NP Bond Research Articles

Effect of Ligand Adsorption on the Electronic Properties of the PbS(100) Surface.

A first-principles density functional theory calculation was carried out to study the adsorption of acetic acid, methyl amine, methanethiol, and hydrogen iodide on the (100) surface of PbS. All four ligands are common capping agents used in colloidal PbS quantum dot-based photovoltaics. Interestingly, among the considered adsorbates, dissociative adsorption was energetically preferred for hydrogen iodide, while associative adsorption was favorable for the rest. Associative adsorption was driven by strong interactions between the electronegative elements (Y) in the respective ligands and the Pb surface atoms via Pb 6p-Y np bond hybridization (n represents the valence quantum number of the respective electronegative elements). Importantly, the adsorption of ligands altered the work function of PbS, with contrasting trends for associative (decrease in the work function) versus dissociative (increase in the work function) adsorption. The changes in the work function correlates well with a corresponding shift in the 5d level of surface Pb atoms. Other important observations include variations in the work function that linearly change with increasing the surface coverage of adsorbed ligands as well as with the strength of the adsorption of ligands.

Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase

All known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3'-amino nucleotides generally act as chain terminators, and no enzymatic pathway for their polymerization has yet been found. Although 3'-amino nucleotides can be chemically coupled to yield stable oligonucleotides containing N3'→P5' phosphoramidate (NP) bonds, no such internucleotide linkages are known to occur in nature. Here, we report that 3'-amino terminated primers are, in fact, slowly extended by the DNA polymerase from B. stearothermophilus in a template-directed manner. When its cofactor is Ca2+ rather than Mg2+, the reaction is fivefold faster, permitting multiple turnover NP bond formation to yield NP-DNA strands from the corresponding 3'-amino-2',3'-dideoxynucleoside 5'-triphosphates. A single active site mutation further enhances the rate of NP-DNA synthesis by an additional 21-fold. We show that DNA-dependent NP-DNA polymerase activity depends on conserved active site residues and propose a likely mechanism for this activity based on a series of crystal structures of bound complexes. Our results significantly broaden the catalytic scope of polymerase activity and suggest the feasibility of a genetic transition between native nucleic acids and NP-DNA.

Synthesis, crystal structure and characterizations of di-μ-cyanido-1:2κ2 N:C;2:3κ2 C:N-bis-(4,7,13,16,21,24-hexa-oxa-1,10-di-aza-bicyclo-[8.8.8]hexacosa-ne)-1κ8 N 1,N 10,O 4,O 7,O 13,O 16,O 21,O 24;3κ8 N 1,N 10,O 4,O 7,O 13,O 16,O 21,O 24-[5,10,15,20-tetra-kis-(4-chloro-phen-yl)porphyrinato-2κ4 N]-2-iron(II)-1,3-dipotassium(I) tetra-hydro-furan disolvate with an unknown solvent.

The title compound, [Fe(C44H24N8Cl4)(CN)2][K2(C18H36N2O6)2]·2C4H8O was synthesized and characterized by single-crystal X-ray diffraction as well as FTIR and UV-vis spectroscopy. The central FeII ion is coordinated by four pyrrole N atoms of the porphyrin core and two C atoms of the cyano groups in a slightly distorted octa-hedral coordination environment. The complex mol-ecule crystallizes with two tetra-hydro-furan solvent mol-ecules, one of which was refined as disordered over two sets of sites with refined occupancies of 0.619 (5) and 0.381 (5). It has a distorted porphyrin core with mean absolute core-atom displacements Ca, Cb, Cm and Cav of 0.32 (3), 0.22 (3), 0.56 (2) and 0.37 (14) Å, respectively. The axial Fe-Ccyano bond lengths are 1.991 (2) and 1.988 (2) Å. The average Fe-Np (Np is a porphyrin N atom) bond length is 1.964 (10) Å. One of the O atoms and several C atoms of the 222 moiety [222 = 4,7,13,16,21,24-hexa-oxa-1,10-di-aza-bicyclo-[8.8.8]hexa-cosa-ne] were refined as disordered over two sets of sites with occupancy ratios of 0.739 (6):0.261 (6) and 0.832 (4):0.168 (4). Additional solvent mol-ecules were found to be highly disordered and their contribution to the scattering was removed using the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9-18], which indicated a solvent cavity of volume 372 Å3 containing approximately 83 electrons. These solvent mol-ecules are not considered in the given chemical formula and other crystal data.

Selective cleaving the N[sbnd]P bond of difluoromethylene phosphabetaines for effective synthesis of β-ketoamides

An unprecedent transition-metal-free protocol for the synthesis of β-ketoamides from β-ketoesters is described. This method involves selective cleaving NP bond of an unusual aminating reagent, [tris(dimethylamino)phosphonio]difluoroacetate (ADFA), which is well known as the difluoromethylene ylide precursor. The process is notable for its operational simplicity and good functional group tolerance.

Crystal structure of bis-(2-methyl-1H-imidazole-κN (3))(meso-tetra-p-tol-ylporphyrinato-κ(4) N)iron(III) perchlorate tetra-hydro-furan sesquisolvate.

In the title compound, [Fe(C48H36N4)(C4H6N2)2]ClO4·1.5C4H8O, the iron(III) metal is coordinated in a distorted octa-hedral geometry by four pyrrole N atoms of the porphyrin ligand in the equatorial plane and two N atoms of 2-methyl-imidazole ligands in the axial sites. The complex has a highly ruffled porphyrin core with mean absolute core-atom displacements C a, C b, C m and C av of 0.25 (5), 0.17 (12), 0.432 (16) and 0.25 (13) Å, respectively. One of the four phenyl groups of the porphyrin is disordered over two sets of sites with refined occupancy ratio of 0.718 (7):0.282 (7). The mean Fe-Np (Np is a porphyrin N atom) bond length [1.975 (9) Å] indicates the low-spin state of the iron atom. The two 2-methyl-imidazole ligands are nearly perpendicular and form a dihedral angle of 86.93 (10)°. The dihedral angles between the 2-methyl-imidazole ligands and the closest Fe-Np vector are 38.04 (9) and 35.00 (7)°. In the crystal, the complex cations inter-act with the perchlorate anions through N-H⋯O hydrogen bonds, forming chains running parallel to [110].

Structural Characterization of Zinc and Iron (II/III) Complexes of a Porphyrin Bearing Two Built-in Nitrogen Bases. An Example of High-Spin Diaqua-Iron(III) Bromo Complex

A bis-strapped porphyrin with two intramolecular nitrogen bases was synthesized, and its zinc(II), iron(II), and iron(III) complexes have been structurally characterized. Whereas the zinc(II) complex is square pyramidal five-coordinate and the iron(II) complex is six-coordinate despite a significant distortion of the macrocycle induced by the rigidity of the straps, the iron(III) complex exhibits a peculiar bis-aqua structure in which no intramolecular axial base is bound to the iron atom in the porphyrin. Furthermore, on one side, the bromide counteranion of the iron is bound inside the cycle formed by a strap and establishes a hydrogen bond with an axially bound water molecule. On the other side, a residual HBr molecule protonates one pyridine base leading to the formation of an intermolecular pyridinium-pyridine hydrogen bond. The large ionic radius of the high-spin iron(III) cation is accommodated in the macrocycle with no displacement of the metal out of the mean porphyrinic plane, with an average Fe-Np bond distance of 2.057 A, and the axial Fe-Ow(aqua) bond distance measured at 2.090 A. As a result, this high-spin iron(III) bis-aqua complex is only lightly distorted.

Blood lead: Its effect on trace element levels and iron structure in hemoglobin

Lead is a ubiquitous environmental pollutant that induce a broad range of physiological and biochemical dysfunctions. The purpose of this study was to investigate its effects on trace elements and the iron structure in hemoglobin. Blood samples were collected from rats that had been exposed to lead. The concentration of trace elements in whole blood and blood plasma was determined by ICP-MS and the results indicate that lead exists mainly in the red blood cells and only about 1–3% in the blood plasma. Following lead exposure, the concentrations of zinc and iron in blood decrease, as does the hemoglobin level. This indicates that the heme biosynthetic pathway is inhibited by lead toxicity and that lead poisoning-associated anemia occurs. The selenium concentration also decreases after lead exposure, which may lead to an increased rate of free radical production. The effect of lead in the blood on iron structure in hemoglobin was determined by EXAFS. After lead exposure, the Fe–O bond length increases by about 0.07 Å and the Fe–Np bond length slightly increases, but the Fe–N ε bond length remains unchanged. This indicates that the blood content of Hb increases, but that the content of HbO 2 decreases.

Interplay of Structure and Vibrational Dynamics in Six-Coordinate Heme Nitrosyls

The isolation of two polymorphic forms of nitrosyl(1-methylimidazole)(tetra-p-fluorophenylporphinato)iron(II) provides a unique opportunity to explore the interplay of structure and vibrational dynamics in six-coordinate {FeNO}7 nitrosyliron porphyrinates. The two species display differing vibrational spectroscopic properties both in νNO (IR) and the iron vibrational modes obtained through the use of nuclear resonance vibrational spectroscopy. Structural characterization of the two complexes has yielded extremely high-quality structures that further confirm that coordination of NO leads to ligand tilting and asymmetry in the equatorial Fe−Np bond distances. The two polymorphic structures (monoclinic and triclinic crystal systems) differ in the relative orientations of the two axial ligands and small but significant differences in coordination group bond distances. Although DFT calculations suggest that the NO/imidazole orientations should be indistinguishable, real experimental (structural and vibrational) differences between the two are found. The observed variation in the axial and equatorial Fe−N bonds is strongly correlated to the dynamics of the Fe−NO unit and other motions of iron. Other structural differences appear to have little effect on the vibrational properties of the two forms. The in-plane motions of iron in CO versus NO heme complexes illustrate distinct dynamic differences.

A cytochrome b model, [Fe(TPP)(4-MeHIm)2][K(222-cryptand)]2Cl2

The mol­ecular structure of the title cytochrome b model, (5-meth­yl-4H-imidazole)(5,10,15,20-tetra­phenyl­porphyrinato)­iron(II) bis­[(222-cryptand)potassium(I)] dichloride, [Fe(C44H28N8)(C4H6N2)2][K(C18H36N2O6)]2Cl2 or [Fe(TPP)(4-MeHIm)2][K(222-cryptand)]2Cl2, is reported. This low-spin FeII tetra­phenyl­porphyrinate is cocrystallized with the salt [K(222-cryptand)]Cl. The crystal structure has iron(II) on an inversion center. The average Fe—Np bond is 1.9952 (8) Å and the Fe—NIm distance is 2.0154 (8) Å. The porphyrin core is saddled; the two imidazole rings have a relative parallel orientation (Np = porphyrinate N atom and Im = imidazole).

Ylidene→Iminophosphine Coordination Complexes and Reversible Dissociation of Dichlorophosphetidines

Chloro-, bromo-, iodo-, and trifluoromethylsulfonyloxy-(2,4,6-tri-tert-butylphenylimino)phosphines (MesNPX; X = Cl, Br, I, OTf) react quantitatively with 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene (Im) to give Lewis acid-base complexes with the general formula MesNP(Im)X. The dichlorophosphetidine (DippNPCl)(2) (Dipp = 2,6-diisopropylphenyl) represents a formal cyclodimer of an iminophosphine and reacts with Im to give a similar complex. The process represents a ligand induced dissociation of the phosphetidine framework and is reversed by the introduction of an appropriate Lewis acid. Solid state structures of RNP(Im)X complexes show that the closest contact between acid and base occurs between phosphorus and carbon in all cases, highlighting them as compounds that contain examples of C-->P coordinate bonds. Association of Im with phosphorus also effects a substantial increase in the P-X distance, but all derivatives maintain a short NP bond, indicating the presence of NP pi-bonding.

Structure of the deoxymyoglobin model [Fe(TPP)(2-MeHIm)] reveals unusual porphyrin core distortions.

The preparation and characterization of the deoxymyoglobin model (2-methylimidazole)(tetraphenylporphinato)iron(II) is described. The preparation and crystallization from chlorobenzene leads to a new crystalline phase that has been structurally characterized. The complex is the most ordered example of a deoxymyoglobin model yet characterized. The X-ray structure determination reveals a number of distortions both in the iron coordination group and in the porphyrin core that result from the steric bulk of the axial ligand. Some of these distortions have been noted previously in related species; however, the demonstration of porphyrin core distortions and an asymmetry in the Fe-N(p) bond distances are new observations. These may have functional significance for this important type of heme protein coordination group. The new structure emphasizes that high-spin iron(II) porphyrinate derivatives display substantial structural pliability with significant variations in iron atom displacements, porphyrin core hole size, and axial and equatorial Fe-N bond lengths. The new complex has also been characterized by zero-field and applied field magnetic Mössbauer spectroscopy. Mössbauer parameters are characteristic for high-spin iron, although they also reveal an extremely rhombic site for iron(II). Crystal data at 130 K for [Fe(TPP)(2-MeHIm)].1.5C(6)H(5)Cl: a = 12.334(3) A, b = 13.515(6) A, c = 14.241(7) A, alpha = 70.62(3) degrees, beta = 88.29(2) degrees, gamma = 88.24(3) degrees, triclinic, space group, P, V = 2238(2) A(3), Z = 2.

Topological Analysis of Chemical Bonding in Cyclophosphazenes

b), and pair density, F (2) (r b1,r b2), are obtained and analyzed. The (NP)3 ring geometry and bonding properties are basically maintained along the cyclotriphosphazenes. The PN distance and the bond critical point properties (electron density, Laplacian, etc.) lie between those of XNPX3, formally a double NP bond, and those of X2NPX4, formally a single NP bond, being much closer to the former than to the latter. The Laplacian of the electron density shows the PN bond to be highly polar, with a clear tendency of the P atoms to lose almost all of their five valence electrons, and a significant concentration of charge along the PN line, even though within the N basin. The charge on the ring N basins, Q(N), remains almost invariant, -2.3 e, in all cyclotriphosphazenes, whereas the charge of the ring P basin, Q(P), varies from +2.9 to +4.0 e, depending on the electronegativity of the -X group. There is an inverse correlation between Q(P) and the PN distance, the more electronegative -X groups shrinking the (NP)3 ring more, even though only slightly. The partition of the pair densities indicates that some 0.63 electron pairs are shared between each P and its two N neighbors in the ring, this value being typical of a polar but largely ionic bonding situation. The three N atoms in the ring share 0.20 electron pairs per N -N group, a small but significant amount, even though no bond path line occurs linking them. The three-dimensional contour surfaces of r 2 F clearly depict the molecular regions having a Lewis basic or acidic character. Ring N atoms behave as weak Lewis bases, whereas ring P atoms are preferred sites for a nucleophilic attack tending to remove, perhaps ionically, a -X group. These topological properties do explain the chemistry of cyclophosphazenes and agree well with the available experimental densities. The AIM analysis supports the main conclusions from the traditional Dewar’s model of phosphazenes.

Biphenyl-Strapped Diphenylporphyrins: Synthesis and Spectroscopic Characterization of a Series of Porphyrins with Ether-Linked Straps. Preliminary CO Binding Properties of Their Iron(II) Derivatives.

The synthesis of a series of meso-5,15-diphenylporphyrins strapped by 2,2'-disubstituted biphenyl units (6H(2), 7H(2), 8H(2)) is described. The biphenyl straps used are linked via their 3,3'-positions by CH(2)O groups to ortho-positions of the phenyl rings of the 5,15-diphenylporphyrins. The straps of these porphyrins have their 2,2'-positions occupied by H (6H(2)), Me (7H(2)), and OMe (8H(2)). The electronic spectral properties of these strapped porphyrins are given, and their conformational properties, which have been studied by (1)H NMR spectroscopy, are described. The synthesis and spectroscopic characterization of several iron(II) and iron(III) derivatives of these porphyrins with different axial bases are also presented. The X-ray structure of the chloroiron(III) derivative of the diphenylporphyrin dianion 6 has been determined. Violet crystals of composition 6-FeCl.CH(3)OH.CH(2)Cl(2) have been obtained by slow evaporation of CH(2)Cl(2)/MeOH solutions of 6-FeCl. These crystals belong to the monoclinic system, space group P2(1)/c, with a = 10.164(3) Å, b = 28.977(9) Å, c = 14.283(4) Å, beta = 106.22(2) degrees, and Z = 4. The iron atom of 6-FeCl is five-coordinate, high-spin. The axial chloride ligand lies opposite to the strap. The average Fe-N(p) bond distance is 2.046(6) Å, and the Fe-Cl bond length equals 2.234(2) Å. The porphyrin is slightly domed and ruffled with the iron atom lying at 0.45(1) Å out of the 4N(p) mean-plane and 0.49(1) Å out of the 24-atom core mean-plane of the porphyrin ring. Ferrous carbonyl adducts of these porphyrins have been obtained in various solvents in the presence or absence of nitrogenous bases. Their structures have been studied by (1)H NMR and IR spectroscopy. Two CO stretching vibrations differing by 20 cm(-)(1) occur in the IR spectra of 6-Fe(CO)(B) (B = py, ImH, NMeIm). The possible origin of these two nu(CO) bands is discussed.

Tilt/Asymmetry in Nitrosyl Metalloporphyrin Complexes: The Cobalt Case.

The high-resolution crystal structure for [Co(OEP)(NO)] shows that the axial Co−N(NO) vector is tilted from the normal to the porphyrin plane. The off-axis tilt is correlated with an asymmetry in the equatorial Co−Np bond distances.

Methyl 3-(triphenylphosphoranylideneamino)pyrazine-2-carboxylate: synthesis, crystal structure and use in pteridin-4(3H)ones synthesis

The title iminophosphorane 6 has been prepared from methyl 3-aminopyrazine-2-carboxylate 1 by a modified Kirsanov method using a triphenylphosphine–hexachloroethane–triethylamine system. The crystal structure of 6 illustrated an iminophosphorane function (NP bond). 2,3-Disubstituted pteridin-4(3H)-ones were obtained in a one-pot reaction of 6 with isocyanates, followed by heterocyclization on addition of alcohols or amines.

A novel synthesis and properties of N-bis(trifluoromethyl)nitroxy-iminophosphine, (CF 3) 2NONPH

(CF 3) 2NONPH, synthesized by a novel method involving the reactions of (CF 3) 2NONO and PH 3, underwent cleavage of the NONP bond by HI to give INPH and substitution reactions with the (CF 3) 2NO radical to afford RNPR, where R = ON(CF 3) 2. While INPH gave the relatively stable addition product, INHPHI, with HI, the addition product RNHPRI, derived from RNPR, proved to be unstable even at low temperatures.

Attempts to prepare alkylidene zirconium complexes by α-hydrogen atom abstraction

We prepared several new neopentyl halide complexes of zirconium in order to test whether they could be induced to lose neopentane and give neopentylidene complexes by adding phosphorus or nitrogen donor ligands. ZrNp 2X 2 (X  Cl or Br) can be prepared in ether and isolated as a dietherate (an oil). It reacts with L (L  PMe 3, PMe 2Ph, NEt 3, 1 2 DMPE, 1 2 TMEDA) to give ZrNp 2X 2L 2. ZrNp 3Cl can be prepared by adding MgNp 2 to ZrNp 2Cl 2(ether) 2 and isolated by sublimation in 25% yield. On adding PMe 3 or TMEDA, it disproportionates to ZrNp 4 and ZrNp 2Cl 2L 2. ZrCp″NpCl 2 (Cp″ = η 5-C 5Me 5), ZrCp″Np 2Cl, and ZrCp″Np 3 were prepared by adding MgNp 2 to ZrCp″Cl 3. Only the last is a solid, only the first forms an adduct, ZrCp″NpCl 2(PMe 3). None of the complexes decomposed to tractable products in the presence of L. Photolysis of ZrNp 2Cl 2(PMe 3) 2 yielded [Zr(PMe 3) 2Cl 3] 2 by an apparently complex reaction initiated by homolytic ZrNp bond fission.