Pyrrole Nitrogen Atoms Research Articles

Synthesis and Twin Polymerization of Si(OCH2py)4 for Nitrogen‐containing Carbon Materials

AbstractThe synthesis and twin polymerization (TP) of Si(OCH2py)4 (3 a, py=2‐cC5H4N; 3 b, py=3‐cC5H4N; 3 c, py=4‐cC5H4N) is discussed. The solid state structures of 3 b, c were confirmed by single‐crystal X‐ray crystallography showing non‐conventional H‐bonding, forming 2D chains (3 b) or 3D networks (3 c). Thermally induced TP of 3 a–c and their simultaneous polymerization with 2,2‘‐spiro‐bi[4H‐1,3,2‐benzodioxasiline] (4) is described. The resulting hybrid materials were characterized by 1H, 13C{1H}, and 29Si{1H} CP MAS NMR spectroscopy confirming the transformation of the SiOCH2 moieties into CH2 groups enabling the formation of the respective polymers. These results were supported by HAADF‐STEM studies, displaying micro‐structuring. Nitrogen‐containing porous carbon materials C_1–C_3 show surface areas of 1300 and 1700 m2 g−1, large pore volumes between 0.6–1.2 cm3 g−1, and nitrogen contents of up to 3.1 at‐%. X‐ray photoemission spectroscopy reveal that pyrrolic, pyridine, and pyridone nitrogen atoms are present. If equimolar amounts of 3 a–c and 4 are simultaneously polymerized in the presence of [Pd(OAc)2] (5), then the Pd nanoparticle‐decorated material Pd@C_3 (900 m2 g−1) was obtained, which showed k values of −0.083 and −0.066 min−1 in the reduction of methylene blue and methyl orange, proving the accessibility of the Pd NPs.

Phenanthrodiazaporphyrins: 1,10-Phenanthroline-Embedded Diazaporphyrin Analogues

Abstract A series of metal-free and metallo-diazaporphyrin analogues embedded with a 1,10-phenanthroline unit were synthesized and characterized. The molecular structure of the Ni(II) complex determined by single-crystal X-ray diffraction analysis confirmed its monocationic character in which the metal center adopts a typical square planar geometry binding with the pyrrole and phenanthroline nitrogen atoms. The spectroscopic and electrochemical studies, as well as molecular orbital calculations suggested that the metal complexes can be classified as 4nπ non-aromatic compounds.

Fullerphene Nanosheets: A Bottom‐Up 2D Material for Single‐Carbon‐Atom‐Level Molecular Discrimination

AbstractUltrathin 2D nanoporous materials offer enhanced sensitivity and high spatial resolution in sensing applications making them important for the selective discrimination of guest molecules. Here bottom‐up fabrication is reported of a novel molecularly‐thin nitrogen‐doped 2D fullerphene. Thermal annealing at 700 °C of a bottom‐up assembled fullerene C60‐ethylenediamine (EDA) thin film results in formation of a nitrogen‐doped ultrathin carbon film, fullerphene, which exhibits a hierarchically micro/mesoporous structure at its surfaces. N‐doping of fullerphene is dominated by pyrrolic and quaternary nitrogen atoms, which allow selective and repetitive adsorption and desorption of low‐molecular‐weight carboxylic acid vapors through noncovalent interactions. The large surface area (655.2 m2 g–1) and pore volume (0.659 cc g–1) offered by the hierarchical micro/mesoporous architecture leads to superior sensitivity of fullerphene to formic acid over acetic acid in the vapor phase demonstrating that novel 2D fullerphene provides an attractive platform for the discrimination of carboxylic acids at the single‐carbon‐atom level.

Construction of Electrochemical Aptamer Sensor Based on Pt-Coordinated Titanium-Based Porphyrin MOF for Thrombin Detection.

In this work, a Pt-coordinated titanium-based porphyrin metal organic framework (Ti-MOF-Pt) was prepared by embedding single-atom Pt through strong interactions between the four pyrrole nitrogen atoms in the rigid backbone of the porphyrin. The synthesized Ti-MOF-Pt was characterized by TEM, XRD, FTIR and BET. Then, the Ti-MOF-Pt has been used for glassy carbon electrode surface modification and consequently used for construction of a thrombin aptamer sensor. The high surface area provides by MOF and excellent electrochemical property provided by Pt enhance the sensing performance. After optimization of amount of aptamer, hybridization time and specific reaction time, the fabricated aptamer sensor exhibited a linear relationship with the logarithm of the thrombin concentration in the range of 4 pM to 0.2 μM. The detection limit can be calculated as 1.3 pM.

A Defective Nanotube Molecule of C552 H496 N24 with Pyridinic and Pyrrolic Nitrogen Atoms.

A 3-nm molecule comprising a cylindrical core and cross-shaped rims was designed and synthesized by developing a modular synthetic route. By using a cyclic precursor from previous studies as a starting material, multiple carbazole units were installed at the rims of the defective cylinder. The defective cylinder was synthetically doped with two types of nitrogen atoms, that is, pyridinic and pyrrolic nitrogen atoms, which resulted in solvatochromic shifts in fluorescence by charge-transfer interactions. The structure of the large, C552 H496 N24 molecule was fully disclosed by crystallographic analyses, and the unique helical arrangement of nitrogen-doped cylinders in the crystal was revealed.

A Defective Nanotube Molecule of C552H496N24 with Pyridinic and Pyrrolic Nitrogen Atoms

AbstractA 3‐nm molecule comprising a cylindrical core and cross‐shaped rims was designed and synthesized by developing a modular synthetic route. By using a cyclic precursor from previous studies as a starting material, multiple carbazole units were installed at the rims of the defective cylinder. The defective cylinder was synthetically doped with two types of nitrogen atoms, that is, pyridinic and pyrrolic nitrogen atoms, which resulted in solvatochromic shifts in fluorescence by charge‐transfer interactions. The structure of the large, C552H496N24 molecule was fully disclosed by crystallographic analyses, and the unique helical arrangement of nitrogen‐doped cylinders in the crystal was revealed.

Synthesis of Open‐Cage Fullerenes with Pyrrole, Pyrrolone, Pyridinone, Iminofuran, and Pyranone Fragments Embedded on the Rim of the Orifice

AbstractAn open‐cage fullerene derivative with a pyranone and a diiminopentanone moiety was prepared. Further reaction with aniline could convert the pyranone moiety into a pyrrole moiety through the pyridinone moiety as an intermediate. During the process, decarboxylation and dehydroxylation aromatization reactions also took place on the diiminopentanone moiety and the two adjacent hydroxyl groups, thus forming iminofuran or pyrrolone moiety on the rim of the open‐cage fullerene. Protonation experiment showed that the imino nitrogen atom on the rim of the orifice is more basic than the pyrrole nitrogen atom. The lone pair of the pyrrole nitrogen is partially conjugated with the π system of the fullerene cage as shown by single crystal X‐ray structures.

Anchoring an Fe Dimer on Nitrogen-Doped Graphene toward Highly Efficient Electrocatalytic Ammonia Synthesis.

Electrochemical reduction of N2 to NH3 based on sustainable energy is a green technique to produce decentralized and on-demand ammonia. In this work, taking graphene as a design platform, we explore the dual-atom catalysts (DACs) via embedding two homonuclear transition metal (TM) atoms into graphene decorated with four neighboring pyrrolic nitrogen atoms (TM2N4@graphene) to computationally screen the qualified nitrogen reduction reaction (NRR) catalysts. On the basis of the activity, selectivity, and stability of 15 homonuclear DACs of TM2N4@graphene, Fe2N4@graphene is identified as the most efficient NRR catalyst with a limiting potential of only -0.32 V. Electronic structure analysis demonstrates that the low oxidation state of Fe (+1) remarkably activates the molecular N2, which contributes to its excellent NRR catalytic activity. Moreover, the kinetic studies reveal all of the NRR elementary steps exhibiting barriers smaller than that of the hydrogen evolution reaction (HER), showing that HER is effectively suppressed. In addition, we find that the integral crystal orbital Hamilton population (ICOHP) can be used as a descriptor to describe the Gibbs free energy of each step for its NRR performance. This work not only provides theoretical guidance for designing DACs for NRR but also promotes the understanding of DACs for N2 fixation.

Bis(1-methyl-imidazole)[meso-α,α,α,α-tetra-kis(o-nicotinamido-phen-yl)porphinato]iron(II)-1-methyl-imidazole-tetra-hydro-furan (1/1/1.5).

In the title compound, [FeII(C68H44N12O4)(C4H6N2)2]·C4H6N2·1.5C4H8O, the central FeII ion is coordinated by four pyrrole N atoms of the porphyrin core and two N atoms of the 1-methyl-imidazole ligands in the axial sites. One 1-methyl-imidazole and one and a half tetra-hydro-furan solvent mol-ecules are also present in the asymmetric unit. The complex exhibits a near planar porphyrin core conformation, in which the iron centre is slightly displaced towards the hindered porphyrin side (0.01 Å). The average Fe-Np (Np refers to the pyrrole nitro-gen atoms in the porphyrin) bond length is 1.990 (9) Å, and the axial Fe-NIm (NIm refers to the imidazole nitro-gen atoms) bond lengths are 1.993 (3) and 2.004 (3) Å. The dihedral angle between the two coordinated 1-methyl-imidazole planes is 56.6 (2)°. The dihedral angles between the 1-methyl-imidazole planes and the planes of the closest Fe-Np vector are 16.8 (2) and 39.8 (2)°. N-H⋯N and N-H⋯O inter-actions are observed in the crystal structure.

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. It is suggested that the absorption change of this subfamily is caused by the bilin C15-Z/C15-E photoisomerization and a subsequent change in the bilin protonation state. However, structural information and direct evidence of the bilin protonation state are lacking. Here, we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a "bucket" consisting of hydrophobic residues, in which the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A- through C-rings coplanar and the D-ring tilted. Three pyrrole nitrogens of the A- through C-rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen bonded in the β-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the bucket, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the "leaky bucket" structure functions as a proton exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.

Mass Spectra of New Heterocycles: XXII. Electron Impact and Chemical Ionization of 1-Alkyl(cycloalkyl, alkoxyalkyl)-5-[(alkyl, allyl, benzyl)sulfanyl]-1H-pyrrol-2-amines

Fragmentation of 1-alkyl(cycloalkyl, alkoxyalkyl)-5-[(alkyl, allyl, benzyl)sulfanyl]-1H-pyrrol-2-amines under electron impact (70 eV) and chemical ionization (with methane as reactant gas) has been studied for the first time. All the examined compounds under electron impact generated the molecular ion [M]+· (Irel 5–90%) whose primary fragmentation involved mainly cleavage of the C–S bond in the SR4 substituent with elimination of R4 radical (except for 1-isopropyl- and 1-cycloalkyl-1H-pyrrol-2-amines). The main pathway of the decomposition of 1-isopropyl(cycloalkyl)-N,N-dimethyl-5-[(methyl, allyl)sulfanyl]-1H-pyrrol-2-amines was cleavage of the C–N bond with both elimination of the R1 radical from the pyrrole nitrogen atom and fragmentation of the pyrrole ring through elimination of imine (or aziridine) molecule and formation of odd-electron [M – NR1]+· radical cation. Chemical ionization of the title compounds involved protonation, charge exchange, and electrophilic addition processes and elimination of Me (Et) and SMe (SEt) radicals from the [M + H]+ ions.

Computational Study of Actinyl Ion Complexation with Dipyriamethyrin Macrocyclic Ligands.

Relativistic density functional theory has been employed to characterize [AnO2(L)]0/-1 complexes, where An = U, Np, Pu, and Am, and L is the recently reported hexa-aza porphyrin analogue, termed dipyriamethyrin, which contains six nitrogen donor atoms (four pyrrolic and two pyridine rings). Shorter axial (An═O) and longer equatorial (An-N) bond lengths are observed when going from AnVI to AnV. The actinide to pyrrole nitrogen bonds are shorter as compared to the bonds to the pyridine nitrogens; the former also play a dominant role in the formation of the actinyl (VI and V) complexes. Natural population analysis shows that the pyrrole nitrogen atoms in all the complexes carry higher negative charges than the pyridine nitrogens. Upon binding actinyl ions with the ligand a significant ligand-to-metal charge transfer takes place in all the actinyl (VI and V) complexes. The formation energy of the actinyl(VI,V) complexes in the gas-phase is found to decrease in the order of UO2L > PuO2L > NpO2L > AmO2L. This trend is consistent with results for the formation of complexes in dichloromethane solution. The calculated ΔG and ΔH values are negative for all the complexes. Energy decomposition analysis (EDA) indicates that the interactions between actinyl(V/VI) and ligand are mainly controlled by electrostatic components over covalent orbital interactions, and the covalent character gradually decreases from U to Am for both pentavalent and hexavalent actinyl complexes.

Coordination Polymer of Cobalt (ΙΙ) Nitrate with Imidazole: Synthesis, Properties and Crystal Structure

Layered metal-organic polymer [Co(L)6](NO3)2 was obtained (where, L = C3H4N2) and structurally characterized by X-Ray diffraction (XRD) analysis. Crystals have trigonal structure: a = b = 12.3555(10) Ǻ, c = 14.4833(3) Ǻ; α = β = 90˚; γ = 120˚; V = 1914.78(5) Ǻ; R3, Z = 3. The structure of the complex consists of discrete [Co(L)6]2+ cations and anions. The Co2+ ion has a centrosymmetric octahedron configuration with a coordination site—CoN6. The ligand is coordinated monodentate through the pyridine nitrogen atom (N3) to the Co2+ ion with an average Co-N bond distance of 2.1590 Ǻ. Molecules in the coordination polymer are additionally linked by intermolecular hydrogen bonds through the pyrrole nitrogen atom (-N-H) and oxygen of the nitrate group with the formation of a polymer chain of the type: N-H…O. The chains are linked in layers along the (001) plane.

A two-dimensional porous conjugated porphyrin polymer for uniform lithium deposition.

Uniform lithium deposition is a benefit to achieving high-energy-density lithium metal batteries. There are many effective methods to suppress the dendritic growth of metallic lithium and promote the application of the lithium anode. However, the designation of lithiophilic sites at the atomic level remains a huge challenge. Herein, a two-dimensional porous conjugated porphyrin polymer linked by two acetylenic linkages from an in situ coupling reaction has been prepared on copper foil and employed as the lithiophilic host. The four electron-rich pyrrolic nitrogen atoms in the porphyrin building block and the linkage electron-rich sp-hybridized carbon atoms were regarded as precise lithiophilic sites, resulting in a decreased nucleation overpotential and dendrite free morphology. With uniform lithium deposition, the electrochemical performance of the electrode was significantly improved in regard to the overpotential, coulombic efficiency and lifespan. This work expands the precise construction of lithiophilic sites at the atomic level and benefits to further development of high-energy density lithium metal batteries.

Building-up novel coordination polymer with magnesium porphyrin: Synthesis, molecular structure, photophysical properties and spectroscopic characterization. Potential application as antibacterial agent

The new meso-tetraphenylporphyrin magnesium(II) polymer compound with the formula {[MgII(TPP)(4,4′-bpy)]}n.n[MgII(TPP)(4,4′-bpy)2] (I), (TPP) = meso-tetraphenylporphyrinato and 4,4′-bipy = 4,4′-bipyridine) was synthetized and characterized by IR, UV–visible, photoluminescence and 1H NMR spectroscopy studies, single-crystal XRD analyses and cyclic voltammetry. From the X-ray data, it was established that the central metal Mg2+ is located on an inversion center, being octahedrally coordinated to four pyrrole nitrogen atoms of the porphyrin ring and the nitrogen atoms of the two 4,4′-bipyridine axial ligand situated in trans positions with respect to the metal center. The crystal of (I) is made by [MgII(TPP)(4,4′-bipy)2] monomer complexes and {[MgII(TPP)(4,4′-bpy)]}n polymers linked together via CH…π type intermolecular interactions leading to a three-dimensional network. The UV–visible spectrum of (I) shows that the Soret band value (432 nm) is redshifted compared to the free base H2TPP while the λmax values of the Q bands are in the range 570–610 nm. The optical gap of (I) was estimated at 2.00 eV and the cyclic voltammogram of the title compound presents two reversible oxidation waves and one reversible reduction wave. The HOMO and LUMO energy values were deduced from the voltammogram which are −4.94 and −3.06 eV respectively. The use of [MgII(TPP)(DMF)] starting material compound, {[MgII(TPP)(4,4′-bpy)]}n.n[MgII(TPP)(4,4′-bpy)2] (I) and the [MgII(TPP)(HTMA)2] (HTMA = hexamethylenetetramine) (II) as novel significant antibacterial agents was also tested.

Superresilient Hard Carbon Nanofabrics for Sodium-Ion Batteries.

Developing supermechanically resilient hard carbon materials that can quickly accommodate sodium ions is highly demanded in fabricating durable anodes for wearable sodium-ion batteries. Here, an interconnected spiral nanofibrous hard carbon fabric with both remarkable resiliency (e.g., recovery rate as high as 1200 mm s-1 ) and high Young's modulus is reported. The hard carbon nanofabrics are prepared by spinning and then carbonizing the reaction product of polyacrylonitrile and polar molecules (melamine). The resulting unique hard carbon possesses a highly disordered carbonaceous structure with enlarged interlayer spacing contributed from the strong electrostatic repulsion of dense pyrrolic nitrogen atoms. Its excellent resiliency remains after intercalation/deintercalation of sodium ions. The outstanding sodium-storage performance of the derived anode includes excellent gravimetric capacity, high-power capability, and long-term cyclic stability. More significantly, with a high loading mass, the hard carbon anode displays a high-power capacity (1.05 mAh cm-2 at 2 A g-1 ) and excellent cyclic stability. This study provides a unique strategy for the design and fabrication of new hard carbon materials for advanced wearable energy storage systems.

Heteroleptic cobalt(II) complex with nitrogen-rich macrocycles — Structure, bioactivity and DFT modelling

We herein discuss the synthesis and characterization of a novel mononuclear cobalt(II) complex CoII(TPBP)(HTMA)2 with the N-donor ligands; hexamethylenetetramine HTMA and meso-tetrakis[4-(benzoyloxy) phenylporphyrin H2TPBP. Firstly, molecular structure and supramolecular assembly have been thoroughly described. The basic core (porphyrin macrocycle) is nearly planar and the cobalt coordination centre sits in slightly distorted octahedral environment occupied by four pyrrolic nitrogen atoms (NPy) and two HTMA nitrogens (NHTMA). On the basis of quantum chemical density-functional theory calculations, metal—ligand charge-transfer interaction (MLCTI), spin density distribution and chemical reactivity character have been also highlighted. Finally, the bio-activity of free porphyrin and their cobalt complexes was evaluated in vitro, by examining their inhibitory effect against some yeasts and fungal strains, and their ability to scavenge 1,1-diphenyl-picrylhydrazyl DPPH radical. This research could provide rich insights into the structural, electronic and (bio)chemical features of analogues macrocyclic metal complexes.

Synthesis and characterization of antimony(V)-oxo corrole complexes

Two corrolato-antimony(III) complexes have been prepared for the first time and characterized by a series of spectroscopic techniques. Both the complexes have been oxidized by iodosobenzene and the corresponding oxidized derivatives have been isolated and thoroughly characterized. All the four antimony complexes, including two corrolato-antimony(III) complexes and two (corrolato)(oxo)antimony(V) complexes are diamagnetic in nature as is evident from their “normal” chemical shifts. For one of the structurally characterized corrolato-antimony(III) complexes, we have obtained two different conformers in two different solvents with slightly different bond lengths and angles. SbIII corroles are dome shaped and the deviation of SbIII ion with respect to the plane consisting four pyrrolic nitrogen atoms is ~0.963–0.966 Å. The two corrolato-antimony(III) complexes exhibited split Soret bands in the range of 440–462 nm due to the low symmetric nature of these molecules. The two (corrolato)(oxo)antimony(V) complexes exhibited single Soret band in the range of 408–413 nm. All the four antimony complexes displayed weak emission in the range of 630–650 nm and a shoulder at 690–710 nm in CH2Cl2. These emission bands are assigned as fluorescence bands due to the observation of smaller Stokes shift in reference to the lowest energy Q-type bands.

Structure-function study of a novel inhibitor of the casein kinase 1 family in Arabidopsis thaliana.

Casein kinase 1 (CK1) is an evolutionarily conserved protein kinase family among eukaryotes. Studies in non‐plants have shown CK1‐dependent divergent biological processes, but the collective knowledge regarding the biological roles of plant CK1 lags far behind other members of the Eukarya. One reason for this is that plants have many more genes encoding CK1 than do animals. To accelerate our understanding of the plant CK1 family, a strong CK1 inhibitor that efficiently inhibits multiple members of the CK1 protein family in vivo (i.e., in planta) is required. Here, we report a novel, specific, and effective CK1 inhibitor in Arabidopsis. Using circadian period‐lengthening activity as an estimation of the CK1 inhibitor effect in vivo, we performed a structure–activity relationship study of analogues of the CK1 inhibitor PHA767491 (1,5,6,7‐tetrahydro‐2‐(4‐pyridinyl)‐4H‐pyrrolo[3,2‐c]pyridin‐4‐one hydrochloride). A propargyl group at the pyrrole nitrogen atom (AMI‐212) or a bromine atom at the pyrrole C3 position (AMI‐23) had stronger CK1 inhibitory activity than PHA767491. A hybrid molecule of AMI‐212 and AMI‐23 (AMI‐331) was about 100‐fold more inhibitory than the parent molecule PHA767491. Affinity proteomics using an AMI‐331 probe showed that the targets of AMI‐331 inhibition are mostly CK1 kinases. As such, AMI‐331 is a potent and selective CK1 inhibitor that shows promise in the research of CK1 in plants.

Characterization of nitrogen-containing aromatics in Baiyinhua lignite and its soluble portions from thermal dissolution

Abstract Soluble portions (SPs) 1–4 (SP1–SP4) were afforded from sequentially dissolution and alkanolyses of Baiyinhua lignite (BL) in cyclohexane, CH3OH, CH3CH2OH, and (CH3)2CHOH at 300 °C. They were analyzed with a gas chromatograph/mass spectrometer and quadrupole exactive orbitrap mass spectrometer (QEOTMS) with an atmosphere pressure chemical ionization source in positive-ion mode, while BL was characterized with an X-ray photoelectron spectrometer (XRPES). The results show that the yields of SP2 and SP3 are much higher than those of SP1 and SP4, and the total SP yield is ca. 39.0%. According to the analysis with XRPES, pyrrolic nitrogen atoms are the most abundant nitrogen existing forms in BL. Thousands of nitrogen-containing aromatics (NCAs) were resolved with QEOTMS and their molecular masses are mainly in the range of 200–450 u. The main NCAs are N1O1 and N1O2 class species with double bond equivalent values of 4–18 and carbon numbers of 7–30. The nitrogen atoms appear in pyridines, quinolines, benzoquinolines or acridine, and dibenzoquinolines or naphthoquinolines, while the oxygen atoms exist in methoxy and furan rings.