Nucleophilic Addition-Elimination at the Acyl Carbon
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De Novo Biosynthesis of Terminal Alkyne-Labeled Natural Products
De novo biosynthesis of terminal alkyne-labeled natural products Xuejun Zhu1,2, Joyce Liu2,3, Wenjun Zhang1,2,4* 1Department of Chemical and Biomolecular Engineering, 2Energy Biosciences Institute, 3Department of Bioengineering, University of California, Berkeley, CA 94720, USA. 4Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. *e-mail:[email protected] 1 Abstract: The terminal alkyne is a functionality widely used in organic synthesis, pharmaceutical science, material science, and bioorthogonal chemistry. This functionality is also found in acetylenic natural products, but the underlying biosynthetic pathways for its formation are not well understood. Here we report the characterization of the first carrier protein- dependent terminal alkyne biosynthetic machinery in microbes. We further demonstrate that this enzymatic machinery can be exploited for the in situ generation and incorporation of terminal alkynes into two natural product scaffolds in E. coli. These results highlight the prospect for tagging major classes of natural products, including polyketides and polyketide/non-ribosomal peptide hybrids, using biosynthetic pathway engineering. 2 Natural products are important small molecules widely used as drugs, pesticides, herbicides, and biological probes. Tagging natural products with a unique chemical handle enables the visualization, enrichment, quantification, and mode of action study of natural products through bioorthogonal chemistry1-4. One prevalent bioorthogonal reaction is -
Elimination Reactions E1, E2, E1cb and Ei
Elimination Reactions Dr. H. Ghosh Surendranath College, Kol-9 ________________________________________________ E1, E2, E1cB and Ei (pyrolytic syn eliminations); formation of alkenes and alkynes; mechanisms (with evidence), reactivity, regioselectivity (Saytzeff/Hofmann) and stereoselectivity; comparison between substitution and elimination. Substitution Reactions Elimination Reactions Elimination happens when the nucleophile attacks hydrogen instead of carbon Strong Base favor Elimination Bulky Nucleophile/Base favor Elimination High Temperature favors Elimination We know- This equation says that a reaction in which ΔS is positive is more thermodynamically favorable at higher temperature. Eliminations should therefore be favoured at high temperature Keep in Mind---- Mechanism Classification E1 Mechanism- Elimination Unimolecular E1 describes an elimination reaction (E) in which the rate-determining step is unimolecular (1) and does not involve the base. The leaving group leaves in this step, and the proton is removed in a separate second step E2 Mechanism- Elimination Bimolecular E2 describes an elimination (E) that has a bimolecular (2) rate-determining step that must involve the base. Loss of the leaving group is simultaneous with removal of the proton by the base Bulky t-butoxide—ideal for promoting E2 as it’s both bulky and a strong base (pKaH = 18). Other Organic Base used in Elimination Reaction These two bases are amidines—delocalization of one nitrogen’s lone pair on to the other, and the resulting stabilization of the protonated amidinium ion, E1 can occur only with substrates that can ionize to give relatively stable carbocations—tertiary, allylic or benzylic alkyl halides, for example. E1-Elimination Reaction not possible here The role of the leaving group Since the leaving group is involved in the rate-determining step of both E1 and E2, in general, any good leaving group will lead to a fast elimination. -
Phospholipid:Diacylglycerol Acyltransferase: an Enzyme That Catalyzes the Acyl-Coa-Independent Formation of Triacylglycerol in Yeast and Plants
Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants Anders Dahlqvist*†‡, Ulf Ståhl†§, Marit Lenman*, Antoni Banas*, Michael Lee*, Line Sandager¶, Hans Ronne§, and Sten Stymne¶ *Scandinavian Biotechnology Research (ScanBi) AB, Herman Ehles Va¨g 2 S-26831 Svaloˆv, Sweden; ¶Department of Plant Breeding Research, Swedish University of Agricultural Sciences, Herman Ehles va¨g 2–4, S-268 31 Svalo¨v, Sweden; and §Department of Plant Biology, Uppsala Genetic Center, Swedish University of Agricultural Sciences, Box 7080, S-750 07 Uppsala, Sweden Edited by Christopher R. Somerville, Carnegie Institution of Washington, Stanford, CA, and approved March 31, 2000 (received for review February 15, 2000) Triacylglycerol (TAG) is known to be synthesized in a reaction that acid) and epoxidated fatty acid (vernolic acid) in TAG in castor uses acyl-CoA as acyl donor and diacylglycerol (DAG) as acceptor, bean (Ricinus communis) and the hawk’s-beard Crepis palaestina, and which is catalyzed by the enzyme acyl-CoA:diacylglycerol respectively. Furthermore, a similar enzyme is shown to be acyltransferase. We have found that some plants and yeast also present in the yeast Saccharomyces cerevisiae, and the gene have an acyl-CoA-independent mechanism for TAG synthesis, encoding this enzyme, YNR008w, is identified. which uses phospholipids as acyl donors and DAG as acceptor. This reaction is catalyzed by an enzyme that we call phospholipid:dia- Materials and Methods cylglycerol acyltransferase, or PDAT. PDAT was characterized in Yeast Strains and Plasmids. The wild-type yeast strains used were microsomal preparations from three different oil seeds: sunflower, either FY1679 (MAT␣ his3-⌬200 leu2-⌬1 trp1-⌬6 ura3-52) (9) or castor bean, and Crepis palaestina. -
Chapter 21 the Chemistry of Carboxylic Acid Derivatives
Instructor Supplemental Solutions to Problems © 2010 Roberts and Company Publishers Chapter 21 The Chemistry of Carboxylic Acid Derivatives Solutions to In-Text Problems 21.1 (b) (d) (e) (h) 21.2 (a) butanenitrile (common: butyronitrile) (c) isopentyl 3-methylbutanoate (common: isoamyl isovalerate) The isoamyl group is the same as an isopentyl or 3-methylbutyl group: (d) N,N-dimethylbenzamide 21.3 The E and Z conformations of N-acetylproline: 21.5 As shown by the data above the problem, a carboxylic acid has a higher boiling point than an ester because it can both donate and accept hydrogen bonds within its liquid state; hydrogen bonding does not occur in the ester. Consequently, pentanoic acid (valeric acid) has a higher boiling point than methyl butanoate. Here are the actual data: INSTRUCTOR SUPPLEMENTAL SOLUTIONS TO PROBLEMS • CHAPTER 21 2 21.7 (a) The carbonyl absorption of the ester occurs at higher frequency, and only the carboxylic acid has the characteristic strong, broad O—H stretching absorption in 2400–3600 cm–1 region. (d) In N-methylpropanamide, the N-methyl group is a doublet at about d 3. N-Ethylacetamide has no doublet resonances. In N-methylpropanamide, the a-protons are a quartet near d 2.5. In N-ethylacetamide, the a- protons are a singlet at d 2. The NMR spectrum of N-methylpropanamide has no singlets. 21.9 (a) The first ester is more basic because its conjugate acid is stabilized not only by resonance interaction with the ester oxygen, but also by resonance interaction with the double bond; that is, the conjugate acid of the first ester has one more important resonance structure than the conjugate acid of the second. -
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. -
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. -
11 Carboxylic Acids and Derivatives
CARBOXYLIC ACIDS AND NITRILES Chapters 20, 21 Organic Chemistry, 8th Edition John McMurry 1 CARBOXYLIC ACID DERIVATIVES 2 CARBOXYLIC ACID DERIVATIVES R C N nitrile R = CH3 acetonitrile 3 STRUCTURE AND BONDING 4 NOMENCLATURE—THE IUPAC SYSTEM heptanoic acid benzoic acid cyclopentane carboxylic acid 4,5-dimethyl 3-pentenoic 3-bromobenzoic p-toluic 1-methyl- hexanoic acid acid acid acid cyclopropanecarboxylic acid 5 NOMENCLATURE-COMMON NAMES προτοσ πιον 6 NOMENCLATURE-POLYIACIDS Oxalis acetosella Malon Succinum HOOC COOH COOH propane-1,2,3-tricarboxylic acid 7 PHYSICAL PROPERTIES • Carboxylic acids exhibit dipole-dipole interactions because they have polar C—O and O—H bonds. • They also exhibit intermolecular hydrogen bonding. • In the gas phase and in apolar solvents, carboxylic acids often exist as dimers held together by two intermolecular hydrogen bonds. 8 PHYSICAL PROPERTIES 9 ACIDITY OF CARBOXYLIC ACIDS The acetate anion has two C—O bonds of equal length (1.27 Å) and intermediate between the length of a C—O single bond (1.36 Å) and C=O (1.21 Å). 10 CARBOXYLIC ACIDS—STRONG ORGANIC BRØNSTED-LOWRY ACIDS 11 THE INDUCTIVE EFFECT IN ALIPHATIC CARBOXYLIC ACIDS 12 THE INDUCTIVE EFFECT IN ALIPHATIC CARBOXYLIC ACIDS 13 SUBSTITUTED BENZOIC ACIDS 14 SUBSTITUTED BENZOIC ACIDS 15 PREPARATION OF CARBOXYLIC ACIDS [1] Oxidation of 1° alcohols [2] Oxidation of alkyl benzenes 16 PREPARATION OF CARBOXYLIC ACIDS [3] From alkyl halides CN CN- i. NaOH + ii.H3O Br COOH i. CO2 Mg + ii. H3O MgBr R MgBr R OMgBr H O+ R OH 3 + Mg++ + Br- O C O O O 17 PREPARATION OF CARBOXYLIC ACIDS [5] From alkyl halides. -
Amine-Catalyzed Hydrolyses of Cyclodextrin Cinnamates
Proc. Natl. Acad. Sci. USA Vol. 73, No. 9, pp. 2969-2972, September 1976 Chemistry Amine-catalyzed hydrolyses of cyclodextrin cinnamates (cyclodextrin-catalyzed ester hydrolysis/acyl-cyclodextrin/acceleration of deacylation/enzyme model) MAKOTO KOMIYAMA AND MYRON L. BENDER Division of Biochemistry, Department of Chemistry, Northwestern University, Evanston, Illinois 60201 Contributed by Myron L. Bender, July 6,1976 ABSTRACT Hydrolyses of 6B-cyclodextrin cinnamate EXPERIMENTAL (#CDC) and a-cyclodextrin cinnamate were catalyzed by amines such as 1,4-diazabicyclo(2.2.2)octane, triethylamine, quinucli- Materials. #CDC and aCDC were kindly furnished by Y. dine, piperidine, diisobutylamine, and n-butylamine. The rate constant of hydrolyses of the #CDC-amine complexes follows Kurono. They were recrystallized before use. The purity of the order: 1,4-diazabicyclo(2.2.2)octane > n-butylamine > qui- fCDC and aCDC were found to be higher than 96% and-98%, nuclidine > piperidine > triethylamine >> diisobutylamine. The respectively, by absorption spectroscopy at 273 nm, which is ratio of the catalytic rate constant for the ,8CDC/1,4-diazabi- the isosbestic point between trans-cinnamic acid and (3CDC cyclo(2.2.2)octane complex to the spontaneous rate constant for or aCDC. Aza2bicOct was purified by recrystallization and had ,8CDC is about 6-fold and is almost independent of pH below a melting point of 158° see ref. Other pH 11.5; but, it then drastically increases with pH above pH 11.5, (159-160° reported, 5). up to 57-fold at pH 13.6 which is much higer than previous reagents were purchased from the Aldrich Chemical Co. attempts. -
Amide Activation: an Emerging Tool for Chemoselective Synthesis
Featuring work from the research group of Professor As featured in: Nuno Maulide, University of Vienna, Vienna, Austria Amide activation: an emerging tool for chemoselective synthesis Let them stand out of the crowd – Amide activation enables the chemoselective modification of a large variety of molecules while leaving many other functional groups untouched, making it attractive for the synthesis of sophisticated targets. This issue features a review on this emerging field and its application in total synthesis. See Nuno Maulide et al., Chem. Soc. Rev., 2018, 47, 7899. rsc.li/chem-soc-rev Registered charity number: 207890 Chem Soc Rev View Article Online REVIEW ARTICLE View Journal | View Issue Amide activation: an emerging tool for chemoselective synthesis Cite this: Chem. Soc. Rev., 2018, 47,7899 Daniel Kaiser, Adriano Bauer, Miran Lemmerer and Nuno Maulide * It is textbook knowledge that carboxamides benefit from increased stabilisation of the electrophilic carbonyl carbon when compared to other carbonyl and carboxyl derivatives. This results in a considerably reduced reactivity towards nucleophiles. Accordingly, a perception has been developed of amides as significantly less useful functional handles than their ester and acid chloride counterparts. Received 27th April 2018 However, a significant body of research on the selective activation of amides to achieve powerful DOI: 10.1039/c8cs00335a transformations under mild conditions has emerged over the past decades. This review article aims at placing electrophilic amide activation in both a historical context and in that of natural product rsc.li/chem-soc-rev synthesis, highlighting the synthetic applications and the potential of this approach. Creative Commons Attribution 3.0 Unported Licence. -
Pentachloride Hazard Summary Identification
Common Name: PHOSPHORUS PENTACHLORIDE CAS Number: 10026-13-8 RTK Substance number: 1525 DOT Number: UN 1806 Date: August 1999 ----------------------------------------------------------------------- ----------------------------------------------------------------------- HAZARD SUMMARY * Phosphorus Pentachloride can affect you when breathed * Exposure to hazardous substances should be routinely in. evaluated. This may include collecting personal and area * Phosphorus Pentachloride is a CORROSIVE air samples. You can obtain copies of sampling results CHEMICAL and contact can severely irritate and burn the from your employer. You have a legal right to this skin and eyes with possible eye damage. information under OSHA 1910.1020. * Breathing Phosphorus Pentachloride can irritate the nose * If you think you are experiencing any work-related health and throat. problems, see a doctor trained to recognize occupational * Breathing Phosphorus Pentachloride can irritate the diseases. Take this Fact Sheet with you. lungs causing coughing and/or shortness of breath. Higher exposures can cause a build-up of fluid in the lungs WORKPLACE EXPOSURE LIMITS (pulmonary edema), a medical emergency, with severe OSHA: The legal airborne permissible exposure limit shortness of breath. (PEL) is 1 mg/m3 averaged over an 8-hour * Exposure to Phosphorus Pentachloride can cause workshift. headache, dizziness, weakness, nausea and vomiting. * Phosphorus Pentachloride may damage the liver and NIOSH: The recommended airborne exposure limit is kidneys. 1 mg/m3 averaged over a 10-hour workshift. * Phosphorus Pentachloride is a REACTIVE CHEMICAL and an EXPLOSION HAZARD. ACGIH: The recommended airborne exposure limit is 0.85 mg/m3 averaged over an 8-hour workshift. IDENTIFICATION Phosphorus Pentachloride is a white to pale yellow, WAYS OF REDUCING EXPOSURE crystalline solid with a pungent odor. -
Hydrolysis of Amides: a Kinetic Study of Substituent Effects on the Acidic and Basic Hydrolysis of Aliphatic Amides
University of Wollongong Research Online University of Wollongong Thesis Collection 1954-2016 University of Wollongong Thesis Collections 1969 Hydrolysis of amides: a kinetic study of substituent effects on the acidic and basic hydrolysis of aliphatic amides Grahame Leslie Jackson Wollongong University College Follow this and additional works at: https://ro.uow.edu.au/theses University of Wollongong Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorise you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: This work is copyright. Apart from any use permitted under the Copyright Act 1968, no part of this work may be reproduced by any process, nor may any other exclusive right be exercised, without the permission of the author. Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. A court may impose penalties and award damages in relation to offences and infringements relating to copyright material. Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form. Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong. Recommended Citation Jackson, Grahame Leslie, Hydrolysis of amides: a kinetic study of substituent effects on the acidic and basic hydrolysis of aliphatic amides, Doctor of Philosophy thesis, Department of Chemistry, University of Wollongong, 1969.