irradiation. The following observations were made: (1) for Al/Al specimens, 2.6 sec of HPU irradiation will screen weak bond conditions due to improper preparation of bonding surfaces; (2) for composite/composite specimens, 2.0 sec of HPU irradiation will disrupt weak bonds due to under-cured conditions; (3) for Al honeycomb core with composite skin structure, 3.5 sec of HPU irradiation will disrupt weak bonds due to bad adhesive or oils contamination of bonding surfaces; and (4) for Nomex honeycomb with Al skin structure, 1.3 sec of HPU irradiation will disrupt weak bonds due to bad adhesive.

  17. Light metal alanates and amides for reversible hydrogen storage applications

    NASA Astrophysics Data System (ADS)

    Lu, Jun

    Hydrogen is undoubtedly one of the key alternatives to replace petroleum products as a clean energy carrier for both transportation and stationary applications. Although there have been numerous material systems studied as potential candidates for hydrogen storage applications, none of the materials known to date has demonstrated sufficient hydrogen capacity or efficiency in the required operating temperature ranges. There are still considerable opportunities for the discovery of new materials that could lead to advances in science as well as commercial technologies in this area. In this study, two new hydrogen-storage systems, i.e. alanate/amide and LiMgN, are investigated. Firstly, we found that if LiAlH4 and LiNH2 are allowed to react in a proper molar ratio, the LiH that forms as an intermediate product of the dehydrogenation of LiAlH4 can subsequently react with LiNH2 to release H2 at temperatures below 300°C, much lower than that without LiNH2. However, this system is only partially reversible. The difficulty of reversing the reaction is attributed to the irreversibility of the dehydrogenation reaction of LiAlH4 to Li3AlH6. Further experimental results showed that the reversible storage capacity of the combined alanate/amide material system is increased to 7.0 wt% under 300°C, if LiNH2 were reacted with Li3AlH6, instead of LiAlH4, in a 3:1 molar ratio. We also found that the re-formation of Li3AlH 6 depends strongly on the heating rate during the hydrogenation process. To improve the kinetic and thermodynamic properties of the Li-Al-N-H systems, the reaction between Li3AlH6 and Mg(NH2) 2 was studied based on the understanding of the destabilizing effect of amide on alanates. The Li-Al-Mg-N-H system would have better kinetic properties than the Li-Al-N-H system due to the addition of Mg, based on the published research results on the comparison between the Li-Mg-N-H and Li-N-H systems. A reversible 6.2 wt% H2 storage capacity has been demonstrated under the

  18. Concerted Amidation of Activated Esters: Reaction Path and Origins of Selectivity in the Kinetic Resolution of Cyclic Amines via N-Heterocyclic Carbenes and Hydroxamic Acid Cocatalyzed Acyl Transfer

    PubMed Central

    2015-01-01

    The N-heterocyclic carbene and hydroxamic acid cocatalyzed kinetic resolution of cyclic amines generates enantioenriched amines and amides with selectivity factors up to 127. In this report, a quantum mechanical study of the reaction mechanism indicates that the selectivity-determining aminolysis step occurs via a novel concerted pathway in which the hydroxamic acid plays a key role in directing proton transfer from the incoming amine. This modality was found to be general in amide bond formation from a number of activated esters including those generated from HOBt and HOAt, reagents that are broadly used in peptide coupling. For the kinetic resolution, the proposed model accurately predicts the faster reacting enantiomer. A breakdown of the steric and electronic control elements shows that a gearing effect in the transition state is responsible for the observed selectivity. PMID:25050843

  19. Influence of superheated water on the hydrogen bonding and crystallography of piperazine-based (Co)polyamides.

    PubMed

    Vinken, Esther; Terry, Ann E; Spoelstra, Anne B; Koning, Cor E; Rastogi, Sanjay

    2009-05-01

    Here we demonstrate that superheated water is a solvent for polyamide 2,14 and piperazine-based copolyamides up to a piperazine content of 62 mol %. The incorporation of piperazine allows for a variation of the hydrogen bond density without altering the crystal structure (i.e., the piperazine units cocrystallize with the PA2,14 units (Hoffmann, S.; Vanhaecht, B.; Devroede, J.; Bras, W.; Koning, C. E.; Rastogi, S. Macromolecules 2005, 38, 1797-1803). It is shown that the crystallization of PA2,14 from superheated water greatly influences the crystal structure. Water molecules incorporated in the PA2,14 crystal lattice cause a slip on the hydrogen bonded planes, resulting in a coexistence of a triclinic and a monoclinic crystal structure. On heating above the Brill transition, the water molecules exit from the lattice, restoring the triclinic crystal structure. With increasing piperazine content, and hence decreasing hydrogen bond density, the dissolution temperature decreases. It is only possible to grow single crystals from superheated water up to a piperazine content of 62 mol %. For these single crystals, the incorporation of water molecules in the vicinity of the amide group is seen by the presence of COO- stretch vibrations with FTIR spectroscopy. These vibrations disappear on heating above the Brill transition temperature, and the water molecules leave the amide groups. For copolyamides with more than 62 mol % piperazine, no Brill transition is observed, no single crystals can be grown from water, and no water molecules are observed in the vicinity of the amide groups (Vinken, E.; Terry, A. E.; Hoffmann, S.; Vanhaecht, B.; Koning, C. E.; Rastogi, S. Macromolecules 2006, 39, 2546-2552). The high piperazine content (co)polyamides have fewer hydrogen bond donors and are therefore less likely to have interactions with the water molecules. This work demonstrates the relation among the Brill transition, the dissolution of polyamide in superheated water, and its

  20. Hydrogen Bond-Assisted Supramolecular Self-Assembly of Doubly Discotic Supermolecules Based on Porphyrin and Triphenylene

    SciTech Connect

    Miao, J.; Zhu, L

    2010-01-01

    Hydrogen bonding is a powerful driving force for the supramolecular self-assembly of discotic mesogens, and molecular shape also plays an important role in such systems. To study these effects, doubly discotic supermolecules have been synthesized by linking a meso-tetraphenylporphine-4,4{prime},4{double_prime},4(triple prime)-tetracarboxylic acid (Py) core with four triphenylenes (Tp) arms via either amide or ester bonds. The spacer length between the Py core and Tp disks was C6 and C10, and the alkyl arm length in the Tp disks was C5 and C12, respectively. Compared to the ester-linked Py(Tp){sub 4} supermolecules, the amide-linked samples exhibited rich crystalline and liquid-crystalline phases, suggesting that the intracolumnar hydrogen-bonding among trans amide bonds was the primary driving force for the self-assembly. X-ray diffraction (XRD) was used to understand the supramolecular self-assembly of the amide-linked Py(Tp){sub 4} doubly discotic supermolecules. When the spacer length was no shorter than or similar to the triphenylene alkyl arm length, a rectangular boardlike molecular shape was adopted and thus lamellar structures were obtained. When the spacer length was much shorter than the triphenylene alkyl arms, an ellipsoidal overall molecular shape resulted, and thus a regular columnar phase was obtained. From this study, we speculated that hydrogen-bond-induced microphase separation between moieties with different electron affinities in doubly discotic supermolecules may be useful for the practical applications of organic electronics.