Chapter 20: Carboxylic Acids and Nitriles the Importance of Carboxylic Acids
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Alkyldihydropyrones, New Polyketides Synthesized by a Type III Polyketide Synthase from Streptomyces Reveromyceticus
The Journal of Antibiotics (2014) 67, 819–823 & 2014 Japan Antibiotics Research Association All rights reserved 0021-8820/14 www.nature.com/ja ORIGINAL ARTICLE Alkyldihydropyrones, new polyketides synthesized by a type III polyketide synthase from Streptomyces reveromyceticus Teruki Aizawa1, Seung-Young Kim1, Shunji Takahashi2,3, Masahiko Koshita1, Mioka Tani1, Yushi Futamura3, Hiroyuki Osada2,3 and Nobutaka Funa1 Genome sequencing allows a rapid and efficient identification of novel catalysts that produce novel secondary metabolites. Here we describe the catalytic properties of dihydropyrone synthase A (DpyA), a novel type III polyketide synthase encoded in a linear plasmid of Streptomyces reveromyceticus. Heterologous expression of dpyA led to the accumulation of alkyldihydropyrones A (1), B (2), C (3) and D (4), which are novel dihydropyran compounds that exhibit weak cytotoxicity against the leukemia cell line HL-60. DpyA catalyzes the condensation of b-hydroxyl acid thioester and methylmalonyl-CoA to yield a triketide intermediate that then undergoes lactonization of a secondary alcohol and a thioester to give alkyldihydropyrone. The Journal of Antibiotics (2014) 67, 819–823; doi:10.1038/ja.2014.80; published online 2 July 2014 INTRODUCTION Very recently, Tang et al.11 discovered that presulficidin, which is Type III polyketide synthase (PKS), which is widely distributed synthesized by Cpz6, a type III PKS from the caprazamycin among higher plants, fungi and bacteria, catalyzes the assembly of biosynthetic cluster, relays sulfonate from 30-phosphoadenine-50- primary metabolites such as acyl-CoA compounds to synthesize phosphosulfate to caprazamycin. structurally complex polyketides.1 The reaction catalyzed by type III Genome sequence analyses of Streptomyces species have shown that PKS starts with the formation of a thioester bond between the the number of biosynthetic gene clusters encoded on the chromosome catalytic center cysteine and an acyl group derived from a starter is much higher than the number of secondary metabolites isolated substrate. -
The Reaction of Aminonitriles with Aminothiols: a Way to Thiol-Containing Peptides and Nitrogen Heterocycles in the Primitive Earth Ocean
life Article The Reaction of Aminonitriles with Aminothiols: A Way to Thiol-Containing Peptides and Nitrogen Heterocycles in the Primitive Earth Ocean Ibrahim Shalayel , Seydou Coulibaly, Kieu Dung Ly, Anne Milet and Yannick Vallée * Univ. Grenoble Alpes, CNRS, Département de Chimie Moléculaire, Campus, F-38058 Grenoble, France; [email protected] (I.S.); [email protected] (S.C.); [email protected] (K.D.L.); [email protected] (A.M.) * Correspondence: [email protected] Received: 28 September 2018; Accepted: 18 October 2018; Published: 19 October 2018 Abstract: The Strecker reaction of aldehydes with ammonia and hydrogen cyanide first leads to α-aminonitriles, which are then hydrolyzed to α-amino acids. However, before reacting with water, these aminonitriles can be trapped by aminothiols, such as cysteine or homocysteine, to give 5- or 6-membered ring heterocycles, which in turn are hydrolyzed to dipeptides. We propose that this two-step process enabled the formation of thiol-containing dipeptides in the primitive ocean. These small peptides are able to promote the formation of other peptide bonds and of heterocyclic molecules. Theoretical calculations support our experimental results. They predict that α-aminonitriles should be more reactive than other nitriles, and that imidazoles should be formed from transiently formed amidinonitriles. Overall, this set of reactions delineates a possible early stage of the development of organic chemistry, hence of life, on Earth dominated by nitriles and thiol-rich peptides (TRP). Keywords: origin of life; prebiotic chemistry; thiol-rich peptides; cysteine; aminonitriles; imidazoles 1. Introduction In ribosomes, peptide bonds are formed by the reaction of the amine group of an amino acid with an ester function. -
Organic Chemistry
Wisebridge Learning Systems Organic Chemistry Reaction Mechanisms Pocket-Book WLS www.wisebridgelearning.com © 2006 J S Wetzel LEARNING STRATEGIES CONTENTS ● The key to building intuition is to develop the habit ALKANES of asking how each particular mechanism reflects Thermal Cracking - Pyrolysis . 1 general principles. Look for the concepts behind Combustion . 1 the chemistry to make organic chemistry more co- Free Radical Halogenation. 2 herent and rewarding. ALKENES Electrophilic Addition of HX to Alkenes . 3 ● Acid Catalyzed Hydration of Alkenes . 4 Exothermic reactions tend to follow pathways Electrophilic Addition of Halogens to Alkenes . 5 where like charges can separate or where un- Halohydrin Formation . 6 like charges can come together. When reading Free Radical Addition of HX to Alkenes . 7 organic chemistry mechanisms, keep the elec- Catalytic Hydrogenation of Alkenes. 8 tronegativities of the elements and their valence Oxidation of Alkenes to Vicinal Diols. 9 electron configurations always in your mind. Try Oxidative Cleavage of Alkenes . 10 to nterpret electron movement in terms of energy Ozonolysis of Alkenes . 10 Allylic Halogenation . 11 to make the reactions easier to understand and Oxymercuration-Demercuration . 13 remember. Hydroboration of Alkenes . 14 ALKYNES ● For MCAT preparation, pay special attention to Electrophilic Addition of HX to Alkynes . 15 Hydration of Alkynes. 15 reactions where the product hinges on regio- Free Radical Addition of HX to Alkynes . 16 and stereo-selectivity and reactions involving Electrophilic Halogenation of Alkynes. 16 resonant intermediates, which are special favor- Hydroboration of Alkynes . 17 ites of the test-writers. Catalytic Hydrogenation of Alkynes. 17 Reduction of Alkynes with Alkali Metal/Ammonia . 18 Formation and Use of Acetylide Anion Nucleophiles . -
Packet of Wiser Reports on Acetone Acetonitrile
Ac&tone ^Hazmat - NFPA Hazard Classification Page 1 of Acetone CAS RN: 67-64-1 Hazmat - NFPA Hazard Classification SOMS DocID 2085807 Health: 1 (Slight) Materials that, on exposure, would cause significant irritation, but only minor residual injury, including those requiring the use of an approved air-purifying respirator. These materials are only slightly hazardous to health and only breathing protection is needed. Flammability: 3 (Severe) rhis degree includes Class IB and 1C flammable liquids and materials that can be easily ignited under almost all normal temperature conditions. Water may be ineffective in controlling or extinguishing fires in such materials. Instability: 0 (Minimal) This degree includes materials that are normally stable, even under fire exposure conditions, and that do not react with water.- Norma lire fighting procedures may be used. Printed by WISER for Windows (v2.3.231, database v2.108) HHS/NIH, National Library of Medicine AR000018 iile://C:\Documents and Settings\Gham\Application Data\National Library of Medicine\WISER\2.3.231.628... 9/27/20 Acetone ^Key Info Page 1 of Acetone CAS RN: 67-64-1 Key Info FLAMMABLE LIQUIDS (Polar / Water-Miscible) • HIGHLY FLAMMABLE: Easily ignited by heat, sparks or flames • CAUTION: Very low flash point; use of water spray when fighting fire may be inefficient Printed by WISER for Windows (v2.3.231, database v2.108) HHS/NIH, National Library of Medicine AR000019 file://C:\Documents and Settings\Gham\Application Data\National Library of Medicine\WISER\2.3.231.628../ 9/27/20 Acetone - -Hazmat - Explosive Limits / Potential Page 1 of Acetone CAS RIM: 67-64-1 Hazmat - Explosive Limits / Potential Highly flammable liquid. -
The Relative Rates of Thiol–Thioester Exchange and Hydrolysis for Alkyl and Aryl Thioalkanoates in Water
Orig Life Evol Biosph (2011) 41:399–412 DOI 10.1007/s11084-011-9243-4 PREBIOTIC CHEMISTRY The Relative Rates of Thiol–Thioester Exchange and Hydrolysis for Alkyl and Aryl Thioalkanoates in Water Paul J. Bracher & Phillip W. Snyder & Brooks R. Bohall & George M. Whitesides Received: 14 April 2011 /Accepted: 16 June 2011 / Published online: 5 July 2011 # Springer Science+Business Media B.V. 2011 Abstract This article reports rate constants for thiol–thioester exchange (kex), and for acid- mediated (ka), base-mediated (kb), and pH-independent (kw) hydrolysis of S-methyl thioacetate and S-phenyl 5-dimethylamino-5-oxo-thiopentanoate—model alkyl and aryl thioalkanoates, respectively—in water. Reactions such as thiol–thioester exchange or aminolysis could have generated molecular complexity on early Earth, but for thioesters to have played important roles in the origin of life, constructive reactions would have needed to compete effectively with hydrolysis under prebiotic conditions. Knowledge of the kinetics of competition between exchange and hydrolysis is also useful in the optimization of systems where exchange is used in applications such as self-assembly or reversible binding. For the alkyl thioester S-methyl thioacetate, which has been synthesized in −5 −1 −1 −1 −1 −1 simulated prebiotic hydrothermal vents, ka = 1.5×10 M s , kb = 1.6×10 M s , and −8 −1 kw = 3.6×10 s . At pH 7 and 23°C, the half-life for hydrolysis is 155 days. The second- order rate constant for thiol–thioester exchange between S-methyl thioacetate and 2- −1 −1 sulfonatoethanethiolate is kex = 1.7 M s . -
Photoionization Studies of Reactive Intermediates Using Synchrotron
Photoionization Studies of Reactive Intermediates using Synchrotron Radiation by John M.Dyke* School of Chemistry University of Southampton SO17 1BJ UK *e-mail: [email protected] 1 Abstract Photoionization of reactive intermediates with synchrotron radiation has reached a sufficiently advanced stage of development that it can now contribute to a number of areas in gas-phase chemistry and physics. These include the detection and spectroscopic study of reactive intermediates produced by bimolecular reactions, photolysis, pyrolysis or discharge sources, and the monitoring of reactive intermediates in situ in environments such as flames. This review summarises advances in the study of reactive intermediates with synchrotron radiation using photoelectron spectroscopy (PES) and constant-ionic-state (CIS) methods with angular resolution, and threshold photoelectron spectroscopy (TPES), taking examples mainly from the recent work of the Southampton group. The aim is to focus on the main information to be obtained from the examples considered. As future research in this area also involves photoelectron-photoion coincidence (PEPICO) and threshold photoelectron-photoion coincidence (TPEPICO) spectroscopy, these methods are also described and previous related work on reactive intermediates with these techniques is summarised. The advantages of using PEPICO and TPEPICO to complement and extend TPES and angularly resolved PES and CIS studies on reactive intermediates are highlighted. 2 1.Introduction This review is organised as follows. After an Introduction to the study of reactive intermediates by photoionization with fixed energy photon sources and synchrotron radiation, a number of Case Studies are presented of the study of reactive intermediates with synchrotron radiation using angle resolved PES and CIS, and TPE spectroscopy. -
Esters Introduction Structurally, an Ester Is a Compound That Has an Alkoxy (OR) Group Attached to the Carbonyl Group
Esters Introduction Structurally, an ester is a compound that has an alkoxy (OR) group attached to the carbonyl group. O R C O R' R may be H, alkyl or aryl, while R’ may be alkyl or aryl only. Esters are widespread in nature. Many of the fragrances of flowers and fruits are due to the esters present. Ethyl butanoate is the chief component that accounts for the pineapple-like aroma and flavour of pineapples. 1:18 PM 1 Nomenclature of Esters Names of esters consist of two words that reflect the composite structure of the ester. The first word is derived from the alkyl group of the alcohol component, and the second word from the carboxylate group of the carboxylic acid component of the ester. The name of the carboxylate portion is derived by substituting the -ic acid suffix of the parent carboxylic acid with the –ate suffix. The alkyl group is cited first followed by the carboxylate group separated by a space. An ester is thus named as an alkyl 1:18 PM alkanoate. 2 IUPAC Nomenclature of Esters Examples 1:18 PM 3 Synthesis of Esters Preparative Strategies Highlighted below are some of the most common strategies by which esters are prepared. The esters are commonly prepared from the reaction of carboxylic acids, acid chlorides and acid anhydrides with alcohols. 1:18 PM 4 Synthesis of Esters Acid-Catalysed Esterification of a Carboxylic Acid and an Alcohol The acid-catalysed reaction of carboxylic acids and alcohols provides esters. Typically, a catalytic amount of a strong inorganic (mineral) acid such as H2SO4, HCl and H3PO4 is used. -
Chloroform 18.08.2020.Pdf
Chloroform Chloroform, or trichloromethane, is an organic compound with formula CHCl3. It is a colorless, sweet-smelling, dense liquid that is produced on a large scale as a precursor to PTFE. It is also a precursor to various refrigerants. It is one of the four chloromethanes and a trihalomethane. It is a powerful anesthetic, euphoriant, anxiolytic and sedative when inhaled or ingested. Formula: CHCl₃ IUPAC ID: Trichloromethane Molar mass: 119.38 g/mol Boiling point: 61.2 °C Density: 1.49 g/cm³ Melting point: -63.5 °C The molecule adopts a tetrahedral molecular geometry with C3v symmetry. Chloroform volatilizes readily from soil and surface water and undergoes degradation in air to produce phosgene, dichloromethane, formyl chloride, carbon monoxide, carbon dioxide, and hydrogen chloride. Its half-life in air ranges from 55 to 620 days. Biodegradation in water and soil is slow. Chloroform does not significantly bioaccumulate in aquatic organisms. Production:- In industry production, chloroform is produced by heating a mixture of chlorine and either chloromethane (CH3Cl) or methane (CH4). At 400–500 °C, a free radical halogenation occurs, converting these precursors to progressively more chlorinated compounds: CH4 + Cl2 → CH3Cl + HCl CH3Cl + Cl2 → CH2Cl2 + HCl CH2Cl2 + Cl2 → CHCl3 + HCl Chloroform undergoes further chlorination to yield carbon tetrachloride (CCl4): CHCl3 + Cl2 → CCl4 + HCl The output of this process is a mixture of the four chloromethanes (chloromethane, dichloromethane, chloroform, and carbon tetrachloride), which can then be separated by distillation. Chloroform may also be produced on a small scale via the haloform reaction between acetone and sodium hypochlorite: 3 NaClO + (CH3)2CO → CHCl3 + 2 NaOH + CH3COONa Deuterochloroform[ Deuterated chloroform is an isotopologue of chloroform with a single deuterium atom. -
Fundamentals of Theoretical Organic Chemistry Lecture 9
Fund. Theor. Org. Chem 1 SE Fundamentals of Theoretical Organic Chemistry Lecture 9 1 Fund. Theor. Org. Chem 2 SE 2.2.2 Electrophilic substitution The reaction which takes place between a reactant with an electronegative carbon and an electropositive reagent forming a polarized covalent bond is called electrophilic. In addition, if substitution occurs (i.e. there is a similar polarized covalent bond on the electronegative carbon, which breaks up during the reaction, so the reagent „substitutes” the „old” group or the leaving group) then this specific reaction is called electrophilic substitution. The electronegative carbon is called the reaction centre. In general, the good reactant are molecules having electronegative carbons like aromatic compounds, alkenes and other compounds containing electron-rich double bonds. These are called Lewis bases. On the contrary, good electrophilic reagents are electron poor compounds/molecule groups like acid-halides, which easily form covalent bond with an electronegative centre, thus creating a new molecule. These are often referred to as Lewis acids. According to molecular orbital (MO) theory the driving force for the electrophilic substitution (SE) is a Lewis complex formation involving the LUMO of the Lewis Acid Reagent and the HOMO of the Lewis Base Reactant. Reactant Reagent LUMO LUMO HOMO Lewis base Lewis acid Lewis complex Types of reactions: There are four types of reactions as illustrated below: 2 Fund. Theor. Org. Chem 3 SE Table. 2.2.2-1. Saturated Aromatic SE1 SE1 (Ar) SE2 SE2 (Ar) SE reaction on saturated atom: (1)Unimolecular electrophilic substitution (SE1): The reaction proceeds in two steps. After the departure of the leaving group, the negatively charged reaction intermediate will combine with the reagent. -
Hydrogen Atom Transfer-Mediated Cyclisations of Nitriles
Hydrogen Atom Transfer-Mediated Cyclisations of Nitriles Oliver J. Turner,*[a,b] John A. Murphy,*[b] David. J. Hirst[a] and Eric P. A. Talbot*[a]† Abstract: Hydrogen atom transfer-mediated intramolecular C-C coupling reactions between alkenes and nitriles, using PhSiH3 and catalytic Fe(acac)3, are described. This introduces a new strategic bond disconnection for ring-closing reactions, forming ketones via imine intermediates. Of note is the scope of the reaction, including formation of sterically hindered ketones, spirocycles and fused cyclic systems. In the early 1960s, Kwiatek and Seyler first reported the use of metal hydrides as catalysts in the hydrogenation of α,β- unsaturated compounds.[1,2] The discovery by Halpern,[3] later elegantly developed by Norton,[4] that metal-hydride hydrogen atom transfer (HAT) proceeded by a free-radical mechanism opened the door to a wide range of alkene hydrofunctionalisation reactions. But it was the pioneering work by Mukaiyama[5] on the catalytic hydration of alkenes, using Co(acac)2 and oxygen, that sparked wider interest in the field of alkene hydrofunctionalisation. As a result, there now exists an extensive ‘toolkit’ for the addition of hydrogen and a functional group to an alkene with Markovnikov selectivity and high chemo-selectivity using cobalt, manganese and iron complexes.[6,7] Efforts have also been made to extend HAT methodologies to C-C bond formation, both in an intra- and intermolecular fashion: Baran’s group developed a general C-C coupling reaction, utilising electron-deficient alkenes as capable radical acceptors (Scheme 1ai).[8–10] Hydropyridylation of alkenes by intramolecular Minisci reaction was recently demonstrated by Starr,[11] which allows for the formation of structures such as Scheme 1. -
Nitrile Synthesis with Aldoxime Dehydratases: a Biocatalytic Platform with Applications in Asymmetric Synthesis, Bulk Chemicals, and Biorefineries
molecules Review Nitrile Synthesis with Aldoxime Dehydratases: A Biocatalytic Platform with Applications in Asymmetric Synthesis, Bulk Chemicals, and Biorefineries Pablo Domínguez de María Sustainable Momentum, SL, Av. Ansite 3, 4–6, 35011 Las Palmas de Gran Canaria, Canary Islands, Spain; [email protected]; Tel.: +34-6-0956-5237 Abstract: Nitriles comprise a broad group of chemicals that are currently being industrially produced and used in fine chemicals and pharmaceuticals, as well as in bulk applications, polymer chemistry, solvents, etc. Aldoxime dehydratases catalyze the cyanide-free synthesis of nitriles starting from aldoximes under mild conditions, holding potential to become sustainable alternatives for industrial processes. Different aldoxime dehydratases accept a broad range of aldoximes with impressive high substrate loadings of up to >1 Kg L−1 and can efficiently catalyze the reaction in aqueous media as well as in non-aqueous systems, such as organic solvents and solvent-free (neat substrates). This paper provides an overview of the recent developments in this field with emphasis on strategies that may be of relevance for industry and sustainability. When possible, potential links to biorefineries and to the use of biogenic raw materials are discussed. Keywords: biocatalysis; green chemistry; nitriles; aldoxime dehydratases; sustainability Citation: Domínguez de María, P. Nitrile Synthesis with Aldoxime Dehydratases: A Biocatalytic Platform with Applications in Asymmetric Synthesis, Bulk 1. Aldoxime Dehydratases as Biocatalysts for the Cyanide-Free Synthesis of Nitriles Chemicals, and Biorefineries. Nitriles comprise an important group of chemicals that are widely spread in industry Molecules 2021, 26, 4466. in a broad range of sectors, being used as products, solvents, polymers, commodities, or https://doi.org/10.3390/ as starting materials for the production of other chemicals such as amines, amides, etc. -
Fermentation and Ester Taints
Fermentation and Ester Taints Anita Oberholster Introduction: Aroma Compounds • Grape‐derived –provide varietal distinction • Yeast and fermentation‐derived – Esters – Higher alcohols – Carbonyls – Volatile acids – Volatile phenols – Sulfur compounds What is and Esters? • Volatile molecule • Characteristic fruity and floral aromas • Esters are formed when an alcohol and acid react with each other • Few esters formed in grapes • Esters in wine ‐ two origins: – Enzymatic esterification during fermentation – Chemical esterification during long‐term storage Ester Formation • Esters can by formed enzymatically by both the plant and microbes • Microbes – Yeast (Non‐Saccharomyces and Saccharomyces yeast) – Lactic acid bacteria – Acetic acid bacteria • But mainly produced by yeast (through lipid and acetyl‐CoA metabolism) Ester Formation Alcohol function Keto acid‐Coenzyme A Ester Ester Classes • Two main groups – Ethyl esters – Acetate esters • Ethyl esters = EtOH + acid • Acetate esters = acetate (derivative of acetic acid) + EtOH or complex alcohol from amino acid metabolism Ester Classes • Acetate esters – Ethyl acetate (solvent‐like aroma) – Isoamyl acetate (banana aroma) – Isobutyl acetate (fruit aroma) – Phenyl ethyl acetate (roses, honey) • Ethyl esters – Ethyl hexanoate (aniseed, apple‐like) – Ethyl octanoate (sour apple aroma) Acetate Ester Formation • 2 Main factors influence acetate ester formation – Concentration of two substrates acetyl‐CoA and fusel alcohol – Activity of enzyme responsible for formation and break down reactions • Enzyme activity influenced by fermentation variables – Yeast – Composition of fermentation medium – Fermentation conditions Acetate/Ethyl Ester Formation – Fermentation composition and conditions • Total sugar content and optimal N2 amount pos. influence • Amount of unsaturated fatty acids and O2 neg. influence • Ethyl ester formation – 1 Main factor • Conc. of precursors – Enzyme activity smaller role • Higher fermentation temp formation • C and N increase small effect Saerens et al.