The Porphyrin Handbook
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Spectroscopy of Porphyrins
BORIS F. KIM and JOSEPH BOHANDY SPECTROSCOPY OF PORPHYRINS Porphyrins are an important class of compounds that are of interest in molecular biology because of the important roles they play in vital biochemical systems such as biochemical energy conversion in animals, oxygen transport in blood, and photosynthetic energy conversion in plants. We are studying the physical properties of the energy states of porphyrins using the techniques of ex perimental and theoretical spectroscopy with the aim of contributing to a basic understanding of their biochemical behavior. INTRODUCTION Metalloporphin Porphyrins are a class of complex organic chemical compounds found in such diverse places as crude oil, plants, and human beings. They are, in most cases, tailored to carry out vital chemical transformations in intricate biochemical or biophysical systems. They are the key constituents of chlorophyll in plants and of hemoglobin in animals. Without them, life would y be impossible. t Free base porphin These molecules display a wide range of chemical and physical properties that depend on the structural details of the particular porphyrin molecule. All por ~x phyrins are vividly colored and absorb light in the visible and ultraviolet regions of the spectrum. Some exhibit luminescence, paramagnetism, photoconduc tion, or semiconduction. Spme are photosensitizers Wavelength (nanometers) or catalysts. Scientists from several disciplines have been interested in unraveling the principles that cause Fig. 1-The chemical structures for the two forms of por· this diversity of properties. phin are shown on the left. A carbon atom and a hydrogen The simplest compound of all porphyrins is por atom are understood to be at each apex not attached to a nitrogen atom. -
Electronic Spectroscopy of Free Base Porphyrins and Metalloporphyrins
Absorption and Fluorescence Spectroscopy of Tetraphenylporphyrin§ and Metallo-Tetraphenylporphyrin Introduction The word porphyrin is derived from the Greek porphura meaning purple, and all porphyrins are intensely coloured1. Porphyrins comprise an important class of molecules that serve nature in a variety of ways. The Metalloporphyrin ring is found in a variety of important biological system where it is the active component of the system or in some ways intimately connected with the activity of the system. Many of these porphyrins synthesized are the basic structure of biological porphyrins which are the active sites of numerous proteins, whose functions range from oxygen transfer and storage (hemoglobin and myoglobin) to electron transfer (cytochrome c, cytochrome oxidase) to energy conversion (chlorophyll). They also have been proven to be efficient sensitizers and catalyst in a number of chemical and photochemical processes especially photodynamic therapy (PDT). The diversity of their functions is due in part to the variety of metals that bind in the “pocket” of the porphyrin ring system (Fig. 1). Figure 1. Metallated Tetraphenylporphyrin Upon metalation the porphyrin ring system deprotonates, forming a dianionic ligand (Fig. 2). The metal ions behave as Lewis acids, accepting lone pairs of electrons ________________________________ § We all need to thank Jay Stephens for synthesizing the H2TPP 2 from the dianionic porphyrin ligand. Unlike most transition metal complexes, their color is due to absorption(s) within the porphyrin ligand involving the excitation of electrons from π to π* porphyrin ring orbitals. Figure 2. Synthesis of Zn(TPP) The electronic absorption spectrum of a typical porphyrin consists of a strong transition to the second excited state (S0 S2) at about 400 nm (the Soret or B band) and a weak transition to the first excited state (S0 S1) at about 550 nm (the Q band). -
Porphyrins & Bile Pigments
Bio. 2. ASPU. Lectu.6. Prof. Dr. F. ALQuobaili Porphyrins & Bile Pigments • Biomedical Importance These topics are closely related, because heme is synthesized from porphyrins and iron, and the products of degradation of heme are the bile pigments and iron. Knowledge of the biochemistry of the porphyrins and of heme is basic to understanding the varied functions of hemoproteins in the body. The porphyrias are a group of diseases caused by abnormalities in the pathway of biosynthesis of the various porphyrins. A much more prevalent clinical condition is jaundice, due to elevation of bilirubin in the plasma, due to overproduction of bilirubin or to failure of its excretion and is seen in numerous diseases ranging from hemolytic anemias to viral hepatitis and to cancer of the pancreas. • Metalloporphyrins & Hemoproteins Are Important in Nature Porphyrins are cyclic compounds formed by the linkage of four pyrrole rings through methyne (==HC—) bridges. A characteristic property of the porphyrins is the formation of complexes with metal ions bound to the nitrogen atom of the pyrrole rings. Examples are the iron porphyrins such as heme of hemoglobin and the magnesium‐containing porphyrin chlorophyll, the photosynthetic pigment of plants. • Natural Porphyrins Have Substituent Side Chains on the Porphin Nucleus The porphyrins found in nature are compounds in which various side chains are substituted for the eight hydrogen atoms numbered in the porphyrin nucleus. As a simple means of showing these substitutions, Fischer proposed a shorthand formula in which the methyne bridges are omitted and a porphyrin with this type of asymmetric substitution is classified as a type III porphyrin. -
Takuzo Aida Deputy Director, RIKEN Center for Emergent Matter Science Professor, School of Engineering, the University of Tokyo
19 Japan Academy Prize to: Takuzo Aida Deputy Director, RIKEN Center for Emergent Matter Science Professor, School of Engineering, The University of Tokyo for “Studies on Precision Hierarchical Design of Innovative Soft Materials” Outline of the work: Prof. Takuzo Aida is a world-leading scientist involved in the development of innovative soft materials. Prof. Aida has been intensely engaged in exploiting the interactions between materials sciences and other scientific disciplines such as physics and life science. While researchers’ focus in molecular science is now shifting from highly diluted and well-equilibrated molecular systems to more complex, non-equilibrated systems in highly condensed phases, Prof. Aida discovered extrusion polymerization of olefins in 1999 using catalyst-immobilized nanoscopic channels of mesoporous silica (ref. 32). When ethylene is allowed to polymerize, polymer chains that are produced in nanopores are not allowed to fold but extruded unidirectionally like spider silk. The chains then assemble together into extended-chain crystalline fibers having ultrahigh mechanical properties. In general, highly anisotropic hierarchical structural ordering can provide materials with extraordinary properties. However, this process is known to be interfered by kinetic traps that emerge in the transition from nano to mesoscopic size regimes. Based on the seminal discovery of extrusion polymerization, Prof. Aida noticed how multivalent interactions and physical perturbations are useful for avoiding kinetic traps that prevent hierarchical structural ordering in highly condensed systems and properly connect the missing link between nano and meso-scale phenomena. From then on, he has been promoting this immature research field and has accomplished numerous seminal achievements for creating innovative soft materials. -
Scientific Program (Oral Presentations)
Oral Presentations Monday, July 12, 2010 Opening of Program and Chirality Award Lecture (Hall A) 16:50 – 17:10 Opening and Chirality Medal Ceremony 17:10 – 18:10 [Chirality Medal Award Lecture] BIOACTIVE NATURAL PRODUCTS AND CHIRALITY Kenji Mori Emeritus Professor, The University of Tokyo, Japan Chirality Medal Reception (Main Hall A) 18:10 – 21:00 Chirality Medal Reception Tuesday, July 13, 2010 Plenary Session 1 (Hall A) Chairperson: Kazuhiko Saigo 08:40 – 09:30 [PL-1] PROTEIN SURFACE RECOGNITION: A SUPRAMOLECULAR APPROACH TO CONTROLLING BIOLOGICAL FUNCTION Andrew D. Hamilton Department of Chemistry, University of Oxford, UK 09:30 – 10:00 COFFEE BREAK (Hall C) Parallel Session A1 (Hall A) Chairperson: Jérôme Lacour 10:00 – 10:30 [IL-A1] INTELLIGENT NANOFIBERS WITH SUPRAMOLECULAR CHIRALITY Myongsoo Lee Center for Supramolecular Nano-Assembly and Department of Chemistry, Seoul National University, Korea 10:30 – 11:00 [IL-A2] CHIRALITY FOR MATERIALS SCIENCE Takuzo Aida School of Engineering, The University of Tokyo, Japan Parallel Session A2 (Hall A) Chairperson: Myongsoo Lee 11:00 – 11:20 [O-A1] SUPRAMOLECULAR MRI CONTRAST AGENTS Pol Besenius, Anja R.A. Palmans, E.W. Meijer Laboratory of Macromolecular and Organic Chemistry and Institute of Complex Molecular Systems, Eindhoven University of Technology, Netherlands 22nd International Symposium on Chirality (Chirality2010) Oral Presentations 11:20 – 11:40 [O-A2] PYRIDINOPHANE CATALYSIS FOR ASYMMETRIC CYCLOPROPANATION WITH COPPER CARBENOID COCATALYSIS Hiroko Tanaka, Nobuhiro Kanomata Department of Chemistry and Biochemistry, Waseda University, Japan 11:40 – 12:00 [O-A3] THE SHAPE MATTERS: A DRAMATIC DEPENDENCE OF CHIROPTICAL RESPONSE ON THE CONFORMATION OF CHIRAL OLIGOMERS José Lorenzo Alonso-Gómez1, Ana G. -
Emerging Applications of Porphyrins and Metalloporphyrins in Biomedicine and Diagnostic Magnetic Resonance Imaging
biosensors Review Emerging Applications of Porphyrins and Metalloporphyrins in Biomedicine and Diagnostic Magnetic Resonance Imaging Muhammad Imran 1,*, Muhammad Ramzan 2,*, Ahmad Kaleem Qureshi 1, Muhammad Azhar Khan 2 and Muhammad Tariq 3 1 Department of Chemistry, Baghdad-Ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan; [email protected] 2 Department of Physics, Baghdad-Ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan; [email protected] 3 Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan; [email protected] * Correspondence: [email protected] (M.I.); [email protected] (M.R.) Received: 26 September 2018; Accepted: 17 October 2018; Published: 19 October 2018 Abstract: In recent years, scientific advancements have constantly increased at a significant rate in the field of biomedical science. Keeping this in view, the application of porphyrins and metalloporphyrins in the field of biomedical science is gaining substantial importance. Porphyrins are the most widely studied tetrapyrrole-based compounds because of their important roles in vital biological processes. The cavity of porphyrins containing four pyrrolic nitrogens is well suited for the binding majority of metal ions to form metalloporphyrins. Porphyrins and metalloporphyrins possess peculiar photochemical, photophysical, and photoredox properties which are tunable through structural modifications. Their beneficial photophysical properties, such as the long wavelength of emission and absorption, high singlet oxygen quantum yield, and low in vivo toxicity, have drawn scientists’ interest to discover new dimensions in the biomedical field. Applications of porphyrins and metalloporphyrins have been pursued in the perspective of contrast agents for magnetic resonance imaging (MRI), photodynamic therapy (PDT) of cancer, bio-imaging, and other biomedical applications. -
10Th ISMSC-2015 Strasbourg, France (June 28Th - July 2Nd, 2015)
10th ISMSC-2015 Strasbourg, France (June 28th - July 2nd, 2015) Code Presenting Author Title Authors Perspectives in Chemistry: From Supramolecular Chemistry towards PL-1 Jean-Marie Lehn Jean-Marie Lehn Adaptive Chemistry PL-2 E.W. (Bert) Meijer Folding of Macromolecules; Functional single-chain polymer nanoparticles E.W. (Bert) Meijer PL-3 Samuel Stupp Bio-Inspired Supramolecular Materials Samuel Stupp Functional Materials Constructed by Combining Traditional Polymers and PL-4 Feihe Huang Feihe Huang, Xiaofan Ji, Mingming Zhang, Xiaodong Chi Host-Guest Molecular Recognition Motifs Supramolecular Liquid-Crystalline Materials for Energy, Water, and PL-5 Takashi Kato Takashi Kato Environment PL-6 Tanja Weil Programmed Self-Assembly of Bioactive Architectures Tanja Weil, David Y. W. Ng PL-7 Paul D. Beer Interlocked Host Molecules for Anion Recognition and Sensing Paul D. Beer PL-8 Takuzo Aida Rational Strategy for Chain-Growth Supramolecular Polymerization Takuzo Aida IL-1 Pablo Ballester Mechanically Interlocked Molecules Containing Calix[4]pyrrole Scaffolds Pablo Ballester IL-2 Davide Bonifazi Supramolecular Colorlands Davide Bonifazi IL-3 Kentaro Tanaka Columnar Liquid Crystalline Macrocycles Kentaro Tanaka IL-4 Ian Manners Recent Advances in “Living” Crystallization-Driven Self-Assembly Ian Manners Light-driven catenation and intermolecular communication in solution and Nathan D. McClenaghan, A. Tron, R. Bofinger, J. IL-5 Nathan McClenaghan nanocapsules Thevenot, S. Lecommandoux, J.H.R. Tucker Supramolecular Chemistry and Photophysics of Light-Harvesting IL-6 Harry Anderson Harry Anderson Nanorings Jeroen J. L. M. IL-7 Supramolecular Protein Assemblies, from Cages to Tubes Jeroen J. L. M. Cornelissen Cornelissen Light-driven liquids, particles, and interfaces: from microfluidics to coffee IL-8 Damien Baigl Damien Baigl rings B.C. -
Vitamin B12 Promotes Porphyrin Production in Acne-Associated P
UCLA UCLA Electronic Theses and Dissertations Title Porphyrin production and regulation in different Propionibacterium acnes lineages contribute to acne vulgaris pathogenesis Permalink https://escholarship.org/uc/item/9g02d15m Author Johnson, Tremylla Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Porphyrin production and regulation in different Propionibacterium acnes lineages contribute to acne vulgaris pathogenesis A dissertation submitted in partial satisfaction of the requirement for the degree Doctor of Philosophy in Molecular and Medical Pharmacology by Tremylla A. Johnson 2017 © Copyright by Tremylla A. Johnson 2017 ABSTRACT OF THE DISSERTATION Porphyrin production and regulation in different Propionibacterium acnes lineages contribute to acne vulgaris pathogenesis by Tremylla A. Johnson Doctor of Philosophy in Molecular & Medical Pharmacology University of California, Los Angeles, 2017 Professor Huiying Li, Chair Propionibacterium acnes is a dominant human skin commensal. It has been implicated in acne pathogenesis, but its role remains unclear. Recent metagenomic studies have revealed that certain P. acnes strains are highly associated with acne, while some others are associated with healthy skin. Little information exists about P. acnes strain-level differences beyond the genomic differences. In this study, I revealed that acne-associated type IA P. acnes strains produced significantly higher levels of porphyrins (a metabolite important in acne development) than health-associated strains (type II). Strains of type IA-1 and type IA-2 produced similar levels of porphyrins. Moreover, porphyrin production in these P. acnes strains is modulated by vitamin B12. On the other hand, health-associated type II strains produced low levels of ii porphyrins and did not respond to vitamin B12. -
Seunghyun Sim Bas Van Genabeek Takuzo Aida Bert Meijer
In association with NASA Takuzo Aida December 10, 2019 Seunghyun Sim Bas van Genabeek Bert Meijer Tokyo University Caltech SyMO-Chem Eindhoven University . cmeacs.org In association with NASA ACS GLOBAL OUTSTANDING GRADUATE STUDENT & MENTOR AWARDS IN POLYMER SCIENCE AND ENGINEERING SPONSORED BY CME Seunghyun Sim Bas van Genabeek Postdoc Researcher Caltech SyMO-Chem Takuzo Aida Bert Meijer Prof. Tokyo University Distinguished Professor Riken Group Director Eindhoven University . December 10, 2019 cmeacs.org In association with NASA 2:00 pm – Awards Presentation and Talk on Engineering self-assembly of protein polymers for functional materials. Seunghyun Sim – Proteins are monodisperse polymers that fold into a specific nanoscale structure. These state-of-art nanoscale machineries exert highly precise mechanical motions and process environmental inputs by the combination of allosteric effects. My research focuses on finding interdisciplinary solutions for designing a library of functional protein materials, mainly from the principles in supramolecular chemistry, molecular biology, and polymer science. In this symposium, I will discuss the design of protein-based macromolecular architectures in multiple dimensions, understanding their property for the therapeutic application, and in situ synthesis of extracellular protein network by living organisms for generating engineered living materials. Profile – Seunghyun Sim graduated from Seoul National University with B.S. degrees in Chemistry and Biological Sciences in 2012. She conducted her doctoral research with professor Takuzo Aida at the University of Tokyo and received her M.Eng. and Ph.D. in 2017. Her thesis work focused on engineering protein-based supramolecular nanostructures and functions. She is currently a postdoctoral fellow at California Institute of Technology in the lab of professor David Tirrell. -
Expanding the Eggshell Colour Gamut: Uroerythrin and Bilirubin from Tinamou (Tinamidae) Eggshells Randy Hamchand1, Daniel Hanley2, Richard O
www.nature.com/scientificreports OPEN Expanding the eggshell colour gamut: uroerythrin and bilirubin from tinamou (Tinamidae) eggshells Randy Hamchand1, Daniel Hanley2, Richard O. Prum3 & Christian Brückner1* To date, only two pigments have been identifed in avian eggshells: rusty-brown protoporphyrin IX and blue-green biliverdin IXα. Most avian eggshell colours can be produced by a mixture of these two tetrapyrrolic pigments. However, tinamou (Tinamidae) eggshells display colours not easily rationalised by combination of these two pigments alone, suggesting the presence of other pigments. Here, through extraction, derivatization, spectroscopy, chromatography, and mass spectrometry, we identify two novel eggshell pigments: yellow–brown tetrapyrrolic bilirubin from the guacamole- green eggshells of Eudromia elegans, and red–orange tripyrrolic uroerythrin from the purplish-brown eggshells of Nothura maculosa. Both pigments are known porphyrin catabolites and are found in the eggshells in conjunction with biliverdin IXα. A colour mixing model using the new pigments and biliverdin reproduces the respective eggshell colours. These discoveries expand our understanding of how eggshell colour diversity is achieved. We suggest that the ability of these pigments to photo- degrade may have an adaptive value for the tinamous. Birds’ eggs are found in an expansive variety of shapes, sizes, and colourings 1. Te diverse array of appearances found across Aves is achieved—in large part—through a combination of structural features, solid or patterned colorations, the use of two diferent dyes, and diferential pigment deposition. Eggshell pigments are embedded within the white calcium carbonate matrix of the egg and within a thin outer proteinaceous layer called the cuticle2–4. Tese pigments are believed to play a key role in crypsis5,6, although other, possibly dynamic 7,8, roles in inter- and intra-species signalling5,9–12 are also possible. -
To a Protoporphyrin. Thus, Type I Porphyrinogens Or Their Respective Porphyrins Reduced Production Oftype III Porphyrin and Hemo
A SUGGESTED CONTROL GENE MECHANISM FOR THE EXCESSIVE PRODUCTION OF TYPES I AND III PORPHYRINS IN CONGENJ TAL ERYTHROPOIETIC PORPHYRIA* BY C. J. WATSON, W. RUNGE, L. TADDEINI, IRENE BOSSENMAIER, AND RUTH CARDINAL DEPARTMENT OF MEDICINE, UNIVERSITY OF MINNESOTA, MINNEAPOLIS Communicated June 19, 1964 The curious phenotype of erythropoietic porphyria, both human and bovine, is directly related to the large amounts of type I porphyrins produced by the develop- ing red cells of the bone marrow. The excessive uroporphyrin (URO-) I is respon- sible for the photocutaneous manifestations, as well as the red urine, teeth, and bones. The spleen enlarges and is at least partly responsible for the increased destruction of circulating red cells so often observed. This stimulates erythro- poiesis and heightened formation of porphyrins, as described elsewhere.1-3 It has been proposed4-7 that the genetic error is a deficiency of uroporphyrinogen (UPG) isomerase. This enzyme directs cyclization to UPG III, of the polypyrryl methane first formed from porphobilinogen (PBG) by PBG deaminase. UPG III is preferentially converted by a decarboxylase to coproporphyrinogen (CPG) III and this by virtue of a coproporphyrinogenase (CPGase), to the corresponding protoporphyrin (PROTO-) and heme. In the absence or relative paucity of isomerase the polypyrryl methane from PBG cyclizes to UPG I, and is decarboxyl- ated in varying proportion to CPG I. With possible rare and minor exceptions,8 the specificity of CPGase for type III is maintained, and CPG-I is not converted to a protoporphyrin. Thus, type I porphyrinogens or their respective porphyrins are excreted or accumulated. This has been discussed in recent reviews.4-7 If the inborn error were an isomerase deficiency, a markedly reduced production of type III porphyrin and hemoglobin might be anticipated. -
Elucidation of the Origin of Chiral Amplification in Discrete Molecular Polyhedra
ARTICLE DOI: 10.1038/s41467-017-02605-x OPEN Elucidation of the origin of chiral amplification in discrete molecular polyhedra Yu Wang 1, Hongxun Fang1, Ionut Tranca2, Hang Qu1, Xinchang Wang1, Albert J. Markvoort 2, Zhongqun Tian1 & Xiaoyu Cao1 Chiral amplification in molecular self-assembly has profound impact on the recognition and separation of chiroptical materials, biomolecules, and pharmaceuticals. An understanding of 1234567890():,; how to control this phenomenon is nonetheless restricted by the structural complexity in multicomponent self-assembling systems. Here, we create chiral octahedra incorporating a combination of chiral and achiral vertices and show that their discrete nature makes these octahedra an ideal platform for in-depth investigation of chiral transfer. Through the con- struction of dynamic combinatorial libraries, the unique possibility to separate and char- acterise each individual assembly type, density functional theory calculations, and a theoretical equilibrium model, we elucidate that a single chiral unit suffices to control all other units in an octahedron and how this local amplification combined with the distribution of distinct assembly types culminates in the observed overall chiral amplification in the system. Our combined experimental and theoretical strategy can be applied generally to quantify discrete multi-component self-assembling systems. 1 State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, iChEM and Key Laboratory of Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China. 2 Institute for Complex Molecular Systems and Computational Biology Group, Eindhoven University of Technology, PO Box 5135600 MB Eindhoven, The Netherlands. Yu Wang and Hongxun Fang contributed equally to this work.