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Porphyrin Ring (porphyrin + ring)
Selected AbstractsPorphyrin "Lego Block" Strategy To Construct Directly meso,, Doubly Linked Porphyrin Rings,ANGEWANDTE CHEMIE, Issue 21 2010Jianxin Song Dr. Eingerastet: Die Suzuki-Miyaura-Kupplung von ,,,,-diborylierten mit meso,meso,-dibromierten Porphyrinblöcken wird für den Aufbau direkt doppelt meso-,-verknüpfter Porphyrinringe genutzt, darunter zweier Tetraporphyrinringe, Hexaporphyrinringe und eines verbrückten Heptaporphyrins (siehe Bild). [source] Computational study of the solvation of protoporphyrin IX and its Fe2+ complexINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008Teobaldo Cuya Guizado Abstract Molecular dynamics (MD) simulations of a well known hydrophobic structure, the heme (ferroprotoporphyrin IX) and its precursor in the heme synthesis, protoporphyrin IX (PPIX) are presented. The objective of the present study is to determine the stability of both structures in an aqueous medium, as well as the structure-solvent relation, hydration shells, and discuss their implications for biological processes. The density functional theory (DFT) is used for the electronic and structural characterization of both PPIX and its Fe2+ complex. A classical approach based on the Gromacs package is used for the MD. The radial distribution function g(r) is used to examine the allocation of water molecules around different regions of the porphyrins. The calculations demonstrate the heterogeneous character of the porphyrins with respect to the affinity with water molecules, the general hydrophobic character of the porphyrin ring bonded or not to the ion Fe, the hydrophilic character of the carboxylic oxygen that is unchanged upon iron binding, and the low hydrophilicity of Fe2+ in the heme. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Density functional study of the heme moiety of cytochrome c,,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Anil Kumar Abstract A model of cytochrome c (Cyt-c) including the porphyrin ring, a methionine residue (Met), and the imidazole ring of histidine (His), the latter two being situated above and below the iron (Fe) atom of the porphyrin ring, was studied using Density Functional Theory (DFT). The geometries of the model Cyt-c complex with the Fe atom in two different charge states were fully optimized, i.e., in singlet and triplet states for Fe and in doublet and quartet states for Fe3+. The B3LYP method of DFT along with the 3-21G* basis set for C, H, N, and O atoms and the Lanl2dz basis set for the Fe atom was used. We found that with Fe3+, the doublet spin state is the ground state and the quartet state lies slightly above it. The geometry of the singlet spin state is similar to that of the doublet and quartet states. However, methionine has different conformations when Fe has zero charge (singlet, triplet states) relative to the situation when Fe has +3 charges (doublet, quartet states). The Met chain is folded instead of remaining extended in going from the singlet or triplet spin state to the doublet or quartet state and the folding is stabilized by an intramolecular CH..O hydrogen bond. The optimized geometrical parameters of the model of Cyt-c are usually in satisfactory agreement with those observed experimentally. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Unsolvated 5,10,15,20-tetra-4-pyridylporphyrin, its sesquihydrate and its 2-chlorophenol disolvate: conformational versatility of the ligandACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Sophia Lipstman Unsolvated 5,10,15,20-tetra-4-pyridylporphyrin, C40H26N8, (I), its sesquihydrate, C40H26N8·1.514H2O, (II), and its 2-chlorophenol disolvate, C40H26N8·2C6H5ClO, (III), reveal different conformational features of the porphyrin core. In (I), the latter is severely deformed from planarity, apparently in order to optimize the intermolecular interactions and efficient crystal packing of the molecular entities. The molecular framework has a C1 symmetry. In (II), the porphyrin molecules are located on symmetry axes, preserving the marked deformation from planarity of the porphyrin core. The molecular units are interlinked into a single-framework supramolecular architecture by hydrogen bonding to one another via molecules of water, which lie on twofold rotation axes. In (III), the porphyrin molecules are located across centres of inversion and are characterized by a planar conformation of the 24-membered macrocyclic porphyrin ring. Two trans -related pyridyl substituents are hydrogen bonded to the 2-chlorophenol solvent molecules. The interporphyrin organization in (III) is similar to that observed for many other tetraarylporphyrin compounds. However, the organization observed in (I) and (II) is different and of a type rarely observed before. This study reports for the first time the crystal structure of the unsolvated tetrapyridylporphyrin. [source] Truncated hemoglobins: trimming the classical ,three-over-three' globin fold to a minimal sizeBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 3 2001Mario Milani Abstract Truncated hemoglobins (trHbs) host the heme in a ,two-over-two' ,-helical sandwich which results from extensive editing of the classical ,three-over-three' globin fold. The three-dimensional structure of trHbs is based on four main ,-helices, arranged in a sort of ,-helical bundle composed of two antiparallel helix pairs (B/E and G/H). Most notably, trHbs deviate from the conventional globin fold in that they display an extended loop substituting for the heme proximal F-helix observed in globins. Moreover, since efficient adaptation of a 110,130 amino acid trHb chain to host the porphyrin ring firstly requires specific chain flexibility, trHbs contain three invariant Gly-based motifs. Inspection of the trHb three-dimensional trHb structures shows that an apparent protein cavity or tunnel would connect the protein surface to an inner region very close to the heme distal site. Such a structural feature, never observed before in (non) vertebrate globins, may have substantial implications for ligand diffusion and binding properties in trHbs. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved. [source] Crystallization and preliminary X-ray crystallographic analysis of a new crystal form of hydroxylamine oxidoreductase from Nitrosomonas europaeaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Peder E. Cedervall Hydroxylamine oxidoreductase (HAO) from Nitrosomonas europaea is a homotrimeric protein that catalyzes the oxidation of hydroxylamine to nitrite. Each monomer, with a molecular weight of 67.1,kDa, contains seven c -type hemes and one heme P460, the porphyrin ring of which is covalently linked to a tyrosine residue from an adjacent subunit. HAO was first crystallized and structurally characterized at a resolution of 2.8,Å in 1997. The structure was solved in space group P63 and suffered from merohedral twinning. Here, a crystallization procedure is presented that yielded untwinned crystals belonging to space group P21212, which diffracted to 2.25,Å resolution and contained one trimer in the asymmetric unit. The unit-cell parameters were a = 140.7, b = 142.6, c = 107.4,Å. [source] Novel Zinc Porphyrin Sensitizers for Dye-Sensitized Solar Cells: Synthesis and Spectral, Electrochemical, and Photovoltaic PropertiesCHEMISTRY - A EUROPEAN JOURNAL, Issue 6 2009Cheng-Wei Lee Abstract Novel meso - or ,-derivatized porphyrins with a carboxyl group have been designed and synthesized for use as sensitizers in dye-sensitized solar cells (DSSCs). The position and nature of a bridge connecting the porphyrin ring and carboxylic acid group show significant influences on the spectral, electrochemical, and photovoltaic properties of these sensitizers. Absorption spectra of porphyrins with a phenylethynyl bridge show that both Soret and Q,bands are red-shifted with respect to those of porphyrin 6. This phenomenon is more pronounced for porphyrins 3 and 4, which have a ,-conjugated electron-donating group at the meso position opposite the anchoring group. Upon introduction of an ethynylene group at the meso position, the potential at the first oxidation alters only slightly whereas that for the first reduction is significantly shifted to the positive, thus indicating a decreased HOMO,LUMO gap. Quantum-chemical (DFT) results support the spectroelectrochemical data for a delocalization of charge between the porphyrin ring and the amino group in the first oxidative state of diarylamino-substituted porphyrin 5, which exhibits the best photovoltaic performance among all the porphyrins under investigation. From a comparison of the cell performance based on the same TiO2 films, the devices made of porphyrin 5 coadsorbed with chenodeoxycholic acid (CDCA) on TiO2 in ratios [5]/[CDCA]=1:1 and 1:2 have efficiencies of power conversion similar to that of an N3 -based DSSC, which makes this green dye a promising candidate for colorful DSSC applications. [source] Single-Step Electron Transfer on the Nanometer Scale: Ultra-Fast Charge Shift in Strongly Coupled Zinc Porphyrin,Gold Porphyrin DyadsCHEMISTRY - A EUROPEAN JOURNAL, Issue 11 2008Jérôme Fortage Dr. Abstract The synthesis, electrochemical properties, and photoinduced electron transfer processes of a series of three novel zinc(II),gold(III) bisporphyrin dyads (ZnPSAuP+) are described. The systems studied consist of two trisaryl porphyrins connected directly in the meso position via an alkyne unit to tert -(phenylenethynylene) or penta(phenylenethynylene) spacers. In these dyads, the estimated center to center interporphyrin separation distance varies from 32 to 45,Å. The absorption, emission, and electrochemical data indicate that there are strong electronic interactions between the linked elements, thanks to the direct attachment of the spacer on the porphyrin ring through the alkyne unit. At room temperature in toluene, light excitation of the zinc porphyrin results in almost quantitative formation of the charge shifted state .+ZnPSAuP., whose lifetime is in the order of hundreds of picoseconds. In this solvent, the charge-separated state decays to the ground state through the intermediate population of the zinc porphyrin triplet excited state. Excitation of the gold porphyrin leads instead to rapid energy transfer to the triplet ZnP. In dichloromethane the charge shift reactions are even faster, with time constants down to 2,ps, and may be induced also by excitation of the gold porphyrin. In this latter solvent, the longest charge-shifted lifetime (,=2.3,ns) was obtained with the penta-(phenylenethynylene) spacer. The charge shift reactions are discussed in terms of bridge-mediated super-exchange mechanisms as electron or hole transfer. These new bis-porphyrin arrays, with strong electronic coupling, represent interesting molecular systems in which extremely fast and efficient long-range photoinduced charge shift occurs over a long distance. The rate constants are two to three orders of magnitude larger than for corresponding ZnPAuP+ dyads linked via meso -phenyl groups to oligo-phenyleneethynylene spacers. This study demonstrates the critical impact of the attachment position of the spacer on the porphyrin on the electron transfer rate, and this strategy can represent a useful approach to develop molecular photonic devices for long-range charge separations. [source] Reaction Mechanism of Porphyrin Metallation Studied by Theoretical MethodsCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2005Yong Shen Dr. Abstract We have studied the reaction mechanism for the insertion of Mg2+ and Fe2+ into a porphyrin ring with density functional calculations with large basis set and including solvation, zero-point and thermal effects. We have followed the reaction from the outer-sphere complex, in which the metal is coordinated with six water molecules and the porphyrin is doubly protonated, until the metal ion is inserted into the deprotonated porphyrin ring with only one water ligand remaining. This reaction involves the stepwise displacement of five water molecules and the removal of two protons from the porphyrin ring. In addition, a step seems to be necessary in which a porphyrin pyrrolenine nitrogen atom changes its interaction from a hydrogen bond to a metal-bound solvent molecule to a direct coordination to the metal ion. If the protons are taken up by a neutral imidazole molecule, the deprotonation reactions are exothermic with minimal barriers. However, with a water molecule as an acceptor, they are endothermic. The ligand exchange reactions were approximately thermoneutral (±20 kJ,mol,1, with one exception) with barriers of up to 72 kJ,mol,1 for Mg and 51 kJ,mol,1 for Fe. For Mg, the highest barrier was found for the formation of the first bond to the porphyrin ring. For Fe, a higher barrier was found for the formation of the second bond to the porphyrin ring, but this barrier is probably lower in solution. No evidence was found for an initial pre-equilibrium between a planar and a distorted porphyrin ring. Instead, the porphyrin becomes more and more distorted as the number of metal,porphyrin bonds increase (by up to 191 kJ,mol,1). This strain is released when the porphyrin becomes deprotonated and the metal moves into the ring plane. Implications of these findings for the chelatase enzymes are discussed. [source] Fluorescence Quenching of Pheophytin-a by Copper(II) IonsCHINESE JOURNAL OF CHEMISTRY, Issue 3 2009Mingbo HU Abstract A method was developed for determination of Cu(II) ions quantitatively by measuring fluorescent intensity of pheophytin-a (Pheoa) solution. The Pheoa was obtained by de-intercalation of magnesium from the porphyrin ring of chlorophyll-a (Chla) extracted from fresh spinach leaves. Its two UV-Vis absorption peaks at 505 and 535 nm in acetone solution have been observed but disappeared when the acetone solution of Pheoa was mixed with a Cu(II) ion aqueous solution. A fluorescence quenching phenomenon was thus observed when the acetone solution of Pheoa was mixed with an aqueous solution of Cu(II) ions. However, other physiologically relevant cations rarely caused any quenching fluorescence of Pheoa under the same experimental conditions. Kinetics of the fluorescence fading process was investigated by measuring the effects of Cu(II) ion concentration, reaction time and reaction temperature on the fluorescence intensity of the Pheoa acetone solution. An activation energy of (10±1) kJ·mol,1 was estimated from Arrhenius empirical relation assuming that the interaction between the Pheoa and the Cu(II) ions was the first order reaction. The calibration graph obtained with the fluorescence was linear over the Cu(II) concentration range of 8.0×10,5,8.0×10,7 mol·dm,3 with a detection limit of 8.0×10,7 mol·dm,3 for Cu(II) ion. [source] Time-dependent density functional calculations of the Q-like bands of phenylene-linked free-base and zinc porphyrin dimersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2001Yoichi Yamaguchi Abstract Time-dependent density functional theory (TDDFT) calculations have been performed on the excitation energies and oscillator strengths of the Q-like bands of three structural isomers of phenylene-linked free-base (FBP) and zinc (ZnP) porphyrin dimers. The TDDFT calculated results on the low-lying excited states of the reference monomers, FBP and ZnP, are in excellent agreement with previously calculated and experimental results. It is found that the 1,3- and 1,4-phenylene-linked dimers have monomerlike Q bands that are slightly red-shifted compared to the monomers and new Q, bands comprised of the cross-linked excitations from the FBP (ZnP) ring to the ZnP (FBP) ring at considerably lower energies than the monomer Q bands. For the 1,2-phenylene-linked dimer, the direct ,,, interaction between porphyrin rings caused by the van der Waals repulsion between them provides strong mixing of the Q, bands with the Q bands, which causes its minimum excitation energy to be red-shifted by 0.05 eV compared to the other isomers. The oscillator strengths of the Q, bands are also unexpectedly found to be as strong as those of the Q bands in the dimers. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem 84: 338,347, 2001 [source] Aided Self-Assembly of Porphyrin Nanoaggregates into Ring-Shaped ArchitecturesCHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2004Marga C. Lensen Abstract The formation of micrometer-sized, highly ordered porphyrin rings on surfaces has been investigated. The porphyrin-based nanoarchitectures are formed by deposition from evaporating solutions through a surface dewetting process which can be tuned by variations in the substitution pattern of the molecules used, the coating of the surface and the conditions under which the evaporation takes place. Control over the combined self-assembly and surface dewetting results in nanorings possessing a defined internal architecture. The ordering of the molecules within the rings has been studied by a variety of microscopy techniques (TEM, AFM, fluorescence microscopy) and the exact ordering of the porphyrins within the rings has been quantified. [source] | ||||||||||||||||||||||