NMR resonance splitting of urea in stretched hydrogels: proton exchange and (1)H/(2)H isotopologues.

PubMed

Kuchel, Philip W; Naumann, Christoph; Chapman, Bogdan E; Shishmarev, Dmitry; Håkansson, Pär; Bacskay, George; Hush, Noel S

2014-10-01

Urea at ∼12 M in concentrated gelatin gel, that was stretched, gave (1)H and (2)H NMR spectral splitting patterns that varied in a predictable way with changes in the relative proportions of (1)H2O and (2)H2O in the medium. This required consideration of the combinatorics of the two amide groups in urea that have a total of four protonation/deuteration sites giving rise to 16 different isotopologues, if all the atoms were separately identifiable. The rate constant that characterized the exchange of the protons with water was estimated by back-transformation analysis of 2D-EXSY spectra. There was no (1)H NMR spectral evidence that the chiral gelatin medium had caused in-equivalence in the protons bonded to each amide nitrogen atom. The spectral splitting patterns in (1)H and (2)H NMR spectra were accounted for by intra-molecular scalar and dipolar interactions, and quadrupolar interactions with the electric field gradients of the gelatin matrix, respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

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

2015-08-06

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.

Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water.

PubMed

Cheng, Xian; Shkel, Irina A; Molzahn, Cristen; Lambert, David; Karim, Rezwana; Record, M Thomas

2018-04-17

Alkylureas display hydrocarbon and amide groups, the primary functional groups of proteins. To obtain the thermodynamic information that is needed to analyze interactions of amides and proteins with nucleobases and nucleic acids, we quantify preferential interactions of alkylureas with nucleobases differing in the amount and composition of water-accessible surface area (ASA) by solubility assays. Using an established additive ASA-based analysis, we interpret these thermodynamic results to determine interactions of each alkylurea with five types of nucleobase unified atoms (carbonyl sp 2 O, amino sp 3 N, ring sp 2 N, methyl sp 3 C, and ring sp 2 C). All alkylureas interact favorably with nucleobase sp 2 C and sp 3 C atoms; these interactions become more favorable with an increasing level of alkylation of urea. Interactions with nucleobase sp 2 O are most favorable for urea, less favorable for methylurea and ethylurea, and unfavorable for dialkylated ureas. Contributions to overall alkylurea-nucleobase interactions from interactions with each nucleobase atom type are proportional to the ASA of that atom type with proportionality constant (interaction strength) α, as observed previously for urea. Trends in α-values for interactions of alkylureas with nucleobase atom types parallel those for corresponding amide compound atom types, offset because nucleobase α-values are more favorable. Comparisons between ethylated and methylated ureas show interactions of amide compound sp 3 C with nucleobase sp 2 C, sp 3 C, sp 2 N, and sp 3 N atoms are favorable while amide sp 3 C-nucleobase sp 2 O interactions are unfavorable. Strongly favorable interactions of urea with nucleobase sp 2 O but weakly favorable interactions with nucleobase sp 3 N indicate that amide sp 2 N-nucleobase sp 2 O and nucleobase sp 3 N-amide sp 2 O hydrogen bonding (NH···O═C) interactions are favorable while amide sp 2 N-nucleobase sp 3 N interactions are unfavorable. These favorable amide-nucleobase hydrogen bonding interactions are prevalent in specific protein-nucleotide complexes.

Understanding the directed ortho lithiation of (R)-Ph₂P(=NCO₂Me)NHCH(Me)Ph. NMR spectroscopic and computational study of the structure of the N-lithiated species.

PubMed

Casimiro, M; García-López, J; Iglesias, M J; López-Ortiz, F

2014-10-14

A multinuclear magnetic resonance ((1)H, (7)Li, (13)C, (15)N, (31)P) and DFT computational study at the M06-2X(SMD,THF)/6-311+G(d,p)//B3LYP/6-31G(d) level of the structure of a N-lithiated phosphinimidic amide (R)-Ph2P(=NCO2Me)NHCH(Me)Ph 13 has been performed. In THF solution it exists as an equilibrium mixture of monomers and dimers. The monomers consist of a six-membered ring formed by coordination of the lithium atom with the deprotonated nitrogen and the oxygen atom of the carbonyl group. This coordination mode is in contrast to the standard N,N-chelation observed in N-lithiated N,N'-bis(trimethylsilyl)phosphinimidic amides. The calculations showed that the metallacycle adopts a twist-boat conformation and that the lithium atom is in a tetrahedral environment involving O,N-chelation by the ligand and coordination to two/one THF molecules in the monomer/dimer. Dimerization takes place through O-Li bridges. For all species two series of isomers have been identified, which originated by restricted rotation of the methoxy group and ring inversion. The twist-boat conformational interconversion seems to be operating for explaining the pattern of signals observed in the (7)Li and (31)P NMR spectra. The structure found for the most stable dimer is analogous to the molecular structure reported for a related C(α)-lithiated phosphazene 20. The structural study revealed that the chiral side-arm of the N-lithiated species is oriented to the outer face of the pro-S P-phenyl ring, which shows one ortho-proton very close to the nitrogen atom of the carbamate moiety. In this conformation, proton abstraction by a base is highly favoured, in agreement with the experimental results.

DNA mobility modifier

DOEpatents

Barron, Annelise

2002-01-01

Polyamides comprising at least one hydrophilic C.sub.1 -C.sub.10 hydrocarbyl substituent on an amide nitrogen atom, and methods for producing and using the same is provided. In particular, polyamides of the formula: ##STR1## and methods for using the same for altering the ratio of charge/translational frictional drag of binding polymers to allow electrophoretic separation of polynucleotides or analogs thereof in a non-sieving liquid medium is provided, where a, q, L.sup.1, P.sup.1, Q.sup.1, R, R.sup.1, R.sup.10 and R.sup.11 are those described herein.

DNA mobility modifier

DOEpatents

Barron, Annelise E.

2004-04-20

Polyamides comprising at least one hydrophilic C.sub.1 -C.sub.10 hydrocarbyl substituent on an amide nitrogen atom, and methods for producing and using the same is provided. In particular, polyamides of the formula: ##STR1## and methods for using the same for altering the ratio of charge/translational frictional drag of binding polymers to allow electrophoretic separation of polynucleotides or analogs thereof in a non-sieving liquid medium is provided, where a, q, L.sup.1, P.sup.1, Q.sup.1, R, R.sup.1, R.sup.10 and R.sup.11 are those described herein.

Iron(II)-catalyzed amidation of aldehydes with iminoiodinanes at room temperature and under microwave-assisted conditions.

PubMed

Ton, Thi My Uyen; Tejo, Ciputra; Tania, Stefani; Chang, Joyce Wei Wei; Chan, Philip Wai Hong

2011-06-17

A method for the amidation of aldehydes with PhI=NTs/PhI=NNs as the nitrogen source and an inexpensive iron(II) chloride + pyridine as the in situ formed precatalyst under mild conditions at room temperature or microwave assisted conditions is described. The reaction was operationally straightforward and accomplished in moderate to excellent product yields (20-99%) and with complete chemoselectivity with the new C-N bond forming only at the formylic C-H bond in substrates containing other reactive functional groups. By utilizing microwave irradiation, comparable product yields and short reaction times of 1 h could be accomplished. The mechanism is suggested to involve insertion of a putative iron-nitrene/imido group to the formylic C-H bond of the substrate via a H-atom abstraction/radical rebound pathway mediated by the precatalyst [Fe(py)(4)Cl(2)] generated in situ from reaction of FeCl(2) with pyridine.

Synthesis, biological evaluation, and structure-activity relationship of clonazepam, meclonazepam, and 1,4-benzodiazepine compounds with schistosomicidal activity.

PubMed

Menezes, Carla M S; Rivera, Gildardo; Alves, Marina A; do Amaral, Daniel N; Thibaut, Jean Pierre B; Noël, François; Barreiro, Eliezer J; Lima, Lídia M

2012-06-01

The inherent morbidity and mortality caused by schistosomiasis is a serious public health problem in developing countries. Praziquantel is the only drug in therapeutic use, leading to a permanent risk of parasite resistance. In search for new schistosomicidal drugs, meclonazepam, the 3-methyl-derivative of clonazepam, is still considered an interesting lead-candidate because it has a proven schistosomicidal effect in humans but adverse effects on the central nervous system did not allow its clinical use. Herein, the synthesis, in vitro biological evaluation, and molecular modeling of clonazepam, meclonazepam, and analogues are reported to establish the first structure-activity relationship for schistosomicidal benzodiazepines. Our findings indicate that the amide moiety [N(1) H-C(2) (=O)] is the principal pharmacophoric unit of 1,4-benzodiazepine schistosomicidal compounds and that substitution on the amide nitrogen atom (N(1) position) is not tolerated. © 2012 John Wiley & Sons A/S.

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures.

PubMed

Otani, Yuko; Watanabe, Satoshi; Ohwada, Tomohiko; Kitao, Akio

2017-01-12

In this study, the solution structures of the homooligomers of a conformationally constrained bicyclic proline-type β-amino acid were studied by means of molecular dynamics (MD) calculations in explicit methanol and water using the umbrella sampling method. The ratio of trans-amide and cis-amide was estimated by NMR and the rotational barrier of the amide of acetylated bicyclic amino acid monomer was estimated by two-dimensional (2D) exchange spectroscopy (EXSY) or line-shape analysis. A bias potential was introduced with respect to the amide torsion angle ω to enhance conformational exchange including isomerization of amide bonds by lowering the rotation energy barrier. After determination of reweighting parameters to best reproduce the experimental results of the monomer amide, the free energy profile around the amide torsion angle ω was obtained from the MD trajectory by reweighting of the biased probability density. The MD simulation results support the existence of invertomers of nitrogen-pyramidalized amide. Furthermore, extended structures with a high fraction of trans-amide conformation appear to be increasingly stabilized as the oligomer is elongated, both in methanol and in water. Our conformational analysis of natural and non-natural tertiary-amide-based peptide oligomers indicates that these oligomers preferentially adopt a limited number of conformations.

Self-penetration--a structural compromise between single networks and interpenetration: magnetic properties and crystal structures of

PubMed

Jensen; Price; Batten; Moubaraki; Murray

2000-09-01

The three-dimensional coordination polymers [Mn(dca)2(H2O)] (1) and [M(dca)(tcm)], M =Co (2), Ni (3), Cu (4), dca =dicyanamide, N(CN)2-, tcm = tricyanomethanide, C(CN)3-, have isomorphous structures. In 1 half the dca ligands coordinate directly (through all three nitrogen atoms) to three Mn atoms (all metal atoms are six-coordinate), while the other half coordinate to two Mn atoms (through the nitrile nitrogens) and hydrogen bond to water molecules coordinated to a third Mn atom (through the amide nitrogen). This dca. H2O structural moiety is disordered over a mirror plane, and is replaced by the structurally equivalent tcm ligand in compounds 2-4. The resulting structures display a new self-penetrating 3,6-connected (2:1) network topology that can be related to, but is different from, the rutile net. The self-penetrating [M(dca)(tcm)] network can be viewed as a structural compromise between the two interpenetrating rutile-like networks of [M(tcm)2] and the single rutile-like network of alpha-[M(dca)2]. The temperature and field dependence of the DC and AC magnetic susceptibilities and magnetisations has been measured for complexes 1-4. Compounds 1-3 exhibit long-range magnetic order with critical temperatures of 6.3 K for 1, 3.5 K for 2 and 8.0 K for 3. The Cu11 compound 4 does not order and is essentially a paramagnet. Hysteresis measurements of coercive field and remnant magnetisation show that 1, 2 and 3 are soft magnets, 1 being a canted-spin antiferromagnet (weak ferromagnet), while 2 and 3 are ferromagnets that display some unusual features in their high-field magnetisation isotherms in comparison to their related alpha-[M(dca)2] phases.

Condensation Reactions and Formation of Amides, Esters, and Nitriles Under Hydrothermal Conditions

NASA Astrophysics Data System (ADS)

Rushdi, Ahmed I.; Simoneit, Bernd R. T.

2004-06-01

Hydrothermal pyrolysis experiments were performed to assess condensation (dehydration) reactions to amide, ester, and nitrile functionalities from lipid precursors. Beside product formation, organic compound alteration and stability were also evaluated. Mixtures of nonadecanoic acid, hexadecanedioic acid, or hexadecanamide with water, ammonium bicarbonate, and oxalic acid were heated at 300°C for 72 h. In addition, mixtures of ammonium bicarbonate and oxalic acid solutions were used to test the abiotic formation of organic nitrogen compounds at the same temperature. The resulting products were condensation compounds such as amides, nitriles, and minor quantities of N-methylalkyl amides, alkanols, and esters. Mixtures of alkyl amide in water or oxalic acid yielded mainly hydrolysis and dehydration products, and with ammonium bicarbonate and oxalic acid the yield of condensation products was enhanced. The synthesis experiments with oxalic acid and ammonium bicarbonate solutions yielded homologous series of alkyl amides, alkyl amines, alkanes, and alkanoic acids, all with no carbon number predominances. These organic nitrogen compounds are stable and survive under the elevated temperatures of hydrothermal fluids.

‘Umpolung’ Reactivity in Semiaqueous Amide and Peptide Synthesis

PubMed Central

Shen, Bo; Makley, Dawn M.; Johnston, Jeffrey N.

2010-01-01

The amide functional group is one of Nature’s key functional and structural elements, most notably within peptides. Amides are also key intermediates in the preparation of a diverse range of therapeutic small molecules. Its construction using available methods focuses principally upon dehydrative approaches, although oxidative and radical-based methods are representative alternatives. During the carbon-nitrogen bond forming step in most every example, the carbon and nitrogen bear electrophilic and nucleophilic character, respectively. Here we show that activation of amines and nitroalkanes with an electrophilic iodine source in wet THF can lead directly to amide products. Preliminary observations support a mechanistic construct in which reactant polarity is reversed (umpolung) during C-N bond formation relative to traditional approaches. The use of nitroalkanes as acyl anion equivalents provides a conceptually innovative approach to amide and peptide synthesis, and one that might ultimately provide for efficient peptide synthesis that is fully reliant on enantioselective methods. PMID:20577205

Synthesis of novel naphthoquinone aliphatic amides and esters and their anticancer evaluation.

PubMed

Kongkathip, Boonsong; Akkarasamiyo, Sunisa; Hasitapan, Komkrit; Sittikul, Pichamon; Boonyalai, Nonlawat; Kongkathip, Ngampong

2013-02-01

Fourteen new naphthoquinone aliphatic amides and seventeen naphthoquinone aliphatic esters were synthesized in nine to ten steps from 1-hydroxy-2-naphthoic acid with 9-25% overall yield for the amides, and 16-21% overall yield for the esters. The key step of the amide synthesis is a coupling reaction between amine and various aliphatic acids using 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM) as a coupling agent while for the ester synthesis, DCC/DMAP or CDI was used as the coupling reagent between aliphatic acids and naphthoquinone alcohol. Both naphthoquinone amides and esters were evaluated for their anticancer activity against KB cells. It was found that naphthoquinone aliphatic amides showed stronger anticancer activity than those of the esters when the chains are longer than 7-carbon atoms. The optimum chain of amides is expected to be 16-carbon atoms. In addition, naphthoquinone aliphatic esters with α-methyl on the ester moiety possessed much stronger anticancer activity than the straight chains. Decatenation assay revealed that naphthoquinone amide with 16-carbon atoms chain at 15 μM and 20 μM can completely inhibit hTopoIIα activity while at 10 μM the enzyme activity was moderately inhibited. Molecular docking result also showed the same trend as the cytotoxicity and decatenation assay. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

The Atmospheric Fate of Organic Nitrogen Compounds

NASA Astrophysics Data System (ADS)

Borduas, Nadine

Organic nitrogen compounds are present in our atmosphere from biogenic and anthropogenic sources and have impacts on air quality and climate. Due to recent advances in instrumentation, these compounds are being detected in the gas and particle phases, raising questions as to their source, processing and sinks in the environment. With their recently identified role as contributors to aerosol formation and growth, their novel large scale use as solvents in carbon capture and storage (CCS) technology and their emissions from cigarette smoke, it is now important to address the gaps in our understanding of the fate of organic nitrogen. Experimentally and theoretically, I studied the chemical atmospheric fate of specific organic nitrogen compounds in the amine, amide and isocyanate families, yielding information that can be used in chemical transport models to assess the fate of this emerging class of atmospheric molecules. I performed kinetic laboratory studies in a smog chamber to measure the room temperature rate coefficient for reaction with the hydroxyl radical of monoethanolamine, nicotine, and five different amides. I employed online-mass spectrometry techniques to quantify the oxidation products. I found that amines react quickly with OH radicals with lifetimes of a few hours under sunlit conditions, producing amides as oxidation products. My studies on amides revealed that they have much longer lifetimes in the atmosphere, ranging from a few hours to a week. Photo-oxidation of amides produces isocyanates and I investigated these mechanisms in detail using ab initio calculations. Furthermore, I experimentally measured isocyanic acid's Henry's Law constant as well as its hydrolysis rate constants to better understand its sinks in the atmosphere. Finally, I re-examined the structure-activity relationship (SAR) of organic nitrogen molecules for improved model parameterizations.

Backbone dynamics of a model membrane protein: measurement of individual amide hydrogen-exchange rates in detergent-solubilized M13 coat protein using /sup 13/C NMR hydrogen/deuterium isotope shifts

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

Henry, G.D.; Weiner, J.H.; Sykes, B.D.

Hydrogen-exchange rates have been measured for individual assigned amide protons in M13 coat protein, a 50-residue integral membrane protein, using a /sup 13/C nuclear magnetic resonance (NMR) equilibrium isotope shift technique. The locations of the more rapidly exchanging amides have been determined. In D/sub 2/O solutions, a peptide carbonyl resonance undergoes a small upfield isotope shift (0.08-0.09 ppm) from its position in H/sub 2/O solutions; in 1:1 H/sub 2/O/D/sub 2/O mixtures, the carbonyl line shape is determined by the exchange rate at the adjacent nitrogen atom. M13 coat protein was labeled biosynthetically with /sup 13/C at the peptide carbonyls ofmore » alanine, glycine, phenylalanine, proline, and lysine, and the exchange rates of 12 assigned amide protons in the hydrophilic regions were measured as a function of pH by using the isotope shift method. This equilibrium technique is sensitive to the more rapidly exchanging protons which are difficult to measure by classical exchange-out experiments. In proteins, structural factors, notably H bonding, can decrease the exchange rate of an amide proton by many orders of magnitude from that observed in the freely exposed amides of model peptides such as poly(DL-alanine). With corrections for sequence-related inductive effects, the retardation of amide exchange in sodium dodecyl sulfate solubilized coat protein has been calculated with respect to poly(DL-alanine). The most rapidly exchanging protons, which are retarded very little or not at all, are shown to occur at the N- and C-termini of the molecule. A model of the detergent-solubilized coat protein is constructed from these H-exchange data which is consistent with circular dichroism and other NMR results.« less

Nafion®-catalyzed microwave-assisted Ritter reaction: An atom-economic solvent-free synthesis of amides

EPA Science Inventory

An atom-economic solvent-free synthesis of amides by the Ritter reaction of alcohols and nitriles under microwave irradiation is reported. This green protocol is catalyzed by solid supported Nafion®NR50 with improved efficiency and reduced waste production.

Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

PubMed Central

Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

1999-01-01

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039

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.

Vibrational, NMR and quantum chemical investigations of acetoacetanilde, 2-chloroacetoacetanilide and 2-methylacetoacetanilide.

PubMed

Arjunan, V; Kalaivani, M; Senthilkumari, S; Mohan, S

2013-11-01

The vibrational assignment and analysis of the fundamental modes of the compounds acetoacetanilide (AAA), 2-chloroacetoacetanilide (2CAAA) and 2-methylacetoacetanilide (2MAAA) have been performed. Density functional theory studies have been carried out with B3LYP method utilising 6-311++G(**) and cc-pVTZ basis sets to determine structural, thermodynamic and vibrational characteristics of the compounds and also to understand the influence of chloro and methyl groups on the characteristic frequencies of amide (CONH) group. Intramolecular hydrogen bond exists in acetoacetanilide and o-substituted acetoacetanilide molecules and the N⋯O distance is found to be around 2.7Å. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecules were determined and the same have been calculated using the gauge independent atomic orbital (GIAO) method. The energies of the frontier molecular orbitals have been determined. In AAA, 2CAAA and 2MAAA molecules, the nN→πCO(∗) interaction between the nitrogen lone pair and the amide CO antibonding orbital gives strong stabilization of 64.75, 62.84 and 64.18kJmol(-1), respectively. The blue shift in amide-II band of 2MAAA is observed by 45-50cm(-1) than that of AAA. The steric effect of ortho methyl group significantly operating on the NH bond properties. The amide-III, the CN stretching mode of methyl and chloro substituted acetoacetanilide compounds are not affected by the substitution while the amide-V band, the NH out of plane bending mode of 2-chloroacetoacetanilide compound is shifted to a higher frequency than that of AAA. The substituent chlorine plays significantly and the blue shift in o-substituted compounds than the parent in the amide-V vibration is observed. The amide-VI, CO out of plane bending modes of 2MAAA and 2CAAA are significantly raised than that of AAA. A blue shift of amide-VI, CO out of plane bending modes of 2MAAA and 2CAAA than AAA is observed. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Synthesis, Structure, and Physical Properties for a Series of Monomeric Iron(III) Hydroxo Complexes with Varying Hydrogen-Bond Networks

PubMed Central

Mukherjee, Jhumpa; Lucas, Robie L.; Zart, Matthew K.; Powell, Douglas R.; Day, Victor W.; Borovik, A. S.

2013-01-01

Mononuclear iron(III) complexes with terminal hydroxo ligands are proposed to be important species in several metalloproteins, but they have been difficult to isolate in synthetic systems. Using a series of amidate/ureido tripodal ligands, we have prepared and characterized monomeric FeIIIOH complexes with similar trigonal-bipyramidal primary coordination spheres. Three anionic nitrogen donors define the trigonal plane, and the hydroxo oxygen atom is trans to an apical amine nitrogen atom. The complexes have varied secondary coordination spheres that are defined by intramolecular hydrogen bonds between the FeIIIOH unit and the urea NH groups. Structural trends were observed between the number of hydrogen bonds and the Fe–Ohydroxo bond distances: the more intramolecular hydrogen bonds there were, the longer the Fe–O bond became. Spectroscopic trends were also found, including an increase in the energy of the O–H vibrations with a decrease in the number of hydrogen bonds. However, the FeIII/II reduction potentials were constant throughout the series (∼2.0 V vs [Cp2Fe]0/+1), which is ascribed to a balancing of the primary and secondary coordination-sphere effects. PMID:18498155

Nanoengineered analytical immobilized metal affinity chromatography stationary phase by atom transfer radical polymerization: Separation of synthetic prion peptides

PubMed Central

McCarthy, P.; Chattopadhyay, M.; Millhauser, G.L.; Tsarevsky, N.V.; Bombalski, L.; Matyjaszewski, K.; Shimmin, D.; Avdalovic, N.; Pohl, C.

2010-01-01

Atom transfer radical polymerization (ATRP) was employed to create isolated, metal-containing nanoparticles on the surface of non-porous polymeric beads with the goal of developing a new immobilized metal affnity chromatography (IMAC) stationary phase for separating prion peptides and proteins. Transmission electron microscopy was used to visualize nanoparticles on the substrate surface. Individual ferritin molecules were also visualized as ferritin–nanoparticle complexes. The column's resolving power was tested by synthesizing peptide analogs to the copper binding region of prion protein and injecting mixtures of these analogs onto the column. As expected, the column was capable of separating prion-related peptides differing in number of octapeptide repeat units (PHGGGWGQ), (PHGGGWGQ)2, and (PHGGGWGQ)4. Unexpectedly, the column could also resolve peptides containing the same number of repeats but differing only in the presence of a hydrophilic tail, Q → A substitution, or amide nitrogen methylation. PMID:17481564

Chemical shift and electric field gradient tensors for the amide and carboxyl hydrogens in the model peptide N-acetyl-D,L-valine. Single-crystal deuterium NMR study.

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

Gerald, R. E., II; Bernhard, T.; Haeberlen, U.

1993-01-01

Solid-state NMR spectroscopy is well established as a method for describing molecular structure with resolution on the atomic scale. Many of the NMR observables result from anisotropic interactions between the nuclear spin and its environment. These observables can be described by second-rank tensors. For example, the eigenvalues of the traceless symmetric part of the hydrogen chemical shift (CS) tensor provide information about the strength of inter- or intramolecular hydrogen bonding. On the other hand, the eigenvectors of the deuterium electric field gradient (EFG) tensor give deuteron/proton bond directions with an accuracy rivalled only by neutron diffraction. In this paper themore » authors report structural information of this type for the amide and carboxyl hydrogen sites in a single crystal of the model peptide N-acetyl-D,L-valine (NAV). They use deuterium NMR to infer both the EFG and CS tensors at the amide and carboxyl hydrogen sites in NAV. Advantages of this technique over multiple-pulse proton NMR are that it works in the presence of {sup 14}N spins which are very hard to decouple from protons and that additional information in form of the EFG tensors can be derived. The change in the CS and EFG tensors upon exchange of a deuteron for a proton (the isotope effect) is anticipated to be very small; the effect on the CS tensors is certainly smaller than the experimental errors. NAV has served as a model peptide before in a variety of NMR studies, including those concerned with developing solid-state NMR spectroscopy as a method for determining the structure of proteins. NMR experiments on peptide or protein samples which are oriented in at least one dimension can provide important information about the three-dimensional structure of the peptide or the protein. In order to interpret the NMR data in terms of the structure of the polypeptide, the relationship of the CS and EFG tensors to the local symmetry elements of an amino acide, e.g., the peptide plane, is essential. The main purpose of this work is to investigate this relationship for the amide hydrogen CS tensor. The amide hydrogen CS tensor will also provide orientational information for peptide bonds in proteins complementary to that from the nitrogen CS and EFG tensors and the nitrogen-hydrogen heteronuclear dipole-dipole coupling which have been used previously to determine protein structures by solid-state NMR spectroscopy. This information will be particularly valuable because the amide hydrogen CS tensor is not axially symmetric. In addition, the use of the amide hydrogen CS interaction in high-field solid-state NMR experiments will increase the available resolution among peptide sites.« less

A Specific Peptide with Calcium-Binding Capacity from Defatted Schizochytrium sp. Protein Hydrolysates and the Molecular Properties.

PubMed

Cai, Xixi; Yang, Qian; Lin, Jiaping; Fu, Nanyan; Wang, Shaoyun

2017-03-29

Marine microorganisms have been proposed as a new kind of protein source. Efforts are needed in order to transform the protein-rich biological wastes left after lipid extraction into value-added bio-products. Thus, the utilization of protein recovered from defatted Schizochytrium sp. by-products presents an opportunity. A specific peptide Tyr-Leu (YL) with calcium-binding capacity was purified from defatted Schizochytrium sp. protein hydrolysates through gel filtration chromatography and RP-HPLC. The calcium-binding activity of YL reached 126.34 ± 3.40 μg/mg. The calcium-binding mechanism was investigated through ultraviolet, fluorescence and infrared spectroscopy. The results showed that calcium ions could form dative bonds with carboxyl oxygen atoms and amino nitrogen atoms as well as the nitrogen and oxygen atoms of amide bonds. YL-Ca exhibited excellent thermal stability and solubility, which was beneficial for its absorption and transport in the basic intestinal tract of the human body. Moreover, the cellular uptake of calcium in Caco-2 cells showed that YL-Ca could enhance calcium uptake efficiency and protect calcium ions against precipitation caused by dietary inhibitors such as tannic acid, oxalate, phytate and metal ions. The findings indicate that the by-product of Schizochytrium sp. is a promising source for making peptide-calcium bio-products as algae-based functional supplements for human beings.

Benchmarking lithium amide versus amine bonding by charge density and energy decomposition analysis arguments.

PubMed

Engelhardt, Felix; Maaß, Christian; Andrada, Diego M; Herbst-Irmer, Regine; Stalke, Dietmar

2018-03-28

Lithium amides are versatile C-H metallation reagents with vast industrial demand because of their high basicity combined with their weak nucleophilicity, and they are applied in kilotons worldwide annually. The nuclearity of lithium amides, however, modifies and steers reactivity, region- and stereo-selectivity and product diversification in organic syntheses. In this regard, it is vital to understand Li-N bonding as it causes the aggregation of lithium amides to form cubes or ladders from the polar Li-N covalent metal amide bond along the ring stacking and laddering principle. Deaggregation, however, is more governed by the Li←N donor bond to form amine adducts. The geometry of the solid state structures already suggests that there is σ- and π-contribution to the covalent bond. To quantify the mutual influence, we investigated [{(Me 2 NCH 2 ) 2 (C 4 H 2 N)}Li] 2 ( 1 ) by means of experimental charge density calculations based on the quantum theory of atoms in molecules (QTAIM) and DFT calculations using energy decomposition analysis (EDA). This new approach allows for the grading of electrostatic Li + N - , covalent Li-N and donating Li←N bonding, and provides a way to modify traditional widely-used heuristic concepts such as the -I and +I inductive effects. The electron density ρ ( r ) and its second derivative, the Laplacian ∇ 2 ρ ( r ), mirror the various types of bonding. Most remarkably, from the topological descriptors, there is no clear separation of the lithium amide bonds from the lithium amine donor bonds. The computed natural partial charges for lithium are only +0.58, indicating an optimal density supply from the four nitrogen atoms, while the Wiberg bond orders of about 0.14 au suggest very weak bonding. The interaction energy between the two pincer molecules, (C 4 H 2 N) 2 2- , with the Li 2 2+ moiety is very strong ( ca. -628 kcal mol -1 ), followed by the bond dissociation energy (-420.9 kcal mol -1 ). Partitioning the interaction energy into the Pauli (Δ E Pauli ), dispersion (Δ E disp ), electrostatic (Δ E elstat ) and orbital (Δ E orb ) terms gives a 71-72% ionic and 25-26% covalent character of the Li-N bond, different to the old dichotomy of 95 to 5%. In this regard, there is much more potential to steer the reactivity with various substituents and donor solvents than has been anticipated so far.

N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

USGS Publications Warehouse

Thorn, K.A.; Cox, L.G.

2009-01-01

The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS 15N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprised the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by 15N NMR. Liquid state 15N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (1H-15N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.

N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

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

Thorn, Kevin A.; Cox, Larry G.

2009-02-28

The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS ¹⁵N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprisedmore » the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by ¹⁵N NMR. Liquid state ¹⁵N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (¹H–¹⁵N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.« less

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

PubMed Central

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

2011-01-01

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

Late Stage Azidation of Complex Molecules

PubMed Central

2016-01-01

Selective functionalization of complex scaffolds is a promising approach to alter the pharmacological profiles of natural products and their derivatives. We report the site-selective azidation of benzylic and aliphatic C–H bonds in complex molecules catalyzed by the combination of Fe(OAc)2 and a PyBox ligand. The same system also catalyzes the trifluoromethyl azidation of olefins to form derivatives of natural products containing both fluorine atoms and azides. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Azides obtained by functionalization of C–H and C=C bonds were converted to the corresponding amines, amides, and triazoles, thus providing a wide variety of nitrogen-containing complex molecules. PMID:27800554

Ultraviolet irradiation effects incorporation of nitrate and nitrite nitrogen into aquatic natural organic matter

USGS Publications Warehouse

Thorn, Kevin A.; Cox, Larry G.

2012-01-01

One of the concerns regarding the safety and efficacy of ultraviolet radiation for treatment of drinking water and wastewater is the fate of nitrate, particularly its photolysis to nitrite. In this study, 15N NMR was used to establish for the first time that UV irradiation effects the incorporation of nitrate and nitrite nitrogen into aquatic natural organic matter (NOM). Irradiation of 15N-labeled nitrate in aqueous solution with an unfiltered medium pressure mercury lamp resulted in the incorporation of nitrogen into Suwannee River NOM (SRNOM) via nitrosation and other reactions over a range of pH from approximately 3.2 to 8.0, both in the presence and absence of bicarbonate, confirming photonitrosation of the NOM. The major forms of the incorporated label include nitrosophenol, oxime/nitro, pyridine, nitrile, and amide nitrogens. Natural organic matter also catalyzed the reduction of nitrate to ammonia on irradiation. The nitrosophenol and oxime/nitro nitrogens were found to be susceptible to photodegradation on further irradiation when nitrate was removed from the system. At pH 7.5, unfiltered irradiation resulted in the incorporation of 15N-labeled nitrite into SRNOM in the form of amide, nitrile, and pyridine nitrogen. In the presence of bicarbonate at pH 7.4, Pyrex filtered (cutoff below 290–300 nm) irradiation also effected incorporation of nitrite into SRNOM as amide nitrogen. We speculate that nitrosation of NOM from the UV irradiation of nitrate also leads to production of nitrogen gas and nitrous oxide, a process that may be termed photo-chemodenitrification. Irradiation of SRNOM alone resulted in transformation or loss of naturally abundant heterocyclic nitrogens.

Fatty Amide Determination in Neutral Molecular Fractions of Green Crude Hydrothermal Liquefaction Oils From Algal Biomass

DOE PAGES

Palardy, Oliver; Behnke, Craig; Laurens, Lieve M. L.

2017-07-05

Even though hydrothermal liquefaction (HTL) is a promising route to produce crude oils (referred to as 'green crude'), the molecular composition of the nitrogen fraction of such green crude oils is not fully understood. The goal of this work was to identify and quantify the fraction of fatty amides in green crude oils obtained from five different samples derived from Desmodesmus armatus, Tetraselmis sp., and Chlorella sp. biomass treated under different HTL conditions (260 or 340 degrees C as batch or continuous processes). The goal of this work was to elucidate the nature of the high nitrogen content of themore » green crude oils. We identified at least 19 distinct fatty amides present in green crude oils and quantified them based on relevant standards in purified fractions after functional group-based separation and enrichment. It was not known how much these compounds contributed to the oils or which molecular fraction they are associated with. We found that fatty amides exclusively partitioned with the neutral fraction of the oils and belonged mainly to one of five categories, based on their functional group substitution, i.e., fatty amides, monomethyl, dimethyl, monoethanolamide, and diethanolamide. The quantification of fatty amides in the neutral oil fraction was based on respective fatty amide standards, after verification of consistency in response factors between molecules with different substitutions of the amide group. Here, we found that the amount of fatty amides found in each of the five samples varied considerably and ranged between 1.4 and 3.0% of the green crude oils, with the highest levels detected in the sample with the highest oil content, after HTL of biomass derived from a nutrient deprived Chlorella sp. culture.« less

The Influence of Varied Amide Bond Positions on Hydraphile Ion Channel Activity

PubMed Central

Weber, Michelle E.; Wang, Wei; Steinhardt, Sarah E.; Gokel, Michael R.; Leevy, W. Matthew; Gokel, George W.

2008-01-01

Hydraphile compounds have been prepared in which certain of the amine nitrogens have been replaced by amide residues. The amide bonds are present either in the sidearm, the side chain, or the central relay. Sodium cation transport through phospholipid vesicles mediated by each hydraphile was assessed. All of the amide-containing hydraphiles showed increased levels of Na+ transport compared to the parent compound, but the most dramatic rate increase was observed for sidearm amine to amide replacement. We attribute this enhancement to stabilization of the sidearm in the bilayer to achieve a better conformation for ion conduction. Biological studies of the amide hydraphiles with E. coli and B. subtilis showed significant toxicity only with the latter. Further, the consistency between the efficacies of ion transport and toxicity previously observed for non-amidic hydraphiles was not in evidence. PMID:19169369

Quantification and enzyme targets of fatty acid amides from duckweed root exudates involved in the stimulation of denitrification.

PubMed

Sun, Li; Lu, Yufang; Kronzucker, Herbert J; Shi, Weiming

2016-07-01

Fatty acid amides from plant root exudates, such as oleamide and erucamide, have the ability to participate in strong plant-microbe interactions, stimulating nitrogen metabolism in rhizospheric bacteria. However, mechanisms of secretion of such fatty acid amides, and the nature of their stimulatory activities on microbial metabolism, have not been examined. In the present study, collection, pre-treatment, and determination methods of oleamide and erucamide in duckweed root exudates are compared. The detection limits of oleamide and erucamide by gas chromatography (GC) (10.3ngmL(-1) and 16.1ngmL(-1), respectively) are shown to be much lower than those by liquid chromatography (LC) (1.7 and 5.0μgmL(-1), respectively). Quantitative GC analysis yielded five times larger amounts of oleamide and erucamide in root exudates of Spirodela polyrrhiza when using a continuous collection method (50.20±4.32 and 76.79±13.92μgkg(-1) FW day(-1)), compared to static collection (10.88±0.66 and 15.27±0.58μgkg(-1) FW day(-1)). Furthermore, fatty acid amide secretion was significantly enhanced under elevated nitrogen conditions (>300mgL(-1)), and was negatively correlated with the relative growth rate of duckweed. Mechanistic assays were conducted to show that erucamide stimulates nitrogen removal by enhancing denitrification, targeting two key denitrifying enzymes, nitrate and nitrite reductases, in bacteria. Our findings significantly contribute to our understanding of the regulation of nitrogen dynamics by plant root exudates in natural ecosystems. Copyright © 2016 Elsevier GmbH. All rights reserved.

Direct amidation of esters with nitroarenes

NASA Astrophysics Data System (ADS)

Cheung, Chi Wai; Ploeger, Marten Leendert; Hu, Xile

2017-03-01

Esters are one of the most common functional groups in natural and synthetic products, and the one-step conversion of the ester group into other functional groups is an attractive strategy in organic synthesis. Direct amidation of esters is particularly appealing due to the omnipresence of the amide moiety in biomolecules, fine chemicals, and drug candidates. However, efficient methods for direct amidation of unactivated esters are still lacking. Here we report nickel-catalysed reductive coupling of unactivated esters with nitroarenes to furnish in one step a wide range of amides bearing functional groups relevant to the development of drugs and agrochemicals. The method has been used to expedite the syntheses of bio-active molecules and natural products, as well as their post-synthetic modifications. Preliminary mechanistic study indicates a reaction pathway distinct from conventional amidation methods using anilines as nitrogen sources. The work provides a novel and efficient method for amide synthesis.

Copper(II)-catalyzed amidations of alkynyl bromides as a general synthesis of ynamides and Z-enamides. An intramolecular amidation for the synthesis of macrocyclic ynamides.

PubMed

Zhang, Xuejun; Zhang, Yanshi; Huang, Jian; Hsung, Richard P; Kurtz, Kimberly C M; Oppenheimer, Jossian; Petersen, Matthew E; Sagamanova, Irina K; Shen, Lichun; Tracey, Michael R

2006-05-26

A general and efficient method for the coupling of a wide range of amides with alkynyl bromides is described here. This novel amidation reaction involves a catalytic protocol using copper(II) sulfate-pentahydrate and 1,10-phenanthroline to direct the sp-C-N bond formation, leading to a structurally diverse array of ynamides including macrocyclic ynamides via an intramolecular amidation. Given the surging interest in ynamide chemistry, this atom economical synthesis of ynamides should invoke further attention from the synthetic organic community.

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

Palardy, Oliver; Behnke, Craig; Laurens, Lieve M. L.

Even though hydrothermal liquefaction (HTL) is a promising route to produce crude oils (referred to as 'green crude'), the molecular composition of the nitrogen fraction of such green crude oils is not fully understood. The goal of this work was to identify and quantify the fraction of fatty amides in green crude oils obtained from five different samples derived from Desmodesmus armatus, Tetraselmis sp., and Chlorella sp. biomass treated under different HTL conditions (260 or 340 degrees C as batch or continuous processes). The goal of this work was to elucidate the nature of the high nitrogen content of themore » green crude oils. We identified at least 19 distinct fatty amides present in green crude oils and quantified them based on relevant standards in purified fractions after functional group-based separation and enrichment. It was not known how much these compounds contributed to the oils or which molecular fraction they are associated with. We found that fatty amides exclusively partitioned with the neutral fraction of the oils and belonged mainly to one of five categories, based on their functional group substitution, i.e., fatty amides, monomethyl, dimethyl, monoethanolamide, and diethanolamide. The quantification of fatty amides in the neutral oil fraction was based on respective fatty amide standards, after verification of consistency in response factors between molecules with different substitutions of the amide group. Here, we found that the amount of fatty amides found in each of the five samples varied considerably and ranged between 1.4 and 3.0% of the green crude oils, with the highest levels detected in the sample with the highest oil content, after HTL of biomass derived from a nutrient deprived Chlorella sp. culture.« less

The generalized anomeric effect in the 1,3-thiazolidines: Evidence for both sulphur and nitrogen as electron donors. Crystal structures of various N-acylthiazolidines including mercury(II) complexes. Possible relevance to penicillin action

NASA Astrophysics Data System (ADS)

Chandrasekhar, Sosale; Chopra, Deepak; Gopalaiah, Kovuru; Guru Row, Tayur N.

2007-06-01

Evidence for the generalized anomeric effect (GAE) in the N-acyl-1,3-thiazolidines, an important structural motif in the penicillins, was sought in the crystal structures of N-(4-nitrobenzoyl)-1,3-thiazolidine and its (2:1) complex with mercuric chloride, N-acetyl-2-phenyl-1,3-thiazolidine, and the (2:1) complex of N-benzoyl-1,3-thiazolidine with mercuric bromide. An inverse relationship was generally observed between the C2- N and C2- S bond lengths of the thiazolidine ring, supporting the existence of the GAE. (Maximal bond length changes were ˜0.04 Å for C2- N3, S1- C2, and ˜0.08 Å for N3- C6.) Comparison with N-acylpyrrolidines and tetrahydrothiophenes indicates that both the nitrogen-to-sulphur and sulphur-to-nitrogen GAE's operate simultaneously in the 1,3-thiazolidines, the former being dominant. (This is analogous to the normal and exo-anomeric effects in pyranoses, and also leads to an interesting application of Baldwin's rules.) The nitrogen-to-sulphur GAE is generally enhanced in the mercury(II) complexes (presumably via coordination at the sulphur); a 'competition' between the GAE and the amide resonance of the N-acyl moiety is apparent. There is evidence for a 'push-pull' charge transfer between the thiazolidine moieties in the mercury(II) complexes, and for a 'back-donation' of charge from the bromine atoms to the thiazolidine moieties in the HgBr 2 complex. (The sulphur atom appears to be sp 2 hybridised in the mercury(II) complexes, possibly for stereoelectronic reasons.) These results are apparently relevant to the mode of action of the penicillins.

Visible-light-promoted redox neutral C-H amidation of heteroarenes with hydroxylamine derivatives.

PubMed

Qin, Qixue; Yu, Shouyun

2014-07-03

A room temperature redox neutral direct C-H amidation of heteroarenes has been achieved. Hydroxylamine derivatives, which are easily accessed, have been employed as tunable nitrogen sources. These reactions were enabled by a visible-light-promoted single-electron transfer pathway without a directing group. A variety of heteroarenes, such as indoles, pyrroles, and furans, could go through this amidation with high yields (up to 98%). These reactions are highly regioselective, and all the products were isolated as a single regioisomer.

Conformation-Specific Spectroscopy of a Prototypical γ-PEPTIDE-WATER Complex: Ac-γ2-hPhe-NHMe-(H2O)1

NASA Astrophysics Data System (ADS)

Buchanan, Evan G.; James, William H., III; Zwier, Timothy S.; Guo, Li; Gellman, Samuel H.

2010-06-01

The prototypical γ-peptide, Ac-γ2-hPhe-NHMe, has been previously studied in a supersonic jet expansion, with three different conformers observed. Two of the monomers form nine atom, intramolecular hydrogen bonded rings, which differ by the position of the aromatic chromophore relative to the backbone. The third monomer conformer has no intramolecular H-bonds, but forms instead an intramolecular, amide-amide stacked structure unique to the γ-peptide backbone. This talk focuses attention on the conformation-specific IR spectra of the Ac-γ2-hPhe-NHMe-(H2O)1 complex, which is observed to form six unique conformational isomers, all of which preserve the two distinct monomer structural motifs. Three conformers are assigned to the nine atom intramolecular hydrogen bond family with the water hydrogen bonded to it as donor in different locations. The other three belong to the amide-amide stacking family with the water forming a bridge between the two amide planes. Infrared photodissocation of the water molecule from the complex to form γ-peptide monomer conformations will also be discussed.

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 force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

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 monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Efficient Amide-Aldehyde-Alkene Condensation: Synthesis for the N-Allyl Amides.

PubMed

Quan, Zheng-Jun; Wang, Xi-Cun

2016-02-01

The allylamine skeleton represents a significant class of biologically active nitrogen compounds that are found in various natural products and drugs with well-recognized pharmacological properties. In this personal account, we will briefly discuss the synthesis of allylamine skeletons. We will focus on showing a general protocol for Lewis acid-catalyzed N-allylation of electron-poor N-heterocyclic amides and sulfonamide via an amide-aldehyde-alkene condensation reaction. The substrate scope with respect to N-heterocyclic amides, aldehydes, and alkenes will be discussed. This method is also capable of preparing the Naftifine motif from N-methyl-1-naphthamide or methyl (naphthalene-1-ylmethyl)carbamate, with paraformaldehyde and styrene in a one-pot manner. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bistable or oscillating state depending on station and temperature in three-station glycorotaxane molecular machines.

PubMed

Busseron, Eric; Romuald, Camille; Coutrot, Frédéric

2010-09-03

High-yield, straightforward synthesis of two- and three-station [2]rotaxane molecular machines based on an anilinium, a triazolium, and a mono- or disubstituted pyridinium amide station is reported. In the case of the pH-sensitive two-station molecular machines, large-amplitude movement of the macrocycle occurred. However, the presence of an intermediate third station led, after deprotonation of the anilinium station, and depending on the substitution of the pyridinium amide, either to exclusive localization of the macrocycle around the triazolium station or to oscillatory shuttling of the macrocycle between the triazolium and monosubstituted pyridinium amide station. Variable-temperature (1)H NMR investigation of the oscillating system was performed in CD(2)Cl(2). The exchange between the two stations proved to be fast on the NMR timescale for all considered temperatures (298-193 K). Interestingly, decreasing the temperature displaced the equilibrium between the two translational isomers until a unique location of the macrocycle around the monosubstituted pyridinium amide station was reached. Thermodynamic constants K were evaluated at each temperature: the thermodynamic parameters DeltaH and DeltaS were extracted from a Van't Hoff plot, and provided the Gibbs energy DeltaG. Arrhenius and Eyring plots afforded kinetic parameters, namely, energies of activation E(a), enthalpies of activation DeltaH( not equal), and entropies of activation DeltaS( not equal). The DeltaG values deduced from kinetic parameters match very well with the DeltaG values determined from thermodynamic parameters. In addition, whereas signal coalescence of pyridinium hydrogen atoms located next to the amide bond was observed at 205 K in the oscillating rotaxane and at 203 K in the two-station rotaxane with a unique location of the macrocycle around the pyridinium amide, no separation of (1)H NMR signals of the considered hydrogen atoms was seen in the corresponding nonencapsulated thread. It is suggested that the macrocycle acts as a molecular brake for the rotation of the pyridinium-amide bond when it interacts by hydrogen bonding with both the amide NH and the pyridinium hydrogen atoms at the same time.

Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results.

PubMed

Hahn, Seungsoo

2016-10-28

The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.

Infrared Fingerprints of nN → σ*NH Hyperconjugation in Hydrazides.

PubMed

Andrade, Laize A F; Silla, Josué M; Cormanich, Rodrigo A; Freitas, Matheus P

2017-12-01

An earlier study demonstrated that hyperconjugation operates in hydrazides by analyzing the N-H stretching mode in gas phase infrared (IR) spectroscopy, and then observing two very distinct bands corresponding to isolated isomers experiencing or not the n N → σ* N-H electron delocalization. The present work reports a chemical method to obtain insight on the hyperconjugation in hydrazide derivatives from solution IR spectroscopy. The analogous amides did not show a ν N-H red-shifted band, as the electron donor orbital in the above hyperconjugative interaction does not exist. In addition, the effect of electron withdrawing groups bonded to a nitrogen atom, namely the trifluoroacetyl and the methanesulfonyl groups, was analyzed on the conformational isomerism and on the ability to induce a stronger hyperconjugation in the resulting compounds.

Preparation and Characterization of Polyimide/Organoclay Nanocomposites

NASA Technical Reports Server (NTRS)

Delozier, D. M.; Orwoll, R. A.; Cahoon, J. F.; Johnston, N. J.; Smith, J. G., Jr.; Connell, J. W.

2002-01-01

Organically modified montmorrrillonite clay, containing a long chain aliphatic quarternary ammonium cation, was used to prepare polyimide/organoclay hybrids. Several approaches were examined in an attempt to achieve fully exfoliated nanocomposites. These included simple mixing of the clay in a pre-made high molecular weight poly(amide acid) solution; simple mixing followed by sonication of the organoclay/poly(amide acid) solutions; and the preparation of high molecular weight poly(amide acid)s in the presence of the organoclay dispersed in N-methyl-2-pyrrolidinone (NMP). The best results were obtained using the in-situ polymerization approach. The resulting nanocomposite films (both amide acid and imide), containing 3-8% by weight of organoclay, were characterized by differential scanning calorimetry (DSC), dynamic thermogravimetric analysis (TGA), transmission electron microscopy (TEM), X-ray diffraction (XRD), and thin film tensile properties. A significant degree of dispersion was observed in the nanocomposite films of the amide acid and the imide. After thermal treatment of amide acid films to effect imidization, in both air and nitrogen, the films were visually darker than control films without clay and the level of clay dispersion appeared to have decreased. In the latter case, the separation between the layers of the clay decreased to a spacing less than that present in the original organoclay. These observations suggest that thermal degradation of the aliphatic quarternary ammonium cation occurred likely during thermal treatment to effect imidization and solvent removal. These thermal degradation effects were less pronounced when thermal treatment was performed under nitrogen. The polyimide/organoclay hybrid films exhibited higher room temperature tensile moduli and lower strength and elongation to break than the control films.

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

PubMed

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

2018-05-18

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

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.

Application of Fourier transform infrared (FT-IR) spectroscopy in determination of microalgal compositions.

PubMed

Meng, Yingying; Yao, Changhong; Xue, Song; Yang, Haibo

2014-01-01

Fourier transform infrared spectroscopy (FT-IR) was applied in algal strain screening and monitoring cell composition dynamics in a marine microalga Isochrysis zhangjiangensis during algal cultivation. The content of lipid, carbohydrate and protein of samples determined by traditional methods had validated the accuracy of FT-IR method. For algal screening, the band absorption ratios of lipid/amide I and carbo/amide I from FT-IR measurements allowed for the selection of Isochrysis sp. and Tetraselmis subcordiformis as the most potential lipid and carbohydrate producers, respectively. The cell composition dynamics of I. zhangjiangensis measured by FT-IR revealed the diversion of carbon allocation from protein to carbohydrate and neutral lipid when nitrogen-replete cells were subjected to nitrogen limitation. The carbo/amide I band absorption ratio had also been demonstrated to depict physiological status under nutrient stress in T. subcordiformis. FT-IR serves as a tool for the simultaneous measurement of lipid, carbohydrate, and protein content in cell. Copyright © 2013 Elsevier Ltd. All rights reserved.

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 ().

Future riverine nitrogen export to US coastal regions: Prospects for improving water quality amid population growth.

EPA Science Inventory

Excess nitrogen (N) in the environment degrades ecosystems and adversely affects human health. Here we examine predictions of contemporary (2000) and future (2030) coastal N loading in the continental US by the Nutrient Export from WaterSheds (NEWS) model. Future scenarios were b...

The ozonolysis of primary aliphatic amines in single and multicomponent fine particles

NASA Astrophysics Data System (ADS)

Zahardis, J.; Geddes, S.; Petrucci, G. A.

2007-10-01

The oxidative processing by ozone of the particulate amines octadecylamine (ODA) and hexadecylamine (HDA) is reported. Ozonolysis of these amines resulted in strong NO2- and NO3- ion signals that increased with ozone exposure as monitored by photoelectron resonance capture ionization aerosol mass spectrometry. These products suggest a mechanism of progressive oxidation of the particulate amines to nitro alkanes. Additionally, a strong ion signal at 125 m/z is assigned to the ion NO3-(HNO3). For ozonized mixed particles containing ODA or HDA + oleic acid (OL), with pO3≥3×10^{-7 atm, imine, secondary amide, and tertiary amide products were measured. These products most likely arise from reactions of amines with aldehydes (for imines) and stabilized Criegee intermediates (SCI) or secondary ozonides (for amides) from the fatty acid. The routes to amides via SCI and/or secondary ozonides was shown to be more important than comparable amide forming reactions between amines and organic acids, using azelaic acid as a test compound. Finally, direct evidence is provided for the formation of a surface barrier in the ODA + OL reaction system that resulted in the retention of OL at high ozone exposures (up to 10-3 atm for 17 s). This effect was not observed in HDA + OL or single component OL particles, suggesting that it may be a species-specific surfactant effect from an in situ generated amide or imine. Implications to tropospheric chemistry, including particle bound amines as sources of oxidized gas phase nitrogen species (e.g. NO2, NO3), formation of nitrogen enriched HULIS via ozonolysis of amines and source apportionment are discussed.}

The ozonolysis of primary aliphatic amines in fine particles

NASA Astrophysics Data System (ADS)

Zahardis, J.; Geddes, S.; Petrucci, G. A.

2008-02-01

The oxidative processing by ozone of the particulate amines octadecylamine (ODA) and hexadecylamine (HDA) is reported. Ozonolysis of these amines resulted in strong NO2- and NO3- ion signals that increased with ozone exposure as monitored by photoelectron resonance capture ionization aerosol mass spectrometry. These products suggest a mechanism of progressive oxidation of the particulate amines to nitroalkanes. Additionally, a strong ion signal at 125 m/z is assigned to the ion NO3- (HNO3). For ozonized mixed particles containing ODA or HDA + oleic acid (OL), with pO3≥3×10-7 atm, imine, secondary amide, and tertiary amide products were measured. These products most likely arise from reactions of amines with aldehydes (for imines) and stabilized Criegee intermediates (SCI) or secondary ozonides (for amides) from the fatty acid. The routes to amides via SCI and/or secondary ozonides were shown to be more important than comparable amide forming reactions between amines and organic acids, using azelaic acid as a test compound. Finally, direct evidence is provided for the formation of a surface barrier in the ODA + OL reaction system that resulted in the retention of OL at high ozone exposures (up to 10-3 atm for 17 s). This effect was not observed in HDA + OL or single component OL particles, suggesting that it may be a species-specific surfactant effect from an in situ generated amide or imine. Implications to tropospheric chemistry, including particle bound amines as sources of oxidized gas phase nitrogen species (e.g.~NO2, NO3), formation of nitrogen enriched HULIS via ozonolysis of amines and source apportionment are discussed.

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.

The carbon functional group budget of a peatland

NASA Astrophysics Data System (ADS)

Moody, Catherine; Worrall, Fred; Clay, Gareth; Apperley, David

2016-04-01

Organic matter samples were taken from each organic matter reservoir and fluvial flux found in a peatland and analysed by elemental analysis for carbon, hydrogen, nitrogen and oxygen content, and by 13C solid state nuclear magnetic resonance (NMR) for functional group composition. The samples analysed were: aboveground, belowground, heather, mosses and sedges, litter layer, four different depths from a peat core, and monthly samples of fluvial particulate and dissolved organic matter. All organic matter samples were taken from a 100% peat catchment within Moor House National Nature Reserve in the North Pennines, UK. The proportion of carbon atoms from each of the eight carbon functional groups (C-alkyl, N-alkyl/methoxyl C, O-alkyl, O2-alkyl/acetal C, aromatic/unsaturated C, phenolic C, aldehyde/ketone C and amide/carboxyl C) from each type of organic matter were combined with an existing carbon budget from the same site, to give a functional group carbon budget. The budget results show that the ecosystem is accumulating N-alkyl/methoxyl C, O-alkyl, O2-alkyl/acetal C and phenolic C groups, but losing C-alkyl, aromatic/unsaturated C, amide/carboxyl C and aldehyde/ketone C. Comparing the functional group compositions between the sampled organic matter pools shows that DOM arises from two distinct sources; from the peat itself and from a vegetation source.

Production mechanism of atomic nitrogen in atmospheric pressure pulsed corona discharge measured using two-photon absorption laser-induced fluorescence

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

Teramoto, Yoshiyuki; Ono, Ryo; Oda, Tetsuji

To study the production mechanism of atomic nitrogen, the temporal profile and spatial distribution of atomic nitrogen are measured in atmospheric pressure pulsed positive corona discharge using two-photon absorption laser-induced fluorescence. The absolute atomic nitrogen density in the streamer filaments is estimated from decay rate of atomic nitrogen in N{sub 2} discharge. The results indicate that the absolute atomic nitrogen density is approximately constant against discharge energy. When the discharge voltage is 21.5 kV, production yield of atomic nitrogen produced by an N{sub 2} discharge pulse is estimated to be 2.9 - 9.8 Multiplication-Sign 10{sup 13} atoms and the energymore » efficiency of atomic nitrogen production is estimated to be about 1.8 - 6.1 Multiplication-Sign 10{sup 16} atoms/J. The energy efficiency of atomic nitrogen production in N{sub 2} discharge is constant against the discharge energy, while that in N{sub 2}/O{sub 2} discharge increases with discharge energy. In the N{sub 2}/O{sub 2} discharge, two-step process of N{sub 2} dissociation plays significant role for atomic nitrogen production.« less

Mild and Selective Hydrozirconation of Amides to Aldehydes Using Cp2Zr(H)Cl

PubMed Central

Spletstoser, Jared T.; White, Jonathan M.; Tunoori, Ashok Rao; Georg, Gunda I.

2008-01-01

An investigation of the use of Cp2Zr(H)Cl (Schwartz’s reagent) to reduce a variety of amides to the corresponding aldehydes under very mild reaction conditions and in high yields is reported. A range of tertiary amides, including Weinreb’s amide, can be converted directly to the corresponding aldehydes with remarkable chemoselectivity. Primary and secondary amides proved to be viable substrates for reduction as well, although the yields were somewhat diminished compared to the corresponding tertiary amides. Results from NMR experiments suggested the presence of a stable, 18-electron zirconacycle intermediate that presumably affords the aldehyde upon water or silica gel workup. A series of competition experiments revealed a preference of the reagent for substrates in which the lone pair of the nitrogen is electron releasing and thus more delocalized across the amide bond by resonance. This trend accounts for the observed excellent selectivity for tertiary amides versus esters. Experiments regarding the solvent dependence of the reaction suggested a kinetic profile similar to that postulated for the hydrozirconation of alkenes and alkynes. Addition of p-anisidine to the reaction intermediate resulted in the formation of the corresponding imine mimicking the addition of water that forms the aldehyde. PMID:17315870

Role of glutamine in cobinamide biosynthesis in Propionibacterium shermanii

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

Eliseev, A.A.; Pushkin, A.V.; Belozerova, E.V.

1987-01-10

The role of glutamine as a possible donor of amide groups in the biosynthesis of vitamin B/sub 12/ was investigated. In the incubation of P. shermanii cells preliminarily exhausted with respect to nitrogen on media containing ammonium sulfate or asparagine, the glutamine synthetase inhibitor methionine sulfoximine suppressed the formation of cobinamide (factor B) from the monoamide of cobiric acid (by 75 and 59%, respectively). At the same time, the inhibitor did not affect cobinamide synthesis on a medium with glutamine. The amide group of glutamine, labeled with /sup 13/N, was used for the amidation of corrinoids four times as efficientlymore » as the amine group. It was concluded that a glutamine-dependent synthetase, which catalyzes the amidation of cobiric acids with the formation of cobinamide, functions in cells of propionic acid bacteria.« less

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.

Quantitative analysis of nitrogen containing compounds in microalgae based bio-oils using comprehensive two-dimensional gas-chromatography coupled to nitrogen chemiluminescence detector and time of flight mass spectrometer.

PubMed

Toraman, Hilal E; Franz, Kristina; Ronsse, Frederik; Van Geem, Kevin M; Marin, Guy B

2016-08-19

Insight in the composition of the algae derived bio-oils is crucial for the development of efficient conversion processes and better upgrading strategies for microalgae. Comprehensive two-dimensional gas chromatography (GC×GC) coupled to nitrogen chemiluminescence detector (NCD) and time-of-flight mass spectrometer (TOF-MS) allows to obtain the detailed quantitative composition of the nitrogen containing compounds in the aqueous and the organic fraction of fast pyrolysis bio-oils from microalgae. Normal phase (apolar×mid-polar) and reverse phase column (polar×apolar) combination are investigated to optimize the separation of the detected nitrogen containing compounds. The reverse phase column combination gives the most detailed information in terms of the nitrogen containing compounds. The combined information from the GC×GC-TOF-MS (qualitative) and GC×GC-NCD (quantitative) with the use of a well-chosen internal standard, i.e. caprolactam, enables the identification and quantification of nitrogen containing compounds belonging to 13 different classes: amines, imidazoles, amides, imides, nitriles, pyrazines, pyridines, indoles, pyrazoles, pyrimidines, quinolines, pyrimidinediones and other nitrogen containing compounds which were not assigned to a specific class. The aqueous fraction mostly consists of amines (4.0wt%) and imidazoles (2.8wt%) corresponding to approximately 80wt% of the total identified nitrogen containing compounds. On the other hand, the organic fraction shows a more diverse distribution of nitrogen containing compounds with the majority of the compounds quantified as amides (3.0wt%), indoles (2.0wt%), amines (1.7wt%) and imides (1.3wt%) corresponding to approximately 65wt% of the total identified nitrogen containing compounds. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural study of salt forms of amides; paracetamol, benzamide and piperine

NASA Astrophysics Data System (ADS)

Kennedy, Alan R.; King, Nathan L. C.; Oswald, Iain D. H.; Rollo, David G.; Spiteri, Rebecca; Walls, Aiden

2018-02-01

Single crystal x-ray diffraction has been used to investigate the structures of six complexes containing O-atom protonated cations derived from the pharmaceutically relevant amides benzamide (BEN), paracetamol (PAR) and piperine (PIP). The structures of the salt forms [PAR(H)][SO3C6H4Cl], [BEN(H)][O3SC6H4Cl] and [BEN(H)][Br]·H2O are reported along with those of the hemi-halide salt forms [PAR(H)][I3]. PAR, [PIP(H)][I3]·PIP and [PIP(H)][I3]0·5[I]0.5. PIP. The structure of the cocrystal BEN. HOOCCH2Cl is also presented for comparison. The geometry of the amide group is found to systematically change upon protonation, with the Cdbnd O distance increasing and the Csbnd N distance decreasing. The hemi-halide species all feature strongly hydrogen bonded amide(H)/amide pairs. The amide group Cdbnd O and Csbnd N distances for both elements of each such pair are intermediate between those found for simple neutral amide and protonated amide forms. It was found that crystallising paracetamol from aqueous solutions containing Ba2+ ions gave orthorhombic paracetamol.

The mechanism and high-free-energy transition state of lac repressor–lac operator interaction

PubMed Central

Sengupta, Rituparna; Capp, Michael W.; Shkel, Irina A.

2017-01-01

Abstract Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)–lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O. Strikingly, three solutes which stabilize RO by favoring burial/dehydration of amide oxygens and anionic phosphate oxygens all reduce kd without affecting ka significantly. The lack of stabilization of TS by these solutes indicates that O phosphates remain hydrated in TS and that TS preferentially buries aromatic carbons and amide nitrogens while leaving amide oxygens exposed. In our proposed mechanism, DNA-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic interactions of RO and burying aromatic carbons. Nucleation of hinge helices creates TS, burying sidechain amide nitrogens. Post-TS, hinge helices assemble and the DBD-hinge helix-O-DNA module docks on core repressor, partially dehydrating phosphate oxygens and tightening all interfaces to form RO. PMID:29036376

Formation of the nitrogen aggregates in annealed diamond by neutron irradiation

NASA Astrophysics Data System (ADS)

Mita, Y.; Nisida, Y.; Okada, M.

2018-02-01

Neutron heavy irradiation was performed on synthetic diamonds contain nitrogen atoms in isolated substitutional form (called "type Ib diamond") and they were annealed under a pressure of 6 GPa. A large number of nitrogen B-aggregate which consists of four substitutional nitrogen atoms symmetrically surrounding a vacancy was formed within 30 m from single nitrogen atoms. Furthermore it is observed that, in these diamonds, single nitrogen atoms coexist with the B-aggregates, which is unexplainable by the simple nitrogen aggregation model.

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

PubMed

Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

2015-07-30

Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol.

PubMed

Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

2016-12-30

Amides are important atmospheric organic-nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N -methylformamide, N , N -dimethylformamide, acetamide, N -methylacetamide and N , N -dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH-amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O-H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

PubMed Central

Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

2016-01-01

Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components. PMID:28042825

Oxygen-Controlled Catalysis by Vitamin B12 -TiO2 : Formation of Esters and Amides from Trichlorinated Organic Compounds by Photoirradiation.

PubMed

Shimakoshi, Hisashi; Hisaeda, Yoshio

2015-12-14

An oxygen switch in catalysis of the cobalamin derivative (B12 )-TiO2 hybrid catalyst for the dechlorination of trichlorinated organic compounds has been developed. The covalently bound B12 on the TiO2 surface transformed trichlorinated organic compounds into an ester and amide by UV light irradiation under mild conditions (in air at room temperature), while dichlorostilbenes (E and Z forms) were formed in nitrogen from benzotrichloride. A benzoyl chloride was formed as an intermediate of the ester and amide, which was detected by GC-MS. The substrate scope of the synthetic strategy is demonstrated with a range of various trichlorinated organic compounds. A photo-duet reaction utilizing the hole and conduction band electron of TiO2 in B12 -TiO2 for the amide formation was also developed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Halochromism, ionochromism, solvatochromism and density functional study of a synthesized copper(II) complex containing hemilabile amide derivative ligand.

PubMed

Golchoubian, Hamid; Moayyedi, Golasa; Reisi, Neda

2015-03-05

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 CuO to CuN 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 CuN/CuO 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 CuO isomer is more stable than its linkage isomer and conversely in alkaline aqueous solution. Copyright © 2014 Elsevier B.V. All rights reserved.

Topological control of supramolecular crystal structures of phenylene bis-monothiooxamate derivatives and in vitro anticancer activity

NASA Astrophysics Data System (ADS)

da Cunha, Tamyris T.; Oliveira, Willian X. C.; Marzano, Ivana M.; Pinheiro, Carlos B.; Pereira-Maia, Elene Cristina; Pereira, Cynthia L. M.

2017-12-01

This paper describes the synthesis, physical characterization, X-ray crystal structures and antitumoral activity against human carcionogenic cells of three new diethyl ester acid derivatives of phenylene bis-monothiooxamate compounds, namely Et2H2opbta (1), Et2H2mpbta (2) and Et2H2ppbta (3) [opbta = N,N‧-1,2-phenylenebis(2-thiooxamate), mbpta = N,N‧-1,3-phenylenebis(2-thiooxamate) and ppbta = N,N‧-1,4-phenylenebis(2-thiooxamate)]. Compounds 1-3 were obtained under mild conditions by reaction of the corresponding N,N‧-phenylenebis(oxamate) analogues and Lawesson's reagent resulting in the formation of Cdbnd S bonds at the carbonyl amide functions. Crystal structures of 1-3 consist of 1D supramolecular assemblies of centrosymmetric H2Et2ppbta (3) or noncentrosymmetric chiral H2Et2opbta (1) and H2Et2mpbta (2) molecules with opposite helical chirality (M and P enantiomers) resulting from intermolecular Nsbnd H⋯O (1 and 3) or Nsbnd H⋯S (2) hydrogen bonds between the amide hydrogen atoms and the carbonyl ester oxygen or thionyl amide sulfur atoms from the thiooxamate moieties respectively, together with weak S⋯S bonds between the thionyl amide sulfur atoms (1). The cytotoxicity of H2Et2xpbta [x = o (1), m (2) and p (3)] against chronic myelogenous leukemia cells was evaluated and the bioactivity follows the order 1 ≫ 2 > 3, compound 1 being six and ten times more active than 2 and 3, respectively.

Possibility of Salicornia europaea use for the human liquid wastes inclusion into BLSS intrasystem mass exchange

NASA Astrophysics Data System (ADS)

Tikhomirova, Natalia A.; Ushakova, Sofya A.; Tikhomirov, Alexander A.; Kalacheva, Galina S.; Gros, Jean-Bernard

One of the ways of solving the problem of the human liquid wastes utilization in bioregenerative life support systems (BLSS) can be the use of halophytic vegetable plant Salicornia europaea capable of accumulating sodium chloride in rather high concentrations. Since the most specific higher plant function in BLSS, which at present cannot be substituted by physicochemical processes, appears to be the biosynthesis of a wide spectrum of nutritive substances necessary for a human, the object of the given work was the investigation of the S. europaea productivity, biochemical and mineral composition when grown under close to optimal BLSS vegetative component conditions. As the use of human urine after its preliminary physicochemical processing is supposed to be the mineral solution basis for the S. europaea cultivation, it is necessary to clear up the effect of reduced nitrogen on plants growth. Ground research was carried out. Biochemical composition of the S. europaea edible part showed that crude protein was contained in the highest degree. At that the content of crude protein (24% per dry weight) and cellulose (4.7% per dry weight) was higher in the plants grown on solutions containing amide nitrogen in comparison with the plants grown on solutions with nitrate nitrogen (15.4%—3.1% correspondingly). The water-soluble sugar contents were not high in the S. europaea edible part and depending on the nitrogen nutrition form they amounted to 1.1% (amide nitrogen) and 1.5% (nitrate nitrogen). The polysaccharide number (except cellulose) was rather higher and varied from 7.7% to 8.2%. Although the lipid content in the S. europaea plants was relatively low (7% per dry weight), it was shown that the plant lipids are characterized by a high nonsaturation degree mainly due to alpha linolenic and linoleic acids. Nitrogen nutrition form did not significantly affect the S. europaea productivity, and dry edible biomass of one plant was 8.6 g. Sodium and its concentrations predominated in the plant mineral composition and amounted in average to 9% per dry weight. Thus the S. europaea being the vegetable plant it can be the source of several biochemical substances and essential fatty acids. The present work also considers the influence of nitrate and amide forms of nitrogen on S. europaea biochemical and mineral composition.

40 CFR 442.2 - General definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., organic chemicals including: alcohols, aldehydes, formaldehydes, phenols, peroxides, organic salts, amines, amides, other nitrogen compounds, other aromatic compounds, aliphatic organic chemicals, glycols, glycerines, and organic polymers; refractory organic compounds including: ketones, nitriles, organo-metallic...

IDAWG: Metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells

PubMed Central

Orlando, Ron; Lim, Jae-Min; Atwood, James A.; Angel, Peggi M.; Fang, Meng; Aoki, Kazuhiro; Alvarez-Manilla, Gerardo; Moremen, Kelley W.; York, William S.; Tiemeyer, Michael; Pierce, Michael; Dalton, Stephen; Wells, Lance

2012-01-01

Robust quantification is an essential component of comparative –omic strategies. In this regard, glycomics lags behind proteomics. Although various isotope-tagging and direct quantification methods have recently enhanced comparative glycan analysis, a cell culture labeling strategy, that could provide for glycomics the advantages that SILAC provides for proteomics, has not been described. Here we report the development of IDAWG, Isotopic Detection of Aminosugars With Glutamine, for the incorporation of differential mass tags into the glycans of cultured cells. In this method, culture media containing amide-15N-Gln is used to metabolically label cellular aminosugars with heavy nitrogen. Because the amide side chain of Gln is the sole source of nitrogen for the biosynthesis of GlcNAc, GalNAc, and sialic acid, we demonstrate that culturing mouse embryonic stems cells for 72 hours in the presence of amide-15N-Gln media results in nearly complete incorporation of 15N into N-linked and O-linked glycans. The isotopically heavy monosaccharide residues provide additional information for interpreting glycan fragmentation and also allow quantification in both full MS and MS/MS modes. Thus, IDAWG is a simple to implement, yet powerful quantitative tool for the glycomics toolbox. PMID:19449840

Interplay of Nitrogen-Atom Inversion and Conformational Inversion in Enantiomerization of 1H-1-Benzazepines.

PubMed

Ramig, Keith; Subramaniam, Gopal; Karimi, Sasan; Szalda, David J; Ko, Allen; Lam, Aaron; Li, Jeffrey; Coaderaj, Ani; Cavdar, Leyla; Bogdan, Lukasz; Kwon, Kitae; Greer, Edyta M

2016-04-15

A series of 2,4-disubstituted 1H-1-benzazepines, 2a-d, 4, and 6, were studied, varying both the substituents at C2 and C4 and at the nitrogen atom. The conformational inversion (ring-flip) and nitrogen-atom inversion (N-inversion) energetics were studied by variable-temperature NMR spectroscopy and computations. The steric bulk of the nitrogen-atom substituent was found to affect both the conformation of the azepine ring and the geometry around the nitrogen atom. Also affected were the Gibbs free energy barriers for the ring-flip and the N-inversion. When the nitrogen-atom substituent was alkyl, as in 2a-c, the geometry of the nitrogen atom was nearly planar and the azepine ring was highly puckered; the result was a relatively high-energy barrier to ring-flip and a low barrier to N-inversion. Conversely, when the nitrogen-atom substituent was a hydrogen atom, as in 2d, 4, and 6, the nitrogen atom was significantly pyramidalized and the azepine ring was less puckered; the result here was a relatively high energy barrier to N-inversion and a low barrier to ring-flip. In these N-unsubstituted compounds, it was found computationally that the lowest-energy stereodynamic process was ring-flip coupled with N-inversion, as N-inversion alone had a much higher energy barrier.

Nitrogen diffusion in hafnia and the impact of nitridation on oxygen and hydrogen diffusion: A first-principles study

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

Sathiyanarayanan, Rajesh, E-mail: rajessat@in.ibm.com, E-mail: rajesh.sathiyanarayanan@gmail.com; Pandey, R. K.; Murali, K. V. R. M.

2015-01-21

Using first-principles simulations, we have computed incorporation energies and diffusion barriers of ammonia, the nitrogen molecule and atomic nitrogen in monoclinic hafnia (m-HfO{sub 2}). Our calculations show that ammonia is likely to dissociate into an NH{sub 2} molecular unit, whereas the nitrogen molecule remains as a molecule either in the interstitial space or at an oxygen lattice site. The lowest energy pathway for the diffusion of atomic nitrogen interstitials consists of the hopping of the nitrogen interstitial between neighboring three-coordinated lattice oxygen atoms that share a single Hf atom, and the barrier for such hops is determined by a switchingmore » mechanism. The substitutional nitrogen atom shows a preference for diffusion through the doubly positive oxygen vacancy-mediated mechanism. Furthermore, we have investigated the impact of nitrogen atoms on the diffusion barriers of oxygen and hydrogen interstitials in m-HfO{sub 2}. Our results show that nitrogen incorporation has a significant impact on the barriers for oxygen and hydrogen diffusion: nitrogen atoms attract oxygen and hydrogen interstitials diffusing in the vicinity, thereby slowing down (reducing) their diffusion (diffusion length)« less

15N-CPMAS nuclear magnetic resonace spectroscopy and biological stability of soil organic nitrogen in whole soil and particle-size fractions

Treesearch

R.J. DiCosty; D.P. Weliky; S.J. Anderson; E.A. Paul

2003-01-01

Soil organic nitrogen was quantified by solid-state 15N cross-polarization nuclear magnetic resonance spectroscopy (NMR) during a 14-month laboratory incubation of a sandy loam soil amended with 15N-clover. In whole soil and particle-size fractions, the clover-derived N was always 85-90% amide, 5 10% guanidinium N of...

Nitrate reduction

DOEpatents

Dziewinski, Jacek J.; Marczak, Stanislaw

2000-01-01

Nitrates are reduced to nitrogen gas by contacting the nitrates with a metal to reduce the nitrates to nitrites which are then contacted with an amide to produce nitrogen and carbon dioxide or acid anions which can be released to the atmosphere. Minor amounts of metal catalysts can be useful in the reduction of the nitrates to nitrites. Metal salts which are formed can be treated electrochemically to recover the metals.

Purification, characterization, gene cloning and nucleotide sequencing of D: -stereospecific amino acid amidase from soil bacterium: Delftia acidovorans.

PubMed

Hongpattarakere, Tipparat; Komeda, Hidenobu; Asano, Yasuhisa

2005-12-01

The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40 degrees C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45 degrees C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd2+, Ag+, Zn2+, Hg2+ and As3+ . The NH2 terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.

Chloro-, methyl-, and (tetrahydroborato)tris((hexamethyldisilyl)amido)thorium(IV) and -uranium(IV). Crystal structure of (tetrahydroborato)tris((hexamethyldisilyl)amido)thorium(IV)

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

Turner, H.W.; Andersen, R.A.; Zalkin, A.

1979-05-01

Reaction of sodium (hexamethyldisilyl)amide with thorium tetrachloride or uranium tetrachloride yields chlorotris-((hexamethyldisilyl)amido)thorium(IV) or -uranium(IV), respectively. The chloroamides of thorium or uranium react with dimethylmagnesium or methyllithium yielding the methyl derivatives MeTh(N(SiMe/sub 3/)/sub 2/)/sub 3/ or MeU(N(SiMe/sub 3/)/sub 2/)/sub 3/, respectively. The chloro compounds yield BH/sub 4/M(N(SiMe/sub 3/)/sub 2/)/sub 3/ upon reaction with lithium tetrahydroborate, where M is thorium or uranium. Infrared spectra of the tetrahydroborate derivatives suggest that BH/sub 4/ is bonded in a tridentate fashion in both compounds, the metal atoms being six-coordinate. Single-crystal X-ray analysis of the thorium borohydride confirms the infrared result. The white BH/sub 4/Th(N(Si(CH/sub 3/))/submore » 2/)/sub 3/ crystals are rhombohedral with cell dimensions a/sub r/ = 11.137 A and ..cap alpha../sub r/ = 113.61/sup 0/; the triply primitive hexagonal cell has a/sub h/ = 18.640 (3) A c/sub h/ = 8.604 (1) A, V = 2489 A/sup 3/, Z = 3, and D/sub x/ = 1.40 g/cm/sup 3/, space group R3m. The structure was refined by full-matrix least squares to a conventional R factor of 0.031 for 1014 data. The Th atom is on a threefold axis 2.32 A from three nitrogen atoms and 2.61 A from the boron atom, a distance which represents a triple bridge bond between Th and B. The three (dimethylsilyl)amide ligands are disordered by a mirror plane parallel to the threefold axis. CH/sub 3/Th(N(Si(CH/sub 3/)/sub 3/)/sub 2/)/sub 3/ is isomorphous with BH/sub 4/Th(N(Si(CH/sub 3/)/sub 3/)/sub 2/)/sub 3/ with cell dimensions a/sub h/ = 18.68 (1) A and c/sub h/ = 8.537 (6) A. The diffraction data yielded integral'' = 12.16 +- 0.33 e for the imaginary scattering term for Th with Cu K..cap alpha.. radiation.« less

Design and optimization of selective azaindole amide M1 positive allosteric modulators.

PubMed

Davoren, Jennifer E; O'Neil, Steven V; Anderson, Dennis P; Brodney, Michael A; Chenard, Lois; Dlugolenski, Keith; Edgerton, Jeremy R; Green, Michael; Garnsey, Michelle; Grimwood, Sarah; Harris, Anthony R; Kauffman, Gregory W; LaChapelle, Erik; Lazzaro, John T; Lee, Che-Wah; Lotarski, Susan M; Nason, Deane M; Obach, R Scott; Reinhart, Veronica; Salomon-Ferrer, Romelia; Steyn, Stefanus J; Webb, Damien; Yan, Jiangli; Zhang, Lei

2016-01-15

Selective activation of the M1 receptor via a positive allosteric modulator (PAM) is a new approach for the treatment of the cognitive impairments associated with schizophrenia and Alzheimer's disease. A novel series of azaindole amides and their key pharmacophore elements are described. The nitrogen of the azaindole core is a key design element as it forms an intramolecular hydrogen bond with the amide N-H thus reinforcing the bioactive conformation predicted by published SAR and our homology model. Representative compound 25 is a potent and selective M1 PAM that has well aligned physicochemical properties, adequate brain penetration and pharmacokinetic (PK) properties, and is active in vivo. These favorable properties indicate that this series possesses suitable qualities for further development and studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

In situ Generated Ruthenium Catalyst Systems Bearing Diverse N-Heterocyclic Carbene Precursors for Atom-Economic Amide Synthesis from Alcohols and Amines.

PubMed

Cheng, Hua; Xiong, Mao-Qian; Cheng, Chuan-Xiang; Wang, Hua-Jing; Lu, Qiang; Liu, Hong-Fu; Yao, Fu-Bin; Chen, Cheng; Verpoort, Francis

2018-02-16

The transition-metal-catalyzed direct synthesis of amides from alcohols and amines is herein demonstrated as a highly environmentally benign and atom-economic process. Among various catalyst systems, in situ generated N-heterocyclic carbene (NHC)-based ruthenium (Ru) halide catalyst systems have been proven to be active for this transformation. However, these existing catalyst systems usually require an additional ligand to achieve satisfactory results. In this work, through extensive screening of a diverse variety of NHC precursors, we discovered an active in situ catalyst system for efficient amide synthesis without any additional ligand. Notably, this catalyst system was found to be insensitive to the electronic effects of the substrates, and various electron-deficient substrates, which were not highly reactive with our previous catalyst systems, could be employed to afford the corresponding amides efficiently. Furthermore, mechanistic investigations were performed to provide a rationale for the high activity of the optimized catalyst system. NMR-scale reactions indicated that the rapid formation of a Ru hydride intermediate (signal at δ=-7.8 ppm in the 1 H NMR spectrum) after the addition of the alcohol substrate should be pivotal in establishing the high catalyst activity. Besides, HRMS analysis provided possible structures of the in situ generated catalyst system. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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. Copyright © 2015, Pisithkul et al.

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

Phenolic amides are potent inhibitors of De Novo nucleotide biosynthesis

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

Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.

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 exposuremore » 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. Furthermore, 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.« less

Phenolic amides are potent inhibitors of De Novo nucleotide biosynthesis

DOE PAGES

Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; ...

2015-06-12

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 exposuremore » 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. Furthermore, 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.« less

In vivo detection of 13C isotopomer turnover in the human brain by sequential infusion of 13C labeled substrates

NASA Astrophysics Data System (ADS)

Li, Shizhe; Zhang, Yan; Ferraris Araneta, Maria; Xiang, Yun; Johnson, Christopher; Innis, Robert B.; Shen, Jun

2012-05-01

This study demonstrates the feasibility of simultaneously detecting human brain metabolites labeled by two substrates infused in a sequential order. In vivo 13C spectra of carboxylic/amide carbons were acquired only during the infusion of the second substrate. This approach allowed dynamic detection of 13C labeling from two substrates with considerably different labeling patterns. [2-13C]glucose and [U-13C6]glucose were used to generate singlet and doublet signals of the same carboxylic/amide carbon atom, respectively. Because of the large one-bond 13C-13C homonuclear J coupling between a carboxylic/amide carbon and an aliphatic carbon (˜50 Hz), the singlet and doublet signals of the same carboxylic/amide carbon were well distinguished. The results demonstrated that different 13C isotopomer patterns could be simultaneously and distinctly measured in vivo in a clinical setting at 3 T.

Metal aminocarboxylate coordination polymers with chain and layered structures.

PubMed

Dan, Meenakshi; Rao, C N R

2005-11-18

The synthesis and structures of metal aminocarboxylates prepared in acidic, neutral, or alkaline media have been explored with the purpose of isolating coordination polymers with linear chain and two-dimensional layered structures. Metal glycinates of the formulae [CoCl2(H2O)2(CO2CH2NH3)] (I), [MnCl2(CO2CH2NH3)2] (II), and [Cd3Cl6(CO2CH2NH3)4] (III) with one-dimensional chain structures have been obtained by the reaction of the metal salts with glycine in an acidic medium under hydro/solvothermal conditions. These chain compounds contain glycine in the zwitterionic form. 4-Aminobutyric acid transforms to a cyclic amide under such reaction conditions, and the amide forms a chain compound of the formula [CdBr2(C4H7NO)2] (IV). Glycine in the zwitterionic form also forms a two-dimensional layered compound of the formula [Mn(H2O)2(CO2CH2NH3)2]Br2 (V). 6-Aminocaproic acid under alkaline conditions forms layered compounds with metals at room temperature, the metal being coordinated both by the amino nitrogen and the carboxyl oxygen atoms. Of the two layered compounds [Cd{CO2(CH2)5NH2}2]2 H2O (VI) and [Cu{CO2(CH2)5NH2}2]2 H2O (VII), the latter has voids in which water molecules reside.

A Continuous Flow System for the Measurement of Ambient Nitrogen Oxides [NO + NO2] Using Rhodamine B Hydrazide as a Chemosensor.

PubMed

Malingappa, Pandurangappa; Yarradoddappa, Venkataramanappa

2014-01-01

A new chemosensor has been used to monitor atmospheric nitrogen oxides [NO + NO2] at parts per billion (ppb) level. It is based on the catalytic reaction of nitrogen oxides with rhodamine B hydrazide (RBH) to produce a colored compound through the hydrolysis of the amide bond of the molecule. A simple colorimeter has been used to monitor atmospheric nitrogen dioxide at ppb level. The air samples were purged through a sampling cuvette containing RBH solution using peristaltic pump. The proposed method has been successfully applied to monitor the ambient nitrogen dioxide levels at traffic junction points within the city limits and the results obtained are compared with the standard Griess-Ilosvay method.

Vibrational Spectra of Cryogenic Peptide Ions Using H_2 Predissociation Spectroscopy

NASA Astrophysics Data System (ADS)

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

2011-06-01

H_2 predissociation spectroscopy was used to collect the vibrational spectra of the model protonated peptides, GlyGly, GlySar, SarGly and SarSar (Gly=glycine and Sar=sarcosine). H_2 molecules were condensed onto protonated peptide ions in a quadrupole ion trap cooled to approximately 10 K. The resulting spectra yielded clearly resolved vibrational transitions throughout the mid IR region, 600-4200 Cm-1, with linewidths of approximately 6 Cm-1. Protonation nominally occurred on the amino terminus giving rise to an intramolecular H-bond between the protonated amine and the neighboring amide oxygen. The sarcosine containing peptides incorporate a methyl group onto either the amino group or the amide nitrogen causing the peptide backbone to adopt a different structure, resulting in the shifts in the amide I and II bands and the N-H stretches.

Excitation of atomic nitrogen by electron impact

NASA Technical Reports Server (NTRS)

Stone, E. J.; Zipf, E. C.

1972-01-01

Absolute cross sections were measured for the excitation of the N I(1134, 1164, 1168, 1200, 1243, and 1743 A) multiplets by electron impact on atomic nitrogen. The presence of vibrationally excited molecular nitrogen in the discharged gas was confirmed, and its effect on the measurements is discussed. The ratio of the oscillator strengths of the 1200 and 1134 A resonance transitions is presented, as well as the branching ratio for the N I(1311/1164 A) multiplets. Striking differences in the distribution of intensity between the spectra of atomic nitrogen and molecular nitrogen excited by energetic electrons suggest an optical method for measuring the density of atomic nitrogen in the upper atmosphere.

Synthesis of actinide nitrides, phosphides, sulfides and oxides

DOEpatents

Van Der Sluys, William G.; Burns, Carol J.; Smith, David C.

1992-01-01

A process of preparing an actinide compound of the formula An.sub.x Z.sub.y wherein An is an actinide metal atom selected from the group consisting of thorium, uranium, plutonium, neptunium, and americium, x is selected from the group consisting of one, two or three, Z is a main group element atom selected from the group consisting of nitrogen, phosphorus, oxygen and sulfur and y is selected from the group consisting of one, two, three or four, by admixing an actinide organometallic precursor wherein said actinide is selected from the group consisting of thorium, uranium, plutonium, neptunium, and americium, a suitable solvent and a protic Lewis base selected from the group consisting of ammonia, phosphine, hydrogen sulfide and water, at temperatures and for time sufficient to form an intermediate actinide complex, heating said intermediate actinide complex at temperatures and for time sufficient to form the actinide compound, and a process of depositing a thin film of such an actinide compound, e.g., uranium mononitride, by subliming an actinide organometallic precursor, e.g., a uranium amide precursor, in the presence of an effectgive amount of a protic Lewis base, e.g., ammonia, within a reactor at temperatures and for time sufficient to form a thin film of the actinide compound, are disclosed.

Structure-Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics.

PubMed

Kaczor, Agnieszka A; Silva, Andrea G; Loza, María I; Kolb, Peter; Castro, Marián; Poso, Antti

2016-04-05

Structure-based virtual screening using a D2 receptor homology model was performed to identify dopamine D2 receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D2 ligands were identified (47.6% success rate, among them D2 receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5-HT2A receptors. The affinity (Ki values) of the compounds ranged from 58 nm to about 24 μM. Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D2 receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D2 pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20-fold binding selectivity for the D2 receptor over the D3 receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling of recovery mechanism of ozone zero phenomenaby adding small amount of nitrogen in atmospheric pressure oxygen dielectric barrier discharges

NASA Astrophysics Data System (ADS)

Akashi, Haruaki; Yoshinaga, Tomokazu

2013-09-01

Ozone zero phenomena in an atmospheric pressure oxygen dielectric barrier discharges have been one of the major problems during a long time operation of ozone generators. But it is also known that the adding a small amount of nitrogen makes the recover from the ozone zero phenomena. To make clear the mechanism of recovery, authors have been simulated the discharges with using the results of Ref. 3. As a result, the recovery process can be seen and ozone density increased. It is found that the most important species would be nitrogen atoms. The reaction of nitrogen atoms and oxygen molecules makes oxygen atoms which is main precursor species of ozone. This generation of oxygen atoms is effective to increase ozone. The dependence of oxygen atom density (nO) and nitrogen atom density (nN) ratio was examined in this paper. In the condition of low nN/nO ratio case, generation of nitrogen oxide is low, and the quenching of ozone by the nitrogen oxide would be low. But in the high ratio condition, the quenching of ozone by nitrogen oxide would significant. This work was supported by KAKENHI(23560352).

Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon

NASA Astrophysics Data System (ADS)

Keiluweit, Marco; Bougoure, Jeremy J.; Zeglin, Lydia H.; Myrold, David D.; Weber, Peter K.; Pett-Ridge, Jennifer; Kleber, Markus; Nico, Peter S.

2012-10-01

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of these materials to classic bulk extraction methods. To address this issue, we used advanced visualization tools to examine transformation pathways of chitin-rich fungal cell wall residues as they interact with microorganisms, soil organic matter and mineral surfaces. Our goal was to document initial micro-scale dynamics of the incorporation of 13C- and 15N-labeled chitin into fungi-dominated microenvironments in O-horizons of old-growth forest soils. At the end of a 3-week incubation experiment, high-resolution secondary ion mass spectrometry imaging of hyphae-associated soil microstructures revealed a preferential association of 15N with Fe-rich particles. Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM/NEXAFS) of the same samples showed that thin organic coatings on these soil microstructures are enriched in aliphatic C and amide N on Fe (hydr)oxides, suggesting a concentration of microbial lipids and proteins on these surfaces. A possible explanation for the results of our micro-scale investigation of chemical and spatial patterns is that amide N from chitinous fungal cell walls was assimilated by hyphae-associated bacteria, resynthesized into proteinaceous amide N, and subsequently concentrated onto Fe (hydr)oxide surfaces. If confirmed in other soil ecosystems, such rapid association of microbial N with hydroxylated Fe oxide surfaces may have important implications for mechanistic models of microbial cycling of C and N.

Precise control of atomic nitrogen production in an electron cyclotron resonance plasma using N2/noble gas mixtures

NASA Astrophysics Data System (ADS)

Fan, Z. Y.; Newman, N.

1998-07-01

The atomic nitrogen flux and impacting ion kinetic energy are two important parameters which influence the quality of deposited nitride films using reactive growth. In this letter, a method is described to control the flux and kinetic energy of atomic and molecular nitrogen ions using an electron cyclotron resonance plasma with N2/Ar and N2/Ne gas mixtures. The results clearly show that the addition of neon to nitrogen plasma can remarkably enhance the production rate of atomic nitrogen due to Penning ionization involving the metastable state of Ne. In contrast, the addition of argon significantly decreases the rate.

A Continuous Flow System for the Measurement of Ambient Nitrogen Oxides [NO + NO2] Using Rhodamine B Hydrazide as a Chemosensor

PubMed Central

Malingappa, Pandurangappa; Yarradoddappa, Venkataramanappa

2014-01-01

A new chemosensor has been used to monitor atmospheric nitrogen oxides [NO + NO2] at parts per billion (ppb) level. It is based on the catalytic reaction of nitrogen oxides with rhodamine B hydrazide (RBH) to produce a colored compound through the hydrolysis of the amide bond of the molecule. A simple colorimeter has been used to monitor atmospheric nitrogen dioxide at ppb level. The air samples were purged through a sampling cuvette containing RBH solution using peristaltic pump. The proposed method has been successfully applied to monitor the ambient nitrogen dioxide levels at traffic junction points within the city limits and the results obtained are compared with the standard Griess-Ilosvay method. PMID:25210422

Highly Chemoselective Reduction of Amides (Primary, Secondary, Tertiary) to Alcohols using SmI2/Amine/H2O under Mild Conditions

PubMed Central

2014-01-01

Highly chemoselective direct reduction of primary, secondary, and tertiary amides to alcohols using SmI2/amine/H2O is reported. The reaction proceeds with C–N bond cleavage in the carbinolamine intermediate, shows excellent functional group tolerance, and delivers the alcohol products in very high yields. The expected C–O cleavage products are not formed under the reaction conditions. The observed reactivity is opposite to the electrophilicity of polar carbonyl groups resulting from the nX → π*C=O (X = O, N) conjugation. Mechanistic studies suggest that coordination of Sm to the carbonyl and then to Lewis basic nitrogen in the tetrahedral intermediate facilitate electron transfer and control the selectivity of the C–N/C–O cleavage. Notably, the method provides direct access to acyl-type radicals from unactivated amides under mild electron transfer conditions. PMID:24460078

Precision synthesis of colloidal inorganic nanocrystals using metal and metalloid amides

NASA Astrophysics Data System (ADS)

Yarema, Maksym; Caputo, Riccarda; Kovalenko, Maksym V.

2013-08-01

Rational selection of molecular precursors is the key consideration in the synthesis of inorganic nanocrystals and nanoparticles. This review highlights the state-of-the-art and future potential of metal amides as precursors in the solution-phase synthesis of monodisperse colloidal nanocrystals of metals and metal alloys, as well as metal oxides and chalcogenides. We exclusively focus on homoleptic metal and metalloid alkylamides M(NR2)n and silylamides M[N(SiMe3)2]n as predominant choice of element-nitrogen bonded precursors, which are often advantageous to commonly used metal-oxygen and metal-carbon bonded counterparts. In particular, these amides are highly reactive in oxidation, reduction and metathesis reactions; they are oxygen-free, easy-to-make and/or commercially available. A comprehensive literature review is complemented by our theoretical studies on the thermal stability of metal silylamides using molecular dynamics simulations.

Halogenated fatty amides - A brand new class of disinfection by-products.

PubMed

Kosyakov, Dmitry S; Ul'yanovskii, Nikolay V; Popov, Mark S; Latkin, Tomas B; Lebedev, Albert T

2017-12-15

An array of similar halogenated nitrogen-containing compounds with elemental composition C n H 2n NO 2 X, C n H 2n-2 NO 2 X and C n H 2n-1 NOX 2 (X = Cl, Br; n = 16, 18, 22) was detected in drinking water with high performance liquid chromatography - high resolution mass spectrometry (HPLC-HRMS) method. Compounds of this type were never mentioned among disinfection by-products. Tandem mass spectrometry allowed referring them to halohydrines or dihalogenated fatty amides, the products of conjugated electrophilic addition of halogens to the double bonds of unsaturated fatty amides. The proposed structures were confirmed by conducting aqueous chlorination with standard solution of oleamide. These compounds may be considered as a brand new class of disinfection by products, while their toxicities require special study. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ab initio study of the barrier to internal rotation in simple amides. 1. N, N-dimethylformamide and N, N-dimethylcarbamic halogenides

NASA Astrophysics Data System (ADS)

Vassilev, Nikolay G.; Dimitrov, Valentin S.

1999-06-01

Free energies of activation for rotation about the amide C-N bond in X-C(O)N(CH 3) 2 (X=H, F, Cl and Br) were calculated at the MP2(fc)/6-31+G*//6-31G* and MP2(fc)/6-311++G**//6-311++G** levels and compared with NMR gas-phase data. The results of calculations indicate that the repulsion between X and methyl group in ground state and the repulsion between X or oxygen and nitrogen lone pair in transition states (TS) are largely responsible for the difference in the free energies of the studied amides. For X=H (DMF), the anti TS is more stable; for the cases X=Cl, Br, the syn TS is more stable, while for the case X=F the two transition states are energetically almost equivalent.

2-Methyl-2-phenyl-1-(pyrrolidin-1-yl)propan-1-one.

PubMed

Ren, Dong-Mei

2013-05-01

In the title compound, C14H19NO, the dihedral angle between the benzene ring and the plane of the amide group is 80.6 (1)°. In the crystal, mol-ecules are connected via weak C-H⋯O hydrogen bonds, forming chains along the c-axis direction. The conformation of the five-memebred ring is an envelope, with one of the ring C atoms adjacent to the ring N atom as the flap atom.

[Effect of Long-Term Fertilization on Organic Nitrogen Functional Groups in Black Soil as Revealed by Synchrotron-Based X-Ray Absorption Near-Edge Structure Spectroscopy].

PubMed

Li, Hui; Gao, Qiang; Wang, Shuai; Zhu, Ping; Zhang, Jin-jing; Zhao, Yi-dong

2015-07-01

Nitrogen (N) is a common limiting nutrient in crop production. The N content of soil has been used as an important soil fertility index. Organic N is the major form of N in soil. In most agricultural surface soils, more than 90% of total N occurs in organic forms. Therefore, understanding the compositional characteristics of soil organic N functional groups can provide the scientific basis for formulating the reasonable farmland management strategies. Synchrotron radiation soft X-ray absorption near-edge structure (N K-edge XANES) spectroscopy is the most powerful tool to characterize in situ organic N functional groups compositions in soil. However, to our most knowledge, no studies have been conducted to examine the organic N functional groups compositions of soil using N K-edge XANES spectroscopy under long-term fertilization practices. Based on a long-term field experiment (started in 1990) in a black soil (Gongzhuling, Northeast China), we investigated the differences in organic N functional groups compositions in bulk soil and clay-size soil fraction among fertilization patterns using synchrotron-based N K- edge XANES spectroscopy. Composite soil samples (0-20 cm) were collected in 2008. The present study included six treatments: farmland fallow (FALL), no-fertilization control (CK), chemical nitrogen, phosphorus, and potassium fertilization (NPK), NPK in combination with organic manure (NPKM), 1.5 times of NPKM (1.5 NPKM), and NPK in combination with maize straw (NPKS). The results showed that N K-edge XANES spectra of all the treatments under study exhibited characteristic absorption peaks in the ranges of 401.2-401.6 and 402.7-403.1 eV, which were assigned as amides/amine-N and pyrrole-N, respectively. These characteristic absorption peaks were more obvious in clay-size soil fraction than in bulk soil. The results obtained from the semi-quantitative analysis of N K-edge XANES spectra indicated that the relative proportion of amides/amine-N was the highest in both bulk soil and clay-size soil fraction, and it was the most major forms in soil organic nitrogen functional groups. Compared with the FALL treatment, the relative proportion of amide/amine-N was lower whereas that of Pyrrole-N was higher in the CK treatment. In the treatments with combined chemical fertilizers and organic manure, the relative proportion of amide/amine-N decreased with increasing application rates of organic manure, while that of Pyrrole-N had an opposite trend. In bulk soil, the relative proportion of amide/amine-N was the highest for the NPKS treatment than for the other treatments. On the other hand, the relative proportion of nitrile/aromatic-N was the highest for the Fallow treatment than for the other treatments in clay-size soil fraction. It is feasible to use N K-edge XANES spectroscopy for characterizing in situ the changes of organic N functional groups in soil under different fertilization practices.

Restricted amide rotation with steric hindrance induced multiple conformations

NASA Astrophysics Data System (ADS)

Krishnan, V. V.; Vazquez, Salvador; Maitra, Kalyani; Maitra, Santanu

2017-12-01

The Csbnd N bond character is dependent directly upon the resonance-contributor structure population driven by the delocalized nitrogen lone-pair of electrons. In the case of N, N-dibenzyl-ortho-toluamide (o-DBET), the molecule adopts subpopulations of conformers with distinct NMR spectral features, particularly at low temperatures. This conformational adaptation is unique to o-DBET, while the corresponding meta- and para- forms do not show such behavior. Variable-temperature (VT) NMR, two-dimensional exchange spectroscopy (EXSY), and qualitative molecular modeling studies are used to demonstrate how multiple competing interactions such as restricted amide rotation and steric hindrance effects can lead to versatile molecular adaptations in the solution state.

Copper complexes of anionic nitrogen ligands in the amidation and imidation of aryl halides.

PubMed

Tye, Jesse W; Weng, Zhiqiang; Johns, Adam M; Incarvito, Christopher D; Hartwig, John F

2008-07-30

Copper(I) imidate and amidate complexes of chelating N,N-donor ligands, which are proposed intermediates in copper-catalyzed amidations of aryl halides, have been synthesized and characterized by X-ray diffraction and detailed solution-phase methods. In some cases, the complexes adopt neutral, three-coordinate trigonal planar structures in the solid state, but in other cases they adopt an ionic form consisting of an L 2Cu (+) cation and a CuX 2 (-) anion. A tetraalkylammonium salt of the CuX 2 (-) anion in which X = phthalimidate was also isolated. Conductivity measurements and (1)H NMR spectra of mixtures of two complexes all indicate that the complexes exist predominantly in the ionic form in DMSO and DMF solutions. One complex was sufficiently soluble for conductance measurements in less polar solvents and was shown to adopt some degree of the ionic form in THF and predominantly the neutral form in benzene. The complexes containing dative nitrogen ligands reacted with iodoarenes and bromoarenes to form products from C-N coupling, but the ammonium salt of [Cu(phth) 2] (-) did not. Similar selectivities for stoichiometric and catalytic reactions with two different iodoarenes and faster rates for the stoichiometric reactions implied that the isolated amidate and imidate complexes are intermediates in the reactions of amides and imides with haloarenes catalyzed by copper complexes containing dative N,N ligands. These amidates and imidates reacted much more slowly with chloroarenes, including chloroarenes that possess more favorable reduction potentials than some bromoarenes and that are known to undergo fast dissociation of chloride from the chloroarene radical anion. The reaction of o-(allyloxy)iodobenzene with [(phen) 2Cu][Cu(pyrr) 2] results in formation of the C-N coupled product in high yield and no detectable amount of the 3-methyl-2,3-dihydrobenzofuran or 3-methylene-2,3-dihydrobenzofuran products that would be expected from a reaction that generated free radicals. These data and computed reaction barriers argue against mechanisms in which the haloarene reacts with a two-coordinate anionic copper species and mechanisms that start with electron transfer to generate a free iodoarene radical anion. Instead, these data are more consistent with mechanisms involving cleavage of the carbon-halogen bond within the coordination sphere of the metal.

Atomic Oxygen (AO) and Nitrogen (AN) In-situ Flux Sensor

DTIC Science & Technology

2016-03-10

AFRL-AFOSR-VA-TR-2016-0126 DURIP 09) AN ATOMIC OXYGEN FLUX MONITOR FOR USE IN THE SEARCH FOR NEW AND BETT Malcolm Beasley LELAND STANFORD JUNIOR UNIV...Grant # FA9550-01-1-0433 M. R. Beasley, PI Stanford University Project Title: Atomic Oxygen (AO) and Nitrogen (AN) In-situ Flux Sensor...of actively controlled in-situ sources of atomic oxygen and nitrogen suitable for MBE application. The goal of this DURIP was to work with a

Construction of an N-nitroso database for assessing dietary intake

USDA-ARS?s Scientific Manuscript database

Dietary N-nitroso compounds are carcinogens synthesized during food processing from two main classes of precursors, oxides of nitrogen and amines or amides. Quantification of the dietary intake of N-nitroso compounds is significant to human cancers, including those of the stomach and upper gastro-in...

Ultraviolet absorption experiment MA-059

NASA Technical Reports Server (NTRS)

Donahue, T. M.; Hudson, R. D.; Anderson, J.; Kaufman, F.; Mcelroy, M. B.

1976-01-01

The ultraviolet absorption experiment performed during the Apollo Soyuz mission involved sending a beam of atomic oxygen and atomic nitrogen resonance radiation, strong unabsorbable oxygen and nitrogen radiation, and visual radiation, all filling the same 3 deg-wide field of view from the Apollo to the Soyuz. The radiation struck a retroreflector array on the Soyuz and was returned to a spectrometer onboard the Apollo. The density of atomic oxygen and atomic nitrogen between the two spacecraft was measured by observing the amount of resonance radiation absorbed when the line joining Apollo and Soyuz was perpendicular to their velocity with respect to the ambient atmosphere. Information concerning oxygen densities was also obtained by observation of resonantly fluorescent light. The absorption experiments for atomic oxygen and atomic nitrogen were successfully performed at a range of 500 meters, and abundant resonance fluorescence data were obtained.

METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

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

John J. Kilbane III

The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project will focus on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate amidase. The objective of the final phase of the project will bemore » to develop derivative CN bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. The project is on schedule and no major difficulties have been encountered. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments have resulted in the isolation of promising cultures that may be capable of cleaving C-N bonds in aromatic amides, several amidase genes have been cloned and are currently undergoing directed evolution to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. Future research will address expression of these genes in Rhodococcus erythropolis. Enrichment culture experiments and directed evolution experiments continue to be a main focus of research activity and further work is required to obtain an appropriate amidase that will selectively cleave C-N bonds in aromatic substrates. Once an appropriate amidase gene is obtained it must be combined with genes encoding an enzyme capable of converting carbazole to 2'aminobiphenyl-2,3-diol: specifically carA genes. The carA genes from two sources have been cloned and are ready for construction of C-N bond cleavage pathway. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum.« less

Adsorption Energies of Carbon, Nitrogen, and Oxygen Atoms on the Low-temperature Amorphous Water Ice: A Systematic Estimation from Quantum Chemistry Calculations

NASA Astrophysics Data System (ADS)

Shimonishi, Takashi; Nakatani, Naoki; Furuya, Kenji; Hama, Tetsuya

2018-03-01

We propose a new simple computational model to estimate the adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3 P), nitrogen (4 S), and oxygen (3 P) atoms based on quantum chemistry calculations. The adsorption energies were estimated to be 14,100 ± 420 K for carbon, 400 ± 30 K for nitrogen, and 1440 ± 160 K for oxygen. The adsorption energy of oxygen is consistent with experimentally reported values. We found that the binding of a nitrogen atom is purely physisorption, while that of a carbon atom is chemisorption, in which a chemical bond to an O atom of a water molecule is formed. That of an oxygen atom has a dual character, with both physisorption and chemisorption. The chemisorption of atomic carbon also implies the possibility of further chemical reactions to produce molecules bearing a C–O bond, though this may hinder the formation of methane on water ice via sequential hydrogenation of carbon atoms. These properties would have a large impact on the chemical evolution of carbon species in interstellar environments. We also investigated the effects of newly calculated adsorption energies on the chemical compositions of cold dense molecular clouds with the aid of gas-ice astrochemical simulations. We found that abundances of major nitrogen-bearing molecules, such as N2 and NH3, are significantly altered by applying the calculated adsorption energy, because nitrogen atoms can thermally diffuse on surfaces, even at 10 K.

Bias in bonding behavior among boron, carbon, and nitrogen atoms in ion implanted a-BN, a-BC, and diamond like carbon films

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

Genisel, Mustafa Fatih; Uddin, Md. Nizam; Say, Zafer

2011-10-01

In this study, we implanted N{sup +} and N{sub 2}{sup +} ions into sputter deposited amorphous boron carbide (a-BC) and diamond like carbon (DLC) thin films in an effort to understand the chemical bonding involved and investigate possible phase separation routes in boron carbon nitride (BCN) films. In addition, we investigated the effect of implanted C{sup +} ions in sputter deposited amorphous boron nitride (a-BN) films. Implanted ion energies for all ion species were set at 40 KeV. Implanted films were then analyzed using x-ray photoelectron spectroscopy (XPS). The changes in the chemical composition and bonding chemistry due to ion-implantationmore » were examined at different depths of the films using sequential ion-beam etching and high resolution XPS analysis cycles. A comparative analysis has been made with the results from sputter deposited BCN films suggesting that implanted nitrogen and carbon atoms behaved very similar to nitrogen and carbon atoms in sputter deposited BCN films. We found that implanted nitrogen atoms would prefer bonding to carbon atoms in the films only if there is no boron atom in the vicinity or after all available boron atoms have been saturated with nitrogen. Implanted carbon atoms also preferred to either bond with available boron atoms or, more likely bonded with other implanted carbon atoms. These results were also supported by ab-initio density functional theory calculations which indicated that carbon-carbon bonds were energetically preferable to carbon-boron and carbon-nitrogen bonds.« less

The Kinetics of Nitrogen Atom Recombination

ERIC Educational Resources Information Center

Brown, G. Ronald; Winkler, C. A.

1977-01-01

Describes a study of the kinetics of the recombination of nitrogen atoms in which concentration-time relations are determined directly by utilizing visual observations of emissions to make gas phase titrations of N atoms with NO. (MLH)

Salt forms of the pharmaceutical amide dihydrocarbamazepine.

PubMed

Buist, Amanda R; Kennedy, Alan R

2016-02-01

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

Normal Mode Analysis of Polytheonamide B

NASA Astrophysics Data System (ADS)

Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

2007-09-01

Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.

Does the position of the electron-donating nitrogen atom in the ring system influence the efficiency of a dye-sensitized solar cell? A computational study.

PubMed

Biswas, Abul Kalam; Barik, Sunirmal; Das, Amitava; Ganguly, Bishwajit

2016-06-01

We have reported a number of new metal-free organic dyes (2-6) that have cyclic asymmetric benzotripyrrole derivatives as donor groups with peripheral nitrogen atoms in the ring, fluorine and thiophene groups as π-spacers, and a cyanoacrylic acid acceptor group. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were employed to examine the influence of the position of the donor nitrogen atom and π-conjugation on solar cell performance. The calculated electron-injection driving force (ΔG inject), electron-regeneration driving force (ΔG regen), light-harvesting efficiency (LHE), dipole moment (μ normal), and number of electrons transferred (∆q) indicate that dyes 3, 4, and 6 have significantly higher efficiencies than reference dye 1, which exhibits high efficiency. We also extended our comparison to some other reported dyes, 7-9, which have a donor nitrogen atom in the middle of the ring system. The computed results suggest that dye 6 possesses a higher incident photon to current conversion efficiency (IPCE) than reported dyes 7-9. Thus, the use of donor groups with peripheral nitrogen atoms appears to lead to more efficient dyes than those in which the nitrogen atom is present in the middle of the donor ring system. Graphical Abstract The locations of the nitrogen atoms in the donor groups in the designed dye molecules have an important influence on DSSC efficiency.

Design, Synthesis, and Biological Evaluation of Peptidomimetic N-Substituted Cbz-4-Hyp-Hpa-Amides as Novel Inhibitors of Plasmodium falciparum.

PubMed

Bacherikov, Valeriy A; Chittiboyina, Amar G; Avery, Mitchell A

2017-08-01

A new series of peptidomimetic N-substituted Cbz-4-Hyp-Hpa-amides were designed, synthesized, and evaluated for inhibition of the Plasmodium falciparum. Substituents on the N-atom of the amide group were selected alkyl-, allyl-, aryl-, 2-hydroxyethyl-, 2-cyanoethyl-, cyanomethyl-, 2-hydroxyethyl-, 2,2-diethoxyethyl-, or 2-ethoxy-2-oxoethylamino groups, and about of 40 new compounds were synthesized and evaluated for antiplasmodial activity in vitro. Antimalarial activity has been investigated as for the final peptide mimetics, and their immediate predecessors, carrying TBDMS or TBDPS protecting groups on 4-hydroxyproline residue and 18 derivatives exhibited toxicity against P. falciparum. Of these agents, compound 23e was shown to have potent antimalarial activity with IC 50 528 ng/ml. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

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

PubMed

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

2009-10-07

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

Analysis of the critical step in catalytic carbodiimide transformation: proton transfer from amines, phosphines, and alkynes to guanidinates, phosphaguanidinates, and propiolamidinates with Li and Al catalysts.

PubMed

Rowley, Christopher N; Ong, Tiow-Gan; Priem, Jessica; Richeson, Darrin S; Woo, Tom K

2008-12-15

While lithium amides supported by tetramethylethylenediamine (TMEDA) are efficient catalysts in the synthesis of substituted guanidines via the guanylation of an amine with carbodiimide, as well as the guanylation of phosphines and conversion of alkynes into propiolamidines, aluminum amides are only efficient catalysts for the guanylation of amides. Density functional theory (DFT) calculations were used to explain this difference in activity. The origin of this behavior is apparent in the critical step where a proton is transferred from the substrate to a metal guanidinate. The activation energies of these steps are modest for amines, phosphines, and alkynes when a lithium catalyst was used, but are prohibitively high for the analogous reactions with phosphines and alkynes for aluminum amide catalysts. Energy decomposition analysis (EDA) indicates that these high activations energies are due to the high energetic cost of the detachment of a chelating guanidinate nitrogen from the aluminum in the proton transfer transition state. Amines are able to adopt an ideal geometry for facile proton transfer to the aluminum guanidinate and concomitant Al-N bond formation, while phosphines and alkynes are not.

Investigating a physical basis for spectroscopic estimates of leaf nitrogen concentration

USGS Publications Warehouse

Kokaly, R.F.

2001-01-01

The reflectance spectra of dried and ground plant foliage are examined for changes directly due to increasing nitrogen concentration. A broadening of the 2.1-??m absorption feature is observed as nitrogen concentration increases. The broadening is shown to arise from two absorptions at 2.054 ??m and 2.172 ??m. The wavelength positions of these absorptions coincide with the absorption characteristics of the nitrogen-containing amide bonds in proteins. The observed presence of these absorption features in the reflectance spectra of dried foliage is suggested to form a physical basis for high correlations established by stepwise multiple linear regression techniques between the reflectance of dry plant samples and their nitrogen concentration. The consistent change in the 2.1-??m absorption feature as nitrogen increases and the offset position of protein absorptions compared to those of other plant components together indicate that a generally applicable algorithm may be developed for spectroscopic estimates of nitrogen concentration from the reflectance spectra of dried plant foliage samples. ?? 2001 Published by Elsevier Science Ireland Ltd.

Deviation from Normal Boltzmann Distribution of High-lying Energy Levels of Iron Atom Excited by Okamoto-cavity Microwave-induced Plasmas Using Pure Nitrogen and Nitrogen-Oxygen Gases.

PubMed

Wagatsuma, Kazuaki

2015-01-01

This paper describes several interesting excitation phenomena occurring in a microwave-induced plasma (MIP) excited with Okamoto-cavity, especially when a small amount of oxygen was mixed with nitrogen matrix in the composition of the plasma gas. An ion-to-atom ratio of iron, which was estimated from the intensity ratio of ion to atomic lines having almost the same excitation energy, was reduced by adding oxygen gas to the nitrogen MIP, eventually contributing to an enhancement in the emission intensities of the atomic lines. Furthermore, Boltzmann plots for iron atomic lines were observed in a wide range of the excitation energy from 3.4 to 6.9 eV, indicating that plots of the atomic lines having lower excitation energies (3.4 to 4.8 eV) were well fitted on a straight line while those having more than 5.5 eV deviated upwards from the linear relationship. This overpopulation would result from any other excitation process in addition to the thermal excitation that principally determines the Boltzmann distribution. A Penning-type collision with excited species of nitrogen molecules probably explains this additional excitation mechanism, in which the resulting iron ions recombine with captured electrons, followed by cascade de-excitations between closely-spaced excited levels just below the ionization limit. As a result, these high-lying levels might be more populated than the low-lying levels of iron atom. The ionization of iron would be caused less actively in the nitrogen-oxygen plasma than in a pure nitrogen plasma, because excited species of nitrogen molecule, which can provide the ionization energy in a collision with iron atom, are consumed through collisions with oxygen molecules to cause their dissociation. It was also observed that the overpopulation occurred to a lesser extent when oxygen gas was added to the nitrogen plasma. The reason for this was also attributed to decreased number density of the excited nitrogen species due to collisions with oxygen molecule.

Influence of ring size on the cognition-enhancing activity of DM235 and MN19, two potent nootropic drugs.

PubMed

Guandalini, L; Martini, E; Di Cesare Mannelli, L; Dei, S; Manetti, D; Scapecchi, S; Teodori, E; Ghelardini, C; Romanelli, M N

2012-03-01

A series of analogs of DM235 and MN19, characterized by rings with different size, have been prepared and evaluated for their nootropic activity in the mouse passive-avoidance test. It was found that the optimal ring size for the analogs of DM235, showing endocyclic both amidic groups, is 6 or 7 atoms. For the compounds structurally related to MN19, carrying an exocyclic amide group, the piperidine ring is the moiety which gives the most interesting compounds. Copyright © 2012 Elsevier Ltd. All rights reserved.

Single- and double-photoionization cross sections of atomic nitrogen from threshold to 31 A

NASA Technical Reports Server (NTRS)

Samson, James A. R.; Angel, G. C.

1990-01-01

The relative photoionization cross section of atomic nitrogen for the production of singly and doubly charged ions has been measured from 44.3 to 275 A and from 520 to 852 A. The results have been made absolute by normalization to one-half of the molecular nitrogen cross section at short wavelengths. The smoothed atomic nitrogen cross sections sigma can be accurately represented, at short wavelengths, by the equation sigma(Mb) = 36,700 x (E exp-2.3) as a function of the photon energy E (eV), thereby allowing the cross sections to be extrapolated to the nitrogen K edge at 31 A.

Strategy for designing stable and powerful nitrogen-rich high-energy materials by introducing boron atoms.

PubMed

Wu, Wen-Jie; Chi, Wei-Jie; Li, Quan-Song; Li, Ze-Sheng

2017-06-01

One of the most important aims in the development of high-energy materials is to improve their stability and thus ensure that they are safe to manufacture and transport. In this work, we theoretically investigated open-chain N 4 B 2 isomers using density functional theory in order to find the best way of stabilizing nitrogen-rich molecules. The results show that the boron atoms in these isomers are aligned linearly with their neighboring atoms, which facilitates close packing in the crystals of these materials. Upon comparing the energies of nine N 4 B 2 isomers, we found that the structure with alternating N and B atoms had the lowest energy. Structures with more than one nitrogen atom between two boron atoms had higher energies. The energy of N 4 B 2 increases by about 50 kcal/mol each time it is rearranged to include an extra nitrogen atom between the two boron atoms. More importantly, our results also show that boron atoms stabilize nitrogen-rich molecules more efficiently than carbon atoms do. Also, the combustion of any isomer of N 4 B 2 releases more heat than the corresponding isomer of N 4 C 2 does under well-oxygenated conditions. Our study suggests that the three most stable N 4 B 2 isomers (BN13, BN24, and BN34) are good candidates for high-energy molecules, and it outlines a new strategy for designing stable boron-containing high-energy materials. Graphical abstract The structural characteristics, thermodynamic stabilities, and exothermic properties of nitrogen-rich N 4 B 2 isomers were investigated by means of density functional theory.

Two-photon absorption laser-induced fluorescence measurements of atomic nitrogen in a radio-frequency atmospheric-pressure plasma jet

NASA Astrophysics Data System (ADS)

Wagenaars, E.; Gans, T.; O'Connell, D.; Niemi, K.

2012-08-01

The first direct measurements of atomic nitrogen species in a radio-frequency atmospheric-pressure plasma jet (APPJ) are presented. Atomic nitrogen radicals play a key role in new plasma medicine applications of APPJs. The measurements were performed with a two-photon absorption laser-induced fluorescence diagnostic, using 206.65 nm laser photons for the excitation of ground-state N atoms and observing fluorescence light around 744 nm. The APPJ was run with a helium gas flow of 1 slm and varying small admixtures of molecular nitrogen of 0-0.7 vol%. A maximum in the measured N concentration was observed for an admixture of 0.25 vol% N2.

Process for making ultra-fine ceramic particles

DOEpatents

Stangle, Gregory C.; Venkatachari, Koththavasal R.; Ostrander, Steven P.; Schulze, Walter A.

1995-01-01

A process for producing ultra-fine ceramic particles in which droplets are formed from a ceramic precursor mixture containing a metal cation, a nitrogen-containing fuel, a solvent, and an anion capable of participating in an anionic oxidation-reduction reaction with the nitrogen containing fuel. The nitrogen-containing fuel contains at least three nitrogen atoms, at least one oxygen atom, and at least one carbon atom. The ceramic precursor mixture is dried to remove at least 85 weight percent of the solvent, and the dried mixture is then ignited to form a combusted powder.

Rhodium-catalyzed Chemo- and Regioselective Cross-dimerization of Two Terminal Alkynes

PubMed Central

Xu, Hua-Dong; Zhang, Ren-Wei; Li, Xiaoxun; Huang, Suyu; Tang, Weiping; Hu, Wen-Hao

2013-01-01

Cross-dimerization of terminal arylacetylenes and terminal propargylic alcohols/amides has been achieved in the effect of a rhodium catalyst. This method features high chemo- and regioselectivities rendering convenient and atom economical access to functionalized enynes. PMID:23356993

Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

NASA Astrophysics Data System (ADS)

Nguyen, Huong T. H.; Tureček, František

2017-07-01

Peptide cation-radical fragment ions of the z-type, [●AXAR+], [●AXAK+], and [●XAR+], where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS3-near-ultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO-NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [yn]+ type. Compared with collision-induced dissociation, UVPD yielded less side-chain dissociations even for residues that are sensitive to radical-induced side-chain bond cleavages. The backbone dissociations are triggered by transitions to second ( B) excited electronic states in the peptide ion R-CH●-CONH- chromophores that are resonant with the 355-nm photon energy. Electron promotion increases the polarity of the B excited states, R-CH+-C●(O-)NH-, and steers the reaction to proceed by transfer of protons from proximate acidic Cα and amide nitrogen positions.

Synthesis, spectroscopic, thermal and anticancer studies of metal-antibiotic chelations: Ca(II), Fe(III), Pd(II) and Au(III) chloramphenicol complexes

NASA Astrophysics Data System (ADS)

Al-Khodir, Fatima A. I.; Refat, Moamen S.

2016-09-01

Four Ca(II), Fe(III), Pd(II) and Au(III) complexes of chloramphenicol drug have been synthesized and well characterized using elemental analyses, (infrared, electronic, and 1H-NMR) spectra, magnetic susceptibility measurement, and thermal analyses. Infrared spectral data show that the chloramphenicol drug coordinated to Ca(II), Pd(II) and Au(III) metal ions through two hydroxyl groups with 1:1 or 1:2 M ratios, but Fe(III) ions chelated towards chloramphenicol drug via the oxygen and nitrogen atoms of amide group with 1:2 ratio based on presence of keto↔enol form. The X-ray powder diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscopy (TEM) techniques were used to identify the nano-size particles of both iron(III) and gold(III) chloramphenicol complexes. The antimicrobial assessments of the chloramphenicol complexes were scanned and collected the results against of some kind of bacteria and fungi. The cytotoxic activity of the gold(III) complex was tested against the human colon carcinoma (HCT-116) and human hepatocellular carcinoma (HepG-2) tumor cell lines.

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia.

PubMed

Lardi, Martina; Pessi, Gabriella

2018-05-18

Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).

Additives and method for controlling clathrate hydrates in fluid systems

DOEpatents

Sloan, Jr., Earle Dendy; Christiansen, Richard Lee; Lederhos, Joseph P.; Long, Jin Ping; Panchalingam, Vaithilingam; Du, Yahe; Sum, Amadeu Kun Wan

1997-01-01

Discussed is a process for preventing clathrate hydrate masses from detrimentally impeding the possible flow of a fluid susceptible to clathrate hydrate formation. The process is particularly useful in the natural gas and petroleum production, transportation and processing industry where gas hydrate formation can cause serious problems. Additives preferably contain one or more five member, six member and/or seven member cyclic chemical groupings. Additives include polymers having lactam rings. Additives can also contain polyelectrolytes that are believed to improve conformance of polymer additives through steric hinderance and/or charge repulsion. Also, polymers having an amide on which a C.sub.1 -C.sub.4 group is attached to the nitrogen and/or the carbonyl carbon of the amide may be used alone, or in combination with ring-containing polymers for enhanced effectiveness. Polymers having at least some repeating units representative of polymerizing at least one of an oxazoline, an N-substituted acrylamide and an N-vinyl alkyl amide are preferred.

Additives and method for controlling clathrate hydrates in fluid systems

DOEpatents

Sloan, E.D. Jr.; Christiansen, R.L.; Lederhos, J.P.; Long, J.P.; Panchalingam, V.; Du, Y.; Sum, A.K.W.

1997-06-17

Discussed is a process for preventing clathrate hydrate masses from detrimentally impeding the possible flow of a fluid susceptible to clathrate hydrate formation. The process is particularly useful in the natural gas and petroleum production, transportation and processing industry where gas hydrate formation can cause serious problems. Additives preferably contain one or more five member, six member and/or seven member cyclic chemical groupings. Additives include polymers having lactam rings. Additives can also contain polyelectrolytes that are believed to improve conformance of polymer additives through steric hindrance and/or charge repulsion. Also, polymers having an amide on which a C{sub 1}-C{sub 4} group is attached to the nitrogen and/or the carbonyl carbon of the amide may be used alone, or in combination with ring-containing polymers for enhanced effectiveness. Polymers having at least some repeating units representative of polymerizing at least one of an oxazoline, an N-substituted acrylamide and an N-vinyl alkyl amide are preferred.

Novel type of ornithine-glutathione double conjugate excreted as a major metabolite into the bile of rats administered clebopride.

PubMed

Ishizuka, T; Komiya, I; Hiratsuka, A; Watabe, T

1990-06-01

Rats orally given radioactive Clebopride [[14C]CP; N-(1'-benzyl-4'-piperidyl)-2-[14C]methoxy-4-amino-5-chlorobenzamide++ +], an antiulcer agent, excreted a novel type of ornithine (Orn)-GSH double conjugate in the bile as a major metabolite [( 14C]BMCP), corresponding to 18% of the dose. The present study provides the first evidence for Orn conjugation of a xenobiotic in mammals and demonstrates that the structure of the radioactive conjugate differs fundamentally from those known in birds and reptiles. The structure of the biliary metabolite, [14C]BMCP, purified to homogeneity by silica gel thin layer and reverse phase high pressure liquid chromatography, was elucidated as S-[2-ornithylamino-4-[14C]methoxy-5-(1'-methyl-4'-piperidylamin o) carboxyphenyl]glutathione, based mainly on the following facts: 1) BMCP showed a protonated molecular ion (M + H)+ peak at m/z 683 in the secondary ion mass spectrum and 2) [14C]BMCP afforded Orn, glutamic acid, glycine, S-(2-amino-4-[14C]methoxy-5-carboxyphenyl)cysteine [( 14C]AMCC), and 1-methyl-4-aminopiperidine (MAP) quantitatively, in an equal molar ratio, by complete hydrolysis with peptidase. Thus, BMCP was a metabolite with three enzymatically hydrolyzable amide bonds in addition to the one existing originally in the parent structure of the drug, which produces MAP by peptic digestion. Of the three additional amide bonds of BMCP, one was a novel type of bond formed by condensation of the alpha-carboxylic acid group of Orn with the primary aromatic amino group of the drug and the other two were in the S-glutathionyl residue, substituted for the chlorine atom vicinal to the Orn-conjugating primary amino group in the aromatic ring and affording glutamic acid, glycine, and the S-cysteine conjugate AMCC by hydrolysis of BMCP with the peptidase. Substitution of a methyl group for the benzyl group at the piperidine ring nitrogen atom, leading to the formation of MAP by peptic digestion, also occurred during metabolism of CP to BMCP.

Ultraviolet absorption: Experiment MA-059. [measurement of atmospheric species concentrations

NASA Technical Reports Server (NTRS)

Donahue, T. M.; Hudson, R. D.; Rawlins, W. T.; Anderson, J.; Kaufman, F.; Mcelroy, M. B.

1977-01-01

A technique devised to permit the measurement of atmospheric species concentrations is described. This technique involves the application of atomic absorption spectroscopy and the quantitative observation of resonance fluorescence in which atomic or molecular species scatter resonance radiation from a light source into a detector. A beam of atomic oxygen and atomic nitrogen resonance radiation, strong unabsorbable oxygen and nitrogen radiation, and visual radiation was sent from Apollo to Soyuz. The density of atomic oxygen and atomic nitrogen between the two spacecraft was measured by observing the amount of resonance radiation absorbed when the line joining Apollo and Soyuz was perpendicular to their velocity with respect to the ambient atmosphere. Results of postflight analysis of the resonance fluorescence data are discussed.

Space Environmentally Durable Polyimides and Copolyimides

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Smith, Joseph G. (Inventor); Hergenrother, Paul M. (Inventor); Watson, Kent A. (Inventor); Thompson, Craig M. (Inventor)

2006-01-01

Polyimides displaying low color in thin films, atomic oxygen resistance, vacuum ultraviolet radiation resistance, solubility in organic solvents in the imide form, high glass transition (T(sub g)) temperatures, and high thermal stability are provided. The poly(amide acid)s, copoly(amide acid)s, polyimides and copolyimides are prepared by the reaction of stoichiometric ratios of an aromatic &anhydride with diamines which contain phenylphosphine oxide groups in polar aprotic solvents. Controlled molecular weight oligomeric (amide acid)s and imides can be prepared by offsetting the stoichiometry according to the Carothers equation using excess diamine and endcapping with aromatic anhydrides. The polyimide materials can be processed into various material forms such as thin films, fibers, foams, threads, adhesive film, coatings, dry powders, and fiber coated prepreg, and uses include thin film membranes on antennas, second-surface mirrors, thermal optical coatings, and multilayer thermal insulation (MLI) blanket materials.

Space Environmentally Durable Polyimides and Copolyimides

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor); Hergenrother, Paul M. (Inventor); Watson, Kent A. (Inventor); Thompson, Craig M. (Inventor)

2005-01-01

Polyimides displaying low color in thin films, atomic oxygen resistance, vacuum ultraviolet radiation resistance, solubility in organic solvents in the imide form, high glass transition (T(sub g)) temperatures, and high thermal stability are provided. The poly(amide acid)s, copoly(amide acid)s, polyimides and copolyimides are prepared by the reaction of stoichiometric ratios of an aromatic dianhydride with diamines which contain phenylphosphine oxide groups in polar aprotic solvents. Controlled molecular weight oligomeric (amide acid)s and imides can be prepared by offsetting the stoichiometry according to the Carothers equation using excess diamine and endcapping with aromatic anhydrides The polyimide materials can be processed into various material forms such as thin films, fibers, foams, threads, adhesive film, coatings, dry powders, and fiber coated prepreg, and uses include thin film membranes on antennas, second-surface mirrors, thermal optical coatings, and multilayer thermal insulation (MLI) blanket materials.

Infrared multiple photon dissociation spectroscopy of group I and group II metal complexes with Boc-hydroxylamine.

PubMed

Dain, Ryan P; Gresham, Gary; Groenewold, Gary S; Steill, Jeffrey D; Oomens, Jos; Van Stipdonk, Michael J

2013-08-30

Hydroxamates are essential growth factors for some microbes, acting primarily as siderophores that solubilize iron for transport into a cell. Here we determined the intrinsic structure of 1:1 complexes between Boc-protected hydroxylamine and group I ([M(L)](+)) and group II ([M(L-H)](+)) cations, where M and L are the cation and ligand, respectively, which are convenient models for the functional unit of hydroxamate siderphores. The relevant complex ions were generated by electrospray ionization (ESI) and isolated and stored in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Infrared spectra of the isolated complexes were collected by monitoring (infrared) photodissociation yield as a function of photon energy. Experimental spectra were then compared to those predicted by density functional theory (DFT) calculations. The infrared multiple photon dissociation (IRMPD) spectra collected are in good agreement with those predicted to be lowest-energy by DFT. The spectra for the group I complexes contain six resolved absorptions that can be attributed to amide I and II type and hydroxylamine N-OH vibrations. Similar absorptions are observed for the group II cation complexes, with shifts of the amide I and amide II vibrations due to the change in structure with deprotonation of the hydroxylamine group. IRMPD spectroscopy unequivocally shows that the intrinsic binding mode for the group I cations involves the O atoms of the amide carbonyl and hydroxylamine groups of Boc-hydroxylamine. A similar binding mode is preferred for the group II cations, except that in this case the metal ion is coordinated by the O atom of the deprotonated hydroxylamine group. Copyright © 2013 John Wiley & Sons, Ltd.

Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

PubMed

Torres, A E; Fomine, S

2015-04-28

The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.

Reactivity of amino acid anions with nitrogen and oxygen atoms.

PubMed

Wang, Zhe-Chen; Li, Ya-Ke; He, Sheng-Gui; Bierbaum, Veronica M

2018-02-14

For many decades, astronomers have searched for biological molecules, including amino acids, in the interstellar medium; this endeavor is important for investigating the hypothesis of the origin of life from space. The space environment is complex and atomic species, such as nitrogen and oxygen atoms, are widely distributed. In this work, the reactions of eight typical deprotonated amino acids (glycine, alanine, cysteine, proline, aspartic acid, histidine, tyrosine, and tryptophan) with ground state nitrogen and oxygen atoms are studied by experiment and theory. These amino acid anions do not react with nitrogen atoms. However, the reactions of these ions with oxygen atoms show an intriguing variety of ionic products and the reaction rate constants are of the order of 10 -10 cm 3 s -1 . Density functional calculations provide detailed mechanisms of the reactions, and demonstrate that spin conversion is essential for some processes. Our study provides important data and insights for understanding the kinetic and dynamic behavior of amino acids in space environments.

AuNx stabilization with interstitial nitrogen atoms: A Density Functional Theory Study

NASA Astrophysics Data System (ADS)

Quintero, J. H.; Gonzalez-Hernandez, R.; Ospina, R.; Mariño, A.

2017-06-01

Researchers have been studying 4d and 5d Series Transition Metal Nitrides lately as a result of the experimental production of AuN, PtN, CuN. In this paper, we used the Density Functional Theory (DFT) implementing a pseudopotential plane-wave method to study the incorporation of nitrogen atoms in the face-centered cube (fcc) lattice of gold (Au). First, we took the fcc structure of gold, and gradually located the nitrogen atoms in tetrahedral (TH) and octahedral (OH) interstitial sites. AuN stabilized in: 2OH (30%), 4OH and 4TH (50%), 4OH - 2TH (close to the wurtzite structure) and 6TH (60%). This leads us to think that AuN behaves like a Transition Metal Nitride since the nitrogen atoms look for tetrahedral sites.

THE EFFECTS OF INITIAL ABUNDANCES ON NITROGEN IN PROTOPLANETARY DISKS

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

Schwarz, Kamber R.; Bergin, Edwin A.

2014-12-20

The dominant form of nitrogen provided to most solar system bodies is currently unknown, though available measurements show that the detected nitrogen in solar system rocks and ices is depleted with respect to solar abundances and the interstellar medium. We use a detailed chemical/physical model of the chemical evolution of a protoplanetary disk to explore the evolution and abundance of nitrogen-bearing molecules. Based on this model, we analyze how initial chemical abundances provided as either gas or ice during the early stages of disk formation influence which species become the dominant nitrogen bearers at later stages. We find that amore » disk with the majority of its initial nitrogen in either atomic or molecular nitrogen is later dominated by atomic and molecular nitrogen as well as NH{sub 3} and HCN ices, where the dominant species varies with disk radius. When nitrogen is initially in gaseous ammonia, it later becomes trapped in ammonia ice except in the outer disk where atomic nitrogen dominates. For a disk with the initial nitrogen in the form of ammonia ice, the nitrogen remains trapped in the ice as NH{sub 3} at later stages. The model in which most of the initial nitrogen is placed in atomic N best matches the ammonia abundances observed in comets. Furthermore, the initial state of nitrogen influences the abundance of N{sub 2}H{sup +}, which has been detected in protoplanetary disks. Strong N{sub 2}H{sup +} emission is found to be indicative of an N{sub 2} abundance greater than n{sub N{sub 2}}/n{sub H{sub 2}}>10{sup −6} in addition to tracing the CO snow line. Our models also indicate that NO is potentially detectable, with lower N gas abundances leading to higher NO abundances.« less

Acid-Base Interactions of Polystyrene Sulfonic Acid in Amorphous Solid Dispersions Using a Combined UV/FTIR/XPS/ssNMR Study.

PubMed

Song, Yang; Zemlyanov, Dmitry; Chen, Xin; Nie, Haichen; Su, Ziyang; Fang, Ke; Yang, Xinghao; Smith, Daniel; Byrn, Stephen; Lubach, Joseph W

2016-02-01

This study investigates the potential drug-excipient interactions of polystyrene sulfonic acid (PSSA) and two weakly basic anticancer drugs, lapatinib (LB) and gefitinib (GB), in amorphous solid dispersions. Based on the strong acidity of the sulfonic acid functional group, PSSA was hypothesized to exhibit specific intermolecular acid-base interactions with both model basic drugs. Ultraviolet (UV) spectroscopy identified red shifts, which correlated well with the color change observed in lapatinib-PSSA solutions. Fourier transform infrared (FTIR) spectra suggest the protonation of the quinazoline nitrogen atom in both model compounds, which agrees well with data from the crystalline ditosylate salt of lapatinib. X-ray photoelectron spectroscopy (XPS) detected increases in binding energy of the basic nitrogen atoms in both lapatinib and gefitinib, strongly indicating protonation of these nitrogen atoms. (15)N solid-state NMR spectroscopy provided direct spectroscopic evidence for protonation of the quinazoline nitrogen atoms in both LB and GB, as well as the secondary amine nitrogen atom in LB and the tertiary amine nitrogen atom in GB. The observed chemical shifts in the LB-PSSA (15)N spectrum also agree very well with the lapatinib ditosylate salt where proton transfer is known. Additionally, the dissolution and physical stability behaviors of both amorphous solid dispersions were examined. PSSA was found to significantly improve the dissolution of LB and GB and effectively inhibit the crystallization of LB and GB under accelerated storage conditions due to the beneficial strong intermolecular acid-base interaction between the sulfonic acid groups and basic nitrogen centers.

Thermoluminescence Dynamics During Destructions of Porous Structures Formed by Nitrogen Nanoclusters in Bulk Superfluid Helium

NASA Astrophysics Data System (ADS)

Meraki, Adil; Mao, Shun; McColgan, Patrick T.; Boltnev, Roman E.; Lee, David M.; Khmelenko, Vladimir V.

2016-11-01

We studied the dynamics of thermoluminescence during destruction of porous structures formed by nanoclusters of nitrogen molecules containing high concentrations of stabilized nitrogen atoms. The porous structures were formed in bulk superfluid helium by injection of the products of discharges in nitrogen-helium gas mixtures through the liquid helium surface. Fast recombination of nitrogen atoms during warming-up led to explosive destruction of the porous structures accompanied by bright flashes. Intense emissions from the α -group of nitrogen atoms, the β -group of oxygen atoms and the Vegard-Kaplan bands of N_2 molecules were observed at the beginning of destruction. At the end of destruction the M- and β -bands of NO molecules as well as bands of O_2 molecules were also observed. Observation of the emissions from NO molecules at the end of destruction was explained by processes of accumulation of NO molecules in the system due to the large van der Waals interaction of NO molecules. For the first time, we observed the emission of the O_2 molecules at the end of destruction of the porous nitrogen structures as a result of the (NO)_2 dimer formation in solid nitrogen and subsequent processes leading to the appearance of excited O_2 molecules.

Mixing of gaseous reactants in chemical generation of atomic iodine for COIL: two-dimensional study

NASA Astrophysics Data System (ADS)

Jirasek, Vit; Spalek, Otomar; Kodymova, Jarmila; Censky, Miroslav

2003-11-01

Two-dimensional CFD model was applied for the study of mixing and reaction between gaseous chlorine dioxide and nitrogen monoxide diluted with nitrogen during atomic iodine generation. The influence of molecular diffusion on the production of atomic chlorine as a precursor of atomic iodine was predominantly studied. The results were compared with one-dimensional modeling of the system.

Electrochemical CO 2 Reduction with Atomic Iron-Dispersed on Nitrogen-Doped Graphene

DOE PAGES

Zhang, Chenhao; Yang, Shize; Wu, Jingjie; ...

2018-03-25

Electrochemical reduction of CO 2 provides an opportunity to reach a carbon-neutral energy recycling regime, in which CO 2 emissions from fuel use are collected and converted back to fuels. The reduction of CO 2 to CO is the first step toward the synthesis of more complex carbon-based fuels and chemicals. Therefore, understanding this step is crucial for the development of high-performance electrocatalyst for CO 2 conversion to higher order products such as hydrocarbons. In this paper, atomic iron dispersed on nitrogen-doped graphene (Fe/NG) is synthesized as an efficient electrocatalyst for CO 2 reduction to CO. Fe/NG has a lowmore » reduction overpotential with high Faradic efficiency up to 80%. The existence of nitrogen-confined atomic Fe moieties on the nitrogen-doped graphene layer is confirmed by aberration-corrected high-angle annular dark-field scanning transmission electron microscopy and X-ray absorption fine structure analysis. The Fe/NG catalysts provide an ideal platform for comparative studies of the effect of the catalytic center on the electrocatalytic performance. Finally, the CO 2 reduction reaction mechanism on atomic Fe surrounded by four N atoms (Fe–N 4) embedded in nitrogen-doped graphene is further investigated through density functional theory calculations, revealing a possible promotional effect of nitrogen doping on graphene.« less

Electrochemical CO 2 Reduction with Atomic Iron-Dispersed on Nitrogen-Doped Graphene

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

Zhang, Chenhao; Yang, Shize; Wu, Jingjie

Electrochemical reduction of CO 2 provides an opportunity to reach a carbon-neutral energy recycling regime, in which CO 2 emissions from fuel use are collected and converted back to fuels. The reduction of CO 2 to CO is the first step toward the synthesis of more complex carbon-based fuels and chemicals. Therefore, understanding this step is crucial for the development of high-performance electrocatalyst for CO 2 conversion to higher order products such as hydrocarbons. In this paper, atomic iron dispersed on nitrogen-doped graphene (Fe/NG) is synthesized as an efficient electrocatalyst for CO 2 reduction to CO. Fe/NG has a lowmore » reduction overpotential with high Faradic efficiency up to 80%. The existence of nitrogen-confined atomic Fe moieties on the nitrogen-doped graphene layer is confirmed by aberration-corrected high-angle annular dark-field scanning transmission electron microscopy and X-ray absorption fine structure analysis. The Fe/NG catalysts provide an ideal platform for comparative studies of the effect of the catalytic center on the electrocatalytic performance. Finally, the CO 2 reduction reaction mechanism on atomic Fe surrounded by four N atoms (Fe–N 4) embedded in nitrogen-doped graphene is further investigated through density functional theory calculations, revealing a possible promotional effect of nitrogen doping on graphene.« less

A theoretical investigation on the neutral Cu(I) phosphorescent complexes with azole-based and phosphine mixed ligand

NASA Astrophysics Data System (ADS)

Ding, Xiao-Li; Shen, Lu; Zou, Lu-Yi; Ma, Ming-Shuo; Ren, Ai-Min

2018-04-01

A theoretical study on a series of neutral heteroleptic Cu(I) complexes with different azole-pyridine-based N^N ligands has been presented to get insight into the effect of various nitrogen atoms in the azole ring on photophysical properties. The results reveal that the highest occupied molecular orbital (HOMO) levels and the emission wavelengths of these complexes are mainly governed by the nitrogen atom number in azole ring. With the increasing number of nitrogen atom , the electron density distribution of HOMO gradually extend from the N^N ligand to the whole molecule, meanwhile, the improved contribution from Cu(d) orbits in HOMO results in an effective mixing of various charge transfermodes, and hence, the fast radiative decay(kr) and the slow non-radiative decay rate(knr) are achieved. The photoluminescence quantum yield (PLQY) show an apparent dependence on the nitrogen atom number in the five-membered nitrogen heterocycles. However, the increasing number of nitrogen atoms is not necessary for increasing PLQY. The complex 3 with 1,2,4-triazole-pyridine-based N^N ligands is considered to be a potential emitter with high phosphorescence efficiency. Finally, we hope that our investigations will contribute to systematical understanding and guiding for material molecular engineering.

Amide proton spin-lattice relaxation in polypeptides. A field-dependence study of the proton and nitrogen dipolar interactions in alumichrome.

PubMed

Llinás, M; Klein, M P; Wüthrich, K

1978-12-01

The proton nuclear magnetic resonance (NMR) spin-lattice relaxation of all six amides of deferriferrichrome and of various alumichromes dissolved in hexadeutero-dimethylsulfoxide have been investigated at 100, 220, and 360 MHz. We find that, depending on the type of residue (glycyl or ornithyl), the amide proton relaxation rates are rather uniform in the metal-free cyclohexapeptide. In contrast, the (1)H spinlattice relaxation times (T(1)'s) are distinct in the Al(3+)-coordination derivative. Similar patterns are observed in a number of isomorphic alumichrome homologues that differ in single-site residue substitutions, indicating that the spin-lattice relaxation rate is mainly determined by dipole-dipole interactions within a rigid molecular framework rather than by the specific primary structures. Analysis of the data in terms of (1)H-(1)H distances (r) calculated from X-ray coordinates yields a satisfactory linear fit between T(1) (-1) and Sigmar(-6) at the three magnetic fields. Considering the very sensitive r-dependence of T(1), the agreement gives confidence, at a quantitative level, both on the fitness of the crystallographic model to represent the alumichromes' solution conformation and on the validity of assuming isotropic rotational motion for the globular metallopeptides. An extra contribution to the amide proton T(1) (-1) is proposed to mainly originate from the (1)H-(14)N dipolar interaction: this was supported by comparison with measurements on an (15)N-enriched peptide. The nitrogen dipolar contribution to the peptide proton relaxation is discussed in the context of {(1)H}-(1)H nuclear Overhauser enhancement (NOE) studies because, especially at high fields, it can be dominant in determining the amide proton relaxation rates and hence result in a decreased effectiveness for the (1)H-(1)H dipolar mechanism to cause NOE's. From the slope and intersect values of T(1) (-1) vs. Sigmar(-6) linear plots, a number of independent estimates of tau(r), the rotational correlation time, were derived. These and the field-dependence of the T(1)'s yield a best estimate approximately 0.37 ns, in good agreement with 0.38 ns [unk] [unk] 0.41 ns, previously determined from (13)C and (15)N spin-lattice relaxation data.

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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water.

PubMed

Farag, Marwa H; Zúñiga, José; Requena, Alberto; Bastida, Adolfo

2013-05-28

Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ~85%-90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.

Enhanced paramagnetism of mesoscopic graphdiyne by doping with nitrogen.

PubMed

Zhang, Mingjia; Wang, Xiaoxiong; Sun, Huijuan; Wang, Ning; Lv, Qing; Cui, Weiwei; Long, Yunze; Huang, Changshui

2017-09-14

The new two-dimensional graphitic material, graphdiyne, has attracted great interest recently due to the superior intrinsic semiconductor properties. Here we investigate the magnetism of pure graphdiyne material and find it demonstrating a remarkable paramagnetic characteristic, which can be attributed to the appearance of special sp-hybridized carbon atoms. On this basis, we further introduce nitrogen with 5.29% N/C ratio into graphdiyne followed by simply annealing in a dopant source and realize a twofold enhancement of saturation moment at 2 K. Associate with the density of states calculation, we investigate the influence of the nitrogen atom doping sites on paramagnetism, and further reveal the important role of doped nitrogen atom on benzene ring in improving local magnetic moment. These results can not only help us deeply understand the intrinsic magnetism of graphdiyne, but also open an efficient way to improve magnetism of graphdiyne by hetero atom doping, like nitrogen doping, which may promote the potential application of graphdiyne in spintronics.

Determination of the line shapes of atomic nitrogen resonance lines by magnetic scans

NASA Technical Reports Server (NTRS)

Lawrence, G. M.; Stone, E. J.; Kley, D.

1976-01-01

A technique is given for calibrating an atomic nitrogen resonance lamp for use in determining column densities of atoms in specific states. A discharge lamp emitting the NI multiplets at 1200 A and 1493 A is studied by obtaining absorption by atoms in a magnetic field (0-2.5 T). This magnetic scanning technique enables the determination of the absorbing atom column density, and an empirical curve of growth is obtained because the atomic f-value is known. Thus, the calibrated lamp can be used in the determination of atomic column densities.

Odd nitrogen production by meteoroids

NASA Technical Reports Server (NTRS)

Park, C.; Menees, G. P.

1978-01-01

The process by which odd nitrogen species (atomic nitrogen and nitric oxide) are formed during atmospheric entry of meteoroids is analyzed theoretically. An ablating meteoroid is assumed to be a point source of mass with a continuum regime evolving in its wake. The amounts of odd nitrogen species, produced by high-temperature reactions of air in the continuum wake, are calculated by numerical integration of chemical rate equations. Flow properties are assumed to be uniform across the wake, and 29 reactions involving five neutral species and five singly ionized species are considered, as well as vibrational and electron temperature nonequilibrium phenomena. The results, when they are summed over the observed mass, velocity, and entry-angle distribution of meteoroids, provide odd-nitrogen-species annual global production rates as functions of altitude. The peak production of nitric oxide is found to occur at an altitude of about 85 km; atomic nitrogen production peaks at about 95 km. The total annual rate for nitric oxide is 40 million kg; for atomic nitrogen it is 170 million kg.

Synthesis of Rhodamines from Fluoresceins Using Pd-Catalyzed C–N Cross-Coupling

PubMed Central

2011-01-01

A unified, convenient, and efficient strategy for the preparation of rhodamines and N,N′-diacylated rhodamines has been developed. Fluorescein ditriflates were found to undergo palladium-catalyzed C–N cross-coupling with amines, amides, carbamates, and other nitrogen nucleophiles to provide direct access to known and novel rhodamine derivatives, including fluorescent dyes, quenchers, and latent fluorophores. PMID:22091952

New Data for Modeling Hypersonic Entry into Earth's Atmosphere: Electron-impact Ionization of Atomic Nitrogen

NASA Astrophysics Data System (ADS)

Savin, Daniel Wolf; Ciccarino, Christopher

2017-06-01

Meteors passing through Earth’s atmosphere and space vehicles returning to Earth from beyond orbit enter the atmosphere at hypersonic velocities (greater than Mach 5). The resulting shock front generates a high temperature reactive plasma around the meteor or vehicle (with temperatures greater than 10,000 K). This intense heat is transferred to the entering object by radiative and convective processes. Modeling the processes a meteor undergoes as it passes through the atmosphere and designing vehicles to withstand these conditions requires an accurate understanding of the underlying non-equilibrium high temperature chemistry. Nitrogen chemistry is particularly important given the abundance of nitrogen in Earth's atmosphere. Line emission by atomic nitrogen is a major source of radiative heating during atomspheric entry. Our ability to accurately calculate this heating is hindered by uncertainties in the electron-impact ionization (EII) rate coefficient for atomic nitrogen.Here we present new EII calculations for atomic nitrogen. The atom is treated as a 69 level system, incorporating Rydberg values up to n=20. Level-specific cross sections are from published B-Spline R-Matrix-with-Pseudostates results for the first three levels and binary-encounter Bethe (BEB) calculations that we have carried out for the remaining 59 levels. These cross section data have been convolved into level-specific rate coefficients and fit with the commonly-used Arrhenius-Kooij formula for ease of use in hypersonic chemical models. The rate coefficient data can be readily scaled by the relevant atomic nitrogen partition function which varies in time and space around the meteor or reentry vehicle. Providing data up to n=20 also enables modelers to account for the density-dependent lowering of the continuum.

Influence of Mechanical Stretching on Adsorption Properties of Nitrogen-Doped Graphene

NASA Astrophysics Data System (ADS)

Dolinskii, I. Yu.; Katin, K. P.; Grishakov, K. S.; Prudkovskii, V. S.; Kargin, N. I.; Maslov, M. M.

2018-04-01

This paper presents the results of quantum chemical modeling of chemisorption of atomic hydrogen and epoxy, carboxyl, and hydroxyl functional groups on nitrogen-doped graphene. It is shown that the substitutional nitrogen atom does not bind to adsorbing groups directly, but significantly increases the adsorption activity of neighboring carbon atoms. Mechanical stretching of doped graphene reduces the adsorption energy of all the aforementioned radicals. This reduction is significantly greater for the epoxy group than for the other functional groups. The results obtained confirm that, upon a sufficient stretching of a nitrogen-doped graphene sheet, the dissociation of molecular hydrogen and oxygen with subsequent precipitation of the resulting radicals onto graphene can be energetically favorable.

Kinetics of Fast Atoms in the Terrestrial Atmosphere

NASA Technical Reports Server (NTRS)

Kharchenko, Vasili A.; Dalgarno, A.; Mellott, Mary (Technical Monitor)

2002-01-01

This report summarizes our investigations performed under NASA Grant NAG5-8058. The three-year research supported by the Geospace Sciences SR&T program (Ionospheric, Thermospheric, and Mesospheric Physics) has been designed to investigate fluxes of energetic oxygen and nitrogen atoms in the terrestrial thermosphere. Fast atoms are produced due to absorption of the solar radiation and due to coupling between the ionosphere and the neutral thermospheric gas. We have investigated the impact of hot oxygen and nitrogen atoms on the thermal balance, chemistry and radiation properties of the terrestrial thermosphere. Our calculations have been focused on the accurate quantitative description of the thermalization of O and N energetic atoms in collisions with atom and molecules of the ambient neutral gas. Upward fluxes of oxygen and nitrogen atoms, the rate of atmospheric heating by hot oxygen atoms, and the energy input into translational and rotational-vibrational degrees of atmospheric molecules have been evaluated. Altitude profiles of hot oxygen and nitrogen atoms have been analyzed and compared with available observational data. Energetic oxygen atoms in the terrestrial atmosphere have been investigated for decades, but insufficient information on the kinetics of fast atmospheric atoms has been a main obstacle for the interpretation of observational data and modeling of the hot geocorona. The recent development of accurate computational methods of the collisional kinetics is seen as an important step in the quantitative description of hot atoms in the thermosphere. Modeling of relaxation processes in the terrestrial atmosphere has incorporated data of recent observations, and theoretical predictions have been tested by new laboratory measurements.

Enhanced nitrogen diffusion induced by atomic attrition

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

Ochoa, E.A.; Figueroa, C.A.; Czerwiec, T.

2006-06-19

The nitrogen diffusion in steel is enhanced by previous atomic attrition with low energy xenon ions. The noble gas bombardment generates nanoscale texture surfaces and stress in the material. The atomic attrition increases nitrogen diffusion at lower temperatures than the ones normally used in standard processes. The stress causes binding energy shifts of the Xe 3d{sub 5/2} electron core level. The heavy ion bombardment control of the texture and stress of the material surfaces may be applied to several plasma processes where diffusing species are involved.

Tracing the atomic nitrogen abundance in star-forming regions with ammonia deuteration

NASA Astrophysics Data System (ADS)

Furuya, Kenji; Persson, Magnus V.

2018-06-01

Partitioning of elemental nitrogen in star-forming regions is not well constrained. Most nitrogen is expected to be partitioned among atomic nitrogen (N I), molecular nitrogen (N_2), and icy N-bearing molecules, such as NH_3 and N_2. N I is not directly observable in the cold gas. In this paper, we propose an indirect way to constrain the amount of N I in the cold gas of star-forming clouds, via deuteration in ammonia ice, the [ND2H/NH2D]/[NH2D/NH3] ratio. Using gas-ice astrochemical simulations, we show that if atomic nitrogen remains as the primary reservoir of nitrogen during cold ice formation stages, the [ND2H/NH2D]/[NH2D/NH3] ratio is close to the statistical value of 1/3 and lower than unity, whereas if atomic nitrogen is largely converted into N-bearing molecules, the ratio should be larger than unity. Observability of ammonia isotopologues in the inner hot regions around low-mass protostars, where ammonia ice has sublimated, is also discussed. We conclude that the [ND2H/NH2D]/[NH2D/NH3] ratio can be quantified using a combination of Very Large Array and Atacama Large Millimeter/submillimeter Array observations with reasonable integration times, at least towards IRAS 16293-2422, where high molecular column densities are expected.

Application of INEPT nitrogen-15 and silicon-29 nuclear magnetic resonance spectrometry to derivatized fulvic acids

USGS Publications Warehouse

Thorn, K.A.; Folan, D.W.; Arterburn, J.B.; Mikita, M.A.; MacCarthy, P.

1989-01-01

Use of the INEPT experiment has been examined in two derivatization studies of the Suwannee River fulvic acid. In the first study, the fulvic acid was derivatized with 15N enriched hydroxylamine. The quantitative 15N NMR spectrum, acquired with a 45° pulse angle, 2.0 second pulse delay and inverse gated decoupling, showed that oximes (390-340 ppm) were the major derivatives, followed by nitriles (270-240 ppm), hydroxamic acids (170-160 ppm), secondary amides (150-115 ppm), and lactams (115-90 ppm). The INEPT 15N NMR spectrum was acquired using refocussing delays and polarization transfer times optimized for signal enhancement of singly protonated nitrogens. INEPT greatly enhanced the amide and lactam resonances, and showed that resonances downfield of 180 ppm in the quantitative spectrum represented nonprotonated nitrogens. In the second study, the fulvic acid was first methylated with diazomethane and then silylated with hexamethyldisilazane. The 29Si NMR spectra exhibited two major peaks, from approximately 33 to 22 ppm, representing silyl esters of carboxylic acids, and from 22 to 13 ppm, representing silyl ethers of alcohols and phenols. The INEPT 29Si NMR spectrum was virtually identical to the quantitative 29Si spectrum, acquired with a 90° pulse angle, 5.0 second pulse delay, inverse gated decoupling, and relaxation reagent. INEPT therefore can be used for quantitative analysis of trimethylsilyl derivatives of the fulvic acid, saving spectrometer time and eliminating the need for relaxation reagents.

A significant abiotic pathway for the formation of unknown nitrogen in nature

NASA Astrophysics Data System (ADS)

Jokic, A.; Schulten, H.-R.; Cutler, J. N.; Schnitzer, M.; Huang, P. M.

2004-03-01

The global nitrogen cycle is of prime importance in natural ecosystems. However, the origin and nature of up to one-half of total soil N remains obscure despite all attempts at elucidation. Our data provide, for the first time, unequivocal evidence that the promoting action of Mn (IV) oxide on the Maillard reaction (sugar-amino acid condensation) under ambient conditions results in the abiotic formation of heterocyclic N compounds, which are often referred to as unknown nitrogen, and of amides which are apparently the dominant N moieties in nature. The information presented is of fundamental significance in understanding the role of mineral colloids in abiotic transformations of organic N moieties, the incorporation of N in the organic matrix of fossil fuels, and the global N cycle.

METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

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

John J. Kilbane II

The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project was focused on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate deaminase. The objective of the final phase of the project will bemore » to develop derivative C-N bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments resulted in the isolation of microbial cultures that utilize aromatic amides as sole nitrogen sources, several amidase genes were cloned and were included in directed evolution experiments to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. During the second year of the project (October, 2003-September, 2004) enrichment culture experiments succeeded in isolating a mixed bacterial culture that can utilize 2-aminobiphenyl as a sole nitrogen source, directed evolution experiments were focused on the aniline dioxygenase enzyme that is capable of deaminating aniline, and expression vectors were constructed to enable the expression of genes encoding C-N bond cleaving enzymes in Rhodococcus hosts. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum. Aromatic compounds such as carbazole are representative of the difficult-to-treat organonitrogen compounds most commonly encountered in petroleum. There are two C-N bonds in carbazole and the construction of a metabolic pathway for the removal of nitrogen from carbazole will require enzymes capable cleaving both C-N bonds. A multi-component enzyme, carbazole dioxygenase, which can selectively cleave the first C-N bond has been identified and the genes that encode this enzyme have been cloned, sequenced, and are being expressed in Rhodococcus erythropolis, a bacterial culture that tolerates exposure to petroleum. An enzyme capable of selectively cleaving the second C-N bond in carbazole has not yet been identified, but enrichment culture experiments have recently succeeded in isolating a bacterial culture that is a likely candidate and may possess a suitable enzyme. Research in the near future will verify if a suitable enzyme for the cleavage of the second C-N bond in carbazole has indeed been found, then the genes encoding a suitable enzyme will be identified, cloned, and sequenced. Ultimately genes encoding enzymes for selective cleavage of both C-N bonds in carbazole will be assembled into a new metabolic pathway and the ability of the resulting bacterial culture to remove nitrogen from petroleum will be determined.« less

Atomic cobalt on nitrogen-doped graphene for hydrogen generation

PubMed Central

Fei, Huilong; Dong, Juncai; Arellano-Jiménez, M. Josefina; Ye, Gonglan; Dong Kim, Nam; Samuel, Errol L.G.; Peng, Zhiwei; Zhu, Zhuan; Qin, Fan; Bao, Jiming; Yacaman, Miguel Jose; Ajayan, Pulickel M.; Chen, Dongliang; Tour, James M.

2015-01-01

Reduction of water to hydrogen through electrocatalysis holds great promise for clean energy, but its large-scale application relies on the development of inexpensive and efficient catalysts to replace precious platinum catalysts. Here we report an electrocatalyst for hydrogen generation based on very small amounts of cobalt dispersed as individual atoms on nitrogen-doped graphene. This catalyst is robust and highly active in aqueous media with very low overpotentials (30 mV). A variety of analytical techniques and electrochemical measurements suggest that the catalytically active sites are associated with the metal centres coordinated to nitrogen. This unusual atomic constitution of supported metals is suggestive of a new approach to preparing extremely efficient single-atom catalysts. PMID:26487368

Access to aliphatic protons as reporters in non-deuterated proteins by solid-state NMR.

PubMed

Vasa, Suresh Kumar; Rovó, Petra; Giller, Karin; Becker, Stefan; Linser, Rasmus

2016-03-28

Interactions within proteins, with their surrounding, and with other molecules are mediated mostly by hydrogen atoms. In fully protonated, inhomogeneous, or larger proteins, however, aliphatic proton shifts tend to show little dispersion despite fast Magic-Angle Spinning. 3D correlations dispersing aliphatic proton shifts by their better resolved amide N/H shifts can alleviate this problem. Using inverse second-order cross-polarization (iSOCP), we here introduce dedicated and improved means to sensitively link site-specific chemical shift information from aliphatic protons with a backbone amide resolution. Thus, even in cases where protein deuteration is impossible, this approach may enable access to various aspects of protein functions that are reported on by protons.

[The Emission Spectroscopy of Nitrogen Discharge under Low Voltage at Room Temperature].

PubMed

Shen, Li-hua; Yu, Chun-xia; Yan, Bei; Zhang, Cheng-xiao

2015-03-01

A set of direct current (DC) discharge device of N2 plasma was developed, carbon nanotubes (CNT) modified ITO electrode was used as anode, aluminum plate as cathode, with -80 μm separation between them. Nitrogen emission spectra was observed at room temperature and low DC voltage (less than 150 V), and the emission spectrometry was used to diagnose the active species of the process of nitrogen discharge. Under DC discharge, the strongest energy band N2 (C3π(u)), the weak Gaydon's Green system N2 (H3 -Φ(u)-G3 Δ(g)) and the emission line of nitrogen atoms (4 p-4 p0) at 820 nm were observed. Found that metastable state of nitrogen molecules were the main factors leading to a series of excited state nitrogen atoms and nitrogen ionization. Compared the emission spectra under DC with that under alternating current (AC) (1.1 kV), and it can be seen that under DC the spectra band of nitrogen atoms can be obviously observed, and there was a molecular band in the range of 500 - 800 nm. The effect of oxygen and hydrogen on the emission spectra of nitrogen was investigated. The results showed that the oxygen inhibited the luminescence intensity of nitrogen, but the shape of spectra unchanged. All of the second positive system, Gaydon's Green system and atomic lines of nitrogen can be observed. The second positive system and Gaydon's Green system of nitrogen will be greatly affected when the volume ratio of nitrogen and hydrogen greatly affected is 1 : 1, which was due to the hydrogen. The hydrogen can depresse nitrogen plasma activation, and make the Gaydon's Green System disappeared. CNT modified ITO electrode can reduce the breakdown voltage, and the optical signal generated by the weakly ionized gas can be observed by the photo-multiplier tube at low voltage of 10 V.

Agreement between experimental and theoretical effects of nitrogen gas flowrate on liquid jet atomization

NASA Technical Reports Server (NTRS)

Ingebo, Robert D.

1987-01-01

Two-phase flows were investigated by using high velocity nitrogen gas streams to atomize small-diameter liquid jets. Tests were conducted primarily in the acceleration-wave regime for liquid jet atomization, where it was found that the loss of droplets due to vaporization had a marked effect on drop size measurements. In addition, four identically designed two-fluid atomizers were fabricated and tested for similarity of spray profiles. A scattered-light scanner was used to measure a characteristic drop diameter, which was correlated with nitrogen gas flowrate. The exponent of 1.33 for nitrogen gas flowrate is identical to that predicted by atomization theory for liquid jet breakup in the acceleration-wave regime. This is higher than the value of 1.2 which was previously obtained at a sampling distance of 4.4 cm downstream of the atomizer. The difference is attributed to the fact that drop-size measurements obtained at a 2.2 cm sampling distance are less effected by vaporization and dispersion of small droplets and therefore should give better agreement with atomization theory. Profiles of characteristic drop diameters were also obtained by making at least five line-of-sight measurements across the spray at several horizontal positions above and below the center line of the spray.

Agreement between experimental and theoretical effects of nitrogen gas flowrate on liquid jet atomization

NASA Technical Reports Server (NTRS)

Ingebo, Robert D.

1987-01-01

Two-phase flows were investigated by using high velocity nitrogen gas streams to atomize small-diameter liquid jets. Tests were conducted primarily in the acceleration-wave regime for liquid jet atomization, where it was found that the loss of droplets due to vaporization had a marked effect on drop-size measurements. In addition, four identically designed two-fluid atomizers were fabricated and tested for similarity of spray profiles. A scattered-light scanner was used to measure a characteristic drop diameter, which was correlated with nitrogen gas flowrate. The exponent of 1.33 for nitrogen gas flowrate is identical to that predicted by atomization theory for liquid jet breakup in the acceleration-wave regime. This is higher than the value of 1.2 which was previously obtained at a smapling distance of 4.4 cm downstream of the atomizer. The difference is attributed to the fact that drop-size measurements obtained at a 2.2 cm sampling distance are less affected by vaporization and dispersion of small droplets and therefore should give better agreement with atomization theory. Profiles of characteristic drop diameters were also obtained by making at least five line-of-sight measurements across the spray at several horizontal positions above and below the center line of the spray.

Diamines Containing Pendent Phenylethynyl Groups

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor); Hergenrother, Paul M. (Inventor)

1997-01-01

Controlled molecular weight imide oligomers and co-oligomers containing pendent phenylethynyl groups (PEPIs) and endcapped with nonreactive or phenylethynyl groups have been prepared by the cyclodehydration of the precursor amide acid oligomers or co-oligomers containing pendent phenylethynyl groups and endcapped with nonreactive or phenylethynyl groups. The amine terminated amide acid oligomers or co-oligomers are prepared from the reaction of dianhydride(s) with an excess of diamine(s) and diamine containing pendent phenylethynyl groups and subsequently endcapped with a phenylethynyl phthalic anhydride or monofunctional anhydride. The anhydride terminated amide acid oligomers and co-oligomers are prepared from the reaction of diamine(s) and diamine containing pendent phenylethynyl group(s) with an excess of dianhydride(s) and subsequently endcapped with a phenylethynyl amine or monofunctional amine. The polymerizations are carried out in polar aprotic solvents such as and N,N-dimethylacetamide under nitrogen at room temperature. The amide acid oligomers or co-oligomers are subsequently cyclodehydrated either thermally or chemically to the corresponding imide oligomers. The polymers and copolymers prepared from these materials exhibit a unique and unexpected combination of properties that includes higher glass transition temperatures after curing and higher retention of neat resin, adhesive and carbon fiber reinforced mechanical properties at temperatures up to 204 C under wet conditions without sacrificing melt flow behavior and processability as compared to similar materials. These materials are useful as adhesives, coatings, films, moldings, and composite matrices.

Nitrosation and nitration of fulvic acid, peat and coal with nitric acid

USGS Publications Warehouse

Thorn, Kevin A.; Cox, Larry G.

2016-01-01

Nitrohumic acids, produced from base extraction of coals and peats oxidized with nitric acid, have received considerable attention as soil ammendments in agriculture. The nitration chemistry however is incompletely understood. Moreover, there is a need to understand the reaction of nitric acid with natural organic matter (NOM) in general, in the context of a variety of environmental and biogeochemical processes. Suwannee River NOM, Suwannee River fulvic acid, and Pahokee Peat fulvic acid were treated with 15N-labeled nitric acid at concentrations ranging from 15% to 22% and analyzed by liquid and solid state 15N NMR spectroscopy. Bulk Pahokee peat and Illinois #6 coal were also treated with nitric acid, at 29% and 40% respectively, and analyzed by solid state 15N NMR spectroscopy. In addition to nitro groups from nitration of aromatic carbon, the 15N NMR spectra of all five samples exhibited peaks attributable to nitrosation reactions. These include nitrosophenol peaks in the peat fulvic acid and Suwannee River samples, from nitrosation of phenolic rings, and N-nitroso groups in the peat samples, from nitrosation of secondary amides or amines, the latter consistent with the peat samples having the highest naturally abundant nitrogen contents. Peaks attributable to Beckmann and secondary reactions of the initially formed oximes were present in all spectra, including primary amide, secondary amide, lactam, and nitrile nitrogens. The degree of secondary reaction product formation resulting from nitrosation reactions appeared to correlate inversely with the 13C aromaticities of the samples. The nitrosation reactions are most plausibly effected by nitrous acid formed from the reduction of nitric acid by oxidizable substrates in the NOM and coal samples.

Nitrosation and Nitration of Fulvic Acid, Peat and Coal with Nitric Acid

PubMed Central

Thorn, Kevin A.; Cox, Larry G.

2016-01-01

Nitrohumic acids, produced from base extraction of coals and peats oxidized with nitric acid, have received considerable attention as soil ammendments in agriculture. The nitration chemistry however is incompletely understood. Moreover, there is a need to understand the reaction of nitric acid with natural organic matter (NOM) in general, in the context of a variety of environmental and biogeochemical processes. Suwannee River NOM, Suwannee River fulvic acid, and Pahokee Peat fulvic acid were treated with 15N-labeled nitric acid at concentrations ranging from 15% to 22% and analyzed by liquid and solid state 15N NMR spectroscopy. Bulk Pahokee peat and Illinois #6 coal were also treated with nitric acid, at 29% and 40% respectively, and analyzed by solid state 15N NMR spectroscopy. In addition to nitro groups from nitration of aromatic carbon, the 15N NMR spectra of all five samples exhibited peaks attributable to nitrosation reactions. These include nitrosophenol peaks in the peat fulvic acid and Suwannee River samples, from nitrosation of phenolic rings, and N-nitroso groups in the peat samples, from nitrosation of secondary amides or amines, the latter consistent with the peat samples having the highest naturally abundant nitrogen contents. Peaks attributable to Beckmann and secondary reactions of the initially formed oximes were present in all spectra, including primary amide, secondary amide, lactam, and nitrile nitrogens. The degree of secondary reaction product formation resulting from nitrosation reactions appeared to correlate inversely with the 13C aromaticities of the samples. The nitrosation reactions are most plausibly effected by nitrous acid formed from the reduction of nitric acid by oxidizable substrates in the NOM and coal samples. PMID:27175784

Direct visualization of atomically precise nitrogen-doped graphene nanoribbons

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

Zhang, Yi; Zhang, Yanfang; Li, Geng

2014-07-14

We have fabricated atomically precise nitrogen-doped chevron-type graphene nanoribbons by using the on-surface synthesis technique combined with the nitrogen substitution of the precursors. Scanning tunneling microscopy and spectroscopy indicate that the well-defined nanoribbons tend to align with the neighbors side-by-side with a band gap of 1.02 eV, which is in good agreement with the density functional theory calculation result. The influence of the high precursor coverage on the quality of the nanoribbons is also studied. We find that graphene nanoribbons with sufficient aspect ratios can only be fabricated at sub-monolayer precursor coverage. This work provides a way to construct atomically precisemore » nitrogen-doped graphene nanoribbons.« less

First-principles calculations of K-shell X-ray absorption spectra for warm dense nitrogen

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

Li, Zi; Zhang, Shen; Kang, Wei

2016-05-15

X-ray absorption spectrum is a powerful tool for atomic structure detection on warm dense matter. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations on warm dense nitrogen along a Hugoniot curve. From the molecular dynamics trajectory, the detailed atomic structures are examined for each thermodynamical condition. The K-shell X-ray absorption spectrum is calculated, and its changes with temperature and pressure along the Hugoniot curve are discussed. The warm dense nitrogen systems may contain isolated nitrogen atoms, N{sub 2} molecules, and nitrogen clusters, which show quite different contributions to the total X-ray spectrum due to their different electronmore » density of states. The changes of X-ray spectrum along the Hugoniot curve are caused by the different nitrogen structures induced by the temperature and the pressure. Some clear signatures on X-ray spectrum for different thermodynamical conditions are pointed out, which may provide useful data for future X-ray experiments.« less

Interaction centres of pyrimidine nucleotides: cytidine-5'-diphosphate (CDP) and cytidine-5'-triphosphate (CTP) in their reactions with tetramines and Cu(II) ions.

PubMed

Gasowska, A

2005-08-01

The interactions between pyrimidine nucleotides: cytidine-5'-diphosphate (CDP) and cytidine-5'-triphosphate (CTP) and Cu(II) ions, spermine (Spm) and 1,11-diamino-4,8-diazaundecane (3,3,3-tet) have been studied. The composition and stability constants of the complexes formed have been determined by means of the potentiometric method, while the centres of interactions in the ligands have been identified by the spectral methods (UV-Vis, Ultraviolet and Visible spectroscopy; EPR, electron spin resonance; NMR). In the systems without metal, formation of the molecular complexes nucleotide-polyamine with the interaction centres at the endocyclic nitrogen atom of purine ring N3, the oxygen atoms of the phosphate group from the nucleotide and protonated nitrogen atoms of the polyamine have been detected. Significant differences have been found in the metallation between the systems with Spm and with 3,3,3-tet. In the systems with spermine, mainly protonated species are formed with the phosphate group of the nucleotide and deprotonated nitrogen atoms of the polyamine making the coordination centres, while the donor nitrogen atom of the nucleotide N3 is involved in the intramolecular interligand interactions, additionally stabilising the complex. In the systems with 3,3,3-tet, the MLL' type species are formed in which the oxygen atoms of the phosphate group and nitrogen atoms of the polyamine are involved in metallation, whereas the N3 atom from the pyrimidine ring of the nucleotide is located outside the inner coordination sphere of copper ion. The main centre of Cu(II) interaction in the nucleotide, both in the system with Spm and 3,3,3-tet is the phosphate group of the nucleotide.

A systematic analysis of atomic protein-ligand interactions in the PDB.

PubMed

Ferreira de Freitas, Renato; Schapira, Matthieu

2017-10-01

As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins - 6444 of which have experimental binding affinity - representing 750 873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C-H···O hydrogen bonds or the relatively frequent amide-π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.

Photoionization research on atomic radiation. 3: The ionization cross section of atomic nitrogen

NASA Technical Reports Server (NTRS)

Comes, F. J.; Elzer, A.

1982-01-01

The photoionization cross section of atomic nitrogen was measured between the ionization limit and 432 A. The experimental values are well fitted by those from a calculation of HENRY due to the dipole velocity approximation. A Rydberg series converging to the 5S-state of the ion is clearly identified from the ionization measurements and is shown to ionize.

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

Antimicrobial properties of analgesic kyotorphin peptides unraveled through atomic force microscopy

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

Ribeiro, Marta M.B.; Franquelim, Henri G.; Torcato, Ines M.

Highlights: Black-Right-Pointing-Pointer New kyotorphin derivatives have antimicrobial properties against S. aureus. Black-Right-Pointing-Pointer Atomic force microscopy show membrane disturbing effects of KTP-NH{sub 2} and IbKTP-NH{sub 2}. Black-Right-Pointing-Pointer None of the KTP derivatives are hemolytic. Black-Right-Pointing-Pointer The minimal peptidic sequence with antimicrobial activity is Tyr-Arg, if amidated. -- Abstract: Antimicrobial peptides (AMPs) are promising candidates as alternatives to conventional antibiotics for the treatment of resistant pathogens. In the last decades, new AMPs have been found from the cleavage of intact proteins with no antibacterial activity themselves. Bovine hemoglobin hydrolysis, for instance, results in AMPs and the minimal antimicrobial peptide sequence was definedmore » as Tyr-Arg plus a positively charged amino acid residue. The Tyr-Arg dipeptide alone, known as kyotorphin (KTP), is an endogenous analgesic neuropeptide but has no antimicrobial activity itself. In previous studies new KTP derivatives combining C-terminal amidation and Ibuprofen (Ib) - KTP-NH{sub 2}, IbKTP, IbKTP-NH{sub 2} - were designed in order to improve KTP brain targeting. Those modifications succeeded in enhancing peptide-cell membrane affinity towards fluid anionic lipids and higher analgesic activity after systemic injection resulted therefrom. Here, we investigated if this affinity for anionic lipid membranes also translates into antimicrobial activity because bacteria have anionic membranes. Atomic force microscopy revealed that KTP derivatives perturbed Staphylococcus aureus membrane structure by inducing membrane blebbing, disruption and lysis. In addition, these peptides bind to red blood cells but are non-hemolytic. From the KTP derivatives tested, amidated KTP proves to be the most active antibacterial agent. The combination of analgesia and antibacterial activities with absence of toxicity is highly appealing from the clinical point of view and broadens the therapeutic potential and application of kyotorphin peptides.« less

A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Qian, Ping

2006-08-14

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.

Electrode structure of a compact microwave driven capacitively coupled atomic beam source

NASA Astrophysics Data System (ADS)

Shimabukuro, Yuji; Takahashi, Hidenori; Wada, Motoi

2018-01-01

A compact magnetic field free atomic beam source was designed, assembled and tested the performance to produce hydrogen and nitrogen atoms. A forced air-cooled solid-state microwave power supply at 2.45 GHz frequency drives the source up to 100 W through a coaxial transmission cable coupled to a triple stub tuner for realizing a proper matching condition to the discharge load. The discharge structure of the source affected the range of operation pressure, and the pressure was reduced by four orders of magnitude through improving the electrode geometry to enhance the local electric field intensity. Optical emission spectra of the produced plasmas indicate production of hydrogen and nitrogen atoms, while the flux intensity of excited nitrogen atoms monitored by a surface ionization type detector showed the signal level close to a source developed for molecular beam epitaxy applications with 500 W RF power.

Collisional-radiative nonequilibrium in partially ionized atomic nitrogen

NASA Technical Reports Server (NTRS)

Kunc, J. A.; Soon, W. H.

1989-01-01

A nonlinear collisional-radiative model for determination of nonequilibrium production of electrons, excited atoms, and bound-bound, dielectronic and continuum line intensities in stationary partially ionized atomic nitrogen is presented. Populations of 14 atomic levels and line intensities are calculated in plasma with T(e) = 8000-15,000 K and N(t) = 10 to the 12th - 10 to the 18th/cu cm. Transport of radiation is included by coupling the rate equations of production of the electrons and excited atoms with the radiation escape factors, which are not constant but depend on plasma conditions.

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

Chumakov, Yu. M.; Tsapkov, V. I., E-mail: vtsapkov@gmail.com; Antosyak, B. Ya.

Nitrato-4-bromo-2-[(2-hydroxyethylimino)methyl]phenolatoimidazolecopper and nitrato-4-chloro-2-[(2-hydroxyethylimino)methyl]phenolatoimidazolecopper were synthesized and studied by X-ray diffraction. The crystals are isostructural. The coordination polyhedron of the copper atom can be described as a distorted square pyramid whose basal plane is formed by the phenolic and alcoholic oxygen atoms and the nitrogen atom of the monodeprotonated tridentate azomethine molecule and the imidazole nitrogen atom. The apex of the copper polyhedron is occupied by the oxygen atom of the nitrato group. The complexes are linked together by hydrogen bonds with the participation of the nitrato groups to form a three-dimensional framework.

NO.sub.x reduction method

DOEpatents

Sekar, Ramanujam R.; Hoppie, Lyle O.

1996-01-01

A method of reducing oxides of nitrogen (NO.sub.X) in the exhaust of an internal combustion engine includes producing oxygen enriched air and nitrogen enriched air by an oxygen enrichment device. The oxygen enriched air may be provided to the intake of the internal combustion engine for mixing with fuel. In order to reduce the amount of NO.sub.X in the exhaust of the internal combustion engine, the molecular nitrogen in the nitrogen enriched air produced by the oxygen enrichment device is subjected to a corona or arc discharge so as to create a plasma and as a result, atomic nitrogen. The resulting atomic nitrogen then is injected into the exhaust of the internal combustion engine causing the oxides of nitrogen in the exhaust to be reduced into nitrogen and oxygen. In one embodiment of the present invention, the oxygen enrichment device that produces both the oxygen and nitrogen enriched air can include a selectively permeable membrane.

A chromatographic estimate of the degree of surface heterogeneity of RPLC packing materials. III. Endcapped amido-embedded reversed phase

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

Gritti, Fabrice; Guiochon, Georges A

2006-01-01

The difference in adsorption behavior between a conventional monomeric endcapped C{sub 18} stationary phase (3.43 {micro}mol/m{sup 2}) and an endcapped polymeric RP-Amide phase (3.31 {micro}mol/m{sup 2}) was investigated. The adsorption isotherms of four compounds (phenol, caffeine, sodium 2-naphthalene sulfonate, and propranololium chloride) were measured by frontal analysis (FA) and the degree of heterogeneity of each phase for each solute was characterized by their adsorption energy distributions (AED), derived using the Expectation-Maximization method. The results show that only certain analytes (phenol and 2-naphthalene sulfonate) are sensitive to the presence of the polar embedded amide groups within the RP phase. Their bindingmore » constants on the amide-bonded phase are significantly higher than on conventional RPLC phases. Furthermore, an additional type of adsorption sites was observed for these two compounds. However, these sites having a low density, their presence does not affect much the retention factors of the two analytes. On the other hand, the adsorption behavior of the other two analytes (caffeine and propranololium chloride) is almost unaffected by the presence of the amide group in the bonded layer. Strong selective interactions may explain these observations. For example, hydrogen-bond interactions between an analyte (e.g., phenol or naphthalene sulfonate) and the carbonyl group (acceptor) or the nitrogen (donor) of the amido-embedded group may take place. No such interactions may take place with either caffeine or the cation propranololium chloride. This study confirms the hypothesis that analytes have ready access to locations deep inside the bonded layer, where the amide groups are present.« less

Selective Radical Amination of Aldehydic C(sp2)–H Bonds with Fluoroaryl Azides via Co(II)-Based Metalloradical Catalysis: Synthesis of N-Fluoroaryl Amides from Aldehydes under Neutral and Nonoxidative Conditions

PubMed Central

Jin, Li-Mei; Lu, Hongjian; Cui, Yuan; Lizardi, Christopher L.; Arzua, Thiago N.; Wojtas, Lukasz; Cui, Xin

2014-01-01

The Co(II) complex of the D2h-symmetric amidoporphyrin 3,5-DitBu-IbuPhyrin, [Co(P1)], has proven to be an effective metalloradical catalyst for intermolecular amination of C(sp2)–H bonds of aldehydes with fluoroaryl azides. The [Co(P1)]-catalyzed process can employ aldehydes as the limiting reagents and operate under neutral and non-oxidative conditions, generating nitrogen gas as the only byproduct. The metalloradical aldehydic C–H amination is suitable for different combinations of aldehydes and fluoroaryl azides, producing the corresponding N-fluoroaryl amides in good to excellent yields. A series of mechanistic studies support a stepwise radical mechanism for the Co(II)-catalyzed intermolecular C–H amination. PMID:25071929

Selective Radical Amination of Aldehydic C(sp2)-H Bonds with Fluoroaryl Azides via Co(II)-Based Metalloradical Catalysis: Synthesis of N-Fluoroaryl Amides from Aldehydes under Neutral and Nonoxidative Conditions.

PubMed

Jin, Li-Mei; Lu, Hongjian; Cui, Yuan; Lizardi, Christopher L; Arzua, Thiago N; Wojtas, Lukasz; Cui, Xin; Zhang, X Peter

2014-06-01

The Co(II) complex of the D 2h -symmetric amidoporphyrin 3,5-Di t Bu-IbuPhyrin, [Co( P1 )], has proven to be an effective metalloradical catalyst for intermolecular amination of C(sp 2 )-H bonds of aldehydes with fluoroaryl azides. The [Co( P1 )]-catalyzed process can employ aldehydes as the limiting reagents and operate under neutral and non-oxidative conditions, generating nitrogen gas as the only byproduct. The metalloradical aldehydic C-H amination is suitable for different combinations of aldehydes and fluoroaryl azides, producing the corresponding N -fluoroaryl amides in good to excellent yields. A series of mechanistic studies support a stepwise radical mechanism for the Co(II)-catalyzed intermolecular C-H amination.

N2 Dissociation In The Mesosphere Due To Secondary Electrons During A Solar Proton Event: The Effect On Atomic Nitrogen and Nitric Oxide

NASA Astrophysics Data System (ADS)

Verronen, P. T.; Shematovich, V. I.; Bisikalo, D. V.; Turunen, E.; Ulich, Th.

Solar proton events have an effect on the middle atmospheric odd nitrogen chem- istry. During a solar proton event high energy protons enter Earth's middle atmosphere where they ionize ambient gas. Ionization leads to production of atomic nitrogen, and further to production of nitric oxide, through ion chemistry. In addition, ionization processes produce secondary electrons that, if possessing 9.76 eV or more energy, dissociate N2 providing an additional source of atomic nitrogen. We have calculated mesospheric N2 dissociation rate due to secondary electrons dur- ing a solar proton event. Further, we have studied the effect on atomic nitrogen and nitric oxide at altitudes between 50 and 90 km. It was found that N2 is efficiently dis- sociated in the lower mesosphere by secondary electrons, with rates up to 103 cm-3 s-1 at 50 km. Thus, secondary electrons significantly add to odd nitrogen produc- tion. As a result of N2 dissociation, atomic nitrogen is greatly enhanced in both N(4S) and N(2D) states by 259% and 1220% maximum increases at 50 km, respectively. This further leads to a maximum increase of 16.5% in NO concentration at 61 km via chemical reactions. In our study a Monte Carlo model was used to calculate the total ionization rate and secondary electrons flux due to precipitating protons. These where then used as input to a detailed ion and neutral chemistry model and a steady-state solution was calcu- lated for two cases: With and without N2 dissociation due to secondary electrons.

Nitrogen spark denoxer

DOEpatents

Ng, Henry K.; Novick, Vincent J.; Sekar, Ramanujam R.

1997-01-01

A NO.sub.X control system for an internal combustion engine includes an oxygen enrichment device that produces oxygen and nitrogen enriched air. The nitrogen enriched air contains molecular nitrogen that is provided to a spark plug that is mounted in an exhaust outlet of an internal combustion engine. As the nitrogen enriched air is expelled at the spark gap of the spark plug, the nitrogen enriched air is exposed to a pulsating spark that is generated across the spark gap of the spark plug. The spark gap is elongated so that a sufficient amount of atomic nitrogen is produced and is injected into the exhaust of the internal combustion engine. The injection of the atomic nitrogen into the exhaust of the internal combustion engine causes the oxides of nitrogen to be reduced into nitrogen and oxygen such that the emissions from the engine will have acceptable levels of NO.sub.X. The oxygen enrichment device that produces both the oxygen and nitrogen enriched air can include a selectively permeable membrane.

Selective observation of biologically important 15N-labeled metabolites in isolated rat brain and liver by 1H-detected multiple-quantum-coherence spectroscopy

NASA Astrophysics Data System (ADS)

Kanamori, Keiko; Ross, Brian D.; Parivar, Farhad

Four cerebral metabolites of importance in neurotransmission, serotonin, L-tryptophan, L-glutamine, and N-acetyl- L-aspartate, and two hepatic urea-cycle intermediates, citrulline and urea, were found to be observable by 1H- 15N heteronuclear multiple-quantum-coherence (HMQC) spectroscopy in aqueous solution at physiological pH and temperature, through the protons spin-coupled to their indole, amide, or ureido nitrogen. Their 1H chemical shifts were well dispersed over a 5-10 ppm region while the 1J 15N- 1H values were 87-99 Hz. For [γ- 15N]glutamine, a 50- to 100-fold increase in sensitivity over direct 15N detection was achieved, in contrast to a 2-fold increase by the polarization-transfer method. In the isolated brain of portacaval-shunted rats, the amide protons of biologically 15N-enriched [γ- 15N]glutamine were observed in 2 min of acquisition, with suppression of proton signals from all other cerebral metabolites. In isolated liver of 15N-enriched control rats, [ 15NIurea protons were observed in 16 min. The HMQC method is likely to be effective for the in vivo study of cerebral and hepatic nitrogen metabolism.

Ammonia fixation by humic substances: A nitrogen-15 and carbon-13 NMR study

USGS Publications Warehouse

Thorn, K.A.; Mikita, M.A.

1992-01-01

The process of ammonia fixation has been studied in three well characterized and structurally diverse fulvic and humic acid samples. The Suwannee River fulvic acid, and the IHSS peat and leonardite humic acids, were reacted with 15N-labelled ammonium hydroxide, and analyzed by liquid phase 15N NMR spectrometry. Elemental analyses and liquid phase 13C NMR spectra also were recorded on the samples before and after reaction with ammonium hydroxide. The largest increase in percent nitrogen occurred with the Suwannee River fulvic acid, which had a nitrogen content of 0.88% before fixation and 3.17% after fixation. The 15N NMR spectra revealed that ammonia reacted similarly with all three samples, indicating that the functional groups which react with ammonia exist in structural configurations common to all three samples. The majority of nitrogcn incorporated into the samples appears to be in the form of indole and pyrrole nitrogen, followed by pyridine, pyrazine, amide and aminohydroquinone nitrogen. Chemical changes in the individual samples upon fixation could not be discerned from the 13C NMR spectra.

Biosynthesis of oleamide.

PubMed

Mueller, Gregory P; Driscoll, William J

2009-01-01

Oleamide (cis-9-octadecenamide) is the prototype long chain primary fatty acid amide lipid messenger. The natural occurrence of oleamide was first reported in human serum in 1989. Subsequently oleamide was shown to accumulate in the cerebrospinal fluid of sleep-deprived cats and to induce sleep when administered to experimental animals. Accordingly, oleamide first became known for its potential role in the mechanisms that mediate the drive to sleep. Oleamide also has profound effects on thermoregulation and acts as an analgesic in several models of experimental pain. Although these important pharmacologic effects are well establish, the biochemical mechanism for the synthesis of oleamide has not yet been defined. This chapter reviews the biosynthetic pathways that have been proposed and highlights two mechanisms which are most supported by experimental evidence: the generation of oleamide from oleoylglycine by the neuropeptide processing enzyme, peptidylglycine alpha-amidating monooxygenase (PAM), and alternatively, the direct amidation of oleic acid via oleoyl coenzyme A by cytochrome c using ammonia as the nitrogen source. The latter mechanism is discussed in the context of apoptosis where oleamide may play a role in regulating gap junction communication. Lastly, several considerations and caveats pertinent to the future study oleamide biosynthesis are discussed.

Optical and Electron Spin Resonance Studies of Destruction of Porous Structures Formed by Nitrogen-Rare Gas Nanoclusters in Bulk Superfluid Helium

NASA Astrophysics Data System (ADS)

McColgan, Patrick T.; Meraki, Adil; Boltnev, Roman E.; Lee, David M.; Khmelenko, Vladimir V.

2017-04-01

We studied optical and electron spin resonance spectra during destruction of porous structures formed by nitrogen-rare gas (RG) nanoclusters in bulk superfluid helium containing high concentrations of stabilized nitrogen atoms. Samples were created by injecting products of a radio frequency discharge of nitrogen-rare gas-helium gas mixtures into bulk superfluid helium. These samples have a high energy density allowing the study of energy release in chemical processes inside of nanocluster aggregates. The rare gases used in the studies were neon, argon, and krypton. We also studied the effects of changing the relative concentrations between nitrogen and rare gas on thermoluminescence spectra during destruction of the samples. At the beginning of the destructions, α -group of nitrogen atoms, Vegard-Kaplan bands of N_2 molecules, and β -group of O atoms were observed. The final destruction of the samples were characterized by a series bright flashes. Spectra obtained during these flashes contain M- and β -bands of NO molecules, the intensities of which depend on the concentration of molecular nitrogen in the gas mixture as well as the type of rare gas present in the gas mixture.

Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms.

PubMed

Seward, Emily A; Kelly, Steven

2016-11-15

Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism's environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood. Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes. Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.

The theoretical investigation of solvent effects on the relative stability and 15N NMR shielding of antidepressant heterocyclic drug

NASA Astrophysics Data System (ADS)

Tahan, Arezoo; Khojandi, Mahya; Salari, Ali Akbar

2016-01-01

The density functional theory (DFT) and Tomasi's polarized continuum model (PCM) were used for the investigation of solvent polarity and its dielectric constant effects on the relative stability and NMR shielding tensors of antidepressant mirtazapine (MIR). The obtained results indicated that the relative stability in the polar solvents is higher than that in non-polar solvents and the most stable structure was observed in the water at the B3LYP/6-311++G ( d, p) level of theory. Also, natural bond orbital (NBO) interpretation demonstrated that by increase of solvent dielectric constant, negative charge on nitrogen atoms of heterocycles and resonance energy for LP(N10) → σ* and π* delocalization of the structure's azepine ring increase and the highest values of them were observed in water. On the other hand, NMR calculations showed that with an increase in negative charge of nitrogen atoms, isotropic chemical shielding (σiso) around them increase and nitrogen of piperazine ring (N19) has the highest values of negative charge and σiso among nitrogen atoms. NMR calculations also represented that direct solvent effect on nitrogen of pyridine ring (N15) is more than other nitrogens, while its effect on N19 is less than other ones. Based on NMR data and NBO interpretation, it can be deduced that with a decrease in the negative charge on nitrogen atoms, the intramolecular effects on them decrease, while direct solvent effect increases.

Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study

DOE PAGES

Chuang, Cheng-Hao; Ray, Sekhar C.; Mazumder, Debarati; ...

2017-02-10

Nitrogen-doped graphene oxides (GO:N x) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH 2) 2 ]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:N x synthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in whichmore » each N-atom trigonally bonds to three distinct sp 2 -hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:N x . The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.« less

Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study

NASA Astrophysics Data System (ADS)

Chuang, Cheng-Hao; Ray, Sekhar C.; Mazumder, Debarati; Sharma, Surbhi; Ganguly, Abhijit; Papakonstantinou, Pagona; Chiou, Jau-Wern; Tsai, Huang-Ming; Shiu, Hung-Wei; Chen, Chia-Hao; Lin, Hong-Ji; Guo, Jinghua; Pong, Way-Faung

2017-02-01

Nitrogen-doped graphene oxides (GO:Nx) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH2)2]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:Nx synthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in which each N-atom trigonally bonds to three distinct sp2-hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:Nx. The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.

A 2:1 co-crystal of 2-methyl-benzoic acid and N,N'-bis-(pyridin-4-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

PubMed

Syed, Sabrina; Jotani, Mukesh M; Halim, Siti Nadiah Abdul; Tiekink, Edward R T

2016-03-01

The asymmetric unit of the title 2:1 co-crystal, 2C8H8O2·C14H14N4O2, comprises an acid mol-ecule in a general position and half a di-amide mol-ecule, the latter being located about a centre of inversion. In the acid, the carb-oxy-lic acid group is twisted out of the plane of the benzene ring to which it is attached [dihedral angle = 28.51 (8)°] and the carbonyl O atom and methyl group lie approximately to the same side of the mol-ecule [hy-droxy-O-C-C-C(H) torsion angle = -27.92 (17)°]. In the di-amide, the central C4N2O2 core is almost planar (r.m.s. deviation = 0.031 Å), and the pyridyl rings are perpendicular, lying to either side of the central plane [central residue/pyridyl dihedral angle = 88.60 (5)°]. In the mol-ecular packing, three-mol-ecule aggregates are formed via hy-droxy-O-H⋯N(pyrid-yl) hydrogen bonds. These are connected into a supra-molecular layer parallel to (12[Formula: see text]) via amide-N-H⋯O(carbon-yl) hydrogen bonds, as well as methyl-ene-C-H⋯O(amide) inter-actions. Significant π-π inter-actions occur between benzene/benzene, pyrid-yl/benzene and pyrid-yl/pyridyl rings within and between layers to consolidate the three-dimensional packing.

Effect of solar proton events in 1978 and 1979 on the odd nitrogen abundance in the middle atmosphere

NASA Technical Reports Server (NTRS)

Jackman, Charles H.; Meade, Paul E.

1988-01-01

Daily average solar proton flux data for 1978 and 1979 are used in a proton energy degradation scheme to derive ion pair production rates and atomic nitrogen production rates. The latter are computed in a form suitable for inclusion in an atmopheric, two-dimensional, time-dependent photochemical model. Odd nitrogen distributions are computed from the model, including atomic nitrogen production from solar protons, and are compared with baseline distributions. The comparisons show that the average effect of the solar protons in 1978 and 1979 was to cause changes in odd nitrogen only above 10 mbar and at latitudes only above about 50 deg in both hemispheres. The influence of the solar proton-produced odd nitrogen on the local abundance of odd nitrogen depends primarily on the background odd nitrogen abundance as well as the altitude and season.

Modification of the G-phonon mode of graphene by nitrogen doping

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

Lukashev, Pavel V., E-mail: pavel.lukashev@uni.edu; Hurley, Noah; Zhao, Liuyan

2016-01-25

The effect of nitrogen doping on the phonon spectra of graphene is analyzed. In particular, we employ first-principles calculations and scanning Raman analysis to investigate the dependence of phonon frequencies in graphene on the concentration of nitrogen dopants. We demonstrate that the G phonon frequency shows oscillatory behavior as a function of nitrogen concentration. We analyze different mechanisms which could potentially be responsible for this behavior, such as Friedel charge oscillations around the localized nitrogen impurity atom, the bond length change between nitrogen impurity and its nearest neighbor carbon atoms, and the long-range interactions of the nitrogen point defects. Wemore » show that the bond length change and the long range interaction of point defects are possible mechanisms responsible for the oscillatory behavior of the G frequency as a function of nitrogen concentration. At the same time, Friedel charge oscillations are unlikely to contribute to this behavior.« less

Reporting of nitrogen-isotope abundances (Technical Report)

USGS Publications Warehouse

Coplen, Tyler B.; Krouse, H.R.; Böhlke, John Karl

1992-01-01

To eliminate possible confusion in the reporting of nitrogen-isotope analyses, the Commission on Atomic Weights and Isotopic Abundances recommends that the value 272 be employed for the 14N/15N value of N2 in air for calculating atom percent 15N from measured δ15N values.

NOx reduction by electron beam-produced nitrogen atom injection

DOEpatents

Penetrante, Bernardino M.

2002-01-01

Deactivated atomic nitrogen generated by an electron beam from a gas stream containing more than 99% N.sub.2 is injected at low temperatures into an engine exhaust to reduce NOx emissions. High NOx reduction efficiency is achieved with compact electron beam devices without use of a catalyst.

Carbon Fibers Conductivity Studies

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Butkus, A. M.

1980-01-01

In an attempt to understand the process of electrical conduction in polyacrylonitrile (PAN)-based carbon fibers, calculations were carried out on cluster models of the fiber consisting of carbon, nitrogen, and hydrogen atoms using the modified intermediate neglect of differential overlap (MINDO) molecular orbital (MO) method. The models were developed based on the assumption that PAN carbon fibers obtained with heat treatment temperatures (HTT) below 1000 C retain nitrogen in a graphite-like lattice. For clusters modeling an edge nitrogen site, analysis of the occupied MO's indicated an electron distribution similar to that of graphite. A similar analysis for the somewhat less stable interior nitrogen site revealed a partially localized II electron distribution around the nitrogen atom. The differences in bonding trends and structural stability between edge and interior nitrogen clusters led to a two-step process proposed for nitrogen evolution with increasing HTT.

Interactions of 1,12-diamino-4,9-dioxadodecane (OSpm) and Cu(II) ions with pyrimidine and purine nucleotides: adenosine-5'-monophosphate (AMP) and cytidine-5'-monophosphate (CMP).

PubMed

Lomozik, L; Gasowska, A; Krzysko, G

2006-11-01

The interactions of Cu(II) ions with adenosine-5'-monophosphate (AMP), cytidine-5'-monophosphate (CMP) and 1,12-diamino-4,9-dioxadodecane (OSpm) were studied. A potentiometric method was applied to determine the composition and stability constants of complexes formed, while the mode of interactions was analysed by spectral methods (ultraviolet and visible spectroscopy (UV-Vis), electron paramagnetic resonance (EPR), (13)C NMR, (31)P NMR). In metal-free systems, molecular complexes nucleotide-polyamine (NMP)H(x)(OSpm) were formed. The endocyclic nitrogen atoms of the purine ring N(1), N(7), the nitrogen atom of the pyrimidine ring N(3), the oxygen atoms of the phosphate group of the nucleotide and the protonated nitrogen atoms of the polyamine were the reaction centres. The mode of interaction of the metal ion with OSpm and the nucleotides (AMP or CMP) in the coordination compounds was established. In the system Cu(II)/OSpm the dinuclear complex Cu(2)(OSpm) forms, while in the ternary systems Cu(II)/nucleotide/OSpm the species type MH(x)LL' and MLL' appear. In the MH(x)LL' type species, the main centres of copper (II) ion binding in the nucleotide are the phosphate groups. The protonated amino groups of OSpm are involved in non-covalent interaction with the nitrogen atoms N(1), N(7) or N(3) of the purine or pyrimidine ring, whereas at higher pH, deprotonated nitrogen atoms of polyamine are engaged in metallation in MLL' species.

Mechanistic investigations of the hydrolysis of amides, oxoesters and thioesters via kinetic isotope effects and positional isotope exchange.

PubMed

Robins, Lori I; Fogle, Emily J; Marlier, John F

2015-11-01

The hydrolysis of amides, oxoesters and thioesters is an important reaction in both organic chemistry and biochemistry. Kinetic isotope effects (KIEs) are one of the most important physical organic methods for determining the most likely transition state structure and rate-determining step of these reaction mechanisms. This method induces a very small change in reaction rates, which, in turn, results in a minimum disturbance of the natural mechanism. KIE studies were carried out on both the non-enzymatic and the enzyme-catalyzed reactions in an effort to compare both types of mechanisms. In these studies the amides and esters of formic acid were chosen because this molecular structure allowed development of methodology to determine heavy-atom solvent (nucleophile) KIEs. This type of isotope effect is difficult to measure, but is rich in mechanistic information. Results of these investigations point to transition states with varying degrees of tetrahedral character that fit a classical stepwise mechanism. This article is part of a special issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2014 Elsevier B.V. All rights reserved.

[Effects of invasive Cenchrus spinifex on nitrogen pools in sandy grassland].

PubMed

Zhang, Ting; Fu, Wei Dong; Zhang, Rui Hai; Song, Zhen; Bai, Chao; Huang, Cheng Cheng; Zhang, Guo Liang

2017-05-18

Cenchrus spinifex is an invasive plant found in large areas of northern China. In this study, we focused on analysis of the effects of C. spinifex on soil nitrogen and plant nitrogen pools in Horqin sandy grassland. In addition, a pot experiment with 15 N tracing techniques was designed to study the biological nitrogen fixation ability of C. spinifex, compared with two native grasses, Elymus dahuricus and Agropyron cristatum. The total soil nitrogen pool in C. spinifex invaded-area increased significantly by 47.5% and 20.8%, and the soil ammonium nitrogen pool decreased significantly by 25.6% and 25.2%, compared with those in bare and native plant Roegneria kamoji areas, respectively. The plant shoot nitrogen pool decreased significantly by 18.7% in C. spinifex compared with native plant R. kamoji. Atom% 15 N, atom% 15 N excess and atom% 15 N weighting excess of C. spinifex were all significantly lower than those of E. dahuricus and A. cristatum. The nitrogen use efficiencies of C. spinifex and E. dahuricus were 48.5% and 47.0%, respectively, and no significant difference was observed. Ndfa of C. spinifex accounted for 60.2%, when growing together with E. dahuricus. These results suggested that the characteristics on the high efficient use for nitrogen of this invasive weed might an ecological adaptation mechanism, leading to successful colonization and spread in Horqin Steppe.

Clarifying atomic weights: A 2016 four-figure table of standard and conventional atomic weights

USGS Publications Warehouse

Coplen, Tyler B.; Meyers, Fabienne; Holden, Norman E.

2017-01-01

To indicate that atomic weights of many elements are not constants of nature, in 2009 and 2011 the Commission on Isotopic Abundances and Atomic Weights (CIAAW) of the International Union of Pure and Applied Chemistry (IUPAC) replaced single-value standard atomic weight values with atomic weight intervals for 12 elements (hydrogen, lithium, boron, carbon, nitrogen, oxygen, magnesium, silicon, sulfur, chlorine, bromine, and thallium); for example, the standard atomic weight of nitrogen became the interval [14.00643, 14.00728]. CIAAW recognized that some users of atomic weight data only need representative values for these 12 elements, such as for trade and commerce. For this purpose, CIAAW provided conventional atomic weight values, such as 14.007 for nitrogen, and these values can serve in education when a single representative value is needed, such as for molecular weight calculations. Because atomic weight values abridged to four figures are preferred by many educational users and are no longer provided by CIAAW as of 2015, we provide a table containing both standard atomic weight values and conventional atomic weight values abridged to four figures for the chemical elements. A retrospective review of changes in four-digit atomic weights since 1961 indicates that changes in these values are due to more accurate measurements over time or to the recognition of the impact of natural isotopic fractionation in normal terrestrial materials upon atomic weight values of many elements. Use of the unit “u” (unified atomic mass unit on the carbon mass scale) with atomic weight is incorrect because the quantity atomic weight is dimensionless, and the unit “amu” (atomic mass unit on the oxygen scale) is an obsolete term: Both should be avoided.

catena-Poly[bis-(sulfamethoxazolium) [[trichloridocadmate(II)]-μ-chlorido] monohydrate].

PubMed

Subashini, Annamalai; Muthiah, Packianathan Thomas; Bocelli, Gabriele; Cantoni, Andrea

2007-12-21

In the title compound, {(C(10)H(12)N(3)O(3)S)(2)[CdCl(4)]·H(2)O}(n), the Cd(II) atom is five-coordinate with a distorted trigonal-bipyramidal geometry formed by chloride ions. The Cd atom and two of the Cl atoms lie on a mirror plane. The cation is protonated on the amino group N atom; it is not coordinated to cadmium, but is hydrogen bonded to the chlorido ligands. Each water mol-ecule bridges two chlorido ligands, generating ring motifs along the -Cd-Cl-Cd- chains. The isoxazole unit and the amide groups are linked through a pair of N-H⋯N hydrogen bonds. The crystal structure is stabilized by N-H⋯O, O-H⋯Cl, C-H⋯N, N-H⋯Cl and C-H⋯O hydrogen bonds.

catena-Poly[bis­(sulfamethoxazolium) [[trichloridocadmate(II)]-μ-chlorido] monohydrate

PubMed Central

Subashini, Annamalai; Muthiah, Packianathan Thomas; Bocelli, Gabriele; Cantoni, Andrea

2008-01-01

In the title compound, {(C10H12N3O3S)2[CdCl4]·H2O}n, the CdII atom is five-coordinate with a distorted trigonal–bipyramidal geometry formed by chloride ions. The Cd atom and two of the Cl atoms lie on a mirror plane. The cation is protonated on the amino group N atom; it is not coordinated to cadmium, but is hydrogen bonded to the chlorido ligands. Each water mol­ecule bridges two chlorido ligands, generating ring motifs along the –Cd—Cl—Cd– chains. The isoxazole unit and the amide groups are linked through a pair of N—H⋯N hydrogen bonds. The crystal structure is stabilized by N—H⋯O, O—H⋯Cl, C—H⋯N, N—H⋯Cl and C—H⋯O hydrogen bonds. PMID:21200590

Very High Performance High Nitrogen Energetic Ingredients and Energetic Polymers for Structural Components

DTIC Science & Technology

2011-12-31

have developed a vastly improved procedure for synthesis of the n- propyl ester that gives essentially quantitative yield and uses concentrated... Synthesis of n- propyl 4-aminofurazan-3-carboxylate. We next turned our attention to the synthesis of the amide. Again, the literature procedure is... synthesis and chemistry of 3-hydroxymethyl-4-amino[1,2,5]oxadiazole and 5) work on energetic polymers for structural components. 15. SUBJECT TERMS

Exceptionally potent inhibitors of fatty acid amide hydrolase: The enzyme responsible for degradation of endogenous oleamide and anandamide

PubMed Central

Boger, Dale L.; Sato, Haruhiko; Lerner, Aaron E.; Hedrick, Michael P.; Fecik, Robert A.; Miyauchi, Hiroshi; Wilkie, Gordon D.; Austin, Bryce J.; Patricelli, Matthew P.; Cravatt, Benjamin F.

2000-01-01

The development of exceptionally potent inhibitors of fatty acid amide hydrolase (FAAH), the enzyme responsible for the degradation of oleamide (an endogenous sleep-inducing lipid), and anandamide (an endogenous ligand for cannabinoid receptors) is detailed. The inhibitors may serve as useful tools to clarify the role of endogenous oleamide and anandamide and may prove to be useful therapeutic agents for the treatment of sleep disorders or pain. The combination of several features—an optimal C12–C8 chain length, π-unsaturation introduction at the corresponding arachidonoyl Δ8,9/Δ11,12 and oleoyl Δ9,10 location, and an α-keto N4 oxazolopyridine with incorporation of a second weakly basic nitrogen provided FAAH inhibitors with Kis that drop below 200 pM and are 102–103 times more potent than the corresponding trifluoromethyl ketones. PMID:10805767

Phenylacetic acid co-crystals with acridine, caffeine, isonicotinamide and nicotinamide: Crystal structures, thermal analysis, FTIR spectroscopy and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Amombo Noa, Francoise M.; Jacobs, Ayesha

2017-07-01

Co-crystals of phenylacetic acid (PAA) with acridine (ACR), caffeine (CAF), isonicotinamide (INM) and nicotinamide (NAM) have been successfully prepared and characterised by single crystal X-ray diffraction, FTIR spectroscopy, thermal analysis and Hirshfeld surface analysis. The ACR, INM and NAM co-crystals with PAA exhibit the carboxylic acid-pyridine heterosynthon. Furthermore the amide-amide supramolecular homosynthon is observed in the PAA co-crystals with INM and NAM as well as Nsbnd H⋯O interactions between the acid and the respective base. The CAF co-crystal exhibits hydrogen bonding between the imidazole nitrogen and the COOH group of the PAA. The compounds demonstrate different stoichiometries; for PAA·ACR and PAA·INM a 1:1 ratio is displayed, a 2:1 in 2PAA·CAF and a 2:2 in the case of 2PAA·2NAM.

Electrostatic Potential Energy within a Protein Monitored by Metal Charge-Dependent Hydrogen Exchange

PubMed Central

Anderson, Janet S.; LeMaster, David M.; Hernández, Griselda

2006-01-01

Hydrogen exchange measurements on Zn(II)-, Ga(III)-, and Ge(IV)-substituted Pyrococcus furiosus rubredoxin demonstrate that the log ratio of the base-catalyzed rate constants (Δ log kex) varies inversely with the distance out to at least 12 Å from the metal. This pattern is consistent with the variation of the amide nitrogen pK values with the metal charge-dependent changes in the electrostatic potential. Fifteen monitored amides lie within this range, providing an opportunity to assess the strength of electrostatic interactions simultaneously at numerous positions within the structure. Poisson-Boltzmann calculations predict an optimal effective internal dielectric constant of 6. The largest deviations between the experimentally estimated and the predicted ΔpK values appear to result from the conformationally mobile charged side chains of Lys-7 and Glu-48 and from differential shielding of the peptide units arising from their orientation relative to the metal site. PMID:17012322

Water-Soluble Phosphinothiols for Traceless Staudinger Ligation and Integration with Expressed Protein Ligation

PubMed Central

Tam, Annie; Soellner, Matthew B.; Raines, Ronald T.

2010-01-01

The traceless Staudinger ligation is an effective means to synthesize an amide bond between two groups of otherwise orthogonal reactivity: a phosphinothioester and an azide. An important application of the Staudinger ligation is in the ligation of peptides at a variety of residues. Here, we demonstrate that the traceless Staudinger ligation can be achieved in water with a water-soluble reagent. Those reagents that provide a high yield of amide product discourage protonation of the nitrogen in the key iminophosphorane intermediate. The most efficacious reagent, bis(p-dimethylaminoethylphenyl)phosphinomethanethiol, mediates the rapid ligation of equimolar substrates in water. This reagent is also able to perform a transthioesterification reaction with the thioester intermediate formed during intein-mediated protein splicing. Hence, the traceless Staudinger ligation can be integrated with expressed protein ligation, extending the reach of modern protein chemistry. PMID:17713909

Gd-Complexes of New Arylpiperazinyl Conjugates of DTPA-Bis(amides): Synthesis, Characterization and Magnetic Relaxation Properties.

PubMed

Ba-Salem, Abdullah O; Ullah, Nisar; Shaikh, M Nasiruzzaman; Faiz, Mohamed; Ul-Haq, Zaheer

2015-04-29

Two new DTPA-bis(amide) based ligands conjugated with the arylpiperazinyl moiety were synthesized and subsequently transformed into their corresponding Gd(III) complexes 1 and 2 of the type [Gd(L)H2O]·nH2O. The relaxivity (R1) of these complexes was measured, which turned out to be comparable with that of Omniscan®, a commercially available MRI contrast agent. The cytotoxicity studies of these complexes indicated that they are non-toxic, which reveals their potential and physiological suitability as MRI contrast agents. All the synthesized ligands and complexes were characterized with the aid of analytical and spectroscopic methods, including elemental analysis, 1H-NMR, FT-IR, XPS and fast atom bombardment (FAB) mass spectrometry.

Synthesis, Antifungal Activity and Structure-Activity Relationships of Novel 3-(Difluoromethyl)-1-methyl-1H-pyrazole-4-carboxylic Acid Amides.

PubMed

Du, Shijie; Tian, Zaimin; Yang, Dongyan; Li, Xiuyun; Li, Hong; Jia, Changqing; Che, Chuanliang; Wang, Mian; Qin, Zhaohai

2015-05-08

A series of novel 3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxylic acid amides were synthesized and their activities were tested against seven phytopathogenic fungi by an in vitro mycelia growth inhibition assay. Most of them displayed moderate to excellent activities. Among them N-(2-(5-bromo-1H-indazol-1-yl)phenyl)-3-(difluoro-methyl)-1-methyl-1H-pyrazole-4-carboxamide (9m) exhibited higher antifungal activity against the seven phytopathogenic fungi than boscalid. Topomer CoMFA was employed to develop a three-dimensional quantitative structure-activity relationship model for the compounds. In molecular docking, the carbonyl oxygen atom of 9m could form hydrogen bonds towards the hydroxyl of TYR58 and TRP173 on SDH.

Direct hydrogenation and one-pot reductive amidation of nitro compounds over Pd/ZnO nanoparticles as a recyclable and heterogeneous catalyst

NASA Astrophysics Data System (ADS)

Hosseini-Sarvari, Mona; Razmi, Zahra

2015-01-01

A novel Pd supported on ZnO nanoparticles was readily synthesized and characterized. The amount of palladium on ZnO is 9.84 wt% which was determined by ICP analysis and atomic absorption spectroscopy (AAS). Percentage of accessible Pd as active catalyst is also estimated to 2.72% based on the thermogravimetric (TG) analysis. This nano-sized Pd/ZnO with an average particle size of 20-25 nm and specific surface area 40.61 m2 g-1 was used as a new reusable heterogeneous catalyst for direct hydrogenation and one-pot reductive amidation of nitro compounds without the use of any ligands under atmospheric pressure. The catalyst can be recovered and recycled several times without marked loss of activity.

Charge-free method of forming nanostructures on a substrate

DOEpatents

Hoffbauer; Mark , Akhadov; Elshan

2010-07-20

A charge-free method of forming a nanostructure at low temperatures on a substrate. A substrate that is reactive with one of atomic oxygen and nitrogen is provided. A flux of neutral atoms of least one of oxygen and nitrogen is generated within a laser-sustained-discharge plasma source and a collimated beam of energetic neutral atoms and molecules is directed from the plasma source onto a surface of the substrate to form the nanostructure. The energetic neutral atoms and molecules in the beam have an average kinetic energy in a range from about 1 eV to about 5 eV.

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

PubMed

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

2017-07-06

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

Synthesis of nitrogen-containing carbon by solution plasma in aniline with high-repetition frequency discharges

NASA Astrophysics Data System (ADS)

Hyun, Koangyong; Ueno, Tomonaga; Saito, Nagahiro

2016-01-01

Nitrogen-containing carbon nanoparticles were synthesized in aniline by solution plasma with high-repetition frequency discharges. We developed a bipolar pulsed power supply that can apply high-repetition frequencies ranging from 25 to 200 kHz. By utilizing high-repetition frequencies, conductive carbons were directly synthesized. The crystallinity was increased and H/C ratio of carbon was decreased. Furthermore, nitrogen atoms were simultaneously embedded in the carbon matrix. Due to the presence of nitrogen atoms, the conductivity and electrocatalytic activity of the samples were remarkably improved compared to that of a pure carbon matrix synthesized from a benzene precursor.

Formation of simple nitrogen hydrides NH and NH2 at cryogenic temperatures through N + NH3→ NH + NH2 reaction: dark cloud chemistry of nitrogen.

PubMed

Nourry, Sendres; Krim, Lahouari

2016-07-21

Although NH3 molecules interacting with ground state nitrogen atoms N((4)S) seem not to be a very reactive system without providing additional energy to initiate the chemical process, we show through this study that, in the solid phase, at very low temperature, NH3 + N((4)S) reaction leads to the formation of the amidogen radical NH2. Such a dissociation reaction previously thought to occur exclusively through UV photon or energetic particle irradiation is in this work readily occurring just by stimulating the mobility of N((4)S)-atoms in the 3-10 K temperature range in the solid sample. The N((4)S)-N((4)S) recombination may be the source of metastable molecular nitrogen N2(A), a reactive species which might trigger the NH3 dissociation or react with ground state nitrogen atoms N((4)S) to form excited nitrogen atoms N((4)P/(2)D) through energy transfer processes. Based on our obtained results, it is possible to propose reaction pathways to explain the NH2 radical formation which is the first step in the activation of stable species such as NH3, a chemical induction process that, in addition to playing an important role in the origin of molecular complexity in interstellar space, is known to require external energy supplies to occur in the gas phase.

Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues.

PubMed

Oda, Akifumi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Takahashi, Ohgi

2018-07-01

Recently, non-enzymatic stereoinversions of aspartic acid (Asp) residues in proteins and peptides have been reported. Here, we performed replica exchange molecular dynamics (REMD) simulations of model peptides (exon 6, 26A-1, and 26A-2) extracted from elastin to investigate their structural features, thereby revealing the factor that influences stereoinversions. For REMD trajectories, we calculated distances between carboxyl carbon in Asp and amide nitrogen in the (n + 1) residue (CN distances). Because bond formation between carbon and nitrogen is indispensable to the formation of a succinimide intermediate the distance between them seems to play an important role in stereoinversion. Moreover, we calculated polar surface areas (PSAs) for the trajectories, finding that CN distances and PSA were different for each peptide, with the longest CN distance and smallest PSA observed for exon 6 peptide, where stereoinversion of Asp is the slowest. Although the average CN distance was shorter for exon 26A-1 peptide than for exon 26A-2 peptide, the number of conformations with CN distances <3.0 Å was greater for exon 26A-2 peptide than for exon 26A-1 peptide. Furthermore, PSA for amide nitrogen of the (n + 1) residue was larger for exon 26A-2 peptide than for exon 26A-1 peptide. These results indicated that the flexibility of Asp and (n + 1) residues and hydrophilicity of peptides, especially in the (n + 1) residue, play important roles in the stereoinversion of Asp. This article is part of a Special Issue entitled: D-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. Copyright © 2018 Elsevier B.V. All rights reserved.

Crystal structures of three 3,4,5-tri-meth-oxy-benzamide-based derivatives.

PubMed

Gomes, Ligia R; Low, John Nicolson; Oliveira, Catarina; Cagide, Fernando; Borges, Fernanda

2016-05-01

The crystal structures of three benzamide derivatives, viz. N-(6-hy-droxy-hex-yl)-3,4,5-tri-meth-oxy-benzamide, C16H25NO5, (1), N-(6-anilinohex-yl)-3,4,5-tri-meth-oxy-benzamide, C22H30N2O4, (2), and N-(6,6-di-eth-oxy-hex-yl)-3,4,5-tri-meth-oxy-benzamide, C20H33NO6, (3), are described. These compounds differ only in the substituent at the end of the hexyl chain and the nature of these substituents determines the differences in hydrogen bonding between the mol-ecules. In each mol-ecule, the m-meth-oxy substituents are virtually coplanar with the benzyl ring, while the p-meth-oxy substituent is almost perpendicular. The carbonyl O atom of the amide rotamer is trans related with the amidic H atom. In each structure, the benzamide N-H donor group and O acceptor atoms link the mol-ecules into C(4) chains. In 1, a terminal -OH group links the mol-ecules into a C(3) chain and the combined effect of the C(4) and C(3) chains is a ribbon made up of screw related R 2 (2)(17) rings in which the ⋯O-H⋯ chain lies in the centre of the ribbon and the tri-meth-oxy-benzyl groups forms the edges. In 2, the combination of the benzamide C(4) chain and the hydrogen bond formed by the terminal N-H group to an O atom of the 4-meth-oxy group link the mol-ecules into a chain of R 2 (2)(17) rings. In 3, the mol-ecules are linked only by C(4) chains.

Energetic Metastable Oxygen and Nitrogen Atoms in the Terrestrial Atmosphere

NASA Technical Reports Server (NTRS)

Kharchenko, Vasili; Dalgarno, A.

2005-01-01

This report summarizes our research performed under NASA Grant NAG5-11857. The three-year grant have been supported by the Geospace Sciences SR&T program. We have investigated the energetic metastable oxygen and nitrogen atoms in the terrestrial stratosphere, mesosphere and thermosphere. Hot atoms in the atmosphere are produced by solar radiation, the solar wind and various ionic reactions. Nascent hot atoms arise in ground and excited electronic states, and their translational energies are larger by two - three orders of magnitude than the thermal energies of the ambient gas. The relaxation kinetics of hot atoms determines the rate of atmospheric heating, the intensities of aeronomic reactions, and the rate of atom escape from the planet. Modeling of the non-Maxwellian energy distributions of metastable oxygen and nitrogen atoms have been focused on the determination of their impact on the energetics and chemistry of the terrestrial atmosphere between 25 and 250 km . At this altitudes, we have calculated the energy distribution functions of metastable O and N atoms and computed non-equilibrium rates of important aeronomic reactions, such as destruction of the water molecules by O(1D) atoms and production of highly excited nitric oxide molecules. In the upper atmosphere, the metastable O(lD) and N(2D) play important role in formation of the upward atomic fluxes. We have computed the upward fluxes of the metastable and ground state oxygen atoms in the upper atmosphere above 250 km. The accurate distributions of the metastable atoms have been evaluated for the day and night-time conditions.

Reactions of Ground State Nitrogen Atoms N(4S) with Astrochemically-Relevant Molecules on Interstellar Dusts

NASA Astrophysics Data System (ADS)

Krim, Lahouari; Nourry, Sendres

2015-06-01

In the last few years, ambitious programs were launched to probe the interstellar medium always more accurately. One of the major challenges of these missions remains the detection of prebiotic compounds and the understanding of reaction pathways leading to their formation. These complex heterogeneous reactions mainly occur on icy dust grains, and their studies require the coupling of laboratory experiments mimicking the extreme conditions of extreme cold and dilute media. For that purpose, we have developed an original experimental approach that combine the study of heterogeneous reactions (by exposing neutral molecules adsorbed on ice to non-energetic radicals H, OH, N...) and a neon matrix isolation study at very low temperatures, which is of paramount importance to isolate and characterize highly reactive reaction intermediates. Such experimental approach has already provided answers to many questions raised about some astrochemically-relevant reactions occurring in the ground state on the surface of dust grain ices in dense molecular clouds. The aim of this new present work is to show the implication of ground state atomic nitrogen on hydrogen atom abstraction reactions from some astrochemically-relevant species, at very low temperatures (3K-20K), without providing any external energy. Under cryogenic temperatures and with high barrier heights, such reactions involving N(4S) nitrogen atoms should not occur spontaneously and require an initiating energy. However, the detection of some radicals species as byproducts, in our solid samples left in the dark for hours at 10K, proves that hydrogen abstraction reactions involving ground state N(4S) nitrogen atoms may occur in solid phase at cryogenic temperatures. Our results show the efficiency of radical species formation stemming from non-energetic N-atoms and astrochemically-relevant molecules. We will then discuss how such reactions, involving nitrogen atoms in their ground states, might be the first key step towards complex organic molecules production in the interstellar medium.

Serum stability of selected decapeptide agonists of KISS1R using pseudopeptides.

PubMed

Asami, Taiji; Nishizawa, Naoki; Ishibashi, Yoshihiro; Nishibori, Kimiko; Nakayama, Masaharu; Horikoshi, Yasuko; Matsumoto, Shin-ichi; Yamaguchi, Masashi; Matsumoto, Hirokazu; Tarui, Naoki; Ohtaki, Tetsuya; Kitada, Chieko

2012-10-15

Metastin/kisspeptin, a 54-amino acid peptide, is the ligand of the G-protein-coupled receptor KISS1R which plays a key role in pathways that regulate reproduction and cell migration in many endocrine and gonadal tissues. The N-terminally truncated decapeptide, metastin(45-54), has 3-10 times higher receptor affinity and intracellular calcium ion-mobilizing activity but is rapidly inactivated in serum. In this study we designed and synthesized stable KISS1R agonistic decapeptide analogs with selected substitutions at positions 47, 50, and 51. Replacement of glycine with azaglycine (azaGly) in which the α-carbon is replaced with a nitrogen atom at position 51 improved the stability of amide bonds between Phe(50)-Gly(51) and Gly(51)-Leu(52) as determined by in vitro mouse serum stability studies. Substitution for tryptophan at position 47 with other amino acids such as serine, threonine, β-(3-pyridyl)alanine, and D-tryptophan (D-Trp), produced analogs that were highly stable in mouse serum. D-Trp(47) analog 13 showed not only high metabolic stability but also excellent KISS1R agonistic activity. Other labile peptides may have increased serum stability using amino acid substitution. Copyright © 2012 Elsevier Ltd. All rights reserved.

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain

PubMed Central

Vugmeyster, Liliya; Ostrovsky, Dmitry

2012-01-01

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13C′ longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, 13C′/13C′−13Cα CSA/dipolar and 13C′/13C′−15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone. PMID:21416162

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

PubMed

Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

2017-01-04

The structures of the mono- and the dihalogenated N -unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide ( ABB ) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer ( A ) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study.

PubMed

Paramasivam, Sivakumar; Gronenborn, Angela M; Polenova, Tatyana

2018-08-01

Chemical shift tensors (CSTs) are an exquisite probe of local geometric and electronic structure. 15 N CST are very sensitive to hydrogen bonding, yet they have been reported for very few proteins to date. Here we present experimental results and statistical analysis of backbone amide 15 N CSTs for 100 residues of four proteins, two E. coli thioredoxin reassemblies (1-73-(U- 13 C, 15 N)/74-108-(U- 15 N) and 1-73-(U- 15 N)/74-108-(U- 13 C, 15 N)), dynein light chain 8 LC8, and CAP-Gly domain of the mammalian dynactin. The 15 N CSTs were measured by a symmetry-based CSA recoupling method, ROCSA. Our results show that the principal component δ 11 is very sensitive to the presence of hydrogen bonding interactions due to its unique orientation in the molecular frame. The downfield chemical shift change of backbone amide nitrogen nuclei with increasing hydrogen bond strength is manifested in the negative correlation of the principal components with hydrogen bond distance for both α-helical and β-sheet secondary structure elements. Our findings highlight the potential for the use of 15 N CSTs in protein structure refinement. Copyright © 2018 Elsevier Inc. All rights reserved.

Charge-free low-temperature method of forming thin film-based nanoscale materials and structures on a substrate

DOEpatents

Hoffbauer, Mark [Los Alamos, NM; Mueller, Alex [Santa Fe, NM

2008-07-01

A method of forming a nanostructure at low temperatures. A substrate that is reactive with one of atomic oxygen and nitrogen is provided. A flux of neutral atoms of at least one of nitrogen and oxygen is generated within a laser-sustained-discharge plasma source and a collimated beam of energetic neutral atoms and molecules is directed from the plasma source onto a surface of the substrate to form the nanostructure. The energetic neutral atoms and molecules in the plasma have an average kinetic energy in a range from about 1 eV to about 5 eV.

Tris-(hydroxyamino)triazines: high-affinity chelating tridentate O,N,O-hydroxylamine ligand for the cis-V(V)O2(+) cation.

PubMed

Nikolakis, Vladimiros A; Exarchou, Vassiliki; Jakusch, Tamás; Woolins, J Derek; Slawin, Alexandra M Z; Kiss, Tamás; Kabanos, Themistoklis A

2010-10-14

The treatment of the trichloro-1,3,5-triazine with N-methylhydroxylamine hydrochloride results in the replacement of the three chlorine atoms of the triazine ring with the function -N(OH)CH(3) yielding the symmetrical tris-(hydroxyamino)triazine ligand H(3)trihyat. Reaction of the ligand H(3)trihyat with NaV(V)O(3) in aqueous solution followed by addition of Ph(4)PCl gave the mononuclear vanadium(V) compound Ph(4)P[V(V)O(2)(Htrihyat)] (1). The structure of compound 1 was determined by X-ray crystallography and indicates that this compound has a distorted square-pyramidal arrangement around vanadium. The ligand Htrihyat(2-) is bonded to vanadium atom in a tridentate fashion at the triazine ring nitrogen atom and the two deprotonated hydroxylamido oxygen atoms. The high electron density of the triazine ring nitrogen atoms, which results from the resonative contribution of electrons of exocyclic nitrogen atoms, leads to a very strong V-N bond. The cis-[V(V)O(2)(Htrihyat)](-) species exhibits high hydrolytic stability in aqueous solution over a wide pH range, 2.5-11.5, as was evidenced by potentiometry.

Influence of attrition milling on nano-grain boundaries

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

Rawers, J.; Cook, D.

1999-03-01

Nanostructured materials have a relatively large proportion of their atoms associated with the grain boundary, and the method used to develop the nano-grains has a strong influence on the resulting grain boundary structure. In this study, attrition milling iron powders and blends of iron powders produced micron-size particles composed of nano-size grains. Mechanical cold-working powder resulted in dislocation generation, multiplication, and congealing that produced grain refinement. As the grain size approached nano-dimensions, dislocations were no longer sustained within the grain and once generated, rapidly diffused to the grain boundary. Dislocations on the grain boundary strained the local lattice structure which,more » as the grain size decreased, became the entire grain. Mechanical alloying of substitutional aluminium atoms into iron powder resulted in the aluminium atoms substituting for iron atoms in the grain boundary cells and providing a grain boundary structure similar to that of the iron powder processed in argon. Attrition milling iron powder in nitrogen gas resulted in nitrogen atoms being adsorbed onto the particle surface. Continued mechanical milling infused the nitrogen atoms into interstitial lattice sites on the grain boundary which also contributed to expanding and straining the local lattice.« less

A 3D QSAR pharmacophore model and quantum chemical structure--activity analysis of chloroquine(CQ)-resistance reversal.

PubMed

Bhattacharjee, Apurba K; Kyle, Dennis E; Vennerstrom, Jonathan L; Milhous, Wilbur K

2002-01-01

Using CATALYST, a three-dimensional QSAR pharmacophore model for chloroquine(CQ)-resistance reversal was developed from a training set of 17 compounds. These included imipramine (1), desipramine (2), and 15 of their analogues (3-17), some of which fully reversed CQ-resistance, while others were without effect. The generated pharmacophore model indicates that two aromatic hydrophobic interaction sites on the tricyclic ring and a hydrogen bond acceptor (lipid) site at the side chain, preferably on a nitrogen atom, are necessary for potent activity. Stereoelectronic properties calculated by using AM1 semiempirical calculations were consistent with the model, particularly the electrostatic potential profiles characterized by a localized negative potential region by the side chain nitrogen atom and a large region covering the aromatic ring. The calculated data further revealed that aminoalkyl substitution at the N5-position of the heterocycle and a secondary or tertiary aliphatic aminoalkyl nitrogen atom with a two or three carbon bridge to the heteroaromatic nitrogen (N5) are required for potent "resistance reversal activity". Lowest energy conformers for 1-17 were determined and optimized to afford stereoelectronic properties such as molecular orbital energies, electrostatic potentials, atomic charges, proton affinities, octanol-water partition coefficients (log P), and structural parameters. For 1-17, fairly good correlation exists between resistance reversal activity and intrinsic basicity of the nitrogen atom at the tricyclic ring system, frontier orbital energies, and lipophilicity. Significantly, nine out of 11 of a group of structurally diverse CQ-resistance reversal agents mapped very well on the 3D QSAR pharmacophore model.

Identification of B-K near edge x-ray absorption fine structure peaks of boron nitride thin films prepared by sputtering deposition

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

Niibe, Masahito; Miyamoto, Kazuyoshi; Mitamura, Tohru

2010-09-15

Four {pi}{sup *} resonance peaks were observed in the B-K near edge x-ray absorption fine structure spectra of boron nitride thin films prepared by magnetron sputtering. In the past, these peaks have been explained as the K-absorption of boron atoms, which are present in environment containing nitrogen vacancies, the number of which is 1-3 corresponding to the three peaks at higher photon energy. However, the authors found that there was a strong correlation between the intensities of these three peaks and that of O-K absorption after wide range scanning and simultaneous measurement of nitrogen and oxygen K-absorptions of the BNmore » films. Therefore, the authors conclude that these three peaks at the higher energy side correspond to boron atoms bound to one-to-three oxygen atoms instead of three nitrogen atoms surrounding the boron atom in the h-BN structure. The result of the first-principles calculation with a simple cluster model supported the validity of this explanation.« less

Titan's atomic nitrogen torus - Inferred properties and consequences for the Saturnian aurora

NASA Astrophysics Data System (ADS)

Barbosa, D. D.

1987-10-01

This paper follows up the lead suggested by Barbosa and Eviatar (1986) that Titanogenic nitrogen ions are a key component of the magnetospheric particle populations and can account for the energetics of the Saturnian aurora without undue assumptions. Nitrogen atoms resulting from electron impact dissociations of N2 (Strobel and Shemansky 1982) escape from Titan and form a large doughnut-shaped ring around the satellite's orbit that is cospatial with the McDonough-Brice (1973) hydrogen cloud. Processes attendant to the ionization and pickup of nitrogen ions include the production of a warm kiloelectronvolt electron population and the excitation of the UV aurora by particle precipitation from the outer magnetosphere.

Ultrafast absorption of intense x rays by nitrogen molecules

NASA Astrophysics Data System (ADS)

Buth, Christian; Liu, Ji-Cai; Chen, Mau Hsiung; Cryan, James P.; Fang, Li; Glownia, James M.; Hoener, Matthias; Coffee, Ryan N.; Berrah, Nora

2012-06-01

We devise a theoretical description for the response of nitrogen molecules (N2) to ultrashort and intense x rays from the free electron laser Linac Coherent Light Source (LCLS). We set out from a rate-equation description for the x-ray absorption by a nitrogen atom. The equations are formulated using all one-x-ray-photon absorption cross sections and the Auger and radiative decay widths of multiply-ionized nitrogen atoms. Cross sections are obtained with a one-electron theory and decay widths are determined from ab initio computations using the Dirac-Hartree-Slater (DHS) method. We also calculate all binding and transition energies of nitrogen atoms in all charge states with the DHS method as the difference of two self-consistent field (SCF) calculations (ΔSCF method). To describe the interaction with N2, a detailed investigation of intense x-ray-induced ionization and molecular fragmentation are carried out. As a figure of merit, we calculate ion yields and the average charge state measured in recent experiments at the LCLS. We use a series of phenomenological models of increasing sophistication to unravel the mechanisms of the interaction of x rays with N2: a single atom, a symmetric-sharing model, and a fragmentation-matrix model are developed. The role of the formation and decay of single and double core holes, the metastable states of N_2^{2+}, and molecular fragmentation are explained.

Optical binding with cold atoms

NASA Astrophysics Data System (ADS)

Máximo, C. E.; Bachelard, R.; Kaiser, R.

2018-04-01

Optical binding is a form of light-mediated forces between elements of matter which emerge in response to the collective scattering of light. Such a phenomenon has been studied mainly in the context of the equilibrium stability of dielectric sphere arrays which move amid dissipative media. In this article, we demonstrate that optically bounded states of a pair of cold atoms can exist, in the absence of nonradiative damping. We study the scaling laws for the unstable-stable phase transition at negative detuning and the unstable-metastable one for positive detuning. In addition, we show that angular momentum can lead to dynamical stabilization with infinite-range scaling.

Polymer amide as an early topology.

PubMed

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.

Recent advances in transition metal-catalyzed N -atom transfer reactions of azides

PubMed Central

Driver, Tom G.

2011-01-01

Transition metal-catalyzed N-atom transfer reactions of azides provide efficient ways to construct new carbon–nitrogen and sulfur–nitrogen bonds. These reactions are inherently green: no additive besides catalyst is needed to form the nitrenoid reactive intermediate, and the by-product of the reaction is environmentally benign N2 gas. As such, azides can be useful precursors for transition metal-catalyzed N-atom transfer to sulfides, olefins and C–H bonds. These methods offer competitive selectivities and comparable substrate scope as alternative processes to generate metal nitrenoids. PMID:20617243

Revealing the Origin of Activity in Nitrogen-Doped Nanocarbons towards Electrocatalytic Reduction of Carbon Dioxide.

PubMed

Xu, Junyuan; Kan, Yuhe; Huang, Rui; Zhang, Bingsen; Wang, Bolun; Wu, Kuang-Hsu; Lin, Yangming; Sun, Xiaoyan; Li, Qingfeng; Centi, Gabriele; Su, Dangsheng

2016-05-23

Carbon nanotubes (CNTs) are functionalized with nitrogen atoms for reduction of carbon dioxide (CO2 ). The investigation explores the origin of the catalyst's activity and the role of nitrogen chemical states therein. The catalysts show excellent performances, with about 90 % current efficiency for CO formation and stability over 60 hours. The Tafel analyses and density functional theory calculations suggest that the reduction of CO2 proceeds through an initial rate-determining transfer of one electron to CO2 , which leads to the formation of carbon dioxide radical anion (CO2 (.-) ). The initial reduction barrier is too high on pristine CNTs, resulting in a very high overpotentials at which the hydrogen evolution reaction dominates over CO2 reduction. The doped nitrogen atoms stabilize the radical anion, thereby lowering the initial reduction barrier and improving the intrinsic activity. The most efficient nitrogen chemical state for this reaction is quaternary nitrogen, followed by pyridinic and pyrrolic nitrogen. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nitrogen plasma-treated multilayer graphene-based field effect transistor fabrication and electronic characteristics

NASA Astrophysics Data System (ADS)

Su, Wei-Jhih; Chang, Hsuan-Chen; Honda, Shin-ichi; Lin, Pao-Hung; Huang, Ying-Sheng; Lee, Kuei-Yi

2017-08-01

Chemical doping with hetero-atoms is an effective method used to change the characteristics of materials. Nitrogen doping technology plays a critical role in regulating the electronic properties of graphene. Nitrogen plasma treatment was used in this work to dope nitrogen atoms to modulate multilayer graphene electrical properties. The measured I-V multilayer graphene-base field-effect transistor characteristics (GFETs) showed a V-shaped transfer curve with the hole and electron region separated from the measured current-voltage (I-V) minimum. GFETs fabricated with multilayer graphene from chemical vapor deposition (CVD) exhibited p-type behavior because of oxygen adsorption. After using different nitrogen plasma treatment times, the minimum in I-V characteristic shifted into the negative gate voltage region with increased nitrogen concentration and the GFET channel became an n-type semiconductor. GFETs could be easily fabricated using this method with potential for various applications. The GFET transfer characteristics could be tuned precisely by adjusting the nitrogen plasma treatment time.

A Complete NMR Spectral Assignment of the Lipid-free Mouse Apolipoprotein A-I (ApoAI) C-terminal Truncation Mutant, ApoAI(1-216)

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

Yang, Yunhuang; Hoyt, David W.; Wang, Jianjun

2007-07-28

Apolipoprotein A-I (apoAI) is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. Upon lipid-binding, apoAI undergoes conformational changes from lipid-free to several different HDL-associated states (1). These different conformational states regulate HDL formation, maturation and transportation. Recent crystal structure of lipid-free human apoAI represents a major progress of structural study of lipid-free apoAI (2). However, no structural is available for lipid-free mouse apoAI (240-residues). Since mouse HDL is homogenous with only HDL2-like size, whereas human HDL is heterogeneous, containing HDL2/HDL3 as its main species, a structuralmore » comparison between human and mouse apoAI may allow us to identify structure basis of HDL size distribution difference between human and mouse. We carried out an NMR structure determination of lipid-free mouse apoAI (1-216) and completely assigned backbone atoms (except backbone amide proton and nitrogen atoms for residues D1, N48, W107, K108, K132, E135, F147, R148, M169 and K203). Secondary structure prediction using backbone NMR parameters indicates that lipid-free mouse apoAI consists of a four helical segments in the N-terminal domain, residues 1-180. In addition, two short helices are also observed between residues 190-195 and 210-215. The helix locations are significantly different from those in the crystal structure of human apoAI, suggesting that mouse apoAI may have a different conformational adaptation upon lipid-binding. BMRB deposit with accession number: 15091.« less

Urease Inhibition in the Presence of N-(n-Butyl)thiophosphoric Triamide, a Suicide Substrate: Structure and Kinetics.

PubMed

Mazzei, Luca; Cianci, Michele; Contaldo, Umberto; Musiani, Francesco; Ciurli, Stefano

2017-10-10

The nickel-dependent enzyme urease is a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria, as well as a negative factor for the efficiency of soil nitrogen fertilization for crop production. The use of urease inhibitors to offset these effects requires knowledge, at a molecular level, of their mode of action. The 1.28 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease with N-(n-butyl)thiophosphoric triamide (NBPT), a molecule largely utilized in agriculture, reveals the presence of the monoamidothiophosphoric acid (MATP) moiety, obtained upon enzymatic hydrolysis of the diamide derivative of NBPT (NBPD) to yield n-butyl amine. MATP is bound to the two Ni(II) ions in the active site of urease using a μ 2 -bridging O atom and terminally bound O and NH 2 groups, with the S atom of the thiophosphoric amide pointing away from the metal center. The mobile flap modulating the size of the active site cavity is found in the closed conformation. Docking calculations suggest that the interaction between urease in the open flap conformation and NBPD involves a role for the conserved αArg339 in capturing and orienting the inhibitor prior to flap closure. Calorimetric and spectrophotometric determinations of the kinetic parameters of this inhibition indicate the occurrence of a reversible slow inhibition mode of action, characterized, for both bacterial and plant ureases, by a very small value of the dissociation constant of the urease-MATP complex. No need to convert NBPT to its oxo derivative NBPTO, as previously proposed, is necessary for urease inhibition.

Cryogenic and Simulated Fuel Jet Breakup in Argon, Helium and Nitrogen Gas Flows

NASA Technical Reports Server (NTRS)

Ingebo, Robert D.

1995-01-01

Two-phase flow atomization of liquid nitrogen jets was experimentally investigated. They were co-axially injected into high-velocity gas flows of helium, nitrogen and argon, respectively, and atomized internally inside a two-fluid fuel nozzle. Cryogenic sprays with relatively high specific surface areas were produced, i.e., ratios of surface area to volume were fairly high. This was indicated by values of reciprocal Sauter mean diameters, RSMD's, as measured with a scattered- light scanning instrument developed at NASA Lewis Research Center. Correlating expressions were derived for the three atomizing gases over a gas temperature range of 111 to 422 K. Also, the correlation was extended to include waterjet breakup data that had been previously obtained in simulating fuel jet breakup in sonic velocity gas flow. The final correlating expression included a new dimensionless molecular-scale acceleration group. It was needed to correlate RSMD data, for LN2 and H2O sprays, with the fluid properties of the liquid jets and atomizing gases used in this investigation.

Evidence for the Formation of Nitrogen-Rich Platinum and Palladium Nitride Nanoparticles

DOE PAGES

Veith, Gabriel M.; Lupini, Andrew R.; Baggetto, Loïc; ...

2013-12-03

Here, we report evidence for the formation of nitrogen-rich precious metal nanoparticles (Pt, Pd) prepared by reactive sputtering of the pure metal in a N 2 plasma. The composition of the nanoparticles varies as a function of particle size and growth conditions. For the smallest particles the nitrogen content appears to be as high as 6.7 N atoms for each Pd atom or 5.9 N atoms for each Pt atom whereas bulk films have nominal compositions of Pt 7.3N and Pd 2.5N. The nanoparticles are metastable in air and moisture, slowly decomposing over several years. This paper describes the synthesismore » of these materials along with experimental evidence of the composition, oxidation state, and growth modes. Moreover, the catalytic properties of these N-rich nanoparticles were accessed by rotating disk electrode electrochemical studies, the liquid phase oxidation of benzyl alcohol and gas phase CO oxidation and support the experimental evidence for the materials composition.« less

Synthesis of High Molecular Weight Para-Phenylene PBI

DTIC Science & Technology

1974-11-01

acid , and the viscous material stirred at 1500 under nitrogen for 3 hours. The flask was then cooled in ice, opened, and 2 g (6.56 mole) of 2 -[p...11 1. Monomers 11 2 . Polymers 18 0 V REFERENCES 23 ILLUSTRATIONS FIGURE PAGE 1. X-RAY DIFFRACTION PATTERN OF ACID INSOLUBLE POLYMER 24 2 . X-RAY...solvents. Other acid derivatives such as esters, amides, and nitriles were also employed as monomers with the same results. NH 2 ,NH 2 - 4HCI + 1- I NH2

CH functionalization of heteroaromatic compounds by transition metal catalysis

NASA Astrophysics Data System (ADS)

Tanba, Shunsuke; Fujiwara, Taiki; Monguchi, Daiki; Mori, Atsunori

2010-06-01

Transition metal-catalyzed CH functioanlization of thiazoles and thiophenes are carried out. The reaction of thiophene with aryl halide in the presence of a palladium catalyst underwent the CC bond forming reaction at the CH bond of thiophene. By employing the reaction head-to-tail-type oligothiophene is synthesized in a stepwise manner. When several azoles are treated with secondary amines and amides in the presence of a copper catalyst, oxidative CH-NH coupling took place to form the carbon-nitrogen bond.

Copper-catalyzed domino cycloaddition/C-N coupling/cyclization/(C-H arylation): an efficient three-component synthesis of nitrogen polyheterocycles.

PubMed

Qian, Wenyuan; Wang, Hao; Allen, Jennifer

2013-10-11

A cat of all trades: A single copper catalyst promoted up to three reaction steps with separate catalytic cycles in a domino sequence (azide-alkyne cycloaddition/Goldberg amidation/Camps cyclization/(CH arylation)) for the rapid construction of complex heterocycles from three simple components under mild conditions. Facile cleavage of the triazole ring enables further elaboration of the condensation products. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Backbone assignment of the little finger domain of a Y-family DNA polymerase.

PubMed

Ma, Dejian; Fowler, Jason D; Suo, Zucai

2011-10-01

Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

Alkyl halide-free heteroatom alkylation and epoxidation facilitated by a recyclable polymer-supported oxidant for the in-flow preparation of diazo compounds.

PubMed

Nicolle, Simon M; Hayes, Christopher J; Moody, Christopher J

2015-03-16

Highly reactive metal carbenes, generated from simple ketones via diazo compounds, including diazo-amides and -phosphonates, using a recyclable reagent in-flow, are transient but versatile electrophiles for heteroatom alkylation reactions and for epoxide formation. The method produces no organic waste, with the only by-products being water, KI and nitrogen, without the attendant hazards of isolation of intermediate diazo compounds. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preferential incorporation of substitutional nitrogen near the atomic step edges in diluted nitride alloys

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

Cornet, C.; Nguyen Thanh, T.; Almosni, S.

We have investigated the influence of the surface roughness on nitrogen incorporation during the molecular beam epitaxy of diluted nitrides, independently of the other growth parameters. GaPN/GaP layers grown simultaneously on surfaces displaying different roughnesses reveal a large difference in nitrogen incorporation despite the same growth temperature and growth rate. The same difference is found on quasi-lattice-matched GaAsPN demonstrating that the phenomenon is not related to any strain-induced mechanisms. The tendency is clearly confirmed when varying the growth conditions. As a direct consequence, the incorporation of substitutional nitrogen near the atomic step edges is found to be 6.7 times moremore » probable than the in-plane nitrogen incorporation. The formation of N-N{sub i} clusters and their stability on the surface is discussed.« less

Synthesis of pyrido[1,2-a]benzimidazoles and other fused imidazole derivatives with a bridgehead nitrogen atom

NASA Astrophysics Data System (ADS)

Begunov, Roman S.; Ryzvanovich, Galina A.

2013-01-01

Main methods for the synthesis of fused imidazole derivatives with a bridgehead nitrogen atom are systematically considered and summarized. The reaction mechanisms that underlie the methods for the synthesis of pyrido[1,2-a]benzimidazoles and related compounds are described. Biological properties and mechanisms of the biological activity of fused azaheterocycles are discussed. The bibliography includes 152 references.

First-principles studies of a photovoltaic material based on silicon heavily codoped with sulfur and nitrogen

NASA Astrophysics Data System (ADS)

Dong, Xiao; Wang, Yongyong; Song, Xiaohui; Yang, Feng

2018-03-01

In silicon co-hyperdoped with nitrogen and sulfur, dopant atoms tend to form dimers in the near-equilibrium process. The dimer that contains substitutional N and S atoms has the lowest formation energy and can form an impurity band that overlaps with the conduction band (CB). When separating the two atoms far apart from each other, the impurity band is clearly isolated from the CB and becomes an intermediate band (IB). The sub-band-gap absorption decreases with the decrease in the substitutional atom distance. The sub-band-gap absorption of the material is the combined effect of the configurations with different N-S distances.

Rice Ferredoxin-Dependent Glutamate Synthase Regulates Nitrogen-Carbon Metabolomes and Is Genetically Differentiated between japonica and indica Subspecies.

PubMed

Yang, Xiaolu; Nian, Jinqiang; Xie, Qingjun; Feng, Jian; Zhang, Fengxia; Jing, Hongwei; Zhang, Jian; Dong, Guojun; Liang, Yan; Peng, Juli; Wang, Guodong; Qian, Qian; Zuo, Jianru

2016-11-07

Plants assimilate inorganic nitrogen absorbed from soil into organic forms as Gln and Glu through the glutamine synthetase/glutamine:2-oxoglutarate amidotransferase (GS/GOGAT) cycle. Whereas GS catalyzes the formation of Gln from Glu and ammonia, GOGAT catalyzes the transfer of an amide group from Gln to 2-oxoglutarate to produce two molecules of Glu. However, the regulatory role of the GS/GOGAT cycle in the carbon-nitrogen balance is not well understood. Here, we report the functional characterization of rice ABNORMAL CYTOKININ RESPONSE 1 (ABC1) gene that encodes a ferredoxin-dependent (Fd)-GOGAT. The weak mutant allele abc1-1 mutant shows a typical nitrogen-deficient syndrome, whereas the T-DNA insertional mutant abc1-2 is seedling lethal. Metabolomics analysis revealed the accumulation of an excessive amount of amino acids with high N/C ratio (Gln and Asn) and several intermediates in the tricarboxylic acid cycle in abc1-1, suggesting that ABC1 plays a critical role in nitrogen assimilation and carbon-nitrogen balance. Five non-synonymous single-nucleotide polymorphisms were identified in the ABC1 coding region and characterized as three distinct haplotypes, which have been highly and specifically differentiated between japonica and indica subspecies. Collectively, these results suggest that ABC1/OsFd-GOGAT is essential for plant growth and development by modulating nitrogen assimilation and the carbon-nitrogen balance. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

Angular distribution of photoelectrons from atomic oxygen, nitrogen and carbon. [in upper atmosphere

NASA Technical Reports Server (NTRS)

Manson, S. J.; Kennedy, D. J.; Starace, A. F.; Dill, D.

1974-01-01

The angular distributions of photoelectrons from atomic oxygen, nitrogen, and carbon are calculated. Both Hartree-Fock and Hartree-Slater (Herman-Skillman) wave functions are used for oxygen, and the agreement is excellent; thus only Hartree-Slater functions are used for carbon and nitrogen. The pitch-angle distribution of photoelectrons is discussed, and it is shown that previous approximations of energy-independent isotropic or sin squared theta distributions are at odds with the authors' results, which vary with energy. This variation with energy is discussed, as is the reliability of these calculations.

N-Acyl derivatives of Asn, new bacterial N-acyl D-amino acids with surfactant activity.

PubMed

Peypoux, F; Laprévote, O; Pagadoy, M; Wallach, J

2004-03-01

New N-acyl D-amino acids were isolated from Bacillus pumilus IM 1801. Their structures were determined by chemical analysis and mass spectrometry. The lipid part was identified as a mixture of fatty acids with 11, 12, 13, 15, and 16 carbon atoms in the iso, anteiso or n configuration linked by an amide bond with a D-asparagine. They exhibited surfactant properties.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Pseudocapacitive Effects of N-Doped Carbon Nanotube Electrodes in Supercapacitors

PubMed Central

Yun, Young Soo; Park, Hyun Ho; Jin, Hyoung-Joon

2012-01-01

Nitrogen- and micropore-containing carbon nanotubes (NMCNTs) were prepared by carbonization of nitrogen-enriched, polymer-coated carbon nanotubes (CNTs), and the electrochemical performances of the NMCNTs with different heteroatom contents were investigated. NMCNTs-700 containing 9.1 wt% nitrogen atoms had a capacitance of 190.8 F/g, which was much higher than that of pristine CNTs (48.4 F/g), despite the similar surface area of the two CNTs, and was also higher than that of activated CNTs (151.7 F/g) with a surface area of 778 m2/g and a nitrogen atom content of 1.2 wt%. These results showed that pseudocapacitive effects play an important role in the electrochemical performance of supercapacitor electrodes.

Rapid solidification of metallic particulates

NASA Technical Reports Server (NTRS)

Grant, N. J.

1982-01-01

In order to maximize the heat transfer coefficient the most important variable in rapid solidification is the powder particle size. The finer the particle size, the higher the solidification rate. Efforts to decrease the particle size diameter offer the greatest payoff in attained quench rate. The velocity of the liquid droplet in the atmosphere is the second most important variable. Unfortunately the choices of gas atmospheres are sharply limited both because of conductivity and cost. Nitrogen and argon stand out as the preferred gases, nitrogen where reactions are unimportant and argon where reaction with nitrogen may be important. In gas atomization, helium offers up to an order of magnitude increase in solidification rate over argon and nitrogen. By contrast, atomization in vacuum drops the quench rate several orders of magnitude.

Atmospheric Pseudohalogen Chemistry

NASA Technical Reports Server (NTRS)

Lary, David John

2004-01-01

Hydrogen cyanide is not usually considered in atmospheric chemical models. The paper presents three reasons why hydrogen cyanide is likely to be significant for atmospheric chemistry. Firstly, HCN is a product and marker of biomass burning. Secondly, it is also likely that lightning is producing HCN, and as HCN is sparingly soluble it could be a useful long-lived "smoking gun" marker of lightning activity. Thirdly, the chemical decomposition of HCN leads to the production of small amounts of the cyanide (CN) and NCO radicals. The NCO radical can be photolyzed in the visible portion of the spectrum yielding nitrogen atoms (N). The production of nitrogen atoms is significant as it leads to the titration of total nitrogen from the atmosphere via N+N->N2, where N2 is molecular nitrogen.

Empirical model of atomic nitrogen in the upper thermosphere

NASA Technical Reports Server (NTRS)

Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.

1977-01-01

Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.

Nitrogen-doped carbon monolith for alkaline supercapacitors and understanding nitrogen-induced redox transitions.

PubMed

Wang, Da-Wei; Li, Feng; Yin, Li-Chang; Lu, Xu; Chen, Zhi-Gang; Gentle, Ian R; Lu, Gao Qing; Cheng, Hui-Ming

2012-04-23

A nitrogen-doped porous carbon monolith was synthesized as a pseudo-capacitive electrode for use in alkaline supercapacitors. Ammonia-assisted carbonization was used to dope the surface with nitrogen heteroatoms in a way that replaced carbon atoms but kept the oxygen content constant. Ammonia treatment expanded the micropore size-distributions and increased the specific surface area from 383 m(2) g(-1) to 679 m(2) g(-1). The nitrogen-containing porous carbon material showed a higher capacitance (246 F g(-1)) in comparison with the nitrogen-free one (186 F g(-1)). Ex situ electrochemical spectroscopy was used to investigate the evolution of the nitrogen-containing functional groups on the surface of the N-doped carbon electrodes in a three-electrode cell. In addition, first-principles calculations were explored regarding the electronic structures of different nitrogen groups to determine their relative redox potentials. We proposed possible redox reaction pathways based on the calculated redox affinity of different groups and surface analysis, which involved the reversible attachment/detachment of hydroxy groups between pyridone and pyridine. The oxidation of nitrogen atoms in pyridine was also suggested as a possible reaction pathway. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomizing-gas temperature effect on cryogenic spray dropsize

NASA Technical Reports Server (NTRS)

Ingebo, Robert D.

1993-01-01

Correlating expressions for two-phase flow breakup of liquid nitrogen, LN2, jets in sonic velocity nitrogen gasflows were obtained for an atomizing-gas temperature range of 111 to 442 K. The correlations were based on characteristic dropsize measurements obtained with a scattered-light scanner. The effect of droplet vaporization on the measurements of the volume-median dropsize was calculated by using previously determined heat and momentum transfer expressions for droplets evaporating in high-velocity gasflow. Finally, the dropsize of the originally unvaporized spray was calculated, normalized with respect to jet diameter and correlated with atomizing-gas flowrate and temperature.

Substrate promiscuity of a rosmarinic acid synthase from lavender (Lavandula angustifolia L.).

PubMed

Landmann, Christian; Hücherig, Stefanie; Fink, Barbara; Hoffmann, Thomas; Dittlein, Daniela; Coiner, Heather A; Schwab, Wilfried

2011-08-01

One of the most common types of modification of secondary metabolites is the acylation of oxygen- and nitrogen-containing substrates to produce esters and amides, respectively. Among the known acyltransferases, the members of the plant BAHD family are capable of acylating a wide variety of substrates. Two full-length acyltransferase cDNAs (LaAT1 and 2) were isolated from lavender flowers (Lavandula angustifolia L.) by reverse transcriptase-PCR using degenerate primers based on BAHD sequences. Recombinant LaAT1 exhibited a broad substrate tolerance accepting (hydroxy)cinnamoyl-CoAs as acyl donors and not only tyramine, tryptamine, phenylethylamine and anthranilic acid but also shikimic acid and 4-hydroxyphenyllactic acid as acceptors. Thus, LaLT1 forms esters and amides like its phylogenetic neighbors. In planta LaAT1 might be involved in the biosynthesis of rosmarinic acid, the ester of caffeic acid and 3,4-dihydroxyphenyllactic acid, a major constituent of lavender flowers. LaAT2 is one of three members of clade VI with unknown function.

Nanopores creation in boron and nitrogen doped polycrystalline graphene: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Izadifar, Mohammadreza; Abadi, Rouzbeh; Nezhad Shirazi, Ali Hossein; Alajlan, Naif; Rabczuk, Timon

2018-05-01

In the present paper, molecular dynamic simulations have been conducted to investigate the nanopores creation on 10% of boron and nitrogen doped polycrystalline graphene by silicon and diamond nanoclusters. Two types of nanoclusters based on silicon and diamond are used to investigate their effect for the fabrication of nanopores. Therefore, three different diameter sizes of the clusters with five kinetic energies of 10, 50, 100, 300 and 500 eV/atom at four different locations in boron or nitrogen doped polycrystalline graphene nanosheets have been perused. We also study the effect of 3% and 6% of boron doped polycrystalline graphene with the best outcome from 10% of doping. Our results reveal that the diamond cluster with diameter of 2 and 2.5 nm fabricates the largest nanopore areas on boron and nitrogen doped polycrystalline graphene, respectively. Furthermore, the kinetic energies of 10 and 50 eV/atom can not fabricate nanopores in some cases for silicon and diamond clusters on boron doped polycrystalline graphene nanosheets. On the other hand, silicon and diamond clusters fabricate nanopores for all locations and all tested energies on nitrogen doped polycrystalline graphene. The area sizes of nanopores fabricated by silicon and diamond clusters with diameter of 2 and 2.5 nm are close to the actual area size of the related clusters for the kinetic energy of 300 eV/atom in all locations on boron doped polycrystalline graphene. The maximum area and the average maximum area of nanopores are fabricated by the kinetic energy of 500 eV/atom inside the grain boundary at the center of the nanosheet and in the corner of nanosheet with diameters of 2 and 3 nm for silicon and diamond clusters on boron and nitrogen doped polycrystalline graphene.

Hydrogen atom scrambling in selectively labeled anionic peptides upon collisional activation by MALDI tandem time-of-flight mass spectrometry.

PubMed

Bache, Nicolai; Rand, Kasper D; Roepstorff, Peter; Ploug, Michael; Jørgensen, Thomas J D

2008-12-01

We have previously shown that peptide amide hydrogens undergo extensive intramolecular migration (i.e., complete hydrogen scrambling) upon collisional activation of protonated peptides (Jørgensen et al. J. Am. Chem. Soc. 2005, 127, 2785-2793). The occurrence of hydrogen scrambling enforces severe limitations on the application of gas-phase fragmentation as a convenient method to obtain information about the site-specific deuterium uptake for proteins and peptides in solution. To investigate whether deprotonated peptides exhibit a lower level of scrambling relative to their protonated counterparts, we have now measured the level of hydrogen scrambling in a deprotonated, selectively labeled peptide using MALDI tandem time-of-flight mass spectrometry. Our results conclusively show that hydrogen scrambling is prevalent in the deprotonated peptide upon collisional activation. The amide hydrogens ((1)H/(2)H) have migrated extensively in the anionic peptide, thereby erasing the original regioselective deuteration pattern obtained in solution.

Production and characterization of a nitrogen-implanted Fe standard to calibrate PIGE measurements

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

Rodrigues, C. L.; Silva, T. F.; Added, N.

2014-11-11

Three calibration standard was produced by ion implantation of nitrogen in samples of Armco iron (99.7% iron). The samples was irradiated with nitrogen ion beams at several different energies (between 4 keV and 40 keV), and the ion doses were adjusted to obtain an uniform depth profile, using simulations with SRIM code. Two standards, one thick and other a foil (1.62mg/cm{sup 2}), was irradiated at same time with total nominal dose of 6.6×10{sup −16} atoms/cm{sup 2} distributed in a region of 100 nm in depth, with an average concentration of 9.0% nitrogen in iron. The third sample uses the samemore » profile, but with a small dose, 1.1×10{sup −16} atoms/cm{sup 2} and average concentration of 1.5% nitrogen. The characterization of the implanted samples was done using RBS and NRA techniques to quantification of nitrogen.« less

Theoretical studies of the nitrogen containing compounds adsorption behavior on Na(I)Y and rare earth exchanged RE(III)Y zeolites.

PubMed

Geng, Wei; Zhang, Haitao; Zhao, Xuefei; Zan, Wenyan; Gao, Xionghou; Yao, Xiaojun

2015-01-01

In this work, the adsorption behavior of nitrogen containing compounds including NH3, pyridine, quinoline, and carbazole on Na(I)Y and rare earth exchanged La(III)Y, Pr(III)Y, Nd(III)Y zeolites was investigated by density functional theory (DFT) calculations. The calculation results demonstrate that rare earth exchanged zeolites have stronger adsorption ability for nitrogen containing compounds than Na(I)Y. Rare earth exchanged zeolites exhibit strongest interaction with quinoline while weakest with carbazole. Nd(III)Y zeolites are found to have strongest adsorption to all the studied nitrogen containing compounds. The analysis of the electronic total charge density and electron orbital overlaps show that nitrogen containing compounds interact with zeolites by π-electrons of the compounds and the exchanged metal atom. Mulliken charge population analysis also proves that adsorption energies are strongly dependent on the charge transfer between the nitrogen containing molecules and exchanged metal atom in the zeolites.

Synergistic cytogenetic and antineoplastic effects by the combined action of esteric steroidal derivatives of nitrogen mustards.

PubMed

Mourelatos, Constantinos; Nikolaropoulos, Sotiris; Fousteris, Manolis; Pairas, Georgios; Argyraki, Maria; Kareli, Dimitra; Dafa, Evaggelia; Mourelatos, Dionisios; Lialiaris, Theodore

2012-06-01

We studied the effect of five newly synthesized steroidal derivatives of nitrogen mustards. These derivatives have as alkylators either P-N, N-bis(2-chloroethyl)aminophenyl-butyrate (CHL) or P-N, N-bis(2-chloroethyl)aminophenyl-acetate (PHE) groups esterified with different modified steroidal nuclei. We examined them alone or in combination, on sister chromatid exchange rates and on human lymphocyte proliferation kinetics. The antitumor activity of these compounds, alone or in combination, was also tested on Leukemia P388-bearing mice. A pronounced cytogenetic and antineoplastic action was demonstrated by the compounds that contain either PHE or CHL as alkylators and are esterified with a steroidal nucleus having added a cholestene group in the 17 position of the D-ring. The exocyclical insertion of an -NHCO- group in the D-ring of the steroidal nucleus esterified with PHE (amide ester of PHE) yielded a compound demonstrating a distinct cytogenetic and antineoplastic effect. In contrast, the ketone group in the D-ring being inserted endocyclically in the steroidal nucleus (androstene) esterified with either CHL or with PHE gave negative cytogenetic and antineoplastic effects. However, the combined action of cholestene esterified with either CHL or with PHE in combination with either the androstene ester of PHE or with the androstene ester of CHL, respectively, gave synergistic cytogenetic and antineoplastic effects. Also the amide ester of PHE in combination with the androstene ester of CHL gave distinct cytogenetic and antineoplastic effects in a synergistic manner.

Organic nitrogen chemistry during low-grade metamorphism

USGS Publications Warehouse

Boudou, J.-P.; Schimmelmann, A.; Ader, M.; Mastalerz, Maria; Sebilo, M.; Gengembre, L.

2008-01-01

Most of the organic nitrogen (Norg) on Earth is disseminated in crustal sediments and rocks in the form of fossil nitrogen-containing organic matter. The chemical speciation of fossil Norg within the overall molecular structure of organic matter changes with time and heating during burial. Progressive thermal evolution of organic matter involves phases of enhanced elimination of Norg and ultimately produces graphite containing only traces of nitrogen. Long-term chemical and thermal instability makes the chemical speciation of Norg a valuable tracer to constrain the history of sub-surface metamorphism and to shed light on the subsurface biogeochemical nitrogen cycle and its participating organic and inorganic nitrogen pools. This study documents the evolutionary path of Norg speciation, transformation and elimination before and during metamorphism and advocates the use of X-ray photoelectron spectroscopy (XPS) to monitor changes in Norg speciation as a diagnostic tool for organic metamorphism. Our multidisciplinary evidence from XPS, stable isotopes, traditional quantitative coal analyses, and other analytical approaches shows that at the metamorphic onset Norg is dominantly present as pyrrolic and pyridinic nitrogen. The relative abundance of nitrogen substituting for carbon in condensed, partially aromatic systems (where N is covalently bonded to three C atoms) increases exponentially with increasing metamorphic grade, at the expense of pyridinic and pyrrolic nitrogen. At the same time, much Norg is eliminated without significant nitrogen isotope fractionation. The apparent absence of Rayleigh-type nitrogen isotopic fractionation suggests that direct thermal loss of nitrogen from an organic matrix does not serve as a major pathway for Norg elimination. Instead, we propose that hot H, O-containing fluids or some of their components gradually penetrate into the carbonaceous matrix and eliminate Norg along a progressing reaction front, without causing nitrogen isotope fractionation in the residual Norg in the unreacted core of the carbonaceous matrix. Before the reaction front can reach the core, an increasing part of core Norg chemically stabilizes in the form of nitrogen atoms substituting for carbon in condensed, partially aromatic systems forming graphite-like structural domains with delocalized ??-electron systems (nitrogen atoms substituting for "graphitic" carbon in natural metamorphic organic matter). Thus, this nitrogen species with a conservative isotopic composition is the dominant form of residual nitrogen at higher metamorphic grade. ?? 2007 Elsevier Ltd. All rights reserved.

Etude des trois molecules H 2P-NH 2, ClHP-NH 2, H 2P-NHCl au moyen d'une methode de pseudopotentiels

NASA Astrophysics Data System (ADS)

Barthelat, M.; Mathis, R.; Mathis, F.

The three molecules H 2P-NH 2, ClHP-NH 2 and H 2P-NHCl have been studied by a pseudo-potential method, with a minimal basis of quality mono-zeta, with 3 d functions on the phosphorus atom. The geometry of each molecule was optimized and the phosphorus-nitrogen rotation barrier calculated. The results of the calculations confirm that the polarity of the phosphorus-nitrogen bond is P +-N -. Three weak interactions appear: a partial coordinative bond between the nitrogen doublet and a 3 d orbital of the phosphorus atom, hyperconjugation between the nitrogen doublet and the P-H bonds, and participation of the 3 d orbital of phosphorus in the P-N bond.

Application of cyanuric chloride-based six new chiral derivatizing reagents having amino acids and amino acid amides as chiral auxiliaries for enantioresolution of proteinogenic amino acids by reversed-phase high-performance liquid chromatography.

PubMed

Bhushan, Ravi; Dixit, Shuchi

2012-04-01

Six dichloro-s-triazine (DCT) reagents having L-Leu, D-Phg, L-Val, L-Met, L-Ala and L-Met-NH(2) as chiral auxiliaries in cyanuric chloride were introduced for enantioseparation of 13 proteinogenic amino acids. Four other DCTs and six monochloro-s-triazine (MCT) reagents having amino acid amides as chiral auxiliaries were also synthesized. These 16 chiral derivatizing reagents (CDRs) were used for synthesis of diastereomers of all the 13 analytes using microwave irradiation, which were resolved by reversed-phase high-performance liquid chromatography (RP-HPLC) using C18 column and gradient eluting mixture of aqueous TFA and acetonitrile with UV detection at 230 nm. It required only 60-90 s for derivatization using microwave irradiation. Better resolution and lower retention times were observed for the diastereomers prepared with CDRs having amino acids as chiral auxiliaries as compared to counterparts prepared with reagents having amino acid amides as chiral auxiliaries. As the best resolution of all the 13 analytes was observed for their diastereomers prepared using the DCT reagent having L-Leu as chiral auxiliary, this CDR was further employed for derivatization of Lys, Tyr, His and Arg followed by RP-HPLC analysis of resulting diastereomers. The results are discussed in light of acid and amide groups of chiral auxiliaries constituting CDRs, electronegativities of the atoms of achiral moieties constituting CDRs and hydrophobicities of side chains of amino acids constituting CDRs and analytes.

Selective reduction of carboxylic acids to aldehydes with hydrosilane via photoredox catalysis.

PubMed

Zhang, Muliang; Li, Nan; Tao, Xingyu; Ruzi, Rehanguli; Yu, Shouyun; Zhu, Chengjian

2017-09-12

The direct reduction of carboxylic acids to aldehydes with hydrosilane was achieved through visible light photoredox catalysis. The combination of both single electron transfer and hydrogen atom transfer steps offers a novel and convenient approach to selective reduction of carboxylic acids to aldehydes. The method also features mild conditions, high yields, broad substrate scope, and good functional group tolerance, such as alkyne, ester, ketone, amide and amine groups.

Polymer useful for an ion exchange membrane

DOEpatents

Liang, Siwei; Lynd, Nathaniel A.

2017-03-14

The present invention provides for a polymer formed by reacting a first reactant polymer, or a mixture of first reactant polymers comprising different chemical structures, comprising a substituent comprising two or more nitrogen atoms (or a functional group/sidechain comprising a two or more nitrogen atoms) with a second reactant polymer, or a mixture of second reactant polymers comprising different chemical structures, comprising a halogen substituent (or a functional group/sidechain comprising a halogen).

Ultraviolet electroluminescence from nitrogen-doped ZnO-based heterojuntion light-emitting diodes prepared by remote plasma in situ atomic layer-doping technique.

PubMed

Chien, Jui-Fen; Liao, Hua-Yang; Yu, Sheng-Fu; Lin, Ray-Ming; Shiojiri, Makoto; Shyue, Jing-Jong; Chen, Miin-Jang

2013-01-23

Remote plasma in situ atomic layer doping technique was applied to prepare an n-type nitrogen-doped ZnO (n-ZnO:N) layer upon p-type magnesium-doped GaN (p-GaN:Mg) to fabricate the n-ZnO:N/p-GaN:Mg heterojuntion light-emitting diodes. The room-temperature electroluminescence exhibits a dominant ultraviolet peak at λ ≈ 370 nm from ZnO band-edge emission and suppressed luminescence from GaN, as a result of the decrease in electron concentration in ZnO and reduced electron injection from n-ZnO:N to p-GaN:Mg because of the nitrogen incorporation. The result indicates that the in situ atomic layer doping technique is an effective approach to tailoring the electrical properties of materials in device applications.

The impact of gas-surface reactions on mass spectrometric measurements of atomic nitrogen. [determination of atmosphere ion sources

NASA Technical Reports Server (NTRS)

Engebretson, M. J.; Mauersberger, K.

1979-01-01

The paper presents a simplified model of the ion source chemistry, explains several details of the data reduction method used in obtaining atomic-nitrogen (N) densities from OSS data, and discusses implications of gas-surface reactions for the design of future satellite-borne mass spectrometers. Because of various surface reactions, N appears in three different forms in the ion source, as N, NO, and NO2. Considering the rather small spin modulation of NO and NO2 in the semi-open ionization chamber used in the OSS instrument, it is not surprising that these reaction products have not been previously identified in closed source instruments as a measure of the presence of atomic nitrogen. Warmup and/or outgassing of the ion source are shown to drastically reduce the NO2 concentration, thereby making possible reliable measurement of ambient N densities.

The influence of the structural orientation of amide linkers on the serum compatibility and lung transfection properties of cationic amphiphiles.

PubMed

Srujan, Marepally; Chandrashekhar, Voshavar; Reddy, Rakesh C; Prabhakar, Rairala; Sreedhar, Bojja; Chaudhuri, Arabinda

2011-08-01

Understanding the structural parameters of cationic amphiphiles which can influence gene transfer efficiencies of cationic amphiphiles continues to remain important for designing efficient liposomal gene delivery reagents. Previously we demonstrated the influence of structural orientation of the ester linker (widely used in covalently tethering the polar head and the non-polar tails) in modulating in vitro gene transfer efficiencies of cationic amphiphiles. However, our previously described cationic amphiphiles with ester linkers failed to deliver genes under in vivo conditions. Herein we report on the development of a highly serum compatible cationic amphiphile with circulation stable amide linker which shows remarkable selectivity in transfecting mouse lung. We also demonstrate that reversing structural orientation of the amide linker adversely affects both serum compatibility and the lung selective gene transfer property. Dynamic laser light scattering and atomic force microscopic studies revealed smaller average hydrodynamic sizes of the liposomes of transfection efficient lipid than those for the liposomes of transfection incompetent analog (148 ± 1 nm vs 214 ± 4 nm). Average surface potential of the liposomes of transfection competent amphiphiles were found to be significantly higher than that for the liposomes of transfection incompetent analog (10.7 ± 5.4 mV vs 2.8 ± 1.3 mV, respectively). Findings in fluorescence resonance energy transfer and dye entrapment experiments support lower rigidity and higher biomembrane fusogenicity of the liposomes of the transfection efficient amphiphiles. Importantly, cationic lipoplexes of the novel amide-linker based amphiphile exhibited higher mouse lung selective gene transfer properties than DOTAP, one of the widely used commercially available liposomal lung transfection kits. In summary, the present findings demonstrate for the first time that amide linker structural orientation profoundly influences the serum compatibility and lung transfection efficiencies of cationic amphiphiles. Copyright © 2011 Elsevier Ltd. All rights reserved.

Energetic Nitrogen Ions within the Inner Magnetosphere of Saturn

NASA Astrophysics Data System (ADS)

Sittler, E. C.; Johnson, R. E.; Richardson, J. D.; Jurac, S.; Moore, M.; Cooper, J. F.; Mauk, B. H.; Smith, H. T.; Michael, M.; Paranicus, C.; Armstrong, T. P.; Tsurutani, B.; Connerney, J. E. P.

2003-05-01

Titan's interaction with Saturn's magnetosphere will result in the energetic ejection of atomic nitrogen atoms into Saturn's magnetosphere due to dissociation of N2 by electrons, ions, and UV photons. The ejection of N atoms into Saturn's magnetosphere will form a nitrogen torus around Saturn with mean density of about 4 atoms/cm3 with source strength of 4.5x1025 atoms/sec. These nitrogen atoms are ionized by photoionization, electron impact ionization and charge exchange reactions producing an N+ torus of 1-4 keV suprathermal ions centered on Titan's orbital position. We will show Voyager plasma observations that demonstrate presence of a suprathermal ion component within Saturn's outer magnetosphere. The Voyager LECP data also reported the presence of inward diffusing energetic ions from the outer magnetosphere of Saturn, which could have an N+ contribution. If so, when one conserves the first and second adiabatic invariant the N+ ions will have energies in excess of 100 keV at Dione's L shell and greater than 400 keV at Enceladus' L shell. Energetic charged particle radial diffusion coefficients are also used to constrain the model results. But, one must also consider the solar wind as another important source of keV ions, in the form of protons and alpha particles, for Saturn's outer magnetosphere. Initial estimates indicate that a solar wind source could dominate in the outer magnetosphere, but various required parameters for this estimate are highly uncertain and will have to await Cassini results for confirmation. We show that satellite sweeping and charged particle precipitation within the middle and outer magnetosphere will tend to enrich N+ ions relative to protons within Saturn's inner magnetosphere as they diffuse radially inward for radial diffusion coefficients that do not violate observations. Charge exchange reactions within the inner magnetosphere can be an important loss mechanism for O+ ions, but to a lesser degree for N+ ions. Initial LECP results using composition data at energies greater than 200 keV/nucl., showed that heavy ions within Saturn's inner magnetosphere dominated over protons, but that contrary to original suggestions that these ions were O+ , we now argue that they are instead N+ ions. With energetic N+ ions bombarding the icy satellite surfaces chemical reactions can occur at the end of the ion tracks and produce nitrogen oxides or other nitrogen containing molecules such that the radiology within the icy surfaces is driven by the impacting energetic nitrogen ions. These can accumulate over the lifetime of the Saturn system.

Surface contamination on LDEF exposed materials

NASA Technical Reports Server (NTRS)

Hemminger, Carol S.

1992-01-01

X-ray photoelectron spectroscopy (XPS) has been used to study the surface composition and chemistry of Long Duration Exposure Facility (LDEF) exposed materials including silvered Teflon (Ag/FEP), Kapton, S13GLO paint, quartz crystal monitors (QCM's), carbon fiber/organic matrix composites, and carbon fiber/Al Alloy composites. In each set of samples, silicones were the major contributors to the molecular film accumulated on the LDEF exposed surfaces. All surfaces analyzed have been contaminated with Si, O, and C; most have low levels (less than 1 atom percent) of N, S, and F. Occasionally observed contaminants included Cl, Na, K, P, and various metals. Orange/brown discoloration observed near vent slots in some Ag/FEP blankets were higher in carbon, sulfur, and nitrogen relative to other contamination types. The source of contamination has not been identified, but amine/amide functionalities were detected. It is probable that this same source of contamination account for the low levels of sulfur and nitrogen observed on most LDEF exposed surfaces. XPS, which probes 50 to 100 A in depth, detected the major sample components underneath the contaminant film in every analysis. This probably indicates that the contaminant overlayer is patchy, with significant areas covered by less that 100 A of molecular film. Energy dispersive x-ray spectroscopy (EDS) of LDEF exposed surfaces during secondary electron microscopy (SEM) of the samples confirmed contamination of the surfaces with Si and O. In general, particulates were not observed to develop from the contaminant overlayer on the exposed LDEF material surfaces. However, many SiO2 submicron particles were seen on a masked edge of an Ag/FEP blanket. In some cases such as the carbon fiber/organic matrix composites, interpretation of the contamination data was hindered by the lack of good laboratory controls. Examination of laboratory controls for the carbon fiber/Al alloy composites showed that preflight contamination was the most significant factor for all the contaminants generally detected at less than 1 atom percent, or detected only occasionally (i.e., all but Si, O, and C). Flight control surfaces, including sample backsides not exposed to space radiation or atomic oxygen flux, have accumulated some contamination on flight (compared to laboratory controls), but experimentally, the LDEF exposed surface contamination levels are generally higher for the contaminants Si and O. For most materials analyzed, Si contamination levels were higher on the leading edge surfaces than on the trailing edge surfaces. This was true even for the composite samples where considerable atomic oxygen erosion of the leading edge surfaces was observed by SEM. It is probable that the return flux associated with atmospheric backscatter resulted in enhanced deposition of silicones and other contaminants on the leading edge flight surfaces relative to the trailing edge. Although the Si concentration data suggested greater on-flight deposition of contaminants on the leading edge surfaces, the XPS analyses did not conclusively show different relative total thicknesses of flight deposited contamination for leading and trailing edge surfaces. It is possible that atomic oxygen reactions on the leading edge resulted in greater volatilization of the carbon component of the deposited silicones, effectively 'thinning' the leading edge deposited overlayer. Unlike other materials, exposed polymers such as Kapton and FEP-type Teflon had very low contamination on the leading edge surfaces. SEM evidence showed that undercutting of the contaminant overlayer and damaged polymer layers occurred during atomic oxygen erosion, which would enhance loss of material from the exposed surface.

On NMR prediction of the effectiveness of p-phenylenediamine antioxidants

NASA Astrophysics Data System (ADS)

Puškárová, Ingrid; Šoral, Michal; Breza, Martin

2015-10-01

NMR shifts of N-phenyl-N‧-alkyl-p-phenylenediamines (PPD) in DMSO have been measured as well as evaluated by B3LYP calculations. According to Simon et al. Molar Antioxidant Effectiveness (AEM) of PPD antioxidants depends on the bond strength of hydrogens to amine nitrogens between aromatic rings (NA), to the side aliphatic chain nitrogens (NB) and to its neighboring tertiary carbon atoms (CT). AEM increases with NMR shifts of HA, HB, NA and probably also of CT atoms whereas NMR shifts of NB atoms exhibit a reverse trend. This is very surprising because similar reactions at A and B sites are supposed.

Direct asymmetric N-specific reaction of nitrosobenzene with aldehydes catalyzed by a chiral primary amine-based organocatalyst.

PubMed

Qin, Long; Li, Lei; Yi, Lei; Da, Chao-Shan; Zhou, Yi-Feng

2011-08-01

Nitroso compounds have two reactive nitrogen and oxygen atoms. It is interesting and important to perform a nitrogen or oxygen selective reaction with interesting substrates. These atom specific reactions are crucial to specifically synthesis of specific compounds. An enantioselective N-specific reaction of nitrosobenzene with unmodified aldehydes was successfully achieved catalyzed first by a variety of primary amine-based organocatalysts with higher yield and enantioselectivity. The bulkier substituted groups of the organocatalyst and two hydrogen bonds from the organocatalyst and the oxygen atom of nitrosobenzene make the reaction preferentially N-specific and predominantly afford R products. Copyright © 2011 Wiley-Liss, Inc.

Microtesla SABRE enables 10% nitrogen-15 nuclear spin polarization.

PubMed

Theis, Thomas; Truong, Milton L; Coffey, Aaron M; Shchepin, Roman V; Waddell, Kevin W; Shi, Fan; Goodson, Boyd M; Warren, Warren S; Chekmenev, Eduard Y

2015-02-04

Parahydrogen is demonstrated to efficiently transfer its nuclear spin hyperpolarization to nitrogen-15 in pyridine and nicotinamide (vitamin B(3) amide) by conducting "signal amplification by reversible exchange" (SABRE) at microtesla fields within a magnetic shield. Following transfer of the sample from the magnetic shield chamber to a conventional NMR spectrometer, the (15)N NMR signals for these molecules are enhanced by ∼30,000- and ∼20,000-fold at 9.4 T, corresponding to ∼10% and ∼7% nuclear spin polarization, respectively. This method, dubbed "SABRE in shield enables alignment transfer to heteronuclei" or "SABRE-SHEATH", promises to be a simple, cost-effective way to hyperpolarize heteronuclei. It may be particularly useful for in vivo applications because of longer hyperpolarization lifetimes, lack of background signal, and facile chemical-shift discrimination of different species.

Microtesla SABRE Enables 10% Nitrogen-15 Nuclear Spin Polarization

PubMed Central

2016-01-01

Parahydrogen is demonstrated to efficiently transfer its nuclear spin hyperpolarization to nitrogen-15 in pyridine and nicotinamide (vitamin B3 amide) by conducting “signal amplification by reversible exchange” (SABRE) at microtesla fields within a magnetic shield. Following transfer of the sample from the magnetic shield chamber to a conventional NMR spectrometer, the 15N NMR signals for these molecules are enhanced by ∼30,000- and ∼20,000-fold at 9.4 T, corresponding to ∼10% and ∼7% nuclear spin polarization, respectively. This method, dubbed “SABRE in shield enables alignment transfer to heteronuclei” or “SABRE-SHEATH”, promises to be a simple, cost-effective way to hyperpolarize heteronuclei. It may be particularly useful for in vivo applications because of longer hyperpolarization lifetimes, lack of background signal, and facile chemical-shift discrimination of different species. PMID:25583142

Synthesis and structural characterization of two half-sandwich nickel(II) complexes with the scorpionate ligands

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

Wang, G.-F., E-mail: wgf1979@126.com, E-mail: s-shuwen@163.com; Zhang, X., E-mail: zhangx@hit.edu.cn; Sun, S.-W.

The synthesis and characterization of two new halfsandwich mononuclear nickel(II) complexes with the scorpionate ligands, [k{sup 3}-N, N',N''-Tp{sup t-Bu}, {sup Me}NiI] (1) and [k{sup 3}-N,N',N''-Tp{sup t-Bu}, {sup Me}NiNO{sub 3}] (2), are reported. These complexes have been fully characterized by elemental analyses and infrared spectra. Their molecular structures were determined by single crystal X-ray diffraction. The nickel(II) ion of complex 1 is in a four-coordinate environment, in which the donor atoms are provided by three nitrogen atoms of a hydrotris(pyrazolyl) borate ligand and one iodide atom, while that of complex 2 is in a five-coordinate environment with three nitrogen atoms frommore » a hydrotris(pyrazolyl)borate ligand and two oxygen atoms from a nitrate ion.« less

Slip-additive migration, surface morphology, and performance on injection moulded high-density polyethylene closures.

PubMed

Dulal, Nabeen; Shanks, Robert; Gengenbach, Thomas; Gill, Harsharn; Chalmers, David; Adhikari, Benu; Pardo Martinez, Isaac

2017-11-01

The amount and distribution of slip agents, erucamide, and behenamide, on the surface of high-density polyethene, is determined by integral characteristics of slip agent structure and polymer morphology. A suite of surface analysis techniques was applied to correlate physicochemical properties with slip-additive migration behaviour and their surface morphology. The migration, surface morphology and physicochemical properties of the slip additives, crystallinity and orientation of polyethene spherulites and interaction between slip additives and high-density polyethene influence the surface characteristics. The high-density polyethene closures were produced with erucamide and behenamide separately and stored until they produced required torque. Surface composition was determined employing spectroscopy and gas chromatography. The distribution of additives was observed under optical, scanning electron and atomic force microscopes. The surface energy, crystallinity and application torque were measured using contact angle, differential scanning calorimeter and a torque force tester respectively. Each slip additive produced a characteristic amide peak at 1645cm -1 in infrared spectroscopy and peaks of oxygen and nitrogen in X-ray photoelectron spectroscopy, suggesting their presence on the surface. The erucamide produced placoid scale-like structures and behenamide formed denticulate structures. The surface erucamide and behenamide responsible for reducing the torque was found to be 15.7µg/cm 2 and 1.7µg/cm 2 . Copyright © 2017 Elsevier Inc. All rights reserved.

Surface chemical study on the covalent attachment of hydroxypropyltrimethyl ammonium chloride chitosan to titanium surfaces

NASA Astrophysics Data System (ADS)

Xu, Xiaofen; Wang, Ling; Guo, Shengrong; Lei, Lei; Tang, Tingting

2011-10-01

An anti-microbial and bioactive coating could not only reduce the probability of infection related to titanium implants but also support the growth of surrounding osteogenic cells. Our previous study has showed that hydroxypropyltrimethyl ammonium chloride chitosan (HACC) with a DS (degrees of substitution) of 18% had improved solubility and significantly higher antibacterial activities against three bacteria which were usually associated with infections in orthopaedics. In the current study, HACC with a DS of 18% coating was bonded to titanium surface by a three-step process. The titanium surface after each individual reaction step was analyzed by X-ray photoelectron spectroscopy (XPS) and attenuated total reflection (ATR) of Fourier-transformed infrared (FT-IR) spectroscopy. The XPS results demonstrated that there were great changes in the atomic ratios of C/Ti, O/Ti, and N/Ti after each reaction step. The XPS high resolution and corresponding devolution spectra of carbon, oxygen, nitrogen, and titanium were also in good coordination with the anticipated reaction steps. Additionally, the absorption bands around 3365 cm -1 (-OH vibration), 1664 cm -1 (Amide I), 1165 cm -1 ( νas, C-O-C bridge), and the broad absorption bands between 958 cm -1 and 1155 cm -1 (skeletal vibrations involving the C-O stretching of saccharide structure of HACC) verified that HACC was successfully attached to titanium surface.

Crystal structures of three 3,4,5-tri­meth­oxy­benzamide-based derivatives

PubMed Central

Gomes, Ligia R.; Low, John Nicolson; Oliveira, Catarina; Cagide, Fernando; Borges, Fernanda

2016-01-01

The crystal structures of three benzamide derivatives, viz. N-(6-hy­droxy­hex­yl)-3,4,5-tri­meth­oxy­benzamide, C16H25NO5, (1), N-(6-anilinohex­yl)-3,4,5-tri­meth­oxy­benzamide, C22H30N2O4, (2), and N-(6,6-di­eth­oxy­hex­yl)-3,4,5-tri­meth­oxy­benzamide, C20H33NO6, (3), are described. These compounds differ only in the substituent at the end of the hexyl chain and the nature of these substituents determines the differences in hydrogen bonding between the mol­ecules. In each mol­ecule, the m-meth­oxy substituents are virtually coplanar with the benzyl ring, while the p-meth­oxy substituent is almost perpendicular. The carbonyl O atom of the amide rotamer is trans related with the amidic H atom. In each structure, the benzamide N—H donor group and O acceptor atoms link the mol­ecules into C(4) chains. In 1, a terminal –OH group links the mol­ecules into a C(3) chain and the combined effect of the C(4) and C(3) chains is a ribbon made up of screw related R 2 2(17) rings in which the ⋯O—H⋯ chain lies in the centre of the ribbon and the tri­meth­oxy­benzyl groups forms the edges. In 2, the combination of the benzamide C(4) chain and the hydrogen bond formed by the terminal N—H group to an O atom of the 4-meth­oxy group link the mol­ecules into a chain of R 2 2(17) rings. In 3, the mol­ecules are linked only by C(4) chains. PMID:27308017

Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins.

PubMed

Zhang, Yu-Juan; Yang, Chun-Lin; Hao, You-Jin; Li, Ying; Chen, Bin; Wen, Jian-Fan

2014-01-25

To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution. Copyright © 2013 Elsevier B.V. All rights reserved.

The π-Electron Delocalization in 2-Oxazolines Revisited: Quantification and Comparison with Its Analogue in Esters

PubMed Central

Fimberger, Martin; Luef, Klaus P.; Payerl, Claudia; Fischer, Roland C.; Stelzer, Franz; Kállay, Mihály; Wiesbrock, Frank

2015-01-01

The single crystal X-ray analysis of the ester-functionalized 2-oxazoline, methyl 3-(4,5-dihydrooxazol-2-yl)propanoate, revealed π-electron delocalization along the N–C–O segment in the 2-oxazoline pentacycle to significant extent, which is comparable to its counterpart along the O–C–O segment in the ester. Quantum chemical calculations based on the experimental X-ray geometry of the molecule supported the conjecture that the N–C–O segment has a delocalized electronic structure similar to an ester group. The calculated bond orders were 1.97 and 1.10 for the N=C and C–O bonds, and the computed partial charges for the nitrogen and oxygen atoms of −0.43 and −0.44 were almost identical. In the ester group, the bond orders were 1.94 and 1.18 for the C–O bonds, while the partial charges of the oxygen atom are −0.49 and −0.41, which demonstrates the similar electronic structure of the N–C–O and O–C–O segments. In 2-oxazolines, despite the higher electronegativity of the oxygen atom (compared to the nitrogen atom), the charges of the hetero atoms oxygen and nitrogen are equalized due to the delocalization, and it also means that a cationic attack on the nitrogen is possible, enabling regioselectivity during the initiation of the cationic ring-opening polymerization of 2-oxazoline monomers, which is a prerequisite for the synthesis of materials with well-defined structures. PMID:28184258

Curare-Like Activity of Mono-Quaternary Salts Containing Adamantyl Residue at the Nitrogen Atom

DTIC Science & Technology

As shown in previous works, mono-quaternary salts of alkamine esters of benzoic and cinnamic acids types and exhibit a pronounced curare like action...A series of methiodides of alkamine esters of benzoic and cinnamic acids were synthesized, containing at the quaternary nitrogen atom a 1-adamantyl...adamantyl causes a change of the substance’s mechanism of action, this applying both to the benzoic acid derivatives and to the cinnamic acid derivatives

CuO nanoparticles catalyzed C-N, C-O, and C-S cross-coupling reactions: scope and mechanism.

PubMed

Jammi, Suribabu; Sakthivel, Sekarpandi; Rout, Laxmidhar; Mukherjee, Tathagata; Mandal, Santu; Mitra, Raja; Saha, Prasenjit; Punniyamurthy, Tharmalingam

2009-03-06

CuO nanoparticles have been studied for C-N, C-O, and C-S bond formations via cross-coupling reactions of nitrogen, oxygen, and sulfur nucleophiles with aryl halides. Amides, amines, imidazoles, phenols, alcohols and thiols undergo reactions with aryl iodides in the presence of a base such as KOH, Cs(2)CO(3), and K(2)CO(3) at moderate temperature. The procedure is simple, general, ligand-free, and efficient to afford the cross-coupled products in high yield.

Interaction and dynamics of (alkylamide + electrolyte) deep eutectics: Dependence on alkyl chain-length, temperature, and anion identity

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

Guchhait, Biswajit; Das, Suman; Daschakraborty, Snehasis

Here we investigate the solute-medium interaction and solute-centered dynamics in (RCONH{sub 2} + LiX) deep eutectics (DEs) via carrying out time-resolved fluorescence measurements and all-atom molecular dynamics simulations at various temperatures. Alkylamides (RCONH{sub 2}) considered are acetamide (CH{sub 3}CONH{sub 2}), propionamide (CH{sub 3}CH{sub 2}CONH{sub 2}), and butyramide (CH{sub 3}CH{sub 2}CH{sub 2}CONH{sub 2}); the electrolytes (LiX) are lithium perchlorate (LiClO{sub 4}), lithium bromide (LiBr), and lithium nitrate (LiNO{sub 3}). Differential scanning calorimetric measurements reveal glass transition temperatures (T{sub g}) of these DEs are ∼195 K and show a very weak dependence on alkyl chain-length and electrolyte identity. Time-resolved and steady statemore » fluorescence measurements with these DEs have been carried out at six-to-nine different temperatures that are ∼100–150 K above their individual T{sub g}s. Four different solute probes providing a good spread of fluorescence lifetimes have been employed in steady state measurements, revealing strong excitation wavelength dependence of probe fluorescence emission peak frequencies. Extent of this dependence, which shows sensitivity to anion identity, has been found to increase with increase of amide chain-length and decrease of probe lifetime. Time-resolved measurements reveal strong fractional power dependence of average rates for solute solvation and rotation with fraction power being relatively smaller (stronger viscosity decoupling) for DEs containing longer amide and larger (weaker decoupling) for DEs containing perchlorate anion. Representative all-atom molecular dynamics simulations of (CH{sub 3}CONH{sub 2} + LiX) DEs at different temperatures reveal strongly stretched exponential relaxation of wavevector dependent acetamide self dynamic structure factor with time constants dependent both on ion identity and temperature, providing justification for explaining the fluorescence results in terms of temporal heterogeneity and amide clustering in these multi-component melts.« less

Study of nitrogen flowing afterglow with mercury vapor injection

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

Mazánková, V., E-mail: mazankova@fch.vutbr.cz; Krčma, F.; Trunec, D.

2014-10-21

The reaction kinetics in nitrogen flowing afterglow with mercury vapor addition was studied by optical emission spectroscopy. The DC flowing post-discharge in pure nitrogen was created in a quartz tube at the total gas pressure of 1000 Pa and discharge power of 130 W. The mercury vapors were added into the afterglow at the distance of 30 cm behind the active discharge. The optical emission spectra were measured along the flow tube. Three nitrogen spectral systems – the first positive, the second positive, and the first negative, and after the mercury vapor addition also the mercury resonance line at 254more » nm in the spectrum of the second order were identified. The measurement of the spatial dependence of mercury line intensity showed very slow decay of its intensity and the decay rate did not depend on the mercury concentration. In order to explain this behavior, a kinetic model for the reaction in afterglow was developed. This model showed that the state Hg(6 {sup 3}P{sub 1}), which is the upper state of mercury UV resonance line at 254 nm, is produced by the excitation transfer from nitrogen N{sub 2}(A{sup 3}Σ{sup +}{sub u}) metastables to mercury atoms. However, the N{sub 2}(A{sup 3}Σ{sup +}{sub u}) metastables are also produced by the reactions following the N atom recombination, and this limits the decay of N{sub 2}(A{sup 3}Σ{sup +}{sub u}) metastable concentration and results in very slow decay of mercury resonance line intensity. It was found that N atoms are the most important particles in this late nitrogen afterglow, their volume recombination starts a chain of reactions which produce excited states of molecular nitrogen. In order to explain the decrease of N atom concentration, it was also necessary to include the surface recombination of N atoms to the model. The surface recombination was considered as a first order reaction and wall recombination probability γ = (1.35 ± 0.04) × 10{sup −6} was determined from the experimental data. Also sensitivity analysis was applied for the analysis of kinetic model in order to reveal the main control parameters in the model.« less

Mg2+ ions: do they bind to nucleobase nitrogens?

PubMed Central

Leonarski, Filip; D'Ascenzo, Luigi; Auffinger, Pascal

2017-01-01

Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg2+ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg2+ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na+, K+, NH4+ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg2+ ions do not bind to N7 atoms. Without much of a surprise, Mn2+, Zn2+ and Cd2+, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn2+ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments. PMID:27923930

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

Designer synthetic media for studying microbial-catalyzed biofuel production

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

Tang, Xiaoyu; da Costa Sousa, Leonardo; Jin, Mingjie

Background: The fermentation inhibition of yeast or bacteria by lignocellulose-derived degradation products, during hexose/pentose co-fermentation, is a major bottleneck for cost-effective lignocellulosic biorefineries. To engineer microbial strains for improved performance, it is critical to understand the mechanisms of inhibition that affect fermentative organisms in the presence of major components of a lignocellulosic hydrolysate. The development of a synthetic lignocellulosic hydrolysate (SH) media with a composition similar to the actual biomass hydrolysate will be an important advancement to facilitate these studies. In this work, we characterized the nutrients and plant-derived decomposition products present in AFEX™ pretreated corn stover hydrolysate (ACH). Themore » SH was formulated based on the ACH composition and was further used to evaluate the inhibitory effects of various families of decomposition products during Saccharomyces cerevisiae 424A (LNH-ST) fermentation. Results: The ACH contained high levels of nitrogenous compounds, notably amides, pyrazines, and imidazoles. In contrast, a relatively low content of furans and aromatic and aliphatic acids were found in the ACH. Though most of the families of decomposition products were inhibitory to xylose fermentation, due to their abundance, the nitrogenous compounds showed the most inhibition. From these compounds, amides (products of the ammonolysis reaction) contributed the most to the reduction of the fermentation performance. However, this result is associated to a concentration effect, as the corresponding carboxylic acids (products of hydrolysis) promoted greater inhibition when present at the same molar concentration as the amides. Due to its complexity, the formulated SH did not perfectly match the fermentation profile of the actual hydrolysate, especially the growth curve. However, the SH formulation was effective for studying the inhibitory effect of various compounds on yeast fermentation. Conclusions: The formulation of SHs is an important advancement for future multi-omics studies and for better understanding the mechanisms of fermentation inhibition in lignocellulosic hydrolysates. The SH formulated in this work was instrumental for defining the most important inhibitors in the ACH. Major AFEX decomposition products are less inhibitory to yeast fermentation than the products of dilute acid or steam explosion pretreatments; thus, ACH is readily fermentable by yeast without any detoxification.« less

Designer synthetic media for studying microbial-catalyzed biofuel production

DOE PAGES

Tang, Xiaoyu; da Costa Sousa, Leonardo; Jin, Mingjie; ...

2015-01-01

Background: The fermentation inhibition of yeast or bacteria by lignocellulose-derived degradation products, during hexose/pentose co-fermentation, is a major bottleneck for cost-effective lignocellulosic biorefineries. To engineer microbial strains for improved performance, it is critical to understand the mechanisms of inhibition that affect fermentative organisms in the presence of major components of a lignocellulosic hydrolysate. The development of a synthetic lignocellulosic hydrolysate (SH) media with a composition similar to the actual biomass hydrolysate will be an important advancement to facilitate these studies. In this work, we characterized the nutrients and plant-derived decomposition products present in AFEX™ pretreated corn stover hydrolysate (ACH). Themore » SH was formulated based on the ACH composition and was further used to evaluate the inhibitory effects of various families of decomposition products during Saccharomyces cerevisiae 424A (LNH-ST) fermentation. Results: The ACH contained high levels of nitrogenous compounds, notably amides, pyrazines, and imidazoles. In contrast, a relatively low content of furans and aromatic and aliphatic acids were found in the ACH. Though most of the families of decomposition products were inhibitory to xylose fermentation, due to their abundance, the nitrogenous compounds showed the most inhibition. From these compounds, amides (products of the ammonolysis reaction) contributed the most to the reduction of the fermentation performance. However, this result is associated to a concentration effect, as the corresponding carboxylic acids (products of hydrolysis) promoted greater inhibition when present at the same molar concentration as the amides. Due to its complexity, the formulated SH did not perfectly match the fermentation profile of the actual hydrolysate, especially the growth curve. However, the SH formulation was effective for studying the inhibitory effect of various compounds on yeast fermentation. Conclusions: The formulation of SHs is an important advancement for future multi-omics studies and for better understanding the mechanisms of fermentation inhibition in lignocellulosic hydrolysates. The SH formulated in this work was instrumental for defining the most important inhibitors in the ACH. Major AFEX decomposition products are less inhibitory to yeast fermentation than the products of dilute acid or steam explosion pretreatments; thus, ACH is readily fermentable by yeast without any detoxification.« less

A large atomic chlorine source inferred from mid-continental reactive nitrogen chemistry.

PubMed

Thornton, Joel A; Kercher, James P; Riedel, Theran P; Wagner, Nicholas L; Cozic, Julie; Holloway, John S; Dubé, William P; Wolfe, Glenn M; Quinn, Patricia K; Middlebrook, Ann M; Alexander, Becky; Brown, Steven S

2010-03-11

Halogen atoms and oxides are highly reactive and can profoundly affect atmospheric composition. Chlorine atoms can decrease the lifetimes of gaseous elemental mercury and hydrocarbons such as the greenhouse gas methane. Chlorine atoms also influence cycles that catalytically destroy or produce tropospheric ozone, a greenhouse gas potentially toxic to plant and animal life. Conversion of inorganic chloride into gaseous chlorine atom precursors within the troposphere is generally considered a coastal or marine air phenomenon. Here we report mid-continental observations of the chlorine atom precursor nitryl chloride at a distance of 1,400 km from the nearest coastline. We observe persistent and significant nitryl chloride production relative to the consumption of its nitrogen oxide precursors. Comparison of these findings to model predictions based on aerosol and precipitation composition data from long-term monitoring networks suggests nitryl chloride production in the contiguous USA alone is at a level similar to previous global estimates for coastal and marine regions. We also suggest that a significant fraction of tropospheric chlorine atoms may arise directly from anthropogenic pollutants.

Imidazoline phosphonic acids

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

Redmore, D.

1972-07-04

Nitrogen-heterocyclic phosphonic acids and derivatives are characterized by aminomethyl (or substituted methyl) phosphonic acids or derivatives thereof bonded directly or indirectly, i.e., through a N-side chain to the nitrogen atom in the heterocyclic ring, for example those containing in the molecule at least one of the following units: ..pi..Equation/sup -/ where represents a heterocyclic ring having a nitrogen atom on the ring; -R'N- represents an amino- terminated side chain attached directly to the ring nitrogen (which side chain may or may not be present); and ..pi..Equation/sup -/ represents a methyl (or substituted methyl) phosphonic acid group where M is hydrogen,more » an alcohol or a salt moiety, and X and Y are hydrogen or a substituted group such as alkyl, aryl, etc., of which one or 2 units may be present depending on the available nitrogen bonded by hydrogens, and to uses for these compounds, for example, as scale inhibitors, corrosion inhibitors, etc. (5 claims)« less

Anhydrous 1:1 proton-transfer compounds of isonipecotamide with picric acid and 3,5-dinitrosalicylic acid: 4-carbamoylpiperidinium 2,4,6-trinitrophenolate and two polymorphs of 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate.

PubMed

Smith, Graham; Wermuth, Urs D

2010-12-01

The structures of the anhydrous 1:1 proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with picric acid and 3,5-dinitrosalicylic acid, namely 4-carbamoylpiperidinium 2,4,6-trinitrophenolate, C(6)H(13)N(2)O(+)·C(6)H(2)N(3)O(7)(-), (I), and 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate [two forms of which were found, the monoclinic α-polymorph, (II), and the triclinic β-polymorph, (III)], C(6)H(13)N(2)O(+)·C(7)H(3)N(2)O(7)(-), have been determined at 200 K. All three compounds form hydrogen-bonded structures, viz. one-dimensional in (II), two-dimensional in (I) and three-dimensional in (III). In (I), the cations form centrosymmetric cyclic head-to-tail hydrogen-bonded homodimers [graph set R(2)(2)(14)] through lateral duplex piperidinium-amide N-H...O interactions. These dimers are extended into a two-dimensional network structure through further interactions with phenolate and nitro O-atom acceptors, including a direct symmetric piperidinium-phenol/nitro N-H...O,O cation-anion association [graph set R(1)(2)(6)]. The monoclinic polymorph, (II), has a similar R(1)(2)(6) cation-anion hydrogen-bonding interaction to (I) but with an additional conjoint symmetrical R(1)(2)(4) interaction as well as head-to-tail piperidinium-amide N-H...O,O hydrogen bonds and amide-carboxyl N-H...O hydrogen bonds, giving a network structure which includes large R(4)(3)(20) rings. The hydrogen bonding in the triclinic polymorph, (III), is markedly different from that of monoclinic (II). The asymmetric unit contains two independent cation-anion pairs which associate through cyclic piperidinium-carboxyl N-H...O,O' interactions [graph set R(1)(2)(4)]. The cations also show the zigzag head-to-tail piperidinium-amide N-H...O hydrogen-bonded chain substructures found in (II), but in addition feature amide-nitro and amide-phenolate N-H...O associations. As well, there is a centrosymmetric double-amide N-H...O(carboxyl) bridged bis(cation-anion) ring system [graph set R(4)(2)(8)] in the three-dimensional framework. The structures reported here demonstrate the utility of the isonipecotamide cation as a synthon with previously unrecognized potential for structure assembly applications. Furthermore, the structures of the two polymorphic 3,5-dinitrosalicylic acid salts show an unusual dissimilarity in hydrogen-bonding characteristics, considering that both were obtained from identical solvent systems.

Lattice Gas Model Based Optimization of Plasma-Surface Processes for GaN-Based Compound Growth

NASA Astrophysics Data System (ADS)

Nonokawa, Kiyohide; Suzuki, Takuma; Kitamori, Kazutaka; Sawada, Takayuki

2001-10-01

Progress of the epitaxial growth technique for GaN-based compounds makes these materials attractive for applications in high temperature/high-power electronic devices as well as in short-wavelength optoelectronic devices. For MBE growth of GaN epilayer, atomic nitrogen is usually supplied from ECR-plasma while atomic Ga is supplied from conventional K-cell. To grow high-quality epilayer, fundamental knowledge of the detailed atomic process, such as adsorption, surface migration, incorporation, desorption and so forth, is required. We have studied the influence of growth conditions on the flatness of the growth front surface and the growth rate using Monte Carlo simulation based on the lattice gas model. Under the fixed Ga flux condition, the lower the nitrogen flux and/or the higher the growth temperature, the better the flatness of the front surface at the sacrifice of the growth rate of the epilayer. When the nitrogen flux is increased, the growth rate reaches saturation value determined from the Ga flux. At a fixed growth temperature, increasing of nitrogen to Ga flux ratio results in rough surface owing to 3-dimensional island formation. Other characteristics of MBE-GaN growth using ECR-plasma can be well reproduced.

Crystal structure of di-methyl-formamidium bis-(tri-fluoro-methane-sulfon-yl)amide: an ionic liquid.

PubMed

Cardenas, Allan Jay P; O'Hagan, Molly

2016-09-01

At 100 K, the title mol-ecular salt, C 3 H 8 NO + ·C 2 F 6 NO 4 S 2 - , has ortho-rhom-bic ( P 2 1 2 1 2 1 ) symmetry; the amino H atom of bis-(tri-fluoro-methane-sulfon-yl)amine (HNTf 2 ) was transferred to the basic O atom of di-methyl-formamide (DMF) when the ionic liquid components were mixed. The structure displays an O-H⋯N hydrogen bond, which links the cation to the anion, which is reinforced by a non-conventional C-H⋯O inter-action, generating an R 2 2 (7) loop. A further very weak C-H⋯O inter-action generates an [001] chain.

Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations.

PubMed

Shi, Qicun; Meroueh, Samy O; Fisher, Jed F; Mobashery, Shahriar

2008-07-23

Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2 kcal x mol(-1) greater than the barrier (22 kcal x mol(-1)) for the formation of the tetrahedral species in acylation. The potential-energy surface for the collapse of the deacylation tetrahedral species gives a 24 kcal x mol(-1) higher energy species for the product, signifying that the complex would readily reorganize and pave the way for the expulsion of the product of the reaction from the active site and the regeneration of the catalyst. These computational data dovetail with the knowledge on the reaction from experimental approaches.

Reactivity of Dimeric Tetrazirconium(IV) Wells-Dawson Polyoxometalate toward Dipeptide Hydrolysis Studied by a Combined Experimental and Density Functional Theory Approach.

PubMed

Ly, Hong Giang T; Mihaylov, Tzvetan; Absillis, Gregory; Pierloot, Kristine; Parac-Vogt, Tatjana N

2015-12-07

Detailed kinetic studies on the hydrolysis of glycylglycine (Gly-Gly) in the presence of the dimeric tetrazirconium(IV)-substituted Wells-Dawson-type polyoxometalate Na14[Zr4(P2W16O59)2(μ3-O)2(OH)2(H2O)4] · 57H2O (1) were performed by a combination of (1)H, (13)C, and (31)P NMR spectroscopies. The catalyst was shown to be stable under a broad range of reaction conditions. The effect of pD on the hydrolysis of Gly-Gly showed a bell-shaped profile with the fastest hydrolysis observed at pD 7.4. The observed rate constant for the hydrolysis of Gly-Gly at pD 7.4 and 60 °C was 4.67 × 10(-7) s(-1), representing a significant acceleration as compared to the uncatalyzed reaction. (13)C NMR data were indicative for coordination of Gly-Gly to 1 via its amide oxygen and amine nitrogen atoms, resulting in a hydrolytically active complex. Importantly, the effective hydrolysis of a series of Gly-X dipeptides with different X side chain amino acids in the presence of 1 was achieved, and the observed rate constant was shown to be dependent on the volume, chemical nature, and charge of the X amino acid side chain. To give a mechanistic explanation of the observed catalytic hydrolysis of Gly-Gly, a detailed quantum-chemical study was performed. The theoretical results confirmed the nature of the experimentally suggested binding mode in the hydrolytically active complex formed between Gly-Gly and 1. To elucidate the role of 1 in the hydrolytic process, both the uncatalyzed and the polyoxometalate-catalyzed reactions were examined. In the rate-determining step of the uncatalyzed Gly-Gly hydrolysis, a carboxylic oxygen atom abstracts a proton from a solvent water molecule and the nascent OH nucleophile attacks the peptide carbon atom. Analogous general-base activity of the free carboxylic group was found to take place also in the case of polyoxometalate-catalyzed hydrolysis as the main catalytic effect originates from the -C═O···Zr(IV) binding.

The Nitrogen Moieties of Dietary Nonessential Amino Acids Are Distinctively Metabolized in the Gut and Distributed to the Circulation in Rats.

PubMed

Nakamura, Hidehiro; Kawamata, Yasuko; Kuwahara, Tomomi; Sakai, Ryosei

2017-08-01

Background: Although previous growth studies in rodents have indicated the importance of dietary nonessential amino acids (NEAAs) as nitrogen sources, individual NEAAs have different growth-promoting activities. This phenomenon might be attributable to differences in the nitrogen metabolism of individual NEAAs. Objective: The aim of this study was to compare nitrogen metabolism across dietary NEAAs with the use of their 15 N isotopologues. Methods: Male Fischer rats (8 wk old) were given 1.0 g amino acid-defined diets containing either 15 N-labeled glutamate, glutamine (amino or amide), aspartate, alanine, proline, glycine, or serine hourly for 5-6 h. Then, steady-state amino acid concentrations and their 15 N enrichments in the gut and in portal and arterial plasma were measured by an amino acid analyzer and LC tandem mass spectrometry, respectively. Results: The intestinal 15 N distribution and portal-arterial balance of 15 N metabolites indicated that most dietary glutamate nitrogen (>90% of dietary input) was incorporated into various amino acids, including alanine, proline, and citrulline, in the gut. Dietary aspartate nitrogen, alanine nitrogen, and amino nitrogen of glutamine were distributed similarly to other amino acids both in the gut and in the circulation. In contrast, incorporation of the nitrogen moieties of dietary proline, serine, and glycine into other amino acids was less than that of other NEAAs, although interconversion between serine and glycine was very active. Cluster analysis of 15 N enrichment data also indicated that dietary glutamate nitrogen, aspartate nitrogen, alanine nitrogen, and the amino nitrogen of glutamine were distributed similarly to intestinal and circulating amino acids. Further, the analysis revealed close relations between intestinal and arterial 15 N enrichment for each amino acid. The steady-state 15 N enrichment of arterial amino acids indicated that substantial amounts of circulating amino acid nitrogen are derived from dietary NEAAs. Conclusions: The present results revealed similarities and differences among NEAAs in terms of their intestinal nitrogen metabolism in rats and indicated substantial entry of dietary NEAA nitrogen into circulating amino acid nitrogen, presumably primarily through metabolism in the gut. © 2017 American Society for Nutrition.

Spatial Concentrations of Silicon Atoms in RF Discharges of Silane.

DTIC Science & Technology

1985-02-18

regions. These profiles were much more sensitive to plasma chemistry changes than profiles obtained from plasma emission. Experiments with nitrogen...addition demonstrated significant changes in the silicon atom profiles near the sheath boundary. Originator supplied keywords include: rf discharge, silane, plasma chemistry , silicon atom, laser-induced fluorescence.

Theoretical study of the alkaline hydrolysis of an aza-β-lactam derivative of clavulanic acid

NASA Astrophysics Data System (ADS)

Garcías, Rafael C.; Coll, Miguel; Donoso, Josefa; Muñoz, Francisco

2003-04-01

DFT calculations based on the hybrid functional B3LYP/6-31+G * were used to study the alkaline hydrolysis of an aza-clavulanic acid, which results from the substitution of the carbon atom at position 6 in clavulanic acid by a nitrogen atom. The presence of the nitrogen atom endows the compound with special properties; in fact, once formed, the tetrahedral intermediate can evolve with cleavage of the N 4-C 7 or N 6-C 7 bond, which obviously leads to different reaction products. These differential bond cleavages may play a central role in the inactivation of β-lactamases, so the compound may be a powerful inactivator of these enzymes.

Mass spectrometric dereplication of nitrogen-containing constituents of black cohosh (Cimicifuga racemosa L.)

PubMed Central

Nikolić, Dejan; Gödecke, Tanja; Chen, Shao-Nong; White, Jerry; Lankin, David C.; Pauli, Guido F.; van Breemen, Richard B.

2011-01-01

Black cohosh preparations are popular dietary supplements among women seeking alternative treatments for menopausal complaints. For decades, triterpene glycosides and phenolic acids have dominated the phytochemical and biomedical research on this plant. In this study, we provide evidence that black cohosh contains an unexpected and highly diverse group of secondary nitrogenous metabolites previously unknown to exist in this plant. Using a dereplication approach that combines accurate mass measurements, database searches and general knowledge of biosynthetic pathways of natural products, we identified or tentatively identified 73 nitrogen-containing metabolites, many of which are new natural products. The identified compounds belong to several structural groups including alkaloids, amides or esters of hydroxycinnamic acids and betains. Among the alkaloids, several classes such as guanidino alkaloids, isoquinolines and β-carbolines were identified. Fragmentation patterns for major compound classes are discussed, which provides a framework for the discovery of these compounds from other sources. Identification of alkaloids as a well-known group of bioactive natural products represents an important advance in better understanding of the pharmacological profile of black cohosh. PMID:22178683

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). Copyright © 2014 John Wiley & Sons, Ltd.

Synthesis of phosphinoferrocene amides and thioamides from carbamoyl chlorides and the structural chemistry of Group 11 metal complexes with these mixed-donor ligands.

PubMed

Fernandes, Tiago A; Solařová, Hana; Císařová, Ivana; Uhlík, Filip; Štícha, Martin; Štěpnička, Petr

2015-02-21

The reaction of in situ generated 1'-(diphenylphosphino)-1-lithioferrocene with carbamoyl chlorides, ClC(E)NMe2, affords the corresponding (thio)amides, Ph2PfcC(E)NMe2 (E = O (), S (); fc = ferrocene-1,1'-diyl). These compounds as well as their analogues, Ph2PfcC(O)NHMe () and Ph2PfcC(O)NH2 (), prepared from 1'-(diphenylphosphino)ferrocene-1-carboxylic acid (Hdpf) were studied as ligands for the Group 11 metal ions. In the reactions with [Cu(MeCN)4][BF4], the amides give rise to bis-chelate complexes of the type [Cu(L-κ(2)O,P)2][BF4]. Similar products, [Ag(L-κ(2)O,P)2]ClO4, are obtained from silver(i) perchlorate and , or . In contrast, the reaction of AgClO4 with produces a unique molecular dimer [Ag()(ClO4-κO)]2, where the metal centres are bridged by the sulfur atoms of the P,S-chelating thioamides. The reactions of with [AuCl(tht)] (tht = tetrahydrothiophene) afford the expected gold(i)-phosphine complexes, [AuCl(L-κP)], containing uncoordinated (thio)amide moieties. Hemilabile coordination of the phosphinoamide ligands in complexes with the soft Group 11 metal ions is established by the crystal structure of a solvento complex, [Cu(-κ(2)O,P)(-κP)(CHCl3-κCl)][BF4], which was isolated serendipitously during an attempted crystallisation of [Cu(-κ(2)O,P)2][BF4]. All of the compounds are characterised by spectroscopic methods, and the structures of several representatives of both the free phosphinoamides and their complexes are determined by X-ray diffraction analysis and further studied by DFT calculations and cyclic voltammetry.

Point defect weakened thermal contraction in monolayer graphene

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

Zha, Xian-Hu; Department of Physics, University of Science and Technology of China, Hefei; USTC-CityU Joint Advanced Research Centre, Suzhou 215123

We investigate the thermal expansion behaviors of monolayer graphene and three configurations of graphene with point defects, namely the replacement of one carbon atom with a boron or nitrogen atom, or of two neighboring carbon atoms by boron-nitrogen atoms, based on calculations using first-principles density functional theory. It is found that the thermal contraction of monolayer graphene is significantly decreased by point defects. Moreover, the corresponding temperature for negative linear thermal expansion coefficient with the maximum absolute value is reduced. The cause is determined to be point defects that enhance the mechanical strength of graphene and then reduce the amplitudemore » and phonon frequency of the out-of-plane acoustic vibration mode. Such defect weakening of graphene thermal contraction will be useful in nanotechnology to diminish the mismatching or strain between the graphene and its substrate.« less

Paramagnetic Attraction of Impurity-Helium Solids

NASA Technical Reports Server (NTRS)

Bernard, E. P.; Boltnev, R. E.; Khmelenko, V. V.; Lee, D. M.

2003-01-01

Impurity-helium solids are formed when a mixture of impurity and helium gases enters a volume of superfluid helium. Typical choices of impurity gas are hydrogen deuteride, deuterium, nitrogen, neon and argon, or a mixture of these. These solids consist of individual impurity atoms and molecules as well as clusters of impurity atoms and molecules covered with layers of solidified helium. The clusters have an imperfect crystalline structure and diameters ranging up to 90 angstroms, depending somewhat on the choice of impurity. Immediately following formation the clusters aggregate into loosely connected porous solids that are submerged in and completely permeated by the liquid helium. Im-He solids are extremely effective at stabilizing high concentrations of free radicals, which can be introduced by applying a high power RF dis- charge to the impurity gas mixture just before it strikes the super fluid helium. Average concentrations of 10(exp 19) nitrogen atoms/cc and 5 x 10(exp 18) deuterium atoms/cc can be achieved this way. It shows a typical sample formed from a mixture of atomic and molecular hydrogen and deuterium. It shows typical sample formed from atomic and molecular nitrogen. Much of the stability of Im-He solids is attributed to their very large surface area to volume ratio and their permeation by super fluid helium. Heat resulting from a chance meeting and recombination of free radicals is quickly dissipated by the super fluid helium instead of thermally promoting the diffusion of other nearby free radicals.

Atomic Layer Deposition of the Solid Electrolyte LiPON

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

Kozen, Alexander C.; Pearse, Alexander J.; Lin, Chuan -Fu

We demonstrate an atomic layer deposition (ALD) process for the solid electrolyte lithium phosphorousoxynitride (LiPON) using lithium tert-butoxide (LiO tBu), H 2O, trimethylphosphate (TMP), and plasma N 2 ( PN 2) as precursors. We use in-situ spectroscopic ellipsometry to determine growth rates for process optimization to design a rational, quaternary precursor ALD process where only certain substrate–precursor chemical reactions are favorable. We demonstrate via in-situ XPS tunable nitrogen incorporation into the films by variation of the PN 2 dose and find that ALD films over approximately 4.5% nitrogen are amorphous, whereas LiPON ALD films with less than 4.5% nitrogen aremore » polycrystalline. Lastly, we characterize the ionic conductivity of the ALD films as a function of nitrogen content and demonstrate their functionality on a model battery electrode—a Si anode on a Cu current collector.« less

Planar field emitters and high efficiency photocathodes based on ultrananocrystalline diamond

DOEpatents

Sumant, Anirudha V.; Baryshev, Sergey V.; Antipov, Sergey P.

2016-08-16

A method of forming a field emitter comprises disposing a first layer on a substrate. The first layer is seeded with nanodiamond particles. The substrate with the first layer disposed thereon is maintained at a first temperature and a first pressure in a mixture of gases which includes nitrogen. The first layer is exposed to a microwave plasma to form a nitrogen doped ultrananocrystalline diamond film on the first layer, which has a percentage of nitrogen in the range of about 0.05 atom % to about 0.5 atom %. The field emitter has about 10.sup.12 to about 10.sup.14 emitting sites per cm.sup.2. A photocathode can also be formed similarly by forming a nitrogen doped ultrananocrystalline diamond film on a substrate similar to the field emitter, and then hydrogen terminating the film. The photocathode is responsive to near ultraviolet light as well as to visible light.

Planar Field Emitters and High Efficiency Photocathodes Based on Ultrananocrystalline Diamond

NASA Technical Reports Server (NTRS)

Sumant, Anirudha V. (Inventor); Baryshev, Sergey V. (Inventor); Antipov, Sergey P. (Inventor)

2016-01-01

A method of forming a field emitter comprises disposing a first layer on a substrate. The first layer is seeded with nanodiamond particles. The substrate with the first layer disposed thereon is maintained at a first temperature and a first pressure in a mixture of gases which includes nitrogen. The first layer is exposed to a microwave plasma to form a nitrogen doped ultrananocrystalline diamond film on the first layer, which has a percentage of nitrogen in the range of about 0.05 atom % to about 0.5 atom %. The field emitter has about 10.sup.12 to about 10.sup.14 emitting sites per cm.sup.2. A photocathode can also be formed similarly by forming a nitrogen doped ultrananocrystalline diamond film on a substrate similar to the field emitter, and then hydrogen terminating the film. The photocathode is responsive to near ultraviolet light as well as to visible light.

Atomic Layer Deposition of the Solid Electrolyte LiPON

DOE PAGES

Kozen, Alexander C.; Pearse, Alexander J.; Lin, Chuan -Fu; ...

2015-07-09

We demonstrate an atomic layer deposition (ALD) process for the solid electrolyte lithium phosphorousoxynitride (LiPON) using lithium tert-butoxide (LiO tBu), H 2O, trimethylphosphate (TMP), and plasma N 2 ( PN 2) as precursors. We use in-situ spectroscopic ellipsometry to determine growth rates for process optimization to design a rational, quaternary precursor ALD process where only certain substrate–precursor chemical reactions are favorable. We demonstrate via in-situ XPS tunable nitrogen incorporation into the films by variation of the PN 2 dose and find that ALD films over approximately 4.5% nitrogen are amorphous, whereas LiPON ALD films with less than 4.5% nitrogen aremore » polycrystalline. Lastly, we characterize the ionic conductivity of the ALD films as a function of nitrogen content and demonstrate their functionality on a model battery electrode—a Si anode on a Cu current collector.« less

Synthesis of nitrogen- and sulfur-codoped 3D cubic-ordered mesoporous carbon with superior performance in supercapacitors.

PubMed

Zhang, Deyi; Zheng, Liweng; Ma, Ying; Lei, Longyan; Li, Qinglin; Li, Yan; Luo, Heming; Feng, Huixia; Hao, Yuan

2014-02-26

In this contribution, nitrogen- and sulfur-codoped 3D cubic-ordered mesoporous carbon (KNOMC) materials with controlled dopant content (10.0-4.6 atom % for nitrogen and 0.94-0.75 atom % for sulfur) are presented, using KIT-6 as the template and pyrrole as the precursor, and its supercapacitive behavior is also investigated. The presented materials exhibit excellent supercapacitive performance by combining electrical double-layer capacitance and pseudocapacitance as well as the enhanced wettability and improved conductivity generated from the incorporation of nitrogen and sulfur into the framework of carbon materials. The specific capacitance of the presented materials reaches 320 F g(-1) at a current density of 1 A g(-1), which is significantly larger than that of the pristine-ordered mesoporous carbon reported in the literature and can even compete with some metal oxides and conducting polymers.

X-ray photoelectron spectroscopic study of sulfur-nitrogen-fluorine compounds

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

Beach, D.B.; Jolly, W.L.; Mews, R.

1984-11-21

The gas-phase core binding energies of NSF, NSF/sub 3/, and several compounds of the types NSF/sub 2/R and F/sub 2/SNR have been determined. Qualitative interpretation of the data shows that N(p..pi..) ..-->.. S(d..pi..) bonding is probably important in the NSF/sub 2/R compounds and in NSF/sub 3/, that the bonding of the sulfur atom in NSF is similar to that in SO/sub 2/, and that the nitrogen atom of NSF/sub 3/ is more negatively charged than that of NSF (in spite of a stronger N-S bond in NSF/sub 3/). Quantitative interpretation of the data for NSF and NSF/sub 3/, together withmore » literature valence ionization potentials, shows that the HOMO of each molecule has principally nitrogen 2p character and is stabilized by interaction with a higher lying sulfur 3d orbital. The approximate atomic orbital contributions to the other molecuar orbitals of these molecules are deduced.« less

FAST TRACK COMMUNICATION: Contrasting characteristics of sub-microsecond pulsed atmospheric air and atmospheric pressure helium-oxygen glow discharges

NASA Astrophysics Data System (ADS)

Walsh, J. L.; Liu, D. X.; Iza, F.; Rong, M. Z.; Kong, M. G.

2010-01-01

Glow discharges in air are often considered to be the ultimate low-temperature atmospheric pressure plasmas for numerous chamber-free applications. This is due to the ubiquitous presence of air and the perceived abundance of reactive oxygen and nitrogen species in air plasmas. In this paper, sub-microsecond pulsed atmospheric air plasmas are shown to produce a low concentration of excited oxygen atoms but an abundance of excited nitrogen species, UV photons and ozone molecules. This contrasts sharply with the efficient production of excited oxygen atoms in comparable helium-oxygen discharges. Relevant reaction chemistry analysed with a global model suggests that collisional excitation of O2 by helium metastables is significantly more efficient than electron dissociative excitation of O2, electron excitation of O and ion-ion recombination. These results suggest different practical uses of the two oxygen-containing atmospheric discharges, with air plasmas being well suited for nitrogen and UV based chemistry and He-O2 plasmas for excited atomic oxygen based chemistry.

Atom probe tomographic mapping directly reveals the atomic distribution of phosphorus in resin embedded ferritin

DOE PAGES

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.; ...

2016-02-29

In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Nitrogen enriched mesoporous organic polymer anchored copper(II) material: an efficient and reusable catalyst for the synthesis of esters and amides from aromatic systems.

PubMed

Molla, Rostam Ali; Iqubal, Md Asif; Ghosh, Kajari; Kamaluddin; Islam, Sk Manirul

2015-04-14

A new copper-grafted mesoporous poly-melamine-formaldehyde (Cu-mPMF) has been synthesized from melamine and paraformaldehyde in DMSO medium, followed by grafting of Cu(ii) at its surface. Cu-mPMF has been characterized by elemental analysis, powder XRD, HR TEM, FE-SEM, N2 adsorption study, FT-IR, UV-vis DRS, TGA-DTA, EPR spectroscopy, Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). The Cu-grafted mesoporous material showed very good catalytic activity in methyl esterification of benzylic alcohols and amidation of nitriles. Moreover, the catalyst is easily recoverable and can be reused seven times without appreciable loss of catalytic activity in the above reactions. The highly dispersed and strongly bound Cu(ii) sites in the Cu-grafted mesoporous polymer could be responsible for the observed high activities of the Cu-mPMF catalyst. Due to strong binding with the functional groups of the polymer, no evidence of leached copper from the catalyst during the course of reaction emerged, suggesting true heterogeneity in the catalytic process.

Cytidine Diphosphoramidate Kinase: An Enzyme Required for the Biosynthesis of the O-Methyl Phosphoramidate Modification in the Capsular Polysaccharides of Campylobacter jejuni.

PubMed

Taylor, Zane W; Raushel, Frank M

2018-04-17

Campylobacter jejuni, a leading cause of gastroenteritis, produces a capsular polysaccharide that is derivatized with a unique O-methyl phosphoramidate (MeOPN) modification. This modification contributes to serum resistance and invasion of epithelial cells. Previously, the first three biosynthetic steps for the formation of MeOPN were elucidated. The first step is catalyzed by a novel glutamine kinase (Cj1418), which catalyzes the adenosine triphosphate (ATP)-dependent phosphorylation of the amide nitrogen of l-glutamine. l-Glutamine phosphate is used by cytidine triphosphate (CTP):phosphoglutamine cytidylyltransferase (Cj1416) to displace pyrophosphate from CTP to generate cytidine diphosphate (CDP)-l-glutamine, which is then hydrolyzed by γ-glutamyl-CDP-amidate hydrolase (Cj1417) to form cytidine diphosphoramidate (CDP-NH 2 ). Here, we show that Cj1415 catalyzes the ATP-dependent phosphorylation of CDP-NH 2 to form 3'-phospho-cytidine-5'-diphosphoramidate. Cj1415 will also catalyze the phosphorylation of adenosine diphosphoramidate (ADP-NH 2 ) and uridine diphosphoramidate (UDP-NH 2 ) but at significantly reduced rates. It is proposed that Cj1415 be named cytidine diphosphoramidate kinase.

Biosynthesis of Nucleoside Diphosphoramidates in Campylobacter jejuni.

PubMed

Taylor, Zane W; Brown, Haley A; Holden, Hazel M; Raushel, Frank M

2017-11-21

Campylobacter jejuni is a pathogenic Gram-negative bacterium and a leading cause of food-borne gastroenteritis. C. jejuni produces a capsular polysaccharide (CPS) that contains a unique O-methyl phosphoramidate modification (MeOPN). Recently, the first step in the biosynthetic pathway for the assembly of the MeOPN modification to the CPS was elucidated. It was shown that the enzyme Cj1418 catalyzes the phosphorylation of the amide nitrogen of l-glutamine to form l-glutamine phosphate. In this investigation, the metabolic fate of l-glutamine phosphate was determined. The enzyme Cj1416 catalyzes the displacement of pyrophosphate from MgCTP by l-glutamine phosphate to form CDP-l-glutamine. The enzyme Cj1417 subsequently catalyzes the hydrolysis of CDP-l-glutamine to generate cytidine diphosphoramidate and l-glutamate. The structures of the two novel intermediates, CDP-l-glutamine and cytidine diphosphoramidate, were confirmed by 31 P nuclear magnetic resonance spectroscopy and mass spectrometry. It is proposed that the enzyme Cj1416 be named CTP:phosphoglutamine cytidylyltransferase and that the enzyme Cj1417 be named γ-glutamyl-CDP-amidate hydrolase.

Isomerization and fragmentation of acetonitrile upon interaction with N(4S) atoms: the chemistry of nitrogen in dense molecular clouds

NASA Astrophysics Data System (ADS)

Mencos, Alejandro; Krim, Lahouari

2016-08-01

We experimentally show that the reaction between ground state nitrogen atoms N(4S) and acetonitrile CH3CN can lead to two distinct chemical pathways that are both thermally activated at very low temperatures. First is CH3CN isomerization which produces CH3NC and H2CCNH. Second is CH3CN decomposition which produces HNC and CH3CNH+CN- fragments, with the possible release of H2. Our results reveal that the mobility of N(4S)-atoms is stimulated in the 3-11 K temperature range, and that its subsequent encounter with one acetonitrile molecule is sufficient for the aforementioned reactions to occur without the need for additional energy to be supplied to the CH3CN + N(4S) system. These findings shed more light on the nitrogen chemistry that can possibly take place in dense molecular clouds, which until now was thought to only involve high-energy processes and therefore be unlikely to occur in such cold and dark interstellar regions. The reaction pathways we propose in this study have very important astrochemical implications, as it was shown recently that the atomic nitrogen might be more abundant, in many interstellar icy grain mantles, than previously thought. Also, these reaction pathways can now be considered within dense molecular clouds, and possibly affect the branching ratios for N-bearing molecules computed in astrochemical modelling.

Injection and trapping of tunnel-ionized electrons into laser-produced wakes.

PubMed

Pak, A; Marsh, K A; Martins, S F; Lu, W; Mori, W B; Joshi, C

2010-01-15

A method, which utilizes the large difference in ionization potentials between successive ionization states of trace atoms, for injecting electrons into a laser-driven wakefield is presented. Here a mixture of helium and trace amounts of nitrogen gas was used. Electrons from the K shell of nitrogen were tunnel ionized near the peak of the laser pulse and were injected into and trapped by the wake created by electrons from majority helium atoms and the L shell of nitrogen. The spectrum of the accelerated electrons, the threshold intensity at which trapping occurs, the forward transmitted laser spectrum, and the beam divergence are all consistent with this injection process. The experimental measurements are supported by theory and 3D OSIRIS simulations.

Results of the AEROS satellite program: Summary

NASA Technical Reports Server (NTRS)

Lammerzahl, P.; Rawer, K.; Roemer, N.

1980-01-01

Published literature reporting aeronomic data collected on two AEROS missions is summarized. The extreme ultraviolet solar radiation and other significant parameters of the thermosphere/ionosphere were investigated. Kinetic pressure, the quantity of atomic nitrogen, and partial densities of helium, oxygen, nitrogen, argon, and atomic nitrogen were determined. The thermal electron population, superthermal energy distribution, plasma density, ion temperature, and composition according to ion types were measured. The chief energy supply in the thermosphere was calculated. Aeronomic calculations showing that variations in the parameters of the ionosphere cannot be correlated with fluctuations of extreme ultraviolet solar radiation were performed. The AEROS data were compared with data from S3-1, ISIS, and AE-C satellites. Models of the thermosphere and ionosphere were developed.

Pathways of assimilation and transfer of fixed nitrogen in coralloid roots of cycad-Nostoc symbioses.

PubMed

Pate, J S; Lindblad, P; Atkins, C A

1988-12-01

Freshly detached coralloid roots of several cycad species were found to bleed spontaneously from xylem, permitting identification of products of nitrogen transfer from symbiotic organ to host. Structural features relevant to the export of fixed N were described for Macrozamia riedlei (Fisch. ex Gaud.) Gardn. the principal species studied. Citrulline (Cit), glutamine (Gln) and glutamic acid (Glu), the latter usually in a lesser amount, were the principal translocated solutes in Macrozamia (5 spp.), Encephalartos (4 spp.) and Lepidozamia (1 sp.), while Gln and a smaller amount of Glu, but no Cit were present in xylem sap of Bowenia (1 sp.),and Cycas (2 spp.). Time-course studies of (15)N enrichment of the different tissue zones and the xylem sap of (15)N2-pulse-fed coralloid roots of M. riedlei showed earlier (15)N incorporation into Gln than into Cit, and a subsequent net decline in the (15)N of Gln of the coralloid-root tissues, whereas Cit labeling continued to increase in inner cortex and stele and in the xylem sap. Hydrolysis of the (15)N-labeled Cit and Gln consistently demonstrated much more intense labeling of the respective carbamyl and amide groups than of the other N-atoms. Coralloid roots of M. riedlei pulse-fed (14)CO2 in darkness showed (14)C labeling of aspartic acid (Asp) and Cit in all tissue zones and of Cit of xylem bleeding sap. Lateral roots and uninfected apogeotropic roots of M. riedlei and M. moorei also incorporated (14)CO2 into Cit. The (14)C of Cit was restricted to the carbamyl-C. Comparable (15)N2 and CO2-feeding studies on corallid roots of Cycas revoluta showed Gln to be the dominant product of N2 fixation, with Asp and alanine as other major (14)C-labeled amino compounds, but a total absence of Cit in labeled or unlabeled form.

Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation

NASA Technical Reports Server (NTRS)

Willey, Ronald J.

1993-01-01

Five kinetic models are compared for their ability to predict recombination coefficients for oxygen and nitrogen atoms over high-temperature reusable surface insulation (HRSI). Four of the models are derived using Rideal-Eley or Langmuir-Hinshelwood catalytic mechanisms to describe the reaction sequence. The fifth model is an empirical expression that offers certain features unattainable through mechanistic description. The results showed that a four-parameter model, with temperature as the only variable, works best with data currently available. The model describes recombination coefficients for oxygen and nitrogen atoms for temperatures from 300 to 1800 K. Kinetic models, with atom concentrations, demonstrate the influence of atom concentration on recombination coefficients. These models can be used for the prediction of heating rates due to catalytic recombination during re-entry or aerobraking maneuvers. The work further demonstrates a requirement for more recombination experiments in the temperature ranges of 300-1000 K, and 1500-1850 K, with deliberate concentration variation to verify model requirements.

Energetic Metastable Oxygen and Nitrogen Atoms in the Terrestrial Atmosphere

NASA Technical Reports Server (NTRS)

Kharchenko, Vasili

2003-01-01

We have investigated the energy distributions of the metastable oxygen atoms in the terrestrial thermosphere. Nascent O(lD) atoms play a fundamental role in the energy balance and chemistry of the terrestrial atmosphere, because they are produced by photo-chemical reactions in the excited electronic states and carry significant translational energies.

Combustor exhaust-emissions and blowout-limits with diesel number 2 and Jet A fuels utilizing air-atomizing and pressure-atomizing nozzles

NASA Technical Reports Server (NTRS)

Ingebo, R. D.; Norgren, C. T.

1975-01-01

The effect of fuel properties on exhaust emissions and blowout limits of a high-pressure combustor segment is evaluated using a splash-groove air-atomizing fuel injector and a pressure-atomizing simplex fuel nozzle to burn both diesel number 2 and Jet A fuels. Exhaust emissions and blowout data are obtained and compared on the basis of the aromatic content and volatility of the two fuels. Exhaust smoke number and emission indices for oxides of nitrogen, carbon monoxide, and unburned hydrocarbons are determined for comparison. As compared to the pressure-atomizing nozzle, the air-atomizing nozzle is found to reduce nitrogen oxides by 20%, smoke number by 30%, carbon monoxide by 70%, and unburned hydrocarbons by 50% when used with diesel number 2 fuel. The higher concentration of aromatics and lower volatility of diesel number 2 fuel as compared to Jet A fuel appears to have the most detrimental effect on exhaust emissions. Smoke number and unburned hydrocarbons are twice as high with diesel number 2 as with Jet A fuel.

Tuning Confinement in Colloidal Silicon Nanocrystals with Saturated Surface Ligands.

PubMed

Carroll, Gerard M; Limpens, Rens; Neale, Nathan R

2018-05-09

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups-alkyls, amides, and alkoxides-on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative to alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands-not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals-are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. These results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.

Tuning Confinement in Colloidal Silicon Nanocrystals with Saturated Surface Ligands

DOE PAGES

Carroll, Gerard M.; Limpens, Rens; Neale, Nathan R.

2018-04-16

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups - alkyls, amides, and alkoxides - on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative tomore » alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands - not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals - are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. Furthermore, these results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.« less

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

Neale, Nathan R; Carroll, Gerard; Limpens, Rens

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups - alkyls, amides, and alkoxides - on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative tomore » alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands - not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals - are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. These results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.« less

Efficient assimilation of cyanobacterial nitrogen by water hyacinth.

PubMed

Qin, Hongjie; Zhang, Zhiyong; Liu, Minhui; Wang, Yan; Wen, Xuezheng; Yan, Shaohua; Zhang, Yingying; Liu, Haiqin

2017-10-01

A 15 N labeling technique was used to study nitrogen transfer from cyanobacterium Microcystis aeruginosa to water hyacinth. 15 N atom abundance in M. aeruginosa peaked (15.52%) after cultivation in 15 N-labeled medium for 3weeks. Over 87% of algal nitrogen was transferred into water hyacinth after the 4-week co-cultivation period. The nitrogen quickly super-accumulated in the water hyacinth roots, and the labeled nitrogen was re-distributed to different organs (i.e., roots, stalks, and leaves). This study provides a new strategy for further research on cyanobacterial bloom control, nitrogen migration, and nitrogen cycle in eutrophic waters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nitrogen electroreduction and hydrogen evolution on cubic molybdenum carbide: a density functional study

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

Matanovic, Ivana; Garzon, Fernando H.

We report in this paper a density functional theory study of the nitrogen electroreduction and hydrogen evolution reactions on cubic molybdenum carbide (MoC) in order to investigate the viability of using this material as an electro-catalyst for ammonia synthesis. Free energy diagrams for associative and dissociative Heyrovsky mechanisms showed that nitrogen reduction on cubic MoC(111) can proceed via an associative mechanism and that small negative potentials of -0.3 V vs. standard hydrogen electrode can onset the reduction of nitrogen to ammonia. Kinetic volcano plots for hydrogen evolution showed that the MoC[110] surface is expected to have a high rate formore » the hydrogen evolution reaction, which could compete with the reduction of nitrogen on cubic MoC. The comparison between the adsorption energies of H-adatoms and N-adatoms also shows that at low potentials adsorption of hydrogen atoms competes with nitrogen adsorption on all the MoC surfaces except the MoC(111) surface. Finally, the hydrogen evolution and accumulation of H-adatoms can be mitigated by introducing carbon vacancies i.e. increasing the ratio of metal to carbon atoms, which will significantly increase the affinity of the catalytic surface for both nitrogen molecules and N-adatoms.« less

Nitrogen electroreduction and hydrogen evolution on cubic molybdenum carbide: a density functional study

DOE PAGES

Matanovic, Ivana; Garzon, Fernando H.

2018-04-26

We report in this paper a density functional theory study of the nitrogen electroreduction and hydrogen evolution reactions on cubic molybdenum carbide (MoC) in order to investigate the viability of using this material as an electro-catalyst for ammonia synthesis. Free energy diagrams for associative and dissociative Heyrovsky mechanisms showed that nitrogen reduction on cubic MoC(111) can proceed via an associative mechanism and that small negative potentials of -0.3 V vs. standard hydrogen electrode can onset the reduction of nitrogen to ammonia. Kinetic volcano plots for hydrogen evolution showed that the MoC[110] surface is expected to have a high rate formore » the hydrogen evolution reaction, which could compete with the reduction of nitrogen on cubic MoC. The comparison between the adsorption energies of H-adatoms and N-adatoms also shows that at low potentials adsorption of hydrogen atoms competes with nitrogen adsorption on all the MoC surfaces except the MoC(111) surface. Finally, the hydrogen evolution and accumulation of H-adatoms can be mitigated by introducing carbon vacancies i.e. increasing the ratio of metal to carbon atoms, which will significantly increase the affinity of the catalytic surface for both nitrogen molecules and N-adatoms.« less

Interfacial phenomena in high-kappa dielectrics

NASA Astrophysics Data System (ADS)

Mathew, Anoop

The introduction of novel high-kappa dielectric materials to replace the traditional SiO2 insulating layer in CMOS transistors is a watershed event in the history of transistor development. Further, replacement of the traditional highly-doped polycrystalline silicon gate electrode with a new set of materials for metal gates complicates the transition and introduces further integration challenges. A whole variety of new material surfaces and interfaces are thus introduced that merit close investigation to determine parameters for optimal device performance. Nitrogen is a key component that improves the performance of a variety of materials for the next generation of these CMOS transistors. Nitrogen is introduced into new gate dielectric materials such as hafnium silicates as well as in potential metal gate materials such as hafnium nitride. A photoemission study of the binding energies of the various atoms in these systems using photoemission reveals the nature of the atomic bonding. The current study compares hafnium silicates of various compositions which were thermally nitrided at different temperatures in ammonia, hafnium nitrides, and thin HfO2 films using photoelectron spectroscopy. A recurring theme that is explored is the competition between oxygen and nitrogen atoms in bonding with hafnium and other atoms. The N 1s photoemission peak is seen to have contributions from its bonding with hafnium, oxygen, and silicon atoms. The Hf 4f and O 1s spectra similarly exhibit signatures of their bonding environment with their neighboring atoms. Angle resolved photoemission and in-situ annealing/argon sputtering experiments are used to elucidate the nature of the bonding and its evolution with processing. A nondestructive profilitng of nitrogen distribution as a function of composition in nitrided hafnium silicates is also constructed using angle resolved photoemission as a function of the take-off angle. These results are corroborated with depth reconstruction obtained using medium energy ion scattering (MEIS). A comparison of samples nitrided at progressively increasing temperatures in an ammonia environment shows substitution of oxygen with nitrogen atoms and increasing penetration of nitrogen into the gate stack. Trends in the binding energy of the the as-prepared hafnium silicates suggest that they are non-phase separated, and the binding energy of the hafnium and silicon track the relative composition. Upon being subject to rapid thermal annealing, the samples are observed to show behavior consistent with phase separation. There is also the evidence of charges at the oxide/Si interface that modify the expected behavior of the shifts in binding energy. In another set of experiments, a one-cycle atomic layer deposition (ALD) growth reaction on the water terminated Si(100) -- (2x1) surface is shown to lead to successful nucleation, high metal oxide coverage, and an abrupt metal-oxide/silicon interface as confirmed by photoemission, reflection high energy electron diffraction (RHEED), and Rutherford back scattering (RBS) measurements. Photoemission results confirm the coordination states of the hafnium and oxygen atoms. A Hf 4f core level shift is observed and assigned to the presence of the Si-O-Hf bonding environment with the more electronegative Si atom inducing the binding energy shift. This Hf 4f shift is smaller than that reported previously for silicates because of the difference of the semiconductor bonding environment. The subspecies *(O)2HfCl2 and *OHfCl3 are seen to be the predominant intermediate species in these reactions and photoemission results provide corroborative evidence for their presence. Experiments indicate that the hydroxyl sites bound to Si(100) are active for adsorption. The abrupt interface could be useful for aggressive Effective Oxide Thickness (EOT) scaling.

Purely substitutional nitrogen on graphene/Pt(111) unveiled by STM and first principles calculations

NASA Astrophysics Data System (ADS)

Gomez-Rodriguez, Jose M.; Martin-Recio, Ana; Romero-Muniz, Carlos; Pou, Pablo; Perez, Ruben

Nitrogen doping of graphene can be an efficient way of tuning its pristine electronic properties. Several techniques have been used to introduce nitrogen atoms on graphene layers. The main problem in most of them is the formation of a variety of C-N species that produce different electronic and structural changes on the 2D layer. Here we report on a method to obtain purely substitutional nitrogen on graphene on Pt(111) surfaces. A detailed experimental study performed in situ, under ultra-high vacuum conditions with scanning tunneling microscopy, low energy electron diffraction and Auger electron spectroscopy of the different steps on the preparation of the sample, has allowed us to gain insight into the optimal parameters for this growth method, that combines ion bombardment and annealing. This experimental work is complemented by first-principles calculations that provide the variation of the projected density of states due to both the metallic substrate and the nitrogen atoms. These calculations enlighten the experimental findings and prove that the species found are graphitic nitrogen. This easy and effective technique leads to the possibility of playing with the amount of dopants and the metallic substrate to obtain the desired doping of the graphene layer.

Gold Nanoparticles Doped with (199) Au Atoms and Their Use for Targeted Cancer Imaging by SPECT.

PubMed

Zhao, Yongfeng; Pang, Bo; Luehmann, Hannah; Detering, Lisa; Yang, Xuan; Sultan, Deborah; Harpstrite, Scott; Sharma, Vijay; Cutler, Cathy S; Xia, Younan; Liu, Yongjian

2016-04-20

Gold nanoparticles have been labeled with various radionuclides and extensively explored for single photon emission computed tomography (SPECT) in the context of cancer diagnosis. The stability of most radiolabels, however, still needs to be improved for accurate detection of cancer biomarkers and thereby monitoring of tumor progression and metastasis. Here, the first synthesis of Au nanoparticles doped with (199)Au atoms for targeted SPECT tumor imaging in a mouse triple negative breast cancer (TNBC) model is reported. By directly incorporating (199)Au atoms into the crystal lattice of each Au nanoparticle, the stability of the radiolabel can be ensured. The synthetic procedure also allows for a precise control over both the radiochemistry and particle size. When conjugated with D-Ala1-peptide T-amide, the Au nanoparticles doped with (199)Au atoms can serve as a C-C chemokine receptor 5 (CCR5)-targeted nanoprobe for the sensitive and specific detection of both TNBC and its metastasis in a mouse tumor model. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum oscillations of nitrogen atoms in uranium nitride

NASA Astrophysics Data System (ADS)

Aczel, A. A.; Granroth, G. E.; MacDougall, G. J.; Buyers, W. J. L.; Abernathy, D. L.; Samolyuk, G. D.; Stocks, G. M.; Nagler, S. E.

2012-10-01

The vibrational excitations of crystalline solids corresponding to acoustic or optic one-phonon modes appear as sharp features in measurements such as neutron spectroscopy. In contrast, many-phonon excitations generally produce a complicated, weak and featureless response. Here we present time-of-flight neutron scattering measurements for the binary solid uranium nitride, showing well-defined, equally spaced, high-energy vibrational modes in addition to the usual phonons. The spectrum is that of a single atom, isotropic quantum harmonic oscillator and characterizes independent motions of light nitrogen atoms, each found in an octahedral cage of heavy uranium atoms. This is an unexpected and beautiful experimental realization of one of the fundamental, exactly solvable problems in quantum mechanics. There are also practical implications, as the oscillator modes must be accounted for in the design of generation IV nuclear reactors that plan to use uranium nitride as a fuel.

Quantum oscillations of nitrogen atoms in uranium nitride.

PubMed

Aczel, A A; Granroth, G E; Macdougall, G J; Buyers, W J L; Abernathy, D L; Samolyuk, G D; Stocks, G M; Nagler, S E

2012-01-01

The vibrational excitations of crystalline solids corresponding to acoustic or optic one-phonon modes appear as sharp features in measurements such as neutron spectroscopy. In contrast, many-phonon excitations generally produce a complicated, weak and featureless response. Here we present time-of-flight neutron scattering measurements for the binary solid uranium nitride, showing well-defined, equally spaced, high-energy vibrational modes in addition to the usual phonons. The spectrum is that of a single atom, isotropic quantum harmonic oscillator and characterizes independent motions of light nitrogen atoms, each found in an octahedral cage of heavy uranium atoms. This is an unexpected and beautiful experimental realization of one of the fundamental, exactly solvable problems in quantum mechanics. There are also practical implications, as the oscillator modes must be accounted for in the design of generation IV nuclear reactors that plan to use uranium nitride as a fuel.

Experimental validation of calculated atomic charges in ionic liquids

NASA Astrophysics Data System (ADS)

Fogarty, Richard M.; Matthews, Richard P.; Ashworth, Claire R.; Brandt-Talbot, Agnieszka; Palgrave, Robert G.; Bourne, Richard A.; Vander Hoogerstraete, Tom; Hunt, Patricia A.; Lovelock, Kevin R. J.

2018-05-01

A combination of X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy has been used to provide an experimental measure of nitrogen atomic charges in nine ionic liquids (ILs). These experimental results are used to validate charges calculated with three computational methods: charges from electrostatic potentials using a grid-based method (ChelpG), natural bond orbital population analysis, and the atoms in molecules approach. By combining these results with those from a previous study on sulfur, we find that ChelpG charges provide the best description of the charge distribution in ILs. However, we find that ChelpG charges can lead to significant conformational dependence and therefore advise that small differences in ChelpG charges (<0.3 e) should be interpreted with care. We use these validated charges to provide physical insight into nitrogen atomic charges for the ILs probed.

The kinetics of the reaction of nitrogen dioxide with iron(II)- and iron(III) cytochrome c.

PubMed

Domazou, Anastasia S; Gebicka, Lidia; Didik, Joanna; Gebicki, Jerzy L; van der Meijden, Benjamin; Koppenol, Willem H

2014-04-01

The reactions of NO2 with both oxidized and reduced cytochrome c at pH 7.2 and 7.4, respectively, and with N-acetyltyrosine amide and N-acetyltryptophan amide at pH 7.3 were studied by pulse radiolysis at 23 °C. NO2 oxidizes N-acetyltyrosine amide and N-acetyltryptophan amide with rate constants of (3.1±0.3)×10(5) and (1.1±0.1)×10(6) M(-1) s(-1), respectively. With iron(III)cytochrome c, the reaction involves only its amino acids, because no changes in the visible spectrum of cytochrome c are observed. The second-order rate constant is (5.8±0.7)×10(6) M(-1) s(-1) at pH 7.2. NO2 oxidizes iron(II)cytochrome c with a second-order rate constant of (6.6±0.5)×10(7) M(-1) s(-1) at pH 7.4; formation of iron(III)cytochrome c is quantitative. Based on these rate constants, we propose that the reaction with iron(II)cytochrome c proceeds via a mechanism in which 90% of NO2 oxidizes the iron center directly-most probably via reaction at the solvent-accessible heme edge-whereas 10% oxidizes the amino acid residues to the corresponding radicals, which, in turn, oxidize iron(II). Iron(II)cytochrome c is also oxidized by peroxynitrite in the presence of CO2 to iron(III)cytochrome c, with a yield of ~60% relative to peroxynitrite. Our results indicate that, in vivo, NO2 will attack preferentially the reduced form of cytochrome c; protein damage is expected to be marginal, the consequence of formation of amino acid radicals on iron(III)cytochrome c. Copyright © 2014 Elsevier Inc. All rights reserved.

Radiative Characteristics of the Pulse-Periodic Discharge Plasma Initiated by Runaway Electrons

NASA Astrophysics Data System (ADS)

Lomaev, M. I.; Beloplotov, D. V.; Tarasenko, V. F.; Sorokin, D. A.

2016-07-01

Results of experimental investigations of amplitude-temporal and spectral characteristics of radiation of a pulse-periodic discharge plasma initiated in nitrogen by runaway electrons are presented. The discharge was initiated by high-voltage nanosecond voltage pulses with repetition frequency of 60 Hz in a sharply inhomogeneous electric field in a gap between the conic potential cathode and the planar grounded aluminum anode. It is established that intensive lines of Al I atoms and Al II atomic ions, lines of N I atoms and N II ions, bands of the first (1+) and second positive (2+) nitrogen systems, as well as bands of cyanogen CN are observed in the emission spectrum of the discharge plasma under the given excitation conditions.

Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma

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

Okada, H.; Kato, M.; Ishimaru, T.

2014-02-20

Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma is investigated. Feasibility of precursors of triethylsilane (TES) and bis(dimethylamino)dimethylsilane (BDMADMS) is discussed based on a calculation of bond energies by computer simulation. Refractive indices of 1.81 and 1.71 are obtained for deposited films with TES and BDMADMS, respectively. X-ray photoelectron spectroscopy (XPS) analysis of the deposited film revealed that TES-based film coincides with the stoichiometric thermal silicon nitride.

PHYSICAL PROPERTIES OF ZIRCONIUM NITRIDE IN THE HOMOGENEITY REGION (in Ukrainian)

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

Samsonov, G.V.; Verkhoglyadova, T.S.

1962-01-01

The x-ray method was used to determine the homogeneity region of zirconium nitride as 40 to 50 at.% (9.5 to 13.3% by weight) of nitrogen. It is also shown that part of the ionic bond in the zirconium nitride lattice increases with a decrease in the nitrogen content in this region, this increase being higher than in the homogeneity region of titunium nitride due to the smaller degree of unfilling of the electron d-shell of the zirconium atom in comparison with that of the titanium atom. (auth)

Isotopic effects in the muon transfer from pmu and dmu to heavier atoms.

PubMed

Dupays, Arnaud

2004-07-23

The results of accurate hyperspherical calculations of the muon-transfer rates from muonic protium and deuterium atoms to nitrogen, oxygen, and neon are reported. Very good agreement with measured rates is obtained and, for the three systems, the isotopic effect is perfectly reproduced. The transfer rate is higher for deuterium in the cases of nitrogen and neon due to constructive interferences between two transfer paths. The lower transfer rate for deuterium in the case of oxygen results from a large resonant contribution. Copyright 2004 The American Physical Society

Secondary benzylation with benzyl alcohols catalyzed by a high-valent heterobimetallic Ir-Sn complex.

PubMed

Podder, Susmita; Choudhury, Joyanta; Roy, Sujit

2007-04-13

A highly efficient secondary benzylation procedure has been demonstrated using a high-valent heterobimetallic complex [Ir2(COD)2(SnCl3)2(Cl)2(mu-Cl)2] 1 as the catalyst in 1,2-dichloroethane to afford the corresponding benzylated products in moderate to excellent yields. The reaction was performed not only with carbon nucleophiles (arenes and heteroarenes) but also with oxygen (alcohol), nitrogen (amide and sulfonamide), and sulfur (thiol) nucleophiles. Mechanistic investigation showed the intermediacy of the ether in this reaction. An electrophilic mechanism is proposed from Hammett correlation.

Theoretical study of nitrogen-doped graphene nanoflakes: Stability and spectroscopy depending on dopant types and flake sizes.

PubMed

Lin, Chih-Kai

2018-03-05

As nitrogen-doped graphene has been widely applied in optoelectronic devices and catalytic reactions, in this work we have investigated where the nitrogen atoms tend to reside in the material and how they affect the electron density and spectroscopic properties from a theoretical point of view. DFT calculations on N-doped hexagonal and rectangular graphene nanoflakes (GNFs) showed that nitrogen atoms locating on zigzag edges are obviously more stable than those on armchair edges or inside flakes, and interestingly, the N-hydrogenated pyridine moiety could be preferable to pure pyridine moiety in large models. The UV-vis absorption spectra of these nitrogen-doped GNFs display strong dependence on flake sizes, where the larger flakes have their major peaks in lower energy ranges. Moreover, the spectra exhibit different connections to various dopant types and positions: the graphitic-type dopant species present large variety in absorption profiles, while the pyridinic-type ones show extraordinary uniform stability and spectra independent of dopant positions/numbers and hence are hardly distinguishable from each other. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

ASN1-encoded asparagine synthetase in floral organs contributes to nitrogen filling in Arabidopsis seeds.

PubMed

Gaufichon, Laure; Marmagne, Anne; Belcram, Katia; Yoneyama, Tadakatsu; Sakakibara, Yukiko; Hase, Toshiharu; Grandjean, Olivier; Clément, Gilles; Citerne, Sylvie; Boutet-Mercey, Stéphanie; Masclaux-Daubresse, Céline; Chardon, Fabien; Soulay, Fabienne; Xu, Xiaole; Trassaert, Marion; Shakiebaei, Maryam; Najihi, Amina; Suzuki, Akira

2017-08-01

Despite a general view that asparagine synthetase generates asparagine as an amino acid for long-distance transport of nitrogen to sink organs, its role in nitrogen metabolic pathways in floral organs during seed nitrogen filling has remained undefined. We demonstrate that the onset of pollination in Arabidopsis induces selected genes for asparagine metabolism, namely ASN1 (At3g47340), GLN2 (At5g35630), GLU1 (At5g04140), AapAT2 (At5g19950), ASPGA1 (At5g08100) and ASPGB1 (At3g16150), particularly at the ovule stage (stage 0), accompanied by enhanced asparagine synthetase protein, asparagine and total amino acids. Immunolocalization confined asparagine synthetase to the vascular cells of the silique cell wall and septum, but also to the outer and inner seed integuments, demonstrating the post-phloem transport of asparagine in these cells to developing embryos. In the asn1 mutant, aberrant embryo cell divisions in upper suspensor cell layers from globular to heart stages assign a role for nitrogen in differentiating embryos within the ovary. Induction of asparagine metabolic genes by light/dark and nitrate supports fine shifts of nitrogen metabolic pathways. In transgenic Arabidopsis expressing promoter Ca MV 35S ::ASN1 fusion, marked metabolomics changes at stage 0, including a several-fold increase in free asparagine, are correlated to enhanced seed nitrogen. However, specific promoter Napin2S ::ASN1 expression during seed formation and a six-fold increase in asparagine toward the desiccation stage result in wild-type seed nitrogen, underlining that delayed accumulation of asparagine impairs the timing of its use by releasing amide and amino nitrogen. Transcript and metabolite profiles in floral organs match the carbon and nitrogen partitioning to generate energy via the tricarboxylic acid cycle, GABA shunt and phosphorylated serine synthetic pathway. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Nitrite fixation by humic substances: Nitrogen-15 nuclear magnetic resonance evidence for potential intermediates in chemodenitrification

USGS Publications Warehouse

Thorn, K.A.; Mikita, M.A.

2000-01-01

Studies have suggested that NO2/-, produced during nitrification and denitrification, can become incorporated into soil organic matter and, in one of the processes associated with chemodenitrification, react with organic matter to form trace N gases, including N2O. To gain an understanding of the nitrosation chemistry on a molecular level, soil and aquatic humic substances were reacted with 15N-labeled NaNO2, and analyzed by liquid phase 15N and 13C nuclear magnetic resonance (NMR). The International Humic Substances Society (IHSS) Pahokee peat and peat humic acid were also reacted with Na15NO2 and analyzed by solid-state 15N NMR. In Suwannee River, Armadale, and Laurentian fulvic acids, phenolic rings and activated methylene groups underwent nitrosation to form nitrosophenols (quinone monoximes) and ketoximes, respectively. The oximes underwent Beckmann rearrangements to 2??amides, and Beckmann fragmentations to nitriles. The nitriles in turn underwent hydrolysis to 1??amides. Peaks tentatively identified as imine, indophenol, or azoxybenzene nitrogens were clearly present in spectra of samples nitrosated at pH 6 but diminished at pH 3. The 15N NMR spectrum of the peat humic acid exhibited peaks corresponding with N-nitroso groups in addition to nitrosophenols, ketoximes, and secondary Beckmann reaction products. Formation of N-nitroso groups was more significant in the whole peat compared with the peat humic acid. Carbon-13 NMR analyses also indicated the occurrence of nitrosative demethoxylation in peat and soil humic acids. Reaction of 15N-NH3 fixated fulvic acid with unlabeled NO2/- resulted in nitrosative deamination of aminohydroquinone N, suggesting a previously unrecognized pathway for production of N2 gas in soils fertilized with NH3.Studies have suggested that NO2-, produced during nitrification and denitrification, can become incorporated into soil organic matter and, in one of the processes associated with chemodenitrification, react with organic matter to form trace N gases, including N2O. To gain an understanding of the nitrosation chemistry on a molecular level, soil and aquatic humic substances were reacted with 15N-labeled NaNO2, and analyzed by liquid phase 15N and 13C nuclear magnetic resonance (NMR). The International Humic Substances Society (IHSS) Pahokee peat and peat humic acid were also reacted with Na15NO2 and analyzed by solid-state 15N NMR. In Suwannee River, Armadale, and Laurentian fulvic acids, phenolic rings and activated methylene groups underwent nitrosation to form nitrosophenols (quinone monoximes) and ketoximes, respectively. The oximes underwent Beckmann rearrangements to 2?? amides, and Beckmann fragmentations to nitriles. The nitriles in turn underwent hydrolysis to 1?? amides. Peaks tentatively identified as imine, indophenol, or azoxybenzene nitrogens were dearly present in spectra of samples nitrosated at pH 6 but diminished at pH 3. The 15N NMR spectrum of the peat humic acid exhibited peaks corresponding with N-nitroso groups in addition to nitrosophenols, ketoximes, and secondary Beckmann reaction products. Formation of N-nitroso groups was more significant in the whole peat compared with the peat humic acid. Carbon-13 NMR analyses also indicated the occurrence of nitrosative demethoxylation in peat and soil humic acids. Reaction of 15N-NH3 fixated fulvic acids with unlabeled NO2- resulted in nitrosative deamination of aminohydroquinone N, suggesting a previously unrecognized pathway for production of N2 gas in soils fertilized with NH3.

Quality-assurance data for routine water analysis in the National Water-Quality Laboratory of the US Geological Survey for water year 1988

USGS Publications Warehouse

Lucey, K.J.

1989-01-01

The US Geological Survey maintains a quality assurance program based on the analysis of reference samples for its National Water Quality Laboratory located in Denver, Colorado. Reference samples containing selected inorganic, nutrient, and precipitation (low-level concentration) constituents are prepared at the Survey 's Water Quality Services Unit in Ocala, Florida, disguised as routine samples, and sent daily or weekly, as appropriate, to the laboratory through other Survey offices. The results are stored permanently in the National Water Data Storage and Retrieval System (WATSTORE), the Survey 's database for all water data. These data are analyzed statistically for precision and bias. An overall evaluation of the inorganic major ion and trace metal constituent data for water year 1988 indicated a lack of precision in the National Water Quality Laboratory for the determination of 8 out of 58 constituents: calcium (inductively coupled plasma emission spectrometry), fluoride, iron (atomic absorption spectrometry), iron (total recoverable), magnesium (atomic absorption spectrometry), manganese (total recoverable), potassium, and sodium (inductively coupled plasma emission spectrometry). The results for 31 constituents had positive or negative bias during water year 1988. A lack of precision was indicated in the determination of three of the six nutrient constituents: nitrate plus nitrite nitrogen as nitrogen, nitrite nitrogen as nitrogen, and orthophosphate as phosphorus. A biased condition was indicated in the determination of ammonia nitrogen as nitrogen, ammonia plus organic nitrogen as nitrogen, and nitrate plus nitrite nitrogen as nitrogen. There was acceptable precision in the determination of all 10 constituents contained in precipitation samples. Results for ammonia nitrogen as nitrogen, sodium, and fluoride indicated a biased condition. (Author 's abstract)

4-Amino-N-(3-meth­oxy­pyrazin-2-yl)benzene­sulfonamide

PubMed Central

Bruni, Bruno; Coran, Silvia A.; Bartolucci, Gianluca; Di Vaira, Massimo

2010-01-01

The overall mol­ecular geometry of the title compound, C11H12N4O3S, is bent, with a dihedral angle of 89.24 (5)° between the best planes through the two aromatic rings. Each mol­ecule behaves as a hydrogen-bond donor toward three different mol­ecules, through its amidic and the two aminic H atoms, and it behaves as a hydrogen-bond acceptor from two other mol­ecules via one of its sulfonamidic O atoms. In the crystal, mol­ecules linked by N—H⋯N and N—H⋯O hydrogen bonds form kinked layers parallel to (001), adjacent layers being connected by van der Waals inter­actions. PMID:21587634

Influence of sulfur oxidation state and steric bulk upon trifluoromethyl ketone (TFK) binding kinetics to carboxylesterases and fatty acid amide hydrolase (FAAH)

PubMed Central

Wheelock, Craig E.; Nishi, Kosuke; Ying, Andy; Jones, Paul D.; Colvin, Michael E.; Olmstead, Marilyn M.; Hammock, Bruce D.

2009-01-01

Carboxylesterases metabolize numerous exogenous and endogenous ester-containing compounds including the chemotherapeutic agent CPT-11, anti-influenza viral agent oseltamivir and many agrochemicals. Trifluoromethyl ketone (TFK)-containing compounds with a sulfur atom beta to the ketone moiety are some of the most potent carboxylesterase and amidase inhibitors identified to date. This study examined the effects of alkyl chain length (i.e., steric effects) and sulfur oxidation state upon TFK inhibitor potency (IC50) and binding kinetics (ki). The selective carboxylesterase inhibitor benzil was used as a non-TFK containing control. These effects were examined using two commercial esterases (porcine and rabbit liver esterase) and two human recombinant esterases (hCE-1 and hCE-2) as well as human recombinant fatty acid amide hydrolase (FAAH). In addition, the inhibition mechanism was examined using a combination of 1H NMR, X-ray crystallography and ab initio calculations. Overall, the data show that while sulfur oxidation state profoundly affects both inhibitor potency and binding kinetics, the steric effects dominate and override the contributions of sulfur oxidation. In addition, the data suggest that inclusion of a sulfur atom beta to the ketone contributes an increase (~5-fold) in inhibitor potency due to effects upon ketone hydration and/or intramolecular hydrogen bond formation. These results provide further information on the nature of the TFK binding interaction and will be useful in increasing our understanding of this basic biochemical process. PMID:18023188

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

PubMed Central

Krylov, Igor B; Vil’, Vera A

2015-01-01

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

New fluorinated rhodamines for optical microscopy and nanoscopy.

PubMed

Mitronova, Gyuzel Yu; Belov, Vladimir N; Bossi, Mariano L; Wurm, Christian A; Meyer, Lars; Medda, Rebecca; Moneron, Gael; Bretschneider, Stefan; Eggeling, Christian; Jakobs, Stefan; Hell, Stefan W

2010-04-19

New photostable rhodamine dyes represented by the compounds 1 a-r and 3-5 are proposed as efficient fluorescent markers with unique combination of structural features. Unlike rhodamines with monoalkylated nitrogen atoms, N',N-bis(2,2,2-trifluoroethyl) derivatives 1 e, 1 i, 1 j, 3-H and 5 were found to undergo sulfonation of the xanthene fragment at the positions 4' and 5'. Two fluorine atoms were introduced into the positions 2' and 7' of the 3',6'-diaminoxanthene fragment in compounds 1 a-d, 1 i-l and 1 m-r. The new rhodamine dyes may be excited with λ=488 or 514 nm light; most of them emit light at λ=512-554 nm (compounds 1 q and 1r at λ=576 and 589 nm in methanol, respectively) and have high fluorescence quantum yields in solution (up to 98 %), relatively long excited-state lifetimes (>3 ns) and are resistant against photobleaching, especially at high laser intensities, as is usually applied in confocal microscopy. Sulfonation of the xanthene fragment with 30 % SO3 in H2SO4 is compatible with the secondary amide bond (rhodamine-CON(Me)CH2CH2COOH) formed with MeNHCH2CH2COOCH3 to providing the sterically unhindered carboxylic group required for further (bio)conjugation reactions. After creating the amino reactive sites, the modified derivatives may be used as fluorescent markers and labels for (bio)molecules in optical microscopy and nanoscopy with very-high light intensities. Further, the new rhodamine dyes are able to pass the plasma membrane of living cells, introducing them as potential labels for recent live-cell-tag approaches. We exemplify the excellent performance of the fluorinated rhodamines in optical microscopy by fluorescence correlation spectroscopy (FCS) and stimulated emission depletion (STED) nanoscopy experiments. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conduction Mechanism and Improved Endurance in HfO2-Based RRAM with Nitridation Treatment

NASA Astrophysics Data System (ADS)

Yuan, Fang-Yuan; Deng, Ning; Shih, Chih-Cheng; Tseng, Yi-Ting; Chang, Ting-Chang; Chang, Kuan-Chang; Wang, Ming-Hui; Chen, Wen-Chung; Zheng, Hao-Xuan; Wu, Huaqiang; Qian, He; Sze, Simon M.

2017-10-01

A nitridation treatment technology with a urea/ammonia complex nitrogen source improved resistive switching property in HfO2-based resistive random access memory (RRAM). The nitridation treatment produced a high performance and reliable device which results in superior endurance (more than 109 cycles) and a self-compliance effect. Thus, the current conduction mechanism changed due to defect passivation by nitrogen atoms in the HfO2 thin film. At a high resistance state (HRS), it transferred to Schottky emission from Poole-Frenkel in HfO2-based RRAM. At low resistance state (LRS), the current conduction mechanism was space charge limited current (SCLC) after the nitridation treatment, which suggests that the nitrogen atoms form Hf-N-Ox vacancy clusters (Vo +) which limit electron movement through the switching layer.

Plasma-chemical processes accompanying discharge in air excited by a microwave beam

NASA Astrophysics Data System (ADS)

Askar'ian, G. A.; Batanov, G. M.; Gritsinin, S. I.; Kossyi, I. A.; Kostinskii, A. Iu.

1990-11-01

Experimental results are presented on plasma-chemical processes of nitrogen oxidation and ozone production accompanying microwave discharge in dry air and in nitrogen-oxygen mixtures. The degree of nitrogen oxidation and the energy expenditure toward the formation of oxides as a function of discharge conditions are established. The experimental results can be explained by assuming oxidation reactions of electron-excited metastable nitrogen molecules by oxygen atoms. Low ozone concentrations in the discharge indicate a significant energy input into the gas.

Cation and anion dependence of stable geometries and stabilization energies of alkali metal cation complexes with FSA(-), FTA(-), and TFSA(-) anions: relationship with physicochemical properties of molten salts.

PubMed

Tsuzuki, Seiji; Kubota, Keigo; Matsumoto, Hajime

2013-12-19

Stable geometries and stabilization energies (Eform) of the alkali metal complexes with bis(fluorosulfonyl)amide, (fluorosulfonyl)(trifluoromethylslufonyl)amide and bis(trifluoromethylsulfonyl)amide (FSA(-), FTA(-) and TFSA(-)) were studied by ab initio molecular orbital calculations. The FSA(-) complexes prefer the bidentate structures in which two oxygen atoms of two SO2 groups have contact with the metal cation. The FTA(-) and TFSA(-) complexes with Li(+) and Na(+) prefer the bidentate structures, while the FTA(-) and TFSA(-) complexes with Cs(+) prefer tridentate structures in which the metal cation has contact with two oxygen atoms of an SO2 group and one oxygen atom of another SO2 group. The two structures are nearly isoenergetic in the FTA(-) and TFSA(-) complexes with K(+) and Rb(+). The magnitude of Eform depends on the alkali metal cation significantly. The Eform calculated for the most stable TFSA(-) complexes with Li(+), Na(+), K(+), Rb(+) and Cs(+) cations at the MP2/6-311G** level are -137.2, -110.5, -101.1, -89.6, and -84.1 kcal/mol, respectively. The viscosity and ionic conductivity of the alkali TFSA molten salts have strong correlation with the magnitude of the attraction. The viscosity increases and the ionic conductivity decreases with the increase of the attraction. The melting points of the alkali TFSA and alkali BETA molten salts also have correlation with the magnitude of the Eform, which strongly suggests that the magnitude of the attraction play important roles in determining the melting points of these molten salts. The anion dependence of the Eform calculated for the complexes is small (less than 2.9 kcal/mol). This shows that the magnitude of the attraction is not the cause of the low melting points of alkali FTA molten salts compared with those of corresponding alkali TFSA molten salts. The electrostatic interactions are the major source of the attraction in the complexes. The electrostatic energies for the most stable TFSA(-) complexes with the five alkali metal cations are -140.3, -119.4, -104.1, -96.9, and -91.1 kcal/mol, respectively. The induction interactions also contribute to the attraction. In particular, the induction interactions are large in the Li(+) complexes. The induction energies for the five complexes are -46.6, -25.2, -17.5, -13.3, and -10.4 kcal/mol, respectively.

Diffusion and reactivity of ground-state nitrogen atoms N(4S) between 3 and 15 K: application to the hydrogen abstraction reaction from methane under non-energetic conditions

NASA Astrophysics Data System (ADS)

Nourry, Sendres; Krim, Lahouari

2015-07-01

We have characterized the CH4 + N(4S) reaction in solid phase, at very low temperature, under non-energetic conditions and where the CH4 and N reactants are in their ground states. A microwave-driven atomic source has been used to generate ground-state nitrogen atoms N(4S), and experiments have been carried out at temperatures as low as 3 K to reduce the mobility of the trapped species in solid phase and hence to freeze the first step of the CH4 + N reaction pathway. Leaving the formed solid sample in the dark for a while allows all trapped reactants to relax to the ground state, specifically radicals and excited species streaming from the plasma discharge. Such a method could be the only possibility of proving that the CH4 + N reaction occurs between CH4 and N reactants in their ground states without any additional energy to initiate the chemical process. The appearance of the CH3 reaction product, just by inducing the mobility of N atoms between 3 and 11 K, translates that a hydrogen abstraction reaction from methane, under non-energetic conditions, will start occurring at very low temperature. The formation of methyl radical, under these experimental conditions, is due to recombination processes N(4S)-N(4S) of ground-state nitrogen atoms without any contribution of cosmic ray particles or high-energy photons.

Radiation of nitrogen molecules in a dielectric barrier discharge with small additives of chlorine and bromine

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

Avtaeva, S. V.; Avdeev, S. M.; Sosnin, E. A.

2010-08-15

Spectral and energy characteristics of nitrogen molecule radiation in dielectric barrier discharges in Ar-N{sub 2}, Ar-N{sub 2}-Cl{sub 2}, and Ar-N{sub 2}-Br{sub 2} mixtures were investigated experimentally. Small additives of molecular chlorine or bromine to an Ar-N{sub 2} mixture are found to increase the radiation intensity of the second positive system of nitrogen. The conditions at which the radiation spectrum predominantly consists of vibronic bands of this system are determined. Using a numerical model of plasmachemical processes, it is shown that, at electron temperatures typical of gas discharges (2-4 eV), a minor additive of molecular chlorine to an Ar-N{sub 2} mixturemore » leads to an increase in the concentrations of electrons, positive ions, and metastable argon atoms. In turn, collisional energy transfer from metastable argon atoms to nitrogen molecules results in the excitation of the N{sub 2}(C{sup 3{Pi}}{sub u}) state.« less

Characterization of ternary bivalent metal complexes with bis(2-hydroxyethyl)iminotris(hydroxymethy)methane (Bis?Tris) and the comparison of five crystal structures of Bis?Tris complexes*1

NASA Astrophysics Data System (ADS)

Inomata, Yoshie; Gochou, Yoshihiro; Nogami, Masanobu; Howell, F. Scott; Takeuchi, Toshio

2004-09-01

Eleven bivalent metal complexes with bis(2-hydroxyethyl)iminotris(hydroxymethy)methane (Bis-Tris:hihm): [M(hihm)(H 2O)]SO 4· nH 2O (M: Co, Ni, Cu, Zn), [MCl(hihm)]Cl· nH 2O (M: Co, Ni, Cu), and [M(HCOO)(hihm)](HCOO) (M: Co, Ni, Cu, Zn) have been prepared and characterized by using their infrared absorption and powder diffuse reflection spectra, magnetic susceptibility, thermal analysis and powder X-ray diffraction analysis. The crystal structures of [Ni(hihm)(H 2O)]SO 4·H 2O ( 2), [Cu(hihm)(H 2O)]SO 4 ( 3), [NiCl(hihm)]Cl·H 2O ( 6), [CuCl(hihm)]Cl ( 7) and [Co(HCOO)(hihm)](HCOO) ( 8) have been determined by single crystal X-ray diffraction analysis. The crystals of [Ni(hihm)(H 2O)]SO 4·H 2O ( 2) and [Cu(hihm)(H 2O)]SO 4 ( 3) are each orthorhombic with the space group P2 12 12 1 and Pna2 1. For both complexes, the metal atom is in a distorted octahedral geometry, ligated by four hydroxyl oxygen atoms, a nitrogen atom and a water molecule. [NiCl(hihm)]Cl·H 2O ( 6) is monoclinic with the space group P2 1/ n. For complex ( 6), the nickel atom is in a distorted octahedral geometry, ligated by four hydroxyl oxygen atoms, a nitrogen atom and a chloride ion. [CuCl(hihm)]Cl ( 7) is orthorhombic with the space group P2 12 12 1. Although in this copper(II) complex the copper atom is ligated by six atoms, it is more reasonable to think that the copper atom is in a trigonal bipyramidal geometry coordinated with five atoms: three hydroxyl oxygen atoms, a nitrogen atom and a chloride ion if the bond distances and angles surrounding the copper atom are taken into consideration. [Co(HCOO)(hihm)](HCOO) ( 8) is monoclinic with the space group P2 1. In cobalt(II) complex ( 8), the cobalt atom is in a distorted octahedral geometry, ligated by four hydroxyl oxygen atoms, a nitrogen atom and an oxygen atom of a formate ion. The structure of complex ( 8) is the same as the structure of [NiCl(hihm)]Cl·H 2O ( 6) except for the formate ion coordinating instead of the chloride ion. [M(hihm)(H 2O)]SO 4·H 2O (M: Co, Zn) ( 1, 4), [CoCl(hihm)]Cl·H 2O ( 5) and [M(HCOO)(hihm)](HCOO) (M: Ni, Cu, Zn) ( 9- 11) seem to have the same structures as the structures of [Ni(hihm)(H 2O)]SO 4·H 2O ( 2), [NiCl(hihm)]Cl·H 2O ( 6) and [Co(HCOO)(hihm)](HCOO) ( 8), respectively, judging by the results of IR and powder diffuse reflection spectra and powder X-ray diffraction analysis. Bis-Tris has coordinated to the metal atoms as a pentadentate ligand in all complexes of which the structures have been determined by single crystal X-ray diffraction analysis in this work.

TIMED/GUVI Observations of Aurora, Ionosphere, Thermosphere and Solar EUV Variations

NASA Astrophysics Data System (ADS)

Zhang, Y.; Paxton, L. J.; Schaefer, R. K.

2017-12-01

The FUV (100-200 nm) emissions from the ionosphere and thermosphere carry rich information of the density and composition of the IT system, aurora and solar EUV flux. The key emissions include atomic hydrogen line (121.6nm), atomic oxygen lines (e.g. 130.4, 135.6, 164.1 nm), atomic nitrogen lines (e.g. 120.0, 149.3, 174.3 nm), molecular nitrogen bands (LBH and VK bands) and nitric oxide ɛ bands. TIMED/GUVI data cover the nearly full FUV range and generate many space weather products (ionosphere, thermosphere, aurora and solar EUV) that extend the products from other missions (such as NASA GOLD and ICON) and help to solve some of MIT (Magnetosphere-Ionosphere-Thermosphere) science problems and serve as validation data sources for models.

Doping and vacancy effects of graphyne on SO2 adsorption.

PubMed

Kim, Sunkyung; Lee, Jin Yong

2017-05-01

The adsorption of sulfur dioxide (SO 2 ) on pristine and modified graphyne (including boron- or nitrogen- doping and introducing a single carbon atom defect) was investigated by density functional theory calculations. The structural, electronic, and magnetic properties of graphyne were changed according to the dopant atom site of doping and vacancy. SO 2 adsorption was obviously affected by modification of graphyne. SO 2 weakly interacted with pristine and nitrogen-doped graphynes. Boron doping at the sp-hybridized carbon site and introducing a single carbon atom vacancy in graphyne brought about a dramatic enhancement in SO 2 adsorption. The strongly chemisorbed SO 2 at these active sites caused deformation of the graphyne structure and electron redistribution, which induced changes in the conductivity and magnetism of graphynes. Copyright © 2017 Elsevier Inc. All rights reserved.

Ask the experts: past, present and future of the rule of five.

PubMed

Baell, Jonathan; Congreve, Miles; Leeson, Paul; Abad-Zapatero, Celerino

2013-05-01

Coined in 1997, by Christopher Lipinki et al., the rule of five (Ro5) comprises a set of parameters that determine drug-likeness for oral delivery. The parameters are as follows: no more than five hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms); no more than ten hydrogen bond acceptors (nitrogen or oxygen atoms); a molecular mass less than 500 Da; and an octanol-water partition coefficient log P no greater than 5. Future Medicinal Chemistry invited a selection of leading researchers to express their views on Lipinski's Ro5, which has influenced drug design for over a decade. Their enlightening responses provide an insight into the current and future role of Ro5, and other rules of thumb, in the evolving world of medicinal chemistry.

Compounds from the Fruits of the Popular European Medicinal Plant Vitex agnus-castus in Chemoprevention via NADP(H):Quinone Oxidoreductase Type 1 Induction.

PubMed

Li, Shenghong; Qiu, Shengxiang; Yao, Ping; Sun, Handong; Fong, Harry H S; Zhang, Hongjie

2013-01-01

As part of our continuing efforts in the search for potential biologically active compounds from medicinal plants, we have isolated 18 compounds including two novel nitrogen containing diterpenes from extracts of the fruits of Vitex agnus-castus. These isolates, along with our previously obtained novel compound vitexlactam A (1), were evaluated for potential biological effects, including cancer chemoprevention. Chemically, the nitrogenous isolates were found to be two labdane diterpene alkaloids, each containing an α , β -unsaturated γ -lactam moiety. Structurally, they were elucidated to be 9 α -hydroxy-13(14)-labden-16,15-amide (2) and 6 β -acetoxy-9 α -hydroxy-13(14)-labden-15,16-amide (3), which were named vitexlactams B and C, respectively. The 15 known isolates were identified as vitexilactone (4), rotundifuran (5), 8-epi-manoyl oxide (6), vitetrifolin D (7), spathulenol (8), cis-dihydro-dehydro-diconiferylalcohol-9-O- β -D-glucoside (9), luteolin-7-O-glucoside (10), 5-hydroxy-3,6,7,4'-tetramethoxyflavone (11), casticin (12), artemetin (13), aucubin (14), agnuside (15), β -sitosterol (16), p-hydroxybenzoic acid (17), and p-hydroxybenzoic acid glucose ester (18). All compound structures were determined/identified on the basis of 1D and/or 2D NMR and mass spectrometry techniques. Compounds 6, 8, 9, and 18 were reported from a Vitex spieces for the first time. The cancer chemopreventive potentials of these isolates were evaluated for NADP(H):quinone oxidoreductase type 1 (QR1) induction activity. Compound 7 demonstrated promising QR1 induction effect, while the new compound vitexlactam (3) was only slightly active.

Compounds from the Fruits of the Popular European Medicinal Plant Vitex agnus-castus in Chemoprevention via NADP(H):Quinone Oxidoreductase Type 1 Induction

PubMed Central

Li, Shenghong; Qiu, Shengxiang; Yao, Ping; Sun, Handong; Fong, Harry H. S.; Zhang, Hongjie

2013-01-01

As part of our continuing efforts in the search for potential biologically active compounds from medicinal plants, we have isolated 18 compounds including two novel nitrogen containing diterpenes from extracts of the fruits of Vitex agnus-castus. These isolates, along with our previously obtained novel compound vitexlactam A (1), were evaluated for potential biological effects, including cancer chemoprevention. Chemically, the nitrogenous isolates were found to be two labdane diterpene alkaloids, each containing an α, β-unsaturated γ-lactam moiety. Structurally, they were elucidated to be 9α-hydroxy-13(14)-labden-16,15-amide (2) and 6β-acetoxy-9α-hydroxy-13(14)-labden-15,16-amide (3), which were named vitexlactams B and C, respectively. The 15 known isolates were identified as vitexilactone (4), rotundifuran (5), 8-epi-manoyl oxide (6), vitetrifolin D (7), spathulenol (8), cis-dihydro-dehydro-diconiferylalcohol-9-O-β-D-glucoside (9), luteolin-7-O-glucoside (10), 5-hydroxy-3,6,7,4′-tetramethoxyflavone (11), casticin (12), artemetin (13), aucubin (14), agnuside (15), β-sitosterol (16), p-hydroxybenzoic acid (17), and p-hydroxybenzoic acid glucose ester (18). All compound structures were determined/identified on the basis of 1D and/or 2D NMR and mass spectrometry techniques. Compounds 6, 8, 9, and 18 were reported from a Vitex spieces for the first time. The cancer chemopreventive potentials of these isolates were evaluated for NADP(H):quinone oxidoreductase type 1 (QR1) induction activity. Compound 7 demonstrated promising QR1 induction effect, while the new compound vitexlactam (3) was only slightly active. PMID:23662135

Land application of tylosin and chlortetracycline swine manure: Impacts to soil nutrients and soil microbial community structure.

PubMed

Stone, James J; Dreis, Erin K; Lupo, Christopher D; Clay, Sharon A

2011-01-01

The land application of aged chortetracycle (CTC) and tylosin-containing swine manure was investigated to determine associated impacts to soil microbial respiration, nutrient (phosphorus, ammonium, nitrate) cycling, and soil microbial community structure under laboratory conditions. Two silty clay loam soils common to southeastern South Dakota were used. Aerobic soil respiration results using batch reactors containing a soil-manure mixture showed that interactions between soil, native soil microbial populations, and antimicrobials influenced CO(2) generation. The aged tylosin treatment resulted in the greatest degree of CO(2) inhibition, while the aged CTC treatment was similar to the no-antimicrobial treatment. For soil columns in which manure was applied at a one-time agronomic loading rate, there was no significant difference in soil-P behavior between either aged CTC or tylosin and the no-antimicrobial treatment. For soil-nitrogen (ammonium and nitrate), the aged CTC treatment resulted in rapid ammonium accumulation at the deeper 40cm soil column depth, while nitrate production was minimal. The aged CTC treatment microbial community structure was different than the no-antimicrobial treatment, where amines/amide and carbohydrate chemical guilds utilization profile were low. The aged tylosin treatment also resulted in ammonium accumulation at 40 cm column depth, however nitrate accumulation also occurred concurrently at 10 cm. The microbial community structure for the aged tylosin was also significantly different than the no-antimicrobial treatment, with a higher degree of amines/amides and carbohydrate chemical guild utilization compared to the no-antimicrobial treatment. Study results suggest that land application of CTC and tylosin-containing manure appears to fundamentally change microbial-mediated nitrogen behavior within soil A horizons.

Covalent nitrogen doping in molecular beam epitaxy-grown and bulk WSe2

NASA Astrophysics Data System (ADS)

Khosravi, Ava; Addou, Rafik; Smyth, Christopher M.; Yue, Ruoyu; Cormier, Christopher R.; Kim, Jiyoung; Hinkle, Christopher L.; Wallace, Robert M.

2018-02-01

Covalent p-type doping of WSe2 thin films grown by molecular beam epitaxy and WSe2 exfoliated from bulk crystals is achieved via remote nitrogen plasma exposure. X-ray photoelectron and Raman spectroscopies indicate covalently bonded nitrogen in the WSe2 lattice as well as tunable nitrogen concentration with N2 plasma exposure time. Furthermore, nitrogen incorporation induces compressive strain on the WSe2 lattice after N2 plasma exposure. Finally, atomic force microscopy and scanning tunneling microscopy reveal that N2 plasma treatment needs to be carefully tuned to avoid any unwanted strain or surface damage.

Biexciton emission from single isoelectronic traps formed by nitrogen-nitrogen pairs in GaAs

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

Takamiya, Kengo; Fukushima, Toshiyuki; Yagi, Shuhei

2013-12-04

We have studied photoluminescence (PL) from individual isoelectronic traps formed by nitrogen-nitrogen (NN) pairs in GaAs. Sharp emission lines due to exciton and biexciton were observed from individual isoelectronic traps in nitrogen atomic-layer doped (ALD) GaAs. The binding energy of biexciton bound to individual isoelectronic traps was approximately 8 meV. Both the exciton and biexciton luminescence lines show completely random polarization and no fine-structure splitting. These results are desirable to the application to the quantum cryptography used in the field of quantum information technology.

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

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.

In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Study on re-sputtering during CN{sub x} film deposition through spectroscopic diagnostics of plasma

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

Liang, Peipei; Yang, Xu; Li, Hui

2015-10-15

A nitrogen-carbon plasma was generated during the deposition of carbon nitride (CN{sub x}) thin films by pulsed laser ablation of a graphite target in a discharge nitrogen plasma, and the optical emission of the generated nitrogen-carbon plasma was measured for the diagnostics of the plasma and the characterization of the process of CN{sub x} film deposition. The nitrogen-carbon plasma was recognized to contain various species including nitrogen molecules and molecular ions excited in the ambient N{sub 2} gas, carbon atoms and atomic ions ablated from the graphite target and CN radicals. The temporal evolution and spatial distribution of the CNmore » emission and their dependence on the substrate bias voltage show two groups of CN radicals flying in opposite directions. One represents the CN radicals formed as the products of the reactions occurring in the nitrogen-carbon plasma, revealing the reactive deposition of CN{sub x} film due to the reactive expansion of the ablation carbon plasma in the discharge nitrogen plasma and the effective formation of gaseous CN radicals as precursors for CN{sub x} film growth. The other one represents the CN radicals re-sputtered from the growing CN{sub x} film by energetic plasma species, evidencing the re-sputtering of the growing film accompanying film growth. And, the re-sputtering presents ion-induced sputtering features.« less

Selective Mono-reduction of Pyrrole-2,5 and 2,4-Dicarboxylates.

PubMed

Yasui, Eiko; Tsuda, Jyunpei; Ohnuki, Satoshi; Nagumo, Shinji

2016-01-01

Pyrrole-2,5-dicarboxylates were rapidly and selectively reduced to the corresponding mono-alcohol using 3 eq of diisobutylaluminum hydride at 0°C. Pyrrole-2,4-dicarboxylate showed the same reactivity; however, the selectivity decreased with pyrrole-3,4-dicarboxylate. When the nitrogen atom of the pyrrole-2,5-dicarboxylate is protected with a benzyl group, selective mono-reduction does not occur. Considering that furan-2,5-dicarboxylates did not give the corresponding mono-alcohol under the same conditions, the unprotected nitrogen atom of pyrrole apparently plays an important role in this selective mono-reduction.

Combustor exhaust-emissions and blowout-limits with diesel number 2 and jet A fuels utilizing air-atomizing and pressure atomizing nozzles

NASA Technical Reports Server (NTRS)

Ingebo, R. D.; Norgren, C. T.

1975-01-01

Experimental tests with diesel number 2 and Jet A fuels were conducted in a combustor segment to obtain comparative data on exhaust emissions and blowout limits. An air-atomizing nozzle was used to inject the fuels. Tests were also made with diesel number 2 fuel using a pressure-atomizing nozzle to determine the effectiveness of the air-atomizing nozzle in reducing exhaust emissions. Test conditions included fuel-air ratios of 0.008 to 0.018, inlet-air total pressures and temperatures of 41 to 203 newtons per square centimeter and 477 to 811 K, respectively, and a reference velocity of 21.3 meters per second. Smoke number and unburned hydrocarbons were twice as high with diesel number 2 as with Jet A fuel. This was attributed to diesel number 2 having a higher concentration of aromatics and lower volatility than Jet A fuel. Oxides of nitrogen, carbon monoxide, and blowout limits were approximately the same for the two fuels. The air-atomizing nozzle, as compared with the pressure-atomizing nozzle, reduced oxides-of-nitrogen by 20 percent, smoke number by 30 percent, carbon monoxide by 70 percent, and unburned hydrocarbons by 50 percent when used with diesel number 2 fuel.

Characteristics of ammonia emission during thermal drying of lime sludge for co-combustion in cement kilns.

PubMed

Liu, Wei; Xu, Jingcheng; Liu, Jia; Cao, Haihua; Huang, Xiang-Feng; Li, Guangming

2015-01-01

Thermal drying was used to reduce sludge moisture content before co-combustion in cement kilns. The characteristics of ammonia (NH3) emission during thermal drying of lime sludge (LS) were investigated in a laboratory-scale tubular dry furnace under different temperature and time conditions. As the temperature increased, the NH3 concentration increased in the temperature range 100-130°C, decreased in the temperature range 130-220°C and increased rapidly at >220°C. Emission of NH3 also increased as the lime dosage increased and stabilized at lime dosages>5%. In the first 60 min of drying experiments, 55% of the NH3 was released. NH3 accounted for about 67-72% of the change in total nitrogen caused by the release of nitrogen-containing volatile compounds (VCs) from the sludge. X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy revealed that the main forms of nitrogen in sludge were amides and amines. The addition of lime (CaO) could cause conversion of N-H, N-O or C-N containing compounds to NH3 during the drying process.

The negative ions emission in nitrogen

NASA Technical Reports Server (NTRS)

Soon, W. H.; Kunc, J. A.

1991-01-01

The contribution of negative atomic ions to continuum radiation in nitrogen plasma is discussed. It is shown that both unstable N(-)(3P) and metastable N(-)(1D) ions have a significant effect on the total production of the continuum radiation at electron temperatures below 12,000 K.

N-type droping of nanocrystalline diamond films with nitrogen and electrodes made therefrom

DOEpatents

Gruen, Dieter M [Downers Grove, IL; Krauss, Alan R [late of Naperville, IL; Auciello, Orlando H [Bolingbrook, IL; Carlisle, John A [Plainfield, IL

2004-09-21

An electrically conducting n-type ultrananocrystalline diamond (UNCD) having no less than 10.sup.19 atoms/cm.sup.3 of nitrogen is disclosed. A method of making the n-doped UNCD. A method for predictably controlling the conductivity is also disclosed.

N-(Quinolin-8-yl)quinoline-2-carbox­amide

PubMed Central

Li, Yanfeng; Zhou, Hongbo; Shen, Xiaoping

2012-01-01

In the title compound, C19H13N3O, the dihedral angle between the two quinoline systems is 11.54 (3)°. The mol­ecular conformation is stabilized by intra­molecular N—H⋯N and C—H⋯O hydrogen bonds, with N—H⋯N being bifurcated towards the two N atoms of the two quinoline rings. In the crystal, there are weak intermolecular π–π inter­actions present involving the quinoline rings [centroid–centroid distance 3.7351 (14) Å]. PMID:22719482

Oligosaccharide Mimetics

NASA Astrophysics Data System (ADS)

Wessel, Hans Peter; Lucas, Susana Dias

The important roles of oligosaccharides in physiological and pathophysiological processes have spurred the development of mimetics. Oligosaccharide mimetics discussed in this chapter may possess a linker of two or more atoms such as amide or urea groups that may lead to isosteric linkage replacements but mostly do not. Larger groups that replace a full sugar unit we refer to as spacers and have grouped molecules with flexible acyclic spacers and more rigid cyclic spacers . The employment of pharmacophore models has led to oligosaccharide mimetics with only one sugar unit or finally without any saccharide unit as exemplified in mimotopes.

Arc Jet Flow Properties Determined from Laser-Induced Fluorescence of Atomic Nitrogen

NASA Technical Reports Server (NTRS)

Fletcher, Douglas; Wercinski, Paul F. (Technical Monitor)

1998-01-01

An laser-spectroscopic investigation of the thermocheMical state of arcjet flows is currently being conducted in the Aerodynamic Heating Facility (AHF) Circlet at NASA Ames Research Center. Downstream of the nozzle exit, but upstream of the test article, Laser-Induced Fluorescence (LIF) of atomic nitrogen is used to assess the nonequilibriuM distribution of flow enthalpy in the free stream. The two-photon LIF technique provides simultaneous measurements of free stream velocity, translational temperature, and nitrogen number density on the flow centerline. Along with information from facility instrumentation, these measurements allow a determination of the free stream total enthalpy, and its apportionment in to thermal, kinetic, and chemical mode contributions. Experimental results are presented and discussed for two different niti-ogen/argon test gas flow runs during which the current is varied while the pressure remains constant .

Amide and Ester-Functionalized Humic Acid for Fuel Combustion Enhancement

NASA Astrophysics Data System (ADS)

Riggs, Mark

Humic acid is a class of naturally occurring molecules composed of large sheet-like regions of cyclic aromatic hydrocarbon networks with surface and edge functional groups including phenols, carboxylic acids, and epoxides. These naturally occurring molecules are found in brown coal deposits near lignite formations. Humic acid has gained attention from the scientific community as a precursor for graphene. Graphene is a 2-dimensional honeycomb structure of fully unsaturated carbon atoms that has exceptional material properties and inherent aromaticity. Graphene's incredible properties are matched by the difficulty associated with reproducibly manufacturing it on a large scale. This issue has limited the use of graphene for commercial applications. The polar functional groups of humic acid contribute to the hydrophilic nature of the molecule, limiting its miscibility in any alkyl-based solvent. Surfactants containing long alkyl chains can affect the miscibility of the molecule in an organic solvent. Surfactants are often difficult to remove from the system. It is theorized that alkylation of the functional sites of humic acid can affect the hydrophilic nature of the molecule, and effectively enable its dispersion into organic solvents without simultaneous incorporation of surfactants. This dissertation investigated the amidation and esterification of humic acid molecules extracted from leonardite. The resulting change in the modified humic acid dispersibility in organic solvents and its potential usage as a fuel additive were evaluated. Butyl, hexyl, octyl, and decyl amide-modified and ester-modified humic acids were synthesized. These products were characterized to confirm successful chemical reaction through thermogravimetric analysis, Fourier-transform infrared spectroscopy, and scanning electron microscopy. The decyl-modified humic acids remained suspended in kerosene mixtures for longer than 1 week. Other organo-humic acids showed varying degrees of flocculation. The modified humic acid samples were diluted with kerosene to identify the influence on combustion properties. Butyl-modified humic acid samples decreased the molar enthalpy of combustion. Hexyl, octyl, and decyl-modified humic acids improved the combustion values. Decyl amide-modified humic acid showed the largest improvement of these mixtures with a 0.9% increase from the expected molar enthalpy of combustion with a loading percentage of 0.36% in kerosene. Octyl amide-modified and octyl ester-modified humic acid mixtures were prepared in 0.05, 0.1, and 1% loading percentage dilutions to study the effect of modified humic acid loading percent on combustion properties. The 0.1% dilution showed the largest increase of the expected molar enthalpy of combustion by 1.14% and 0.4% for amide-modified HA and ester-modified HA, respectively.

Mapping the amide I absorption in single bacteria and mammalian cells with resonant infrared nanospectroscopy

NASA Astrophysics Data System (ADS)

Baldassarre, L.; Giliberti, V.; Rosa, A.; Ortolani, M.; Bonamore, A.; Baiocco, P.; Kjoller, K.; Calvani, P.; Nucara, A.

2016-02-01

Infrared (IR) nanospectroscopy performed in conjunction with atomic force microscopy (AFM) is a novel, label-free spectroscopic technique that meets the increasing request for nano-imaging tools with chemical specificity in the field of life sciences. In the novel resonant version of AFM-IR, a mid-IR wavelength-tunable quantum cascade laser illuminates the sample below an AFM tip working in contact mode, and the repetition rate of the mid-IR pulses matches the cantilever mechanical resonance frequency. The AFM-IR signal is the amplitude of the cantilever oscillations driven by the thermal expansion of the sample after absorption of mid-IR radiation. Using purposely nanofabricated polymer samples, here we demonstrate that the AFM-IR signal increases linearly with the sample thickness t for t \\gt 50 nm, as expected from the thermal expansion model of the sample volume below the AFM tip. We then show the capability of the apparatus to derive information on the protein distribution in single cells through mapping of the AFM-IR signal related to the amide-I mid-IR absorption band at 1660 cm-1. In Escherichia Coli bacteria we see how the topography changes, observed when the cell hosts a protein over-expression plasmid, are correlated with the amide I signal intensity. In human HeLa cells we obtain evidence that the protein distribution in the cytoplasm and in the nucleus is uneven, with a lateral resolution better than 100 nm.

Structure-activity relationship studies on quinoxalin-2(1H)-one derivatives containing thiazol-2-amine against hepatitis C virus leading to the discovery of BH6870.

PubMed

Zhong, Qi-Fei; Liu, Rui; Liu, Gang

2015-11-01

Chronic hepatitis C virus infection represents a serious global public health problem, typically resulting in fibrosis, cirrhosis, and ultimately hepatocellular carcinoma. Based on our previous discovery of lead compound 2 (Liu et al. J Med Chem 54:5747-5768, 2011), 35 new quinoxalinone derivatives were explored in this study. Outline of the structure-activity relationships (SARs) revealed that compound BH6870 (36) showed high anti-HCV potency ([Formula: see text]) and a good cell safety index (SI [Formula: see text]). SARs analysis indicated that quinoxalin-2(1H)-one containing a 4-aryl-substituted thiazol-2-amine moiety was optimal for antiviral activity. Introducing a hydrogen-bond acceptor (such as ester or amide group) at the C-3 position of quinoxalin-2(1H)-one was beneficial for the antiviral potency, and especially, N,N-disubstituted amide was far superior to N-monosubstituted amide. Incorporation of more than one halogen (fluorine or chlorine atom) or a strong electron-withdrawing group on the benzene ring of the thiazole-phenyl moiety might reduce electron atmosphere density further and resulted in a dramatical loss of activity. The NH-group of the lactam moiety was clearly required for anti-HCV activity. Design and synthesis of quinoxalin-2(1H)-one derivatives as new non-nucleoside small-molecule HCV inhibitors. BH6870 (36), showing higher antiviral potency and a good cell safety index, was identified.

Nitrogen containing organic compounds in aerosols: results from TD-PTR-MS measurements during the CALNEX campaign

NASA Astrophysics Data System (ADS)

Holzinger, R.; Timkovsky, J.

2011-12-01

During the CALNEX campaign we deployed a thermal-desorption proton-transfer-reaction mass-spectrometer (TD-PTR-MS) at the Caltech ground site near downtown Los Angeles. The instrument was equipped with a time of flight mass spectrometer and a mass resolution power of ~4000 was realized under field conditions. Mass peaks could be determined at accuracy levels of +/- 3 mDa, which allowed identification by the empirical formula rather than by m/z alone. Over 900 ion species have been detected in aerosols. The largest signals (m/z 18.032, NH4+, and 45.991, NO2+) were attributed to ammonia and nitrate, respectively. 350 ion species accounted for 80% of the total measured mass of organic aerosol species. Of these, 66 species contained one nitrogen atom and 73 species contained two nitrogen atoms. Each group accounted for ~15% of the total measured mass. This suggests a ~30% contribution of nitrogen compounds to the total organic aerosol burden. However, this number could still underestimate the real fraction of nitrogen compounds for two reasons: (1) thermal desorption may cause decomposition of nitrogen compounds. E.g. peroxy nitrates rapidly decompose at temperatures above 100°C and produce NO2 which cannot be detected by the PTR-MS. (2) During protonation nitrogen functional groups may be preferentially lost. E.g. alkyl nitrates typically fragment during protonation in the PTR-MS. A minor fraction of the alkyl nitrates is detected as NO2+ and contributes to the signal at m/z 45.991, however, the majority is detected as alkyl ion without nitrogen. At this point it the overall loss of nitrogen due to these processes is hard to quantify. Our findings suggest that nitrogen chemistry plays a crucial role in producing secondary organic aerosol.

Tunable electronic properties of graphene through controlling bonding configurations of doped nitrogen atoms.

PubMed

Zhang, Jia; Zhao, Chao; Liu, Na; Zhang, Huanxi; Liu, Jingjing; Fu, Yong Qing; Guo, Bin; Wang, Zhenlong; Lei, Shengbin; Hu, PingAn

2016-06-21

Single-layer and mono-component doped graphene is a crucial platform for a better understanding of the relationship between its intrinsic electronic properties and atomic bonding configurations. Large-scale doped graphene films dominated with graphitic nitrogen (GG) or pyrrolic nitrogen (PG) were synthesized on Cu foils via a free radical reaction at growth temperatures of 230-300 °C and 400-600 °C, respectively. The bonding configurations of N atoms in the graphene lattices were controlled through reaction temperature, and characterized using Raman spectroscopy, X-ray photoelectron spectroscopy and scanning tunneling microscope. The GG exhibited a strong n-type doping behavior, whereas the PG showed a weak n-type doping behavior. Electron mobilities of the GG and PG were in the range of 80.1-340 cm(2) V(-1)·s(-1) and 59.3-160.6 cm(2) V(-1)·s(-1), respectively. The enhanced doping effect caused by graphitic nitrogen in the GG produced an asymmetry electron-hole transport characteristic, indicating that the long-range scattering (ionized impurities) plays an important role in determining the carrier transport behavior. Analysis of temperature dependent conductance showed that the carrier transport mechanism in the GG was thermal excitation, whereas that in the PG, was a combination of thermal excitation and variable range hopping.

Tunable electronic properties of graphene through controlling bonding configurations of doped nitrogen atoms

PubMed Central

Zhang, Jia; Zhao, Chao; Liu, Na; Zhang, Huanxi; Liu, Jingjing; Fu, Yong Qing; Guo, Bin; Wang, Zhenlong; Lei, Shengbin; Hu, PingAn

2016-01-01

Single–layer and mono–component doped graphene is a crucial platform for a better understanding of the relationship between its intrinsic electronic properties and atomic bonding configurations. Large–scale doped graphene films dominated with graphitic nitrogen (GG) or pyrrolic nitrogen (PG) were synthesized on Cu foils via a free radical reaction at growth temperatures of 230–300 °C and 400–600 °C, respectively. The bonding configurations of N atoms in the graphene lattices were controlled through reaction temperature, and characterized using Raman spectroscopy, X–ray photoelectron spectroscopy and scanning tunneling microscope. The GG exhibited a strong n–type doping behavior, whereas the PG showed a weak n–type doping behavior. Electron mobilities of the GG and PG were in the range of 80.1–340 cm2 V−1·s−1 and 59.3–160.6 cm2 V−1·s−1, respectively. The enhanced doping effect caused by graphitic nitrogen in the GG produced an asymmetry electron–hole transport characteristic, indicating that the long–range scattering (ionized impurities) plays an important role in determining the carrier transport behavior. Analysis of temperature dependent conductance showed that the carrier transport mechanism in the GG was thermal excitation, whereas that in the PG, was a combination of thermal excitation and variable range hopping. PMID:27325386

The first investigation of Wilms' tumour atomic structure-nitrogen and carbon isotopic composition as a novel biomarker for the most individual approach in cancer disease

PubMed Central

Taran, Katarzyna; Frączek, Tomasz; Sikora-Szubert, Anita; Sitkiewicz, Anna; Młynarski, Wojciech; Kobos, Józef; Paneth, Piotr

2016-01-01

The paper describes a novel approach to investigating Wilms' tumour (nephroblastoma) biology at the atomic level. Isotope Ratio Mass Spectrometry (IRMS) was used to directly assess the isotope ratios of nitrogen and carbon in 84 Wilms' tumour tissue samples from 28 cases representing the histological spectrum of nephroblastoma. Marked differences in nitrogen and carbon isotope ratios were found between nephroblastoma histological types and along the course of cancer disease, with a breakout in isotope ratio of the examined elements in tumour tissue found between stages 2 and 3. Different isotopic compositions with regard to nitrogen and carbon content were observed in blastemal Wilms' tumour, with and without focal anaplasia, and in poorly- and well-differentiated epithelial nephroblastoma. This first assessment of nitrogen and carbon isotope ratio reveals the previously unknown part of Wilms' tumour biology and represents a potential novel biomarker, allowing for a highly individual approach to treating cancer. Furthermore, this method of estimating isotopic composition appears to be the most sensitive tool yet for cancer tissue evaluation, and a valuable complement to established cancer study methods with prospective clinical impact. PMID:27732932

Highly enhanced electrochemical activity of Ni foam electrodes decorated with nitrogen-doped carbon nanotubes for non-aqueous redox flow batteries

NASA Astrophysics Data System (ADS)

Lee, Jungkuk; Park, Min-Sik; Kim, Ki Jae

2017-02-01

Nitrogen-doped carbon nanotubes (NCNTs) are directly grown on the surface of a three-dimensional (3D) Ni foam substrate by floating catalytic chemical vapor deposition (FCCVD). The electrochemical properties of the 3D NCNT-Ni foam are thoroughly examined as a potential electrode for non-aqueous redox flow batteries (RFBs). During synthesis, nitrogen atoms can be successfully doped onto the carbon nanotube (CNT) lattices by forming an abundance of nitrogen-based functional groups. The 3D NCNT-Ni foam electrode exhibits excellent electrochemical activities toward the redox reactions of [Fe (bpy)3]2+/3+ (in anolyte) and [Co(bpy)3]+/2+ (in catholyte), which are mainly attributed to the hierarchical 3D structure of the NCNT-Ni foam electrode and the catalytic effect of nitrogen atoms doped onto the CNTs; this leads to faster mass transfer and charge transfer during operation. As a result, the RFB cell assembled with 3D NCNT-Ni foam electrodes exhibits a high energy efficiency of 80.4% in the first cycle; this performance is maintained up to the 50th cycle without efficiency loss.

The role of nitrogen doping in ALD Ta2O5 and its influence on multilevel cell switching in RRAM

NASA Astrophysics Data System (ADS)

Sedghi, N.; Li, H.; Brunell, I. F.; Dawson, K.; Potter, R. J.; Guo, Y.; Gibbon, J. T.; Dhanak, V. R.; Zhang, W. D.; Zhang, J. F.; Robertson, J.; Hall, S.; Chalker, P. R.

2017-03-01

The role of nitrogen doping on the stability and memory window of resistive state switching in N-doped Ta2O5 deposited by atomic layer deposition is elucidated. Nitrogen incorporation increases the stability of resistive memory states which is attributed to neutralization of electronic defect levels associated with oxygen vacancies. The density functional simulations with the screened exchange hybrid functional approximation show that the incorporation of nitrogen dopant atoms in the oxide network removes the O vacancy midgap defect states, thus nullifying excess defects and eliminating alternative conductive paths. By effectively reducing the density of vacancy-induced defect states through N doping, 3-bit multilevel cell switching is demonstrated, consisting of eight distinctive resistive memory states achieved by either controlling the set current compliance or the maximum voltage during reset. Nitrogen doping has a threefold effect: widening the switching memory window to accommodate the more intermediate states, improving the stability of states, and providing a gradual reset for multi-level cell switching during reset. The N-doped Ta2O5 devices have relatively small set and reset voltages (< 1 V) with reduced variability due to doping.

Synthesis of mesoporous TiO(2-x)N(x) spheres by template free homogeneous co-precipitation method and their photo-catalytic activity under visible light illumination.

PubMed

Parida, K M; Naik, Brundabana

2009-05-01

The article presents preparation, characterization and catalytic activity evaluation of an efficient nitrogen doped mesoporous titania sphere photo-catalyst for degradation of methylene blue (MB) and methyl orange (MO) under visible light illumination. Nitrogen doped titania was prepared by soft chemical route i.e. template free, slow and controlled homogeneous co-precipitation from titanium oxysulfate sulfuric acid complex hydrate, urea, ethanol and water. The molar composition of TiOSO(4) to urea was varied to prepare different atomic % nitrogen doped titania. Mesoporous anatase TiO(2-x)N(x) spheres with average crystallite size of 10 nm and formation of titanium oxynitride center were confirmed from HRTEM, XRD and XPS study. UV-vis DRS showed a strong absorption in the range of 400-500 nm which supports its use in visible spectrum of light. Nitrogen adsorption-desorption study supports the porous nature of the doped material. All the TiO(2-x)N(x) samples showed higher photo-catalytic activity than Degussa P(25) and undoped mesoporous titania. Sample containing around one atomic % nitrogen showed highest activity among the TiO(2-x)N(x) samples.

40 CFR 63.1292 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... added to assist foaming by generating gas beyond that resulting from the isocyanate-water reaction..., material safety data sheets, or engineering calculations. High-pressure mixhead means a mixhead where.... Isocyanate means a reactive chemical grouping composed of a nitrogen atom bonded to a carbon atom bonded to...

Computational study on the functionalization of BNNC with pyrrole molecule

NASA Astrophysics Data System (ADS)

Payvand, Akram; Tavangar, Zahra

2018-05-01

The functionalization of the boron nitride nanocone (BNNC) by pyrrole molecule was studied using B3LYP/6-311+G(d) level of theory. The reaction was studied in three methods in different layers of the nanocone: Diels-Alder cycloaddition, quartet cycloaddition and the reaction of the nitrogen atom of the pyrrole molecule with the boron or nitrogen atom of the BNNC. Thermodynamic quantities, Chemical hardness and potential and electrophilicity index of the functionalized BNNC were studied. The results show that the tip of nanocone has a higher tendency for participation in the reaction and the most favorable product of the reaction between BNNC and pyrrole molecule is produced from the reaction of N atom of pyrrole with the B atom of BNNC. The reaction decreases the energy gap value which leads to increasing the reactivity and conductivity of functionalized nanocone. The calculated NICS values confirm the aromaticity in the pristine nanocone as well as in the functionalized nanocone.

Kankan diamonds (Guinea) III: δ13C and nitrogen characteristics of deep diamonds

NASA Astrophysics Data System (ADS)

Stachel, T.; Harris, J. W.; Aulbach, S.; Deines, P.

Diamonds from the Kankan area in Guinea formed over a large depth profile beginning within the cratonic mantle lithosphere and extending through the asthenosphere and transition zone into the lower mantle. The carbon isotopic composition, the concentration of nitrogen impurities and the nitrogen aggregation level of diamonds representing this entire depth range have been determined. Peridotitic and eclogitic diamonds of lithospheric origin from Kankan have carbon isotopic compositions (δ13C: peridotitic -5.4 to -2.2‰ eclogitic -19.7 to -0.7‰) and nitrogen characteristics (N: peridotitic 17-648 atomic ppm; eclogitic 0-1,313 atomic ppm; aggregation from IaA to IaB) which are generally typical for diamonds of these two suites worldwide. Geothermobarometry of peridotitic and eclogitic inclusion parageneses (worldwide sources) indicates that both suites formed under very similar conditions within the cratonic lithosphere, which is not consistent with a derivation of diamonds with light carbon isotopic composition from subducted organic matter within subducting oceanic slabs. Diamonds containing majorite garnet inclusions fall to the isotopically heavy side (δ13C: -3.1‰ to +0.9‰) of the worldwide diamond population. Nitrogen contents are low (0-126 atomic ppm) and one of the two nitrogen-bearing diamonds shows such a low level of nitrogen aggregation (30% B-centre) that it cannot have been exposed to ambient temperatures of the transition zone (>=1,400 °C) for more than 0.2 Ma. This suggests rapid upward transport and formation of some Kankan diamonds pene-contemporaneous to Cretaceous kimberlite activity. Similar to these diamonds from the asthenosphere and the transition zone, lower mantle diamonds show a small shift towards isotopic heavy compositions (-6.6 to -0.5‰, mode at -3.5‰). As already observed for other mines, the nitrogen contents of lower mantle diamonds were below detection (using FTIRS). The mutual shift of sublithospheric diamonds towards isotopic heavier compositions suggests a common carbon source, which may have inherited an isotopic heavy composition from a component consisting of subducted carbonates.

Kankan diamonds (Guinea) III: δ13C and nitrogen characteristics of deep diamonds

NASA Astrophysics Data System (ADS)

Stachel, T.; Harris, J. W.; Aulbach, S.; Deines, P.

2001-08-01

Diamonds from the Kankan area in Guinea formed over a large depth profile beginning within the cratonic mantle lithosphere and extending through the asthenosphere and transition zone into the lower mantle. The carbon isotopic composition, the concentration of nitrogen impurities and the nitrogen aggregation level of diamonds representing this entire depth range have been determined. Peridotitic and eclogitic diamonds of lithospheric origin from Kankan have carbon isotopic compositions (δ13C: peridotitic -5.4 to -2.2‰ eclogitic -19.7 to -0.7‰) and nitrogen characteristics (N: peridotitic 17-648 atomic ppm; eclogitic 0-1,313 atomic ppm; aggregation from IaA to IaB) which are generally typical for diamonds of these two suites worldwide. Geothermobarometry of peridotitic and eclogitic inclusion parageneses (worldwide sources) indicates that both suites formed under very similar conditions within the cratonic lithosphere, which is not consistent with a derivation of diamonds with light carbon isotopic composition from subducted organic matter within subducting oceanic slabs. Diamonds containing majorite garnet inclusions fall to the isotopically heavy side (δ13C: -3.1‰ to +0.9‰) of the worldwide diamond population. Nitrogen contents are low (0-126 atomic ppm) and one of the two nitrogen-bearing diamonds shows such a low level of nitrogen aggregation (30% B-centre) that it cannot have been exposed to ambient temperatures of the transition zone (>=1,400 °C) for more than 0.2 Ma. This suggests rapid upward transport and formation of some Kankan diamonds pene-contemporaneous to Cretaceous kimberlite activity. Similar to these diamonds from the asthenosphere and the transition zone, lower mantle diamonds show a small shift towards isotopic heavy compositions (-6.6 to -0.5‰, mode at -3.5‰). As already observed for other mines, the nitrogen contents of lower mantle diamonds were below detection (using FTIRS). The mutual shift of sublithospheric diamonds towards isotopic heavier compositions suggests a common carbon source, which may have inherited an isotopic heavy composition from a component consisting of subducted carbonates.

Data analysis in Raman measurements of biological tissues using wavelet techniques

NASA Astrophysics Data System (ADS)

Gaeta, Giovanni M.; Zenone, Flora; Camerlingo, Carlo; Riccio, Roberto; Moro, Gianfranco; Lepore, Maria; Indovina, Pietro L.

2005-03-01

Raman spectroscopy of oral tissues is a promising tool for in vivo diagnosis of oral pathologies, due to the high chemical and structural information content of Raman spectra. However, measurements on biological tissues are usually hindered by low level signals and by the presence of interfering noise and background components due to light diffusion or fluorescence processes. Numerical methods can be used in data analysis, in order to overcome these problems. In this work the wavelet multicomponent decomposition approach has been tested in a series of micro-Raman measurements performed on "in vitro" animal tissue samples. The experimental set-up was mainly composed by a He-Ne laser and a monochromator equipped with a liquid nitrogen cooled CCD equipped with a grating of 1800 grooves/mm. The laser light was focused on the sample surface by means of a 50 X optical objective. The resulting spectra were analysed using a wavelet software package and the contribution of different vibration modes have been singled out. In particular, the C=C stretching mode, and the CH2 bending mode of amide I and amide III and tyrosine contributions were present. The validity of wavelet approach in the data treatment has been also successfully tested on aspirin.

Kinetics and mechanisms of some atomic oxygen reactions

NASA Technical Reports Server (NTRS)

Cvetanovic, R. J.

1987-01-01

Mechanisms and kinetics of some reactions of the ground state of oxygen atoms, O(3P), are briefly summarized. Attention is given to reactions of oxygen atoms with several different types of organic and inorganic compounds such as alkanes, alkenes, alkynes, aromatics, and some oxygen, nitrogen, halogen and sulfur derivatives of these compounds. References to some recent compilations and critical evaluations of reaction rate constants are given.

Density functional theory study of nitrogen atoms and molecules interacting with Fe(1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Nosir, M. A.; Martin-Gondre, L.; Bocan, G. A.; Díez Muiño, R.

2016-09-01

We present Density functional theory (DFT) calculations for the investigation of the structural relaxation of Fe(1 1 1), as well as for the study of the interaction of nitrogen atoms and molecules with this surface. We perform spin polarized DFT calculations using VASP (Vienna Ab-initio Simulation Package) code. We use the supercell approach and up to 19 slab layers for the relaxation of the Fe(1 1 1) surface. We find a contraction of the first two interlayer distances with a relative value of Δ12 = - 7.8 % and Δ23 = - 21.7 % with respect to the bulk reference. The third interlayer distance is however expanded with a relative change of Δ34 = 9.7 % . Early experimental studies of the surface relaxation using Low Energy Electron Diffraction (LEED) and Medium Energy Ion Scattering (MEIS) showed contradictory results, even on the relaxation general trend. Our current theoretical results support the LEED conclusions and are consistent qualitatively with other recent theoretical calculations. In addition, we study the interaction energy of nitrogen atoms and molecules on the Fe(1 1 1) surface. The nitrogen atoms are adsorbed in the hollow site of the unit cell, with an adsorption energy consistent with the one found in previous studies. In addition, we find the three molecularly adsorbed states that are observed experimentally. Two of them correspond to the adsorbed molecule oriented normal to the surface and a third one corresponds to the molecule adsorbed parallel to the surface. We conclude that our results are accurate enough to be used to build a full six-dimensional potential energy surface for the N2 system.

Tetrabenzoporphyrin and -mono-, -cis-di- and Tetrabenzotriazaporphyrin Derivatives: Electrochemical and Spectroscopic Implications of meso CH Group Replacement with Nitrogen.

PubMed

van As, Adele; Joubert, Chris C; Buitendach, Blenerhassitt E; Erasmus, Elizabeth; Conradie, Jeanet; Cammidge, Andrew N; Chambrier, Isabelle; Cook, Michael J; Swarts, Jannie C

2015-06-01

Nonperipherally hexyl-substituted metal-free tetrabenzoporphyrin (2H-TBP, 1a) tetrabenzomonoazaporphyrin (2H-TBMAP, 2a), tetrabenzo-cis-diazaporphyrin (2H-TBDAP, 3a), tetrabenzotriazaporphyrin (2H-TBTAP, 4a), and phthalocyanine (2H-Pc, 5a), as well as their copper complexes (1b-5b), were synthesized. As the number of meso nitrogen atoms increases from zero to four, λmax of the Q-band absorption peak becomes red-shifted by almost 100 nm, and extinction coefficients increased at least threefold. Simultaneously the blue-shifted Soret (UV) band substantially decreased in intensity. These changes were related to the relative electron-density of each macrocycle expressed as the group electronegativity sum of all meso N and CH atom groups, ∑χR. X-ray photoelectron spectroscopy differentiated between the three different types of macrocyclic nitrogen atoms (the Ninner, (NH)inner, and Nmeso) in the metal-free complexes. Binding energies of the Nmeso and Ninner,Cu atoms in copper chelates could not be resolved. Copper insertion lowered especially the cathodic redox potentials, while all four observed redox processes occurred at larger potentials as the number of meso nitrogens increased. Computational chemical methods using density functional theory confirmed 1b to exhibit a Cu(II) reduction prior to ring-based reductions, while for 2b, Cu(II) reduction is the first reductive step only if the nonperipheral substituents are hydrogen. When they are methyl groups, it is the second reduction process; when they are ethyl, propyl, or hexyl, it becomes the third reductive process. Spectro-electrochemical measurements showed redox processes were associated with a substantial change in intensity of at least two main absorbances (the Q and Soret bands) in the UV spectra of these compounds.

Spectroscopic Determination of Trace Contaminants in High-Purity Oxygen

NASA Technical Reports Server (NTRS)

Hornung, Steven

2013-01-01

Oxygen used for extravehicular activities (EVAs) must be free of contaminants because a difference in a few tenths of a percent of argon or nitrogen content can mean significant reduction in available EVA time. These inert gases build up in the extravehicular mobility unit because they are not metabolized or scrubbed from the atmosphere. A prototype optical emission technique capable of detecting argon and nitrogen below 0.1% in oxygen has been developed. This instrument uses a glow discharge in reduced-pressure gas to produce atomic emission from the species present. Because the atomic emission lines from oxygen, nitrogen, and argon are discrete, and in many cases well-separated, trace amounts of argon and nitrogen can be detected in the ultraviolet and visible spectrum. This is a straightforward, direct measurement of the target contaminants, and may lend itself to a device capable of on-orbit verification of oxygen purity. A glow discharge is a plasma formed in a low-pressure (1 to 10 Torr) gas cell between two electrodes. Depending on the configuration, voltages ranging from 200 V and above are required to sustain the discharge. In the discharge region, the gas is ionized and a certain population is in the excited state. Light is produced by the transitions from the excited states formed in the plasma to the ground state. The spectrum consists of discrete, narrow emission lines for the atomic species, and broader peaks that may appear as a manifold for molecular species such as O2 and N2, the wavelengths and intensities of which are a characteristic of each atom. The oxygen emission is dominated by two peaks at 777 and 844 nm.

Miscut dependent surface evolution in the process of N-polar GaN(000 1 bar) growth under N-rich condition

NASA Astrophysics Data System (ADS)

Krzyżewski, Filip; Załuska-Kotur, Magdalena A.; Turski, Henryk; Sawicka, Marta; Skierbiszewski, Czesław

2017-01-01

The evolution of surface morphology during the growth of N-polar (000 1 bar) GaN under N-rich conditions is studied by kinetic Monte Carlo (kMC) simulations for two substrates miscuts 2° and 4°. The results are compared with experimentally observed surface morphologies of (000 1 bar) GaN layers grown by plasma-assisted molecular beam epitaxy. The proposed kMC two-component model of GaN(000 1 bar) surface where both types of atoms, nitrogen and gallium, attach to the surface and diffuse independently shows that at relatively high rates of the step flow (miscut angle < 2 °) the low mobility of gallium adatoms causes surface instabilities and leads to experimentally observed roughening while for low rates of the step flow (miscut 4°), smooth surface can be obtained. In the presence of almost immobile nitrogen atoms under N-rich conditions crystal growth is realized by the process of two-dimensional island nucleation and coalescence. Larger crystal miscut, lower growth rate or higher temperature results in similar effect of the surface smoothening. We show that the surface also smoothens for the growth conditions with very high N-excess. In the presence of large number of nitrogen atoms the mobility of gallium atoms changes locally thus providing easier coalescence of separated island.

Synthesis and application of a new fluorous-tagged ammonia equivalent.

PubMed

Nielsen, Simon D; Smith, Garrick; Begtrup, Mikael; Kristensen, Jesper L

2010-04-19

A novel fluorous-tagged ammonia equivalent has been developed. It is based on a nitrogen-oxygen bond, which can be cleaved in a traceless manner by a molybdenum complex or samarium diiodide. The application in the synthesis of ureas, amides, sulfonamides, and carbamates is described. The scope of the fluorous N-O linker is exemplified by the synthesis of itopride, a drug used for the treatment of functional dyspepsia. Itopride was synthesized with the aid of fluorous purification methods and the product was isolated in good overall yield, with high purity. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Semiconductor to metal transition by tuning the location of N{sub 2}{sup AA} in armchair graphene nanoribbons

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

Chen, Tong; Wang, Ling-Ling, E-mail: llwang@hnu.edu.cn; Li, Quan

2014-02-07

The electronic band structures and transport properties of N{sub 2}{sup AA}-doped armchair graphene nanoribbons (aGNRs) with two quasi-adjacent substitutional nitrogen atoms incorporated in pairs of neighboring carbon atoms in the same sublattice A are investigated by using non-equilibrium Green function formalism in combination with density functional theory. The results show that the coupling effect between the Pz orbitals of carbon and nitrogen atoms plays an important role in the transition between semiconductor and metal by different locations of N{sub 2}{sup AA}-doped aGNRs. And the striking negative differential resistance behaviors can be found in such devices. These tremendous properties suggest potentialmore » application of N{sub 2}{sup AA}-doped aGNRs in graphene-based nanoelectronic devices.« less

A pseudoatom in a cage: trimetallofullerene Y(3)@C(80) mimics y(3)n@c(80) with nitrogen substituted by a pseudoatom.

PubMed

Popov, Alexey A; Zhang, Lin; Dunsch, Lothar

2010-02-23

Y(3)C(80) obtained in the synthesis of nitride clusterfullerenes Y(3)N@C(2n) (2n = 80-88) by the reactive atmosphere method is found to be a genuine trimetallofullerene, Y(3)@C(80), with low ionization potential and divalent state of yttrium atoms. DFT studies of the electronic structure of Y(3)@C(80) show that this molecule mimics Y(3)N@C(80) with the pseudoatom (PA) instead of the nitrogen atom. Topology analysis of the electron density and electron localization function show that yttrium atoms form Y-PA bonds rather than direct Y-Y bonds. Molecular dynamics simulations show that the Y(3)PA cluster is as rigid as Y(3)N and rotates inside the fullerene cage as a single entity.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

2016-03-01

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

Theoretical studies of the transition state structures and free energy barriers for base-catalyzed hydrolysis of amides

PubMed Central

Xiong, Ying; Zhan, Chang-Guo

2010-01-01

The transition state structures and free energy barriers for the rate-determining step (i.e. the formation of a tetrahedral intermediate) of base-catalyzed hydrolysis of a series of amides in aqueous solution have been studied by performing first-principle electronic structure calculations using a hybrid supermolecule-polarizable continuum approach. The calculated results and a revisit of recently reported experimental proton inventory data reveal that the favorable transition state structure optimized for the tetrahedral intermediate formation of hydroxide ion-catalyzed hydrolysis of formamide may have three solvating water molecules remaining on the attacking hydroxide oxygen and two additional water molecules attached to the carbonyl oxygen of formamide. The calculated results have also demonstrated interesting substituent effects on the optimized transition state geometries, on the transition-state stabilization, and on the calculated free energy barriers for the base-catalyzed hydrolysis of amides. When some or all of the hydrogen atoms of formamide are replaced by methyl groups, the total number of water molecules hydrogen-bonding with the attacking hydroxide in the transition state decreases from three for formamide to two for N-methylacetamide, N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA). The larger substituents of the amide hinder the solvent water molecules approaching the attacking hydroxide oxygen in the transition state and, therefore, destabilize the transition state structure and increase the free energy barrier. By using the optimized most favorable transition state structures, the calculated free energy barriers, i.e. 21.6 (or 21.7), 22.7, 23.1, and 26.0 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively, are in good agreement with the available experimental free energy barriers, i.e. 21.2, 21.5, 22.6, and 24.1 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively. PMID:17107116

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

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

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de

2016-03-21

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). Formore » the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.« less

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

Fluorescent chemosensor for pyridine based on N-doped carbon dots.

PubMed

Campos, B B; Abellán, C; Zougagh, M; Jimenez-Jimenez, J; Rodríguez-Castellón, E; Esteves da Silva, J C G; Ríos, A; Algarra, M

2015-11-15

Fluorescent carbon dots (CDs) and its nitrogen doped (N-CDs) nanoparticles have been synthesized from lactose as precursor using a bottom-up hydrothermal methodology. The synthesized nanoparticles have been characterized by elemental analysis, FTIR, Raman, TEM, DLS, XPS, and steady-state and life-time fluorescence. The synthesized carbon nanoparticles, CDs and N-CDs, have a size at about 7.7±2.4 and 50±15nm, respectively, and quantum yields of 8% (CDs) and 11% (N-CDs). These techniques demonstrated the effectiveness of the synthesis procedure and the functionalization of the CDs surface with amine and amide groups in the presence of NH3 in aqueous media. The effect of excitation wavelength and pH on the luminescent properties was studied. Under the optimal conditions, the nitrogen doped nanoparticles can be used as pyridine sensor in aqueous media because they show an enhancement of its fluorescence with a good linear relationship. The analytical method is simple, reproducible and very sensitive for pyridine determination. Copyright © 2015 Elsevier Inc. All rights reserved.

Secondary metabolites from marine microorganisms.

PubMed

Kelecom, Alphonse

2002-03-01

After 40 years of intensive research, chemistry of marine natural products has become a mature field. Since 1995, there are signals of decreased interest in the search of new metabolites from traditional sources such as macroalgae and octocorals, and the number of annual reports on marine sponges stabilized. On the contrary, metabolites from microorganisms is a rapidly growing field, due, at least in part, to the suspicion that a number of metabolites obtained from algae and invertebrates may be produced by associated microorganisms. Studies are concerned with bacteria and fungi, isolated from seawater, sediments, algae, fish and mainly from marine invertebrates such as sponges, mollusks, tunicates, coelenterates and crustaceans. Although it is still to early to define tendencies, it may be stated that the metabolites from microorganisms are in most cases quite different from those produced by the invertebrate hosts. Nitrogenated metabolites predominate over acetate derivatives, and terpenes are uncommon. Among the latter, sesquiterpenes, diterpenes and carotenes have been isolated; among nitrogenated metabolites, amides, cyclic peptides and indole alkaloids predominate.

Ammonia formation by a thiolate-bridged diiron amide complex as a nitrogenase mimic

NASA Astrophysics Data System (ADS)

Li, Yang; Li, Ying; Wang, Baomin; Luo, Yi; Yang, Dawei; Tong, Peng; Zhao, Jinfeng; Luo, Lun; Zhou, Yuhan; Chen, Si; Cheng, Fang; Qu, Jingping

2013-04-01

Although nitrogenase enzymes routinely convert molecular nitrogen into ammonia under ambient temperature and pressure, this reaction is currently carried out industrially using the Haber-Bosch process, which requires extreme temperatures and pressures to activate dinitrogen. Biological fixation occurs through dinitrogen and reduced NxHy species at multi-iron centres of compounds bearing sulfur ligands, but it is difficult to elucidate the mechanistic details and to obtain stable model intermediate complexes for further investigation. Metal-based synthetic models have been applied to reveal partial details, although most models involve a mononuclear system. Here, we report a diiron complex bridged by a bidentate thiolate ligand that can accommodate HN=NH. Following reductions and protonations, HN=NH is converted to NH3 through pivotal intermediate complexes bridged by N2H3- and NH2- species. Notably, the final ammonia release was effected with water as the proton source. Density functional theory calculations were carried out, and a pathway of biological nitrogen fixation is proposed.

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

PubMed Central

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

2014-01-01

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

Synthesis of nitriles via palladium-catalyzed water shuffling from amides to acetonitrile.

PubMed

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

2014-12-07

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

Motion of protons in the central opening of porphyrins

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

Zayats, V.Y.; Lobanov, V.V.; Pinchuk, V.M.

1986-09-01

The distribution of the electrostatic potential of the molecule of porphine (P) and the anions formed by the successive elimination of one and two central protons from it has been studied by the SCF-MO-LCAO method in the all-valence-electron CNDO/2 approximation. The electrostatic potential of the potential of the (P-2HO/sup 2 -/ dianion is characterized by the presence of four minima located at a distance of about 1 A from the nitrogen atoms. The potential in them is equal to -991 kJ/mole. The value of the potential at the center of the opening is -978 kJ/mole. The distribution of the electrostaticmore » potential of the (P-H)/sup -/ anion with a fixed position of the proton near one of the nitrogen atoms is characterized by the presence of a deep valley situated at the oppositely lying nitrogen atom perpendicularly to the N-H bond. The potential of the molecule of P in the plane of the ring does not have negative values, attesting to the energetic unfavorability of the planar conformations of the (P+H)/sup +/ cation.« less

Behaviors of Absolute Densities of N, H, and NH3 at Remote Region of High-Density Radical Source Employing N2-H2 Mixture Plasmas

NASA Astrophysics Data System (ADS)

Chen, Shang; Kondo, Hiroki; Ishikawa, Kenji; Takeda, Keigo; Sekine, Makoto; Kano, Hiroyuki; Den, Shoji; Hori, Masaru

2011-01-01

For an innovation of molecular-beam-epitaxial (MBE) growth of gallium nitride (GaN), the measurements of absolute densities of N, H, and NH3 at the remote region of the radical source excited by plasmas have become absolutely imperative. By vacuum ultraviolet absorption spectroscopy (VUVAS) at a relatively low pressure of about 1 Pa, we obtained a N atom density of 9×1012 cm-3 for a pure nitrogen gas used, a H atom density of 7×1012 cm-3 for a gas composition of 80% hydrogen mixed with nitrogen gas were measured. The maximum density 2×1013 cm-3 of NH3 was measured by quadruple mass spectrometry (QMS) at H2/(N2+H2)=60%. Moreover, we found that N atom density was considerably affected by processing history, where the characteristic instability was observed during the pure nitrogen plasma discharge sequentially after the hydrogen-containing plasma discharge. These results indicate imply the importance of establishing radical-based processes to control precisely the absolute densities of N, H, and NH3 at the remote region of the radical source.

Observation of Landau levels on nitrogen-doped flat graphite surfaces without external magnetic fields

PubMed Central

Kondo, Takahiro; Guo, Donghui; Shikano, Taishi; Suzuki, Tetsuya; Sakurai, Masataka; Okada, Susumu; Nakamura, Junji

2015-01-01

Under perpendicular external magnetic fields, two-dimensional carriers exhibit Landau levels (LLs). However, it has recently been reported that LLs have been observed on graphene and graphite surfaces without external magnetic fields being applied. These anomalous LLs have been ascribed primarily to a strain of graphene sheets, leading to in-plane hopping modulation of electrons. Here, we report the observation of the LLs of massive Dirac fermions on atomically flat areas of a nitrogen-doped graphite surface in the absence of external magnetic fields. The corresponding magnetic fields were estimated to be as much as approximately 100 T. The generation of the LLs at the area with negligible strain can be explained by inequivalent hopping of π electrons that takes place at the perimeter of high-potential domains surrounded by positively charged substituted graphitic-nitrogen atoms. PMID:26549618

Combustor exhaust emissions with air-atomizing splash-groove fuel injectors burning Jet A and Diesel number 2 fuels

NASA Technical Reports Server (NTRS)

Ingebo, R. D.; Norgren, C. T.

1975-01-01

Air-atomizing, splash-groove injectors were shown to improve primary-zone fuel spreading and reduce combustor exhaust emissions for Jet A and diesel number 2 fuels. With Jet A fuel large-orifice, splash-groove injectors the oxides-of-nitrogen emission index was reduced, but emissions of carbon monoxide, unburned hydrocarbons, or smoke were unaffected. Small-orifice, splash-groove injectors did not reduce oxides of nitrogen, but reduced the smoke number and carbon monoxide and unburned-hydrocarbon emission indices. With diesel number 2 fuel, the small-orifice, splash-groove injectors reduced oxides of nitrogen by 19 percent, smoke number by 28 percent, carbon monoxide by 75 percent, and unburned hydrocarbons by 50 percent. Smoke number and unburned hydrocarbons were twice as high with diesel number 2 as with Jet A fuel. Combustor blowout limits were similar for diesel number 2 and Jet A fuels.

Isolated boron and nitrogen sites on porous graphitic carbon synthesized from nitrogen-containing chitosan for supercapacitors.

PubMed

Sun, Li; Fu, Yu; Tian, Chungui; Yang, Ying; Wang, Lei; Yin, Jie; Ma, Jing; Wang, Ruihong; Fu, Honggang

2014-06-01

Separated boron and nitrogen porous graphitic carbon (BNGC) is fabricated by a facile hydrothermal coordination/ZnCl2-activation process from renewable and inexpensive nitrogen-containing chitosan. In this synthetic pathway, chitosan, which has a high nitrogen content, first coordinates with Fe(3+) ions to form chitosan-Fe that subsequently reacts with boric acid (boron source) to generate the BNGC precursor. After simultaneous carbonization and ZnCl2 activation followed by removal of the Fe catalyst, BNGC, containing isolated boron and nitrogen centers and having a high surface area of 1567 m(2)  g(-1) and good conductivity, can be obtained. Results indicate that use of chitosan as a nitrogen-containing carbon source effectively prevents nitrogen atoms from direct combination with boron atoms. In addition, the incorporation of Fe(3+) ions not only endows BNGC with high graphitization, but also favors for nitrogen fixation. Remarkably, the unique microstructure of BNGC enables its use as an advanced electrode material for energy storage. As electrode material for supercapacitors, BNGC shows a high capacitance of 313 F g(-1) at 1 A g(-1), and also long-term durability and coulombic efficiency of >99.5 % after 5000 cycles. Notably, in organic electrolytes, the energy density could be up to 50.1 Wh kg(-1) at a power density of 10.5 kW kg(-1). The strategy developed herein opens a new avenue to prepare BNGC without inactive BN bonds from commercially available chitosan for high-performance supercapacitors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural stability and O{sub 2} dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

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

Yang, Mingye; Wang, Lu, E-mail: lwang22@suda.edu.cn, E-mail: yyli@suda.edu.cn; Li, Min

2015-06-15

By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped) graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM) atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N{sub 4}V {sub 2} forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O{sub 2} dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N,more » the graphitic-N is more favorable to dissociate O{sub 2} molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.« less

Nitrogen-atom endohedral fullerene synthesis with high efficiency by controlling plasma-ion irradiation energy and C60 internal energy

NASA Astrophysics Data System (ADS)

Cho, Soon Cheon; Kaneko, Toshiro; Ishida, Hiroyasu; Hatakeyama, Rikizo

2015-03-01

The nitrogen-atom endohedral fullerene (N@C60) has been synthesized by controlling the plasma ion irradiation energy (Ei) and fullerene (C60) behavior in the sublimation phase. We examined the relationship between the synthesis purity of N@C60 [molar concentration ratio of N@C60 to pristine fullerene (C60)] and Ei, which was controlled by changing the substrate bias voltages (Vsub) and gas pressure (PN2) during the plasma irradiation process. High-density nitrogen-molecular ions (N2+) with a suitable Ei near 80 eV are confirmed to be the optimum condition of the nitrogen plasma for the synthesis of high-purity N@C60. In addition, high sublimation of C60 contributes to a higher yield due to the high internal energy of C60 and the related cage defects that are present under these conditions. As a result, a purity of 0.83% is realized for the first time, which is almost two orders of magnitude higher than that using other methods.

High Energy Density Lithium Primary Cells Using Nitrogen Containing Polymer Positives.

DTIC Science & Technology

1983-12-01

the charges were stabilized on heteroatoms, particularly nitro- gen. A positive charge would be stored in the form of an ammonium ion. in a high...operate reversibly. 2.0 POLYMERIC CATHODES A polymer which might be expected to exemplify charge stabilization by nitrogen is poly-N-methylpyrrole (PMP...This material is electronically conductive and might store one charge per nitrogen atom. ox. PMP;4 N3 red. I N + N+ An additional, seductive attraction

N-Doped Graphene with Low Intrinsic Defect Densities via a Solid Source Doping Technique.

PubMed

Liu, Bo; Yang, Chia-Ming; Liu, Zhiwei; Lai, Chao-Sung

2017-09-30

N-doped graphene with low intrinsic defect densities was obtained by combining a solid source doping technique and chemical vapor deposition (CVD). The solid source for N-doping was embedded into the copper substrate by NH₃ plasma immersion. During the treatment, NH₃ plasma radicals not only flattened the Cu substrate such that the root-mean-square roughness value gradually decreased from 51.9 nm to 15.5 nm but also enhanced the nitrogen content in the Cu substrate. The smooth surface of copper enables good control of graphene growth and the decoupling of height fluctuations and ripple effects, which compensate for the Coulomb scattering by nitrogen incorporation. On the other hand, the nitrogen atoms on the pre-treated Cu surface enable nitrogen incorporation with low defect densities, causing less damage to the graphene structure during the process. Most incorporated nitrogen atoms are found in the pyrrolic configuration, with the nitrogen fraction ranging from 1.64% to 3.05%, while the samples exhibit low defect densities, as revealed by Raman spectroscopy. In the top-gated graphene transistor measurement, N-doped graphene exhibits n-type behavior, and the obtained carrier mobilities are greater than 1100 cm²·V -1 ·s -1 . In this study, an efficient and minimally damaging n-doping approach was proposed for graphene nanoelectronic applications.

Stability and molecular properties of the boron-nitrogen alternating analogs of azulene and naphthalene: a computational study.

PubMed

Catão, Anderson José Lopes; López-Castillo, Alejandro

2017-04-01

In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investigated boron-nitrogen naphthalene (boroazanaphthalene) and two isomers of boron-nitrogen azulene, 1,3,4,6,8-pentaaza-2,3a,5,7,8a-pentaboraazulene (BN-azulene) and 2,3a,5,7,8a-pentaaza-1,3,4,6,8- pentaboraazulene (NB-azulene), are stable systems. However, these molecules have different properties, i.e., different stability, dipole moment, and aromaticity based on the NICS approach. BN-naphthalene has a high dipole moment magnitude showing high polar character, while naphthalene is apolar. BN- and NB-azulene are weakly polar, while ordinary azulene is highly polar in character. Also, substitution of C atoms by B and N atoms decreases the aromaticity. In the case of NB-azulene, the seven-membered ring has anti-aromaticity behavior while both rings of BN-azulene exhibit aromaticity. We expect that the new theoretical data provided in this work will be useful in identifying and characterizing experimentally the compounds investigated, and in helping our understanding of the chemistry of boron-nitrogen molecules. Graphical abstract Boron-nitrogen alternating analogs of azulene. Spectral distinction between isomers.

The passivation of uranium metal surfaces by nitrogen bombardment — the formation of uranium nitride

NASA Astrophysics Data System (ADS)

Allen, Geoffrey C.; Holmes, Nigel R.

1988-05-01

As part of a detailed investigation of the behaviour of metallic uranium in various atmospheres, we have examined the reaction between nitrogen gas and uranium metal. At room temperature there was no evidence of reaction between nitrogen gas and a clean metal surface; the only changes observed could be attributed to reaction between the metal and traces of oxygen (less than 0.1 ppm) in the nitrogen gas. Reaction between the metal and nitrogen was induced, however, by accelerating nitrogen towards the surface using a fast atom gun. The resulting nitrided surface was characterized by X-ray photoelectron spectroscopy, and its oxidation behaviour was monitored over an extended period in UHV and in air.

Study of Surface Cleaning Methods and Pyrolysis Temperature on Nano-Structured Carbon Films using X-ray Photoelectron Spectroscopy

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

Kerber, Pranita B.; Porter, Lisa M.; McCullough, L. A.

2012-10-12

Nanostructured carbon (ns-C) films fabricated by stabilization and pyrolysis of di-block copolymers are of interest for a variety of electrical/electronic applications due to their chemical inertness, high-temperature insensitivity, very high surface area, and tunable electrical resistivity over a wide range [Kulkarni et al., Synth. Met. 159, (2009) 177]. Because of their high porosity and associated high specific surface area, controlled surface cleaning studies are important for fabricating electronic devices from these films. In this study, quantification of surface composition and surface cleaning studies on ns-C films synthesized by carbonization of di-block copolymers of polyacrylonitrile-b-poly(n-butyl acrylate) (PAN-b-PBA) at two different temperaturesmore » were carried out. X-ray photoelectron spectroscopy was used for elemental analysis and to determine the efficacy of various surface cleaning methods for ns-C films and to examine the polymer residues in the films. The in-situ surface cleaning methods included: HF vapor treatment, vacuum annealing, and exposure to UV-ozone. Quantitative analysis of high-resolution XPS scans showed 11 at. % of nitrogen present in the films pyrolyzed at 600 °C, suggesting incomplete denitrogenation of the copolymer films. The nitrogen atomic concentration reduced significantly for films pyrolyzed at 900 °C confirming extensive denitrogenation at that temperature. Furthermore, quantitative analysis of nitrogen sub-peaks indicated higher loss of nitrogen atoms residing at the edge of graphitic clusters relative to that of nitrogen atoms within the graphitic cluster, suggesting higher graphitization with increasing pyrolysis temperature. Of the surface cleaning methods investigated, in-situ annealing of the films at 300 °C for 40 min was found to be the most efficacious in removing adventitious carbon and oxygen impurities from the surface.« less

Study of surface cleaning methods and pyrolysis temperatures on nanostructured carbon films using x-ray photoelectron spectroscopy

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

Kerber, Pranita; Porter, Lisa M.; McCullough, Lynne A.

2012-11-15

Nanostructured carbon (ns-C) films fabricated by stabilization and pyrolysis of diblock copolymers are of interest for a variety of electrical/electronic applications due to their chemical inertness, high-temperature insensitivity, very high surface area, and tunable electrical resistivity over a wide range [Kulkarni et al., Synth. Met. 159, 177 (2009)]. Because of their high porosity and associated high specific surface area, controlled surface cleaning studies are important for fabricating electronic devices from these films. In this study, quantification of surface composition and surface cleaning studies on ns-C films synthesized by carbonization of diblock copolymers of polyacrylonitrile-b-poly(n-butyl acrylate) at two different temperatures weremore » carried out. X-ray photoelectron spectroscopy was used for elemental analysis and to determine the efficacy of various surface cleaning methods for ns-C films and to examine the polymer residues in the films. The in-situ surface cleaning methods included HF vapor treatment, vacuum annealing, and exposure to UV-ozone. Quantitative analysis of high-resolution XPS scans showed 11 at. % nitrogen was present in the films pyrolyzed at 600 Degree-Sign C, suggesting incomplete denitrogenation of the copolymer films. The nitrogen atomic concentration decreased significantly for films pyrolyzed at 900 Degree-Sign C confirming extensive denitrogenation at that temperature. Furthermore, quantitative analysis of nitrogen subpeaks indicated higher loss of nitrogen atoms residing at the edge of graphitic clusters relative to that of nitrogen atoms within the graphitic clusters, suggesting higher graphitization with increasing pyrolysis temperature. Of the surface cleaning methods investigated, in-situ annealing of the films at 300 Degree-Sign C for 40 min was found to be the most efficacious in removing adventitious carbon and oxygen impurities from the surface.« less

Spatially and Temporally Resolved Atomic Oxygen Measurements in Short Pulse Discharges by Two Photon Laser Induced Fluorescence

NASA Astrophysics Data System (ADS)

Lempert, Walter; Uddi, Mruthunjaya; Mintusov, Eugene; Jiang, Naibo; Adamovich, Igor

2007-10-01

Two Photon Laser Induced Fluorescence (TALIF) is used to measure time-dependent absolute oxygen atom concentrations in O2/He, O2/N2, and CH4/air plasmas produced with a 20 nanosecond duration, 20 kV pulsed discharge at 10 Hz repetition rate. Xenon calibrated spectra show that a single discharge pulse creates initial oxygen dissociation fraction of ˜0.0005 for air like mixtures at 40-60 torr total pressure. Peak O atom concentration is a factor of approximately two lower in fuel lean (φ=0.5) methane/air mixtures. In helium buffer, the initially formed atomic oxygen decays monotonically, with decay time consistent with formation of ozone. In all nitrogen containing mixtures, atomic oxygen concentrations are found to initially increase, for time scales on the order of 10-100 microseconds, due presumably to additional O2 dissociation caused by collisions with electronically excited nitrogen. Further evidence of the role of metastable N2 is demonstrated from time-dependent N2 2^nd Positive and NO Gamma band emission spectroscopy. Comparisons with modeling predictions show qualitative, but not quantitative, agreement with the experimental data.

The structure and properties of a nickel-base superalloy produced by osprey atomization-deposition

NASA Astrophysics Data System (ADS)

Bricknell, Rodger H.

1986-04-01

The production of a nickel-base superalloy, René* 80, by the Osprey atomization-deposition process has been investigated. Dense (>99 pct) material with a fine-grained equiaxed microstructure was deposited using either argon or nitrogen as the atomizing gas. Defects present in the material included a chill region at the collector plate interface, entrapped recirculated particles, porosity, and ceramic particles from the melting and dispensing system. In contrast to other rapid solidification techniques, low oxygen pick-ups are noted in the current technique. Tensile strengths above those displayed by castings are found in both nitrogen and argon atomized material, and in both the as-deposited and heat treated conditions. In addition, no profound mid-temperature ductility loss is displayed by this low oxygen material, in contrast to results on other rapidly solidified material with high oxygen contents. These results are explained in terms of oxygen embrittlement. In view of the excellent properties measured, the attractive economics of the process, and the fact that fine control of the gas/metal flow ratio is shown to be unnecessary, it is concluded that atomization-deposition presents an attractive potential production route for advanced alloys.

N-Methylamino Pyrimidyl Amides (MAPA): Highly Reactive, Electronically-Activated Amides in Catalytic N-C(O) Cleavage.

PubMed

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

2017-09-01

Despite recent progress in catalytic cross-coupling technologies, the direct activation of N-alkyl-N-aryl amides has been a challenging transformation. Here, we report the first Suzuki cross-coupling of N-methylamino pyrimidyl amides (MAPA) enabled by the controlled n N → π Ar conjugation and the resulting remodeling of the partial double bond character of the amide bond. The new mode of amide activation is suitable for generating acyl-metal intermediates from unactivated primary and secondary amides.

Spectroscopic Study of the Thermal Degradation of PVP-capped Rh and Pt Nanoparticles in H2 and O2 Environments

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

Borodko, Yuri; Lee, Hyun Sook; Joo, Sang Hoon

2009-09-15

Poly(N-vinylpyrrolidone) (PVP) capped platinum and rhodium nanoparticles (7-12 nm) have been studied with UV-VIS, FTIR and Raman spectroscopy. The absorption bands in the region 190-900 nm are shown to be sensitive to the electronic structure of surface Rh and Pt atoms as well as to the aggregation of the nanoparticles. In-situ FTIR-DRIFT spectroscopy of the thermal decay of PVP stabilized Rh and Pt nanoparticles in H{sub 2} and O{sub 2} atmospheres in temperatures ranging from 30 C-350 C reveal that decomposition of PVP above 200 C, PVP transforms into a 'polyamidpolyene' - like material that is in turn converted intomore » a thin layer of amorphous carbon above 300 C. Adsorbed carbon monoxide was used as a probing molecule to monitor changes of electronic structure of surface Rh and Pt atoms and accessible surface area. The behavior of surface Rh and Pt atoms with ligated CO and amide groups of pyrrolidones resemble that of surface coordination compounds.« less

Ligand-based virtual screening and inductive learning for identification of SIRT1 inhibitors in natural products.

PubMed

Sun, Yunan; Zhou, Hui; Zhu, Hongmei; Leung, Siu-wai

2016-01-25

Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide-dependent deacetylase, and its dysregulation can lead to ageing, diabetes, and cancer. From 346 experimentally confirmed SIRT1 inhibitors, an inhibitor structure pattern was generated by inductive logic programming (ILP) with DMax Chemistry Assistant software. The pattern contained amide, amine, and hetero-aromatic five-membered rings, each of which had a hetero-atom and an unsubstituted atom at a distance of 2. According to this pattern, a ligand-based virtual screening of 1 444 880 active compounds from Chinese herbs identified 12 compounds as inhibitors of SIRT1. Three compounds (ZINC08790006, ZINC08792229, and ZINC08792355) had high affinity (-7.3, -7.8, and -8.6 kcal/mol, respectively) for SIRT1 as estimated by molecular docking software AutoDock Vina. This study demonstrated a use of ILP and background knowledge in machine learning to facilitate virtual screening.

Ligand-based virtual screening and inductive learning for identification of SIRT1 inhibitors in natural products

NASA Astrophysics Data System (ADS)

Sun, Yunan; Zhou, Hui; Zhu, Hongmei; Leung, Siu-Wai

2016-01-01

Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide-dependent deacetylase, and its dysregulation can lead to ageing, diabetes, and cancer. From 346 experimentally confirmed SIRT1 inhibitors, an inhibitor structure pattern was generated by inductive logic programming (ILP) with DMax Chemistry Assistant software. The pattern contained amide, amine, and hetero-aromatic five-membered rings, each of which had a hetero-atom and an unsubstituted atom at a distance of 2. According to this pattern, a ligand-based virtual screening of 1 444 880 active compounds from Chinese herbs identified 12 compounds as inhibitors of SIRT1. Three compounds (ZINC08790006, ZINC08792229, and ZINC08792355) had high affinity (-7.3, -7.8, and -8.6 kcal/mol, respectively) for SIRT1 as estimated by molecular docking software AutoDock Vina. This study demonstrated a use of ILP and background knowledge in machine learning to facilitate virtual screening.

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

Wahid, Ahmad Nazrul Abd, E-mail: a-nazrul@nuclearmalaysia.gov.my; Malaysian Nuclear Agency, Bangi, 43000 Kajang, Selangor; Rahim, Sahibin Abd, E-mail: haiyan@ukm.edu.my

This study was carried out to evaluate the efficiency use of the nitrogen fertilizer on aerobic rice varieties MR219-4 and MR219-9 which were grown aerobically under field capacity water potential at the controlled environment area or shield house. Direct {sup 15}N isotope tracer method was used in this study, whereby the {sup 15}N isotope was utilized as a tracer for nitrogen nutrient uptake. {sup 15}N isotope presence in the samples is determined by using emission spectrometer analysis and percentage of total nitrogen is determined by using Kjeldahl method. {sup 15}N atom access value contained in the sample will be usedmore » in determining the effectiveness of the use of nitrogen in fertilizers through the specific calculation formulas. In this work, the data several data of nitrogen derived from fertilizer (Ndff), total nitrogen, nitrogen uptake and nitrogen use efficiency was obtained.« less

Hexacoordinated nitrogen(V) stabilized by high pressure

PubMed Central

Kurzydłowski, Dominik; Zaleski-Ejgierd, Patryk

2016-01-01

In all of its known connections nitrogen retains a valence shell electron count of eight therefore satisfying the golden rule of chemistry - the octet rule. Despite the diversity of nitrogen chemistry (with oxidation states ranging from + 5 to −3), and despite numerous efforts, compounds containing nitrogen with a higher electron count (hypervalent nitrogen) remain elusive and are yet to be synthesized. One possible route leading to nitrogen’s hypervalency is the formation of a chemical moiety containing pentavalent nitrogen atoms coordinated by more than four substituents. Here, we present theoretical evidence that a salt containing hexacoordinated nitrogen(V), in the form of an NF6− anion, could be synthesized at a modest pressure of 40 GPa (=400 kbar) via spontaneous oxidation of NF3 by F2. Our results indicate that the synthesis of a new class of compounds containing hypervalent nitrogen is within reach of current high-pressure experimental techniques. PMID:27808104

Nitriding of Polymer by Low Energy Nitrogen Neutral Beam Source

NASA Astrophysics Data System (ADS)

Hara, Yasuhiro; Takeda, Keigo; Yamakawa, Koji; Den, Shoji; Toyoda, Hirotaka; Sekine, Makoto; Hori, Masaru

2012-03-01

Nitriding of polyethylene naphthalate (PEN) has been carried out at room temperature using a nitrogen neutral beam with kinetic energy of less than 100 eV. The surface hardness of nitrided samples increased to two times that of the untreated sample, when the acceleration voltage was between 30 and 50 V. The thickness of the hardened polymer layer was estimated to be 1 µm. It was concluded that the hardness enhancement was caused by the diffusion of nitrogen atoms into the polymer.

Polymeric Cd(II), trinuclear and mononuclear Ni(II) complexes of 5-methyl-4-phenyl-1,2,4-triazole-3-thione: Synthesis, structural characterization, thermal behaviour, fluorescence properties and antibacterial activity

NASA Astrophysics Data System (ADS)

Bharty, M. K.; Paswan, S.; Dani, R. K.; Singh, N. K.; Sharma, V. K.; Kharwar, R. N.; Butcher, R. J.

2017-02-01

Syntheses of a polymeric Cd(II) complex, [Cd(mptt)2]n (1), a trinuclear Ni(II) complex, [Ni3(μ-mptt)4(μ-H2O)2(H2O)2(ttfa)2]·3H2O (2) and a mononuclear Ni(II) complex [Ni(mptt)2(en)2] (3) have been performed using the ligand 5-methyl-4-phenyl-1,2,4-triazole-3-thione (Hmptt) and nickel(II)/cadmium(II) salts {ttfa = thenoyltrifluroacetonate). The ligand and the complexes have been characterized by various physicochemical methods in addition to their single crystal X-ray structure. The Cd centre in complex 1 adopts a distorted tetrahedral geometry with one sulfur atom and two mptt ligands provide three nitrogen atoms from three triazole units. The sulfur atom of the ligand binds covalently and overall the ligand acts as uninigative N,S/N,N bidentate moiety. The polymeric structure of complex 1 results from the N atoms of the neighboring triazole units coordinating with the Cd(II) centre. The three Ni(II) centres in the trinuclear Ni(II) complex 2 form a linear arrangement and all have six coordinated arrangements. The middle Ni(II) binds with four deprotonated triazole ring nitrogens and two water molecules form two bridges. The terminal Ni(II) centres bind through two thenoyl oxygens, two triazole nitrogens and water molecules that formed bridges with the middle Ni centre. In complex 3, the nickel(II) centre is covalently bonded through two deprotonated triazole ring nitrogens from two ligand moieties and other four sites are occupied by four nitrogens from two bidentate en ligands. Thermogravimetric analyses (TGA) of the complexes indicated for NiO as the final residue. The bioefficacy of the ligand and complexes 2 and 3 have been examined against the growth of bacteria to evaluate their anti-microbial potential. Complex 2 showed high antibacterial activity as compared to the ligand and complex 3. Complexes 1, 2 and 3 are fluorescent materials with maximum emissions at 425, 421 and 396 nm at an excitation wavelength of 323, 348 and 322 nm, respectively.

Soliton microdynamics of the generation of new-type nonlinear surface vibrations, dissociation, and surfing diffusion in diatomic crystals of the uranium nitride type

NASA Astrophysics Data System (ADS)

Dubovsky, O. A.; Semenov, V. A.; Orlov, A. V.; Sudarev, V. V.

2014-09-01

The microdynamics of large-amplitude nonlinear vibrations of uranium nitride diatomic lattices has been investigated using the computer simulation and neutron scattering methods at temperatures T = 600-2500°C near the thresholds of the dissociation and destruction of the reactor fuel materials. It has been found using the computer simulation that, in the spectral gap between the frequency bands of acoustic and optical phonons in crystals with an open surface, there are resonances of new-type harmonic surface vibrations and a gap-filling band of their genetic successors, i.e., nonlinear surface vibrations. Experimental measurements of the slow neutron scattering spectra of uranium nitride on the DIN-2PI neutron spectrometer have revealed resonances and bands of these surface vibrations in the spectral gap, as well as higher optical vibration overtones. It has been shown that the solitons and bisolitons initiate the formation and collapse of dynamic pores with the generation of surface vibrations at the boundaries of the cavities, evaporation of atoms and atomic clusters, formation of cracks, and destruction of the material. It has been demonstrated that the mass transfer of nitrogen in cracks and along grain boundaries can occur through the revealed microdynamics mechanism of the surfing diffusion of light nitrogen atoms at large-amplitude soliton waves propagating in the stabilizing sublattice of heavy uranium atoms and in the nitrogen sublattice.

Intrinsic Antioxidant Potential of the Aminoindole Structure: A Computational Kinetics Study of Tryptamine.

PubMed

Bentz, Erika N; Lobayan, Rosana M; Martínez, Henar; Redondo, Pilar; Largo, Antonio

2018-06-21

A computational kinetics study of the antioxidant activity of tryptamine toward HO • and HOO • radicals in water at 298 K has been carried out. Density functional methods have been employed for the quantum chemical calculations, and the conventional transition state theory was used for rate constant evaluation. Different mechanisms have been considered: radical adduct formation (RAF), single electron transfer (SET), and hydrogen atom transfer (HAT). For the reaction of tryptamine with the hydroxyl radical, nearly all channels are diffusion-controlled, and the overall rate constant is very high, 6.29 × 10 10 M -1 s -1 . The RAF mechanism has a branching ratio of 55%, followed by the HAT mechanism (31%), whereas the SET mechanism accounts just for 13% of the products. The less hindered carbon atom neighboring to the nitrogen of the indole ring seems to be the preferred site for the RAF mechanism, with a branching ratio of 16%. The overall rate constant for the reaction of tryptamine with the HOO • radical is 3.71 × 10 4 M -1 s -1 , suggesting that it could be a competitive process with other reactions of hydroperoxyl radicals in biological environments. For this reaction only the HAT mechanism seems viable. Furthermore, only two centers may contribute to the HAT mechanism, the nitrogen atom of the indole ring and a carbon atom of the aminoethyl chain, the former accounting for more than 91% of the total products. Our results suggest that tryptamine could have a noticeable scavenging activity toward radicals, and that this activity is mainly related to the nitrogen atom of the indole ring, thus showing the relevance of their behavior in the study of aminoindoles.

Tridentate ligated heteronuclear tin(II) alkoxides for use as base catalysts

DOEpatents

Boyle, Timothy J.

2001-01-01

Tin alkoxide compounds are provided with accessible electrons. The tin alkoxide compound have the general formula (THME).sub.2 Sn.sub.3 (M(L).sub.x).sub.y, where THME is (O--CH.sub.2).sub.3 C(CH.sub.3), M is a metal atom selected from Sn and Ti, L is an organic/inorganic ligand selected from an alkoxide, a phenoxide or an amide, x is selected from 2 and 4 and y is selected from 0 and 1. These compounds have applicability as base catalysts in reactions and in metal-organic chemical vapor depositions processes.

Covalent conjugation of graphene oxide with methotrexate and its antitumor activity

NASA Astrophysics Data System (ADS)

Wojtoniszak, M.; Urbas, K.; Perużyńska, M.; Kurzawski, M.; Droździk, M.; Mijowska, E.

2013-05-01

Here, we have functionalized graphene oxide with anticancer drug methotrexate through amide bonding. A kinetics of the drug release from graphene oxide in physiological solution - phosphate buffered saline (PBS) containing different biocompatible polymers have been investigated. Dispersion of MTX-GO in poly sodium-4-styrene sulfonate and poly ethylene glycol resulted in increase of the release time. The material was characterized with transmission electron microscopy, atomic force microscopy, Raman spectroscopy, Fourier transform infrared spectroscopy and UV-vis spectroscopy. Furthermore, antineoplastic action against human breast adenocarcinoma cell line MCF7 of MTX-GO and empty graphene oxide was explored.

A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

DOE PAGES

Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; ...

2015-07-01

Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategymore » that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N 2S 2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with g z < g x,y. 14N-hyperfine is observed on g z« less

Source Water Identification and Chemical Typing for Nitrogen at the Kissimmee River, Pool C, Florida--Preliminary Assessment

DTIC Science & Technology

2002-01-01

and the mass-spectrometric measurement techniques, in J.R. Gat and R. Gonfiantini, eds., Stable isotope hydrology: Deuterium and oxygen-18 in the water ... cycle , chap. 4, p. 35-84, International Atomic Energy Agency, Vienna, Austria. Heaton, T.H.E., 1986, Isotopic studies of nitrogen pollution in the

Synthesis and crystal structure of new copper(II) metal complex: Noncovalent interactions and electrical conductance properties

NASA Astrophysics Data System (ADS)

Pathak, Sudipta; Chakraborty, Koushik; Ghosh, Surajit; Roy, Kunal; Jana, Barnali; Konar, Saugata

2018-01-01

[Cu(pydc)(apyz)(H2O)2] (1) (where pydcH2 = pyridine-2,6-dicarboxylic acid; apyz = 2- aminopyrazine) has been synthesized and characterized by elemental analysis, IR spectroscopy and single crystal X-ray diffraction techniques. Crystallographic analysis revealed that complex 1 has distorted octahedral geometry with pydcH2 coordinated as tridentate ligands to metal ion through two oxygen atoms of each carboxylate group, nitrogen atom of the pyridine ring and the auxiliary ligand pyrazine nitrogen atom form basal plane and apical positions are occupied by two oxygen atoms of water molecules. In addition, the coordination compounds are connected by a variety of non covalent interactions like OH … π, lone pair … π, π … π and hydrogen bonds. The evaluation of these noncovalent interactions is useful for rationalizing their influence in the crystal packing. In addition, electrical current measured at room temperature on thin film before and after annealed is in the order of 229 μA and 246 μA respectively with bias voltage 1 V.

Surface Functionalization of Polyethylene Granules by Treatment with Low-Pressure Air Plasma.

PubMed

Šourková, Hana; Primc, Gregor; Špatenka, Petr

2018-05-25

Polyethylene granules of diameter 2 mm were treated with a low-pressure weakly ionized air plasma created in a metallic chamber by a pulsed microwave discharge of pulse duration 180 μs and duty cycle 70%. Optical emission spectroscopy showed rich bands of neutral nitrogen molecules and weak O-atom transitions, but the emission from N atoms was below the detection limit. The density of O atoms in the plasma above the samples was measured with a cobalt catalytic probe and exhibited a broad peak at the pressure of 80 Pa, where it was about 2.3 × 10 21 m -3 . The samples were characterized by X-ray photoelectron spectroscopy. Survey spectra showed oxygen on the surface, while the nitrogen concentration remained below the detection limit for all conditions. The high-resolution C1s peaks revealed formation of various functional groups rather independently from treatment parameters. The results were explained by extensive dissociation of oxygen molecules in the gaseous plasma and negligible flux of N atoms on the polymer surface.

Synthesis and structure-activity relationships of fenbufen amide analogs.

PubMed

Lin, Kun-I; Yang, Chao-Hsun; Huang, Chia-Wen; Jian, Jhen-Yi; Huang, Yu-Chun; Yu, Chung-Shan

2010-12-02

The previous discoveries of butyl fenbufen amide analogs with antitumor effects were further examined. The amide analogs with 1, 3, 4 and 8 carbons chains were prepared in 70-80% yield. Fenbufen had no cytotoxic effects at concentrations ranging from 10 to 100 μM. Methyl fenbufen amide had significant cytotoxic effects at a concentration of 100 μM. As the length of the alkyl amide side chain increased, the cytotoxic effects increased, and the octyl fenbufen amide had the greatest cytotoxic effect. After treatment with 30 μM octyl fenbufen amide, nearly seventy percent of the cells lost their viability. At the concentration of 10 μM, fenbufen amide analogs did not show cytotoxicity according to the MTT assay results. The NO scavenging activities of the fenbufen amide analogs were not significantly different from those of fenbufen.

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

PubMed

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

2016-04-05

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

Boron/nitrogen substitution of the central carbon atoms of the biphenalenyl diradical π dimer: a novel 2e-12c bond and large NLO responses.

PubMed

Zhong, Rong-Lin; Zhang, Ji; Muhammad, Shabbir; Hu, Yang-Yang; Xu, Hong-Liang; Su, Zhong-Min

2011-10-10

On the basis of the famous staggered biphenalenyl diradical π dimer 1, the eclipsed biphenalenyl (1a), with no centrosymmetry, was obtained by rotating a layer of 1 by 60° around its central axis. Furthermore, the central carbon atoms of 1 and 1a were substituted by boron and nitrogen atoms to form 2 and 2a with a novel 2e-12c bond. We found that the novel 2e-12c bond is formed by the electron pair of the occupied orbital of the phenalenyl monomer substituted by the nitrogen atom and the unoccupied orbital of the phenalenyl monomer substituted by the boron atom. As a result of the novel 2e-12c bond, 2 and 2a exhibit a fascinating interlayer charge-transfer transition character, which results in a significant difference in the dipole moments (Δμ) between the ground state and the crucial excited state. The values of Δμ for 2 and 2a are 6.4315 and 6.9253 Debye, clearly larger than the values of 0 and 0.0015 Debye for 1 and 1a. Significantly, the boron/nitrogen substitution effect can greatly enhance the first hyperpolarizabilities (β(0) ) of 2 and 2a with a novel 2e-12c bond compared with 1 and 1a with a traditional 2e-12c bond: 0 and 19 a.u. for 1 and 1a are much lower than 3516 and 12272 a.u. for 2 and 2a. Furthermore, the interaction energies (E(int) )of 2 and 2a are larger than those of 1 and 1a, which could be considered as a signature of reliability for the newly designed dimers. Our present work will be beneficial for further theoretical and experimental studies on the properties of molecules with the novel 2e-12c bond. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficiencies for production of atomic nitrogen and oxygen by relativistic proton impact in air

NASA Technical Reports Server (NTRS)

Porter, H. S.; Jackman, C. H.; Green, A. E. S.

1976-01-01

Relativistic electron and proton impact cross sections are obtained and represented by analytic forms which span the energy range from threshold to 1 GeV. For ionization processes, the Massey-Mohr continuum generalized oscillator strength surface is parameterized. Parameters are determined by simultaneous fitting to (1) empirical data, (2) the Bethe sum rule, and (3) doubly differential cross sections for ionization. Branching ratios for dissociation and predissociation from important states of N2 and O2 are determined. The efficiency for the production of atomic nitrogen and oxygen by protons with kinetic energy less than 1 GeV is determined using these branching ratio and cross section assignments.

The production and escape of nitrogen atoms on Mars

NASA Technical Reports Server (NTRS)

Fox, J. L.

1993-01-01

Updated rate coefficients and a revised ionosphere-thermosphere model are used to compute the production rates and densities of odd nitrogen species in the Martian atmosphere. Computed density profiles for N(4S), N(2D), N(2P), and NO are presented. The model NO densities are found to be about a factor of 2-3 less than those measured by the Viking 1 mass spectrometer. Revised values for the escape rates of N atoms from dissociative recombination and ionospheric reactions are also computed. Dissociative recombination is found to be comparable in importance to photodissociation at low solar activity, but it is still the most important escape mechanism for N-14 at high solar activity.

Retrieval of thermospheric atomic oxygen, nitrogen and temperature from the 732 NM emission measured by the ISO on ATLAS 1

NASA Technical Reports Server (NTRS)

Fennelly, Judy A.; Torr, Douglas G.; Torr, Marsha R.; Richards, Phillip G.; Yung, Sopo

1993-01-01

The Imaging Spectrometric Observatory (ISO) was a part of the ATLAS 1 Mission flown on the shuttle Atlantis from March 24 to April 2, 1992. During limb scanning operations, the ISO measured the O+(2P) ion emission at 732 nm. We have used a numerical inversion technique to retrieve thermospheric atomic oxygen, molecular nitrogen and temperature profiles. These preliminary results indicate a lower thermospheric temperature cooler than that predicted by MSIS for the solar conditions during the mission. Although the densities agree at low altitudes, the reduced scale height produces O and N2 densities 25 percent lower than the MSIS at 300 km.

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

Korolev, D. S.; Mikhaylov, A. N.; Belov, A. I.

The composition and structure of silicon surface layers subjected to combined gallium and nitrogen ion implantation with subsequent annealing have been studied by the X-ray photoelectron spectroscopy, Rutherford backscattering, electron spin resonance, Raman spectroscopy, and transmission electron microscopy techniques. A slight redistribution of the implanted atoms before annealing and their substantial migration towards the surface during annealing depending on the sequence of implantations are observed. It is found that about 2% of atoms of the implanted layer are replaced with gallium bonded to nitrogen; however, it is impossible to detect the gallium-nitride phase. At the same time, gallium-enriched inclusions containingmore » ∼25 at % of gallium are detected as candidates for the further synthesis of gallium-nitride inclusions.« less

An analytical study of nitrogen oxides and carbon monoxide emissions in hydrocarbon combustion with added nitrogen, preliminary results

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1979-01-01

The effect of combustor operating conditions on the conversion of fuel-bound nitrogen (FBN) to nitrogen oxides NO sub x was analytically determined. The effect of FBN and of operating conditions on carbon monoxide (CO) formation was also studied. For these computations, the combustor was assumed to be a two stage, adiabatic, perfectly-stirred reactor. Propane-air was used as the combustible mixture and fuel-bound nitrogen was simulated by adding nitrogen atoms to the mixture. The oxidation of propane and formation of NO sub x and CO were modeled by a fifty-seven reaction chemical mechanism. The results for NO sub x and CO formation are given as functions of primary and secondary stage equivalence ratios and residence times.

[Preparation, spectral analysis and photocatalytic activities of TiO2 films codoped with iron and nitrogen].

PubMed

Liu, Wan-bing; Deng, Jian; Zhao, Yu-bao; Xu, Jin-sheng; Zhou, Liang

2009-05-01

Using tetrabutyl titanate as the titanium source, and ammonia and ferric nitrate as the sources of nitrogen and ferrum respectively, iron and nitrogen-codoped nano-TiO2 gelatins were prepared by sol-gel method. The iron and nitrogen-codoped nano-TiO2 complex films were prepared with the obtained gelatins used to coat the surface of cleaned glass slides by several times of dipping-lifting procedure, followed by natural seasoning at room temperature and calcined at 450 degrees C for 3 hours, then the films were characterized by X-ray diffraction (XRD), scanning electron microscope (SEM), X-ray photoelectron spectrum (XPS) and ultraviolet-visible diffuse reflectance spectrum (UV-Vis). The XRD spectra o f samples showed that the Fe-TiO(2-x)Nx, filmswere of anatase structure with a few of oxygen atoms in the lattice of anatase TiO2 substituted by nitrogen atoms, resulting in the distortion of crystal lattice. The SEM image showed that the nanoparticles of the films have a good dispersion characteristic and uniform orbicular shape with an average diameter of about 19 nm. The absorption edges of UV-Vis spectra exhibited a red shift up to 740 nm when the TiO2 films were codoped with iron and nitrogen. The XPS of the Fe-TiO(2-x)Nx film presented a lowering of Ti 2p(3/2) electron binding energy because of the codoping of iron and nitrogen, which then resulted in the widening of the absorption of visible light range. The photocatalytic properties were studied by photocatalytical degradation of sudan I as a model reaction in a self-assembled light-reactor. When the atomic ratio of Fe3+/Ti4+ reached 0.4%, the Fe-TiO(2-x)Nx film showed the highest catalytic performance in degradation of sudan I which was decomposed by up to 97% after 4 hours of photocatalytic reaction. Codoping of nitrogen and appropriate amount of iron in TiO2 enhances photoresponse and utilizing efficiency in visible light region, and then improves the performances of Fe-TiO(2-x)Nx photocatalyst. The complex film catalyst prepared by this method will have potential application in areas of wastewater disposal.

Spectroscopic investigation of H atom transfer in a gas-phase dissociation reaction: McLafferty rearrangement of model gas-phase peptide ions.

PubMed

Van Stipdonk, Michael J; Kerstetter, Dale R; Leavitt, Christopher M; Groenewold, Gary S; Steill, Jeffrey; Oomens, Jos

2008-06-14

Wavelength-selective infrared multiple-photon photodissociation (WS-IRMPD) was used to study isotopically-labeled ions generated by McLafferty rearrangement of nicotinyl-glycine-tert-butyl ester and betaine-glycine-tert-butyl ester. The tert-butyl esters were incubated in a mixture of D(2)O and CH(3)OD to induce solution-phase hydrogen-deuterium exchange and then converted to gas-phase ions using electrospray ionization. McLafferty rearrangement was used to generate the free-acid forms of the respective model peptides through transfer of an H atom and elimination of butene. The specific aim was to use vibrational spectra generated by WS-IRMPD to determine whether the H atom remains at the acid group, or migrates to one or more of the other exchangeable sites. Comparison of the IRMPD results in the region from 1200-1900 cm(-1) to theoretical spectra for different isotopically-labeled isomers clearly shows that the H atom is situated at the C-terminal acid group and migration to amide positions is negligible on the time scale of the experiment. The results of this study suggest that use of the McLafferty rearrangement for peptide esters could be an effective approach for generation of H-atom isotope tracers, in situ, for subsequent investigation of intramolecular proton migration during peptide fragmentation studies.

Twisted Amides: From Obscurity to Broadly Useful Transition-Metal-Catalyzed Reactions by N-C Amide Bond Activation.

PubMed

Liu, Chengwei; Szostak, Michal

2017-05-29

The concept of using amide bond distortion to modulate amidic resonance has been known for more than 75 years. Two classic twisted amides (bridged lactams) ingeniously designed and synthesized by Kirby and Stoltz to feature fully perpendicular amide bonds, and as a consequence emanate amino-ketone-like reactivity, are now routinely recognized in all organic chemistry textbooks. However, only recently the use of amide bond twist (distortion) has advanced to the general organic chemistry mainstream enabling a host of highly attractive N-C amide bond cross-coupling reactions of broad synthetic relevance. In this Minireview, we discuss recent progress in this area and present a detailed overview of the prominent role of amide bond destabilization as a driving force in the development of transition-metal-catalyzed cross-coupling reactions by N-C bond activation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Carboxamide Spleen Tyrosine Kinase (Syk) Inhibitors: Leveraging Ground State Interactions To Accelerate Optimization.

PubMed

Ellis, J Michael; Altman, Michael D; Cash, Brandon; Haidle, Andrew M; Kubiak, Rachel L; Maddess, Matthew L; Yan, Youwei; Northrup, Alan B

2016-12-08

Optimization of a series of highly potent and kinome selective carbon-linked carboxamide spleen tyrosine kinase (Syk) inhibitors with favorable drug-like properties is described. A pervasive Ames liability in an analogous nitrogen-linked carboxamide series was obviated by replacement with a carbon-linked moiety. Initial efforts lacked on-target potency, likely due to strain induced between the hinge binding amide and solvent front heterocycle. Consideration of ground state and bound state energetics allowed rapid realization of improved solvent front substituents affording subnanomolar Syk potency and high kinome selectivity. These molecules were also devoid of mutagenicity risk as assessed via the Ames test using the TA97a Salmonella strain.

Carboxamide Spleen Tyrosine Kinase (Syk) Inhibitors: Leveraging Ground State Interactions To Accelerate Optimization

PubMed Central

2016-01-01

Optimization of a series of highly potent and kinome selective carbon-linked carboxamide spleen tyrosine kinase (Syk) inhibitors with favorable drug-like properties is described. A pervasive Ames liability in an analogous nitrogen-linked carboxamide series was obviated by replacement with a carbon-linked moiety. Initial efforts lacked on-target potency, likely due to strain induced between the hinge binding amide and solvent front heterocycle. Consideration of ground state and bound state energetics allowed rapid realization of improved solvent front substituents affording subnanomolar Syk potency and high kinome selectivity. These molecules were also devoid of mutagenicity risk as assessed via the Ames test using the TA97a Salmonella strain. PMID:27994755

Composition measurements of the topside ionosphere.

PubMed

Hoffman, J H

1967-01-20

Data from a magnetic mass spectrometer flown on the Explorer 31 satellite show that the ionosphere above 1000 kilometers usually consists of hydrogen ions as the predominant species. Between this altitude and perigee (500 kilometers) the dominant ion species shifts to atomic oxygen, with a significant amount of atomic nitrogen ions also present. Helium ions are present in small quantities at all altitudes. Other minor ions observed are those of 2, 7, 8, 15, 18, and 20 atomic mass units.

Characterization of Ar/N2/H2 middle-pressure RF discharge and application of the afterglow region for nitridation of GaAs

NASA Astrophysics Data System (ADS)

Raud, J.; Jõgi, I.; Matisen, L.; Navrátil, Z.; Talviste, R.; Trunec, D.; Aarik, J.

2017-12-01

This work characterizes the production and destruction of nitrogen and hydrogen atoms in RF capacitively coupled middle-pressure discharge in argon/nitrogen/hydrogen mixtures. Input power, electron concentration, electric field strength and mean electron energy were determined on the basis of electrical measurements. Gas temperature and concentration of Ar atoms in 1s states were determined from spectral measurements. On the basis of experimentally determined plasma characteristics, main production and loss mechanisms of H and N atoms were discussed. The plasma produced radicals were applied for the nitridation and oxide reduction of gallium arsenide in the afterglow region of discharge. After plasma treatment the GaAs samples were analyzed using x-ray photoelectron spectroscopy (XPS) technique. Successful nitridation of GaAs sample was obtained in the case of Ar/5% N2 discharge. In this gas mixture the N atoms were generated via dissociative recombination of N2+ created by charge transfer from Ar+. The treatment in Ar/5% N2/1% H2 mixture resulted in the reduction of oxide signals in the XPS spectra. Negligible formation of GaN in the latter mixture was connected with reduced concentration of N atoms, which was, in turn, due to less efficient mechanism of N atom production (electron impact dissociation of N2 molecules) and additional loss channel in reaction with H2.

Growth of nitrogen-doped graphene on copper: Multiscale simulations

NASA Astrophysics Data System (ADS)

Gaillard, P.; Schoenhalz, A. L.; Moskovkin, P.; Lucas, S.; Henrard, L.

2016-02-01

We used multiscale simulations to model the growth of nitrogen-doped graphene on a copper substrate by chemical vapour deposition (CVD). Our simulations are based on ab-initio calculations of energy barriers for surface diffusion, which are complemented by larger scale Kinetic Monte Carlo (KMC) simulations. Our results indicate that the shape of grown doped graphene flakes depends on the temperature and deposition flux they are submitted during the process, but we found no significant effect of nitrogen doping on this shape. However, we show that nitrogen atoms have a preference for pyridine-like sites compared to graphite-like sites, as observed experimentally.

Equilibrium and NMR studies on GdIII, YIII, CuII and ZnII complexes of various DTPA-N,N''-bis(amide) ligands. Kinetic stabilities of the gadolinium(III) complexes.

PubMed

Jászberényi, Zoltán; Bányai, István; Brücher, Ernö; Király, Róbert; Hideg, Kálmán; Kálai, Tamás

2006-02-28

Three DTPA-derivative ligands, the non-substituted DTPA-bis(amide) (L(0)), the mono-substituted DTPA-bis(n-butylamide) (L(1)) and the di-substituted DTPA-bis[bis(n-butylamide)] (L(2)) were synthesized. The stability constants of their Gd3+ complexes (GdL) have been determined by pH-potentiometry with the use of EDTA or DTPA as competing ligands. The endogenous Cu2+ and Zn2+ ions form ML, MHL and M(2)L species. For the complexes CuL(0) and CuL(1) the dissociation of the amide hydrogens (CuLH(-1)) has also been detected. The stability constants of complexes formed with Gd3+, Cu2+ and Zn2+ increase with an increase in the number of butyl substituents in the order ML(0) < ML(1) < ML(2). NMR studies of the diamagnetic YL(0) show the presence of four diastereomers formed by changing the chirality of the terminal nitrogens of their enantiomers. At 323 K, the enantiomerization process, involving the racemization of central nitrogen, falls into the fast exchange range. By the assignment and interpretation of 1H and 13C NMR spectra, the fractions of the diastereomers were found to be equal at pH = 5.8 for YL(0). The kinetic stabilities of GdL(0), GdL(1) and GdL(2) have been characterized by the rates of the exchange reactions occurring between the complexes and Eu3+, Cu2+ or Zn2+. The rates of reaction with Eu3+ are independent of the [Eu3+] and increase with increasing [H+], indicating the rate determining role of the proton assisted dissociation of complexes. The rates of reaction with Cu2+ and Zn2+ increase with rising metal ion concentration, which shows that the exchange can take place with direct attack of Cu2+ or Zn2+ on the complex, via the formation of a dinuclear intermediate. The rates of the proton, Cu2+ and Zn2+ assisted dissociation of Gd3+ complexes decrease with increasing number of the n-butyl substituents, which is presumably the result of steric hindrance hampering the formation or dissociation of the intermediates. The kinetic stabilities of GdL(0) and GdL(1) at pH = 7.4, [Cu2+] = 1 x 10(-6) M and [Zn(2+)] = 1 x 10(-5) M are similar to that of Gd(DTPA)2-, while the complex GdL2 possesses a much higher kinetic stability.

Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

PubMed Central

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-01

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism. PMID:25588215

Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

PubMed

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-12

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

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

PubMed Central

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

2014-01-01

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

Nitrogen-atom endohedral fullerene synthesis with high efficiency by controlling plasma-ion irradiation energy and C{sub 60} internal energy

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

Cho, Soon Cheon; Kaneko, Toshiro, E-mail: kaneko@ecei.tohoku.ac.jp; Ishida, Hiroyasu

2015-03-28

The nitrogen-atom endohedral fullerene (N@C{sub 60}) has been synthesized by controlling the plasma ion irradiation energy (E{sub i}) and fullerene (C{sub 60}) behavior in the sublimation phase. We examined the relationship between the synthesis purity of N@C{sub 60} [molar concentration ratio of N@C{sub 60} to pristine fullerene (C{sub 60})] and E{sub i}, which was controlled by changing the substrate bias voltages (V{sub sub}) and gas pressure (P{sub N2}) during the plasma irradiation process. High-density nitrogen-molecular ions (N{sub 2}{sup +}) with a suitable E{sub i} near 80 eV are confirmed to be the optimum condition of the nitrogen plasma for themore » synthesis of high-purity N@C{sub 60}. In addition, high sublimation of C{sub 60} contributes to a higher yield due to the high internal energy of C{sub 60} and the related cage defects that are present under these conditions. As a result, a purity of 0.83% is realized for the first time, which is almost two orders of magnitude higher than that using other methods.« less

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

One-Step Electrochemical Preparation of Multilayer Graphene Functionalized with Nitrogen

NASA Astrophysics Data System (ADS)

Ustavytska, Olena; Kurys, Yaroslav; Koshechko, Vyacheslav; Pokhodenko, Vitaly

2017-03-01

A new environmentally friendly one-step method for producing multilayer (preferably 7-9 layers) nitrogen-doped graphene (N-MLG) with a slight amount of oxygen-containing defects was developed. The approach is based on the electrochemical exfoliation of graphite electrode in the presence of azide ions under the conditions of electrolysis with pulse changing of the electrode polarization potential. It was found that usage of azide anions lead not only to the exfoliation of graphite but also to the simultaneous functionalization of graphene sheets by nitrogen atoms (as a result of electrochemical decomposition of azide anions with ammonia evolution). Composition, morphology, structure, and electrochemical properties of N-MLG were characterized by C,H,N analysis, transmission electron microscopy, atomic force microscopy, FTIR, UV-Vis, and Raman spectroscopy, as well as cyclic voltammetry. The perspective of using N-MLG as oxygen reduction reaction electrocatalyst and for the electrochemical analysis of biomarkers (dopamine, ascorbic acid, and uric acid) in their mixtures was shown.

An x-ray absorption study of the iron site in bacterial photosynthetic reaction centers.

PubMed Central

Bunker, G; Stern, E A; Blankenship, R E; Parson, W W

1982-01-01

Measurements were made of the extended x-ray absorption fine structure (EXAFS) of the iron site in photosynthetic reaction centers from the bacterium Rhodopseudomonas sphaeroides. Forms with two quinones, two quinones with added o-phenanthroline, and one quinone were studied. Only the two forms containing two quinones maintained their integrity and were analyzed. The spectra show directly that the added o-phenanthroline does not chelate the iron atom. Further analysis indicates that the iron is octahedrally coordinated by nitrogen and/or oxygen atoms located at various distances, with the average value of about 2.14 A. The analysis suggests that most of the ligands are nitrogens and that three of the nitrogen ligands belong to histidine rings. This interpretation accounts for several unusual features of the EXAFS spectrum. We speculate that the quinones are bound to the histidine rings in some manner. Qualitative features of the absorption edge spectra also are discussed and are related to the Fe-ligand distance. PMID:6977382

Supramolecular packing and polymorph screening of N-isonicotinoyl arylketone hydrazones with phenol and amino modifications

NASA Astrophysics Data System (ADS)

Hean, Duane; Michael, Joseph P.; Lemmerer, Andreas

2018-04-01

Thirteen structural variants based on the (E)-N‧-(1-arylethylidene)pyridohydrazide template were prepared, investigated and screened for possible polymorphic behaviour. Four variants showed from Differential Scanning Calorimetry Scans thermal events indicative of new solid-state phases. The thirteen variants included substituents R = sbnd OH or sbnd NH2 placed at ortho, meta and para positions on the phenyl ring; and shifting the pyridyl nitrogen between positions 4-, 3- and 2-. The crystal structures of twelve of the compounds were determined to explore their supramolecular structures. The outcomes of these modifications demonstrated that the pyridyl nitrogen at the 2- position is 'locked' by forming a hydrogen bond with the amide hydrogen; while placing the pyridyl nitrogen at positions 3- and 4- offers a greater opportunity for hydrogen bonding with neighbouring molecules. Such interactions include Osbnd H⋯N, Nsbnd H⋯N, Osbnd H⋯O, Nsbnd H⋯O, Nsbnd H⋯π, π⋯π stacking, as well as other weaker interactions such as Csbnd H⋯N, Csbnd H⋯O, Csbnd H⋯N(pyridyl). When OH or NH2 donors are placed in the ortho position, an intramolecular hydrogen bond is formed between the acceptor hydrazone nitrogen and the respective donor. The meta- and para-positioned donors form an unpredictable array of supramolecular structures by forming hydrogen-bonded chains with the pyridyl nitrogen and carbonyl acceptors respectively. In addition to the intramolecular and chain hydrogen bond formation demonstrated throughout the crystal structures under investigation, larger order hydrogen-bonded rings were also observed in some of the supramolecular aggregations. The extent of the hydrogen-bonded ring formations range from two to six molecular participants depending on the specific crystal structure.

Templated synthesis of copper(II) azacyclam complexes using urea as a locking fragment and their metal-enhanced binding tendencies towards anions.

PubMed

Boiocchi, Massimo; Fabbrizzi, Luigi; Garolfi, Mauro; Licchelli, Maurizio; Mosca, Lorenzo; Zanini, Cristina

2009-10-26

Copper(II) azacyclam complexes 3(2+) and 4(2+) were obtained through a metal-templated procedure involving the pertinent open-chain tetramine, formaldehyde and a phenylurea derivative as a locking fragment. Both metal complexes can establish interactions with anions through the metal centre and the amide NH group. Equilibrium studies in DMSO by a spectrophotometric titration technique were carried out to assess the affinity of 3(2+) and 4(2+) towards anions. While the NH group of an amide model compound and the metal centre of the plain Cu(II)(azacyclam)(2+) complex do not interact at all with anions, 3(2+) and 4(2+) establish strong interactions with oxo anions, profiting from a pronounced cooperative effect. In particular, 1) they form stable 1:1 and 1:2 complexes with H(2)PO(4) (-) ions in a stepwise mode with both hydrogen-bonding and metal-ligand interactions, and 2) in the presence of CH(3)COO(-), they undergo deprotonation of the amido NH group and thus profit from axial coordination of the partially negatively charged carbonyl oxygen atom in a scorpionate binding mode.

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.

PubMed

Ribas-Arino, Jordi; Carvajal, Maria Angels; Chaumont, Alain; Masia, Marco

2012-12-03

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymorphs and polymorphic cocrystals of temozolomide.

PubMed

Babu, N Jagadeesh; Reddy, L Sreenivas; Aitipamula, Srinivasulu; Nangia, Ashwini

2008-07-07

Crystal polymorphism in the antitumor drug temozolomide (TMZ), cocrystals of TMZ with 4,4'-bipyridine-N,N'-dioxide (BPNO), and solid-state stability were studied. Apart from a known X-ray crystal structure of TMZ (form 1), two new crystalline modifications, forms 2 and 3, were obtained during attempted cocrystallization with carbamazepine and 3-hydroxypyridine-N-oxide. Conformers A and B of the drug molecule are stabilized by intramolecular amide N--HN(imidazole) and N--HN(tetrazine) interactions. The stable conformer A is present in forms 1 and 2, whereas both conformers crystallized in form 3. Preparation of polymorphic cocrystals I and II (TMZBPNO 1:0.5 and 2:1) were optimized by using solution crystallization and grinding methods. The metastable nature of polymorph 2 and cocrystal II is ascribed to unused hydrogen-bond donors/acceptors in the crystal structure. The intramolecularly bonded amide N-H donor in the less stable structure makes additional intermolecular bonds with the tetrazine C==O group and the imidazole N atom in stable polymorph 1 and cocrystal I, respectively. All available hydrogen-bond donors and acceptors are used to make intermolecular hydrogen bonds in the stable crystalline form. Synthon polymorphism and crystal stability are discussed in terms of hydrogen-bond reorganization.

Increasing the electron-transfer ability of Cyanidioschyzon merolae ferredoxin by a one-point mutation – A high resolution and Fe-SAD phasing crystal structure analysis of the Asp58Asn mutant

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

Ueno, Yuko; Matsumoto, Takashi; Yamano, Akihito

2013-07-12

Highlights: •A single amino acid change on the ferredoxin surface affects electron transfer. •Precise positions of amide atoms were located utilizing no prior structural data. •Ultra high resolution and SAD phasing may be used for bias-free model building. -- Abstract: Cyanidioschyzon merolae (Cm) is a single cell red algae that grows in rather thermophilic (40–50 °C) and acidic (pH 1–3) conditions. Ferredoxin (Fd) was purified from this algae and characterized as a plant-type [2Fe–2S] Fd by physicochemical techniques. A high resolution (0.97 Å) three-dimensional structure of the CmFd D58N mutant molecule has been determined using the Fe-SAD phasing method tomore » clarify the precise position of the Asn58 amide, as this substitution increases the electron-transfer ability relative to wild-type CmFd by a factor of 1.5. The crystal structure reveals an electro-positive surface surrounding Asn58 that may interact with ferredoxin NADP{sup +} reductase or cytochrome c.« less

Discovery of competing anaerobic and aerobic pathways in umpolung amide synthesis allows for site-selective amide 18O-labeling

PubMed Central

Shackleford, Jessica P.; Shen, Bo; Johnston, Jeffrey N.

2012-01-01

The mechanism of umpolung amide synthesis was probed by interrogating potential sources for the oxygen of the product amide carbonyl that emanates from the α-bromo nitroalkane substrate. Using a series of 18O-labeled substrates and reagents, evidence is gathered to advance two pathways from the putative tetrahedral intermediate. Under anaerobic conditions, a nitro-nitrite isomerization delivers the amide oxygen from nitro oxygen. The same homolytic nitro-carbon fragmentation can be diverted by capture of the carbon radical intermediate with oxygen gas (O2) to deliver the amide oxygen from O2. This understanding was used to develop a straightforward protocol for the preparation of 18O-labeled amides in peptides by simply performing the umpolung amide synthesis reaction under an atmosphere of . PMID:22184227

Microorganisms hydrolyse amide bonds; knowledge enabling read-across of biodegradability of fatty acid amides.

PubMed

Geerts, Roy; Kuijer, Patrick; van Ginkel, Cornelis G; Plugge, Caroline M

2014-07-01

To get insight in the biodegradation and potential read-across of fatty acid amides, N-[3-(dimethylamino)propyl] cocoamide and N-(1-ethylpiperazine) tall oil amide were used as model compounds. Two bacteria, Pseudomonas aeruginosa PK1 and Pseudomonas putida PK2 were isolated with N-[3-(dimethylamino)propyl] cocoamide and its hydrolysis product N,N-dimethyl-1,3-propanediamine, respectively. In mixed culture, both strains accomplished complete mineralization of N-[3-(dimethylamino)propyl] cocoamide. Aeromonas hydrophila PK3 was enriched with N-(1-ethylpiperazine) tall oil amide and subsequently isolated using agar plates containing dodecanoate. N-(2-Aminoethyl)piperazine, the hydrolysis product of N-(1-ethylpiperazine) tall oil amide, was not degraded. The aerobic biodegradation pathway for primary and secondary fatty acid amides of P. aeruginosa and A. hydrophila involved initial hydrolysis of the amide bond producing ammonium, or amines, where the fatty acids formed were immediately metabolized. Complete mineralization of secondary fatty acid amides depended on the biodegradability of the released amine. Tertiary fatty acid amides were not transformed by P. aeruginosa or A. hydrophila. These strains were able to utilize all tested primary and secondary fatty acid amides independent of the amine structure and fatty acid. Read-across of previous reported ready biodegradability results of primary and secondary fatty acid amides is justified based on the broad substrate specificity and the initial hydrolytic attack of the two isolates PK1 and PK3.

Cobalt nanoparticles/nitrogen-doped graphene with high nitrogen doping efficiency as noble metal-free electrocatalysts for oxygen reduction reaction.

PubMed

Liang, Jingwen; Hassan, Mehboob; Zhu, Dongsheng; Guo, Liping; Bo, Xiangjie

2017-03-15

Nitrogen-doped graphene (N/GR) has been considered as active metal-free electrocatalysts for oxygen reduction reaction (ORR). However, the nitrogen (N) doping efficiency is very low and only few N atoms are doped into the framework of GR. To boost the N doping efficiency, in this work, a confined pyrolysis method with high N doping efficiency is used for the preparation of cobalt nanoparticles/nitrogen-doped GR (Co/N/GR). Under the protection of SiO 2 , the inorganic ligand NH 3 in cobalt amine complex ([Co(NH 3 ) 6 ] 3+ ) is trapped in the confined space and then can be effectively doped into the framework of GR without the introduction of any carbon residues. Meanwhile, due to the redox reaction between the cobalt ions and carbon atoms of GR, Co nanoparticles are supported into the framework of N/GR. Due to prevention of GR layer aggregation with SiO 2 , the Co/N/GR with high dispersion provides sufficient surface area and maximum opportunity for the exposure of Co nanoparticles and active sites of N dopant. By combination of enhanced N doping efficiency, Co nanoparticles and high dispersion of GR sheets, the Co/N/GR is remarkably active, cheap and selective noble-metal free catalysts for ORR. Copyright © 2016 Elsevier Inc. All rights reserved.

Chlorine activation indoors and outdoors via surface-mediated reactions of nitrogen oxides with hydrogen chloride

PubMed Central

Raff, Jonathan D.; Njegic, Bosiljka; Chang, Wayne L.; Gordon, Mark S.; Dabdub, Donald; Gerber, R. Benny; Finlayson-Pitts, Barbara J.

2009-01-01

Gaseous HCl generated from a variety of sources is ubiquitous in both outdoor and indoor air. Oxides of nitrogen (NOy) are also globally distributed, because NO formed in combustion processes is oxidized to NO2, HNO3, N2O5 and a variety of other nitrogen oxides during transport. Deposition of HCl and NOy onto surfaces is commonly regarded as providing permanent removal mechanisms. However, we show here a new surface-mediated coupling of nitrogen oxide and halogen activation cycles in which uptake of gaseous NO2 or N2O5 on solid substrates generates adsorbed intermediates that react with HCl to generate gaseous nitrosyl chloride (ClNO) and nitryl chloride (ClNO2), respectively. These are potentially harmful gases that photolyze to form highly reactive chlorine atoms. The reactions are shown both experimentally and theoretically to be enhanced by water, a surprising result given the availability of competing hydrolysis reaction pathways. Airshed modeling incorporating HCl generated from sea salt shows that in coastal urban regions, this heterogeneous chemistry increases surface-level ozone, a criteria air pollutant, greenhouse gas and source of atmospheric oxidants. In addition, it may contribute to recently measured high levels of ClNO2 in the polluted coastal marine boundary layer. This work also suggests the potential for chlorine atom chemistry to occur indoors where significant concentrations of oxides of nitrogen and HCl coexist. PMID:19620710

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

2016-09-02

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.

Atomic hydrogen and nitrogen distributions from atmosphere explorer measurements

NASA Technical Reports Server (NTRS)

Breig, Edward L.

1992-01-01

We were selective as to our approach to research activities, and devoted primary attention to two investigations concerning the global behavior of atomic hydrogen in the Earth's upper atmosphere. We derive the thermospheric concentration of H by applying the condition of charge-exchange equilibrium between hydrogen and oxygen atoms and ions to in-situ measurements of F-region composition and temperature from the series of Atmosphere Explorer (AE) aeronomy satellites. Progress and accomplishments on these chosen research projects are summarized.

Physical Chemistry of Energetic Nitrogen Compounds

DTIC Science & Technology

1993-10-01

2177 (1981). 8. R.F. Heiner, III, H . Helvajian , G.ý. Holloway,-and J.B. Koffend, J. Phys. Chem . 93, 7813 (1989). 9. D.D. Bell and R.D. Coombe, J. Chem...Deuterium Atom Reactions with NFC12 . . . . . . . . . . . . . . . . . . . . . . . . . 15 3. The Reaction of H Atomps with NF2Cl .............. 22 V...or Br,) was admitted downstream such that a portion of the F atoms were converted to H , Cl or Br atoms prior to the admission of HN3 to the flow. When

Amide-N-oxide heterosynthon and amide dimer homosynthon in cocrystals of carboxamide drugs and pyridine N-oxides.

PubMed

Babu, N Jagadeesh; Reddy, L Sreenivas; Nangia, Ashwini

2007-01-01

The carboxamide-pyridine N-oxide heterosynthon is sustained by syn(amide)N-H...O-(oxide) hydrogen bond and auxiliary (N-oxide)C-H...O(amide) interaction (Reddy, L. S.; Babu, N. J.; Nangia, A. Chem. Commun. 2006, 1369). We evaluate the scope and utility of this heterosynthon in amide-containing molecules and drugs (active pharmaceutical ingredients, APIs) with pyridine N-oxide cocrystal former molecules (CCFs). Out of 10 cocrystals in this study and 7 complexes from previous work, amide-N-oxide heterosynthon is present in 12 structures and amide dimer homosynthon occurs in 5 structures. The amide dimer is favored over amide-N-oxide synthon in cocrystals when there is competition from another H-bonding functional group, e.g., 4-hydroxybenzamide, or because of steric factors, as in carbamazepine API. The molecular organization in carbamazepine.quinoxaline N,N'-dioxide 1:1 cocrystal structure is directed by amide homodimer and anti(amide)N-H...O-(oxide) hydrogen bond. Its X-ray crystal structure matches with the third lowest energy frame calculated in Polymorph Predictor (Cerius(2), COMPASS force field). Apart from generating new and diverse supramolecular structures, hydration is controlled in one substance. 4-Picoline N-oxide deliquesces within a day, but its cocrystal with barbital does not absorb moisture at 50% RH and 30 degrees C up to four weeks. Amide-N-oxide heterosynthon has potential utility in both amide and N-oxide type drug molecules with complementary CCFs. Its occurrence probability in the Cambridge Structural Database is 87% among 27 structures without competing acceptors and 78% in 41 structures containing OH, NH, H(2)O functional groups.

Ternary complexes of Zn(II) and Cu(II) with 1-((2-hydroxynaphthalen-1-yl)methylene)-4-phenylthiosemicarbazide in the presence of heterocyclic bases as auxiliary ligands: Synthesis, spectroscopic and structural characterization and antibacterial activity

NASA Astrophysics Data System (ADS)

Azarkish, Mohammad; Akbari, Alireza; Sedaghat, Tahereh; Simpson, Jim

2018-03-01

The new ternary complexes, ZnLL‧ [L = 1-((2-hydroxynaphthalen-1-yl)methylene)-4-phenylthiosemicarbazide and L‧ = imidazole (1), 2, 2‧-bipyridine (2) and 2-methyimidazole (3)], Zn2L2L‧ [L‧ = 4, 4‧-bipy (4)] and CuLL‧ [L‧ = 2, 2‧-bipy (5)] have been synthesized by the reaction of a metal(II) acetate salt with the thiosemicarbazone and in presence of heterocyclic bases as auxiliary ligands. The synthesized compounds were investigated by elemental analysis and IR, 1H NMR, and 13C NMR spectroscopy and complex 5 was structurally characterized by X-ray crystallography. The results indicate the thiosemicarbazone doubly deprotonated and coordinates to metal through the thiolate sulfur, imine nitrogen and phenolic oxygen atoms. The nitrogen atom(s) of the auxiliary ligand complete the coordination sphere. Complex 4 is binuclear with 4, 4‧-bipy acting as a bridging ligand. The structure of 5 is a distorted square pyramid with one of the bipyridine nitrogen atoms in the apical position. This compound creates an inversion dimer in solid state by intermolecular hydrogen bonds of Nsbnd H⋯S type. The in vitro antibacterial activity of the synthesized compounds were evaluated against Gram-positive (B. subtilis and S. aureus) and Gram-negative (P. aeruginosa) bacteria and is compared to that of standard antibacterial drugs. All complexes exhibit good inhibitory effects and are significantly more effective than the parent ligand.

Ozone Depletion, UVB and Atmospheric Chemistry

NASA Technical Reports Server (NTRS)

Stolarski, Richard S.

1999-01-01

The primary constituents of the Earth's atmosphere are molecular nitrogen and molecular oxygen. Ozone is created when ultraviolet light from the sun photodissociates molecular oxygen into two oxygen atoms. The oxygen atoms undergo many collisions but eventually combine with a molecular oxygen to form ozone (O3). The ozone molecules absorb ultraviolet solar radiation, primarily in the wavelength region between 200 and 300 nanometers, resulting in the dissociation of ozone back into atomic oxygen and molecular oxygen. The oxygen atom reattaches to an O2 molecule, reforming ozone which can then absorb another ultraviolet photon. This sequence goes back and forth between atomic oxygen and ozone, each time absorbing a uv photon, until the oxygen atom collides with and ozone molecule to reform two oxygen molecules.

STM observation of the chemical reaction of atomic hydrogen on the N-adsorbed Cu(001) surface

NASA Astrophysics Data System (ADS)

Hattori, Takuma; Yamada, Masamichi; Komori, Fumio

2017-01-01

Chemical reaction of atomic hydrogen with the N-adsorbed Cu(001) surfaces was investigated at room temperature by scanning tunnel microscopy. At the low exposure of atomic hydrogen, it reacted with the N atoms and turned to be the NH species on the surface. The reaction rate is proportional to the amount of the unreacted N atoms. By increasing the exposure of atomic hydrogen from this condition, the amount of nitrogen species on the surface decreased. This is attributed to the formation of ammonia and its desorption from the surface. The NH species on the surface turn to NH3 through the surface NH2 species by atomic hydrogen. Coexistence of the clean Cu surface enhances the rate of ammonia formation owing to atomic hydrogen migrating on the clean surface.