Pyrrole Nitrogen Atoms Research Articles

Synthesis and Characterization of Palladium(II) Complexes of meso-Substituted [14]Tribenzotriphyrin(2.1.1).

Metalation of 6,13,20,21-tetrakis-aryl-22H-[14]tribenzotriphyrin(2.1.1) (TriPs) with PdCl2 provides Pd(II)-TriP complexes in 45-56% yields. The complexes were characterized by mass spectrometry, and UV-visible absorption, magnetic circular dichroism, and (1)H NMR spectroscopy. A single crystal X-ray analysis reveals that the Pd(II)-TriPs adopts a deeply saddled conformation. The palladium(II) ion is coordinated by two pyrrole nitrogen atoms and two chloride ions to form the square-planar coordination environment. The redox properties of the Pd(II)-TriPs were studied by cyclic voltammetry. Each compound undergoes one irreversible and two reversible one-electron reductions. There is a marked red-shift of the main spectral bands, relative to those of the free-base TriP ligand, due to a marked relative stabilization of the LUMO upon coordination by PdCl2.

Homoleptic transition metal complexes of the 7-azaindolide ligand featuring κ(1)-N1 coordination.

Homoleptic complexes of the anion of 7-azaindole (AzaIn) were synthesized and characterized for a series of 3d transition metals. For Mn(II), Fe(II), and Co(II), complexes of formula Na2[M(AzaIn)4]·2L (L = tetrahydrofuran (THF), 2-MeTHF, toluene, or benzene) were isolated by treatment of the corresponding metal chloride salts with 7-azaindole in the presence of sodium hexamethyldisilazide. The complexes adopt tetrahedral geometries with exclusive coordination to the transition metal ion through the pyrrolic N1 nitrogen atoms of the AzaIn ligands. Solid-state structures of the complexes demonstrate that the sodium cations remain tightly associated with the coordination entities through interaction with both the pyrrolic and pyridine nitrogen atoms of the azaindolide ligands. For Fe(II), replacement of the sodium cations by other alkali metal ions (Li or K) generates new complexes that demonstrate similar coordination geometries to the sodium salts. As a means of comparison, the Fe(II) complex of 4-azaindolide was also investigated. Na2[Fe(4-AzaIn)4]·2L adopts a similar solution structure to the 7-azaindolide complexes as judged by NMR spectroscopy and cyclic voltammetry. Density functional theory calculations were performed to investigate the bonding in the 7-azaindolide complexes. Results demonstrate that 7-azaindolide-κ(1)-N1 is a nearly pure sigma donor ligand that features a high degree of ionic character in its bonding to mid 3d transition metal ions.

A Quasi-relativistic Density Functional Theory Study of the Actinyl(VI, V) (An = U, Np, Pu) Complexes with a Six-Membered Macrocycle Containing Pyrrole, Pyridine, and Furan Subunits

Actinyl(VI, V) (An = U, Np and Pu) complexes of the recently reported hybrid macrocycle, cyclo[1]furan[1]pyridine[4]pyrrole (denoted as H4L), have been studied using density functional theory in combination with the small-core scalar-relativistic effective core potentials and corresponding (14s13p10d8f6g)/[ 10s9p5d4f3g] basis sets in the segmented contraction scheme. On the basis of our calculations, the pyrrole nitrogen atoms that possess the shortest An-L bonds and strongest basicity are the main donor atoms that contribute to the formation of actinyl(VI, V) complexes. The natural population analysis (NPA) suggests higher ligand-to-actinyl charge transfer in the actinyl(VI) complexes than in their actinyl(V) analogues, which account for the higher decomposition energies of the former. A significant actinide-to-ligand spin density delocalization in the uranyl(V) and neptunyl(V) complexes was observed owing to the redistribution of spin density caused by complexation. A thermodynamic analysis indicates that the formation of the actinyl(VI, V) complexes are exothermic reactions in CH2Cl2 solvent, where the uranyl cations show the highest selectivity. In aqueous solution containing chloride ions, for complexing with macrocycle H4L, the plutonyl(VI) and uranyl(V) cations possess the highest selectivity among actinyl(VI) and (V) cations, respectively. This work can shed light on the design of macrocycle complexes for actinide recognition and extraction in the future.

N-H Hydrogen Bonding in Porphyrins - from Conformational Design to Supramolecular Chemistry

Typically porphyrin N-H units are not involved in intermolecular hydrogen bonds as they are ‘shielded’ by the macrocycle system. However, two possibilities exist to utilize the pyrrole nitrogen atoms in such bonds: a) Porpho(di)methenes and phlorins (calixphyrin-type systems) contain sp3-hybridized meso positions and the interruption of the aromatic system gives rise to specific cavities and often roof- or bowl-shaped conformations making the core nitrogen and N–H units more accessible for coordination. b) Likewise, saddle-distorted nonplanar porphyrins are very basic and can bind anions and neutral molecules via N-H hydrogen bonds in the core. Similarly, specific conformations and binding motifs can be accessed in porphyrin dications depending on the type, number, regiochemistry and steric bulk of substituents in the respective free base porphyrin. Here we give a brief overview of the different approaches and illustrate their use with regard to the design of ion-pair receptors for small molecules and anions and the formation of potentially functional supramolecular complexes.

The synthesis of some sulfonamides based on 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine

Synthetic protocols for the preparation of 1-oxo-, 3-oxo-, and 1,3-dioxopyrrolo[3,4- c ]pyridines which contain sulfonamide groups linked to the pyrrole nitrogen atom of the pyrrolo[3,4- c ]pyridine cycle by a flexible (CH2)6 aliphatic linker were developed. 1,3-Dioxopyrrolo[3,4- c ]pyridines were obtained from 3,4-pyridinedicarboxylic acid by condensation of intermediate methyl 3-(chlorocarbonyl)isonicotinate with amines. 3-Oxopyrrolo[3,4- c ]pyridines were prepared by regioselective reduction of 1,3-dioxopyrrolo[3,4- c ]pyridines with a tin dust followed by treatment with triethylsilane. 1-Oxopyrrolo[3,4- c ]pyridines were prepared by a synthetic sequence consisting of the treatment of methyl isonicotinate with N -bromosuccinimide and the following condensation of the obtained ethyl 3-bromomethylisonicotinate with primary amines. How to Cite Ikaunieks, M.; Bjorkling, F.; Loza, E. Chem. Heterocycl. Compd. 201 5 , 51 , 658. [ Khim. Geterotsikl. Soedin. 2015 , 51 , 658.] For this article in the English edition see DOI 10.1007/s10593-015-1753-y

N-H Hydrogen Bonding in Porphyrins - from Conformational Design to Supramolecular Chemistry

Typically porphyrin N-H units are not involved in intermolecular hydrogen bonds as they are ‘shielded’ by the macrocycle system. However, two possibilities exist to utilize the pyrrole nitrogen atoms in such bonds. A) Porpho(di)methenes and phlorins (calixphyrin-type systems) contain sp3-hybridized meso positions and the interruption of the aromatic system gives rise to specific cavities and often roof- or bowl-shaped conformations making the core nitrogen and N–H units more accessible for coordination. B) Likewise, saddle-distorted nonplanar porphyrins are very basic and can bind anions and neutral molecules via N-H hydrogen bonds. Similarly, specific conformations and binding motifs can be accessed in porphyrin dications (N22,N24-dihydroporphyrins) depending on the type, number, regiochemistry and steric bulk of substituents in the respective free base porphyrin. The different approaches will be compared and analyzed with regard to the design of ion-pair receptors for small molecules and anions and the formation of functional supramolecular complexes.

Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography.

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.

Spectroscopic and theoretical studies of acid-base behaviors of N-confused porphyrins: effects of meso-aryl substituents.

The acid-base properties of a series of meso-aryl-substituted N-confused porphyrins (NCPs) were examined in aqueous sodium dodecyl sulfate (SDS) micellar solutions by both spectrophotometric methods and theoretical calculations. Reflecting the unsymmetrical structure of NCP having an outward-pointing pyrrolic nitrogen atom, the first and second protonations were distinguishable in the absorption and (1)H NMR spectra, unlike for porphyrins, and the pK3 and pK4 values were determined discretely. The individual basicities of the NCPs were directly related to the inductive effect of para substituents on the meso-phenyl groups: A linear relationship between the pK3 (pK4) and Hammett σpara parameters was revealed. In the case of deprotonation, the structure of monoanionic NCP species was similarly characterized by the absorption and (1)H NMR spectra. For the second deprotonation, the pK1 value was determined to be 11.39 for the NCP derivative with pentafluorophenyl groups. DFT calculations support the changes in electronic structures and aromaticity of the cationic and anionic species. It is demonstrated that NCPs are easily protonated and deprotonated compared to the corresponding regular congeners.

Exploration of the catalytically active site structures of animal biomass-modified on cheap carbon nanospheres for oxygen reduction reaction with high activity, stability and methanol-tolerant performance in alkaline medium

Nitrogen-doped carbon materials are known to exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR). However, the structure of the active site for the ORR remains unknown. In this work, a series of nitrogen-doped carbon nanospheres (N-CNSs) were successfully prepared by using porcine blood protein as specific nitrogen source at different pyrolysis temperatures. The results show that the catalyst with a higher percentage of the planar N species (83.5% in total nitrogen content), possesses outstanding ORR electrocatalytic activity close to the commercial 40% Pt/C catalyst in alkaline media, and significantly superior stability and immunity for methanol crossover than that of 40% Pt/C. Metal Fe particles in the precursor can facilitate the partial transformation of oxidized N to planar N and the joint incorporation of planar pyridinic and pyrrolic N groups into the carbon matrix during high-temperature pyrolysis, which further produces more defective and exposed edges in the carbon structure. It is here proposed that both planar pyridinic and pyrrolic nitrogen atoms may be the N functionalities that are most responsible for the ORR electrocatalytic activity and can function as ORR active sites for as-prepared catalysts.

Molecular assemblies based on strong axial coordination in metal complexes of saddle-distorted dodecaphenylporphyrins

In this mini-review, we have highlighted our works on metal complexes having saddle-distorted dodecaphenylporphyrin (DPP) and its derivative as ligands in the light of enhancement of the Lewis acidity of a metal center coordinated by the porphyrin. The important point through this mini-review is ill-overlap of the out-of-plane lone pairs of pyrrole nitrogen atoms with σ-orbitals of the metal center bound to the saddle-distorted porphyrin core. The enhanced Lewis acidity of the central metal ions enabled us to construct stable molecular complexes through axial coordination using metal–DPP (M(DPP)) moieties ( M = Mo V or Sn IV ) and molecular or ionic entities with Lewis-basic coordination sites, including Keggin-type polyoxometallates (POM), which are known to have weak Lewis basicity and thus hard to coordinate to metal ions. A discrete 1:2 complex with a Ru -substituted POM performs catalytic substrate oxidation reactions in organic solvents. A 1:1 complex between Sn IV ( DPP ) and a Keggin-type POM exhibited photoinduced electron transfer, in which the Sn IV ( DPP ) moiety acts as an electron donor and the POM as an electron acceptor. Besides POM, other electron acceptors, including μ3-oxo trinuclear Ru III clusters and anthraquinone, having carboxyl groups as a linker unit also formed stable complexes with DPP-metal complexes as axial ligands to perform photoinduced electron transfer. Successful photoreactions of the M(DPP)-acceptor complexes are mainly enabled by the enhanced Lewis acidity of the DPP-metal complexes for the stabilization of the assemblies and also by lowering the oxidation potential of the porphyrin ligand to gain larger driving force of electron transfer to form an electron-transfer state with avoiding intersystem crossing. The stability and photochemical behavior are in sharp contrast to those for metal complexes with planar porphyrins as ligands.

Molybdenum complex with bulky chelates as a functional model for molybdenum oxidases.

The novel bulky Schiff base chelate ligand [(4,5-diisopropyl-1H-pyrrole-2-yl)methylene]-4-(tert-butyl)aniline ((iPr2)HL) bearing two isopropyl groups close to the pyrrole nitrogen atom reacts with MoCl2(dme)O2 (dme = 1,2-dimethoxyethane) to give the sterically congested complex Mo(VI)((iPr2)L)2O2 ((iPr2)1; OC-6-4-4 configuration). In spite of the increased steric shielding of the [MoO2] unit (iPr2)1 is active in oxygen-atom transfer to PMe3 and PPh3 to give OPMe3 and OPPh3, respectively. Because of the increased steric bulk of the chelate ligand, formation of dinuclear complexes [Mo(V)((iPr2)L)2O]2(μ-O) ((iPr2)3) by comportionation is effectively prevented in contrast to the highly favored formation of [Mo(V)((H2)L)2O]2(μ-O) ((H2)3) with the less bulky ligand (H2)HL. Instead, the smaller PMe3 ligand coordinates to the resulting pentacoordinate intermediate Mo(IV)((iPr2)L)2O ((iPr2)5), giving the hexacoordinate complex Mo(IV)((iPr2)L)2O(PMe3) ((iPr2)2) with OC-6-3-3 configuration. The larger potential ligands PPh3 and OPPh3 are only able to weakly coordinate to (iPr2)5, giving labile and sensitive Mo(IV)((iPr2)L)2O(L) complexes ((iPr2)6, L = PPh3; (iPr2)7, L = OPPh3). Traces of water and dioxygen in solutions of (iPr2)6/(iPr2)7 yield the di(μ-oxido) complex [Mo(V)((iPr2)L)O]2(μ-O)2 ((iPr2)4) with reduced steric congestion due to dissociation of the bulky chelate ligands. According to electron paramagnetic resonance studies, the much more strongly bound small PMe3 ligand in (iPr2)2 can be slowly liberated by one-electron oxidation to Mo(V), with Ag(+) leaving a free coordination site at Mo(V). Hence, essentially pentacoordinate Mo(IV) and Mo(V) complexes are accessible as a result of the increased steric bulk.

Phosphorus complexes of meso-triaryl-25-oxasmaragdyrins.

The aromatic PO2 complexes of meso-triaryl-25-oxasmaragdyrins were synthesized by treating the free base 25-oxasmaragdyrins with POCl3 in toluene/triethylamine at refluxing temperature. The complexes are stable and characterized by X-ray and different spectroscopic techniques. In these complexes, the phosphorus(V) ion was bound to two pyrrolic nitrogen atoms of the smaragdyrin macrocycle and two oxygen atoms in tetrahedral geometry. The X-ray structure revealed that the smaragdyrin macrocycle showed significant distortion upon insertion of a PO2 unit, and the phosphorus atom lies 1.339 Å above the mean plane defined by three meso-carbon atoms of the macrocycle. These complexes absorb strongly in the visible region and are 2.5 times more strongly fluorescent than free base 25-oxasmaragdyrins. The smaragdyrin macrocycle becomes electron-deficient upon complexation with a PO2 unit because these complexes are easier to reduce but difficult to oxidize compared to free base smaragdyrins. We designed and synthesized a covalently linked BODIPY-PO2-smaragdyrin dyad and demonstrated efficient energy transfer from the BODIPY unit to the PO2-smaragdyrin unit.

A comparative analysis on x-ray structure of cobalamin binding proteins

Vitamin B12 (Cobalamin;Cbl;B12; Figure) is a water soluble vitamin and is an essential component for the growth and development of many eukaryotes and prokaryotes organisms. B12 coordinates a cobalt ion in the center of the ring through the four pyrrole nitrogen atoms, the fifth ligand is dimethylbenzimidazole (DMB) moiety and the sixth ligand can be methyl group, deoxyadenosyl, cyanide or OH-. The structurally diverse groups of B12 binding proteins involved in various important biological functions. B12 adopts either base-on or base-off conformation in B12 binding proteins (Figure). An in-depth analysis on these structures was carried out using PDB coordinates (www.pdb.org) of a carefully chosen database of B12 binding proteins to correlate the overall folding of the molecule with phylogeny, the B12 interactions, and with biological function. The chosen database can be divided into three distinct groups. The first group is B12 transport proteins in mammals and the second is B12 transport proteins in E.Coli. The third group can be broadly clarified as B12-dependent enzymes. Results: The molecular architecture of the B12 binding proteins is diverse. It varies from a two-domain to multi-domain proteins. An analysis on the environment around B12 molecule shows that hydrogen bonds or vander waals interactions are dominant interactions between B12 and protein. Both conventional hydrogen bonds (N-H....X and O-H....X) and weak C-H....X hydrogen bonds play important role in these interactions. The number of protein residues interacting with B12 varies widely from 2 to 18 residues, depending on the nature of biological function. The analysis clearly establishes that B12 is amazingly adoptive to wide range of environments, namely polar, non-polar or charged. The B12 uses its functional groups both at head, corrin ring and in tail region (phosphate or DMB groups) at optimum level to form stable complex with partner proteins. Details will be presented.

Prodigiosin analogue designed for metal coordination: stable zinc and copper pyrrolyldipyrrins.

The pyrrolyldipyrrin motif is found in several naturally occurring prodigiosin pigments. The potential roles of the interactions of prodigiosins with transition metals and the properties of metal-bound pyrrolyldipyrrins, however, have been difficult to assess because of the very limited number of well-characterized stable complexes. Here, we show that the introduction of a meso-aryl substituent and an ethyl ester group during the sequential assembly of the three heterocycles affords a pyrrolyldipyrrin of enhanced coordinating abilities when compared to that of natural prodigiosins. UV–visible absorption studies indicate that this ligand promptly binds Zn(II) ions with 2:1 ligand-to-metal stoichiometry and Cu(II) ions with 1:1 stoichiometry. Notably, no addition of base is required for the formation of the resulting stable complexes. The crystal structures reveal that whereas the tetrahedral zinc center engages two nitrogen donors on each ligand, the pseudosquare planar copper complex features coordination of all three pyrrolic nitrogen atoms and employs the ester group as a neutral ligand. This first example of coordination of a redox-active transition metal within a fully conjugated pyrrolyldipyrrin framework was investigated spectroscopically by electron paramagnetic resonance to show that the 1:1 metal-to-ligand ratio found in the crystal structure is also maintained in solution.

Synthesis and spectrophotometric study of the acid-base and complexing properties of 2,3,7,8,12,13,17,18-Octaethyl-5,10,15,20-tetrakis(4-methoxyphenyl)porphyrin in acetonitrile

2,3,7,8,12,13,17,18-Octaethyl-5,10,15,20-tetrakis(4-methoxyphenyl)porphyrin has been synthesized, and its acid-base and complexing properties in the systems 1,8-diazabicyclo[5.4.0]undec-7-ene-acetonitrile, acetonitrile-Zn(OAc)2, and 1,8-diazabicyclo[5.4.0]undec-7-ene-acetonitrile-Zn(OAc)2 have been studied by spectrophotometry. Titration of 2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(4-methoxyphenyl)porphyrin with 1,8-diazabicyclo[5.4.0]undec-7-ene is accompanied by successive deprotonation of the pyrrole nitrogen atoms with formation of the corresponding mono- and dianion. The overall acid dissociation constant of the title compound has been determined. The complexation of neutral and doubly deprotonated 2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(4-methoxyphenyl)porphyrin with Zn(OAc)2 has been studied, and kinetic parameters for the formation of the zinc complex according to the molecular and ionic mechanisms have been determined. Extra coordination of 1,8-diazabicyclo[5.4.0]undec-7-ene by the zinc complex of 2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(4-methoxyphenyl)porphyrin.

Synthesis, crystal structure, and photoluminescence of a zinc metalloporphyrin

A zinc metalloporphyrin, ZnTCPP(acetone) (1) (TCPP = meso-tetra(4-carboxyphenyl)porphyrin), has been prepared via a solvothermal reaction and structurally characterized by single-crystal X-ray diffraction. Compound 1 features an isolated structure with a planar macrocycle and an embedded zinc ion binded to four pyrrole nitrogen atoms and one acetone oxygen atom. Photoluminescent investigation reveals that compound 1 displays an intensive emission in the red region.

Study of Electronic and Magnetic Properties of Nitrogen Doped Graphene Oxide

The Nitrogen doped graphene oxide (NGO) was synthesized by doping N-atoms on graphene oxide (GO) sheet by using melamine which serves as the nitrogen source, through hydrothermal approach. The insertion of nitrogen atoms into the graphene oxide sheet was confirmed by FT-IR, EDS and Raman spectroscopic techniques. We also probed into the tuned dielectric and magnetic properties of NGO due to the decomposition of oxy functional groups of GO and the insertion of pyridinic, pyrrolic and graphitic type nitrogen atoms into the graphitic structure. The dielectric properties were measured by Broadband Dielectric Spectroscopy (BDS). The magnetic behaviour of the sample was demonstrated by Vibrational Scanning Magnetometer (VSM).

Silicon carbide-derived carbon nanocomposite as a substitute for mercury in the catalytic hydrochlorination of acetylene.

Acetylene hydrochlorination is an important coal-based technology for the industrial production of vinyl chloride, however it is plagued by the toxicity of the mercury chloride catalyst. Therefore extensive efforts have been made to explore alternative catalysts with various metals. Here we report that a nanocomposite of nitrogen-doped carbon derived from silicon carbide activates acetylene directly for hydrochlorination in the absence of additional metal species. The catalyst delivers stable performance during a 150 hour test with acetylene conversion reaching 80% and vinyl chloride selectivity over 98% at 200 °C. Experimental studies and theoretical simulations reveal that the carbon atoms bonded with pyrrolic nitrogen atoms are the active sites. This proof-of-concept study demonstrates that such a nanocomposite is a potential substitute for mercury while further work is still necessary to bring this to the industrial stage. Furthermore, the finding also provides guidance for design of carbon-based catalysts for activation of other alkynes.

Synthesis and Crystal Structure of the Rhenium(I) Tricarbonyl Complex of 5,10,15,20-Tetra-p-tolyl-21,23-dithiaporphyrin

The hexacoordinated rhenium(I) complex of 5,10,15,20-tetra-p-tolyl-21,23-dithiaporphyrin was synthesized, and the crystal structure analysis revealed the unusual binding mode of rhenium(I) to two thiophene sulfur atoms and one of the pyrrole nitrogen atoms of the porphyrin macrocycle.

Molecular Structures and Absorption Spectra Assignment of Corrole NH Tautomers

The individual absorption spectra of the two NH tautomers of 10-(4,6-dichloropyrimidin-5-yl)-5,15-dimesitylcorrole are assigned on the basis of the Gouterman four-orbital model and a quantum chemical TD-DFT study. The assignment indicates that the red-shifted T1 tautomer is the one with protonated pyrrole nitrogen atoms N(21), N(22) and N(23), whereas the blue-shifted T2 tautomer has pyrrole nitrogen atoms N(21), N(22) and N(24) protonated. A wave-like nonplanar distortion of the macrocycle in the ground state is found for both NH tautomers, with the wave axis going through the pyrroles containing N(22) and N(24). The 7C plane determined by the least-squares distances to the carbon atoms C1, C4, C5, C6, C9, C16, and C19 is suggested as a mean corrole macrocycle plane for the analysis of out-of-plane distortions. The magnitude of these distortions is distinctly different for the two NH tautomers, leading to substantial perturbations of their acid-base properties, which are rationalized by the interplay of the degree of out-of-plane distortion of the macrocycle as a whole and the tendency of the pyrrole nitrogen atoms toward pyramidalization, with the former leading to a basicity increase whereas the latter enhances the acidity.