Nitrogen Acceptor Research Articles

Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222.

Denitrification is a respiratory process that produces nitrous oxide as an intermediate, which may escape to the atmosphere before its reduction to dinitrogen through the nitrous oxide reductase NosZ. In this work, the denitrification process carried out by Paracoccus denitrificans PD1222 has been explored through a quantitative proteomic analysis. Under anaerobic conditions, with nitrate as sole nitrogen source, the synthesis of all the enzymes involved in denitrification, the respiratory nitrate, nitrite, nitric oxide, and nitrous oxide reductases, was increased. However, the periplasmic and assimilatory nitrate reductases decreased. Synthesis of transporters for alcohols, D-methionine, sulfate and copper, most of the enzymes involved in the tricarboxylic acid cycle, and proteins involved in other metabolic processes like lysine catabolism, fatty acids degradation and acetyl-CoA synthesis, was increased during denitrification in P. denitrificans PD1222. As consequence, an enhanced production of the central metabolite acetyl-CoA was observed. After establishing the key features of the denitrification proteome, its changes by the influence of a competitive electron acceptor, oxygen, or competitive nitrogen source, ammonium, were evaluated.

Molecular Beam Epitaxy and p-type Doping of ZnMgSTe Quaternary Alloys

ZnS-based ZnMgSTe quaternary alloy layers have been grown by molecular beam epitaxy. The bandgap of ZnMgSTe has been estimated from the reflectance spectra, and it was found that it increases with increasing Mg content, while it decreases with increasing Te content. Nitrogen acceptor doping to $$\hbox {Zn}_{1-x}\hbox {Mg}_x\hbox {S}_{1-y}\hbox {Te}_y$$ layers has also been investigated. The layers with Te content $$y > 0.1$$ were found to be p-type, and the layer with the larger Te content exhibited lower resistivity. From these results, it seems that the ZnMgSTe quaternary alloy with appropriate composition possesses both a wide bandgap and p-type conductivity.

Supramolecular packing and polymorph screening of N-isonicotinoyl arylketone hydrazones with phenol and amino modifications

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 = OH or 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 OH⋯N, NH⋯N, OH⋯O, NH⋯O, NH⋯π, π⋯π stacking, as well as other weaker interactions such as CH⋯N, CH⋯O, CH⋯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.

Identification and tuning of zinc-site nitrogen-related complexes in ZnO material

In this article, the authors have designed an experiment to artificially introduce the recently proposed zinc-site nitrogen complex acceptors. The novel acceptors have been introduced in ZnO film samples grown at an atmosphere with extra-high oxygen partial pressure. The shallowness of the nitrogen complex acceptors has been experimentally verified. The concentration of the nitrogen-related complex acceptors could be tuned by varying the VI/II ratio in gas during growth. The modulation of the carrier concentration has been observed in accordance with the change of the complex concentration. Although theories predict higher formation rate of the complexes as monotonically increasing the oxygen chemical potential, experiments show that oxygen interstitials and/or antisite oxygen would compete the formation of the zinc-site nitrogen acceptors at extra-oxygen-rich gaseous condition.

Evidence for nitrogen-related deep acceptor states in SnO2 grown by chemical vapor deposition

Nitrogen-doped SnO2 thin films were deposited on r-plane sapphire by chemical vapor deposition with different NH3 flow rates. Hydrogen of the precursor led to a dominant unintentional n-type behavior in the as grown samples, i.e., SnO2:N,H. Thermal annealing increased the ratio of N concentration to H concentration in the samples. A significant increase in resistivity and a decrease in carrier concentration, both by almost four orders of magnitude, were observed in the annealed SnO2:N,H thin films. Unfortunately, the carrier type in the samples annealed at the highest temperatures, i.e., with low carrier concentrations of ∼1015 cm−3, could not be determined. Nevertheless, our findings suggest that the samples annealed at the highest temperatures above 500 °C were close to becoming p-type (scenario A) or are even p-type (scenario B). The analysis of temperature-dependent conductivity measurements yielded activation energies in the range of 280 to 350 meV, which must be either due to activation from a deep donor state to the conduction band (scenario A) or due to activation from a nitrogen acceptor state to the valence band (scenario B). Independent of the scenario, our results indicate that achieving stable p-type conductivity by nitrogen doping of SnO2 should be possible.

ESR identification of the nitrogen acceptor in 2H-polytype synthetic MoS2: Dopant level and activation

Multi-frequency electron spin resonance (ESR) study of p-type synthetic 2H MoS2 reveals a previously unreported signal of axial-symmetry [g// = 2.032(2); g⊥ = 2.270(2)] characteristic for a hole-type center in MoS2. It is identified as originating from N acceptor dopants, the N atoms substituting for S sites, with a density of ∼2.3 x 1017 cm-3, thus predominantly accounting for the p-type sample doping. For the applied magnetic field along the c-axis, the signal is mainly comprised of a 14N hyperfine 1:1:1 triplet of splitting A// = 14.7 ± 0.2 G with, on top, a center line accounting for ∼26% of the total signal intensity. The additional observation of a weak half-field signal (g = 3.92) correlating with the main full-field Zeeman response points to the presence of spin S ≥ 1 N agglomerates. The overall signal properties indicate that only ∼74% of the N acceptors occur as isolated decoupled dopants. Monitoring of the ESR signal intensity over a broad temperature range unveils the N dopant as a shallow acceptor of activation energy Ea = 45 ± 7 meV, thus well fit for stable substitutional p-type doping in MoS2-based novel nanoelectronic devices.

Synergistic effects of hydrogen and halogen bonding in co-crystals of dipyridylureas and diiodotetrafluorobenzenes

Herein, we investigate co-crystallization of three linear co-formers that contain urea and pyridyl groups with three regioisomers of diiodotetrafluorobenzene (DITFB) to afford eleven co-crystals. The linear o-, m-, and p- dipyridylureas vary distance and geometry between the urea carbonyl oxygen and two pyridyl nitrogen acceptors, while the donors consist of urea NH groups and the activated halides in DITFB. Electrostatic potential calculations suggest that the o-dipyridylurea co-former presents two significantly different acceptors. In comparison, the acceptors in the m- and p-dipyridylurea co-formers display electrostatic potentials within 5–6 kJ/mol and should be competitive, potentially leading to altered assembly motifs. Overall, ten of the co-crystals consistently display the urea assembly motif as the best acceptor/donor pair. Seven structures were obtained as the predicted 1:1 ratio with halogen bonding interactions linking ditopic halogen bond donors and the pyridyl units through N···I interactions ranging from 78.4 to 83.1% of the van der Waals radii. Modified structures were more likely when there was a structural mismatch with the geometrically challenging o-DITFB donor and m- or p-dipyridylurea co-former. The majority of the co-crystal structures (10/11) demonstrated fully satisfied hydrogen and halogen bonding interactions suggesting that these synthons can be used synergistically to generate complex solid-state structures.

Nitrogen isotopes provide clues to amino acid metabolism in human colorectal cancer cells

Glutamic acid and alanine make up more than 60 per cent of the total amino acids in the human body. Glutamine is a significant source of energy for cells and also a prime donor of nitrogen in the biosynthesis of many amino acids. Several studies have advocated the role of glutamic acid in cancer therapy. Identification of metabolic signatures in cancer cells will be crucial for advancement of cancer therapies based on the cell’s metabolic state. Stable nitrogen isotope ratios (15N/14N, δ15N) are of particular advantage to understand the metabolic state of cancer cells, since most biochemical reactions involve transfer of nitrogen. In our study, we used the natural abundances of nitrogen isotopes (δ15N values) of individual amino acids from human colorectal cancer cell lines to investigate isotope discrimination among amino acids. Significant effects were noticed in the case of glutamic acid, alanine, aspartic acid and proline between cancer and healthy cells. The data suggest that glutamic acid is a nitrogen acceptor while alanine, aspartic acid and proline are nitrogen donors in cancerous cells. One plausible explanation is the transamination of the three acids to produce glutamic acid in cancerous cells.

Shallow acceptor state in ZnO realized by ion irradiation and annealing route

Activation of shallow acceptor state has been observed in ion irradiated and subsequently air annealed polycrystalline ZnO material. Low temperature photoluminescence (PL) spectrum of the sample exhibits clear signature of acceptor bound exciton (ABX) emission at 3.360 eV. The other two samples, pristine and ion irradiated (without annealing), however, do not show acceptor related PL emission in the nearby energy region. Electron transition from shallow donor (most probable site is interstitial zinc for undoped ZnO) to such newly formed shallow acceptor state creates new donor-acceptor pair (DAP) luminescence peak ∼ 3.229 eV. ABX and DAP peak energy positions confirm that the acceptor is N related. The acceptor exciton binding energy has been estimated to be 180 ± 15 meV which is in conformity with earlier reports. The activation of shallow acceptors without any source of atomic nitrogen can only be possible through diffusion of molecular nitrogen inside the sample during annealing. The N2 molecules get trapped at bulk defect sites incorporated by ion irradiation and subsequent annealing. X-ray diffraction (XRD) and Raman spectroscopic (RS) investigation have been employed to probe the changing defective nature of the ZnO samples. Irradiation induced increased disorder has been detected (both by XRD and RS) which is partially removed/modified by annealing at 300 °C. Simultaneous activation of molecular nitrogen acceptor in purposefully defective ZnO is the key finding of this work. Results presented here provide a simple but controlled way of producing shallow acceptor state in ZnO. If optimized through suitable choice of ion, its energy and fluence as well as the annealing temperature, this methodology can trigger further scope to fabricate devices using ZnO epitaxial thin films or nanowires.

Reversible p-type conductivity in H passivated nitrogen and phosphorous codoped ZnO thin films using rapid thermal annealing

We demonstrate reversible p-type nature of pulsed laser deposited (P, N) codoped ZnO thin films using rapid thermal annealing process. As grown thin films exhibited change in conductivity from p to n-type over a span of 120days. Non-annealed n-type thin films contain unintentional donor impurities such as hydrogen and carbon. X-ray photoelectron spectroscopy and Raman measurements conclusively show that hydrogen passivates nitrogen acceptors by forming NH complex. Carbon can be annealed out at 600°C, whereas, the dissociation of NH complex takes place at 800°C. The films revert its p-type nature at an annealing temperature of 800°C.

Combined Experimental and Theoretical Study of the Transient IR Spectroscopy of 7-Hydroxyquinoline in the First Electronically Excited Singlet State.

The photophysics of 7-hydroxyquinoline (7HQ) in protic media results from an interplay of acid-base chemistry, prompted by the effects of photoacidity of the hydroxyl group and photobasicity of the nitrogen atom in the quinoline aromatic system. With ultrafast IR spectroscopic measurements, we follow the proton transfer dynamics of 7HQ in its four possible charged forms in methanol solution. Using deuterated methanol as solvent, we determine deuteron transfer rates from the neutral to the zwitterionic form to be 330 ps, those from the cationic form to the zwitterionic form to be 170 ps, and those from the anionic form to the zwitterionic form to be 600 ps. We compare the observed IR-active fingerprint marker patterns in the electronic ground state and the first electronically excited 1Lb-state with those calculated using density functional theory and time-dependent density functional theory, respectively, and find good correspondence between experimental and calculated transitions. The calculations provide insight into the nature of electronic excitation of these four different charged forms of 7HQ, suggesting the key role of electronic charge distribution changes upon electronic excitation of 7HQ and hydrogen bond changes at the donor hydroxyl and acceptor nitrogen moieties.

Improvement of thermal stability of p‐type ZnO:(Al,N) fabricated by oxidizing Zn3N2:Al thin films

AbstractThe authors report the fabrication of p‐type ZnO thin films with improved thermal stability. The p‐type ZnO thin films were obtained by oxidizing Zn3N2:Al thin films in an oxygen ambient. Both Zn3N2:Al and Zn3N2 thin films were deposited on fused silica substrates at 100 °C by megnetron sputtering. X‐ray diffraction (XRD) measurements showed that the ZnO thin films obtained from by oxiding Zn3N2:Al, have preferred (002) orientation. On the other hand, ZnO films obtained by oxidizing Zn3N2 are polycrystalline. The optical band gap of ZnO (3.294 eV) obtained by annealing Zn3N2:Al thin films is narrower than that of the ZnO (3.31 eV) obtained by annealing Zn3N2. P‐type ZnO films were formed by annealing Zn3N2:Al at temperatures above 600 °C. A maximum hole density of 1.4 x 1016 cm‐3 was obtained in a film annealed at 800 °C. In contrast, only n‐type ZnO can be produced from oxidizing Zn3N2. Our results indicate that the Al can stabilize the nitrogen acceptors in ZnO thin films. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Metal-ion binding via a cyclic network of intramolecular halogen-bonded interactions: a theoretical study

ABSTRACTA cyclic network of four intramolecular C–I…N interactions is shown to bind Na+ and Ca2+ with corresponding binding energies of 57 and 175 kcal/mol, respectively. The halogen-bonded network is built by connecting four molecules of 2-iodoimidazole with acetylene and ethylene as convenient linkers. 2-iodoimidazole provides both the halogen bond donor and the halogen bond acceptor moieties. Each of the four iodine atoms participates in the binding of the metal ion as indicated by the presence of bond paths connecting the metal ion with each one of the halogen atoms in the host, and orthogonal to the C–I…N interactions. A similar intermolecular network of C–I…N interactions is also found to form by the interactions of four 2-iodoimidazole molecules. In contrast to its intramolecular counterpart, the intermolecular C–I…N network is at least partly destroyed upon metal-ion binding as the metal ion competes somewhat successfully for the lone pair of the acceptor nitrogen atoms.

Identification of nitrogen acceptor in Cu2O: First-principles study

The source of p-type carriers observed in nitrogen-doped Cu2O samples [Appl. Phys. Lett. 82, 1060 (2003)] was identified by using accurate hybrid density functional calculations. Similar to the case of ZnO, we found that N is a deep acceptor when substituting for O in Cu2O and cannot be the source of the observed p-type carriers. Detailed investigation of other N-related defects in Cu2O reveals that N2 substitution for Cu, i.e., (N2)Cu, is a shallow acceptor and can give hole carriers in N-doped Cu2O samples. (N2)Cu is not only a shallow acceptor but it also has a lower formation energy than NO in some growth conditions. The calculated emission photo luminescence (PL) peak at 1.89 eV associated with (N2)Cu is also in good agreement with the observed N-related PL peak at ∼1.82 eV in N-doped Cu2O sample. To aid future identification by Raman spectroscopy techniques, the vibrational frequencies of N2 on both Cu and O sites were calculated.

Molecular nitrogen acceptors in ZnO nanowires induced by nitrogen plasma annealing

X-ray absorption near-edge spectroscopy, photoluminescence, cathodoluminescence, and Raman spectroscopy have been used to investigate the chemical states of nitrogen dopants in ZnO nanowires. It is found that nitrogen exists in multiple states: ${\mathrm{N}}_{\mathrm{O}},\phantom{\rule{0.16em}{0ex}}{\mathrm{N}}_{\mathrm{Zn}}$, and loosely bound ${\mathrm{N}}_{2}$ molecule. The results establish a direct link between a donor-acceptor pair emission at 3.232 eV and the concentration of loosely bound ${\mathrm{N}}_{2}$. This work confirms that ${\mathrm{N}}_{2}$ at Zn site is a potential candidate for producing a shallow acceptor state in N-doped ZnO as theoretically predicted by Lambrecht and Boonchun [Phys. Rev. B 87, 195207 (2013)]. Additionally, shallow acceptor states arising from ${\mathrm{N}}_{\mathrm{O}}$ complexes have been ruled out in this paper.

First-principle study on Ag-2N heavy codoped of p-type graphene-like ZnO nanosheet

In this article, two different Ag-2N heavy codoped of graphene-like ZnO nanosheets have been investigated based on first-principles density-functional theory. The geometric optimization, Density of States (DOS) and Band structure (BS) for all models are calculated, respectively. The results indicate that Ag substituted on the cation site (AgZn) exhibit a strong attractive interaction with a nitrogen acceptor located at the nearest-neighbor oxygen site, forming passive Ag-N complex. This study can be a theoretical guidance to improve the electrical conductivity of p-type graphene-like ZnO nanosheet by heavy codoping.

Electrical characterization of In-N codoped p-type ZnO films grown by chemical methods

Preliminary results of the studies of electrical properties of ZnO films, codoped with donor and acceptor pair In-N are reported. The films were grown on Si substrates by chemical route procedures involving a sol-gel followed by hydrothermal treatment at 500°C. For electrical characterization, current-voltage and capacitance-voltage measurements were conducted on MIS structures with embedded ZnO(In,N) films. The estimated doping concentration in the studied films is higher than 1×1016 cm−3 corresponding to a semiconductor with good conductivity. However, the obtained large values of the differential specific resistivity (ρ = 3.2×105 Ωcm) suggest that the nitrogen acceptors in these films are compensated by some kind of donor-type defects.

Electronic structure and magnetic properties of N monodoping and (Ag,N) codoped graphene-like ZnO sheet

We perform first principles density functional theory calculations to investigate the atomic structures, electronic structures and magnetic properties of dopant complexes involving Ag and N in graphene-like ZnO sheet (Gr–ZnO). The results indicate that monodoping of N in Gr–ZnO favours a spin polarised state. Ag substituted on the cation site (AgZn) acts as a single acceptor and exhibits a strong attractive interaction with a nitrogen acceptor located at the nearest neighbour oxygen site, forming passive Ag–N complex. By introducing a higher concentration of nitrogen, Ag–2N complex forms. The ferromagnetism is decreased, but the formation energy can be evidently reduced for the defective system. Our findings suggest that (Ag,N) codoping of Gr–ZnO could turn the ferromagnetic stability and is likely to yield better p-type conductivity.

Study of a 2D coordination polymer of Zn(II) with 5-aminoisophtalic as ligand.

The design, synthesis and characterization of infinite one-, two- and three dimensional coordination polymers have attracted increasing attention in chemistry and material science research due to their potential applications as drug deliver, magnetic and optical sensors [1]. In particular, a series metal-organic frameworks MOFs - (a coordination polymer subclass) with different topological nets such as honey-comb, brick wall, ladder, herringbone, diamondoid and rectangular grids have been comprehensively discussed by Yaghi, Kitagawa and their co-workers [2] and it was observed that the type of metal ion and organic bridge ligand determines the dimensionality and the topology of the network. In this work we report a new 2D coordination polymer obtained by from ZnSO4.7H2O and 5-aminoisophtalic acid (5AIF), using the base diffusion method (DMSO as solvent). The crystal structure was determined from single crystal X-ray diffraction data collect in a Gemini-Oxford diffractometer. The Zn atom is tetrahedrally coordinated with two oxygen and one nitrogen from three different 5AIF molecules and one oxygen from DMSO molecules. The molecular packing indicates the formation of a 2D parallel to (010) forming hydrophilic cavities along [001]. The 2D network is stabilized by intermolecular hydrogen bonds involving the donor hydroxyl group (O3-H3) and the acceptor nitrogen atom (N1). The geometrical features of this new 2D coordination polymer were are all in agreement with similar fragments deposited in CSD [3].

Kinesin spindle protein inhibitors with diaryl amine scaffolds: crystal packing analysis for improved aqueous solubility.

Diaryl amine derivatives have been designed and synthesized as novel kinesin spindle protein (KSP) inhibitors based on planar carbazole-type KSP inhibitors with poor aqueous solubility. The new generation of inhibitors was found to show comparable inhibitory activity and high selectivity for KSP, and this was accompanied with improved solubility. Kinetic analysis and molecular modeling studies suggested that these inhibitors work in an ATP-competitive manner via binding to the secondary allosteric site formed by α4 and α6 helices of KSP. Comparative structural investigations on a series of compounds revealed that the higher solubility of diaryl amine-type inhibitors was attributed to fewer van der Waals interactions in the crystal packing and the hydrogen-bond acceptor nitrogen of the aniline moiety for favorable solvation.