Chain Nitrogen Research Articles

Three-nucleon forces in exotic open-shell isotopes

Advances in the self-consistent Green's function approach to finite nuclei are discussed, including the implementation of three-nucleon forces and the extension to the Gorkov formalism. We report results on binding energies in the nitrogen and fluorine isotopic chains, as well as spectral functions of 22O. The application to medium-mass open-shell systems is illustrated by separation energy spectra of two argon isotopes, which are compared to one-neutron removal experiments.

ChemInform Abstract: Recent Advanced Strategies for Extending the Nitrogen Chain in the Synthesis of High Nitrogen Compounds

AbstractReview: 42 refs.

Evolving Structural Diversity and Metallicity in Compressed Lithium Azide

In pursuit of new stable nitrogen-rich phases and of a possible insulator–metal transition, the ground-state electronic structure of lithium azide, LiN3, is investigated from 1 atm to 300 GPa (∼2-fold compression) using evolutionary crystal structure exploration methods coupled with density functional theoretical calculations. Two new LiN3 phases, containing slightly reduced and well-separated N2 units, are found to be enthalpically competitive with the known lithium azide crystal structure at 1 atm. At pressures above 36 GPa nitrogen-rich assemblies begin to evolve. These incorporate NN bond formation beyond that in N2 or N3–. N6 rings and infinite one-dimensional linear nitrogen chains (structural analogues to polyacetylene) appear. Above 200 GPa quasi-one- and two-dimensional extended puckered hexagonal and decagonal nitrogen layers emerge. The high-pressure phase featuring linear chains may be quenchable to P = 1 atm. With increasing pressure the progression in electrical conductivity is from insulato...

Recent Advanced Strategies for Extending the Nitrogen Chain in the Synthesis of High Nitrogen Compounds

The synthesis and handling of compounds containing long catenated nitrogen chains are challenging for researchers in this field. These challenges arise from their high endothermic, thermodynamic instability, and a serious lack of nitrogen–nitrogen bond-forming reactions. This paper addresses techniques of azo-coupling reaction between the diazonium salt of <i>N</i>-NH₂ and amine derivative to form the longest nitrogen chain (N₁₁). This type of nitrogen–nitrogen bond formation opens a new strategy for the construction of novel compounds containing odd or even numbers of catenated nitrogen atoms (≥9) especially for polynitrogen compounds.

1H NMR and theoretical studies on the conformational equilibrium of tryptophan methyl ester

Abstract Selected 3JHH coupling constants and theoretical calculations were used to explain the conformational equilibrium of L-tryptophan methyl ester (Trp-OMe) in several solvents. The obtained 3JHαHβ values did not exhibit any significant variability and thus indicate that there are no conformational population variations for the side chain of the Trp-O-Me depending on the solvent. Moreover, the potential energy surfaces obtained at the B3LYP/cc-pVDZ theoretical level produced eight energy minima that were analysed by QTAIM and NBO methods. It was possible to conclude that the Trp-OMe conformational preferences were due to hyperconjugative effects involving the nonbonding electron pairs of the main chain nitrogen atom and certain antibonding orbitals ( σ C 4 -C 13 ⁎ , σ C 1 -C 4 ⁎ and σ C 4 -H 12 ⁎ ) and also to the steric effects from the nonbonding electron pairs of oxygen atoms and the main and side chain of this system.

Nitrogen Fate and Transport in a Conventional Onsite Wastewater Treatment System Installed in a Clay Soil: A Nitrogen Chain Model

Nitrogen cycling in clay‐textured soils with onsite wastewater treatment systems (OWTS) is studied and modeled much less often than sand‐ and loam‐textured soils because there is little data on OWTS performance in these soils. Information on the nitrogen loads from these systems is needed for quantification of total maximum daily loads (TMDLs). The objective of this study was to calibrate a 2D HYDRUS model using experimental soil pressure head and vadose zone nitrogen (N) and chloride (Cl) data from a conventional OWTS that was installed in a clay soil in the Piedmont region of Georgia. An N chain model with water‐content dependent first‐order transformation rates for nitrification and denitrification was developed. The overall predicted soil pressure heads and solute concentrations were similar to data collected from the field experiment. The calibrated model made it possible to estimate water and solute fluxes in the drainfield and N losses from the OWTS. The estimated annual N loss from leaching at the lower boundary of the experimental drainfield was 3.8 kg yr−1. Scaled up to an OWTS size typical for GA and a zoning density of 5 homes ha−1, the N load to groundwater would be 57.4 kg ha−1 yr−1, which is comparable to agricultural production losses to groundwater. The model predicted 52% of the N removal in the system was from denitrification, whereas plant uptake and change in N storage accounted for ≤5% of the N loss. These estimates were specific to clay‐textured soils and should be valuable to TMDL developers who need to predict load allocations for nonpoint sources in the Piedmont.

Alternative binding modes of l-histidine guided by metal ions for the activation of the antiterminator protein HutP of Bacillus subtilis

Anti-terminator proteins control gene expression by recognizing control signals within cognate transcripts and then preventing transcription termination. HutP is such a regulatory protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences in hut mRNAs. During the anti-termination process, l-histidine and a divalent ion are required for hutP to bind to the specific sequence within the hut mRNA. Our previous crystal structure of the HutP-l-histidine-Mg(2+)-RNA ternary complex demonstrated that the l-histidine ligand and Mg(2+) bind together such that the backbone nitrogen and carboxyl oxygen of l-histidine coordinate with Mg(2+). In addition to the Mg(2+), other divalent ions are also known to efficiently support the l-histidine-dependent anti-termination of the hut operon, and the best divalent ion is Zn(2+). In this study, we determined the crystal structure of the HutP-l-histidine-Zn(2+) complex and found that the orientation of l-histidine coordinated to Zn(2+) is reversed relative to that of l-histidine coordinated to Mg(2+), i.e., the imidazole side chain nitrogen of l-histidine coordinates to Zn(2+). This alternative binding mode of the l-histidine ligand to a divalent ion provides further insight into the mechanisms responsible for the activation of RNA binding during the hut anti-termination process.

The heat capacity of nitrogen chain in grooves of single-walled carbon nanotube bundles

The heat capacity of bundles of closed-cap single-walled carbon nanotubes with one-dimensional chains of nitrogen molecules adsorbed in the grooves has been first experimentally studied at temperatures from 2 to 40 K using an adiabatic calorimeter. The contribution of nitrogen CN2 to the total heat capacity has been separated. In the region 2–8 K the behavior of the curve CN2(T) is qualitatively similar to the theoretical prediction of the phonon heat capacity of 1D chains of Kr atoms localized in the grooves of SWNT bundles. Below 3 K the dependence CN2(T) is linear. Above 8 K the dependence CN2(T) becomes steeper in comparison with the case of Kr atoms. This behavior of the heat capacity CN2(T) is due to the contribution of the rotational degrees of freedom of the N2 molecules.

Thermal stability of the N10 compound with extended nitrogen chain

1,1′-Azobis(tetrazole) (N10) as a potential eco-friendly material, has the highest nitrogen content among the azo-stabilized poly-nitrogen compounds. The detailed potential energy surface of N10 was thoroughly investigated using M06-2X, MP2 and CCSD(T) calculations, and the main decomposition pathways were calculated by canonical transition state theory modeling. Amongst all the channels studied, ring opening of the N10 compound, followed by N2 elimination to form the linear molecule Im8 is predicted to be the primary decomposition channel. The linear species formed (Im8) is characterized by a successive four-nitrogen atom chain stabilized by two terminal HNC groups. Its thorough decomposition reaction is strongly exothermic with a barrier height of 67.5 kcal mol−1. TST calculations were performed to probe the influence of temperature on the rate coefficients at 1 atm. Based on the thermal decomposition mechanism of N10, the novel species N12 and N14 were explored. These longer nitrogen chain compounds having higher nitrogen content than N10 are strongly expected to improve performance of high energy density materials. It is found that the predicted structures could exist at room temperature by comparison of their energetic barriers with the corresponding primary N2-elimination reaction of N10.

Gas-phase hydrogen deuterium exchange behavior of lysine and its homologs

The gas-phase hydrogen/deuterium exchange behavior for protonated lysine and its three shorter homologs, ornithine (Orn), 2,4-diamino butanoic acid (Daba), and 2,3-diamino propanoic acid (Dapa) were studied in a modified LCQ-DECA ion trap mass spectrometer. The HDX behavior of protonated lysine has been studied previously by several groups. It undergoes five equivalent exchanges, corresponding to the hydrogen atoms attached to the protonated lysine side chain and amine terminus nitrogen, and one slower exchange corresponding to the COOH hydrogen. The shorter homologs also exchange all six labile hydrogen atoms but at different rates. Relative to protonated lysine, DapaH+ exchanges two times faster, DabaH+ exchanges slightly slower, and OrnH+ exchanges nearly 30 times more slowly. High-level hybrid density functional theory calculations attribute this difference to the increased barrier for the relay-type exchange mechanism in OrnH+, relative to the other homologs.

Structure Analysis and Comparative Characterization of the Cytochrome c′ and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum

The thermodynamic and spectroscopic properties of two soluble electron transport proteins, cytochrome (Cyt) c' and flavocytochrome c, isolated from thermophilic purple sulfur bacterium Thermochromatium (Tch.) tepidum were examined and compared with those of the corresponding proteins from a closely related mesophilic bacterium Allochromatium (Alc.) vinosum. These proteins share sequence identities of 82% for the cytochromes c' and 86% for the flavocytochromes c. Crystal structures of the two proteins have been determined at high resolutions. Differential scanning calorimetry and denaturing experiments show that both proteins from Tch. tepidum are thermally and structurally much more stable than their mesophilic counterparts. The denaturation temperature of Tch. tepidum Cyt c' was 22 °C higher than that of Alc. vinosum Cyt c', and the midpoints of denaturation using guanidine hydrochloride were 2.0 and 1.2 M for the Tch. tepidum and Alc. vinosum flavocytochromes c, respectively. The enhanced stabilities can be interpreted on the basis of the structural and sequence information obtained in this study: increased number of hydrogen bonds formed between main chain nitrogen and oxygen atoms, more compact structures and reduced number of glycine residues. Many residues with large side chains in Alc. vinosum Cyt c' are substituted by alanines in Tch. tepidum Cyt c'. Both proteins from Tch. tepidum exhibit high structural similarities to their counterparts from Alc. vinosum, and the different residues between the corresponding proteins are mainly located on the surface and exposed to the solvent. Water molecules are found in the heme vicinity of Tch. tepidum Cyt c' and form hydrogen bonds with the heme ligand and C-terminal charged residues. Similar bound waters are also found in the vicinity of one heme group in the diheme subunit of Tch. tepidum flavocytochrome c. Electron density map of the Tch. tepidum flavocytochrome c clearly revealed the presence of disulfur atoms positioned between two cysteine residues at the active site near the FAD prosthetic group. The result strongly suggests that flavocytochrome c is involved in the sulfide oxidation in vivo. Detailed discussion is given on the relationships between the crystal structures and the spectroscopic properties observed for these proteins.

POLYMERIC NITROGEN CHAINS CONFINED IN CARBON NANOTUBE BUNDLE

The hybrid structure of polymeric nitrogen chains and carbon nanotube bundle (CNTB) is studied using first-principle calculations. Our finite temperature molecular dynamics simulations show the hybrid system to be very stable at room temperature. The detailed electronic structure is also revealed in this study. According to the calculated electronic structure, the room temperature stabilization of the hybrid material has been demonstrated to originate from the electron transfer from carbon nanotubes (CNTS) to polymeric nitrogen chains. The present work provides a new way to synthesize nitrogen-based high-energy-density materials (HEDM).

Theoretical study on novel nitrogen-rich energetic compounds of bis(amino)-azobis(azoles) with tetrazene unit

Six stereoisomers of 5,5'-bis(amino)-1,1'-azobis(tetrazoles) and 30 other structures, including all possible bis(amino)-azobis(azoles) with an N-N=N-N unit, were designed. The molecular geometries were fully optimized at the DFT-B3LYP level with the 6-31++g (d, p) basis set. From the absence of any imaginary frequency in the infrared vibration frequency spectrum, it is predicted that all these studied structures may exist in stable forms. The results of the total energies of the stereoisomers of 5,5'-bis(amino)-1,1'-azobis(tetrazoles) indicate that the two symmetric trans-form structures are more likely to exist than the other four. The pyrolysis process, chemical stability and molecular electrostatic potential were studied via the investigation of their electronic structure. Heats of formation (HOFs) were calculated using the atomization energy method based on the results of the harmonic vibration frequencies, and a linear relationship was found between the HOF and nitrogen chain or nitrogen content. Densities of the title compounds were predicted with the Monte Carlo method. Finally, according to the results of the calculated HOFs and densities, the explosive parameters of these compounds were calculated using the Kamlet-Jacobs formula. 5,5'-Bis(amino)-1,1'-azobis(tetrazoles) and its isomer 5,5'-bis(amino)-2,2'-azobis(tetrazoles) may have potential for use as energetic compounds.

In-situ Attainment of Paramagnetic Behaviour of Poly(Amino-Acetanalide) during Synthesis

Polyaniline and its derivatives have gained significant interest because of their unique electronic property, simple synthesis process and their environmental stability. We report on the cerium (IV) ammonium nitrate mediated synthesis of poly (amino-acetanilide), PAA, using an interfacial polymerization technique in which PAA serves as a guest of the cerium (III) ion, a paramagnetic species produced during the synthesis condition. The cerium (III) ionic species bonded with the chain nitrogen of the PAA and the supramolecular system show the paramagnetic behavior throughout the experimental temperature range 400-1.9 K.

Structural insight into mechanism and diverse substrate selection strategy of L‐ribulokinase

The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k(cat) values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from Bacillus halodurans bound to L-ribulose and investigated its substrate and ATP co-factor binding properties. The polypeptide chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified (447)GGLPQK(452) as the ATP-binding motif within the smaller domain. L-ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of L-ribulokinase with L-ribulose reveals versatile structural features that help explain recognition of various 2-ketopentose substrates and competitive inhibition by L-erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment.

Emergence of Paramagnetism in Organic Macromolecules during Synthesis

Paramagnetism in polyaniline can be generated during synthesis if cerium (IV) ammonium nitrate (CAN) is used as a polymerizing (oxidizing) agent. During the reaction, in situ formation of Ce3+ ions are doped in the spherical polyaniline particles and show paramagnetic behavior throughout the experimental temperature range (400–1.9 K). The result indicated that the Ce3+ ions covalently functionalized with the chain nitrogen of the polyaniline.

Productive performance, nutrient digestion and metabolism of Holstein (Bos taurus) and Nellore (Bos taurus indicus) cattle and Mediterranean Buffaloes (Bubalis bubalis) fed with corn-silage based diets

The objective of this study was to evaluate the productive performance, nutrients digestion and metabolism of three different genetic groups fed with the same diet based on corn silage. 30 heifers in growth were used of three groups of cattle, the following: Nellore (Bos taurus indicus) (n=10), Holstein (Bos taurus taurus) (n=10), and Mediterranean buffaloes (Bubalis bubalis) (n=10). The animals were fed in groups and received the same experimental diet composed of corn silage and concentrate for growing heifers. In the evaluation of animals the performance, consumption and total apparent digestibility of dry matter and nutrients with the aid of internal markers (chromic oxide) and external (iADF), rumen fermentation, excretion of purine derivatives, nitrogen balance and blood metabolites were measured.No differences were observed in animal performance. There were differences in nutrient intake and apparent digestibility of dry matter and nutrients in different groups of cattle. The concentration of ammonia nitrogen (NH3-N) and short chain fatty acids (SCFA) in the rumen were higher and lower, respectively, for the group of buffaloes in relation to other experimental groups evaluated. When considering the excretion of total purine derivatives, buffaloes showed the lowest value compared to other genetic groups evaluated; about 61.76% of the total genetic group Nellore and 57.62% of the total genetic group Holstein with an average of 33.67mmol/day. For the buffaloes, the excretion of xanthine and hypoxanthine observed was of 5.11% of total purine derivatives. There was a better nitrogen balance (g/day) for groups of Holstein heifers and Nellore in relation to the group of buffalo heifers. There were differences in the concentrations of urea and urea nitrogen in serum and liver enzymes where the buffaloes had higher values in relation at the bovines. There is a great metabolic diversity among the experimental groups evaluated and it was more exacerbated among buffaloes and bovines, when submitted to the same diet and same management conditions.

Abstract 2786: Identification and preclinical characterization of EMD 1204831 – A selective c-Met kinase inhibitor in clinical phase 1

Abstract The involvement of the mesenchymal endothelial transition factor (c-Met) in the primary event of oncogenic transformation and the secondary ability to mediate metastatic spread has been convincingly demonstrated in preclinical and early clinical settings. The clinical benefits of c-Met kinase inhibitors with various modes of actions and selectivity profiles are currently under investigation hoping that inhibitors of c-Met might emerge as valuable cancer therapeutics in the future. During an HTS run 3-(diethylamino)propyl N-[3-[[5-(3,4-dimethoxyphenyl)-2-oxo-6H-1,3,4-thiadiazin-3-yl]methyl]phenyl]carbamate was identified as an attractive lead structure with an interesting overall profile (clogD (7.4): 2.5, S (pH 7.4): &amp;gt;100 µg/ml, IC50 (cMet enzyme): 30 nM, IC50 (cMet A549): 800 nM) providing a valid starting point. The co-crystal structure of 1 revealed the binding mode and the essential structural features. The initial HTS hit was bound in a DFG-in conformation interacting with the main chain nitrogen atom of Met1160 within the hinge region and with the main chain nitrogen of Asp1222. After subsequent optimization of potency, efficacy, PK properties and the safety profile of thiadiazinone 1, EMD1204831 was identified as development compound. EMD1204831 is currently being investigated in a phase 1 clinical trial. The pyridazinone EMD1204831 inhibits enzymatic and cellular c-Met kinase activity with IC50 values of 12 nM and 15 nM, respectively. EMD1204831 displayed an exquisite selectivity when tested in vitro against a panel of more than 400 potential off-targets, including kinases, GPCRs, ion channels, transporters and various enzymes. EMD 1204831 demonstrated excellent anti-tumor activity in vivo in a variety of xenograft models, including U87-MG glioblastoma cells (autocrine HGF expression), TPR-Met-transformed mouse fibroblasts (oncogenic Met fusion protein) or Hs746T gastric cancer cells (c-Met gene amplification and HGF-independent activation). Depending on the particular model, complete regressions were observed with doses as low as 6 mg/kg/d administered per os. PK/PD analysis revealed efficient, dose- and time-dependent inhibition of c-Met phosphorylation, reduction of IL-8 and cyclin D1 expression as well as an induction of the cell cycle inhibitor p27. The overall profile of EMD1204831 including first time structural disclosure, some structure activity relationships, in vitro potency, selectivity profile and in-vivo data will be presented. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2786. doi:10.1158/1538-7445.AM2011-2786

General metabolism of Laribacter hongkongensis: a genome-wide analysis

BackgroundLaribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes and pathways of the general metabolism of L. hongkongensis and correlated them with its phenotypic characteristics.ResultsThe L. hongkongensis genome possesses the pentose phosphate and gluconeogenesis pathways and tricarboxylic acid and glyoxylate cycles, but incomplete Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in agreement with its asaccharolytic phenotype. It contains enzymes for biosynthesis and β-oxidation of saturated fatty acids, biosynthesis of all 20 universal amino acids and selenocysteine, the latter not observed in Neisseria gonorrhoeae, Neisseria meningitidis and Chromobacterium violaceum. The genome contains a variety of dehydrogenases, enabling it to utilize different substrates as electron donors. It encodes three terminal cytochrome oxidases for respiration using oxygen as the electron acceptor under aerobic and microaerophilic conditions and four reductases for respiration with alternative electron acceptors under anaerobic conditions. The presence of complete tetrathionate reductase operon may confer survival advantage in mammalian host in association with diarrhea. The genome contains CDSs for incorporating sulfur and nitrogen by sulfate assimilation, ammonia assimilation and nitrate reduction. The existence of both glutamate dehydrogenase and glutamine synthetase/glutamate synthase pathways suggests an importance of ammonia metabolism in the living environments that it may encounter.ConclusionsThe L. hongkongensis genome possesses a variety of genes and pathways for carbohydrate, amino acid and lipid metabolism, respiratory chain and sulfur and nitrogen metabolism. These allow the bacterium to utilize various substrates for energy production and survive in different environmental niches.

Prediction of a stable free standing nitrogen oligomer

Density Functional Theory is used to predict the possibility of a double chain nitrogen oligomer. Calculation of the frequencies of the normal modes for various chain lengths show no negative frequencies indicating the structures are stationary states. The calculations indicate that this nitrogen oligomer can exist without the need to be stabilized inside carbon nanotubes or between graphene planes as has been predicted for other forms of nitrogen oligomers. It is also predicted that the oligomer is semiconducting. The calculations also show that the material is quite stable and on decomposition to n[N 2] is more exothermic than any existing energetic material.