Dynamical Insights Into the Decomposition of 1,2-Dioxetane
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
William D. Mcelroy Papers
http://oac.cdlib.org/findaid/ark:/13030/kt6489r0v5 No online items William D. McElroy Papers Special Collections & Archives, UC San Diego Special Collections & Archives, UC San Diego Copyright 2005 9500 Gilman Drive La Jolla 92093-0175 [email protected] URL: http://libraries.ucsd.edu/collections/sca/index.html William D. McElroy Papers MSS 0483 1 Descriptive Summary Languages: English Contributing Institution: Special Collections & Archives, UC San Diego 9500 Gilman Drive La Jolla 92093-0175 Title: William D. McElroy Papers Identifier/Call Number: MSS 0483 Physical Description: 10.4 Linear feet(19 archives boxes, 11 oversize folders, 6 art bin items) Date (inclusive): 1944-1999 Abstract: Papers of William David McElroy (1917-1999), professor of biochemistry, the fourth chancellor (1972-1980) of the University of California, San Diego; and former director (1969-1971) of the National Science Foundation. Scope and Content of Collection Papers of William David McElroy (1917-1999), professor of biochemistry, the fourth chancellor (1972-1980) of the University of California, San Diego; and former director (1969-1971) of the National Science Foundation. McElroy's significant contributions to biology include isolating and crystallizing the compounds that enable firefly luminescence and for his subsequent research into bacterial bioluminescence. He also wrote, spoke, and worked on problems in areas of environment, pollution, food production, science education, and international science. The papers largely document McElroy's scientific research and include correspondence with the scientific community, various biographical materials including awards and photographs, his trip to China in 1979, writings and reprints related to biochemical and scientific investigation, research materials on bioluminescence, teaching materials, and speeches given both as chancellor and as director of the National Science Foundation. -
Safety Data Sheet
G-Biosciences, St Louis, MO, USA | 1-800-628-7730 | 1-314-991-6034 | [email protected] A Geno Technology, Inc. (USA) brand name Safety Data Sheet Cat. # RC-227 D-Luciferin Firefly, FREE ACID Size: 0.25g think proteins! think G-Biosciences! www.GBiosciences.com D-Luciferin Firefly, potassium salt Safety Data Sheet according to Federal Register / Vol. 77, No. 58 / Monday, March 26, 2012 / Rules and Regulations Date of issue: 05/06/2013 Revision date: 05/11/2017 Version: 7.1 SECTION 1: Identification 1.1. Identification Product form : Substance Trade name : D-Luciferin Firefly, potassium salt CAS-No. : 2591-17-5 Product code : 006A Formula : C11H8N2O3S2 Synonyms : (4S)-4,5-dihydro-2-(6-hydroxy-2-benzothiazolyl)-4-thiazolecarboxylic acid / (S)-2-(6-hydroxy-2- benzothiazolyl)-2-thiazoline-4-carboxylic acid / (S)-4,5-dihydro-2-(6-hydroxybenzothiazol-2- yl)thiazole-4-carboxylic acid / 2-(6-hydroxy-2-benzothiazolyl)-2-thiazoline-4-carcoxylic acid, (S)- / 2-(6-hydroxybenzothiazol-2-yl)-2-thiazoline-4-carboxylic acid / 4,5-dihydro-2-(6-hydroxy-2- benzorhiazolyl)-4-thiazolecarboxylic acid, (4S)- / 4,5-dihydro-2-(6-hydroxy-2-benzothiazolyl)-4- thiazolecarboxylic acid / 4-Thiazolecarboxylic acid, 4,5-dihydro-2-(6-hydroxy-2-benzothiazolyl)-, (S)- / D-(-)-luciferin / D-luciferin / firefly luciferin / liciferin, D-(-)- / luciferin / luciferin, D- Other means of identification : D-Luciferin Firefly, free acid 4,5-Dihydro-2-(6-hydroxy-2-benzothiazolyl)-4-thiazolecarboxylic acid, ST50405784, Luciferin, CHEBI:17165 BIG No : 48631 1.2. Recommended use and restrictions on use Use of the substance/mixture : Luciferin is a common bioluminescent reporter used for in-vivo imaging of the expression of the luc marker gene . -
Transition State Theory. I
MIT OpenCourseWare http://ocw.mit.edu 5.62 Physical Chemistry II Spring 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. 5.62 Spring 2007 Lecture #33 Page 1 Transition State Theory. I. Transition State Theory = Activated Complex Theory = Absolute Rate Theory ‡ k H2 + F "! [H2F] !!" HF + H Assume equilibrium between reactants H2 + F and the transition state. [H F]‡ K‡ = 2 [H2 ][F] Treat the transition state as a molecule with structure that decays unimolecularly with rate constant k. d[HF] ‡ ‡ = k[H2F] = kK [H2 ][F] dt k has units of sec–1 (unimolecular decay). The motion along the reaction coordinate looks ‡ like an antisymmetric vibration of H2F , one-half cycle of this vibration. Therefore k can be approximated by the frequency of the antisymmetric vibration ν[sec–1] k ≈ ν ≡ frequency of antisymmetric vibration (bond formation and cleavage looks like antisymmetric vibration) d[HF] = νK‡ [H2] [F] dt ! ‡* $ d[HF] (q / N) 'E‡ /kT [ ] = ν # *H F &e [H2 ] F dt "#(q 2 N)(q / N)%& ! ‡ $ ‡ ‡* ‡ (q / N) ' q *' q *' g * ‡ K‡ = # trans &) rot ,) vib ,) 0 ,e-E kT H2 qH2 ) q*H2 , gH2 gF "# (qtrans N) %&( rot +( vib +( 0 0 + ‡ Reaction coordinate is antisymmetric vibrational mode of H2F . This vibration is fully excited (high T limit) because it leads to the cleavage of the H–H bond and the formation of the H–F bond. For a fully excited vibration hν kT The vibrational partition function for the antisymmetric mode is revised 4/24/08 3:50 PM 5.62 Spring 2007 Lecture #33 Page 2 1 kT q*asym = ' since e–hν/kT ≈ 1 – hν/kT vib 1! e!h" kT h! Note that this is an incredibly important simplification. -
Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium Sp
Article Cite This: Biochemistry 2019, 58, 1246−1259 pubs.acs.org/biochemistry Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium sp. TCM1 † † † ‡ ‡ Andrew N. Bigley, Dao Feng Xiang, Tamari Narindoshvili, Charlie W. Burgert, Alvan C. Hengge,*, † and Frank M. Raushel*, † Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States ‡ Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States *S Supporting Information ABSTRACT: Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phospho- triesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organo- phosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic hydrolysis mechanism of Sb-PTE, the pH dependence of the reaction and the effects of changing the solvent viscosity were determined. These experiments were complemented by measurement of the primary and ff ff secondary 18-oxygen isotope e ects on substrate hydrolysis and a determination of the e ects of changing the pKa of the leaving group on the magnitude of the rate constants for hydrolysis. Collectively, the results indicated that a single group must be ionized for nucleophilic attack and that a separate general acid is not involved in protonation of the leaving group. -
Bioluminescence Is Produced by a Firefly-Like Luciferase but an Entirely
www.nature.com/scientificreports OPEN New Zealand glowworm (Arachnocampa luminosa) bioluminescence is produced by a Received: 8 November 2017 Accepted: 1 February 2018 frefy-like luciferase but an entirely Published: xx xx xxxx new luciferin Oliver C. Watkins1,2, Miriam L. Sharpe 1, Nigel B. Perry 2 & Kurt L. Krause 1 The New Zealand glowworm, Arachnocampa luminosa, is well-known for displays of blue-green bioluminescence, but details of its bioluminescent chemistry have been elusive. The glowworm is evolutionarily distant from other bioluminescent creatures studied in detail, including the frefy. We have isolated and characterised the molecular components of the glowworm luciferase-luciferin system using chromatography, mass spectrometry and 1H NMR spectroscopy. The purifed luciferase enzyme is in the same protein family as frefy luciferase (31% sequence identity). However, the luciferin substrate of this enzyme is produced from xanthurenic acid and tyrosine, and is entirely diferent to that of the frefy and known luciferins of other glowing creatures. A candidate luciferin structure is proposed, which needs to be confrmed by chemical synthesis and bioluminescence assays. These fndings show that luciferases can evolve independently from the same family of enzymes to produce light using structurally diferent luciferins. Glowworms are found in New Zealand and Australia, and are a major tourist attraction at sites located across both countries. In contrast to luminescent beetles such as the frefy (Coleoptera), whose bioluminescence has been well characterised (reviewed by ref.1), the molecular details of glowworm bioluminescence have remained elusive. Tese glowworms are the larvae of fungus gnats of the genus Arachnocampa, with eight species endemic to Australia and a single species found only in New Zealand2. -
Lecture Outline a Closer Look at Carbocation Stabilities and SN1/E1 Reaction Rates We Learned That an Important Factor in the SN
Lecture outline A closer look at carbocation stabilities and SN1/E1 reaction rates We learned that an important factor in the SN1/E1 reaction pathway is the stability of the carbocation intermediate. The more stable the carbocation, the faster the reaction. But how do we know anything about the stabilities of carbocations? After all, they are very unstable, high-energy species that can't be observed directly under ordinary reaction conditions. In protic solvents, carbocations typically survive only for picoseconds (1 ps - 10–12s). Much of what we know (or assume we know) about carbocation stabilities comes from measurements of the rates of reactions that form them, like the ionization of an alkyl halide in a polar solvent. The key to connecting reaction rates (kinetics) with the stability of high-energy intermediates (thermodynamics) is the Hammond postulate. The Hammond postulate says that if two consecutive structures on a reaction coordinate are similar in energy, they are also similar in structure. For example, in the SN1/E1 reactions, we know that the carbocation intermediate is much higher in energy than the alkyl halide reactant, so the transition state for the ionization step must lie closer in energy to the carbocation than the alkyl halide. The Hammond postulate says that the transition state should therefore resemble the carbocation in structure. So factors that stabilize the carbocation also stabilize the transition state leading to it. Here are two examples of rxn coordinate diagrams for the ionization step that are reasonable and unreasonable according to the Hammond postulate. We use the Hammond postulate frequently in making assumptions about the nature of transition states and how reaction rates should be influenced by structural features in the reactants or products. -
The Colors of Firefly Bioluminescence: Enzyme Configuration and Species Specificity by H
THE COLORS OF FIREFLY BIOLUMINESCENCE: ENZYME CONFIGURATION AND SPECIES SPECIFICITY BY H. H. SELIGER AND W. D. MCELROY MCCOLLUM-PRATT INSTITUTE, JOHNS HOPKINS UNIVERSITY Communicated May 25, 1964 We have previously reported on an unusual stereospecificity of firefly luciferase for a D(-) isomer of firefly luciferin.' While both the D(-) and the L(+) form will react with ATP to liberate pyrophosphate in the reaction E + LH2 + ATP =- E. LH2AMP + PP, (1) only D(-) LH2AMP will react further, in the presence of oxygen, to produce bio- luminescence and an oxidized product. There is also a strong pH dependence of the color of the emitted light;2 in acidic buffer solutions, pH < 6.5, the intensity of the normal yellow-green emission, peaking at 562 ml,, decreases markedly and a low intensity red emission is observed, peaking at 616 miu. This is evidence that enzyme configuration is important in determining the resonance energy levels of the excited state responsible for light emission. Further Evidence for Configurational Changes.-Except for the partial denatura- tion of the enzyme in acidic buffer, the pH effect on the emission spectrum shift is completely reversible. We have been able to observe these same reversible red shifts in emission spectra by increasing the temperature of the reaction, by carrying out the reaction in 0.2 M urea and at normal pH values (7.6) in glycyl glycine buffer, by adding small concentrations of Zn++, Cd++, and Hg++ cations, as chlorides. The normalized emission spectra of the in vitro bioluminescence of purified Photinus pyralis luciferase for various Zn++ concentrations are shown in Figure 1. -
Glossary of Terms Used in Photochemistry, 3Rd Edition (IUPAC
Pure Appl. Chem., Vol. 79, No. 3, pp. 293–465, 2007. doi:10.1351/pac200779030293 © 2007 IUPAC INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY ORGANIC AND BIOMOLECULAR CHEMISTRY DIVISION* SUBCOMMITTEE ON PHOTOCHEMISTRY GLOSSARY OF TERMS USED IN PHOTOCHEMISTRY 3rd EDITION (IUPAC Recommendations 2006) Prepared for publication by S. E. BRASLAVSKY‡ Max-Planck-Institut für Bioanorganische Chemie, Postfach 10 13 65, 45413 Mülheim an der Ruhr, Germany *Membership of the Organic and Biomolecular Chemistry Division Committee during the preparation of this re- port (2003–2006) was as follows: President: T. T. Tidwell (1998–2003), M. Isobe (2002–2005); Vice President: D. StC. Black (1996–2003), V. T. Ivanov (1996–2005); Secretary: G. M. Blackburn (2002–2005); Past President: T. Norin (1996–2003), T. T. Tidwell (1998–2005) (initial date indicates first time elected as Division member). The list of the other Division members can be found in <http://www.iupac.org/divisions/III/members.html>. Membership of the Subcommittee on Photochemistry (2003–2005) was as follows: S. E. Braslavsky (Germany, Chairperson), A. U. Acuña (Spain), T. D. Z. Atvars (Brazil), C. Bohne (Canada), R. Bonneau (France), A. M. Braun (Germany), A. Chibisov (Russia), K. Ghiggino (Australia), A. Kutateladze (USA), H. Lemmetyinen (Finland), M. Litter (Argentina), H. Miyasaka (Japan), M. Olivucci (Italy), D. Phillips (UK), R. O. Rahn (USA), E. San Román (Argentina), N. Serpone (Canada), M. Terazima (Japan). Contributors to the 3rd edition were: A. U. Acuña, W. Adam, F. Amat, D. Armesto, T. D. Z. Atvars, A. Bard, E. Bill, L. O. Björn, C. Bohne, J. Bolton, R. Bonneau, H. -
Bioluminescence in Insect
Int.J.Curr.Microbiol.App.Sci (2018) 7(3): 187-193 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 03 (2018) Journal homepage: http://www.ijcmas.com Review Article https://doi.org/10.20546/ijcmas.2018.703.022 Bioluminescence in Insect I. Yimjenjang Longkumer and Ram Kumar* Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar-848125, India *Corresponding author ABSTRACT Bioluminescence is defined as the emission of light from a living organism K e yw or ds that performs some biological function. Bioluminescence is one of the Fireflies, oldest fields of scientific study almost dating from the first written records Bioluminescence , of the ancient Greeks. This article describes the investigations of insect Luciferin luminescence and the crucial role imparted in the activities of insect. Many Article Info facets of this field are easily accessible for investigation without need for Accepted: advanced technology and so, within the History of Science, investigations 04 February 2018 of bioluminescence played a significant role in the establishment of the Available Online: scientific method, and also were among the many visual phenomena to be 10 March 2018 accounted for in developing a theory of light. Introduction Bioluminescence (BL) serves various purposes, including sexual attraction and When a living organism produces and emits courtship, predation and defense (Hastings and light as a result of a chemical reaction, the Wilson, 1976). This process is suggested to process is known as Bioluminescence - bio have arisen after O2 appearance on Earth at means 'living' in Greek while `lumen means least 30 different times during evolution, as 'light' in Latin. -
An Improved Potential Energy Surface for the H2cl System and Its Use for Calculations of Rate Coefficients and Kinetic Isotope Effects Thomas C
Chemistry Publications Chemistry 8-1996 An Improved Potential Energy Surface for the H2Cl System and Its Use for Calculations of Rate Coefficients and Kinetic Isotope Effects Thomas C. Allison University of Minnesota - Twin Cities Gillian C. Lynch University of Minnesota - Twin Cities Donald G. Truhlar University of Minnesota - Twin Cities Mark S. Gordon Iowa State University, [email protected] Follow this and additional works at: http://lib.dr.iastate.edu/chem_pubs Part of the Chemistry Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ chem_pubs/327. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Chemistry at Iowa State University Digital Repository. It has been accepted for inclusion in Chemistry Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. An Improved Potential Energy Surface for the H2Cl System and Its Use for Calculations of Rate Coefficients and Kinetic Isotope Effects Abstract We present a new potential energy surface (called G3) for the chemical reaction Cl + H2 → HCl + H. The new surface is based on a previous potential surface called GQQ, and it incorporates an improved bending potential that is fit ot the results of ab initio electronic structure calculations. Calculations based on variational transition state theory with semiclassical transmission coefficients corresponding to an optimized multidimensional tunneling treatment (VTST/OMT, in particular improved canonical variational theory with least-action ground-state transmission coefficients) are carried out for nine different isotopomeric versions of the abstraction reaction and six different isotopomeric versions of the exchange reaction involving the H, D, and T isotopes of hydrogen, and the new surface is tested by comparing these calculations to available experimental data. -
Spring 2013 Lecture 13-14
CHM333 LECTURE 13 – 14: 2/13 – 15/13 SPRING 2013 Professor Christine Hrycyna INTRODUCTION TO ENZYMES • Enzymes are usually proteins (some RNA) • In general, names end with suffix “ase” • Enzymes are catalysts – increase the rate of a reaction – not consumed by the reaction – act repeatedly to increase the rate of reactions – Enzymes are often very “specific” – promote only 1 particular reaction – Reactants also called “substrates” of enzyme catalyst rate enhancement non-enzymatic (Pd) 102-104 fold enzymatic up to 1020 fold • How much is 1020 fold? catalyst time for reaction yes 1 second no 3 x 1012 years • 3 x 1012 years is 500 times the age of the earth! Carbonic Anhydrase Tissues ! + CO2 +H2O HCO3− +H "Lungs and Kidney 107 rate enhancement Facilitates the transfer of carbon dioxide from tissues to blood and from blood to alveolar air Many enzyme names end in –ase 89 CHM333 LECTURE 13 – 14: 2/13 – 15/13 SPRING 2013 Professor Christine Hrycyna Why Enzymes? • Accelerate and control the rates of vitally important biochemical reactions • Greater reaction specificity • Milder reaction conditions • Capacity for regulation • Enzymes are the agents of metabolic function. • Metabolites have many potential pathways • Enzymes make the desired one most favorable • Enzymes are necessary for life to exist – otherwise reactions would occur too slowly for a metabolizing organis • Enzymes DO NOT change the equilibrium constant of a reaction (accelerates the rates of the forward and reverse reactions equally) • Enzymes DO NOT alter the standard free energy change, (ΔG°) of a reaction 1. ΔG° = amount of energy consumed or liberated in the reaction 2. -
Brazilian Bioluminescent Beetles: Reflections on Catching Glimpses of Light in the Atlantic Forest and Cerrado
Anais da Academia Brasileira de Ciências (2018) 90(1 Suppl. 1): 663-679 (Annals of the Brazilian Academy of Sciences) Printed version ISSN 0001-3765 / Online version ISSN 1678-2690 http://dx.doi.org/10.1590/0001-3765201820170504 www.scielo.br/aabc | www.fb.com/aabcjournal Brazilian Bioluminescent Beetles: Reflections on Catching Glimpses of Light in the Atlantic Forest and Cerrado ETELVINO J.H. BECHARA and CASSIUS V. STEVANI Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo, SP, Brazil Manuscript received on July 4, 2017; accepted for publication on August 11, 2017 ABSTRACT Bioluminescence - visible and cold light emission by living organisms - is a worldwide phenomenon, reported in terrestrial and marine environments since ancient times. Light emission from microorganisms, fungi, plants and animals may have arisen as an evolutionary response against oxygen toxicity and was appropriated for sexual attraction, predation, aposematism, and camouflage. Light emission results from the oxidation of a substrate, luciferin, by molecular oxygen, catalyzed by a luciferase, producing oxyluciferin in the excited singlet state, which decays to the ground state by fluorescence emission. Brazilian Atlantic forests and Cerrados are rich in luminescent beetles, which produce the same luciferin but slightly mutated luciferases, which result in distinct color emissions from green to red depending on the species. This review focuses on chemical and biological aspects of Brazilian luminescent beetles (Coleoptera) belonging to the Lampyridae (fireflies), Elateridae (click-beetles), and Phengodidae (railroad-worms) families. The ATP- dependent mechanism of bioluminescence, the role of luciferase tuning the color of light emission, the “luminous termite mounds” in Central Brazil, the cooperative roles of luciferase and superoxide dismutase against oxygen toxicity, and the hypothesis on the evolutionary origin of luciferases are highlighted.