Science.gov

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.

  3. 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

  4. 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.

  5. Barriers to rotation adjacent to double bonds. 3. The C-O barrier in formic acid, methyl formate, acetic acid, and methyl acetate. The origin of ester and amide resonance

    SciTech Connect

    Wiberg, K.B.; Laidig, K.E.

    1987-09-30

    The structures of the rotamers about the C-O bonds of formic acid, methyl formate, acetic acid, and methyl acetate were calculated by using the 6-31G* basis set and complete geometrical relaxation. Large basis sets (6-311+G**) and correction for electron correlation were needed in order to obtain calculated barriers that were in good agreement with the available experimental data. The factors that control the geometry at a carbonyl group are considered, and it is shown that an analysis in terms of bond path angles leads to a direct connection with electronegativity. The nature of the interaction between an amino group and a carbonyl, as in an amide, is examined and shown not to involve charge transfer from the nitrogen to the carbonyl oxygen, but rather it involves charge transfer between carbon and nitrogen. The origin of the rotational barrier in esters and of the difference in energy between the E and Z conformers is discussed.

  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. 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.

  8. 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.

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

    PubMed

    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. PMID:26200342

  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. Macrocycle Synthesis by Chloride-Templated Amide Bond Formation.

    PubMed

    Martí-Centelles, Vicente; Burguete, M Isabel; Luis, Santiago V

    2016-03-01

    A new family of pseudopeptidic macrocyclic compounds has been prepared involving an anion-templated amide bond formation reaction at the macrocyclization step. Chloride anion was found to be the most efficient template in the macrocyclization process, producing improved macrocyclization yields with regard to the nontemplated reaction. The data suggest a kinetic effect of the chloride template, providing an appropriate folded conformation of the open-chain precursor and reducing the energy barrier for the formation of the macrocyclic product. PMID:26820908

  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. 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

  14. Strong Bonds Made Weak: Towards the General Utility of Amides as Synthetic Modules.

    PubMed

    Ruider, Stefan A; Maulide, Nuno

    2015-11-16

    Breaking good: The amide bond is widely recognized as the strongest bond among the carboxylic acid derivatives. Therefore, the potential of amides to serve as synthetic building blocks has remained mostly untapped thus far. This Highlight describes a recent breakthrough that enables the catalytic conversion of amides into esters for the first time. PMID:26460213

  15. Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C-N Rotational Pathway.

    PubMed

    Szostak, Roman; Aubé, Jeffrey; Szostak, Michal

    2015-08-21

    Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.

  16. 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.

  17. Instability of Amide Bond Comprising the 2-Aminotropone Moiety: Cleavable under Mild Acidic Conditions.

    PubMed

    Balachandra, Chenikkayala; Sharma, Nagendra K

    2015-08-21

    An unusual hydrolysis/solvolysis of the classical acyclic amide bond, derived from N-troponylaminoethylglycine (Traeg) and α-amino acids, is described under mild acidic conditions. The reactivity of this amide bond is possibly owed to the protonation of the troponyl carbonyl functional group. The results suggest that the Traeg amino acid is a potential candidate for protecting and caging of the amine functional group of bioactive molecules via a cleavable amide bond.

  18. Yttrium (amidate) complexes for catalytic C-N bond formation. Rapid, room temperature amidation of aldehydes.

    PubMed

    Thomson, Jaclyn A; Schafer, Laurel L

    2012-07-14

    Yttrium (amidate) precatalysts are highly active for the mild amidation of aldehydes with amines. Reactions occur at room temperature within 5 min in up to 98% isolated yield. These rare-earth systems are effective for this transformation in the absence of supplementary heat, light, base, or oxidants. The reaction proceeds with functionalized amines and/or aldehydes. A comparison of various amidate precatalysts in combination with reaction monitoring suggests that the targeted amide products formed during the reaction promote the formation of alternative catalytically active amidate species in situ.

  19. Rhodium(III)-Catalyzed Amidation of Unactivated C(sp(3) )-H Bonds.

    PubMed

    Wang, He; Tang, Guodong; Li, Xingwei

    2015-10-26

    Nitrogenation by direct functionalization of C-H bonds represents an important strategy for constructing C-N bonds. Rhodium(III)-catalyzed direct amidation of unactivated C(sp(3) )-H bonds is rare, especially under mild reaction conditions. Herein, a broad scope of C(sp(3) )-H bonds are amidated under rhodium catalysis in high efficiency using 3-substituted 1,4,2-dioxazol-5-ones as the amide source. The protocol broadens the scope of rhodium(III)-catalyzed C(sp(3) )-H activation chemistry, and is applicable to the late-stage functionalization of natural products.

  20. 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

  1. Metal amides as the simplest acid/base catalysts for stereoselective carbon-carbon bond-forming reactions.

    PubMed

    Yamashita, Yasuhiro; Kobayashi, Shū

    2013-07-15

    In this paper, new possibilities for metal amides are described. Although typical metal amides are recognized as strong stoichiometric bases for deprotonation of inert or less acidic hydrogen atoms, transition-metal amides, namely silver and copper amides, show interesting abilities as one of the simplest acid/base catalysts in stereoselective carbon-carbon bond-forming reactions.

  2. 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.

  3. Hydrogen bond stabilities in membrane-reconstituted alamethicin from amide-resolved hydrogen-exchange measurements.

    PubMed Central

    Dempsey, C E; Handcock, L J

    1996-01-01

    Amide-resolved hydrogen-deuterium exchange-rate constants were measured for backbone amides of alamethicin reconstituted in dioleoylphosphatidylcholine vesicles by an exchange-trapping method combined with high-resolution nuclear magnetic resonance spectroscopy. In vesicles containing alamethicin at molar ratios between 1:20 and 1:100 relative to lipid, the exchange-rate constants increased with increasing volume of the D20 buffer in which the vesicles were suspended, indicating that exchange under these conditions is dominated by partitioning of the peptide into the aqueous phase. This was supported by observation of a linear relationship between the exchange-rate constants for amides in membrane-reconstituted alamethicin and those for amides in alamethicin dissolved directly into D2O buffer. Significant protection of amides from exchange with D2O buffer in membrane-reconstituted alamethicin is interpreted in terms of stabilization by helical hydrogen bonding. Under conditions in which amide exchange occurred by partitioning of the peptide into solution, only lower limits for hydrogen-bond stabilities in the membrane were determined; all the potentially hydrogen-bonded amides of alamethicin are at least 1000-fold exchange protected in the membrane-bound state. When partitioning of alamethicin into the aqueous phase was suppressed by hydration of reconstituted vesicles in a limiting volume of water [D2O:dioleoylphosphatidylcholine:alamethicin; 220:1:0.05; (M:M:M)], the exchange-protection factors exhibited helical periodicity with highly exchange-protected, and less well-protected, amides on the nonpolar and polar helix faces, respectively. The exchange data indicate that, under the conditions studied, alamethicin adopts a stable helical structure in DOPC bilayers in which all the potentially hydrogen-bonded amides are stabilized by helical hydrogen bonds. The protection factors define the orientation of the peptide helix with respect to an aqueous phase, which is

  4. Activation of amide N-H bonds by organotransition metal complexes

    SciTech Connect

    Schaad, D.R.

    1992-01-01

    This research was aimed at developing new homogeneous transition metal hydroamination catalysts, specifically for hydroamination reactions involving the addition of amides to olefins. New iron-, ruthenium-, palladium- and platinum-amido complexes were formed via amide N-H bond activation reactions to zerovalent and divalent organotransition metal complexes. Complexes of the general formula trans-MW(amido) (diphosphine)[sub 2] were synthesized by reaction of amides with FeH(C[sub 6]H[sub 4]PPhCH[sub 2]CH[sub 2]PPh[sub 2]) (dppe) and cis-RuHNp(dmpe)[sub 2]. Photolysis of cis-FeH[sub 2](dmpe)[sub 2] or Pt(C[sub 2]O[sub 4] (PEt[sub 3])[sub 2] in the presence of amides yielded trans-FeH(amido)(dmple)[sub 2] and trans-PtH (amido) IPEt[sub 3]) products. Reactions of amides with cis-M(PEtt[sub 3])[sub 2]Me[sub 2] yielded compounds with the general formula M(amido)Me(PEt[sub 3])[sub 2] (M = Pd, Pt). The reaction of M(diphosphine)Me[sub 2] complexes with amides produced compounds with the general formula M(amido)Me(diphosphine) (M = Pd, Pt). Reaction of amides with PtMe[sub 2](COD) yielded complexes with the general formula PtMe(amido)(COD). The compounds were characterized by multinuclear NMR spectroscopy. The reactions were proposed to occur by two routes: oxidative addition of the amid eN-H bond to the metal complex or direct protonation of the metal complex by the N-H bond of the amide. The rate of formation and the stability of the metal-amido products depended on the nature of the metal complex and the amide employed. Only acidic amides reacted with the iron complexes. For the thermal reactions of amides with the metal complexes, the reactions proceeded to completion faster as the acidity of the amide was increased. The new iron-, ruthenium-, palladium- and platinum-amido complexes were inert to further reaction.

  5. 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

  6. 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

  7. 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.

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

    PubMed

    Hummel, Joshua R; Ellman, Jonathan A

    2015-05-15

    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 a broad isocyanate scope and good functional-group compatibility and has been performed on gram scale.

  9. 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

  10. 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

  11. 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

  12. 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 ().

  13. 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

  14. 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

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

    NASA Astrophysics Data System (ADS)

    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 1H NMR, 13C NMR, IR and X-ray single-crystal diffraction. The carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in a centrosymmetric R22(8) ring motifs for BAA-Br and BAA-Cl. However, no carboxylic acid group forms classic Osbnd H ⋯ 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 0.5-3.8 kcal/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 4 kcal/mol.

  16. 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

  17. Role of an amide bond for self-assembly of surfactants.

    PubMed

    Bordes, Romain; Tropsch, Juergen; Holmberg, Krister

    2010-03-01

    Self-assembly in solution and adsorption at the air-water interface and at solid surfaces were investigated for two amino-acid-based surfactants with conductimetry, NMR, tensiometry, quartz crystal microbalance with monitoring of the dissipation (QCM-D), and surface plasmon resonance (SPR). The surfactants studied were sodium N-lauroylglycinate and sodium N-lauroylsarcosinate, differing only in a methyl group on the amide nitrogen for the sarcosinate. Thus, the glycinate but not the sarcosinate surfactant is capable of forming intermolecular hydrogen bonds via the amide group. It was found that the amide bond, N-methylated or not, gave a substantial contribution to the hydrophilicity of the amphiphile. The ability to form intermolecular hydrogen bonds led to tighter packing at the air-water interface and at a hydrophobic surface. It also increased the tendency for precipitation as an acid-soap pair on addition of acid. Adsorption of the surfactants at a gold surface was also investigated and gave unexpected results. The sarcosine-based surfactant seemed to give bilayer adsorption, while the glycine derivative adsorbed as a monolayer.

  18. Iridium(III)-Catalyzed Regioselective Intermolecular Unactivated Secondary Csp(3) -H Bond Amidation.

    PubMed

    Xiao, Xinsheng; Hou, Cheng; Zhang, Zhenhui; Ke, Zhuofeng; Lan, Jianyong; Jiang, Huanfeng; Zeng, Wei

    2016-09-19

    For the first time, a highly regioselective intermolecular sulfonylamidation unactivated secondary Csp(3) -H bond has been achieved using Ir(III) catalysts. The introduced N,N'-bichelating ligand plays a crucial role in enabling iridium-nitrene insertion into a secondary Csp(3) -H bond via an outer-sphere pathway. Mechanistic studies and density functional theory (DFT) calculations demonstrated that a two-electron concerted nitrene insertion was involved in this Csp(3) -H amidation process. This method tolerates a broad range of linear and branched-chain N-alkylamides, and provides efficient access to diverse γ-sulfonamido-substituted aliphatic amines. PMID:27561950

  19. Electrostatic interaction of pi-acidic amides with hydrogen-bond acceptors.

    PubMed

    Li, Yi; Snyder, Lawrence B; Langley, David R

    2003-10-01

    Interactions between N-methylacetamide (NMA) and N-methylated derivatives of uracil, isocyanurate and barbituric acid have been studied using ab initio methods at the local MP2/6-31G** level of theory. The results were compared to similar interactions between the oxygen atom of NMA and the pi-clouds of perfluorobenzene, quinone and trimethyltriazine. The pi-acidic amides of isocyanurate and barbituric acid were found to interact with a hydrogen bond acceptor primarily through electrostatic attractions. These groups may be used as alternatives of a hydrogen bond donor to complement a hydrogen bond acceptor or an anion in molecular recognition and drug design. Examples of such interactions were identified through a search of the CSD database.

  20. Analysis of hydrogen bonds in peptides, based on the hydration affinity of amides

    NASA Astrophysics Data System (ADS)

    Perczel, András; Lengyel, Istvan; Mantsch, Henry H.; Fasman, Gerald D.

    1993-08-01

    The difference in the affinity for water of peptide groups embedded in different molecular environments was investigated. The chemical shift of an amide proton is sensitive to conformational variations, as well as to changes in the molecular environment [D.S. Wishat, B.D. Sykes and F.M. Richards, J. Mol. Biol., 222 (1991) 311-333]. Therefore, if the conformational motions are minimized or excluded, the observed changes in the chemical shift can simply be related to the environmental effects. The conformation(s) of the cyclic β-turn models studied in this work has been previously reported using X-ray, NMR, circular dichroism, and (FT-IR) spectroscopic methods, as well as MD calculations. [M. Hollósi, K.E. Köver, S. Holly, L. Radics and G.D. Fasman, Biopolymers, 26 (1987) 1527-1572; A. Perczel, M. Hollósi, B.M. Foxman and G.D. Fasman, J. Am. Chem. Soc., 113 (1991) 9772-9784; and H.H. Mantsch, A. Perczel, M. Hollósi and G.D. Fasman, Biopolymers, 33 (1993) 201-207]. The backbone of the cyclo[(δ)Ava—Gly—Pro—Aaa—Gly] (where Aaa = Ser(O tBu), Ser or Thr(O tBu), and δ(Ava) is δ-aminovaleric acid) compounds was found to be rigidly incorporated in the structure and to contain two intramolecular hydrogen bonds. These β-turn models also include one (or two) "free" amide group(s) that are not involved in any type of interaction. The "water titration" of these amide groups in acetonitrile, where they are involved in various degrees of hydrogen bonding, revealed their molecular environment. Owing to the rigidity of these structures, the observed changes in the amide proton chemical shifts, during titration were attributed to their involvement in hydrogen bonding. This was confirmed by monitoring the water titration simultaneously with FT-IR spectroscopy. The phenomenon described here, with the proposed characterization of the investigated peptide/water system, comprise an improvement in the NMR method for analyzing the hydrogen bonding of small rigid peptides.

  1. 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.

  2. 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.

  3. 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.

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

    DOE PAGES

    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

  5. Synthesis, Anti-HCV, Antioxidant and Reduction of Intracellular Reactive Oxygen Species Generation of a Chlorogenic Acid Analogue with an Amide Bond Replacing the Ester Bond.

    PubMed

    Wang, Ling-Na; Wang, Wei; Hattori, Masao; Daneshtalab, Mohsen; Ma, Chao-Mei

    2016-06-08

    Chlorogenic acid is a well known natural product with important bioactivities. It contains an ester bond formed between the COOH of caffeic acid and the 3-OH of quinic acid. We synthesized a chlorogenic acid analogue, 3α-caffeoylquinic acid amide, using caffeic and quinic acids as starting materials. The caffeoylquinc acid amide was found to be much more stable than chlorogenic acid and showed anti-Hepatitis C virus (anti-HCV) activity with a potency similar to chlorogenic acid. The caffeoylquinc acid amide potently protected HepG2 cells against oxidative stress induced by tert-butyl hydroperoxide.

  6. Synthesis, Anti-HCV, Antioxidant and Reduction of Intracellular Reactive Oxygen Species Generation of a Chlorogenic Acid Analogue with an Amide Bond Replacing the Ester Bond.

    PubMed

    Wang, Ling-Na; Wang, Wei; Hattori, Masao; Daneshtalab, Mohsen; Ma, Chao-Mei

    2016-01-01

    Chlorogenic acid is a well known natural product with important bioactivities. It contains an ester bond formed between the COOH of caffeic acid and the 3-OH of quinic acid. We synthesized a chlorogenic acid analogue, 3α-caffeoylquinic acid amide, using caffeic and quinic acids as starting materials. The caffeoylquinc acid amide was found to be much more stable than chlorogenic acid and showed anti-Hepatitis C virus (anti-HCV) activity with a potency similar to chlorogenic acid. The caffeoylquinc acid amide potently protected HepG2 cells against oxidative stress induced by tert-butyl hydroperoxide. PMID:27338318

  7. Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion.

    PubMed

    Palermo, Giulia; Campomanes, Pablo; Cavalli, Andrea; Rothlisberger, Ursula; De Vivo, Marco

    2015-01-22

    Herein, we combined classical molecular dynamics (MD) and quantum mechanical/molecular mechanics (QM/MM) simulations to unravel the whole catalytic cycle of fatty acid amide hydrolase (FAAH) in complex with anandamide, the main neurotransmitters involved in the control of pain. While microsecond MD simulations of FAAH in a realistic membrane/water environment provided a solid model for the reactant state of the enzymatic complex (Palermo et al. J. Chem. Theory Comput. 2013, 9, 1202-1213.), QM/MM simulations depict now a highly concerted two-step catalytic mechanism characterized by (1) acyl-enzyme formation after hydrolysis of the substrate amide bond and (2) deacylation reaction with restoration of the catalytic machinery. We found that a crucial event for anandamide hydrolysis is the inversion of the reactive nitrogen of the scissile amide bond, which occurs during the acylation rate-limiting step. We show that FAAH uses an exquisite catalytic strategy to induce amide bond distortion, reactive nitrogen inversion, and amide bond hydrolysis, promoting catalysis to completion. This new strategy is likely to be of general applicability to other amidases/peptidases that show similar catalytic site architectures, providing crucial insights for de novo enzyme design or drug discovery efforts.

  8. Energy relaxation of the amide-I mode in hydrogen-bonded peptide units: a route to conformational change.

    PubMed

    Pouthier, Vincent

    2008-02-14

    A one-site Davydov model involving a C[Double Bond]O group engaged in a hydrogen bond is used to study the amide-I relaxation due to Fermi resonances with a bath of intramolecular normal modes. In the amide-I ground state, the hydrogen bond behaves as a harmonic oscillator whose eigenstates are phonon number states. By contrast, in the amide-I first excited state, the hydrogen bond experiences a linear distortion so that the eigenstates are superimpositions of number states. By assuming the hydrogen bond in thermal equilibrium at biological temperature, it is shown that the amide-I excitation favors the population of these excited states and the occurrence of coherences. Due to the interaction with the bath, the vibron decays according to an exponential or a biexponential law depending on whether the Fermi resonance is wide or narrow. Therefore, each excited state relaxes over a set of number states according to specific pathways. The consequence is twofold. First, the relaxation leads to a redistribution of the number state population which differs from the initial Boltzmann distribution. Then, it allows for coherence transfers so that, although the vibron has disappeared, the hydrogen keeps the memory of its initial distortion and it develops free oscillations.

  9. 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.

  10. 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

  11. Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries.

    PubMed

    Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario

    2016-08-01

    DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.

  12. 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.

  13. Discovery of amide (peptide) bond synthetic activity in Acyl-CoA synthetase.

    PubMed

    Abe, Tomoko; Hashimoto, Yoshiteru; Hosaka, Hideaki; Tomita-Yokotani, Kaori; Kobayashi, Michihiko

    2008-04-25

    Acyl-CoA synthetase, which is one of the acid-thiol ligases (EC 6.2.1), plays key roles in metabolic and regulatory processes. This enzyme forms a carbon-sulfur bond in the presence of ATP and Mg(2+), yielding acyl-CoA thioesters from the corresponding free acids and CoA. This enzyme belongs to the superfamily of adenylate-forming enzymes, whose three-dimensional structures are analogous to one another. We here discovered a new reaction while studying the short-chain acyl-CoA synthetase that we recently reported (Hashimoto, Y., Hosaka, H., Oinuma, K., Goda, M., Higashibata, H., and Kobayashi, M. (2005) J. Biol. Chem. 280, 8660-8667). When l-cysteine was used as a substrate instead of CoA, N-acyl-l-cysteine was surprisingly detected as a reaction product. This finding demonstrated that the enzyme formed a carbon-nitrogen bond (EC 6.3.1 acid-ammonia (or amide) ligase (amide synthase); EC 6.3.2 acid-amino acid ligase (peptide synthase)) comprising the amino group of the cysteine and the carboxyl group of the acid. N-Acyl-d-cysteine, N-acyl-dl-homocysteine, and N-acyl-l-cysteine methyl ester were also synthesized from the corresponding cysteine analog substrates by the enzyme. Furthermore, this unexpected enzyme activity was also observed for acetyl-CoA synthetase and firefly luciferase, indicating the generality of the new reaction in the superfamily of adenylate-forming enzymes.

  14. Simultaneous determination of interfacial molarities of amide bonds, carboxylate groups, and water by chemical trapping in micelles of amphiphiles containing peptide bond models.

    PubMed

    Zhang, Yongliang; Romsted, Laurence S; Zhuang, Lanzhen; de Jong, Sander

    2013-01-15

    Chemical trapping is a powerful approach for obtaining experimental estimates of interfacial molarities of weakly basic nucleophiles in the interfacial regions of amphiphile aggregates. Here, we demonstrate that the chemical probe 4-hexadecyl-2,6-dimethylbenzenediazonium ion (16-ArN(2)(+)) reacts competitively with interfacial water, with the amide carbonyl followed by cleavage of the headgroups from the tail at the amide oxygen, and with the terminal carboxylate groups in micelles of two N-acyl amino-acid amphiphiles, sodium N-lauroylsarcosinate (SLS) and sodium N-lauroylglycinate (SLG), simple peptide bond model amphiphiles. Interfacial molarities (in moles per liter of interfacial volume) of these three groups were obtained from product yields, assuming that selectivity toward a particular nucleophile compared to water is the same in an aqueous reference solution and in the interfacial region. Interfacial carboxylate group molarities are ~1.5 M in both SLS and SLG micelles, but the concentration of the amide carbonyl for SLS micelles is ~4.6-5 times less (ca. 0.7 M) than that of SLG micelles (~3 M). The proton on the secondary N of SLG helps solubilize the amide bond in the aqueous region, but the methyl on the tertiary N of SLS helps solubilize the amide bond in the micellar core, reducing its reaction with 16-ArN(2)(+). Application of chemical trapping to proteins in membrane mimetic interfaces should provide insight into the topology of the protein within the interface because trapping of the amide carbonyl and cleavage at the C-N bond occurs only within the interface, and fragment characterization marks those peptide bonds located within the interface.

  15. 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.

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

    PubMed

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

    2009-10-01

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

  17. 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

  18. Atomic Level Distributed Strain within Graphene Divacancies from Bond Rotations.

    PubMed

    Chen, Qu; Robertson, Alex W; He, Kuang; Gong, Chuncheng; Yoon, Euijoon; Lee, Gun-Do; Warner, Jamie H

    2015-08-25

    Vacancy defects play an important role in influencing the properties of graphene, and understanding their detailed atomic structure is crucial for developing accurate models to predict their impact. Divacancies (DVs) are one of the most common defects in graphene and can take three different structural forms through various sequences of bond rotations to minimize the energy. Using aberration-corrected transmission electron microscopy with monochromation of the electron source, we resolve the position of C atoms in graphene and measure the C-C bond lengths within the three DVs, enabling a map of bond strain to be generated. We show that bond rotations reduce the maximum single bond strain reached within a DV and help distribute the strain over a larger number of bonds to minimize the peak magnitude.

  19. N-methylation of the amide bond by methyltransferase asm10 in ansamitocin biosynthesis.

    PubMed

    Wu, Yingying; Kang, Qianjin; Shang, Guangdong; Spiteller, Peter; Carroll, Brian; Yu, Tin-Wein; Su, Wenjin; Bai, Linquan; Floss, Heinz G

    2011-07-25

    Ansamitocins are potent antitumor agents produced by Actinosynnema pretiosum. As deduced from their structures, an N-methylation on the amide bond is required among the various modifications. The protein encoded by asm10 belongs to the SAM-dependent methyltransferase family. Through gene inactivation and complementation, asm10 was proved to be responsible for the N-methylation of ansamitocins. Asm10 is a 33.0 kDa monomer, as determined by gel filtration. By using N-desmethyl-ansamitocin P-3 as substrate, the optimal temperature and pH for Asm10 catalysis were determined to be 32 °C and 10.0, respectively. Asm10 also showed broad substrate flexibility toward other N-desmethyl-ansamycins and synthetic indolin-2-ones. Through site-directed mutagenesis, Asp154 and Leu155 of Asm10 were confirmed to be essential for its catalysis, possibly through the binding of SAM. The characterization of this unique N-methyltransferase has enriched the toolbox for engineering N-methylated derivatives from both natural and synthetic compounds; this will allow known potential drugs to be modified.

  20. 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

  1. Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation.

    PubMed

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

    2012-04-01

    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.

  2. 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

  3. 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.

  4. 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.

  5. Thermal-sensitive viscosity transition of elongated micelles induced by breaking intermolecular hydrogen bonding of amide groups.

    PubMed

    Morita, Clara; Imura, Yoshiro; Ogawa, Tetsuya; Kurata, Hiroki; Kawai, Takeshi

    2013-05-01

    A heat-induced viscosity transition of novel worm-like micelles of a long alkyl-chain amidoamine derivative (C18AA) bearing intermolecular hydrogen-bonding group was investigated by cryo-TEM, FT-IR, and rheological measurements. At lower temperature, C18AA forms straight elongated micelles with a length on the order of micrometers due to strong intermolecular hydrogen-bonded packing of the amide groups, although the micelles rarely entangle and have low value of zero-shear viscosity. The straight elongated micelles likely became flexible and underwent a morphological transition from straight structure to worm-like structure at a certain temperature, which caused a drastic increase in viscosity due to entanglement of the micelles. This morphological transition was caused by a defect of intermolecular hydrogen bonding between the amide groups on heating. Furthermore, addition of LiCl, which acts as hydrogen-bond breaker, also promoted the viscosity transition, leading to a lowering of the transition temperature.

  6. Amide-mediated hydrogen bonding at organic crystal/water interfaces enables selective endotoxin binding with picomolar affinity.

    PubMed

    Vagenende, Vincent; Ching, Tim-Jang; Chua, Rui-Jing; Thirumoorthi, Navanita; Gagnon, Pete

    2013-05-22

    Since the discovery of endotoxins as the primary toxic component of Gram-negative bacteria, researchers have pursued the quest for molecules that detect, neutralize, and remove endotoxins. Selective removal of endotoxins is particularly challenging for protein solutions and, to this day, no general method is available. Here, we report that crystals of the purine-derived compound allantoin selectively adsorb endotoxins with picomolar affinity through amide-mediated hydrogen bonding in aqueous solutions. Atom force microscopy and chemical inhibition experiments indicate that endotoxin adsorption is largely independent from hydrophobic and ionic interactions with allantoin crystals and is mediated by hydrogen bonding with amide groups at flat crystal surfaces. The small size (500 nm) and large specific surface area of allantoin crystals results in a very high endotoxin-binding capacity (3 × 10(7) EU/g) which compares favorably with known endotoxin-binding materials. These results provide a proof-of-concept for hydrogen bond-based molecular recognition processes in aqueous solutions and establish a practical method for removing endotoxins from protein solutions.

  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. 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

  11. Amide-I relaxation-induced hydrogen bond distortion: An intermediate in electron capture dissociation mass spectrometry of alpha-helical peptides?

    PubMed

    Pouthier, Vincent; Tsybin, Yury O

    2008-09-01

    Electron capture dissociation (ECD) of peptides and proteins in the gas phase is a powerful tool in tandem mass spectrometry whose current description is not sufficient to explain many experimental observations. Here, we attempt to bridge the current understanding of the vibrational dynamics in alpha-helices with the recent experimental results on ECD of alpha-helical peptides through consideration of amide-I relaxation-induced hydrogen bond distortion. Based on a single spine of H-bonded peptide units, we assume that charge neutralization upon electron capture by a charged alpha-helix excites a nearby amide-I mode, which relaxes over a few picoseconds due to Fermi resonances with intramolecular normal modes. The amide-I population plays the role of an external force, which drives the displacements of each peptide unit. It induces a large immobile contraction of the H bonds surrounding the excited site whose lifetime is about the amide-I lifetime. In addition, it creates two lattice deformations describing H bond stretchings, which propagate from the excited region toward both termini of the alpha-helix, get reflected at the termini and yield H bond contractions which move back to the excited region. Consequently, we show that H bonds experience rather large contractions whose amplitude depends on general features such as the position of the amide-I mode, the peptide length and the H bond force constants. When an H bond contraction is sufficiently large, it may promote a hydrogen atom transfer between two neighboring peptide units leading to the formation of a radical at charge site remote carbonyl carbon which is known to be a precursor to the rupture of the corresponding N[Single Bond]C(alpha) bond. The introduced here way of excitation energy generation and transfer may significantly advance ECD understanding and complement existing ECD mechanisms.

  12. 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.

  13. 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.

  14. 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

  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. 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.

  17. 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

  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. Investigation on the Surface-Confined Self-Assembly Stabilized by Hydrogen Bonds of Urea and Amide Groups: Quantitative Analysis of Concentration Dependence of Surface Coverage.

    PubMed

    Nishitani, Nobuhiko; Hirose, Takashi; Matsuda, Kenji

    2015-09-01

    Formation of a hydrogen-bond network via an amide group is a key driving force for the nucleation-elongation-type self-assembly that is often seen in biomolecules and artificial supramolecular assemblies. In this work, rod-coil-like aromatic compounds bearing an amide (1 a-3 a) or urea group (1 u-3 u) were synthesized, and their self-assemblies on a 2-D surface were investigated by scanning tunneling microscopy (STM). According to the quantitative analysis of the concentration dependence of the surface coverage, it was revealed that the strength of the hydrogen bond (i.e., amide or urea) and the number of non-hydrogen atoms in a molecular component (i.e., size of core and length of alkyl side chain) play a primary role in determining the stabilization energy during nucleation and elongation processes of molecular ordering on the HOPG surface.

  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. Mechanochemical Iridium(III)-Catalyzed C-H Bond Amidation of Benzamides with Sulfonyl Azides under Solvent-Free Conditions in a Ball Mill.

    PubMed

    Hermann, Gary N; Becker, Peter; Bolm, Carsten

    2016-03-01

    Mechanochemical conditions have been applied to an iridium(III)-catalyzed C-H bond amidation process for the first time. In the absence of solvent, the mechanochemical activation enables the formation of an iridium species that catalyzes the ortho-selective amidation of benzamides with sulfonyl azides as the nitrogen source. As the reaction proceeds in the absence of organic solvents without external heating and yields the desired products in excellent yields within short reaction times, this method constitutes a powerful, fast, and environmentally benign alternative to the common solvent-based standard approaches.

  3. 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

  4. 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.

  5. 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

  6. Effects of Peptide Backbone Amide-to-Ester Bond Substitution on the Cleavage Frequency in Electron Capture Dissociation and Collision-Activated Dissociation

    NASA Astrophysics Data System (ADS)

    Kjeldsen, Frank; Zubarev, Roman A.

    2011-08-01

    Probing the mechanism of electron capture dissociation on variously modified model peptide polycations has resulted in discovering many ways to prevent or reduce {{N}} - {{{C}}_α } bond fragmentation. Here we report on a rare finding of how to increase the backbone bond dissociation rate. In a number of model peptides, amide-to-ester backbone bond substitution increased the frequency of {{O}} - {{{C}}_α } bond cleavage (an analogue of {{N}} - {{{C}}_α } bonds in normal peptides) by several times, at the expense of reduced frequency of cleavages of the neighboring {{N}} - {{{C}}_α } bonds. In contrast, the ester linkage was only marginally broken in collisional dissociation. These results further highlight the complementarity of the reaction mechanisms in electron capture dissociation (ECD) and collision-activated dissociation (CAD). It is proposed that the effects of amide-to-ester bond substitution on fragmentation are mainly due to the differences in product ion stability (ECD, CAD) as well as proton affinity (CAD). This proposal is substantiated by calculations using density functional theory. The implications of these results in relation to the current understanding of the mechanisms of electron capture dissociation and electron transfer dissociation are discussed.

  7. 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.

  8. 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

  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. 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.

  11. 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…

  12. Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture.

    PubMed

    Penner, Robert C; Andersen, Ebbe S; Jensen, Jens L; Kantcheva, Adriana K; Bublitz, Maike; Nissen, Poul; Rasmussen, Anton M H; Svane, Katrine L; Hammer, Bjørk; Rezazadegan, Reza; Nielsen, Niels Chr; Nielsen, Jakob T; Andersen, Jørgen E

    2014-12-17

    Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each C(α) effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.

  13. 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.

  14. 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.

  15. Electrostatic origin of the cooperative effect on the C dbnd6 O bond lengths and the amide I vibrational frequencies of the N-methylacetamide oligomers

    NASA Astrophysics Data System (ADS)

    Torii, Hajime

    2005-02-01

    The electric fields operating among the molecules in the oligomers of N-methylacetamide are analyzed to see the reasons for the cooperative effect on the Cdbnd6 O bond lengths and the diagonal force constants in the vibrational subspace of the amide I mode. It is suggested that the following three factors are important for the enhancement of the electric field that gives rise to the cooperative effect: (1) the changes in the intermolecular distances (arising from the changes in the hydrogen-bond lengths); (2) the existence of the electric field directly operating between distant molecules, and (3) the polarization of the intervening molecule(s) between distant molecules. It is shown that the third factor is reasonably explained by the dipole-induced dipole mechanism. Some requirements for the correct representation of the electrostatic effects on the structures and the vibrational modes of polypeptides and proteins are proposed on the basis of this result.

  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. Rigid Single Carbon-Carbon Bond That Does Not Rotate in Water.

    PubMed

    Gadogbe, Manuel; Zhou, Yadong; Zou, Shengli; Zhang, Dongmao

    2016-03-10

    Carbon-carbon bond is one of the most ubiquitous molecular building blocks for natural and man-made materials. Rotational isomerization is fundamentally important for understanding the structure and reactivity of chemical and biological molecules. Reported herein is the first demonstration that a single C-C bond does not rotate in water. The two distal C-S bonds in both 1,2-ethanedithiolate ((-)S-CH2-CH2-S(-), 1,2-EDT(2-)) and 2,3-butanedithiolate (2,3-BuDT(2-)) are exclusively in the trans conformer with reference to their respective center single C-C bond. In contrast, both trans and gauche conformers are observed in neutral 1,2-ethanedithiol (1,2-EDT) and 2, 3-butanedithiol (2,3-BuDT). The insight from this work should be important for understanding the charge effect on the molecular conformation in aqueous solutions.

  18. Single-Molecule Rotational Switch on a Dangling Bond Dimer Bearing.

    PubMed

    Godlewski, Szymon; Kawai, Hiroyo; Kolmer, Marek; Zuzak, Rafał; Echavarren, Antonio M; Joachim, Christian; Szymonski, Marek; Saeys, Mark

    2016-09-27

    One of the key challenges in the construction of atomic-scale circuits and molecular machines is to design molecular rotors and switches by controlling the linear or rotational movement of a molecule while preserving its intrinsic electronic properties. Here, we demonstrate both the continuous rotational switching and the controlled step-by-step single switching of a trinaphthylene molecule adsorbed on a dangling bond dimer created on a hydrogen-passivated Ge(001):H surface. The molecular switch is on-surface assembled when the covalent bonds between the molecule and the dangling bond dimer are controllably broken, and the molecule is attached to the dimer by long-range van der Waals interactions. In this configuration, the molecule retains its intrinsic electronic properties, as confirmed by combined scanning tunneling microscopy/spectroscopy (STM/STS) measurements, density functional theory calculations, and advanced STM image calculations. Continuous switching of the molecule is initiated by vibronic excitations when the electrons are tunneling through the lowest unoccupied molecular orbital state of the molecule. The switching path is a combination of a sliding and rotation motion over the dangling bond dimer pivot. By carefully selecting the STM conditions, control over discrete single switching events is also achieved. Combined with the ability to create dangling bond dimers with atomic precision, the controlled rotational molecular switch is expected to be a crucial building block for more complex surface atomic-scale devices. PMID:27504525

  19. Multiple N-methylation of MT-II backbone amide bonds leads to melanocortin receptor subtype hMC1R selectivity; pharmacological and conformational studies

    PubMed Central

    Doedens, Lucas; Opperer, Florian; Cai, Minying; Beck, Johannes G.; Dedek, Matt; Palmer, Erin; Hruby, Victor J.; Kessler, Horst

    2010-01-01

    Multiple N-methylation is a novel technology to improve bioavailability of peptides and increase receptor subtype selectivity. This technique has been applied here to the superpotent but non-selective cyclic peptide MT-II. A library of all possible 31 backbone N-methylated derivatives has been synthesized and tested for binding and activation at melanocortin receptor subtypes 1, 3, 4 and 5. It turned out that selectivity is improved with every introduced N-methyl group, resulting in several N-methylated selective and potent agonists for the hMC1R. The most potent of these derivatives is N-methylated on four out of five amide bonds in the cyclic structure. Its solution structure indicates a strongly preferred backbone conformation which resembles other a-MSH analogs but possesses much less flexibility and in addition distinct differences in the spatial arrangement of individual amino acid side chains. PMID:20496895

  20. 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.

  1. 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.

  2. 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

  3. Structures of Highly Twisted Amides Relevant to Amide N-C Cross-Coupling: Evidence for Ground-State Amide Destabilization.

    PubMed

    Pace, Vittorio; Holzer, Wolfgang; Meng, Guangrong; Shi, Shicheng; Lalancette, Roger; Szostak, Roman; Szostak, Michal

    2016-10-01

    Herein, we show that acyclic amides that have recently enabled a series of elusive transition-metal-catalyzed N-C activation/cross-coupling reactions are highly twisted around the N-C(O) axis by a new destabilization mechanism of the amide bond. A unique effect of the N-glutarimide substituent, leading to uniformly high twist (ca. 90°) irrespective of the steric effect at the carbon side of the amide bond has been found. This represents the first example of a twisted amide that does not bear significant steric hindrance at the α-carbon atom. The (15) N NMR data show linear correlations between electron density at nitrogen and amide bond twist. This study strongly supports the concept of amide bond ground-state twist as a blueprint for activation of amides toward N-C bond cleavage. The new mechanism offers considerable opportunities for organic synthesis and biological processes involving non-planar amide bonds.

  4. Synthesis, conformational analysis, and biological activities of cyclic enkephalins and model cyclic peptides containing thioamides as amide bond replacements

    SciTech Connect

    Sherman, D.B.

    1988-01-01

    This thesis describes the first applications of the thioamide surrogate ({psi}(CSNH)) in model cyclic peptides and cyclic enkephalins. The solution phase synthesis and conformational analysis of two model cyclic endothiopentapeptides, cyclo(D-Phe-Pro{psi} (CSNH)Gly-Pro-Gly) (I) and cyclo(D-Phe-Pro-Gly-Pro{psi}(CSNH)Gly) (II), are reported. The conformations of I and II were analyzed using several 1 and 2D NMR techniques, such as INDOR, temperature and concentration dependence, {sup 1}H-{sup 1}H and {sup 1}H-{sup 13}C COSY, ROESY, and magnetization transfer. Compound I displayed the same general conformation as its parent in CDCl{sub 3}, but the {gamma}-turn hydrogen bond appeared to be weaker, while the {beta}-turn hydrogen bond appeared to be stronger. In DMSO-d{sub 6}, this molecule existed in two conformations in a ratio of 2:1. The major conformer appeared to be the same as that in CDCl{sub 3}, while the second contained at least one cis X-Pro bond, most likely at the Gly{sup 1}-Pro{sup 2} position. Compound II displayed the same conformation as its parent in both solvents. The {gamma}-turn hydrogen bond again appeared to be weaker in CDCl{sub 3}, but comparable with the parent in DMSO-d{sub 6}. Molecular modeling studies of I and II indicated the Pro {psi} angle increased by {approx}6{degree} when a thiocarbonyl was present, thereby reducing steric interactions with the Pro {beta} methylene.

  5. 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

  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. 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

  8. Internal dynamics in halogen-bonded adducts: a rotational study of chlorotrifluoromethane-formaldehyde.

    PubMed

    Gou, Qian; Feng, Gang; Evangelisti, Luca; Vallejo-López, Montserrat; Spada, Lorenzo; Lesarri, Alberto; Cocinero, Emilio J; Caminati, Walther

    2015-03-01

    The rotational spectra of two isotopologues of the 1:1 complex between chlorotrifluoromethane and formaldehyde have been recorded and analyzed by using Fourier-transform microwave spectroscopy. Only one rotamer was detected, with the two constituent molecules held together through a Cl⋅⋅⋅O halogen bond (R(Cl⋅⋅⋅O) = 3.048 Å). The dimer displays two simultaneous large-amplitude intramolecular motions. The internal rotation of formaldehyde around its symmetry axis (V2 = 28(5) cm(-1)) splits all the rotational transitions into two component lines with a relative intensity ratio of 1:3. On the other hand, the almost free internal rotation (V3 ≈ 2.5 cm(-1)) of the CF3 symmetric top increases the "rigid" value of the rotational constant A by almost one order of magnitude. In addition, all the transitions display a hyperfine structure due to the (35)Cl (or (37)Cl) nucleus quadrupole effects. PMID:25630577

  9. HNCO-based measurement of one-bond amide 15N-1H couplings with optimized precision.

    PubMed

    Arbogast, Luke; Majumdar, Ananya; Tolman, Joel R

    2010-02-01

    A pair of 3D HNCO-based experiments have been developed with the aim of optimizing the precision of measurement of (1)J(NH) couplings. Both pulse sequences record (1)J(NH) coupling evolution during the entire constant time interval that (15)N magnetization is dephasing or rephasing with respect to the directly bonded (13)C' nucleus, with (15)N(13)C' multiple quantum coherence maintained during the (13)C' evolution period. The first experiment, designed for smaller proteins, produces an apparent doubling of the (1)J(NH) coupling without any accompanying increases in line width. The second experiment is a J-scaled TROSY-HNCO experiment in which the (1)J(NH) coupling is measured by frequency difference between resonances offset symmetrically about the position of the downfield component of the (15)N doublet (i.e. the TROSY resonance). This experiment delivers significant gains in precision of (1)J(NH) coupling measurement compared to existing J-scaled TROSY-HNCO experiments. With the proper choice of acquisition parameters and sufficient sensitivity to acquire a 3D TROSY-HNCO experiment, it is shown that (1)J(NH) couplings can be measured with a precision which approaches or exceeds the precision of measurement with which the frequency of the TROSY resonance itself can be determined. PMID:20012159

  10. Interatomic potential for directional bonding: The rotated-second-moment approximation

    SciTech Connect

    Kress, J.D.; Voter, A.F. , Los Alamos National Laboratory, Los Alamos, New Mexico 87545 )

    1991-05-15

    An interatomic potential is presented, the rotated-second-moment approximation (RSMA), which incorporates directional bonding through energy moments evaluated over directional atomic orbitals. When nondirectional orbitals are used, RSMA reduces to the standard SMA (which is equivalent to the embedded-atom method), and is thus capable of describing metallic systems. A model RSMA potential is constructed for 3{ital d} transition metals, with only first-neighbor shell interactions, which can correctly predict the experimental trend in the relative stability of the fcc and hcp structures.

  11. Concerted Breaking of Two Hydrogen Bonds in Water Hexamer Prism Revealed from Broadband Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Richardson, Jeremy O.; Perez, Cristobal; Lobsiger, Simon; Reid, Adam A.; Temelso, Berhane; Shields, George C.; Kisiel, Zbigniew; Wales, David J.; Pate, Brooks; Althorpe, Stuart C.

    2016-06-01

    Over the past few years, we have used H218O water substitution to determine the structures of water clusters by molecular rotational spectroscopy. In the case of the water hexamer, the energy difference between the cage and prism structures is calculated to be about 0.1 kcal/mol and this energy difference is of the order of the zero-point energy variation between the isomers. Using rotational spectroscopy we provided experimental evidence for three isomers, i.e, cage, prism and book and established their relative energy ordering. In the special case of the prism hexamer, cluster dynamics causes measurable splitting in rotational transitions resulting from tunneling between discernible equivalent minima. Multiple isotopic substitution measurements involving all 64 possible isotopologues of the water hexamer prism (H218O)n(H216O)6-n were performed in order to identify the water molecules involved in the tunneling motion. The analysis of these tunneling-rotation spectra suggests that there are two distinct tunneling paths that involve concerted motion of two water molecules, implying a prototype scenario involving the breaking of two hydrogen bonds. C. Pérez, et al, Science. 2012, 336 897-901 J. O. Richardson et al, Science. 2016, in press

  12. 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.

  13. Metal cation dependence of interactions with amino acids: bond dissociation energies of Rb(+) and Cs(+) to the acidic amino acids and their amide derivatives.

    PubMed

    Armentrout, P B; Yang, Bo; Rodgers, M T

    2014-04-24

    Metal cation-amino acid interactions are key components controlling the secondary structure and biological function of proteins, enzymes, and macromolecular complexes comprising these species. Determination of pairwise interactions of alkali metal cations with amino acids provides a thermodynamic vocabulary that begins to quantify these fundamental processes. In the present work, we expand a systematic study of such interactions by examining rubidium and cesium cations binding with the acidic amino acids (AA), aspartic acid (Asp) and glutamic acid (Glu), and their amide derivatives, asparagine (Asn) and glutamine (Gln). These eight complexes are formed using electrospray ionization and their bond dissociation energies (BDEs) are determined experimentally using threshold collision-induced dissociation with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy-dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations are conducted at the B3LYP, MP2(full), and M06 levels of theory using def2-TZVPPD basis sets, with results showing reasonable agreement with experiment. At 0 and 298 K, most levels of theory predict that the ground-state conformers for M(+)(Asp) and M(+)(Asn) involve tridentate binding of the metal cation to the backbone carbonyl, amino, and side-chain carbonyl groups, although tridentate binding to the carboxylic acid group and side-chain carbonyl is competitive for M(+)(Asn). For the two longer side-chain amino acids, Glu and Gln, multiple structures are competitive. A comparison of these results to those for the smaller alkali cations, Na(+) and K(+), provides insight into the trends in binding energies associated with the molecular polarizability and dipole moment of the side chain. For all four metal cations, the BDEs are inversely correlated with the size of the metal cation and follow the order Asp < Glu

  14. 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.

  15. 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.

  16. 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

  17. The synthesis of sterically hindered amides.

    PubMed

    Schäfer, Gabriel; Bode, Jeffrey W

    2014-01-01

    Amide bond formation is one of the most important reactions due to the ubiquity of the amide functional group in pharmaceuticals and biologically active compounds. However, even the best existing methods reach their limits when it comes to the synthesis of sterically hindered amides. In this article we summarize our research in the formation of sterically hindered amides. We show that the direct coupling of Grignard reagents to isocyanates provides a facile and robust solution to this long-standing challenge and hope that this methodology will find widespread application in the synthesis of pharmaceuticals and materials. PMID:24983609

  18. 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

  19. 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.

  20. 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.

  1. Insight into shock-induced chemical reaction from the perspective of ring strain and rotation of chemical bonds.

    PubMed

    Tan, Bisheng; Long, Xinping; Li, Jinshan; Nie, Fude; Huang, Jinglun

    2012-12-01

    Density functional theory BLYP/DNP and hyperhomodesmotic equations were employed to calculate ring strain energy, the bond dissociation energy of X-NO(2) (X=C, N) and the charges on the nitro groups of several four-membered and six-membered heterocycle compounds. BLYP/DNP and LST/QST + CG method were also applied to calculate bond rotational energy of X-NO(2) (X=C, N) of above mentioned compounds. It indicated that ring strain energy of four-membered heterocycle nitro compounds is apparently higher than that of six-membered heterocycle nitro compounds. Predictably, ring-opening reactions may preferentially occur for those compounds containing higher ring strain energy under shock. In addition, C-NO(2) bonds in these compounds may rotate easier than N-NO(2) bonds in response to the external shock. As for N-NO(2) bonds in these compounds, they also respond to the external shock by the rotation of N-NO(2) bonds, once to the saddle point of the rotational energy barrier, the whole molecule will become relaxed, N-NO(2) bond becomes weaker and eventually leads to the breakage. When one -C=O, -C=NH or -NH(2) group is introduced to the six-membered heterocycle, the charges on the nitro groups of the new compound decrease drastically, and ring strains increase remarkably. It can be predicted that the new compounds will be more sensitive to shock, and the viewpoint is confirmed by the experimental results of shock sensitivity (small scale gap test) of several explosives.

  2. 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

  3. The pure rotational spectrum of HPS (X̃1A'): chemical bonding in second-row elements.

    PubMed

    Halfen, D T; Clouthier, D J; Ziurys, L M; Lattanzi, V; McCarthy, M C; Thaddeus, P; Thorwirth, S

    2011-04-01

    The pure rotational spectrum of HPS, as well as its (34)S and D isotopologues, has been recorded at microwave, millimeter, and submillimeter wavelengths, the first observation of this molecule in the gas phase. The data were obtained using a combination of millimeter direct absorption, Fourier transform microwave (FTMW), and microwave-microwave double-resonance techniques, which cover the total frequency range from 15 to 419 GHz. Quantum chemical calculations at the B3LYP and CCSD(T) levels were also performed to aid in spectral identification. HPS was created in the direct absorption experiment from a mixture of elemental phosphorus, H(2)S, and Ar carrier gas; DPS was produced by adding D(2). In the FTMW study, these species were generated in a pulsed discharge nozzle from PH(3) and H(2)S or D(2)S, diluted in neon. The spectra recorded for HPS and its isotopologues exhibit clear asymmetric top patterns indicating bent structures; phosphorus hyperfine splittings were also observed in HPS, but not DPS. Analysis of the data yielded rotation, centrifugal distortion, and phosphorus nuclear spin-rotation parameters for the individual species. The r(m) ((1)) structure for HPS, calculated from the rotational constants, is r(H-P) = 1.438(1) Å, r(P-S) = 1.9320(1) Å, and θ(H-P-S) = 101.85(9)°. Empirically correcting for zero-point vibrational effects yields the geometry r(e)(H-P) = 1.4321(2) Å, r(e)(P-S) = 1.9287(1) Å, and θ(e)(H-P-S) = 101.78(1)°, in close agreement with the r(m) ((1)) structure. A small inertial defect was found for HPS indicating a relatively rigid molecule. Based on these data, the bonding in this species is best represented as H-P=S, similar to the first-row analog HNO, as well as HNS and HPO. Therefore, substitution of phosphorus and sulfur for nitrogen and oxygen does not result in a dramatic structural change.

  4. Pd/C-Catalyzed Aminocarbonylation of Aryl Iodides via Oxidative C-N Bond Activation of Tertiary Amines to Tertiary Amides.

    PubMed

    Mane, Rajendra S; Bhanage, Bhalchandra M

    2016-02-01

    This work reports oxidative N-dealkylation/carbonylation of tertiary amines to tertiary amides by using molecular oxygen as a sole oxidant using a Pd/C catalyst. This protocol is free from ligands, additives, bases, and cocatalysts. Different tertiary amines as well as aryl iodides have been examined for this transformation, providing desired products in good to excellent yield. PMID:26756705

  5. [Rh(III)(Cp*)]-catalyzed ortho-selective direct C(sp(2))-H bond amidation/amination of benzoic acids by N-chlorocarbamates and N-chloromorpholines. A versatile synthesis of functionalized anthranilic acids.

    PubMed

    Ng, Fo-Ning; Zhou, Zhongyuan; Yu, Wing-Yiu

    2014-04-01

    A Rh(III) -catalyzed direct ortho-CH amidation/amination of benzoic acids with N-chlorocarbamates/N-chloromorpholines was achieved, giving anthranilic acids in up to 85 % yields with excellent ortho-selectivity and functional-group tolerance. Successful benzoic acid aminations were achieved with carbamates bearing various amide groups including NHCO2 Me, NHCbz, and NHTroc (Cbz=carbobenzyloxy; Troc=trichloroethylchloroformate), as well as secondary amines, such as morpholines, piperizines, and piperidines, furnishing highly functionalized anthranilic acids. A stoichiometric reaction of a cyclometallated rhodium(III) complex of benzo[h]quinoline with a silver salt of N-chlorocarbamate afforded an amido-rhodium(III) complex, which was isolated and structurally characterized by X-ray crystallography. This finding confirmed that the CN bond formation results from the cross-coupling of N-chlorocarbamate with the aryl-rhodium(III) complex. Yet, the mechanistic details regarding the CN bond formation remain unclear; pathways involving 1,2-aryl migration and rhodium(V)- nitrene are plausible. PMID:24596116

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. Catalytic synthesis of amides via aldoximes rearrangement.

    PubMed

    Crochet, Pascale; Cadierno, Victorio

    2015-02-14

    Amide bond formation reactions are among the most important transformations in organic chemistry because of the widespread occurrence of amides in pharmaceuticals, natural products and biologically active compounds. The Beckmann rearrangement is a well-known method to generate secondary amides from ketoximes. However, under the acidic conditions commonly employed, aldoximes RHC=NOH rarely rearrange into the corresponding primary amides RC(=O)NH2. In recent years, it was demonstrated that this atom-economical transformation can be carried out efficiently and selectively with the help of metal catalysts. Several homogeneous and heterogenous systems have been described. In addition, protocols offering the option to generate the aldoximes in situ from the corresponding aldehydes and hydroxylamine, or even from alcohols, have also been developed, as well as a series of tandem processes allowing the access to N-substituted amide products. In this Feature article a comprehensive overview of the advances achieved in this particular research area is presented.

  12. Metal-free catalytic enantioselective C-B bond formation: (pinacolato)boron conjugate additions to α,β-unsaturated ketones, esters, Weinreb amides, and aldehydes promoted by chiral N-heterocyclic carbenes.

    PubMed

    Wu, Hao; Radomkit, Suttipol; O'Brien, Jeannette M; Hoveyda, Amir H

    2012-05-16

    The first broadly applicable metal-free enantioselective method for boron conjugate addition (BCA) to α,β-unsaturated carbonyls is presented. The C-B bond forming reactions are promoted in the presence of 2.5-7.5 mol % of a readily accessible C(1)-symmetric chiral imidazolinium salt, which is converted, in situ, to the catalytically active diastereo- and enantiomerically pure N-heterocyclic carbene (NHC) by the common organic base 1,8-diazabicyclo[5.4.0]undec-7-ene (dbu). In addition to the commercially available bis(pinacolato)diboron [B(2)(pin)(2)], and in contrast to reactions with the less sterically demanding achiral NHCs, the presence of MeOH is required for high efficiency. Acyclic and cyclic α,β-unsaturated ketones, as well as acyclic esters, Weinreb amides, and aldehydes, can serve as suitable substrates; the desired β-boryl carbonyls are isolated in up to 94% yield and >98:2 enantiomer ratio (er). Transformations are often carried out at ambient temperature. In certain cases, such as when the relatively less reactive unsaturated amides are used, elevated temperatures are required (50-66 °C); nonetheless, reactions remain highly enantioselective. The utility of the NHC-catalyzed method is demonstrated through comparison with the alternative Cu-catalyzed protocols; in cases involving a polyfunctional substrate, unique profiles in chemoselectivity are exhibited by the metal-free approach (e.g., conjugate addition vs reaction with an alkyne, allene, or aldehyde). PMID:22559866

  13. 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

  14. 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

  15. 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) .

  16. Phenazinium salt-catalyzed aerobic oxidative amidation of aromatic aldehydes.

    PubMed

    Leow, Dasheng

    2014-11-01

    Amides are prevalent in organic synthesis. Developing an efficient synthesis that avoids expensive oxidants and heating is highly desirable. Here the oxidative amidation of aromatic aldehydes is reported using an inexpensive metal-free visible light photocatalyst, phenazine ethosulfate, at low catalytic loading (1-2 mol %). The reaction proceeds at ambient temperature and uses air as the sole oxidant. The operationally easy procedure provides an economical, green, and mild alternative for the formation of amide bonds.

  17. 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

  18. Synthetic Molecular Motors: Thermal N Inversion and Directional Photoinduced C=N Bond Rotation of Camphorquinone Imines.

    PubMed

    Greb, Lutz; Eichhöfer, Andreas; Lehn, Jean-Marie

    2015-11-23

    The thermal and photochemical E/Z isomerization of camphorquinone-derived imines was studied by a combination of kinetic, structural, and computational methods. The thermal isomerization proceeds by linear N inversion, whereas the photoinduced process occurs through C=N bond rotation with preferred directionality as a result of diastereoisomerism. Thereby, these imines are arguably the simplest example of synthetic molecular motors. The generality of the orthogonal trajectories of the thermal and photochemical pathways allows for the postulation that every suitable chiral imine qualifies, in principle, as a molecular motor driven by light or heat.

  19. 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...

  20. Unraveling the interplay between hydrogen bonding and rotational energy barrier to fine-tune the properties of triazine molecular glasses.

    PubMed

    Laventure, Audrey; De Grandpré, Guillaume; Soldera, Armand; Lebel, Olivier; Pellerin, Christian

    2016-01-21

    Mexylaminotriazine derivatives form molecular glasses with outstanding glass-forming ability (GFA), high resistance to crystallization (glass kinetic stability, GS), and a glass transition temperature (Tg) above room temperature that can be conveniently modulated by selection of the headgroup and ancillary groups. A common feature of all these compounds is their secondary amino linkers, suggesting that they play a critical role in their GFA and GS for reasons that remain unclear because they can simultaneously form hydrogen (H) bonds and lead to a high interconversion energy barrier between different rotamers. To investigate independently and better control the influence of H bonding capability and rotational energy barrier on Tg, GFA and GS, a library of twelve analogous molecules was synthesized with different combinations of NH, NMe and O linkers. Differential scanning calorimetry (DSC) revealed that these compounds form, with a single exception, kinetically stable glasses with Tg values spanning a very broad range from -25 to 94 °C. While variable temperature infrared spectroscopy combined to chemometrics reveals that, on average, around 60% of the NH groups are still H-bonded as high as 40 °C above Tg, critical cooling rates obtained by DSC clearly show that molecules without H-bond donating linkers also present an outstanding GFA, meaning that H bonding plays a dominant role in controlling Tg but is not required to prevent crystallization. It is a high interconversion energy barrier, provoking a distribution of rotamers, that most efficiently promotes both GFA and resistance to crystallization. These new insights pave the way to more efficient glass engineering by extending the possible range of accessible Tg, allowing in particular the preparation of homologous glass-formers with high GS at ambient temperature in either the viscous or vitreous state.

  1. Substrate stereoselectivity of poly(Asp) hydrolase-1 capable of cleaving β-amide bonds as revealed by investigation of enzymatic hydrolysis of stereoisomeric β-tri(Asp)s.

    PubMed

    Hiraishi, Tomohiro; Abe, Hideki; Maeda, Mizuo

    2015-12-01

    We previously reported that poly(Asp) hydrolase-1 (PahZ1KP-2) from Pedobacter sp. KP-2 selectively, but not completely, cleaved the amide bonds between β-Asp units in thermally synthesized poly(Asp) (tPAA). In the present study, the enzymatic hydrolysis of stereoisomeric β-tri(Asp)s by PahZ1KP-2 was investigated to clarify the substrate stereoselectivity of PahZ1KP-2 in the hydrolysis of tPAA. The results suggest the following structural features of PahZ1KP-2 at its substrate binding site: (1) the active site contains four subsites (2, 1, -1, and -2), three of which need to be occupied by Asp units for cleavage to occur; (2) for the hydrolysis to proceed, subsite 1 should be occupied by an L-Asp unit, whereas the other three subsites may accept both L- and D-Asp units; (3) for the two central subsites between which cleavage occurs, the (L-Asp)-(D-Asp) sequence is the most favorable for cleavage.

  2. Amide temperature coefficients in the protein G B1 domain.

    PubMed

    Tomlinson, Jennifer H; Williamson, Mike P

    2012-01-01

    Temperature coefficients have been measured for backbone amide (1)H and (15)N nuclei in the B1 domain of protein G (GB1), using temperatures in the range 283-313 K, and pH values from 2.0 to 9.0. Many nuclei display pH-dependent coefficients, which were fitted to one or two pK(a) values. (1)H coefficients showed the expected behaviour, in that hydrogen-bonded amides have less negative values, but for those amides involved in strong hydrogen bonds in regular secondary structure there is a negative correlation between strength of hydrogen bond and size of temperature coefficient. The best correlation to temperature coefficient is with secondary shift, indicative of a very approximately uniform thermal expansion. The largest pH-dependent changes in coefficient are for amides in loops adjacent to sidechain hydrogen bonds rather than the amides involved directly in hydrogen bonds, indicating that the biggest determinant of the temperature coefficient is temperature-dependent loss of structure, not hydrogen bonding. Amide (15)N coefficients have no clear relationship with structure.

  3. Shear-horizontal waves in a rotated Y-cut quartz plate with an imperfectly bonded mass layer.

    PubMed

    Chen, Yangyang; Du, Jianke; Wang, Ji; Yang, Jiashi

    2011-03-01

    We study shear-horizontal (SH) waves in an unbounded plate of rotated Y-cut quartz carrying a thin mass layer imperfectly or nonrigidly bonded to the surface of the quartz plate. The imperfect interface is described by the socalled shear-lag model that allows the displacement to be discontinuous across the interface. A transcendental frequency equation that determines the dispersion relations of the waves is obtained. Exact and approximate solutions to the frequency equation are presented. The effects of the mass layer and the imperfect interface on the dispersion relations are examined. A quantitative criterion is given which distinguishes whether the combined effect of the mass layer and the imperfect interface raises or lowers the wave frequencies. PMID:21429853

  4. Dissociation energies of the hydrogen-bonded dimers RCN-HF (R = CH3, HCC) determined by rotational spectroscopy

    NASA Astrophysics Data System (ADS)

    Legon, A. C.; Millen, D. J.; North, Hazel M.

    1987-03-01

    The zero-point and equilibrium dissociation energies (D0 and De) of the hydrogen-bonded dimers CH3CN-HF and HCCCN-HF are determined experimentally on the basis of absolute intensity measurements of selected rotational transitions. A Stark-modulated microwave spectrometer is employed with the cooled absorption cell described by Legon et al. (1980). The results are presented in tables and analyzed. Energies determined are D0 = 26.1(0.6) kJ/mol and De = 29.0(0.9) kJ/mol for CH3CN-HF and D0 = 20.4(0.7) kJ/mol and De = 23.4(0.9) kJ/mol for HCCCN-HF. Theoretical De values calculated using the Morse potential function are found to be in much better agreement with the experimental results than those calculated with the Lennard-Jones potential function.

  5. Cu(I) complexes of phosphorous amides

    SciTech Connect

    Nifant'ev, E.E.; Antipin, M.Y.; Blokhin, V.I.; Teleshev, A.T.

    1985-11-01

    The authors prepare and investigate copper complexes of phosphorous amides. The IR spectra of the systems investigated contain an absorption band at 920-940 cm/sup -1/ corresponding to P-N vibrations. The coordinates of the nonhydrogen atoms and their isotropic equivalent temperature factors are given with bond lengths and angles. The general form of the molecule of (IId) with the numbering of atoms, which are represented as probability ellipsoids of the thermal vibrations is shown. Copper complexes of phosphorus amides are phosphorylating agents for mono- and di-hydric alcohols.

  6. Rotation around the glycosidic bond as driving force of proton transfer in protonated 2‧-deoxyriboadenosine monophosphate (dAMP)

    NASA Astrophysics Data System (ADS)

    Shishkin, Oleg V.; Dopieralski, Przemyslaw; Palamarchuk, Gennady V.; Latajka, Zdzislaw

    2010-04-01

    Theoretical investigation of the conformation of 2'-deoxyriboadenosine monophosphate protonated at the N7 atom and stabilized by a very strong C8-H⋯O-P hydrogen bond indicates that this hydrogen bond may be disrupted by rotation of the adenine moiety around the glycosidic bond. A B3LYP/aug-cc-pVDZ scan of the relaxed potential energy surface demonstrates that this rotation is a multi-stage process, accompanying proton transfer from the N7 atom of adenine to the oxygen atom of the phosphate group with a change of conformation of the nucleotide from south/anti to north/syn conformation. Car-Parrinello molecular dynamics simulation indicates that rotation around the glycosidic bond is the preferred way for relaxation of the molecular geometry of this conformer. Both processes, i.e. conformational transition and proton transfer, are strongly coupled. However, the conformer containing a strong C-H⋯O hydrogen bond also corresponds to a local minimum on the Gibbs free energy surface. A specific property of this hydrogen bond is the large variation of the H⋯O distance (ranging from 1.3 to 2.2 Å), which is not caused by proton movement between the carbon and oxygen atoms, but rather by relative motions of the adenine and phosphate moieties.

  7. Millimeter-wave spectroscopy of FeF (X 6Δi): Rotational analysis and bonding study

    NASA Astrophysics Data System (ADS)

    Allen, M. D.; Ziurys, L. M.

    1997-03-01

    The pure rotational spectrum of the FeF radical in its 6Δi ground electronic state has been recorded using millimeter/submillimeter direct absorption techniques. Transitions arising from all six spin-orbit components have been observed in the v=0, 1, and 2 vibrational levels of 56FeF, the main isotopic species, and also in the less abundant 54Fe isotopomer. Hyperfine splittings, arising from the 19F nuclear spin of I=1/2, were resolved in the majority of transitions recorded, and lambda-doubling interactions were observed in the Ω=3/2, 1/2, and -1/2 spin-orbit ladders. The complete data set has been analyzed using a 6Δ Hamiltonian, and rotational, spin-orbit, spin-spin, lambda-doubling, and hyperfine constants determined. This study has conclusively demonstrated that the ground electronic state of FeF is 6Δi. It also suggests that FeF has more covalent character to its bonding than alkaline earth or alkali metal counterparts.

  8. An inertia-capacitance beam substructure formulation based on the bond graph method with application to rotating beams

    NASA Astrophysics Data System (ADS)

    Xing, Yihan; Pedersen, Eilif; Moan, Torgeir

    2011-10-01

    In this paper, a novel inertia-capacitance (IC) beam substructure formulation based on the IC-field presentation from the bond graph method is developed. The IC beam provides a modular, systematic and graphical approach to beam modeling. These features allow the modeler to focus more on the modeling and less on the mathematics. As such, the IC beam is proposed as an alternative to the many existing types of beam models available in the literature. The IC beam is formulated in the center of mass body fixed coordinate system allowing for easy interfacing in a multibody system setting. This floating frame approach is also computationally cheap. Elastic deformations in the IC beam are assumed to be small and described by modal superposition. The formulation couples rigid body and elastic deformations in a nonlinear fashion. The formulation is also compact and efficient. Detailed derivations for a two-dimensional planar IC beam with bending modes are presented. A modal acceleration method based on the decoupling of bending modes is proposed for use in the IC beam. The rotating beam spin-up maneuver problem is solved. The Karnopp-Margolis method is applied to ensure complete integral causality for an efficient numerical system. Geometric substructuring technique is applied to model large deflections. The IC beam is shown to be capable of solving the rotating beam problem accurately and efficiently.

  9. 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

  10. 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

  11. 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.

  12. Poly(ester amide)s from Soybean Oil for Modulated Release and Bone Regeneration.

    PubMed

    Natarajan, Janeni; Dasgupta, Queeny; Shetty, Shreya N; Sarkar, Kishor; Madras, Giridhar; Chatterjee, Kaushik

    2016-09-28

    Designing biomaterials for bone tissue regeneration that are also capable of eluting drugs is challenging. Poly(ester amide)s are known for their commendable mechanical properties, degradation, and cellular response. In this regard, development of new poly(ester amide)s becomes imperative to improve the quality of lives of people affected by bone disorders. In this framework, a family of novel soybean oil based biodegradable poly(ester amide)s was synthesized based on facile catalyst-free melt-condensation reaction. The structure of the polymers was confirmed by FTIR and (1)H -NMR, which indicated the formation of the ester and amide bonds along the polymer backbone. Thermal analysis revealed the amorphous nature of the polymers. Contact angle and swelling studies proved that the hydrophobic nature increased with increase in chain length of the diacids and decreased with increase in molar ratio of sebacic acid. Mechanical studies proved that Young's modulus decreased with decrease in chain lengths of the diacids and increase in molar ratio of sebacic acid. The in vitro hydrolytic degradation and dye release demonstrated that the degradation and release decreased with increase in chain lengths of the diacids and increased with increase in molar ratio of sebacic acid. The degradation followed first order kinetics and dye release followed Higuchi kinetics. In vitro cell studies showed no toxic effects of the polymers. Osteogenesis studies revealed that the polymers can be remarkably efficient because more than twice the amount of minerals were deposited on the polymer surfaces than on the tissue culture polystyrene surfaces. Thus, a family of novel poly(ester amide)s has been synthesized, characterized for controlled release and tissue engineering applications wherein the physical, degradation, and release kinetics can be tuned by varying the monomers and their molar ratios. PMID:27599306

  13. 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

  14. Retinobenzoic acids. 4. Conformation of aromatic amides with retinoidal activity. Importance of trans-amide structure for the activity.

    PubMed

    Kagechika, H; Himi, T; Kawachi, E; Shudo, K

    1989-10-01

    N-Methylation of two retinoidal amide compounds, 4-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)carbamoyl]benz oic acid (3, Am80) and 4-[[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2- naphthalenyl)carbonyl]amino]benzoic acid (5, Am580), resulted in the disappearance of their potent differentiation-inducing activity on human promyelocytic leukemia cell line HL-60. Studies with 1H NMR and UV spectroscopy indicated that large conformational differences exist between the active secondary amides and the inactive N-methyl amides. From a comparison of the spectroscopic results of these amides with those of stilbene derivatives, the conformations of the active amides are expected to resemble that of (E)-stilbene, whereas the inactive amides resemble the Z isomer: 3 (Am80) and 5 (Am580) have a trans-amide bond and their whole structures are elongated, while the N-methylated compounds [4 (Am90) and 6 (Am590)] have a cis-amide bond, resulting in the folding of the two benzene rings. These structures in the crystals were related to those in solution by 13C NMR spectroscopic comparison between the two phases (solid and solution).

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. Amide I vibrational circular dichroism of polypeptides: Generalized fragmentation approximation method

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Kim, Joong-Soo; Cho, Minhaeng

    2005-05-01

    Fragment analyses of vibrational circular dichroic response of dipeptides were carried out recently [Choi and Cho, J. Chem. Phys. 120, 4383 (2004)]. In the present paper, by using a minimal size unit peptide containing two chiral carbons covalently bonded to the peptide group, a generalized fragmentation approximation method is discussed and applied to the calculations of infrared-absorption and vibrational circular dichroism (VCD) intensities of amide I vibrations in various secondary structure polypeptides. Unlike the dipole strength determining IR-absorption intensity, the rotational strength is largely determined by the cross terms that are given by the inner product between the transition electric dipole and the transition magnetic dipole of two different peptides. This explains why the signs and magnitudes of VCD peaks are far more sensitive to the relative orientation and distance between different peptide bonds in a given protein. In order to test the validity of fragmentation approximation, three different segments in a globular protein ubiquitin, i.e., right-handed α-helix, β-sheet, and β-turn regions, were chosen for density-functional theory (DFT) calculations of amide I vibrational properties and the numerically simulated IR-absorption and VCD spectra by using the fragmentation method are directly compared with DFT results. It is believed that the fragmentation approximation method will be of use in numerically simulating vibrational spectra of proteins in solutions.

  3. Amide I'-II' 2D IR spectroscopy provides enhanced protein secondary structural sensitivity.

    PubMed

    Deflores, Lauren P; Ganim, Ziad; Nicodemus, Rebecca A; Tokmakoff, Andrei

    2009-03-11

    We demonstrate how multimode 2D IR spectroscopy of the protein amide I' and II' vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I'-II' 2D IR experiments on poly-l-lysine in the beta-sheet, alpha-helix, and random coil conformations show that a combination of amide I' and II' diagonal and cross peaks can effectively distinguish between secondary structural content, where amide I' infrared spectroscopy alone cannot. The enhanced sensitivity arises from frequency and amplitude correlations between amide II' and amide I' spectra that reflect the symmetry of secondary structures. 2D IR surfaces are used to parametrize an excitonic model for the amide I'-II' manifold suitable to predict protein amide I'-II' spectra. This model reveals that the dominant vibrational interaction contributing to this sensitivity is a combination of negative amide II'-II' through-bond coupling and amide I'-II' coupling within the peptide unit. The empirically determined amide II'-II' couplings do not significantly vary with secondary structure: -8.5 cm(-1) for the beta sheet, -8.7 cm(-1) for the alpha helix, and -5 cm(-1) for the coil.

  4. 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.

  5. Measurements of the rotational spectra of phenol and 2-pyrone and computational studies of the H-bonded phenol-pyrone dimer.

    PubMed

    Tanjaroon, Chakree; Kukolich, Stephen G

    2009-08-13

    Rotational spectra for the a-type transitions of phenol and a-type and b-type transitions of 2-pyrone in the ground vibrational states were measured using pulsed beam Fourier transform (PBFT) microwave spectroscopy. From the observed a-type spectrum of phenol, which exhibited no complicated tunneling doublet splittings, we obtained the following rotational constants: A0 = 5650.494(26), B0 = 2619.2323(7), C0 = 1789.8520(7) MHz. For 2-pyrone, the following rotational constants were obtained: A0 = 5677.6356(10), B0 = 2882.2458(11), C0 = 1912.13275(94) MHz. The centrifugal distortion constant, DeltaJ, for these molecules is less than 0.2 kHz, in good agreement with our predicted, theoretical Delta(J) values. Combined spectral fits using data from this work and previous data provided accurate information on the rotational and centrifugal distortion constants of these molecules. From the measured rotational constants we obtained the following inertial defects (Delta): Delta(2-pyrone) = -0.053 and Delta(phenol) = -0.031 amu A2. The observed negative inertial defect for these planar molecules (normally a small positive value for planar molecules) suggests that the out-of-plane vibrational potential due to the attached OH and O is highly anharmonic. From the measured inertial defect, we calculated the low frequency out-of-plane vibration to be approximately 110 cm(-1). Quantum chemical calculations were performed in combination with the experiments to determine the molecular and spectroscopic properties of phenol, 2-pyrone and the H-bonded, phenol-pyrone dimer. A well-defined theoretical structure was obtained for the phenol-pyrone dimer from the calculations with electron correlation. Structure optimization calculations using Møller-Plesset perturbation theory predicted a stable bent dimer structure with relatively strong interaction energy in the 28-32 kJ mol(-1) range. This novel, phenol-pyrone dimer forms a single O...HO hydrogen bond with length about 1.87-1.93 A, and

  6. 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

  7. Advances in the chemistry of sulphenic acid amides

    NASA Astrophysics Data System (ADS)

    Koval', I. V.

    1990-04-01

    Results of recent investigations in the area of sulphenic acid amides have been systematised and correlated in the review. Reactions of sulphenamides occurring with the generation of anions, radicals and nitrenes have been considered, as well as reactions accompanied by fussion of the S-N bond and oxidation of the sulphur atom. The bibliography contains 95 references.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. Influence of receptor flexibility on intramolecular H-bonding interactions.

    PubMed

    Sun, Hongmei; Guo, Kai; Gan, Haifeng; Li, Xin; Hunter, Christopher A

    2015-08-01

    Atropisomers of a series of zinc tetraphenyl porphyrins were synthesized and used as supramolecular receptors. Rotation around the porphyrin-meso phenyl bonds is restricted by installing ortho-chlorine substituents on the phenyl groups. The chlorine substituents allowed chromatographic separation of atropisomers, which did not interconvert at room temperature. The porphyrin meso phenyl groups were also equipped with phenol groups, which led to the formation of intramolecular H-bonds when the zinc porphyrins were bound to pyridine ligands equipped with ester or amide side arms. Binding of the pyridine ligands with the conformationally locked chloroporphyrins was compared with the corresponding unsubstituted porphyrins, which are more flexible. The association constants of 150 zinc porphyrin-pyridine complexes were measured in two different solvents, toluene and 1,1,2,2-tetrachloroethane (TCE). These association constants were then used to construct 120 chemical double mutant cycles to quantify the influence of chlorine substitution on the free energy of intramolecular H-bonds formed between the phenol side arms of the porphyrins and the ester or amide side arms of the pyridine ligands. Conformational restriction leads to increases in the stability of some complexes and decreases in the stability of others with variations in the free energy contribution due to intramolecular H-bonding of -5 to +6 kJ mol(-1).

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. Three centered hydrogen bonds of the type C=O···H(N)···X-C in diphenyloxamide derivatives involving halogens and a rotating CF3 group: NMR, QTAIM, NCI and NBO studies.

    PubMed

    Lakshmipriya, A; Rama Chaudhari, Sachin; Shahi, Abhishek; Arunan, E; Suryaprakash, N

    2015-03-21

    The existence of three centered C=O···H(N)···X-C hydrogen bonds (H-bonds) involving organic fluorine and other halogens in diphenyloxamide derivatives has been explored by NMR spectroscopy and quantum theoretical studies. The three centered H-bond with the participation of a rotating CF3 group and the F···H-N intramolecular hydrogen bonds, a rare observation of its kind in organofluorine compounds, has been detected. It is also unambiguously established by a number of one and two dimensional NMR experiments, such as temperature perturbation, solvent titration, (15)N-(1)H HSQC, and (19)F-(1)H HOESY, and is also confirmed by theoretical calculations, such as quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) and non-covalent interaction (NCI).

  1. 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

  2. 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.

  3. 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

  4. On the temperature dependence of amide I frequencies of peptides in solution.

    PubMed

    Amunson, Krista E; Kubelka, Jan

    2007-08-23

    The temperature dependence of the amide I vibrational frequencies of peptides in solution was investigated. In D2O, the amide I' bands of both an alpha-helical oligopeptide, the random-coil poly(L-lysine), and the simplest amide, N-methyl acetamide (NMA), exhibit linear frequency shifts of approximately 0.07 cm(-1)/degrees C with increasing temperature. Similar amide I frequency shifts are also observed for NMA in both polar (acetonitrile and DMSO) and nonpolar (1,4-dioxane) organic solvents, thus ruling out hydrogen-bonding strength as the cause of these effects. The experimental NMA amide I frequencies in the organic solvents can be accurately described by a simple theory based on the Onsager reaction field with temperature-dependent solvent dielectric properties and a solute molecular cavity. DFT-level calculations (BPW91/cc-pVDZ) for NMA with an Onsager reaction field confirm the significant contribution of the molecular cavity to the predicted amide I frequencies. Comparison of the computations to experimental data shows that the frequency-dependent response of the reaction field, taken into account by the index of refraction, is crucial for describing the amide I frequencies in polar solvents. The poor predictions of the model for the NMA amide I band in D2O might be due, in part, to the unknown temperature dependence of the refractive index of D2O in the mid-IR range, which was approximated by the available values in the visible region.

  5. Thioamides: versatile bonds to induce directional and cooperative hydrogen bonding in supramolecular polymers.

    PubMed

    Mes, Tristan; Cantekin, Seda; Balkenende, Dirk W R; Frissen, Martijn M M; Gillissen, Martijn A J; De Waal, Bas F M; Voets, Ilja K; Meijer, E W; Palmans, Anja R A

    2013-06-24

    The amide bond is a versatile functional group and its directional hydrogen-bonding capabilities are widely applied in, for example, supramolecular chemistry. The potential of the thioamide bond, in contrast, is virtually unexplored as a structuring moiety in hydrogen-bonding-based self-assembling systems. We report herein the synthesis and characterisation of a new self-assembling motif comprising thioamides to induce directional hydrogen bonding. N,N',N''-Trialkylbenzene-1,3,5-tris(carbothioamide)s (thioBTAs) with either achiral or chiral side-chains have been readily obtained by treating their amide-based precursors with P2S5. The thioBTAs showed thermotropic liquid crystalline behaviour and a columnar mesophase was assigned. IR spectroscopy revealed that strong, three-fold, intermolecular hydrogen-bonding interactions stabilise the columnar structures. In apolar alkane solutions, thioBTAs self-assemble into one-dimensional, helical supramolecular polymers stabilised by three-fold hydrogen bonding. Concentration- and temperature-dependent self-assembly studies performed by using a combination of UV and CD spectroscopy demonstrated a cooperative supramolecular polymerisation mechanism and a strong amplification of supramolecular chirality. The high dipole moment of the thioamide bond in combination with the anisotropic shape of the resulting cylindrical aggregate gives rise to sufficiently strong depolarised light scattering to enable depolarised dynamic light scattering (DDLS) experiments in dilute alkane solution. The rotational and translational diffusion coefficients, D(trans) and D(rot), were obtained from the DDLS measurements, and the average length, L, and diameter, d, of the thioBTA aggregates were derived (L = 490 nm and d = 3.6 nm). These measured values are in good agreement with the value L(w) = 755 nm obtained from fitting the temperature-dependent CD data by using a recently developed equilibrium model. This experimental verification

  6. Transesterification and amide cis-trans isomerization in Zn and Cd complexes of the chelating amino acid ligand Boc-Asp(Dpa)-OBzl.

    PubMed

    Niklas, Nicole; Zahl, Achim; Alsfasser, Ralf

    2007-01-01

    The amino acid derivative Boc-Asp-OBzl (Boc=N-butyloxycarbonyl; Asp=aspartic acid; Bzl=benzyl) was functionalized by coupling its carboxylate side chain to dipicolylamine. This yielded the tridentate nitrogen donor ligand Boc-Asp(Dpa)-OBzl (-OBzl). The compound -OBzl contains three different carbonyl groups: a tertiary amide linkage between Asp and Dpa, a C-terminal benzyl ester function, and an N-terminal urethane protecting group. NMR spectra were used to compare the reactivity of these moieties. The Boc protecting group gives rise to two isomers, (E, 9%) and (Z, 91%). Coordination of Cd(NO3)2 and Zn(NO3)2 yielded the complexes and. These compounds have significantly reduced barriers to rotation about the tertiary amide C-N bond compared with the free ligand (-OBzl:18.5 kcal mol-1 in CDBr3;: 12.9 kcal mol-1 in (CD3)2CO;: 13.8 kcal mol-1 in (CD3)2CO). Both complexes readily undergo transesterification in methanol or CD3OD. Experimental pseudo-first order rate constants were determined in CD3OD and (CD3)2CO:CD3OD (3:1;). It was found that the zinc complex (k=(2.28+/-0.02)x10(-4) s-1) is significantly more reactive than the cadmium complex (k=(1.41+/-0.03)x10(-6) s-1). In order to study their tertiary amide cis-trans isomerization, the cadmium complex [(-OCH3)Cd(NO3)2] was synthesized, and the zinc complex [(-OCD3)Zn(NO3)2] was generated in situ in (CD3)2CO:CD3OD (3:1). The barriers to rotation were determined (:14.1 kcal mol-1 in CD3OD;: 13.4 kcal mol-1 in (CD3)2CO:CD3OD (3:1)). Our results show that the stronger Lewis-acid zinc(II) is significantly more active than cadmium(II) in the acceleration of the transesterification. This is in marked contrast to the tertiary amide bond rotation which is comparably fast with both metal ions. PMID:17160185

  7. Lanthanide(III) complexation with an amide derived pyridinophane.

    PubMed

    Castro, Goretti; Bastida, Rufina; Macías, Alejandro; Pérez-Lourido, Paulo; Platas-Iglesias, Carlos; Valencia, Laura

    2015-02-16

    Herein we report a detailed investigation of the solid state and solution structures of lanthanide(III) complexes with the 18-membered pyridinophane ligand containing acetamide pendant arms TPPTAM (TPPTAM = 2,2',2″-(3,7,11-triaza-1,5,9(2,6)-tripyridinacyclododecaphane-3,7,11-triyl)triacetamide). The ligand crystallizes in the form of a clathrated hydrate, where the clathrated water molecule establishes hydrogen-bonding interactions with the amide NH groups and two N atoms of the macrocycle. The X-ray structures of 13 different Ln(3+) complexes obtained as the nitrate salts (Ln(3+) = La(3+)-Yb(3+), except Pm(3+)) have been determined. Additionally, the X-ray structure of the La(3+) complex obtained as the triflate salt was also obtained. In all cases the ligand provides 9-fold coordination to the Ln(3+) ion, ten coordination being completed by an oxygen atom of a coordinated water molecule or a nitrate or triflate anion. The bond distances of the metal coordination environment show a quadratic change along the lanthanide series, as expected for isostructural series of Ln(3+) complexes. Luminescence lifetime measurements obtained from solutions of the Eu(3+) and Tb(3+) complexes in H2O and D2O point to the presence of a water molecule coordinated to the metal ion in aqueous solutions. The analysis of the Ln(3+)-induced paramagnetic shifts indicates that the complexes are ten-coordinated throughout the lanthanide series from Ce(3+) to Yb(3+), and that the solution structure is very similar to the structures observed in the solid state. The complexes of the light Ln(3+) ions are fluxional due to a fast Δ(λλλλλλ) ↔ Λ(δδδδδδ) interconversion that involves the inversion of the macrocyclic ligand and the rotation of the acetamide pendant arms. The complexes of the small Ln(3+) ions are considerably more rigid, the activation free energy determined from VT (1)H NMR for the Lu(3+) complex being ΔG(⧧)298 = 72.4 ± 5.1 kJ mol(-1).

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    PubMed

    Ichikawa, Akio; Ono, Hiroshi; Mikata, Yuji

    2015-07-16

    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.

  15. Cleavage kinetics and anchor linked intermediates in solid phase peptide amide synthesis.

    PubMed

    Dürr, H; Beck-Sickinger, A G; Schnorrenberg, G; Rapp, W; Jung, G

    1991-08-01

    Kinetics and cleavage conditions of peptide amide synthesis were studied using the anchor molecules 5-(4'-aminomethyl-3',5'-dimethoxyphenoxy)valeric acid (4-ADPV-OH) and 5-(2'-aminomethyl-3'-5'-dimethoxyphenoxy) valeric acid (2-ADPV-OH). Unexpectedly the anchor amide alanyl-4-ADPV-NH2 was isolated and characterized as an intermediate during the cleavage with trifluoroacetic acid (TFA) of alanyl-4-ADPV-alanyl-aminomethyl-polystyrene to yield the alanine amide. As a matter of fact the NH--CH alpha bond of the alanyl spacer has to be cleaved to form this intermediate. Using TFA-dichloromethane (1:9) alanyl-4-ADPV-NH2 was obtained as a cleavage product in 50% yield within 60 min, whereas the isomeric alanyl-2-ADPV-NH2 was formed more slowly under these mild conditions. At high TFA concentration no difference between the 2- and 4-ADPV anchor was observed in the rate of formation of the free alanine amide. The presence of tryptophan amide in the cleavage mixture resulted in an anchor alkylated tryptophan amide, which remains stable in acidic solution but disappears rapidly in the presence of the resin. A low TFA/high TFA cleavage procedure is recommended for peptide amid synthesis applying the ADPV anchor.

  16. 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

  17. 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

  18. Empirical modeling of the peptide amide I band IR intensity in water solution

    NASA Astrophysics Data System (ADS)

    Bouř, Petr; Keiderling, Timothy A.

    2003-12-01

    An empirical correction to amide group vacuum force fields is proposed in order to account for the influence of the aqueous environment on the C=O stretching vibration (amide I). The dependence of the vibrational absorption spectral intensities on the geometry is studied with density functional theory methods at the BPW91/6-31G** level for N-methyl acetamide interacting with a variety of of water molecule clusters hydrogen bonded to it. These cluster results are then generalized to form an empirical correction for the force field and dipole intensity of the amide I (C=O stretch) mode. As an example of its extension, the method is applied to a larger (β-turn model) peptide molecule and its IR spectrum is simulated. The method provides realistic bandwidths for the amide I bands if the spectra are generated from the ab initio force field corrected by perturbation from an ensemble of solvent geometries obtained using molecular dynamic simulations.

  19. The rotational spectrum and structure for the argon-cyclopentadienyl thallium van der Waals complex: experimental and computational studies of noncovalent bonding in an organometallic pi-complex.

    PubMed

    Tanjaroon, Chakree; Daly, Adam M; Kukolich, Stephen G

    2008-08-01

    The rotational spectrum of a noble gas-organometallic complex was measured using a pulse molecular beam Fourier transform microwave spectrometer. Rotational transitions for the neutral argon-cyclopentadienyl thallium weakly bound complex were measured in the 4-9 GHz range. Analysis of the spectrum showed that the complex is a prolate symmetric-top rotor with C(5V) symmetry. The experimentally determined molecular parameters for Ar-C(5)H(5) (205)Tl are B=372.4479(3) MHz, D(J)=0.123(2) kHz, and D(JK)=0.45(2) kHz. For Ar-C(5)H(5) (203)Tl, B=373.3478(5) MHz, D(J)=0.113(3) kHz, and D(JK)=0.37(3) kHz. Using a pseudodiatomic model with Lennard-Jones potential yields an approximate binding energy of 339 cm(-1). The argon atom is located on the a-axis of the C(5)H(5)Tl monomer, directly opposite from the thallium metal atom. The measured separation distance between argon and the cyclopentadienyl ring is R=3.56 A. The overall size of the cluster is about 6 A, measuring from argon to thallium. Relatively small D(J) and D(JK) centrifugal distortion constants were observed for the complex, indicating that the structure of Ar-C(5)H(5)Tl is somewhat rigid. MP2 calculations were used to investigate the possible structures and binding energies of the argon-cyclopentadienyl thallium complex. Calculated, counterpoise corrected binding energies are evaluated at R=3.56 A for Ar-C(5)H(5)Tl range from 334 to 418 cm(-1). The experimental binding energy epsilon=339 cm(-1) for Ar-C(5)H(5)Tl falls within this range. The higher-level MP2/aug-cc-pVTZ-PP (thallium)/aug-cc-pVTZ(Ar, C, H) calculation with variable R yielded R(e)=3.46 A and binding energy of 535 cm(-1). Our estimated binding energy for argon-cyclopentadienyl thallium is very similar to the binding energy of argon-benzene. Calculations for the new van der Waals complexes, Ar(C(5)H(5)Tl)(2) and (C(5)H(5)Tl)(2), have been obtained, providing further information on the structures and bonding properties of previously observed

  20. Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin.

    PubMed

    Sodt, Alexander J; Pastor, Richard W; Lyman, Edward

    2015-09-01

    All-atom simulation data are presented for ternary mixtures of palmitoyl sphingomyelin (PSM), cholesterol, and either palmitoyl oleoyl phosphatidyl choline or dioleoyl phosphatidyl choline (DOPC). For comparison, data for a mixture of dipalmitoyl phosphatidyl choline (DPPC), cholesterol, and DOPC are also presented. Compositions corresponding to the liquid-ordered phase, the liquid-disordered phase, and coexistence of the two phases are simulated for each mixture. Within the liquid-ordered phase, cholesterol is preferentially solvated by DOPC if it is available, but if DOPC is replaced by POPC, cholesterol is preferentially solvated by PSM. In the DPPC mixtures, cholesterol interacts preferentially with the saturated chains via its smooth face, whereas in the PSM mixtures, cholesterol interacts preferentially with PSM via its rough face. Interactions between cholesterol and PSM have a very particular character: hydrogen bonding between cholesterol and the amide of PSM rotates the tilt of the amide plane, which primes it for more robust hydrogen bonding with other PSM. Cholesterol-PSM hydrogen bonding also locally modifies the hexagonal packing of hydrocarbon chains in the liquid-ordered phase of PSM mixtures.

  1. 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.

  2. Oligonuclear ferrocene amides: mixed-valent peptides and potential redox-switchable foldamers.

    PubMed

    Siebler, Daniel; Linseis, Michael; Gasi, Teuta; Carrella, Luca M; Winter, Rainer F; Förster, Christoph; Heinze, Katja

    2011-04-11

    Trinuclear ferrocene tris-amides were synthesized from an Fmoc- or Boc-protected ferrocene amino acid, and hydrogen-bonded zigzag conformations were determined by NMR spectroscopy, molecular modelling, and X-ray diffraction. In these ordered secondary structures orientation of the individual amide dipole moments approximately in the same direction results in a macrodipole moment similar to that of α-helices composed of α-amino acids. Unlike ordinary α-amino acids, the building blocks in these ferrocene amides with defined secondary structure can be sequentially oxidized to mono-, di-, and trications. Singly and doubly charged mixed-valent cations were probed experimentally by Vis/NIR, paramagnetic ¹H NMR and Mössbauer spectroscopy and investigated theoretically by DFT calculations. According to the appearance of intervalence charge transfer (IVCT) bands in solution, the ferrocene/ferrocenium amides are described as Robin-Day class II mixed-valent systems. Mössbauer spectroscopy indicates trapped valences in the solid state. The secondary structure of trinuclear ferrocene tris-amides remains intact (coiled form) upon oxidation to mono- and dications according to DFT calculations, while oxidation to the trication should break the intramolecular hydrogen bonding and unfold the ferrocene peptide (uncoiled form).

  3. Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2013-04-01

    The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm-1 for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm-1. These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.

  4. UV raman examination of alpha-helical peptide water hydrogen bonding.

    PubMed

    Pimenov, Konstantin V; Bykov, Sergei V; Mikhonin, Aleksandr V; Asher, Sanford A

    2005-03-01

    UV resonance Raman spectra (UVRS) of an alpha-helical, 21 residue, mainly Ala peptide (AP) in the dehydrated solid state were compared to those in aqueous solution at different temperatures. The UVRS amide band frequencies of a dehydrated solid alpha-helix peptide show frequency shifts compared to those in aqueous solution due to the loss of amide backbone hydrogen bonding to water; the amide II and amide III bands of the solid alpha-helix downshift, while the amide I band upshifts. The shifts are identical in direction but smaller than those that occur for alpha-helices in aqueous solution as the temperature increases; water hydrogen bonding strengths decrease as the temperature increases. The UV Raman amide band frequency shifts can be used to monitor alpha-helix hydrogen bonding. PMID:15740105

  5. 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

  6. Peptide backbone cleavage by α-amidation is enhanced at methionine residues.

    PubMed

    Hellwig, Michael; Löbmann, Katja; Orywol, Tom

    2015-01-01

    Cleavage reactions at backbone loci are one of the consequences of oxidation of proteins and peptides. During α-amidation, the Cα -N bond in the backbone is cleaved under formation of an N-terminal peptide amide and a C-terminal keto acyl peptide. On the basis of earlier works, a facilitation of α-amidation by the thioether group of adjacent methionine side chains was proposed. This reaction was characterized by using benzoyl methionine and benzoyl alanyl methionine as peptide models. The decomposition of benzoylated amino acids (benzoyl-methionine, benzoyl-alanine, and benzoyl-methionine sulfoxide) to benzamide in the presence of different carbohydrate compounds (reducing sugars, Amadori products, and reductones) was studied during incubation for up to 48 h at 80 °C in acetate-buffered solution (pH 6.0). Small amounts of benzamide (0.3-1.5 mol%) were formed in the presence of all sugars and from all benzoylated species. However, benzamide formation was strongly enhanced, when benzoyl methionine was incubated in the presence of reductones and Amadori compounds (3.5-4.2 mol%). The reaction was found to be intramolecular, because α-amidation of a similar 4-methylbenzoylated amino acid was not enhanced in the presence of benzoyl-methionine and carbohydrate compounds. In the peptide benzoyl-alanyl-methionine, α-amidation at the methionine residue is preferred over α-amidation at the benzoyl peptide bond. We propose here a mechanism for the enhancement of α-amidation at methionine residues.

  7. 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

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

    PubMed

    Byrd, Katherine M

    2015-01-01

    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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. Phenyl-ring rotational disorder in the two-dimensional hydrogen-bonded structure of the 1:1 proton-transfer salt of the diazo-dye precursor 4-(phenyldiazenyl)aniline (aniline yellow) with L-tartaric acid.

    PubMed

    Smith, Graham; Wermuth, Urs D; Young, David J

    2010-07-01

    In the structure of the 1:1 proton-transfer compound from the reaction of L-tartaric acid with the azo-dye precursor aniline yellow [4-(phenyldiazenyl)aniline], namely 4-(phenyldiazenyl)anilinium (2R,3R)-3-carboxy-2,3-dihydroxypropanoate, C(12)H(12)N(3)(+) x C(4)H(5)O(6)(-), the asymmetric unit contains two independent 4-(phenyldiazenyl)anilinium cations and two hydrogen L-tartrate anions. The structure is unusual in that all four phenyl rings of the two cations have identical rotational disorder with equal occupancy of the conformations. The two hydrogen L-tartrate anions form independent but similar chains through head-to-tail carboxyl-carboxylate O-H...O hydrogen bonds [graph set C(7)], which are then extended into a two-dimensional hydrogen-bonded sheet structure through hydroxy O-H...O hydrogen-bonded links. The anilinium groups of the 4-(phenyldiazenyl)anilinium cations are incorporated into the sheets and also provide internal hydrogen-bonded extensions, while their aromatic tails are layered in the structure without significant association except for weak pi-pi interactions [minimum ring centroid separation = 3.844 (3) A]. The hydrogen L-tartrate residues of both anions exhibit the common short intramolecular hydroxy-carboxylate O-H...O hydrogen bonds. This work provides a solution to the unusual disorder problem inherent in the structure of this salt, as well as giving another example of the utility of the hydrogen tartrate anion in the generation of sheet substructures in molecular assembly processes.

  14. 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).

  15. 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

  16. 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

  17. 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

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    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.

  20. 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

  1. 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

  2. The vibration-rotation spectrum of D 12CP in the region of the ν2 band: The spectroscopic constants for the states 00 00, 01 10, 02 00, and 02 20 and the bond lengths of the molecule

    NASA Astrophysics Data System (ADS)

    Lavigne, Jacques; Pépin, Claude; Cabana, Aldée

    1984-03-01

    The vibration-rotation spectrum of DCP has been recorded with a resolution of 0.004 cm -1 in the spectral region extending from 575 to 475 cm -1. The fundamental band ν2 and the "hot" bands from the vibrational level (01 10) to the levels (02 00) and (02 20) have been identified and analyzed. A total of 347 infrared transitions have been measured and their wavenumbers together with 13 microwave or millimeter-wave frequencies have been fit simultaneously to obtain 15 spectroscopic constants including those arising from l-type doubling and l-type resonance. The agreement between the calculated and measured wavenumbers of nonblended lines is usually within 1 × 10 -4 cm -1. These constants, used in conjunction with the ones previously obtained for the molecule, allow the calculation of the anharmonicity constants x22 and g22 and of the second-order vibration-rotation interaction constants γ22 and γ11. Although many of the γ's are still missing because an insufficient number of bands have been analyzed, the equilibrium bond lengths for the molecule have been recalculated using the improved set of first-order vibration-rotation interaction constants: re(CH) = 1.06596(11)Å and re(CP) = 1.540452(18)Å.

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

    PubMed

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

    2015-10-01

    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.

  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. 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

  7. BINDING OF THE RESPIRATORY CHAIN INHIBITOR ANTIMYCIN TO THE MITOCHONDRIAL bc1 COMPLEX: A NEW CRYSTAL STRUCTURE REVEALS AN ALTERED INTRAMOLECULAR HYDROGEN-BONDING PATTERN.

    PubMed Central

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

    2006-01-01

    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-salicylamide 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 2.28 Å 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 αA helix. PMID:16024040

  8. 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

  9. Self-assembly and antimicrobial activity of long-chain amide-functionalized ionic liquids in aqueous solution.

    PubMed

    Garcia, M Teresa; Ribosa, Isabel; Perez, Lourdes; Manresa, Angeles; Comelles, Francesc

    2014-11-01

    Surface active amide-functionalized ionic liquids (ILs) consisting of a long alkyl chain (C6C14) connected to a polar head group (methylimidazolium or pyridinium cation) via an amide functional group were synthesized and their thermal stability, micellar properties and antimicrobial activity in aqueous solution investigated. The incorporation of an amide group increased the thermal stability of the functionalized ionic liquids compared to simple alkyl chain substituted ionic liquids. The surface activity and aggregation behaviour in aqueous solution of amide-functionalized ionic liquids were examined by tensiometry, conductivity and spectrofluorimetry. Amide-functionalized ILs displayed surface activity and their critical micelle concentration (cmc) in aqueous media decreased with the elongation of the alkyl side chain as occurs for typical surfactants. Compared to non-functionalized ILs bearing the same alkyl chain, ionic liquids with an amide moiety possess higher surface activity (pC20) and lower cmc values. The introduction of an amide group in the hydrophobic chain close to the polar head enhances adsorption at the air/water interface and micellization which could be attributed to the H-bonding in the headgroup region. The antimicrobial activity was evaluated against a panel of representative Gram-negative and Gram-positive bacteria and fungi. Amide-functionalized ILs with more than eight carbon atoms in the side chain showed broad antimicrobial activity. Antibacterial activities were found to increase with the alkyl chain length being the C12 homologous the most effective antimicrobial agents. The introduction of an amide group enhanced significantly the antifungal activity as compared to non-functionalized ILs.

  10. 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.

    PubMed

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

    2011-12-14

    The ground-state rotational spectra of two weakly bound complexes B···ICF(3) (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···ICF(3) and both the C and O atoms in OC···ICF(3) lie along the C(3) axis of ICF(3). The rotational constant B(0), the centrifugal distortion constants D(J) and D(JK), and the iodine nuclear quadrupole coupling constant χ(aa)(I) were determined for each of the isotopologues (84)Kr···ICF(3), (86)Kr···ICF(3), (16)O(12)C···ICF(3), (16)O(13)C···ICF(3), and (18)O(12)C···ICF(3). Interpretation of the spectroscopic constants reveals that the carbon atom of CO is adjacent to I and participates in the weak bond in OC···ICF(3). 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···ICF(3) and OC···ICF(3), respectively, and to the quadratic force constants for stretching of the weak bond k(σ) = 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 k(σ) values, and the angular geometries of the pair of complexes B···ICF(3) and B···ICl for a given B are compared when B = Kr, CO, H(2)O, H(2)S, or NH(3). The comparison reveals that the iodine bond in B···ICF(3) is systematically longer and weaker than that of B···ICl, while the angular geometry of the B···I moiety is isomorphic in B···ICF(3) and B···ICl for a given B. It is concluded that -CF(3) is less effective than -Cl as an electron-withdrawing group when attached to an I atom and that the angular geometries of the B···ICF(3) can be predicted by means of a simple rule that holds for many hydrogen- and halogen-bonded complexes.

  11. 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

  12. 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

  13. Construction of Electrochemical Chiral Interfaces with Integrated Polysaccharides via Amidation.

    PubMed

    Bao, Liping; Chen, Xiaohui; Yang, Baozhu; Tao, Yongxin; Kong, Yong

    2016-08-24

    Polysaccharides of sodium carboxymethyl cellulose (CMC) and chitosan (CS) were integrated together via amidation reactions between the carboxyl groups on sodium CMC and the amino groups on CS. Compared with individual sodium CMC and CS, the integrated polysaccharides with a mass ratio of 1:1, CMC-CS (1:1), exhibited a three-dimensional (3D) porous network structure, resulting in a significantly enhanced hydrophility due to the exposed polar functional groups in the CMC-CS (1:1). Chiral interfaces were constructed with the integrated polysaccharides and used for electrochemical enantiorecognition of tryptophan (Trp) isomers. The CMC-CS (1:1) chiral interfaces exhibited excellent selectivity toward the Trp isomers owing to the highly hydrophilic feature of CMC-CS (1:1) and the different steric hindrance during the formation of H bonds between Trp isomers and CMC-CS (1:1). Also, the optimization in the preparation of integrated polysaccharides such as mass ratio and combination mode (amidation or electrostatic interactions) was investigated. The CMC-CS (1:1) presented the ability of determining the percentage of d-Trp in racemic mixtures, and thus, the proposed electrochemical chiral interfaces could be regarded as a potential biosensing platform for enantiorecognition of chiral compounds. PMID:27487166

  14. On the additivity of bond dipole moments. Stark effect studies of the rotationally resolved electronic spectra of aniline, benzonitrile, and aminobenzonitrile

    NASA Astrophysics Data System (ADS)

    Borst, David R.; Korter, Timothy M.; Pratt, David W.

    2001-12-01

    We study the influence of an applied electric field on the fully resolved electronic spectra of aniline (AN), benzonitrile (BN), and 4-aminobenzonitrile (ABN) in the gas phase. Using these data, we test the commonly held but rarely proven assumption that the total dipole moment of a polyatomic molecule is the vector sum of bond dipole moments, localized in different parts of the molecule. We find that μa(ABN)≈ μa(AN)+ μa(BN) in the excited S 1 state, but not in the ground S 0 state. Possible reasons for this non-additivity are discussed.

  15. Establishing the ellipsoidal geometry of a benzoic acid-based amphiphile via dimer switching: insights from intramolecular rotation and facial H-bond torsion.

    PubMed

    Ramesh, Nivarthi; Sarangi, Nirod Kumar; Patnaik, Archita

    2013-05-01

    Soft molecular ellipsoids conceived from 3,4-di(dodecyloxy)benzoic acid (DDBA) amphiphile draw attention to monomer structure design, intramolecular -COOH headgroup twist (ϕ°) and cyclic-acyclic dimer switching through facial H-bond torsion (ψ°). Generically, precipitation in hydrogen bonded systems has been the prime phenomenon once the critical aggregation concentrations were reached in the bulk solution. DDBA was no exception to this generalization. It formed precipitates in chloroform and methanol with no specific geometry but with cyclic dimer motifs in them. On the contrary, surface pressure modulated interfacial aggregation with ellipsoidal geometry followed acyclic dimerization (catemer motif) with various levels of headgroup torsion, established through real-time polarization modulated infrared reflection-absorption spectroscopy (IRRAS) and density functional theory (DFT) calculations, that estimated the energy costs for these unexplored pathways. The reaction coordinates ϕ° and ψ° in consonance with 2D surface pressure modulation thus directed the shape anisotropy during the dynamic self-assembly of DDBA. Changes in subphase pH and metal ionic environment had a derogatory effect on the ellipsoid formation, the structural requirement for which strictly followed a stringent need for twin alkyl chains in an asymmetric unit cell, as 4-dodecyloxybenzoic acid (MABA) with a single alkyl chain formed exclusively spherical assemblies with no dimer modulation. The investigation thus reports unexplored energy pathways toward ellipsoidal geometry of the amphiphile in the course of its interfacial aggregation.

  16. 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)

  17. 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

  18. 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

  19. Infrared amide I' band of the coiled coil.

    PubMed

    Reisdorf, W C; Krimm, S

    1996-02-01

    The Fourier transform infrared (FTIR) spectra of several coiled-coil proteins have been shown to possess unusual features in the amide I' region. Band maxima occur in the vicinity of 1630 cm-1, with component bands at higher frequency. This is well below the observed band at 1650 cm-1 found in standard alpha-helical polypeptides such as poly-L-alanine. Normal mode calculations on models of the coiled-coil structure have been performed to investigate this issue. We find that the observed band profile can be reproduced with very small random variation on the phi, psi of tropomyosin. We believe that the shift to lower frequency is due to additional hydrogen bonding of the solvent accessible backbone CO groups to water.

  20. An unusual intramolecular transfer of the fluorobenzyl cation between two remote amidic nitrogen atoms induced by collision in the gas phase.

    PubMed

    Yan, Zhengyin; Tounge, Brett; Caldwell, Gary W

    2012-01-15

    A highly unusual rearrangement in collision-induced dissociation mass spectrometry is reported that involves intramolecular transfer of the fluorobenzyl cation between two remote amidic nitrogen atoms separated by five chemical bonds. The same intramolecular transfer was also observed for two related analogs. It is postulated that the ionic reactions are initiated by protonation of the first amidic nitrogen, resulting in formation of the fluorobenzyl cation and a neutral partner that are maintained together in the gas phase by electrostatic interactions as an intermediate ion-neutral complex. In the ion-neutral complex, the nascent fluorobenzyl cation approaches geometrically to the second amidic nitrogen atom on the neutral partner, and subsequently forms a new C-N bond and an isomeric precursor ion as the charge is retained on the amidic nitrogen. The newly formed isomeric precursor ion eventually undergoes the final fragmentation by amide bond cleavage. Alternatively, the ionic reactions proceed through a direct intramolecular transfer mechanism by which the molecular ion adopts to a ring-like configuration in the gas phase, so that both the donor and recipient nitrogens are geometrically close to each other within a bonding distance to permit a direct transfer between two sites even though they are separated by multiple chemical bonds.

  1. 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

  2. Peptide sweeteners. 3. Effect of modifying the peptide bond on the sweet taste of L-aspartyl-L-phenylalanine methyl ester and its analogues.

    PubMed

    MacDonald, S A; Willson, C G; Chorev, M; Vernacchia, F S; Goodman, M

    1980-04-01

    A series of analogues designed to assess the importance of the amide bond in the dipeptide sweetener L-aspartyl-L-phenylalanine methyl ester has been synthesized and tested. The peptide bond was methylated, replaced by an ester bond, or reversed. all of these modifications produced compounds that did not have a sweet taste. We conclude that the steric, electronic, and directional characteristics of the amide bond are essential for biological activity in the dipeptide sweeteners. PMID:7381839

  3. Peptide sweeteners. 3. Effect of modifying the peptide bond on the sweet taste of L-aspartyl-L-phenylalanine methyl ester and its analogues.

    PubMed

    MacDonald, S A; Willson, C G; Chorev, M; Vernacchia, F S; Goodman, M

    1980-04-01

    A series of analogues designed to assess the importance of the amide bond in the dipeptide sweetener L-aspartyl-L-phenylalanine methyl ester has been synthesized and tested. The peptide bond was methylated, replaced by an ester bond, or reversed. all of these modifications produced compounds that did not have a sweet taste. We conclude that the steric, electronic, and directional characteristics of the amide bond are essential for biological activity in the dipeptide sweeteners.

  4. A Novel Reaction Mediated by Human Aldehyde Oxidase: Amide Hydrolysis of GDC-0834

    PubMed Central

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

    2015-01-01

    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

  5. 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

  6. 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.

  7. Enzymes utilizing glutamine as an amide donor.

    PubMed

    Zalkin, H; Smith, J L

    1998-01-01

    Amide nitrogen from glutamine is a major source of nitrogen atoms incorporated biosynthetically into other amino acids, purine and pyrimidine bases, amino-sugars, and coenzymes. A family comprised of at least sixteen amidotransferases are known to catalyze amide nitrogen transfer from glutamine to their acceptor substrates. Recent fine structural advances, largely as a result of X-ray crystallography, now provide structure-based mechanisms that help to explain fundamental aspects of the catalytic and regulatory interactions of several of these aminotransferases. This chapter provides an overview of this recent progress made on the characterization of amidotransferase structure and mechanism. PMID:9559052

  8. 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

  9. 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.

  10. Solvent-Driven Conformational Exchange for Amide-Linked Bichromophoric BODIPY Derivatives.

    PubMed

    Thakare, Shrikant; Stachelek, Patrycja; Mula, Soumyaditya; More, Ankush B; Chattopadhyay, Subrata; Ray, Alok K; Sekar, Nagaiyan; Ziessel, Raymond; Harriman, Anthony

    2016-09-26

    The fluorescence lifetime and quantum yield are seen to depend in an unexpected manner on the nature of the solvent for a pair of tripartite molecules composed of two identical boron dipyrromethene (BODIPY) residues attached to a 1,10-phenanthroline core. A key feature of these molecular architectures concerns the presence of an amide linkage that connects the BODIPY dye to the heterocyclic platform. The secondary amide derivative is more sensitive to environmental change than is the corresponding tertiary amide. In general, increasing solvent polarity, as measured by the static dielectric constant, above a critical threshold tends to reduce fluorescence but certain hydrogen bond accepting solvents exhibit anomolous behaviour. Fluorescence quenching is believed to arise from light-induced charge transfer between the two BODIPY dyes, but thermodynamic arguments alone do not explain the experimental findings. Molecular modelling is used to argue that the conformation changes in strongly polar media in such a way as to facilitate improved rates of light-induced charge transfer. These solvent-induced changes, however, differ remarkably for the two types of amide. PMID:27529596

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. The nature of the bond between peptide and carrier molecule determines the immunogenicity of the construct.

    PubMed

    Beekman, N J; Schaaper, W M; Langeveld, J P; Boshuizen, R S; Meloen, R H

    2001-09-01

    The influence of the nature of the bond between a peptide and a (lipidic) carrier molecule on the immunogenicity of that construct was investigated. As types of bonds a thioester-, a disulfide-, an amide- and a thioether bond were investigated. As carrier molecules a peptide, an N-palmitoylated peptide or a C(16)-hydrocarbon chain were used. The biostability of the bond between peptide and carrier molecule is thioether > amide > disulfide > thioester. However, the immunogenic potency of the constructs used was found to be thioester > disulfide > amide > thioether. In conclusion, a construct with a bond between peptide and (lipidic) carrier molecule that is more susceptible to biological degradation is more immunogenic when used in a peptide-based vaccine than a bond that is less susceptible to biological degradation. PMID:11576330

  16. 40 CFR 721.10680 - Fatty 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 amides (generic). 721.10680... Substances § 721.10680 Fatty acid amides (generic). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substances identified generically as fatty acid amides (PMNs...

  17. 40 CFR 721.10686 - Fatty 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 amides (generic). 721.10686... Substances § 721.10686 Fatty acid amides (generic). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substances identified generically as fatty acid amides (PMNs...

  18. 40 CFR 721.10691 - Fatty acid amide (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Fatty acid amide (generic). 721.10691... Substances § 721.10691 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-13-267) is...

  19. 40 CFR 721.10320 - Fatty acid amide (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 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...

  20. 40 CFR 721.10687 - Fatty acid amide hydrochlorides (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Fatty acid amide hydrochlorides... Specific Chemical Substances § 721.10687 Fatty acid amide hydrochlorides (generic). (a) Chemical substance... fatty acid amide hydrochlorides (PMNs P-13-201, P-13-203, P-13-204, P-13-205, P-13-206, P-13-207,...

  1. 40 CFR 721.10320 - Fatty acid amide (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 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...

  2. 40 CFR 721.10463 - Fatty 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 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...

  3. 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...

  4. 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...

  5. Crystal structures and spectroscopic properties of ester amide and diamide of squaric acid with prolinamide

    NASA Astrophysics Data System (ADS)

    Kolev, Tsonko; Seidel, Rüdiger W.; Mayer-Figge, Heike; Spiteller, Michael; Sheldrick, William S.; Koleva, Bojidarka B.

    2009-04-01

    We report the synthesis, spectroscopic and structural elucidation of two prolinamide derivatives of squaric acid, i.e. prolinamide ester amide of squaric acid ethyl ester ( 1) and prolinamide diamide of squaric acid dihydrate ( 2). Both compounds crystallize in non-centrosymmetric space groups, monoclinic P2 1 ( 1) and orthorhombic P2 12 12 1 ( 2), respectively. For first time in the literature the crystal structure of homodiamide of amino acid amide of squaric acid is reported. The data for heterodiamides is also absent. Supramolecular zig-zag chains by hydrogen bonds of H 2N-C dbnd O⋯HNH (3.020 Å) and HNH⋯O dbnd C (Sq) (2.972 Å) types with the participation of amide and squaric acid (Sq) fragments, -C dbnd O-NH 2 and O dbnd C (Sq) are refined in ( 1). A helix supramolecular structure is formed in ( 2) by moderate intermolecular HNH⋯O dbnd C(NH 2) hydrogen bond with length of 2.947 Å. The two crystallographical non-equivalent water molecules stabilized the helix by interactions of types HOH⋯O dbnd C (Sq) (2.917 Å), HOH⋯O dbnd C(NH 2) (2.899 Å), H 2O⋯NH 2(C dbnd O) (2.972 Å), respectively. Optical and magnetic properties are investigated with a view to explain the correlation structure-properties of the newly synthesized molecules.

  6. 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

  7. Design, synthesis and molecular docking of amide and urea derivatives as Escherichia coli PDHc-E1 inhibitors.

    PubMed

    He, Jun-Bo; Ren, Yan-Liang; Sun, Qiu-Shuang; You, Ge-Yun; Zhang, Li; Zou, Peng; Feng, Ling-Ling; Wan, Jian; He, Hong-Wu

    2014-06-15

    By targeting the ThDP binding site of Escherichia coli PDHc-E1, two new 'open-chain' classes of E. coli PDHc-E1 inhibitors, amide and urea derivatives, were designed, synthesized, and evaluated. The amide derivatives of compound 6d, with 4-NO2 in the benzene ring, showed the most potent inhibition of E. coli PDHc-E1. The urea derivatives displayed more potent inhibitory activity than the corresponding amide derivatives with the same substituent. Molecular docking studies confirmed that the urea derivatives have more potency due to the two hydrogen bonds formed by two NH of urea with Glu522. The docking results also indicate it might help us to design more efficient PDHc-E1 inhibitors that could interact with Glu522.

  8. 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.

  9. 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

  10. 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.

  11. Strength of a bifurcated H bond

    PubMed Central

    Feldblum, Esther S.; Arkin, Isaiah T.

    2014-01-01

    Macromolecules are characterized by their particular arrangement of H bonds. Many of these interactions involve a single donor and acceptor pair, such as the regular H-bonding pattern between carbonyl oxygens and amide H+s four residues apart in α-helices. The H-bonding potential of some acceptors, however, leads to the phenomenon of overcoordination between two donors and one acceptor. Herein, using isotope-edited Fourier transform infrared measurements and density functional theory (DFT) calculations, we measured the strength of such bifurcated H bonds in a transmembrane α-helix. Frequency shifts of the 13C=18O amide I mode were used as a reporter of the strength of the bifurcated H bond from a thiol and hydroxyl H+ at residue i + 4. DFT calculations yielded very similar frequency shifts and an energy of −2.6 and −3.4 kcal/mol for the thiol and hydroxyl bifurcated H bonds, respectively. The strength of the intrahelical bifurcated H bond is consistent with its prevalence in hydrophobic environments and is shown to significantly impact side-chain rotamer distribution. PMID:24591597

  12. 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.

  13. 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

  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. DFT-based simulations of IR amide I' spectra for a small protein in solution. Comparison of explicit and empirical solvent models.

    PubMed

    Grahnen, Johan A; Amunson, Krista E; Kubelka, Jan

    2010-10-14

    Infrared (IR) amide I' spectra are widely used for investigations of the structural properties of proteins in aqueous solution. For analysis of the experimental data, it is necessary to separate the spectral features due to the backbone conformation from those arising from other factors, in particular the interaction with solvent. We investigate the effects of solvation on amide I' spectra for a small 40-residue helix-turn-helix protein by theoretical simulations based on density functional theory (DFT). The vibrational force fields and intensity parameters for the protein amide backbone are constructed by transfer from smaller heptaamide fragments; the side chains are neglected in the DFT calculations. Solvent is modeled at two different levels: first as explicit water hydrogen bonded to the surface amide groups, treated at the same DFT level, and, second, using the electrostatic map approach combined with molecular dynamics (MD) simulation. Motional narrowing of the spectral band shapes due to averaging over the fast solvent fluctuation is introduced by use of the time-averaging approximation (TAA). The simulations are compared with the experimental amide I', including two (13)C isotopically edited spectra, corrected for the side-chain signals. Both solvent models are consistent with the asymmetric experimental band shape, which arises from the differential solvation of the amide backbone. However, the effects of (13)C isotopic labeling are best captured by the gas-phase calculations. The limitations of the solvent models and implications for the theoretical simulations of protein amide vibrational spectra are discussed.

  16. Uncovering the Sensitivity of Amide-II Vibration to Peptide-Ion Interactions.

    PubMed

    Zhao, Juan; Wang, Jianping

    2016-09-15

    In this work, linear infrared spectroscopy was used to examine the effect of salt on the amide-II mode in a model β-peptide (N-ethylpropionamide, NEPA) in its deuterated form, to reveal the sensitivity of this mode in reporting peptide-ion interactions. In comparison to the case of NEPA in water, the amide-II spectra mainly showed a red-shifted component in four typical saline solutions (NaCl, CaCl2, MgCl2, and AlCl3) examined in this work. Our results suggest that highly populated hydrated ion complexes under high salt concentration conditions destroy the hydration layer of the model peptide and result in mostly a salting-out state of the peptide. Molecular dynamics simulations suggest that the hydrated cation mainly interacts with the peptide backbone on the amide C═O side, whereas the hydrated anion interacts on the amide N-H side. As the amide-II mode is mainly a combination of the C-N stretching and N-H in-plane-bending vibrations, this mode is advantageous in being responsive to ionic interaction from both the C═O and N-H sides. Such a dual sensitivity should be very useful in probing the breaking and/or formation of the interamide hydrogen bond between the C═O and N-H groups, which is a very important interaction involved in the solvation and stabilization, as well as folding/unfolding of proteins. PMID:27537202

  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. A Simple Primary Amide for the Selective Recovery of Gold from Secondary Resources.

    PubMed

    Doidge, Euan D; Carson, Innis; Tasker, Peter A; Ellis, Ross J; Morrison, Carole A; Love, Jason B

    2016-09-26

    Waste electrical and electronic equipment (WEEE) such as mobile phones contains a plethora of metals of which gold is by far the most valuable. Herein a simple primary amide is described that achieves the selective separation of gold from a mixture of metals typically found in mobile phones by extraction into toluene from an aqueous HCl solution; unlike current processes, reverse phase transfer is achieved simply using water. Phase transfer occurs by dynamic assembly of protonated and neutral amides with [AuCl4 ](-) ions through hydrogen bonding in the organic phase, as shown by EXAFS, mass spectrometry measurements, and computational calculations, and supported by distribution coefficient analysis. The fundamental chemical understanding gained herein should be integral to the development of metal-recovery processes, in particular through the use of dynamic assembly processes to build complexity from simplicity.

  19. A Simple Primary Amide for the Selective Recovery of Gold from Secondary Resources.

    PubMed

    Doidge, Euan D; Carson, Innis; Tasker, Peter A; Ellis, Ross J; Morrison, Carole A; Love, Jason B

    2016-09-26

    Waste electrical and electronic equipment (WEEE) such as mobile phones contains a plethora of metals of which gold is by far the most valuable. Herein a simple primary amide is described that achieves the selective separation of gold from a mixture of metals typically found in mobile phones by extraction into toluene from an aqueous HCl solution; unlike current processes, reverse phase transfer is achieved simply using water. Phase transfer occurs by dynamic assembly of protonated and neutral amides with [AuCl4 ](-) ions through hydrogen bonding in the organic phase, as shown by EXAFS, mass spectrometry measurements, and computational calculations, and supported by distribution coefficient analysis. The fundamental chemical understanding gained herein should be integral to the development of metal-recovery processes, in particular through the use of dynamic assembly processes to build complexity from simplicity. PMID:27554437

  20. A simple primary amide for the selective recovery of gold from secondary resources

    DOE PAGES

    Doidge, Euan D.; Carson, Innis; Tasker, Peter A.; Ellis, Ross J.; Morrison, Carole A.; Love, Jason B.

    2016-08-24

    Waste electrical and electronic equipment (WEEE) such as mobile phones contains a plethora of metals of which gold is by far the most valuable. Herein a simple primary amide is described that achieves the selective separation of gold from a mixture of metals typically found in mobile phones by extraction into toluene from an aqueous HCl solution; unlike current processes, reverse phase transfer is achieved simply using water. Phase transfer occurs by dynamic assembly of protonated and neutral amides with [AuCl4]– ions through hydrogen bonding in the organic phase, as shown by EXAFS, mass spectrometry measurements, and computational calculations, andmore » supported by distribution coefficient analysis. In conclusion, the fundamental chemical understanding gained herein should be integral to the development of metal-recovery processes, in particular through the use of dynamic assembly processes to build complexity from simplicity.« less

  1. Selective rhodium-catalyzed reduction of tertiary amides in amino acid esters and peptides.

    PubMed

    Das, Shoubhik; Li, Yuehui; Bornschein, Christoph; Pisiewicz, Sabine; Kiersch, Konstanze; Michalik, Dirk; Gallou, Fabrice; Junge, Kathrin; Beller, Matthias

    2015-10-12

    Efficient reduction of the tertiary amide bond in amino acid derivatives and peptides is described. Functional group selectivity has been achieved by applying a commercially available rhodium precursor and bis(diphenylphosphino)propane (dppp) ligand together with phenyl silane as a reductant. This methodology allows for specific reductive derivatization of biologically interesting peptides and offers straightforward access to a variety of novel peptide derivatives for chemical biology studies and potential pharmaceutical applications. The catalytic system tolerates a variety of functional groups including secondary amides, ester, nitrile, thiomethyl, and hydroxy groups. This convenient hydrosilylation reaction proceeds at ambient conditions and is operationally safe because no air-sensitive reagents or highly reactive metal hydrides are needed. PMID:26189442

  2. Selective rhodium-catalyzed reduction of tertiary amides in amino acid esters and peptides.

    PubMed

    Das, Shoubhik; Li, Yuehui; Bornschein, Christoph; Pisiewicz, Sabine; Kiersch, Konstanze; Michalik, Dirk; Gallou, Fabrice; Junge, Kathrin; Beller, Matthias

    2015-10-12

    Efficient reduction of the tertiary amide bond in amino acid derivatives and peptides is described. Functional group selectivity has been achieved by applying a commercially available rhodium precursor and bis(diphenylphosphino)propane (dppp) ligand together with phenyl silane as a reductant. This methodology allows for specific reductive derivatization of biologically interesting peptides and offers straightforward access to a variety of novel peptide derivatives for chemical biology studies and potential pharmaceutical applications. The catalytic system tolerates a variety of functional groups including secondary amides, ester, nitrile, thiomethyl, and hydroxy groups. This convenient hydrosilylation reaction proceeds at ambient conditions and is operationally safe because no air-sensitive reagents or highly reactive metal hydrides are needed.

  3. Titanocene(III)-Catalyzed Three-Component Reaction of Secondary Amides, Aldehydes, and Electrophilic Alkenes.

    PubMed

    Zheng, Xiao; He, Jiang; Li, Heng-Hui; Wang, Ao; Dai, Xi-Jie; Wang, Ai-E; Huang, Pei-Qiang

    2015-11-01

    An umpolung Mannich-type reaction of secondary amides, aliphatic aldehydes, and electrophilic alkenes has been disclosed. This reaction features the one-pot formation of C-N and C-C bonds by a titanocene-catalyzed radical coupling of the condensation products, from secondary amides and aldehydes, with electrophilic alkenes. N-substituted γ-amido-acid derivatives and γ-amido ketones can be efficiently prepared by the current method. Extension to the reaction between ketoamides and electrophilic alkenes allows rapid assembly of piperidine skeletons with α-amino quaternary carbon centers. Its synthetic utility has been demonstrated by a facile construction of the tricyclic core of marine alkaloids such as cylindricine C and polycitorol A.

  4. /sup 17/O NMR spectroscopy: torsion angle relationships in aryl carboxylic esters, acids, and amides

    SciTech Connect

    Baumstark, A.L.; Balakrishnan, P.; Dotrong, M.; McCloskey, C.J.; Oakley, M.G.; Boykin, D.W.

    1987-02-18

    /sup 1/ /sup 7/O NMR spectroscopic data (natural abundance in acetonitrile at 75/sup 0/C) were obtained for the following series of electronically similar, sterically hindered compounds: aromatic methyl esters, aromatic carboxylic acids, and aromatic amides. Torsional angles were calculated by the molecular mechanics (MM2) method. Linear regression analysis of the estimated torsion angles and the /sup 17/O chemical shift data for each series yielded the following results (series, slope delta/degree, correlation coefficient): esters (C=O), 0.70, 0.997; esters (-0-), 0.43, 0.992; acids (-CO/sub 2/H), 0.56, 0.994; amides (C=O), 0.84, 0.942; N,N-dimethylamides (C=O), 0.6, 0.991. The results are discussed in terms of minimization of repulsive van der Waals interactions by rotation of the functional group out of the plane of the aromatic ring.

  5. The amide III vibrational circular dichroism band as a probe to detect conformational preferences of alanine dipeptide in water.

    PubMed

    Mirtič, Andreja; Merzel, Franci; Grdadolnik, Jože

    2014-07-01

    The conformational preferences of blocked alanine dipeptide (ADP), Ac-Ala-NHMe, in aqueous solution were studied using vibrational circular dichroism (VCD) together with density functional theory (DFT) calculations. DFT calculations of three most representative conformations of ADP surrounded by six explicit water molecules immersed in a dielectric continuum have proven high sensitivity of amide III VCD band shape that is characteristic for each conformation of the peptide backbone. The polyproline II (PII ) and αR conformation of ADP are associated with a positive VCD band while β conformation has a negative VCD band in amide III region. Knowing this spectral characteristic of each conformation allows us to assign the experimental amide III VCD spectrum of ADP. Moreover, the amide III region of the VCD spectrum was used to determine the relative populations of conformations of ADP in water. Based on the interpretation of the amide III region of VCD spectrum we have shown that dominant conformation of ADP in water is PII which is stabilized by hydrogen bonded water molecules between CO and NH groups on the peptide backbone.

  6. 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.

  7. 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

  8. 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.

  9. Interaction geometries and energies of hydrogen bonds to C[double bond]O and C[double bond]S acceptors: a comparative study.

    PubMed

    Wood, Peter A; Pidcock, Elna; Allen, Frank H

    2008-08-01

    The occurrence, geometries and energies of hydrogen bonds from N-H and O-H donors to the S acceptors of thiourea derivatives, thioamides and thiones are compared with data for their O analogues - ureas, amides and ketones. Geometrical data derived from the Cambridge Structural Database indicate that hydrogen bonds to the C[double bond]S acceptors are much weaker than those to their C[double bond]O counterparts: van der Waals normalized hydrogen bonds to O are shorter than those to S by approximately 0.25 A. Further, the directionality of the approach of the hydrogen bond with respect to S, defined by the C[double bond]S...H angle, is in the range 102-109 degrees , much lower than the analogous C[double bond]O...H angle which lies in the range 127-140 degrees . Ab initio calculations using intermolecular perturbation theory show good agreement with the experimental results: the differences in hydrogen-bond directionality are closely reproduced, and the interaction energies of hydrogen bonds to S are consistently weaker than those to O, by approximately 12 kJ mol(-1), for each of the three compound classes. There are no CSD examples of hydrogen bonds to aliphatic thiones, (Csp(3))(2)C=S, consistent with the near-equality of the electronegativities of C and S. Thioureas and thioamides have electron-rich N substituents replacing the Csp(3) atoms. Electron delocalization involving C[double bond]S and the N lone pairs then induces a significant >C(delta+)[double bond]S(delta-) dipole, which enables the formation of the medium-strength C[double bond]S...H bonds observed in thioureas and thioamides.

  10. Acid-promoted chemoselective introduction of amide functionality onto aromatic compounds mediated by an isocyanate cation generated from carbamate.

    PubMed

    Sumita, Akinari; Kurouchi, Hiroaki; Otani, Yuko; Ohwada, Tomohiko

    2014-10-01

    Carbamates have been used as precursors of isocyanates, but heating in the presence of strong acids is required because cleavage of the C-O bond in carbamates is energy-demanding even in acid media. Direct amidation of aromatic compounds by isocyanate cations generated at room temperature from carbamoyl salicylates in trifluoromethanesulfonic acid (TfOH) was examined. Carbamates with ortho-salicylate as an ether group (carbamoyl salicylates) showed dramatically accelerated O-C bond dissociation in TfOH, which resulted in facile generation of the isocyanate cation. These chemoselective intermolecular aromatic amidation reactions proceeded even at room temperature and showed good compatibility with other electrophilic functionalities and high discrimination between N-monosubstituted carbamate and N,N-disubstituted carbamate. The reaction rates of secondary and tertiary amide formation were markedly different, and this difference was utilized to achieve successive (tandem) amidation reactions of molecules with an N-monosubstituted carbamate and an N,N-disubstituted carbamate with two kinds of aromatic compounds.

  11. 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

  12. 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…

  13. Sticker Bonding.

    ERIC Educational Resources Information Center

    Frazier, Laura Corbin

    2000-01-01

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

  14. Carbonyl-carbonyl interactions and amide π-stacking as the directing motifs of the supramolecular assembly of ethyl N-(2-acetylphenyl)oxalamate in a synperiplanar conformation.

    PubMed

    Cabrera-Pérez, Laura C; García-Báez, Efrén V; Franco-Hernández, Marina O; Martínez-Martínez, Francisco J; Padilla-Martínez, Itzia I

    2015-05-01

    The title compound, C12H13NO4, is one of the few examples that exhibits a syn conformation between the amide and ester carbonyl groups of the oxalyl group. This conformation allows the engagement of the amide H atom in an intramolecular three-centred hydrogen-bonding S(6)S(5) motif. The compound is self-assembled by C=O...C=O and amide-π interactions into stacked columns along the b-axis direction. The concurrence of both interactions seems to be responsible for stabilizing the observed syn conformation between the carbonyl groups. The second dimension, along the a-axis direction, is developed by soft C-H...O hydrogen bonding. Density functional theory (DFT) calculations at the B3LYP/6-31G(d,p) level of theory were performed to support the experimental findings.

  15. 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.

  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. 40 CFR 721.10682 - Fatty acid amide hydrochlorides (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Fatty acid amide hydrochlorides... Specific Chemical Substances § 721.10682 Fatty acid amide hydrochlorides (generic). (a) Chemical substances... fatty acid amide hydrochlorides (PMNs P-13-63, P-13-64, P-13-65, P-13-69, P-13-70, P-13-71, P-13-72,...

  18. Cp*Co(III)-Catalyzed Dehydrative C-H Allylation of 6-Arylpurines and Aromatic Amides Using Allyl Alcohols in Fluorinated Alcohols.

    PubMed

    Bunno, Youka; Murakami, Nanami; Suzuki, Yudai; Kanai, Motomu; Yoshino, Tatsuhiko; Matsunaga, Shigeki

    2016-05-01

    Cp*Co(III)-catalyzed C-H allylation of various aromatic C-H bonds using allyl alcohols as allylating reagents is described. Improved reaction conditions using fluorinated alcohol solvents afforded efficient directed C-H allylation of 6-arylpurines, benzamides, and a synthetically useful Weinreb amide with good functional group compatibility.

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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}.

  4. Rotational spectrum of tryptophan.

    PubMed

    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 (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.

  5. 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.

  6. Rotational Spectrum of Tryptophan

    NASA Astrophysics Data System (ADS)

    Sanz, M. Eugenia; Cabezas, Carlos; Mata, Santiago; Alonso, José L.

    2014-06-01

    The rotational spectrum of the natural amino acid tryptophan has been observed using a recently constructed LA-MB-FTMW spectrometer, specifically designed to optimize the detection of heavier molecules at a lower frequency range. Independent analyses of the rotational spectra of individual conformers have conducted to a definitive identification of two different conformers of tryptophan, with one of the observed conformers never reported before. The experimental values of the 14N nuclear quadrupole coupling constants have been found capital in the discrimination of the conformers. Both observed conformers are stabilized by a O-H\\cdotsN hydrogen bond in the side chain and a N-H\\cdotsπ interaction forming a chain that reinforces the strength of hydrogen bonds through cooperative effects.

  7. 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.

  8. 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

  9. 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

  10. AMID: autonomous modeler of intragenic duplication.

    PubMed

    Kummerfeld, Sarah K; Weiss, Anthony S; Fekete, Alan; Jermiin, Lars S

    2003-01-01

    Intragenic duplication is an evolutionary process where segments of a gene become duplicated. While there has been much research into whole-gene or domain duplication, there have been very few studies of non-tandem intragenic duplication. The identification of intragenically replicated sequences may provide insight into the evolution of proteins, helping to link sequence data with structure and function. This paper describes a tool for autonomously modelling intragenic duplication. AMID provides: identification of modularly repetitive genes; an algorithm for identifying repeated modules; and a scoring system for evaluating the modules' similarity. An evaluation of the algorithms and use cases are presented.

  11. 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

  12. 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...

  13. 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

  14. Theoretical study on the properties of linear and cyclic amides in gas phase and water solution.

    PubMed

    Aparicio-Martínez, S; Hall, K R; Balbuena, P B

    2006-07-27

    The structural and energetic properties of a group of selected amides, of well-known importance for the design of efficient clathrate inhibitors, are calculated with Hartree-Fock and density functional theory, B3LYP, theoretical levels, and a 6-311++g** basis set in the gas phase and a water solution. The conformational behavior of the molecules is studied through the scanning of the torsional potential energy surfaces and by the analysis of the differences in the energetic and structural properties between the isomers. The properties of the amides in water solution are determined within a self-consistent reaction field approach with a polarizable continuum model that allows the calculation of the different contributions to the free energy of solvation. The calculated barriers to rotation are in good agreement with the available experimental data and the comparison of the gas and water results shows the strong effect of the solute polarization. The properties of different amide-water complexes are calculated and compared with available experimental information.

  15. Glutamic Acid Selective Chemical Cleavage of Peptide Bonds.

    PubMed

    Nalbone, Joseph M; Lahankar, Neelam; Buissereth, Lyssa; Raj, Monika

    2016-03-01

    Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.

  16. 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

  17. 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

  18. 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.

  19. Development of a novel amide-silica stationary phase for the reversed-phase HPLC separation of different classes of phytohormones.

    PubMed

    Aral, Hayriye; Aral, Tarık; Ziyadanoğulları, Berrin; Ziyadanoğulları, Recep

    2013-11-15

    A novel amide-bonded silica stationary phase was prepared starting from N-Boc-phenylalanine, cyclohexylamine and spherical silica gel (4 µm, 60 Å). The amide ligand was synthesised with high yield. The resulting amide bonded stationary phase was characterised by SEM, IR and elemental analysis. The resulting selector bearing a polar amide group is used for the reversed-phase chromatography separation of different classes of thirteen phytohormones (plant hormones). The chromatographic behaviours of these analytes on the amide-silica stationary phase were compared with those of RP-C18 column under same conditions. The effects of different separation conditions, such as mobile phase, pH value, flow rate and temperature, on the separation and retention behaviours of the 13 phytohormones in this system were studied. The optimum separation was achieved using reversed-phase HPLC gradient elution with an aqueous mobile phase containing pH=6.85 potassium phosphate buffer (20 mM) and acetonitrile with a 22 °C column temperature. Under these experimental conditions, the 12 phytohormones could be separated and detected at 230 or 270 nm within 26 min.

  20. 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

  1. Helix bending in alamethicin: molecular dynamics simulations and amide hydrogen exchange in methanol.

    PubMed Central

    Gibbs, N; Sessions, R B; Williams, P B; Dempsey, C E

    1997-01-01

    Molecular dynamics simulations of alamethicin in methanol were carried out with either a regular alpha-helical conformation or the x-ray crystal structure as starting structures. The structures rapidly converged to a well-defined hydrogen-bonding pattern with mixed alpha-helical and 3(10)-helical hydrogen bonds, consistent with NMR structural characterization, and did not unfold throughout the 1-ns simulation, despite some sizable backbone fluctuations involving reversible breaking of helical hydrogen bonds. Bending of the helical structure around residues Aib10-Aib13 was associated with reversible flips of the peptide bonds involving G11 (Aib10-G11 or G11-L12 peptide bonds), yielding discrete structural states in which the Aib10 carbonyl or (rarely) the G11 carbonyl was oriented away from the peptide helix. These peptide bond reversals could be accommodated without greatly perturbing the adjacent helical structure, and intramolecular hydrogen bonding was generally maintained in bent states through the formation of new (non-alpha or 3[10]) hydrogen bonds with good geometries: G11 NH-V9 CO (inverse gamma turn), Aib13 NH-Aib8 CO (pi-helix) and, rarely, L12 NH- Q7 NH (pi-helix). These observations may reconcile potentially conflicting NMR structural information for alamethicin in methanol, in which evidence for conformational flexibility in the peptide sequence before P14 (G11-Aib13) contrasts with the stability of backbone amide NH groups to exchange with solvent. Similar reversible reorientation of the Thr11-Gly12 peptide bond of melittin is also observed in dynamics simulations in methanol (R. B. Sessions, N. Gibbs, and C. E. Dempsey, submitted). This phenomenon may have some role in the orientation of the peptide carbonyl in solvating the channel lumen in membrane ion channel states of these peptides. Images FIGURE 1 FIGURE 2 PMID:9168025

  2. The rotational spectrum of tyrosine.

    PubMed

    Pérez, Cristóbal; Mata, Santiago; Cabezas, Carlos; López, Juan C; Alonso, José L

    2015-04-23

    In this work neutral tyrosine has been generated in the gas phase by laser ablation of solid samples, and its most abundant conformers characterized through their rotational spectra. Their identification has been made by comparison between the experimental and ab initio values of the rotational and quadrupole coupling constants. Both conformers are stabilized by an O-H•••N hydrogen bond established within the amino acid skeleton chain and an additional weak N-H•••π hydrogen bond. The observed conformers differ in the orientation of the phenolic -OH group.

  3. 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

  4. 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%).

  5. 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

  6. Rotational testing.

    PubMed

    Furman, J M

    2016-01-01

    The natural stimulus for the semicircular canals is rotation of the head, which also might stimulate the otolith organs. Vestibular stimulation usually induces eye movements via the vestibulo-ocular reflex (VOR). The orientation of the subject with respect to the axis of rotation and the orientation of the axis of rotation with respect to gravity together determine which labyrinthine receptors are stimulated for particular motion trajectories. Rotational testing usually includes the measurement of eye movements via a video system but might use a subject's perception of motion. The most common types of rotational testing are whole-body computer-controlled sinusoidal or trapezoidal stimuli during earth-vertical axis rotation (EVAR), which stimulates primarily the horizontal semicircular canals bilaterally. Recently, manual impulsive rotations, known as head impulse testing (HIT), have been developed to assess individual horizontal semicircular canals. Most types of rotational stimuli are not used routinely in the clinical setting but may be used in selected research environments. This chapter will discuss clinically relevant rotational stimuli and several types of rotational testing that are used primarily in research settings. PMID:27638070

  7. 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

  8. 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).

  9. 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

  10. Discovery of a novel series of potent MK2 non-ATP competitive inhibitors using 1,2-substituted azoles as cis-amide isosteres.

    PubMed

    Xiao, Dong; Zhu, Xiaohong; Sofolarides, Michael; Degrado, Sylvia; Shao, Ning; Rao, Ashwin; Chen, Xiao; Aslanian, Robert; Fossetta, James; Tian, Fang; Trivedi, Prashant; Lundell, Daniel; Palani, Anandan

    2014-08-01

    A unified strategy was conceived and implemented to deliver conformationally constrained anilides based on their preferred cis-amide conformers. The imidazole/triazole mimicing amide bonds were designed, building upon an earlier discovery of a novel series of tricyclic lactams MK2 kinase inhibitors. This approach enabled rapid, modular synthesis of structurally novel analogs. The efficient SAR development led to the discovery of low molecular weight and potent MK2 non-ATP competitive inhibitors with good ligand efficiency, which led to improved permeability and oral exposure in rats.

  11. 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

  12. 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

  13. Characterizing the Intramolecular H-bond and Secondary Structure in Methylated GlyGlyH+ with H2 Predissociation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Leavitt, Christopher M.; Wolk, Arron B.; Kamrath, Michael Z.; Garand, Etienne; van Stipdonk, Michael J.; Johnson, Mark A.

    2011-11-01

    We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH+•(H2)1,2, GlySarH+•(D2)2, SarGlyH+•(H2)2, and SarSarH+•(D2)2, generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H2 (D2) molecules in a linear action regime throughout the 700-4200 cm-1 range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N-H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110o) about the peptide backbone.

  14. Novel inhibitors of fatty acid amide hydrolase.

    PubMed

    Sit, S Y; Conway, Charlie; Bertekap, Robert; Xie, Kai; Bourin, Clotilde; Burris, Kevin; Deng, Hongfeng

    2007-06-15

    A class of bisarylimidazole derivatives are identified as potent inhibitors of the enzyme fatty acid amide hydrolase (FAAH). Compound 17 (IC(50)=2 nM) dose-dependently (0.1-10mg/kg, iv) potentiates the effects of exogenous anandamide (1 mg/kg, iv) in a rat thermal escape test (Hargreaves test), and shows robust antinociceptive activity in animal models of persistent (formalin test) and neuropathic (Chung model) pain. Compound 17 (20 mg/kg, iv) demonstrates activity in the formalin test that is comparable to morphine (3mg/kg, iv), and is dose-dependently inhibited by the CB1 antagonist SR141716A. In the Chung model, compound 17 shows antineuropathic effects similar to high-dose (100 mg/kg) gabapentin. FAAH inhibition shows potential utility for the clinical treatment of persistent and neuropathic pain.

  15. Copoly(imide-amides) containing hexafluoroisopropylidene

    NASA Technical Reports Server (NTRS)

    Irvin, David J.; Cassidy, Patrick E.; Cameron, Mitch L.

    1990-01-01

    The incorporation of the hexafluoroisopropylidene (HFIP or 6F) group into polymer backbones brings about important and useful changes in properties. These differences include increased thermal and environmental resistance and solubility and decreased dielectric constant and color. Several types of backbones have been substrates for the inclusion of HFIP and all results have reflected impressive property benefits. This project involved the incorporation of 6F groups into a poly(imide-amide) backbone by the condensation of a 6F-containing dianhydride with 4-aminobenzoic acid to yield a diimide terminated with two carboxylic acid groups. This diacid trimer was then polymerized with various diamines. The polymers were obtained in yields of 86-94 percent and with viscosities of 0.90-2.26 dL/g. They were stable to above 500 C and clear, colorless films could be cast from DMAc.

  16. 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

  17. 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.

  18. 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.

  19. 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…

  20. New organic semiconductors with imide/amide-containing molecular systems.

    PubMed

    Liu, Zitong; Zhang, Guanxin; Cai, Zhengxu; Chen, Xin; Luo, Hewei; Li, Yonghai; Wang, Jianguo; Zhang, Deqing

    2014-10-29

    Due to their high electron affinities, chemical and thermal stabilities, π-conjugated molecules with imide/amide frameworks have received considerable attentions as promising candidates for high-performance optoelectronic materials, particularly for organic semiconductors with high carrier mobilities. The purpose of this Research News is to give an overview of recent advances in development of high performance imide/amide based organic semiconductors for field-effect transistors. It covers naphthalene diimide-, perylene diimide- and amide-based conjugated molecules and polymers for organic semiconductors. PMID:24633804

  1. New organic semiconductors with imide/amide-containing molecular systems.

    PubMed

    Liu, Zitong; Zhang, Guanxin; Cai, Zhengxu; Chen, Xin; Luo, Hewei; Li, Yonghai; Wang, Jianguo; Zhang, Deqing

    2014-10-29

    Due to their high electron affinities, chemical and thermal stabilities, π-conjugated molecules with imide/amide frameworks have received considerable attentions as promising candidates for high-performance optoelectronic materials, particularly for organic semiconductors with high carrier mobilities. The purpose of this Research News is to give an overview of recent advances in development of high performance imide/amide based organic semiconductors for field-effect transistors. It covers naphthalene diimide-, perylene diimide- and amide-based conjugated molecules and polymers for organic semiconductors.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. Herringbone Array of Hydrogen-bonded Ribbons in 2-ethoxybenzamide from High-resolution X-ray Powder Diffraction

    SciTech Connect

    Pagola, S.; Stephens, P

    2009-01-01

    In 2-ethoxybenzamide, C{sub 9}H{sub 11}NO{sub 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.

  8. 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...

  9. 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##

  10. Synthesis of chemically bonded graphene/carbon nanotube composites and their application in large volumetric capacitance supercapacitors.

    PubMed

    Jung, Naeyoung; Kwon, Soongeun; Lee, Dongwook; Yoon, Dong-Myung; Park, Young Min; Benayad, Anass; Choi, Jae-Young; Park, Jong Se

    2013-12-17

    Chemically bonded graphene/carbon nanotube composites as flexible supercapacitor electrode materials are synthesized by amide bonding. Carbon nanotubes attached along the edges and onto the surface of graphene act as spacers to increase the electrolyte-accessible surface area. Our lamellar structure electrodes demonstrate the largest volumetric capacitance (165 F cm(-3) ) ever shown by carbon-based electrodes. PMID:24105733

  11. Synthesis of chemically bonded graphene/carbon nanotube composites and their application in large volumetric capacitance supercapacitors.

    PubMed

    Jung, Naeyoung; Kwon, Soongeun; Lee, Dongwook; Yoon, Dong-Myung; Park, Young Min; Benayad, Anass; Choi, Jae-Young; Park, Jong Se

    2013-12-17

    Chemically bonded graphene/carbon nanotube composites as flexible supercapacitor electrode materials are synthesized by amide bonding. Carbon nanotubes attached along the edges and onto the surface of graphene act as spacers to increase the electrolyte-accessible surface area. Our lamellar structure electrodes demonstrate the largest volumetric capacitance (165 F cm(-3) ) ever shown by carbon-based electrodes.

  12. 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

  13. Rotational Energy.

    ERIC Educational Resources Information Center

    Lockett, Keith

    1988-01-01

    Demonstrates several objects rolling down a slope to explain the energy transition among potential energy, translational kinetic energy, and rotational kinetic energy. Contains a problem from Galileo's rolling ball experiment. (YP)

  14. 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.

  15. The binding of amide substrate analogues to phospholipase A2. Studies by 13C-nuclear-magnetic-resonance and infrared spectroscopy.

    PubMed Central

    Slaich, P K; Primrose, W U; Robinson, D H; Wharton, C W; White, A J; Drabble, K; Roberts, G C

    1992-01-01

    (R)-(2-dodecanamidoisohexyl)phosphocholine (DAHPC), labelled with 13C at the amide carbonyl group, has been synthesized and its binding to bovine pancreatic phospholipase A2 (PLA2) studied by n.m.r. and i.r. spectroscopy. Two-dimensional 1H-n.m.r. spectra show that, in the presence of Ca2+, DAHPC binds to the active site of the enzyme in a similar manner to other phospholipid amide substrate analogues. The environment of the labelled carbonyl group has been investigated by a combination of 13C n.m.r. and difference-Fourier-transform i.r. spectroscopy. The carbonyl resonance shifts 3 p.p.m. downfield on the binding of DAHPC to PLA2. The carbonyl absorption frequency decreases by 14-18 cm-1, accompanied by a marked sharpening of the absorption band. These results indicate that the carbonyl bond undergoes significant polarization in the enzyme-ligand complex, facilitated by the enzyme-bound Ca2+ ion. This suggests that ground-state strain is likely to promote catalysis in the case of substrate binding. Simple calculations, based on the i.r. data, indicate that the carbonyl bond is weakened by 5-9 kJ.mol-1. This is the first report of observation of the amide vibration of a bound ligand against the strong background of protein amide vibrations. PMID:1445261

  16. 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

  17. Conformational properties of amphotericin B amide derivatives--impact on selective toxicity.

    PubMed

    Resat, H; Sungur, F A; Baginski, M; Borowski, E; Aviyente, V

    2000-10-01

    Even though it is highly toxic, Amphotericin B (AmB), an amphipathic polyene macrolide antibiotic, is used in the treatment of severe systemic fungal infections as a life-saving drug. To examine the influence of conformational factors on selective toxicity of these compounds, we have investigated the conformational properties of five AmB amide derivatives. It was found that the extended conformation with torsional angles (phi,psi)=(290 degrees,180 degrees) is a common minimum of the potential energy surfaces (PES) of unsubstituted AmB and its amide derivatives. The extended conformation of the studied compounds allows for the formation of an intermolecular hydrogen bond network between adjacent antibiotic molecules in the open channel configuration. Therefore, the extended conformation is expected to be the dominant conformer in an open AmB (or its amide derivatives) membrane channel. The derivative compounds for calculations were chosen according to their selective toxicity compared to AmB and they had a wide range of selective toxicity. Except for two AmB derivatives, the PES maps of the derivatives reveal that the molecules can coexist in more than one conformer. Taking into account the cumulative conclusions drawn from the earlier MD simulation studies of AmB membrane channel, the results of the potential energy surface maps, and the physical considerations of the molecular structures, we hypothesize a new model of structure-selective toxicity of AmB derivatives. In this proposed model the presence of the extended conformation as the only well defined global conformer for AmB derivatives is taken as the indicator of their higher selective toxicity. This model successfully explains our results. To further test our model, we also investigated an AmB derivative whose selective toxicity has not been experimentally measured before. Our prediction for the selective toxicity of this compound can be tested in experiments to validate or invalidate the proposed model

  18. Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide

    NASA Astrophysics Data System (ADS)

    Yatsyna, Vasyl; Bakker, Daniël J.; Feifel, Raimund; Rijs, Anouk M.; Zhaunerchyk, Vitali

    2016-09-01

    Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.

  19. Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide.

    PubMed

    Yatsyna, Vasyl; Bakker, Daniël J; Feifel, Raimund; Rijs, Anouk M; Zhaunerchyk, Vitali

    2016-09-14

    Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.

  20. Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide.

    PubMed

    Yatsyna, Vasyl; Bakker, Daniël J; Feifel, Raimund; Rijs, Anouk M; Zhaunerchyk, Vitali

    2016-09-14

    Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments. PMID:27634262

  1. Bonds Boom.

    ERIC Educational Resources Information Center

    Reynolds, Cathryn

    1989-01-01

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

  2. 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.

  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. Selective formation of secondary amides via the copper-catalyzed cross-coupling of alkylboronic acids with primary amides.

    PubMed

    Rossi, Steven A; Shimkin, Kirk W; Xu, Qun; Mori-Quiroz, Luis M; Watson, Donald A

    2013-05-01

    For the first time, a general catalytic procedure for the cross-coupling of primary amides and alkylboronic acids is demonstrated. The key to the success of this reaction was the identification of a mild base (NaOSiMe3) and oxidant (di-tert-butyl peroxide) to promote the copper-catalyzed reaction in high yield. This transformation provides a facile, high-yielding method for the monoalkylation of amides. PMID:23611591

  5. Calorimetric Investigation of Hydrogen Bonding of Formamide and Its Methyl Derivatives in Organic Solvents and Water

    NASA Astrophysics Data System (ADS)

    Varfolomeev, Mikhail A.; Rakipov, Ilnaz T.; Solomonov, Boris N.

    2013-04-01

    Formamide and its derivatives have a large number of practical applications; also they are structural fragments of many biomolecules. Hydrogen bonds strongly affect their physicochemical properties. In the present work a calorimetric study of formamide and its methyl derivatives was carried out. Enthalpies of solution at infinite dilution of formamide, N-methylformamide, and N, N-dimethylformamide in organic solvents at 298.15 K were measured. The relationships between the obtained enthalpies of solvation and the structure of the studied compounds were observed. Hydrogen-bond enthalpies of amides with chlorinated alkanes, ethers, ketones, esters, nitriles, amines, alcohols, and water were determined. The strength of hydrogen bonds of formamide, N-methylformamide, and N, N-dimethylformamide with proton donor solvents is practically equal. Enthalpies of hydrogen bonds of formamide with the proton acceptor solvents are two times larger in magnitude than the enthalpies of N-methylformamide. The process of hydrogen bonding of amides in aliphatic alcohols and water is complicated. The obtained enthalpies of hydrogen bonding in aliphatic alcohols vary considerably from the amide structure due to the competition between solute-solvent and solvent-solvent hydrogen bonds. Fourier transform infrared spectroscopic measurements were carried out to explain the calorimetric data. Hydration enthalpies of methyl derivatives of formamides contain a contribution of the hydrophobic effect. New thermochemical data on the hydrogen bonding of formamides may be useful for predicting the properties of biomacromolecules.

  6. Giant Zn14 molecular building block in hydrogen-bonded network with permanent porosity for gas uptake.

    PubMed

    Mondal, Suvendu Sekhar; Bhunia, Asamanjoy; Kelling, Alexandra; Schilde, Uwe; Janiak, Christoph; Holdt, Hans-Jürgen

    2014-01-01

    In situ imidazolate-4,5-diamide-2-olate linker generation leads to the formation of a [Zn14(L2)12(O)(OH)2(H2O)4] molecular building block (MBB) with a Zn6 octahedron inscribed in a Zn8 cube. The MBBs connect by amide-amide hydrogen bonds to a 3D robust supramolecular network which can be activated for N2, CO2, CH4, and H2 gas sorption.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. Enhanced Cellular Uptake and Pharmacokinetic Characteristics of Doxorubicin-Valine Amide Prodrug.

    PubMed

    Park, Yohan; Park, Ju-Hwan; Park, Suryeon; Lee, Song Yi; Cho, Kwan Hyung; Kim, Dae-Duk; Shim, Won-Sik; Yoon, In-Soo; Cho, Hyun-Jong; Maeng, Han-Joo

    2016-09-22

    In this study, we synthesized the valine (Val)-conjugated amide prodrug of doxorubicin (DOX) by the formation of amide bonds between DOX and Val. The synthesis of the DOX-Val prodrug was identified by a proton nuclear magnetic resonance (¹H-NMR) assay. In the MCF-7 cells (human breast adenocarcinoma cell; amino acid transporter-positive cell), the cellular accumulation efficiency of DOX-Val was higher than that of DOX according to the flow cytometry analysis data. Using confocal laser scanning microscopy (CLSM) imaging, it was confirmed that DOX-Val as well as DOX was mainly distributed in the nucleus of cancer cells. DOX-Val was intravenously administered to rats at a dose of 4 mg/kg, and the plasma concentrations of DOX-Val (prodrug) and DOX (formed metabolite) were quantitatively determined. Based on the systemic exposure (represented as area under the curve (AUC) values) of DOX-Val (prodrug) and DOX (formed metabolite), approximately half of DOX-Val seemed to be metabolized into DOX. However, it is expected that the remaining DOX-Val may exert improved cellular uptake efficiency in cancer cells after its delivery to the cancer region.

  14. Enhanced Cellular Uptake and Pharmacokinetic Characteristics of Doxorubicin-Valine Amide Prodrug.

    PubMed

    Park, Yohan; Park, Ju-Hwan; Park, Suryeon; Lee, Song Yi; Cho, Kwan Hyung; Kim, Dae-Duk; Shim, Won-Sik; Yoon, In-Soo; Cho, Hyun-Jong; Maeng, Han-Joo

    2016-01-01

    In this study, we synthesized the valine (Val)-conjugated amide prodrug of doxorubicin (DOX) by the formation of amide bonds between DOX and Val. The synthesis of the DOX-Val prodrug was identified by a proton nuclear magnetic resonance (¹H-NMR) assay. In the MCF-7 cells (human breast adenocarcinoma cell; amino acid transporter-positive cell), the cellular accumulation efficiency of DOX-Val was higher than that of DOX according to the flow cytometry analysis data. Using confocal laser scanning microscopy (CLSM) imaging, it was confirmed that DOX-Val as well as DOX was mainly distributed in the nucleus of cancer cells. DOX-Val was intravenously administered to rats at a dose of 4 mg/kg, and the plasma concentrations of DOX-Val (prodrug) and DOX (formed metabolite) were quantitatively determined. Based on the systemic exposure (represented as area under the curve (AUC) values) of DOX-Val (prodrug) and DOX (formed metabolite), approximately half of DOX-Val seemed to be metabolized into DOX. However, it is expected that the remaining DOX-Val may exert improved cellular uptake efficiency in cancer cells after its delivery to the cancer region. PMID:27669201

  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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Cations bind only weakly to amides in aqueous solutions.

    PubMed

    Okur, Halil I; Kherb, Jaibir; Cremer, Paul S

    2013-04-01

    We investigated salt interactions with butyramide as a simple mimic of cation interactions with protein backbones. The experiments were performed in aqueous metal chloride solutions using two spectroscopic techniques. In the first, which provided information about contact pair formation, the response of the amide I band to the nature and concentration of salt was monitored in bulk aqueous solutions via attenuated total reflection Fourier transform infrared spectroscopy. It was found that molar concentrations of well-hydrated metal cations (Ca(2+), Mg(2+), Li(+)) led to the rise of a peak assigned to metal cation-bound amides (1645 cm(-1)) and a decrease in the peak associated with purely water-bound amides (1620 cm(-1)). In a complementary set of experiments, the effect of cation identity and concentration was investigated at the air/butyramide/water interface via vibrational sum frequency spectroscopy. In these studies, metal ion-amide binding led to the ordering of the adjacent water layer. Such experiments were sensitive to the interfacial partitioning of cations in either a contact pair with the amide or as a solvent separated pair. In both experiments, the ordering of the interactions of the cations was: Ca(2+) > Mg(2+) > Li(+) > Na(+) ≈ K(+). This is a direct cationic Hofmeister series. Even for Ca(2+), however, the apparent equilibrium dissociation constant of the cation with the amide carbonyl oxygen was no tighter than ∼8.5 M. For Na(+) and K(+), no evidence was found for any binding. As such, the interactions of metal cations with amides are far weaker than the analogous binding of weakly hydrated anions.

  1. Diffusion bonding

    DOEpatents

    Anderson, Robert C.

    1976-06-22

    1. A method for joining beryllium to beryllium by diffusion bonding, comprising the steps of coating at least one surface portion of at least two beryllium pieces with nickel, positioning a coated surface portion in a contiguous relationship with an other surface portion, subjecting the contiguously disposed surface portions to an environment having an atmosphere at a pressure lower than ambient pressure, applying a force upon the beryllium pieces for causing the contiguous surface portions to abut against each other, heating the contiguous surface portions to a maximum temperature less than the melting temperature of the beryllium, substantially uniformly decreasing the applied force while increasing the temperature after attaining a temperature substantially above room temperature, and maintaining a portion of the applied force at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. Protein Immobilization on Carbon Nanotubes Via a Two-Step Process of Diimide-Activated Amidation

    SciTech Connect

    Jiang, Kuiyang; Schadler, Linda S.; Siegel, Richard W.; Zhang, Xinjie; Zhang, Haifeng; Terrones, Mauricio

    2004-11-06

    Carbon nanotubes exhibit interesting electrical, structural and mechanical properties that make them highly promising nanoscale building blocks for the construction of novel functional materials. Many potential applications have been proposed, such as conductive and high-strength composites, field emission displays, fuel cells, sensors, and hydrogen storage media. In addition, biosensors for detecting abnormalities and bio-fuel cells for embedded devices are among the most exciting applications. In order to create the synergy between the biomolecules and nanotubes required to realize these applications, biomolecules, such as proteins and DNAs, must be connected to the carbon nanotubes. This connection can be non-covalent interaction or covalent bonding. There have been several reports on the immobilization of biomolecules on carbon nanotubes, and most of them use non-covalent interaction. The best stability, accessibility and selectivity, however, will be achieved through covalent bonding because of its capability to control the location of the biomolecule, improve stability, accessibility and selectivity and reduce leaching. In the present study, we report the covalent bonding of proteins to nitrogen-doped multiwalled carbon nanotubes (CNx MWNTs) via a two-step process of diimide-activated amidation between the carboxylic acid groups on CNx MWNTs and the amine groups on proteins.

  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. 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.

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

    PubMed

    Wang, Weizhou; Ji, Baoming; Zhang, Yu

    2009-07-16

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

  11. 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)

  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.

  13. 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

  14. Mechanism of fluorescence quenching of tyrosine derivatives by amide group

    NASA Astrophysics Data System (ADS)

    Wiczk, Wiesław; Rzeska, Alicja; Łukomska, Joanna; Stachowiak, Krystyna; Karolczak, Jerzy; Malicka, Joanna; Łankiewicz, Leszek

    2001-06-01

    The difference between fluorescence lifetimes of the following amino acids: phenylalanine (Phe), tyrosine (Tyr), ( O-methyl)tyrosine (Tyr(Me)), (3-hydroxy)tyrosine (Dopa), (3,4-dimethoxy)phenylalanine (Dopa(Me) 2) and their amides was used to testify the mechanism of fluorescence quenching of aromatic amino acids by the amide group. On the basis of the Marcus theory of photoinduced electron transfer parabolic relationships between ln kET and ionization potentials reduced by energy of excitation ( IP-E ∗0,0) for the above-mentioned amino acids were obtained. This finding indicates the occurrence of photoinduced electron transfer from the excited chromophore group to the amide group.

  15. Relationship between chemical structure and supramolecular effective molarity for formation of intramolecular H-bonds.

    PubMed

    Sun, Hongmei; Hunter, Christopher A; Navarro, Cristina; Turega, Simon

    2013-09-01

    Effective molarity (EM) is a key parameter that determines the efficiency of a range of supramolecular phenomena from the folding of macromolecules to multivalent ligand binding. Coordination complexes formed between zinc porphyrins equipped H-bond donor sites and pyridine ligands equipped with H-bond acceptor sites have allowed systematic quantification of EM values for the formation of intramolecular H-bonds in 240 different systems. The results provide insights into the relationship of EM to supramolecular architecture, H-bond strength, and solvent. Previous studies on ligands equipped with phosphonate diester and ether H-bond acceptors were inconclusive, but the experiments described here on ligands equipped with phosphine oxide, amide, and ester H-bond acceptors resolve these ambiguities. Chemical double-mutant cycles were used to dissect the thermodynamic contributions of individual H-bond interactions to the overall stabilities of the complexes and hence determine the values of EM, which fall in the range 1-1000 mM. Solvent has little effect on EM, and the values measured in toluene and 1,1,2,2-tetrachloroethane are similar. For H-bond acceptors that have similar geometries but different H-bond strengths (amide and ester), the values of EM are very similar. For H-bond acceptors that have different geometries but similar H-bond strengths (amide and phosphonate diester), there is little correlation between the values of EM. These results imply that supramolecular EMs are independent of solvent and intrinsic H-bond strength but depend on supramolecular architecture and geometric complementarity.

  16. Anchor-linked intermediates in peptide amide synthesis are caused by dimeric anchors on the solid supports.

    PubMed

    Flechsler, I; Beck-Sickinger, A G; Stephan, H; Sheppard, R; Jung, G

    1995-01-01

    Cleavage and kinetic studies have been carried out using commercially obtained H-Tyr(tBu)-5-(4'-aminomethyl-3',5'-dimethoxyphenoxy)valeric acid-TentaGelS (H-Tyr(tBu)-4-ADPV-TentaGelS) and H-Tyr (tBu)-4-ADPV-Ala-aminomethyl-resin (H-Tyr(tBu)-4-ADPV-AM-resin) prepared from commercially available resin and loaded with commercially available Fmoc-4-ADPV-OH amide anchor. Cleavage with pure trifluoroacetic acid (TFA) gave the intermediate H-Tyr-4-ADPV-NH2, which was then degraded to H-Tyr-NH2, and cleavage with TFA/dichloromethane (1:9) yielded H-Tyr-4-ADPV-NH2 which could be isolated in preparative amounts. Cleavage reactions with 15N-labelled H-Ala-4-ADPV-(15N)-Gly-AM-resin yielded the intermediate H-Ala-4-ADPV-NH2, which contained no 15N as demonstrated by 1H-NMR. The analysis of the commercial Fmoc-4-ADPV-OH amide anchor showed the presence of Fmoc-4-ADPV-4-ADPV-OH as an impurity in high amounts. This dimeric anchor molecule is the cause of formation of the anchor-linked peptide intermediate obtained during the cleavage from the resin. The particularly high acid-lability of the amide bond between the two ADPV moieties was utilized to synthesize sidechain and C-terminally 4-ADPV protected pentagastrin on a double-anchor resin, and to cleave it using 5% trifluoroacetic acid in dichloromethane. This method may offer a new way for the synthesis of protected peptide amides with improved solubility to be used in fragment condensation.

  17. Synthesis and antituberculosis activity of new fatty acid amides.

    PubMed

    D'Oca, Caroline Da Ros Montes; Coelho, Tatiane; Marinho, Tamara Germani; Hack, Carolina Rosa Lopes; Duarte, Rodrigo da Costa; da Silva, Pedro Almeida; D'Oca, Marcelo Gonçalves Montes

    2010-09-01

    This work reports the synthesis of new fatty acid amides from C16:0, 18:0, 18:1, 18:1 (OH), and 18:2 fatty acids families with cyclic and acyclic amines and demonstrate for the first time the activity of these compounds as antituberculosis agents against Mycobacterium tuberculosis H(37)Rv, M. tuberculosis rifampicin resistance (ATCC 35338), and M. tuberculosis isoniazid resistance (ATCC 35822). The fatty acid amides derivate from ricinoleic acid were the most potent one among a series of tested compounds, with a MIC 6.25 microg/mL for resistance strains.

  18. 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

  19. 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

  20. 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.

  1. Hydrogen bonding in peptide secondary structures

    NASA Astrophysics Data System (ADS)

    Varga, Zoltán; Kovács, Attila

    Hydrogen bonding interactions in various peptide secondary structures (β-sheet, 27-ribbon, 310-helix, α-helix, π-helix, β-turn II, and γ-turn) have been investigated in small oligopeptides by quantum chemical calculations at the B3LYP/6-31G** level. Besides the primary O...HN interactions, the optimized structures revealed the importance of N...HN hydrogen bonding in several structures. The effect of substitution on the energy and structural properties was investigated comparing the properties of glycine, alanine, valine, and serine. The aliphatic substituents generally weaken the hydrogen bonds, the strongest effects being observed in crowded valine conformers. Additional hydrogen bonding interactions introduced by the OH group of serine can both strengthen (by polarizing the amide moiety through N...H interaction) and weaken (constraining the CO oxygen by O...HO interaction) the backbone hydrogen bonds. The effect of water as a polarizable medium on the energy properties was assessed by the COSMO model.

  2. 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.

  3. 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

  4. Chemoselective esterification and amidation of carboxylic acids with imidazole carbamates and ureas.

    PubMed

    Heller, Stephen T; Sarpong, Richmond

    2010-10-15

    Imidazole carbamates and ureas were found to be chemoselective esterification and amidation reagents. A wide variety of carboxylic acids were converted to their ester or amide analogues by a simple synthetic procedure in high yields.

  5. Rh(III)-Catalyzed C-H Amidation of Indoles with Isocyanates.

    PubMed

    Jeong, Taejoo; Han, Sangil; Mishra, Neeraj Kumar; Sharma, Satyasheel; Lee, Seok-Yong; Oh, Joa Sub; Kwak, Jong Hwan; Jung, Young Hoon; Kim, In Su

    2015-07-17

    The rhodium(III)-catalyzed direct amidation of indoles and pyrroles with aryl and alkyl isocyanates is described. These transformations provide a facile and efficient construction of C2-amidated N-heterocyclic scaffolds.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. Acidizing using N-vinyl lactum/unsaturated amide copolymers

    SciTech Connect

    Burns, L.D.; Stahl, G.A.

    1987-09-01

    A process is described for acidizing a subterranean formation penetrated by at least one well comprising injecting into the formation, without a crosslinking agent, a water soluble thickened acid composition comprising: (1) water; (2) acid; and (3) a linear copolymer prepared from the monomers consisting of a N-vinyl lactam monomer and an alpha, beta-unsaturated amide monomer.

  14. 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

  15. 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)-...

  16. 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.

  17. 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

  18. 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

  19. 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....

  20. 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....

  1. 40 CFR 721.10589 - Unsaturated fatty acids, amides with polyethylenepolyamine (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Unsaturated fatty acids, amides with... Specific Chemical Substances § 721.10589 Unsaturated fatty acids, amides with polyethylenepolyamine... identified generically as unsaturated fatty acids, amides with polyethylenepolyamine (PMN P-11-106)...

  2. 40 CFR 721.10590 - Fatty acids, amides with triethylentetramine (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Fatty acids, amides with... Specific Chemical Substances § 721.10590 Fatty acids, amides with triethylentetramine (generic). (a... generically as fatty acids, amides with triethylentetramine (PMN P-11-107) is subject to reporting under...

  3. 40 CFR 721.10589 - Unsaturated fatty acids, amides with polyethylenepolyamine (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Unsaturated fatty acids, amides with... Specific Chemical Substances § 721.10589 Unsaturated fatty acids, amides with polyethylenepolyamine... identified generically as unsaturated fatty acids, amides with polyethylenepolyamine (PMN P-11-106)...

  4. 40 CFR 721.10590 - Fatty acids, amides with triethylentetramine (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Fatty acids, amides with... Specific Chemical Substances § 721.10590 Fatty acids, amides with triethylentetramine (generic). (a... generically as fatty acids, amides with triethylentetramine (PMN P-11-107) is subject to reporting under...

  5. 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...

  6. 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...

  7. 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)...

  8. 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...

  9. 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...

  10. 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)...

  11. 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....

  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, 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....

  14. 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.

  15. Synthesis, structure, and reactivity of tris(amidate) mono(amido) and tetrakis(amidate) complexes of group 4 transition metals.

    PubMed

    Payne, Philippa R; Thomson, Robert K; Medeiros, Diane M; Wan, Geoff; Schafer, Laurel L

    2013-11-28

    The syntheses of a series of tris(amidate) mono(amido) titanium and zirconium complexes are reported. The binding motif of the amidate ligand has been determined to depend on the size of the metal centre for these sterically demanding N,O-chelating ligands; the larger zirconium metal centre supports three κ(2)-(N,O) bound amidate ligands while the titanium analogue has one ligand bound in a κ(1)-(O) fashion to alleviate steric strain. Reactivity studies indicate that, despite high steric crowding about the tris(amidate) mono(amido) zirconium metal centre, transamination of the reactive dimethylamido ligand can be achieved using aniline. This complex is also an active precatalyst for intramolecular alkene hydroamination, in which protonolysis of one amidate ligand in the presence of excess amine is observed as an initiation step prior to catalytic turnover. Eight-coordinate homoleptic κ(2)-amidate complexes of zirconium and hafnium have also been prepared.

  16. 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

  17. 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

  18. 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.

  19. Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: Linear and nonlinear vibrational spectra

    NASA Astrophysics Data System (ADS)

    Kwac, Kijeong; Lee, Hochan; Cho, Minhaeng

    2004-01-01

    By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al. [S. Woutersen, Y. Mu, G. Stock, and P. Hamm, Chem. Phys. 266, 137 (2001)].

  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. Communication: Creation of molecular vibrational motions via the rotation-vibration coupling.

    PubMed

    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.

  2. 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

  3. Poly(ortho ester amides): Acid-labile Temperature-responsive Copolymers for Potential Biomedical Applications

    PubMed Central

    Tang, Rupei; Palumbo, R. Noelle; Ji, Weihang; Wang, Chun

    2009-01-01

    A new, convenient pathway is developed to synthesize highly hydrolytically labile poly(ortho ester amide) (POEA) copolymers that overcomes some of the major weaknesses of the traditional methods of synthesizing poly(ortho esters) and their derivatives. A diamine monomer containing a built-in, stabilized ortho ester group was synthesized and was used for polycondensation with diacid esters, giving rise to a series of POEA copolymers with unique stimuli-responsive properties. The POEA undergoes temperature-responsive, reversible sol-gel phase transition in water. Phase diagrams of the POEA/H2O mixture reveal the concentration-dependent existence of different phases, including hydrogel and opaque or clear solution. Such behavior may be attributed to the temperature-dependent hydrogen-bonding involving the amide groups in the POEA backbone and hydrophobic interactions between POEA chains, and it is tunable by selecting diacid monomers with different chemical structures. The kinetics of POEA mass loss in physiological aqueous buffers and release of a model macromolecular drug, fluorescently labeled dextran, are nearly zero-order, suggesting predominantly surface-restricted polymer erosion. The rates of polymer erosion and drug release are much faster at pH 5.0 than pH 7.4. No cytotoxicity was found for the polymer extracts and the polymer degradation products at concentrations as high as 1 mg/ml. The normal morphology of fibroblasts cultured directly in contact with POEA films was not altered. These novel acid-labile temperature-responsive POEA copolymers may be potentially useful for a wide range of biomedical applications such as minimal invasive delivery of controlled-release drug formulations that respond to biological temperature and acidic-pH environments in cells and tissues. PMID:19281150

  4. 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.

  5. 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.

  6. 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.

  7. 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)

  8. 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…

  9. 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.

  10. 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

  11. In vivo behavior of hydrogel beads based on amidated pectins.

    PubMed

    Munjeri, O; Collett, J H; Fell, J T; Sharma, H L; Smith, A M

    1998-01-01

    Radio-labeled hydrogel beads, based on amidated pectin, have been produced by adding droplets of an amidated pectin solution to calcium chloride. Incorporation of model drugs into the beads and measurement of the dissolution rate showed that the properties of the beads were unaffected by the incorporation of the radiolabel. The labeled beads were used to carry out an in vivo study of their behavior in the gastrointestinal tract using human volunteers. The volunteers were given the beads after an overnight fast and images were obtained at frequent intervals during transit through the upper gastrointestinal tract and the colon. The beads exhibited rapid gastric emptying and proceeded to pass through the small intestine individually before regrouping at the ileo-caecal junction. Once in the colon, the beads again proceeded as individuals and evidence of the degradation of the beads was observed.

  12. Synthesis of Carfentanil Amide Opioids Using the Ugi Multicomponent Reaction

    PubMed Central

    Váradi, András; Palmer, Travis C.; Haselton, Nathan; Afonin, Daniel; Subrath, Joan J.; Le Rouzic, Valerie; Hunkele, Amanda; Pasternak, Gavril W.; Marrone, Gina F.; Borics, Attila; Majumdar, Susruta

    2015-01-01

    We report a novel approach to synthesize carfentanil amide analogues utilizing the isocyanide-based four-component Ugi multicomponent reaction. A small library of bis-amide analogues of carfentanil was created using N-alkylpiperidones, aniline, propionic acid, and various aliphatic isocyanides. Our lead compound showed high affinity for mu (MOR) and delta opioid receptors (DOR) with no appreciable affinity for kappa (KOR) receptors in radioligand binding assays. The compound was found to be a mixed MOR agonist/partial DOR agonist in [35S]GTPγS functional assays, and it showed moderate analgesic potency in vivo. The compound showed no visible signs of physical dependence or constipation in mice. In addition, it produced less respiratory depression than morphine. Most mixed MOR/DOR opioids reported in the literature are peptides and thereby systemically inactive. Our approach utilizing a multicomponent reaction has the promise to deliver potent and efficacious small-molecule analgesics with potential clinical utility. PMID:26148793

  13. Simulations of the temperature dependence of amide I vibration.

    PubMed

    Kaminský, Jakub; Bouř, Petr; Kubelka, Jan

    2011-01-13

    For spectroscopic studies of peptide and protein thermal denaturation it is important to single out the contribution of the solvent to the spectral changes from those originated in the molecular structure. To obtain insights into the origin and size of the temperature solvent effects on the amide I spectra, combined molecular dynamics and density functional simulations were performed with the model N-methylacetamide molecule (NMA). The computations well reproduced frequency and intensity changes previously observed in aqueous NMA solutions. An empirical correction of vacuum frequencies in single NMA molecule based on the electrostatic potential of the water molecules provided superior results to a direct density functional average obtained for a limited number of solute-solvent clusters. The results thus confirm that the all-atom quantum and molecular mechanics approach captures the overall influence of the temperature dependent solvent properties on the amide I spectra and can improve the accuracy and reliability of molecular structural studies.

  14. 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.

  15. 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

  16. Accumulation of hydroxycinnamic acid amides in winter wheat under snow.

    PubMed

    Jin, Shigeki; Yoshida, Midori; Nakajima, Takashi; Murai, Akio

    2003-06-01

    It was found that the content of antifungal compounds p-coumaroylagmatine [1-(trans-4'-hydroxycinnamoylamino)-4-guanidinobutane] and p-coumaroyl-3-hydroxyagmatine [1-(trans-4'-hydroxycinnamoylamino)-3-hydroxy-4-guanidinobutane] in the crown of winter wheat (Triticum aestivum L. cv Chihokukomugi) significantly increased under snow cover. This finding suggests that the accumulation of these hydroxycinnamic acid amides was caused by winter stress and related to protecting the plant against snow mold under snow cover.

  17. 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

  18. Carbazole and amide alkaloids from the stems of Clausena lansium.

    PubMed

    Du, Yi-Qian; Liu, Hang; Li, Chuang-Jun; Yang, Jing-Zhi; Ma, Jie; Zhang, Dan; Sun, Hua; Zhang, Dong-Ming

    2015-01-01

    Two new carbazole alkaloids, claulansine S (1) and claulansine T (2), and one new amide alkaloid, clauamide A (3), together with four known analogues (4-7) were isolated from the stems of Clausena lansium. Their structures were elucidated on the basis of spectroscopic analyses, including UV, IR, and NMR experiments (HSQC, HMBC, and NOE experiments). Compounds 4 and 6 showed moderate hepatoprotective activities. PMID:26095884

  19. Ab initio studies of structural features not easily amenable to experiment. 23. Molecular structures and conformational analysis of the dipeptide N-acetyl-N'-methyl glycyl amide and the significance of local geometries for peptide structures

    NASA Astrophysics Data System (ADS)

    Schäfer, Lothar; Van Alsenoy, C.; Scarsdale, J. N.

    1982-02-01

    The molecular structures of four conformations of N-acetyl-N'-methyl glycyl amide were refined by geometrically unconstrained ab initio gradient relaxation on the 4-21G level. The most stable form I contains a seven-membered ring closed by hydrogen bonding. A second local minimum II is less than 1 kcal/mol above I and represents the fully extended form with a five-membered hydrogen bonded ring. The two other minima refined, III and IV, are open forms which are 4-5 kcal/mol less stable than I. The refined geometries make it possible to estimate the significance of local geometries, in contrast to standard geometry, in the various conformations. It is found that bond distances in different conformations can vary by up to 0.02 Å, and important backbone bond angles can vary by up to 7°. Except for the symmetrical form II, small deviations from amide planarity (H-N-C = 0 angles of 3-10°) are the rule, even though the equilibrium structure of the unperturbed amide group in 4-21G space is planar. It can be concluded that local geometry relaxations at different points of the potential energy surface of a peptide system can amount to several Kcal/mol per residue and should be an important aspect of protein conformational analysis.

  20. 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

  1. 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

  2. Reactivity of a Nickel(II) Bis(amidate) Complex with meta-Chloroperbenzoic Acid: Formation of a Potent Oxidizing Species.

    PubMed

    Corona, Teresa; Pfaff, Florian F; Acuña-Parés, Ferran; Draksharapu, Apparao; Whiteoak, Christopher J; Martin-Diaconescu, Vlad; Lloret-Fillol, Julio; Browne, Wesley R; Ray, Kallol; Company, Anna

    2015-10-12

    Herein, we report the formation of a highly reactive nickel-oxygen species that has been trapped following reaction of a Ni(II) precursor bearing a macrocyclic bis(amidate) ligand with meta-chloroperbenzoic acid (HmCPBA). This compound is only detectable at temperatures below 250 K and is much more reactive toward organic substrates (i.e., C-H bonds, C=C bonds, and sulfides) than previously reported well-defined nickel-oxygen species. Remarkably, this species is formed by heterolytic O-O bond cleavage of a Ni-HmCPBA precursor, which is concluded from experimental and computational data. On the basis of spectroscopy and DFT calculations, this reactive species is proposed to be a Ni(III) -oxyl compound.

  3. Reactivity of a Nickel(II) Bis(amidate) Complex with meta-Chloroperbenzoic Acid: Formation of a Potent Oxidizing Species.

    PubMed

    Corona, Teresa; Pfaff, Florian F; Acuña-Parés, Ferran; Draksharapu, Apparao; Whiteoak, Christopher J; Martin-Diaconescu, Vlad; Lloret-Fillol, Julio; Browne, Wesley R; Ray, Kallol; Company, Anna

    2015-10-12

    Herein, we report the formation of a highly reactive nickel-oxygen species that has been trapped following reaction of a Ni(II) precursor bearing a macrocyclic bis(amidate) ligand with meta-chloroperbenzoic acid (HmCPBA). This compound is only detectable at temperatures below 250 K and is much more reactive toward organic substrates (i.e., C-H bonds, C=C bonds, and sulfides) than previously reported well-defined nickel-oxygen species. Remarkably, this species is formed by heterolytic O-O bond cleavage of a Ni-HmCPBA precursor, which is concluded from experimental and computational data. On the basis of spectroscopy and DFT calculations, this reactive species is proposed to be a Ni(III) -oxyl compound. PMID:26311073

  4. Synthesis and characterization of thermally stable aromatic polyamides and poly(1,3,4-oxadiazole-amide)s nanoparticles containing pendant substituted bezamides

    PubMed Central

    2013-01-01

    Background The introduction of pendent bulky groups along the polymer backbone results in a less ordered polymer matrix and increases the solubility characteristics without affecting thermal properties. The inclusion of chromogenic chemical moieties in the chains can give rise to the luminescent converter material which permits the preparation of materials with potential applications. Aromatic polymers containing heterocyclic rings in the main chain are known for their high thermal resistance, good hydrolytic stability, low dielectric and tough mechanical properties. There is currently much research directed towards the discovery of new blue light-emitting polymers, with characteristics of high efficiency and high reliability. Herein, we describe the preparation of aromatic polyamides and poly (1,3,4-oxadiazole-amide)s nanoparticles with pendant structures comprised of m- and p-acetoxybenzamide groups, where the acetoxybenzamide groups act as signaling units due to their fluorescent and chromogenic characteristics. Results Aromatic polyamides and poly(1,3,4-oxadiazole-amide)s nanoparticles with pendant structures comprised of m- and p-acetoxybenzamide groups were successfully prepared and characterized using different analytical methods. Most polyamides were obtained as well-separated spherical nanoparticles while aramide containing pyridine produced aggregated particles attributed to the molecular self assembly via H-bond directed organization of molecular precursors. The thermal behavior of all polymers exhibited two major thermal decompositions due to the subsequent breakage of the acetoxy group in the lateral chain and cleavage of the main amide bonds. Photoluminescence studies revealed that the blue emissions for the polyamide derived from benzidine were blue-shifted (shifted to a lower wavelength) compared to that of polyamides containing flexible linkages. Conclusions We report the synthesis of aromatic polyamides and poly(1,3,4-oxadiazole-amide

  5. 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.

  6. 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

  7. 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

  8. 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 ...

  9. 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

  10. 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.

  11. 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

  12. 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

  13. Drosophila melanogaster as a model system to study long-chain fatty acid amide metabolism

    PubMed Central

    Jeffries, Kristen A.; Dempsey, Daniel R.; Behari, Anita L.; Anderson, Ryan L.; Merkler, David J.

    2014-01-01

    Long-chain fatty acid amides are cell-signaling lipids identified in mammals and, recently, in invertebrates, as well. Many details regarding fatty acid amide metabolism remain unclear. Herein, we demonstrate that Drosophila melanogaster is an excellent model system for the study long-chain fatty acid amide metabolism as we have quantified the endogenous levels of N-acylglycines, N-acyldopamines, N-acylethanolamines, and primary fatty acid amides by LC/QTOF-MS. Growth of Drosophila melanogaster on media supplemented with [1-13C]-palmitate lead to a family of 13C-palmitate-labeled fatty acid amides in the fly heads. The [1-13C]-palmitate feeding studies provide insight into the biosynthesis of the fatty acid amides. PMID:24650760

  14. Synthesis and Structure of a New Lithium Amide Ligand Precursor: A Tridentate Nitrogen-Based Donor Set of the Formula N(SiMe(2)CH(2)NMe(2))(2). Synthesis and Structure of the Group 4 Amides MCl(3)[N(SiMe(2)CH(2)NMe(2))(2)] (M = Ti, Zr, Hf).

    PubMed

    Fryzuk, Michael D.; Hoffman, Vera; Kickham, James E.; Rettig, Steven J.; Gambarotta, Sandro

    1997-07-30

    The new lithium amide LiN(SiMe(2)CH(2)NMe(2))(2) was prepared by reaction of NH(3) with the corresponding silylamine Me(2)NSiMe(2)CH(2)NMe(2) followed by addition of butyllithium. This lithium derivative exists as a dimer in the solid state wherein the two lithium ions are bridged by the two amido units with the amine arms of each unit bonded to opposite lithium centers in an overall pseudo D(2) structure; however, in solution, a fluxional process serves to interconvert the enantiomeric forms of the dimer unit. The coordination chemistry of the lithium amide dimer has been investigated; reaction with a series of group 4 starting halides, MCl(4), leads to the corresponding complexes MCl(3)[N(SiMe(2)CH(2)NMe(2))(2)], where M = Ti, Zr, and Hf. The structures of these starting trihalides in solution and in the solid state are presented. PMID:11670025

  15. 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

  16. FT-IR and computer modeling study of hydrogen bonding in N-alkyl acrylamide-toluene binary mixtures

    NASA Astrophysics Data System (ADS)

    Rumyantsev, Misha; Kazantsev, Oleg A.; Kamorina, Sofia I.; Kamorin, Denis M.; Sivokhin, Alexey P.

    2016-10-01

    Degree of hydrogen bonding driven self-association of N-(n-butyl)acrylamide, N-(n-octyl)acrylamide, N-(sec-octyl)acrylamide and N-(tert-octyl)acrylamide in toluene was investigated using IR spectroscopy and computer modeling methods. Consistent results were demonstrated in the treatment of the Amide-I (νC=O), Amide-II (δN-H and νC-N) and Amide-A (νN-H) absorption bands in IR spectra. Thus, the content of non-bonded (free) amide groups decreases from 83-98% to 8-20% and the content of linear polyassociates increases to 80-90% with an increase in monomer concentration from 0.5 wt% to 50 wt%. The content of cyclic dimers was equal to the value between 5 and 10% regardless of the initial monomer concentration. Dependences of the association degree and the content of the linear polyassociates on the concentration were found to be similar for all of the studied amides.

  17. 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

  18. 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.

  19. 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

  20. Catalyst-free synthesis of sodium amide nanoparticles encapsulated in silica gel

    NASA Astrophysics Data System (ADS)

    Ogilvie, Alexander D.; Makepeace, Joshua W.; Hore, Katie; Ramirez-Cuesta, Anibal J.; Apperley, David C.; Mitchels, John M.; Edwards, Peter P.; Sartbaeva, Asel

    2013-12-01

    Crystalline sodium amide nanoparticles encapsulated in an amorphous silica framework were formed by ammoniation of a precursor material, silica gel loaded with metallic sodium, under mild conditions and without catalysis. This ammoniation was performed in situ on TOSCA beamline at ISIS, RAL, using anhydrous gaseous ammonia. The resulting material exhibits no pyrophoricity and much reduced air- and moisture-sensitivity compared to the bulk amide. The nanoparticles formed will offer a greatly increased surface area for chemical reactions where amide is currently used as an important ingredient for industrial applications. We anticipate that this method of sodium amide production will have a diversity of applications.

  1. Treatment of Bile Acid Amidation Defects with Glycocholic Acid

    PubMed Central

    Heubi, James E.; Setchell, Kenneth D.R.; Jha, Pinky; Buckley, Donna; Zhang, Wujuan; Rosenthal, Philip; Potter, Carol; Horslen, Simon; Suskind, David

    2014-01-01

    Bile acid amidation defects were predicted to present with fat/fat soluble vitamin malabsorption with minimal cholestasis. We identified and treated 5 patients (1 male/4 females) from 4 families with defective bile acid amidation due to a genetically confirmed deficiency in bile acid CoA:amino acid N-acyl transferase (BAAT) with the conjugated bile acid, glycocholic acid (GCA). Fast atom bombardment-mass spectrometry analysis of urine and bile at baseline revealed predominantly unconjugated cholic acid and absence of the usual glycine and taurine conjugated primary bile acids. Treatment with 15 mg/kg GCA resulted in total duodenal bile acid concentrations of 23.3 ± 19.1 mmol/L (mean ± SD) and 63.5 ± 4.0% of the bile acids were secreted in bile in the conjugated form of which GCA represented 59.6 ± 9.3% of the total biliary bile acids. Unconjugated cholic acid continued to be present in high concentrations in bile because of partial intestinal deconjugation of orally administered GCA. Serum total bile acid concentrations did not significantly differ between pretreatment and post-treatment samples and serum contained predominantly unconjugated cholic acid. These findings confirmed efficient intestinal absorption, hepatic extraction and biliary secretion of the administered GCA. Oral tolerance tests for vitamin D2 (1000 IU vitamin D2/kg) and tocopherol (100 IU/kg tocopherol acetate) demonstrated improvement in fat-soluble vitamin absorption after GCA treatment. Growth improved in 3/3 growth-delayed prepubertal patients. Conclusions: Oral glycocholic acid therapy is safe and effective in improving growth and fat-soluble vitamin absorption in children and adolescents with inborn errors of bile acid metabolism due to amidation defects. PMID:25163551

  2. 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.

  3. Yakushinamides, Polyoxygenated Fatty Acid Amides That Inhibit HDACs and SIRTs, from the Marine Sponge Theonella swinhoei.

    PubMed

    Takada, Kentaro; Imae, Yasufumi; Ise, Yuji; Ohtsuka, Susumu; Ito, Akihiro; Okada, Shigeru; Yoshida, Minoru; Matsunaga, Shigeki

    2016-09-23

    Yakushinamides A (1) and B (2), prolyl amides of polyoxygenated fatty acids, have been isolated from the marine sponge Theonella swinhoei as inhibitors of HDACs and SIRTs. Their planar structures were determined by interpretation of the NMR data of the intact molecules and tandem FABMS data of the methanolysis products. For the assignment of the relative configurations of the three contiguous oxymethine carbons in 1 and 2, Kishi's universal NMR database was applied to the methanolysis products. During the assignments of relative configurations of the isolated 1-hydroxy-3-methyl moiety in 1 and the isolated 1-hydroxy-2-methyl moiety in 2, we found diagnostic NMR features to distinguish each pair of diastereomers. The absolute configurations of 1 and 2 were determined by a combination of the modified Mosher's method and Marfey's method. Although the modified Mosher's method was successfully applied to the methanolysis product of 1, this method gave an ambiguous result at C-20 when applied to the methanolysis product of 2, even after oxidative cleavage of the C-14 and C-15 bond. PMID:27548648

  4. Novel palladium complex-catalyzed reaction of magnesium amides with allylic electrophiles

    SciTech Connect

    Dzhemilev, U.M.; Ibragimov, A.G.; Minsker, D.L.; Muslukhov, R.R.

    1987-08-20

    In order to develop an efficient method for the synthesis of higher order unsaturated tertiary amines, and also to explore a new method for the formation of C-N bonds, they have investigated the transition metal complex-catalyzed reaction of magnesium amides with electrophiles; the electrophiles selected for study included allyl ethers and esters, as well as sulfones, sulfides and quaternized allylamines. The effects of the nature and structure of the catalyst components, as well as of the reaction conditions, on product yield were examined in the case of the reaction of diethyl (bromomagnesium)amine with diallyl ether, and revealed that the highest yield of diethylallyl-amine (I) was achieved using Pd(acac)/sub 2/ (3-5 mole %) and Ph/sub 3/P (1:2) as catalyst in THF solution at 50/sup 0/C for 5 h. Other transition metal (Ni, Fe, Zr, Ti, Cu) compounds were also examined as catalysts, but the yield of (I) did not exceed 15% with these compounds. Bimetallic catalysts based on Zr (Cp/sub 2/ZrCl, Py/sub 2/ZrCl/sub 6/, (RO)/sub 4/Zr) and Ni (Ni(acac)/sub 2/ and NiCl/sub 2/) were successful in forming (I) from diethyl (bromomagnesium)amine and diallyl ether in 60% yield.

  5. Amide derivatives of sulfonamides and isoniazid: synthesis and biological evaluation.

    PubMed

    Husain, Asif

    2009-01-01

    In the present study, various amide derivatives of sulfanilamide, sulfamethoxazole, sulfadiazine, dapsone and isoniazid have been synthesized by condensing them with appropriate 4-oxo-4-(4-substituted phenyl)butanoic acid moiety. The compounds have been evaluated for their antiinflammatory, ulcerogenic and antibacterial activities. Their structures were established on the basis of elemental analysis, 1H NMR and mass spectral data. Some of the compounds were found to have significant antiinflammatory and antibacterial activities. Additionally, these derivatives were low in their ulcerogenic action, which is the main side effect of commonly used NSAIDs. PMID:19894647

  6. 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.

  7. 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.

  8. Physical Limit to Concentration Sensing Amid Spurious Ligands

    NASA Astrophysics Data System (ADS)

    Mora, Thierry

    2015-07-01

    To adapt their behavior in changing environments, cells sense concentrations by binding external ligands to their receptors. However, incorrect ligands may bind nonspecifically to receptors, and when their concentration is large, this binding activity may interfere with the sensing of the ligand of interest. Here, I derive analytically the physical limit to the accuracy of concentration sensing amid a large number of interfering ligands. A scaling transition is found when the mean bound time of correct ligands is twice that of incorrect ligands. I discuss how the physical bound can be approached by a cascade of receptor states generalizing kinetic proofreading schemes.

  9. Amide proton exchange of a dynamic loop in cell extracts.

    PubMed

    Smith, Austin E; Sarkar, Mohona; Young, Gregory B; Pielak, Gary J

    2013-10-01

    Intrinsic rates of exchange are essential parameters for obtaining protein stabilities from amide (1) H exchange data. To understand the influence of the intracellular environment on stability, one must know the effect of the cytoplasm on these rates. We probed exchange rates in buffer and in Escherichia coli lysates for the dynamic loop in the small globular protein chymotrypsin inhibitor 2 using a modified form of the nuclear magnetic resonance experiment, SOLEXSY. No significant changes were observed, even in 100 g dry weight L(-1) lysate. Our results suggest that intrinsic rates from studies conducted in buffers are applicable to studies conducted under cellular conditions.

  10. The halogen bond: an interim perspective.

    PubMed

    Legon, Anthony C

    2010-07-28

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

  11. Metal complexes with varying intramolecular hydrogen bonding networks

    PubMed Central

    Lacy, David C.; Mukherjee, Jhumpa; Lucas, Robie L.; Day, Victor W.; Borovik, A.S.

    2013-01-01

    Alfred Werner described the attributes of the primary and secondary coordination spheres in his development of coordination chemistry. To examine the effects of the secondary coordination sphere on coordination chemistry, a series of tripodal ligands containing differing numbers of hydrogen bond (H-bond) donors were used to examine the effects of H-bonds on Fe(II), Mn(II)–acetato, and Mn(III)–OH complexes. The ligands containing varying numbers of urea and amidate donors allowed for systematic changes in the secondary coordination spheres of the complexes. Two of the Fe(II) complexes that were isolated as their Bu4N+ salts formed dimers in the solid-state as determined by X-ray diffraction methods, which correlates with the number of H-bonds present in the complexes (i.e., dimerization is favored as the number of H-bond donors increases). Electron paramagnetic resonance (EPR) studies suggested that the dimeric structures persist in acetonitrile. The Mn(II) complexes were all isolated as their acetato adducts. Furthermore, the synthesis of a rare Mn(III)–OH complex via dioxygen activation was achieved that contains a single intramolecular H-bond; its physical properties are discussed within the context of other Mn(III)–OH complexes. PMID:24904193

  12. 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

  13. 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

  14. Interaction of Thioamides, Selenoamides, and Amides With Diiodine

    PubMed Central

    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 · I2 and D · I2 · I2, respectively, (D is the ligand donor) (ii) iodonium salts of {[D2 − I]+[In]−} (n = 3, 7) and {[D2 − I]+[FeCl4]−} formulae and (iii) disulfides of the categories (a) [D − D], (b) {[D − DH]+[I3]−} have been isolated and characterized. A compound of formula {[D2 − I]+[I3]−[D · I2]} 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)I2]. 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. 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.

  16. [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

  17. Amidated pectin based hydrogels: synthesis, characterization and cytocompatibility study.

    PubMed

    Mishra, R K; Singhal, J P; Datt, M; Banthia, A K

    2007-01-01

    The design and development of pectin-based hydrogels were attempted through the chemical modification of pectin with diethanolamine (DA). Diethanolamine modified pectin (DAMP) was synthesized by the chemical modification of pectin with varying concentrations of DA (1:1,1:2,1:3 and 1:4) at 5 oC in methanol. The modified product was used for the preparation of the hydrogel with glutaraldehyde (GA) reagent. The prepared hydrogels were characterized by Fourier transform infrared (FTIR) spectroscopy; organic elemental analysis, and X-ray diffraction (XRD), and swelling, hemocompatibility and cytocompatibility studies of the prepared hydrogels were also done. FTIR spectroscopy indicated the presence of primary and secondary amide absorption bands. The XRD pattern of the DAMP hydrogel clearly indicated that there was a considerable increase in crystallinity as compared to parent pectin. The degree of amidation (DA) and molar and mass reaction yields (Ym and Yn) was calculated based on the results of organic elemental analysis. Drug release studies from the hydrogel membranes were also evaluated in a Franz's diffusion cell. The hydrogels demonstrated good water holding properties and were found to be compatible with B-16 melanoma cells and human blood.

  18. Poly(ester amide)s based on (L)-lactic acid oligomers and α-amino acids: influence of the α-amino acid side chain in the poly(ester amide)s properties.

    PubMed

    Fonseca, Ana C; Coelho, Jorge F J; Valente, Joana F A; Correia, Tiago R; Correia, Ilídio J; Gil, Maria H; Simões, Pedro N

    2013-01-01

    Novel biodegradable and low cytotoxic poly(ester amide)s (PEAs) based on α-amino acids and (L)-lactic acid (L-LA) oligomers were successfully synthesized by interfacial polymerization. The chemical structure of the new polymers was confirmed by spectroscopic analyses. Further characterization suggests that the α-amino acid plays a critical role on the final properties of the PEA. L-phenylalanine provides PEAs with higher glass transition temperature, whereas glycine enhances the crystallinity. The hydrolytic degradation in PBS (pH = 7.4) at 37 °C also depends on the α-amino acid, being faster for glycine-based PEAs. The cytotoxic profiles using fibroblast human cells indicate that the PEAs did not elicit an acute cytotoxic effect. The strategy presented in this work opens the possibility of synthesizing biodegradable PEAs with low citotoxicity by an easy and fast method. It is worth to mention also that the properties of these materials can be fine-tuned only by changing the α-amino acid.

  19. 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.

  20. Bond percolation in films

    NASA Astrophysics Data System (ADS)

    Korneta, W.; Pytel, Z.

    1988-04-01

    Bond percolation in films with simple cubic structure is considered. It is assumed that the probability of a bond being present between nearest-neighbor sites depends on the distances to surfaces. Based on the relation between the Potts model and the bond percolation model, and using the mean-field approximation, the phase diagram and profiles of the percolation probability have been obtained.