Organic Chemistry by Robert C
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Common Names for Selected Aromatic Groups
More Nomenclature: Common Names for Selected Aromatic Groups Phenyl group = or Ph = C6H5 = Aryl = Ar = aromatic group. It is a broad term, and includes any aromatic rings. Benzyl = Bn = It has a -CH2- (methylene) group attached to the benzene ring. This group can be used to name particular compounds, such as the one shown below. This compound has chlorine attached to a benzyl group, therefore it is called benzyl chloride. Benzoyl = Bz = . This is different from benzyl group (there is an extra “o” in the name). It has a carbonyl attached to the benzene ring instead of a methylene group. For example, is named benzoyl chloride. Therefore, it is sometimes helpful to recognize a common structure in order to name a compound. Example: Nomenclature: 3-phenylpentane Example: This is Amaize. It is used to enhance the yield of corn production. The systematic name for this compound is 2,4-dinitro-6-(1-methylpropyl)phenol. Polynuclear Aromatic Compounds Aromatic rings can fuse together to form polynuclear aromatic compounds. Example: It is two benzene rings fused together, and it is aromatic. The electrons are delocalized in both rings (think about all of its resonance form). Example: This compound is also aromatic, including the ring in the middle. All carbons are sp2 hybridized and the electron density is shared across all 5 rings. Example: DDT is an insecticide and helped to wipe out malaria in many parts of the world. Consequently, the person who discovered it (Muller) won the Nobel Prize in 1942. The systematic name for this compound is 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)ethane. -
Chiral Proton Catalysis: Design and Development of Enantioselective Aza-Henry and Diels-Alder Reactions
CHIRAL PROTON CATALYSIS: DESIGN AND DEVELOPMENT OF ENANTIOSELECTIVE AZA-HENRY AND DIELS-ALDER REACTIONS Ryan A. Yoder Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy in the Department of Chemistry, Indiana University June 2008 Accepted by the Graduate Faculty, Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Doctoral Committee _____________________________ Jeffrey N. Johnston, Ph.D. _____________________________ Daniel J. Mindiola, Ph.D. _____________________________ David R. Williams, Ph.D. _____________________________ Jeffrey Zaleski, Ph.D. April 24, 2008 ii © 2008 Ryan A. Yoder ALL RIGHTS RESERVED iii DEDICATION This work is dedicated to my parents, David and Doreen Yoder, and my sister, LeeAnna Loudermilk. Their unwavering love and support provided the inspiration for me to pursue my dreams. The sacrifices they have made and the strength they have shown continue to motivate me to be a better person each and every day. Thank you mom, dad, and little sis for being the rocks that I can lean on and the foundation that allowed me to find the happiness I have today. Without you, none of this would have been possible. iv ACKNOWLEDGEMENTS First and foremost I want to thank my research advisor, Professor Jeffrey N. Johnston. I am incredibly grateful for his mentoring and guidance throughout my time in the Johnston group. He has instilled in me a solid foundation in the fundamentals of organic chemistry and at the same time has taught me how to apply innovative and creative solutions to complex problems. -
(+)-Obafluorin, a B-Lactone Antibiotic
Illinois Wesleyan University Digital Commons @ IWU Honors Projects Chemistry 4-26-1996 Pursuit of a Chiral Amino Aldehyde Intermediate in the Synthesis of (+)-Obafluorin, a B-Lactone Antibiotic Jim Cwik '96 Illinois Wesleyan University Follow this and additional works at: https://digitalcommons.iwu.edu/chem_honproj Part of the Chemistry Commons Recommended Citation Cwik '96, Jim, "Pursuit of a Chiral Amino Aldehyde Intermediate in the Synthesis of (+)- Obafluorin, a B-Lactone Antibiotic" (1996). Honors Projects. 15. https://digitalcommons.iwu.edu/chem_honproj/15 This Article is protected by copyright and/or related rights. It has been brought to you by Digital Commons @ IWU with permission from the rights-holder(s). You are free to use this material in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This material has been accepted for inclusion by faculty at Illinois Wesleyan University. For more information, please contact [email protected]. ©Copyright is owned by the author of this document. Pursuit of a Chiral Amino Aldehyde Intermediate in the Synthesis of (+)-Obafluorin, a p-Lactone Antibiotic Jim Cwik Dr. Jeffrey A. Frick, Research Advisor Submitted in Partial Fulfillment of the Requirement for Research Honors in Chemistry and Chemistry 499 Illinois Wesleyan University April 26, 1996 - Table of Contents I. List of Spectral Data , 2 II. Abstract. 3 III. Background 4 IV. Introduction 6 V. -
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 -
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. -
Fischer Carbene Complexes in Organic Synthesis Ke Chen 1/31/2007
Baran Group Meeting Fischer Carbene Complexes in Organic Synthesis Ke Chen 1/31/2007 Ernst Otto Fischer (1918 - ) Other Types of Stabilized Carbenes: German inorganic chemist. Born in Munich Schrock carbene, named after Richard R. Schrock, is nucleophilic on November 10, 1918. Studied at Munich at the carbene carbon atom in an unpaired triplet state. Technical University and spent his career there. Became director of the inorganic Comparision of Fisher Carbene and Schrock carbene: chemistry institute in 1964. In the 1960s, discovered a metal alkylidene and alkylidyne complexes, referred to as Fischer carbenes and Fischer carbynes. Shared the Nobel Prize in Chemistry with Geoffery Wilkinson in 1973, for the pioneering work on the chemistry of organometallic compounds. Schrock carbenes are found with: Representatives: high oxidation states Isolation of first transition-metal carbene complex: CH early transition metals Ti(IV), Ta(V) 2 non pi-acceptor ligands Cp2Ta CH N Me LiMe Me 2 2 non pi-donor substituents CH3 (CO) W CO (CO)5W 5 (CO)5W A.B. Charette J. Am. Chem. Soc. 2001, 123, 11829. OMe O E. O. Fischer, A. Maasbol, Angew. Chem. Int. Ed., 1964, 3, 580. Persistent carbenes, isolated as a crystalline solid by Anthony J. Arduengo in 1991, can exist in the singlet state or the triplet state. Representative Fischer Carbenes: W(CO) Cr(CO) 5 5 Fe(CO)4 Mn(CO)2(MeCp) Co(CO)3SnPh3 Me OMe Ph Ph Ph NEt2 Ph OTiCp2Cl Me OMe Foiled carbenes were defined as "systems where stabilization is Fischer carbenes are found with : obtained by the inception of the facile reaction which is foiled by the impossibility of attaining the final product geometry". -
UNITED STATES PATENT Office PREPARATION of BETA-Akoxy MONO Carboxylcacds Frederick E
Patented July 4, 1944 UNITED STATES PATENT office PREPARATION OF BETA-AKOxY MONO CARBOXYLCACDs Frederick E. King, Akron, Ohio, assignor to The B. F. Goodrich Company, New corporation of New York . York, N. Y., a No Drawing. Application August 5, 1941, Sera No. 405,512 4 Claims. (CL 260-535) This invention relates to a novel process for at least one hydrogen atom on the alpha carbon the preparation of beta-alkoxy derivatives of atom, for example, beta-lactones of saturated monocarboxylic acids, particularly beta-alkoxy aliphatic monocarboxylic acids such as beta-hy derivatives of saturated aliphatic monocarboxylic droxypropionic acid lactone, commonly known as acids such as beta-alkoxy proponic acids, and to 5 hydracrylic acid lactone, beta-hydroxy butyric the conversion of such acids into alkyl esters of acid lactone, alpha-methyl hydracrylic acid lac alpha beta unsaturated monocarboxylic acids tone, beta-hydroxy n-valeric acid actone, beta such as the alkyl esters of acrylic and meth hydroxy alpha-methyl butyric acid lactone, al acrylic acids. - - pharethyl hydracrylic acid lactone, beta-hydroxy In a copending application Serial No. 393,671, 0 isovaleric acid lactone, beta-hydroxy n-caproic filed May 15, 1941, an economical method of pre acid lactone, beta-hydroxy alpha-methyl valeric paring lactones of beta-hydroxy Carboxylic acids acid lactone, beta-methyl beta-ethyl hydracrylic from the reaction of a ketene with a carbonyl acid lactone, alpha-methyl beta-ethylhydracrylic compound such as an aldehyde or ketone has acid lactone, alpha-propyl -
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 . -
Chapter 7, Haloalkanes, Properties and Substitution Reactions of Haloalkanes Table of Contents 1
Chapter 7, Haloalkanes, Properties and Substitution Reactions of Haloalkanes Table of Contents 1. Alkyl Halides (Haloalkane) 2. Nucleophilic Substitution Reactions (SNX, X=1 or 2) 3. Nucleophiles (Acid-Base Chemistry, pka) 4. Leaving Groups (Acid-Base Chemistry, pka) 5. Kinetics of a Nucleophilic Substitution Reaction: An SN2 Reaction 6. A Mechanism for the SN2 Reaction 7. The Stereochemistry of SN2 Reactions 8. A Mechanism for the SN1 Reaction 9. Carbocations, SN1, E1 10. Stereochemistry of SN1 Reactions 11. Factors Affecting the Rates of SN1 and SN2 Reactions 12. --Eliminations, E1 and E2 13. E2 and E1 mechanisms and product predictions In this chapter we will consider: What groups can be replaced (i.e., substituted) or eliminated The various mechanisms by which such processes occur The conditions that can promote such reactions Alkyl Halides (Haloalkane) An alkyl halide has a halogen atom bonded to an sp3-hybridized (tetrahedral) carbon atom The carbon–chlorine and carbon– bromine bonds are polarized because the halogen is more electronegative than carbon The carbon-iodine bond do not have a per- manent dipole, the bond is easily polarizable Iodine is a good leaving group due to its polarizability, i.e. its ability to stabilize a charge due to its large atomic size Generally, a carbon-halogen bond is polar with a partial positive () charge on the carbon and partial negative () charge on the halogen C X X = Cl, Br, I Different Types of Organic Halides Alkyl halides (haloalkanes) sp3-hybridized Attached to Attached to Attached -
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. -
Catalytic, Asymmetric Synthesis of Β-Lactams
J. Am. Chem. Soc. 2000, 122, 7831-7832 7831 Catalytic, Asymmetric Synthesis of â-Lactams Table 1. Diastereoselectivity in the Nucleophile-Catalyzed Reaction of Methylphenylketene 3b with Imine 2a Andrew E. Taggi, Ahmed M. Hafez, Harald Wack, Brandon Young, William J. Drury, III, and Thomas Lectka* Department of Chemistry Johns Hopkins UniVersity, 3400 North Charles Street Baltimore, Maryland 21218 ReceiVed May 22, 2000 The paramount importance of â-lactams (1) to pharmaceutical science and biochemistry has been well established.1 New chiral â-lactams are in demand as antibacterial agents, and their recent discovery as mechanism-based serine protease inhibitors2 has kept interest in their synthesis at a high level.3 However, most chiral methodology is auxiliary-based; only one catalytic, asymmetric synthesis of the â-lactam ring system is known, affording product a - ° in modest enantioselectivity.4 Many asymmetric auxiliary-based Reactions run with 10 mol% catalyst at 78 C and allowed to slowly warm to room temperature overnight. â-lactam syntheses rely on the reaction of imines with ketenes, a 3 process that generally proceeds without a catalyst. We recently catalyzed by 10 mol % bifunctional amine 4a gave a cis/trans dr accomplished a catalyzed reaction of imines and ketenes by of 3/97. A significant role for the H-bond contact in 4a is sug- making the imine component non-nucleophilic, as in electron- gested, as the sterically similar catalyst 4b, which does not contain deficient imino ester 2a.5 In this contribution, we report the ) 6 a hydrogen bond donor, gave low diastereoselectivity (dr 34/ catalytic, asymmetric reaction of imine 2a and ketenes 3 to 66). -
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.