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Amide Groups (amide + groups)
Selected AbstractsEuIII -Doping of Lamellar Bilayer and Amorphous Mono-Amide Cross-Linked Alkyl/Siloxane HybridsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 18 2010Silvia C. Nunes Abstract Two structurally different but chemically similar families of alkyl/siloxane mono-amidosil hosts, represented by m-A(x) [where x = 14 or 8 represents the number of CH2 groups of the pendant alkyl chains directly bonded to the carbonyl group of the amide cross-link] have been doped with a wide range of concentrations of Eu(CF3SO3)3. Mono-amidosils m-A(x)nEu(CF3SO3)3 with n,,,10 (where n is the molar ratio of carbonyl groups per Eu3+ ion) have been analyzed. The m-A(8)nEu(CF3SO3)3 mono-amidosils are transparent and amorphous films, in which the alkyl chains adopt gauche conformations. In contrast, the m-A(14)nEu(CF3SO3)3 mono-amidosils are solid powders; here the lamellar bilayer hierarchical structure of m-A(14) coexists with a new lamellar phase in which the Eu3+ ions are bonded to carbonyl oxygen atoms of the amide groups. At n = 10 the hydrogen-bonded associations formed are highly ordered and considerably stronger than those found in the less concentrated hybrids and in the nondoped matrices. "Free" and weakly coordinated triflate ions occur in all the mono-amidosil samples. The hybrids are white light emitters (maximum quantum yield: 0.08,±,0.01), presenting a broad emission band in the blue/purplish-blue spectral region (ascribed to the hybrid host) superimposed on the 5D0,7F0,4 Eu3+ intra-4f6 transitions. Two Eu3+ local coordination sites (named A and B) have been discerned in both systems. Site A is attributed to weakly coordinated Eu3+/CF3SO3, ion pairs, whereas site B involves Eu3+ coordination to the oxygen atoms of the C=O groups, of the CF3SO3, ions and of the water molecules. For site B, the long-range order of the hybrid host induces distinct features in the energy of the 5D0,7F0,4 transitions, the 5D0 lifetime and the degree of covalency of the Eu3+,first-ligand bonds. [source] Iron(III) Chelation: Tuning of the pH Dependence by Mixed LigandsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 14 2003Anne-Marie Albrecht-Gary Abstract The iron(III) chelating properties of two heteropodands with 8-hydroxyquinoline and catechol binding groups were examined and compared to those of the corresponding homopodal analogues, O-TRENSOX and TRENCAMS. Like the parent homopodands, the two heteropodands are based on the TREN scaffold and the chelating units are connected by amide groups, TRENSOX2CAMS having two 8-hydroxyquinoline and one catechol arms and TRENSOXCAMS2 one 8-hydroxyquinoline and two catechol moieties. The aqueous coordination chemistry of these ligands was examined by potentiometric and spectrophotometric methods in combination with 1H NMR spectroscopy. The respective pFeIII values showed a cooperative effect of the mixed chelating units. Moreover, the pFeIII dependence on pH showed that the mixed ligands exhibit a higher complexing ability than the parent ligands over the pH range 5,9 which is of biological relevance. This result could be of great interest for medical applications. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Roles of adenine anchoring and ion pairing at the coenzyme B12 -binding site in diol dehydratase catalysisFEBS JOURNAL, Issue 24 2008Ken-ichi Ogura The X-ray structure of the diol dehydratase,adeninylpentylcobalamin complex revealed that the adenine moiety of adenosylcobalamin is anchored in the adenine-binding pocket of the enzyme by hydrogen bonding of N3 with the side chain OH group of Ser,224, and of 6-NH2, N1 and N7 with main chain amide groups of other residues. A salt bridge is formed between the ,-NH2 group of Lys,135 and the phosphate group of cobalamin. To assess the importance of adenine anchoring and ion pairing, Ser,224 and Lys,135 mutants of diol dehydratase were prepared, and their catalytic properties investigated. The S,224A, S,224N and K,135E mutants were 19,2% as active as the wild-type enzyme, whereas the K,135A, K,135Q and K,135R mutants retained 58,76% of the wild-type activity. The presence of a positive charge at the ,135 residue increased the affinity for cobalamins but was not essential for catalysis, and the introduction of a negative charge there prevented the enzyme,cobalamin interaction. The S,224A and S,224N mutants showed a kcat/kinact value that was less than 2% that of the wild-type, whereas for Lys,135 mutants this value was in the range 25,75%, except for the K,135E mutant (7%). Unlike the wild-type holoenzyme, the S,224N and S,224A holoenzymes showed very low susceptibility to oxygen in the absence of substrate. These findings suggest that Ser,224 is important for cobalt,carbon bond activation and for preventing the enzyme from being inactivated. Upon inactivation of the S,224A holoenzyme during catalysis, cob(II)alamin accumulated, and a trace of doublet signal due to an organic radical disappeared in EPR. 5,-Deoxyadenosine was formed from the adenosyl group, and the apoenzyme itself was not damaged. This inactivation was thus considered to be a mechanism-based one. [source] Microheterogeneity of recombinant human phenylalanine hydroxylase as a result of nonenzymatic deamidations of labile amide containing amino acidsFEBS JOURNAL, Issue 20 2000Effects on catalytic, stability properties The microheterogeneity of recombinant human phenylalanine hydroxylase (hPAH) was investigated by isoelectric focusing and 2D electrophoresis. When expressed in Escherichia coli four main components (denoted hPAH I-IV) of ,,50 kDa were observed on long-term induction at 28,37 °C with isopropyl thio-,- d -galactoside (IPTG), differing in pI by about 0.1 pH unit. A similar type of microheterogeneity was observed when the enzyme was expressed (1 h at 37 °C) in an in vitro transcription-translation system, including both its nonphosphorylated and phosphorylated forms which were separated on the basis of a difference in mobility on SDS/PAGE. Experimental evidence is presented that the microheterogeneity is the result of nonenzymatic deamidations of labile amide containing amino acids. When expressed in E. coli at 28 °C, the percentage of the acidic forms of the enzyme subunit increased as a function of the induction time with IPTG, representing about 50% on 8 h induction. When the enzyme obtained after 2 h induction (containing mainly hPAH I) was incubated in vitro, its conversion to the acidic components (hPAH II,IV) revealed a pH and temperature dependence characteristic of a nonenzymatic deamidation of asparagine residues in proteins, with the release of ammonia. Comparing the microheterogeneity of the wild-type and a truncated form of the enzyme expressed in E. coli, it is concluded that the labile amide groups are located in the catalytic domain as defined by crystal structure analysis [Erlandsen, H., Fusetti, F., Martínez, A., Hough, E., Flatmark, T. & Stevens, R. C. (1997) Nat. Struct. Biol. 4, 995,1000]. It is further demonstrated that the progressive deamidations which occur in E. coli results in a threefold increase in the catalytic efficiency (Vmax/[S]0.5) of the enzyme and an increased susceptibility to limited tryptic proteolysis, characteristic of a partly activated enzyme. The results also suggest that deamidation may play a role in the long term regulation of the catalytic activity and the cellular turnover of this enzyme. [source] A Stimuli-Responsive, Photoluminescent, Anthracene-Based Liquid Crystal: Emission Color Determined by Thermal and Mechanical ProcessesADVANCED FUNCTIONAL MATERIALS, Issue 12 2009Yoshimitsu Sagara Abstract Here, a photoluminescent liquid crystal that exhibits a change of emission color on the metastable,stable phase transition induced by external stimuli is prepared. A 2,6-diethynylanthracene derivative with amide groups and dendritic side chains exhibits a columnar phase on slow cooling from the isotropic phase and shows blue emission in this columnar phase. In contrast, a cubic phase is obtained by rapid cooling from the isotropic phase. In the cubic phase, the 2,6-diethynylanthracene cores form excimers, resulting in yellow emission. While the columnar phase is a stable liquid-crystalline (LC) phase, the cubic phase is a metastable LC phase. It is found that a change of the photoluminescent color from yellow to blue is observed on the cubic-columnar phase transition induced by heating or mechanical shearing for this 2,6-diethynylanthracene derivative in the cubic phase. This change of photoluminescent color is ascribed to the inhibition of excimer formation on the metastable,stable LC phase transition. [source] Synthesis of Cyclic Peptides by Photochemical Decarboxylation of N -Phthaloyl Peptides in Aqueous SolutionHELVETICA CHIMICA ACTA, Issue 12 2002The synthesis of a variety of cyclic peptides from N -phthaloyl-protected di-, tri-, tetra-, and pentapeptides with different aminocarboxylic acid tethers by photodecarboxylation , initiated by intramolecular electron transfer , has been explored in aqueous media. The progress and the chemoselectivity of the follow-up processes after CO2 extrusion were traced by the respective pH/time-profiles, as well as by the overall change in pH after completion of the reaction. The competition between cyclization and simple oxidative decarboxylation depends on spacer length and geometry, H-bonding interaction between the electron accepting phthalimide CO groups and amide H-atoms, as well as the geometric reorganization coupled with the radical combination step and the formation of the lactam rings. With progressing reaction, hydrolysis of the phthalimide chromophore becomes an increasingly important side reaction due to the constant increase in pH. The use of phosphate-buffered aqueous media consequently improved the cyclization yields. The ground-state interactions between amide groups and the terminal COO, group with the imide CO groups were studied for the model system [N -(phthaloyl)glycyl]sarcosine (1) by NMR spectroscopy where the amide (E/Z)-equilibrium depends on the presence of carboxylate vs. free carboxylic acid, demonstrating the role of H-bonding and metal coordination. [source] PDK1 and PKB/Akt: Ideal Targets for Development of New Strategies to Structure-Based Drug DesignIUBMB LIFE, Issue 3 2003Thomas Harris Abstract Growth factor binding events to receptor tyrosine kinases result in activation of phosphatidylinositol 3-kinase (PI3K), and activated PI3K generates the membrane-bound second messengers phosphatidylinositol 3,4-diphosphate [PI(3,4)P2] and PI(3,4,5)P3, which mediate membrane translocation of the phosphoinositide-dependent kinase-1 (PDK1) and protein kinase B (PKB, also known as Akt). In addition to the kinase domain, PDK1 and PKB contain a pleckstrin homology (PH) domain that binds to the second messenger, resulting in the phosphorylation and activation of PKB by PDK1. Recent evidence indicates that constitutive activation of PKB contributes to cancer progression by promoting proliferation and increased cell survival. The indicating of PDK1 and PKB as primary targets for discovery of anticancer drugs, together with the observations that both PDK1 and PKB contain small-molecule regulatory binding sites that may be in proximity to the kinase active site, make PDK1 and PKB ideal targets for the development of new strategies to structure-based drug design. While X-ray structures have been reported for the kinase domains of PDK1 and PKB, no suitable crystals have been obtained for either PDK1 or PKB with their PH domains intact. In this regard, a novel structure-based strategy is proposed, which utilizes segmental isotopic labeling of the PH domain in combination with site-directed spin labeling of the kinase active site. Then, long-range distance restraints between the 15N-labeled backbone amide groups of the PH domain and the unpaired electron of the active site spin label can be determined from magnetic resonance studies of the enhancement effect that the paramagnetic spin label has on the nuclear relaxation rates of the amide protons. The determination of the structure and position of the PH domain with respect to the known X-ray structure of the kinase active site could be useful in the rational design of potent and selective inhibitors of PDK1 and PKB by 'linking' the free energies of binding of substrate (ATP) analogs with analogs of the inositol polar head group of the phospholipid second messenger. The combined use of X-ray crystallography, segmental isotopic and spin labeling, and magnetic resonance studies can be further extended to the study of other dynamic multidomain proteins and targets for structure-based drug design. IUBMB Life, 55: 117-126, 2003 [source] Surface modification of PHBV films with different functional groups: Thermal properties and in vitro degradationJOURNAL OF APPLIED POLYMER SCIENCE, Issue 1 2010Yu Ke Abstract Polyacrylamide was photografted on solution-cast poly(3-hydroxybutyric acid- co -3-hydroxyvaleric acid) (PHBV) films (amide-PHBV), on which amide groups were transformed into amine groups through Hofmann degradation reaction (amine-PHBV), followed by collagen coupling reaction to prepare collagen-modified PHBV (collagen-PHBV). Amide-, amine-, and collagen-PHBV had higher water absorption and d -spacing values than PHBV, and melting temperatures and enthalpies decreased in the order of collagen-PHBV < amine-PHBV < amide-PHBV < PHBV. Thermal decomposition kinetics of PHBV component in the films has been investigated by means of nonisothermal thermogravimetric and derivative thermogravimetric studies. Applying the Avrami-Erofeev equation with index of 2/5 as the probable kinetic function, the suitable activation energy was calculated by the Friedman method through linear fitting (correlation coefficient > 0.98). The activation energy of PHBV was lower than that of amide-PHBV but higher than that of amine- and collagen-PHBV. Being incubated in phosphate-buffered saline at 37°C, the modified PHBV films showed more weight loss than PHBV during 360 days; however, pH of degradation fluids was nearly neutral as the initial pH was recorded at 7.2. The modified PHBV films with different functional groups may provide an improved biodegradation rate for various cytocompatible biomaterials constructs. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010 [source] Synthesis of amidocrownophanes with 27- and 28-membered rings and their molecular recognition toward urea and its derivativesJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2005Kazuhisha Hiratani Novel crownophanes with 27- and 28-membered rings having two hydroxyl groups, two amide groups, and aromatic moieties such as naphthalene, pyridine, and phenyl rings were successfully synthesized by a one-step reaction from the corresponding macrocyclic polyethers via "tandem Claisen rearrengement" in moderate yields. They can solubilize urea and its derivatives into chloroform solution, while the corresponding macrocyclic polyethers do not solubilize them. According to NMR studies, crownophanes 1 and 2 interact with urea and its derivatives forming 1:1 complexes. [source] Direct analysis of 15N-label in amino and amide groups of glutamine and asparagineJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2007Anne Marie Scharff-Poulsen Abstract A novel method for on-line determination of the amount and position of 15N-labeling in complex mixtures of amino acids is presented. Underivatized amino acids were analyzed by ion-pair chromatography in combination with mass spectrometry. This enables the direct determination of the 15N label distribution. The fragmentation pathways of the nitrogen moieties of glutamine (Gln) and asparagine (Asn) were studied in detail using all mono 15N isotopomers, which led to a method for differentiating between 15N-amide and 15N-amino labeling. The fragmentation involving the amino and amide groups of Gln led to distinct ion structures. The equivalent fragmentation pattern was not observed for Asn. Instead, the amide group of Asn was eliminated as HNCO in a secondary process. The developed analytical method was evaluated by analysis of a range of standard mixtures taking into account different levels of 15N abundance and distribution between the amino and amide groups. The detection limit (3 SD) for the presence of a 15N label was 0.7 and 1.0% for Gln and Asn, respectively. The determination of the positional labeling follows a nonlinear function. A representative example at 30% 15N was used as a benchmark resulting in average relative standard deviations of 2.7 and 15% for Gln and Asn, respectively. The corresponding expectation windows for the positional labeling were found to be 2 and 12%, respectively. Copyright © 2006 John Wiley & Sons, Ltd. [source] FTIR-spectroscopic characterization of humic acids and humin fractions obtained by advanced NaOH, Na4P2O7, and Na2CO3 extraction proceduresJOURNAL OF PLANT NUTRITION AND SOIL SCIENCE, Issue 4 2007Michael Tatzber Abstract Aim of our study was the development of the methodological basis for the characterization of humic fractions of a long-term field experiment. Humic acids (HAs) were extracted from three layers of a nontilled soil using three different extractants (1 M NaOH, 0.1 M Na4P2O7, 1 M Na2CO3), and the humin fraction was enriched. NaOH as extractant for FTIR analysis of humic substances yields higher resolved IR spectra, especially in the important regions of stretching vibrations including aromatic and aliphatic groups and in the fingerprint area including amides, aliphats, and aromats than the other extractants. The NaOH extraction has lower extraction yields as compared to Na4P2O7 and Na2CO3 and represents a different part of the soil organic matter (SOM). This is reflected by lower C : N ratios and higher E4 : E6 and fulvic acid,to,humic acid ratios as compared to the other extractants. The FTIR band areas of HA fraction obtained by NaOH showed an increase of the aromatic and carbonyl groups and a decrease of amide groups with increasing soil depth. Aliphatic groups showed contradicting results: The bands of the stretching vibrations increased, and the band of the bending vibrations decreased. We assume that band interactions in the bending vibrations were responsible for that phenomenon under the assumption of an increase of aliphatic groups with increasing soil depth. The IR bands of the enriched humin fraction showed a decreasing trend in case of both aliphatic bands deriving from stretching vibrations and an increase of aromatic characteristics with depth. Our study led to the conclusion that HA fractions obtained by 1 M NaOH represent a small and dynamic fraction indicated by the measured yields in combination with values of Nt, C : N, E4 : E6 ratios, and ratios of fulvic acids (FA) to HA. The humin fraction has a high contribution to the total organic C and represents a more stabilized fraction of SOM which still shows changes in its aromatic and aliphatic characteristics with soil depth. [source] Structure, Morphology and Properties of a Novel Molecular Composite by In-Situ Blending of Anionic Polyamide 6 with a Polyamide Copolymer Containing Rigid SegmentsMACROMOLECULAR MATERIALS & ENGINEERING, Issue 2 2007Xiaochun Wang Abstract Molten caprolactam, in which a polyamide copolymer (HPN) containing rigid segments was dissolved, was polymerized by means of anionic ROP to in produce polyamide (PA, nylon) 6 blends with HPN in situ. A novel molecular composite was achieved in which toughness and strength were simultaneously improved, as well as modulus, compared to virgin PA6. In view of the interchange reaction between PA6 and PA1212 (and PA66) in blends fabricated in the same way, it was deduced that a similar reaction between PA6 and HPN took place during the blending and led to copolymerization between the two components. The formation of copolymers was verified by their single glass transition and single melting peak, measured through DMA and DSC, respectively. DSC analysis also showed that the occurrence of the interchange reaction inhibited the crystallization and suppressed the melting point of PA6. Analysis by FT-IR spectroscopy indicated that the difference in the distance between the amide groups for PA6 and HPN induced a decrease in the amount and strength of hydrogen bonding. Moreover, characterization by POM and XRD revealed that the spherulite size of the PA6 crystals decreased dramatically and the amount of , crystal increased slightly with the majority of crystallites being , crystals. Furthermore, it was found through the observation of the morphology by SEM that no phase separation existed in the composites. On the basis of detailed analysis and a comparison between the in situ PA6/PA66 and PA6/HPN blends, it is believed that the combination of markedly decreasing spherulite size and similar segmental mobility resulted in the simultaneous improvement of mechanical properties for the in situ PA6/HPN blends. [source] HALS in polyamide 6 polymerizationMACROMOLECULAR SYMPOSIA, Issue 1 2003Roberto Filippini Fantoni Abstract The use of Hindered Amine Light Stabilizers (HALS) directly in polyamide 6 polymerization can cause some problems. The following two problems were the focus of our project: 1) We investigated, from a theoretical point of view, the results of introducing directly one of the precursors of HALS into polyamide 6 polymerization. For the investigation, 4 amino-2,2,6,6-tetramethylpiperidine (triaceton-diamine or TAD) was chosen. We considered the TAD chain-ending effects and their influence on the total amount of amino chain-endings that can be titrated, a parameter of primary importance in the fibre field. 2) We examined the amide interchange reaction in the case of an HALS containing two amide groups, using a product available on the market, N,N,-bis(tetramethyl-4-piperidyl)isophtalamide. In this case we were able to generate a couple of equations that allows one to calculate the quantity of amide interchanged HALS. This was done by comparing the results (molecular weight and chain-endings analysis) of polymerization with and without HALS. [source] Temperature dependencies of amide 1H- and 15N-chemical shifts in hyaluronan oligosaccharidesMAGNETIC RESONANCE IN CHEMISTRY, Issue 5 2007Charles D. Blundell Abstract Temperature coefficients (,,/,T) of amide chemical shifts of N -acetylglucosamine residues have been measured in a range of oligosaccharides of the important vertebrate polysaccharide hyaluronan. Odd- and even-numbered oligosaccharides with glucuronic acid, ,-4,5-unsaturated glucuronic acid and N -acetylglucosamine at the termini were investigated. All amide proton temperature coefficients were only slightly less negative (,6.9 to , 9.1 ppb/ °C) than those of amide protons in free exchange with water (,, 11 ppb/ °C), indicating an absence of persistent intramolecular hydrogen bonds. With the exception of amide groups in reducing-terminal N -acetylglucosamine rings, all amide proton environments have the same temperature coefficient (,6.9 ppb/ °C), irrespective of differences in amide group chemical shifts and 3JHH coupling constants, i.e. they do not sense subtle differences in orientation of the amide group. Amide nitrogen temperature coefficients report the same phenomena but with greater sensitivity. These data provide a set of reference values for temperature coefficients measured in other carbohydrates with acetamido sugars. Copyright © 2007 John Wiley & Sons, Ltd. [source] Experimental charge-density study of paracetamol , multipole refinement in the presence of a disordered methyl groupACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009Joanna M. B A high-resolution single-crystal X-ray study of paracetamol has been performed at 85,K. Different approaches to modeling the experimental electron density (ED) were tested for the dynamically disordered portions of the molecule in order to check to what extent it is possible to obtain a proper ED distribution in the ordered part. Models were examined in which the methyl-group ED was built from pseudoatoms taken from the University at Buffalo Pseudoatom Databank or the Invariom database, with multipole parameters for the remaining atoms being obtained from free refinement. The ,, restricted multipolar model (KRMM) and free ,, refinements were compared; restriction of the ,, parameters was essential in order to obtain values of the electrostatic interaction energy consistent with the results of theoretical single-point periodic calculations. After simultaneous use of KRMM refinement and the databases to model the methyl group, the bond critical point properties and interaction electrostatic energy values were found to be closer to those obtained from theory. Additionally, some discrepancies in the ED distribution and dipole moment among transferred aspherical atom model refinements utilizing both theoretical databases and parameters from theoretical periodic calculations are shown. Including the influence of the crystal field in the periodic calculations increases the ED in the hydroxyl and amide groups, thus leading to higher values of the electrostatic interaction energy, changes in the electrostatic potential values mapped on the isodensity surface and changes in the shape of the anisotropic displacement parameters with respect to results found for both database models. [source] Influence of ionomeric compatibilizers on the morphology and properties of amorphous polyester/polyamide blendsPOLYMER ENGINEERING & SCIENCE, Issue 9 2004Gregory C. Gemeinhardt The utilization of sulfonated polyester ionomers as minor-component compatibilizers in blends of an amorphous polyester and polyamide was investigated. The blends were prepared using twin-screw extrusion and compared to solution blends to investigate the effect of elevated temperatures and shear mixing on blend miscibility and/or phase behavior. The phase domain sizes of the solution blends with respect to ionomer content were studied using small angle light scattering (SALS) and phase contrast optical microscopy. The thermal and mechanical properties of the extruded blends were investigated using dynamic mechanical analysis (DMA) and tensile testing while the morphology was investigated using environmental scanning electron microscopy (ESEM). The interactions between the sulfonate group of the ionomer and the polyamide were characterized using FT-IR spectroscopy. Binary blends of the amorphous polyester and polyamide were immiscible with poor mechanical properties, while blends containing the polyester ionomer as a minor-component compatibilizer showed a significant reduction in the dispersed domain sizes and enhanced ultimate mechanical properties. The compatibilization mechanism is attributed to specific interactions between the sulfonate groups on the polyester ionomer and the amide groups of the polyamide. Polym. Eng. Sci. 44:1721,1731, 2004. © 2004 Society of Plastics Engineers. [source] Swelling behavior of pH- and temperature-sensitive copolymers containing 2-hydroxy-ethyl methacrylate and N -vinyl-2-pyrrolidone crosslinked with new crosslinkersPOLYMER INTERNATIONAL, Issue 11 2004Prof. Ayman M Atta Abstract Copolymers of 2-hydroxyethyl methacrylate (HEMA) and N -vinyl-2-pyrrolidone (VP) and homopolymers of HEMA and VP were crosslinked in the presence of different mol% of melamine trimethacrylamide (MMAm) and melamine triacrylamide (MAAm) as crosslinkers by bulk radical polymerization. The resultant xerogels were characterized by extracting the soluble fractions and measuring the equilibrium water content. Lower critical solution transition temperatures (LCST) were measured by DSC. The properties of crosslinked HEMA and VP copolymers, VP and HEMA series were evaluated in terms of compositional drift of polymerization, heterogeneous crosslinking, and chemical structure of the relevant components. Soluble fractions of the crosslinked networks were reduced by varying the MAAm and MMAm concentrations. The influence of environmental conditions such as temperature and pH on the swelling behavior of these polymeric gels was investigated. The swelling behaviors of the resulting gels show pH sensitivity. This behavior is explained on the basis that amide groups of VP or crosslinkers could be hydrolyzed to form negatively charged carboxylate ion groups in the produced networks in response to an external pH variation. Copyright © 2004 Society of Chemical Industry [source] Control of helix sense in protein-mimicking backbone by the noncovalent chiral effectTHE CHEMICAL RECORD, Issue 3 2007Yoshihito Inai Abstract We have reviewed our previous work regarding induction or control of a peptide helix sense through chiral stimulus to the peptide chain terminus. An optically inactive 310 -helix designed mainly with unusual ,-amino acid residues was commonly employed. Such an N-terminal-free peptide generates a preferred helix sense by chiral acid molecule. A helix sense pre-directed in chiral sequence is also influenced or controlled by the chiral sign of such external molecule. Here free amide groups in the 310 -helical N-terminus participate in the formation of a multipoint coordinated complex. The terminal asymmetry produces the noncovalent chiral domino effect (NCDE) to influence the whole helix sense. The NCDE-mediated control of helicity provides the underlying chiral nature of protein-mimicking helical backbones: notably, chiral recognition at the terminus and modulation of helical propensity through chiral stimulus. The above items from our previous reports have been outlined and reviewed together with their significance in biopolymer science and chiral chemistry. © 2007 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 7: 191,202; 2007: Published online in Wiley Inter-Science (www.interscience.wiley.com) DOI 10.1002/tcr.20116 [source] Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2000W. D. Samuel Motherwell The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of ,,,,, 105° allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH2 spacers, this conformation leads to a parallel ladder with rings of equal size. If , approaches ,60° and , 180°, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH2 spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks. [source] l -Isoleucyl- l -asparagine 1.094-hydrate: a hybrid hydrogen-bonding patternACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Carl Henrik Görbitz The title compound, C10H20N3O4·1.094H2O, crystallizes with two dipeptide molecules in the asymmetric unit, each participating in two head-to-tail chains with hydrogen bonds between the terminal amino and carboxylate groups. As with many other dipeptides, the resulting structure is divided into distinct layers, but as the amide groups of the two peptide molecules participate in different types of interaction, the observed hydrogen bonds within a peptide main-chain layer (as distinct from the side-chain/solvent regions) cannot adapt to any of the four basic patterns observed previously for dipeptides. Instead, a rare hybrid pattern is formed. [source] Herringbone array of hydrogen-bonded ribbons in 2-ethoxybenzamide from high-resolution X-ray powder diffractionACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009Silvina Pagola In 2-ethoxybenzamide, C9H11NO2, 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. [source] 6-(2-Chloroacetamido)hexanoic acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2006Carolina Gastone Crystals of the title compound, C8H14ClNO3, belong to the space group Cc and are characterized by an asymmetric unit containing two molecules, both with a twisted conformation. The molecular packing is stabilized by N,H,O=C hydrogen bonds between the amide groups of molecules with the same conformation. In addition, hydrogen-bonded cyclic carboxylic acid dimers are established between molecules with a different conformation. The ClCH2,CONH bond has a cis conformation in order to favour an intramolecular Cl,HN electrostatic interaction. Weak intra- and intermolecular CH2,O=C interactions are also present. [source] How comb-type poly(maleic acid alkylamide- co -,-olefin) assemble in waxy oils and improve flowing abilityASIA-PACIFIC JOURNAL OF CHEMICAL ENGINEERING, Issue 5 2009Jun Xu Abstract Wax deposition in pipelines restricts flow and even leads to plugging during oil transportation. This paper aims to improve the flowing ability of cold waxy oils using comb-type copolymers to interact with main components of waxy oil: long-chain n -paraffins and asphaltenes. A series of comb-type poly(maleic acid alkylamide- co -,-olefin) (MAC) with different side-chain lengths were synthesized by copolymerization of ,-olefin and maleic anhydride followed by amidation with alkylamine. Their effects on the rheological property (yield stress) and crystallization behaviors of both model waxy oils and crude oils were observed by rheology, differential scanning calorimetry (DSC), and optical microscopy. MACs reduced the yield stress of oils and the crystal size of long-chain n -paraffins, and improved the flowing ability of oils at 0 °C significantly. The MACs either self-assemble to nucleate the crystallization of long-chain n -paraffins or co-crystallize with them by the nonpolar side chains and inhibit the growth of paraffin crystals by the layer of the polar parts, while the carboxyl and amide groups interact with polar aromatic asphaltenes to prevent their aggregation upon cooling. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd. [source] The structure of PhaZ7 at atomic (1.2,Å) resolution reveals details of the active site and suggests a substrate-binding modeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Sachin Wakadkar Poly-(R)-hydroxyalkanoates (PHAs) are bacterial polyesters that are degraded by a group of enzymes known as PHA depolymerases. Paucimonas lemoignei PhaZ7 depolymerase is the only extracellular depolymerase that has been described as being active towards amorphous PHAs. A previously determined crystal structure of PhaZ7 revealed an ,/,-hydrolase fold and a Ser-His-Asp catalytic triad. In order to address questions regarding the catalytic mechanism and substrate binding, the atomic resolution structure of PhaZ7 was determined after cocrystallization with the protease inhibitor PMSF. The reported structure has the highest resolution (1.2,Å) of currently known depolymerase structures and shows a sulfur dioxide molecule covalently attached to the active-site residue Ser136. Structural comparison with the free PhaZ7 structure (1.45,Å resolution) revealed no major changes in the active site, suggesting a preformed catalytic triad. The oxyanion hole was found to be formed by the amide groups of Met137 and Asn49. Nine well ordered water molecules were located in the active site. Manual docking of a substrate trimer showed that the positions of these water molecules coincide well with the substrate atoms. It is proposed that these water molecules are displaced upon binding of the substrate. Furthermore, conformational changes were identified after comparison with a previously determined PhaZ7 dimer structure in a different space group. The changes were located in surface loops involved in dimer formation, indicating some flexibility of these loops and their possible involvement in polyester binding. [source] Degree of blockiness of amide groups as indicator for difference in physical behavior of amidated pectinsBIOPOLYMERS, Issue 1 2006Stéphanie E. Guillotin Abstract Thickening and gelling properties of commercial amidated pectins depend on the degree of amidation and methyl-esterification, but also the distribution of these groups is of great importance. Methods have been developed during the last few years to determine the distribution of methyl esters over the pectic backbone. We applied the strategies developed for the analysis of high methyl-esterified pectins for studying the distribution of amide groups in amidated pectins. Low methyl-esterified amidated (LMA) pectins were digested before and after removal of methyl esters by an endo -polygalacturonase to determine the degree of blockiness of the substituents. The nature of the substituents (amide groups compared to methyl esters) did not modify the behavior of the enzyme. Oligomers released were separated by using high-performance anion exchange chromatography and pulsed amperometric detection (HPAEC,PAD) at pH 5. Fractions collected after on-line desalting were identified by using MALDI,TOF mass spectrometry. Oligomers were found to elute from the column as a function of their total charge. For the same overall charge and size, oligomers with methyl esters eluted before oligomers with amide groups. Both amide groups and methyl esters of the LMA pectins studied were found to be semirandomly distributed over the pectic backbone, but this may vary according to the amidation process used. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 29,37, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] A Dual-Response [2]Rotaxane Based on a 1,2,3-Triazole Ring as a Novel Recognition StationCHEMISTRY - A EUROPEAN JOURNAL, Issue 47 2009Haiyan Zheng Abstract Two novel multilevel switchable [2]rotaxanes containing an ammonium and a triazole station have been constructed by a CuI -catalyzed azide,alkyne cycloaddition reaction. The macrocycle of [2]rotaxane containing a C6-chain bridge between the two hydrogen bonding stations exhibits high selectivity for the ammonium cation in the protonated form. Interestingly, the macrocycle is able to interact with the two recognition stations when the bridge between them is shortened. Upon deprotonation of both [2]rotaxanes, the macrocycle moves towards the triazole recognition site due to the hydrogen-bond interaction between the triazole nitrogen atoms and the amide groups in the macrocycle. Upon addition of chloride anion, the conformation of [2]rotaxane is changed because of the cooperative recognition of the chloride anion by a favorable hydrogen-bond donor from both the macrocycle isophthalamide and thread triazole CH proton. [source] Conformational Flexibility of Tetralactam Macrocycles and Their Intermolecular Hydrogen-Bonding Patterns in the Solid StateCHEMISTRY - A EUROPEAN JOURNAL, Issue 20 2009Sascha Abstract Flexible rigidity: Tetralactam macrocycles of the Hunter type bear a rigid scaffold (see space-filling representation), but can still widely adapt to the properties of a guest molecule inside their cavities. X-ray crystal structures of a series of differently substituted macrocycles reveal a remarkably broad variety of intermolecular hydrogen-bonding patterns organizing the macrocycles in the crystals in intriguingly different ways. Despite their rigid scaffold, tetralactam macrocycles (TLMs) display a remarkable degree of conformational flexibility, as revealed by analysis of the corresponding X-ray crystal structures. This flexibility is not limited to the rotatability of the TLM amide groups but also applies to the m -xylene rings, and it thus has a great impact on the overall shape of the macrocycle cavity. The conformational properties of the TLMs give rise to a broad variety of intermolecular hydrogen-bonding patterns, including infinite ladders, an interesting catemer motif, and short CH,,,OC hydrogen bonds. These results are in accord with previous theoretical calculations, support a structural model proposed earlier for an interpretation of scanning tunneling microscopy images, and substantially contribute to the understanding of the adaptability of macrocyclic scaffolds, which is crucial for guest binding or templated syntheses with TLMs. [source] Two Multi-armed Neutral Receptors for ,,, -Dicarboxylate AnionsCHINESE JOURNAL OF CHEMISTRY, Issue 4 2006Jin-Long Wu Abstract Two new multi-armed neutral receptors 1 and 2 containing thiourea and amide groups were synthesized by simple steps in good yields. Receptors 1 and 2 have a better selectivity and higher association constants for malonate anion than other anions examined by the present work. In particular, distinct color changes were observed upon addition of dicarboxylate anions to the solution of 1 in DMSO. The UV-Vis and fluorescence spectra data indicate that a 1:2 stoichiometry complex was formed between compound 1 or 2 and dicarboxylate anions of shorter carbon chain, and a 1:1 stoichiometry complex was formed between compound 1 or 2 and dicarboxylate anions of longer carbon chain through hydrogen bonding interactions. [source] | |||||||||||||||||||||||||||||||