Carbonyl Chemistry - Fundamentals
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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 -
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. -
Aldehydes and Ketones
12 Aldehydes and Ketones Ethanol from alcoholic beverages is first metabolized to acetaldehyde before being broken down further in the body. The reactivity of the carbonyl group of acetaldehyde allows it to bind to proteins in the body, the products of which lead to tissue damage and organ disease. Inset: A model of acetaldehyde. (Novastock/ Stock Connection/Glow Images) KEY QUESTIONS 12.1 What Are Aldehydes and Ketones? 12.8 What Is Keto–Enol Tautomerism? 12.2 How Are Aldehydes and Ketones Named? 12.9 How Are Aldehydes and Ketones Oxidized? 12.3 What Are the Physical Properties of Aldehydes 12.10 How Are Aldehydes and Ketones Reduced? and Ketones? 12.4 What Is the Most Common Reaction Theme of HOW TO Aldehydes and Ketones? 12.1 How to Predict the Product of a Grignard Reaction 12.5 What Are Grignard Reagents, and How Do They 12.2 How to Determine the Reactants Used to React with Aldehydes and Ketones? Synthesize a Hemiacetal or Acetal 12.6 What Are Hemiacetals and Acetals? 12.7 How Do Aldehydes and Ketones React with CHEMICAL CONNECTIONS Ammonia and Amines? 12A A Green Synthesis of Adipic Acid IN THIS AND several of the following chapters, we study the physical and chemical properties of compounds containing the carbonyl group, C O. Because this group is the functional group of aldehydes, ketones, and carboxylic acids and their derivatives, it is one of the most important functional groups in organic chemistry and in the chemistry of biological systems. The chemical properties of the carbonyl group are straightforward, and an understanding of its characteristic reaction themes leads very quickly to an understanding of a wide variety of organic reactions. -
Chemistry 0310 - Organic Chemistry 1 Chapter 6
Dr. Peter Wipf Chemistry 0310 - Organic Chemistry 1 Chapter 6. SN2 Reactions Nucleophilic substitution reactions occur when nucleophiles (electron-rich species) displace leaving groups on electrophiles (electron-poor species). The net result is the substitution of one group for another bonded to a carbon atom. Nucleophilicity is increased by a negative charge and an increase in the polarizability. The greater the size and the lower the electronegativity of an atom, the greater its polarizability. Leaving groups are stable species that can be detached with their bonding electrons from a molecule during reaction. Most good leaving groups are the conjugate bases of strong acids. Sulfonates (mesylates, tosylates, triflates, etc.) are popular leaving groups since they can be readily obtained from alcohols. Solvents also influence nucleophilicity. SN2 reactions are second-order reactions whose rates depend o the concentration of both the alkyl halide and the nucleophile. The transition state of the one-step SN2 process involves a trigonal bipyramidal carbon and results in an overall inversion of configuration. The order of reactivity of alkyl halides and alkyl sulfonates in SN2 reactions is CH3>1°>2°>3°. The activation energy, DG‡, determines the rate of a reaction: k = koexp(-DG‡/RT). The overall change in free energy, DG, determines the position of the thermodynamic equilibrium. A positive sign of DG is characteristic for an endergonic reaction, a negative DG is found for an exergonic process. The rate of a reaction can be measured and provides information about its mechanism. The reaction order is the sum of the exponents in the rate equation. Relative Leaving Group Abilities: Leaving Group Common Name krel AcO acetate 1 x 10-10 Cl chloride 0.0001 Br bromide 0.001 I iodide 0.01 O mesylate 1.00 H3C S O O O tosylate 0.70 H3C S O O O brosylate 2.62 Br S O O O nosylate 13 O2N S O O O fluorosulfate 29,000 F S O O O triflate 56,000 CF3 S O O O nonaflate 120,000 C4F9 S O O. -
Chapter 14 – Aldehydes and Ketones
Chapter 14 – Aldehydes and Ketones 14.1 Structures and Physical Properties of Aldehydes and Ketones Ketones and aldehydes are related in that they each possess a C=O (carbonyl) group. They differ in that the carbonyl carbon in ketones is bound to two carbon atoms (RCOR’), while that in aldehydes is bound to at least one hydrogen (H2CO and RCHO). Thus aldehydes always place the carbonyl group on a terminal (end) carbon, while the carbonyl group in ketones is always internal. Some common examples include (common name in parentheses): O O H HH methanal (formaldehyde) trans-3-phenyl-2-propenal (cinnamaldehyde) preservative oil of cinnamon O O propanone (acetone) 3-methylcyclopentadecanone (muscone) nail polish remover a component of one type of musk oil Simple aldehydes (e.g. formaldehyde) typically have an unpleasant, irritating odor. Aldehydes adjacent to a string of double bonds (e.g. 3-phenyl-2-propenal) frequently have pleasant odors. Other examples include the primary flavoring agents in oil of bitter almond (Ph- CHO) and vanilla (C6H3(OH)(OCH3)(CHO)). As your book says, simple ketones have distinctive odors (similar to acetone) that are typically not unpleasant in low doses. Like aldehydes, placing a collection of double bonds adjacent to a ketone carbonyl generally makes the substance more fragrant. The primary flavoring agent in oil of caraway is just a such a ketone. 2 O oil of carraway Because the C=O group is polar, small aldehydes and ketones enjoy significant water solubility. They are also quite soluble in typical organic solvents. 14.2 Naming Aldehydes and Ketones Aldehydes The IUPAC names for aldehydes are obtained by using rules similar to those we’ve seen for other functional groups (e.g. -
Carbonyl Compounds
CARBONYL COMPOUNDS PART-4, PPT-4, SEM-3 Dr. Kalyan Kumar Mandal Associate Professor St. Paul’s C. M. College Kolkata CONTENTS: CARBONYL COMPOUNDS PART-4 • Formation of Acetal/Ketal • Formation of Thioacetal Reaction of Carbonyl Compounds with Alcohols • Carbonyl compounds react with alcohols. The product of this reaction is known as a hemiacetal, because it is halfway to an acetal. This reaction is analogous to hydrate formation from aldehydes and ketones. The mechanism follows in the footsteps of hydrate formation: ROH is used instead of HOH (water). This Lecture is prepared by Dr. K. K. Mandal, SPCMC, Kolkata Formation of Cyclic Hemiacetal • Hemiacetal formation is reversible, and they are stabilized by the same special structural features as those of hydrates. However, hemiacetals can also gain stability by being cyclic. • Cyclic hemiacetal is formed when the carbonyl group and the attacking hydroxyl group are part of the same molecule. The reaction is an intramolecular (within the same molecule) addition, as opposed to the intermolecular (between two molecules) ones. This is an example of ring-chain tautomerism. This Lecture is prepared by Dr. K. K. Mandal, SPCMC, Kolkata Formation of Cyclic Hemiacetal • Although the cyclic hemiacetal is more stable, it is still in equilibrium with some of the open-chain hydroxyaldehyde form. Its stability, and how easily it forms, depend on the size of the ring. • Five- and six-membered rings involve less strain (their bonds are free to adopt 109° or 120° angles) in comparison to the three- membered rings, and therefore five or six-membered hemiacetals are very common. -
Leaving Group of Substrate Important
1 Recap... • Last two lectures we looked at substitution reactions • We found that there we two (extreme) mechanisms • SN1 H H H H H PhS R H R Br R SPh Br • And SN2 H H H H PhS + Br R Br PhS R • We looked at many of the factors that influenced which ..mechanism was operating... • Now we will turn our attention to elimination reactions 2 Elimination reactions NaOH NaOH or low Br H2O OH concentration • You have seen SN1 substitution • Reaction not sped up by altering nucleophile - it is not in RDS • In fact if we increase the amount / concentration of nucleophile we get the following... high O H + + + Br Br OH concentration H H • We observe an elimination reaction • Overall HBr is lost from the molecule • Isn't chemistry fun - these are the same conditions as substitution! • Next two lectures will look at the mechanisms for elimination • And how we control the nature of the reaction we observe... 3 Elimination, bimolecular E2 O H Br HO Br H H • E2 - Elimination bimolecular or 2nd order reaction • 2 molecules in the RDS or transition state H H H H H C H C H H C Br Br H O H C H O H C C H H H H C H C H H H • Two molecules in the rate determining step • So both the base and the substrate control the reaction • Both carbon skeleton & leaving group of substrate important In substitutions nucleophile acts as a nucleophile & attacks carbon In eliminations nucleophile acts as a base & attacks proton 4 Elimination, bimolecular E2: MO • Little confusing as need bonding & anti-bonding in same diagram! • Orbitals need to be parallel for maximum overlap -
Carbonyl Chemistry I: Additions to Carbonyl Groups
Paul Bracher Chem 30 – Section 4 Carbonyl Chemistry I: Additions to Carbonyl Groups Section Agenda 1) Lessons from Exam I, Course Feedbeck Mechanism on Web Site 2) Carbonyl Groups: Structure, Bonding, Molecular Orbitals, Geometry, Reactivity 3) Handout: In-Section Problem Set 4) Handout: In-Section Solution Set 5) Weekly Office Hours: Thursday, 3-4PM and 8-9PM, in Bauer Lobby Structure and Bonding · Carbonyl carbons are roughly sp2 hybridized Molecular Orbital Picture and planar with bond angles near 120 degrees bonding p orbital antibonding p* orbital · The C=O p bond is formed by the overlap of two unhybridized p orbitals. The bond is polarized due to the different electronegativities of carbon and oxygen. 105 o Resonance Model O O Bürgi-Dunitz angle · Another way to picture carbonyl groups is I II through an MO picture. Since the coefficient of · Resonance form II suggests that the carbon pO’s contribution is greater in pC=O, then atom is surrounded by less negative charge conservation of blending atomic orbitals into density than oxygen, rendering the carbon more molecular orbitals tells you that pC must be a electrophilic. larger contributor to the p*C=O orbital. · When reagents add to carbonyl double bonds, · The larger coefficient on oxygen in the filled the nucleophile attacks the carbon atom. orbital explains why the oxygen atom behaves as a Lewis base (it commonly complexes with · Due to the increased negative charge density Lewis acids). The larger coefficient on carbon on oxygen, Lewis acids (such as protons) in the empty antibonding orbital explains why it commonly complex with oxygen. -
2 Reactions Observed with Alkanes Do Not Occur with Aromatic Compounds 2 (SN2 Reactions Never Occur on Sp Hybridized Carbons!)
Reactions of Aromatic Compounds Aromatic compounds are stabilized by this “aromatic stabilization” energy Due to this stabilization, normal SN2 reactions observed with alkanes do not occur with aromatic compounds 2 (SN2 reactions never occur on sp hybridized carbons!) In addition, the double bonds of the aromatic group do not behave similar to alkene reactions Aromatic Substitution While aromatic compounds do not react through addition reactions seen earlier Br Br Br2 Br2 FeBr3 Br With an appropriate catalyst, benzene will react with bromine The product is a substitution, not an addition (the bromine has substituted for a hydrogen) The product is still aromatic Electrophilic Aromatic Substitution Aromatic compounds react through a unique substitution type reaction Initially an electrophile reacts with the aromatic compound to generate an arenium ion (also called sigma complex) The arenium ion has lost aromatic stabilization (one of the carbons of the ring no longer has a conjugated p orbital) Electrophilic Aromatic Substitution In a second step, the arenium ion loses a proton to regenerate the aromatic stabilization The product is thus a substitution (the electrophile has substituted for a hydrogen) and is called an Electrophilic Aromatic Substitution Energy Profile Transition states Transition states Intermediate Potential E energy H Starting material Products E Reaction Coordinate The rate-limiting step is therefore the formation of the arenium ion The properties of this arenium ion therefore control electrophilic aromatic substitutions (just like any reaction consider the stability of the intermediate formed in the rate limiting step) 1) The rate will be faster for anything that stabilizes the arenium ion 2) The regiochemistry will be controlled by the stability of the arenium ion The properties of the arenium ion will predict the outcome of electrophilic aromatic substitution chemistry Bromination To brominate an aromatic ring need to generate an electrophilic source of bromine In practice typically add a Lewis acid (e.g. -
Organic Chemistry/Fourth Edition: E-Text
CHAPTER 17 ALDEHYDES AND KETONES: NUCLEOPHILIC ADDITION TO THE CARBONYL GROUP O X ldehydes and ketones contain an acyl group RC± bonded either to hydrogen or Ato another carbon. O O O X X X HCH RCH RCRЈ Formaldehyde Aldehyde Ketone Although the present chapter includes the usual collection of topics designed to acquaint us with a particular class of compounds, its central theme is a fundamental reaction type, nucleophilic addition to carbonyl groups. The principles of nucleophilic addition to alde- hydes and ketones developed here will be seen to have broad applicability in later chap- ters when transformations of various derivatives of carboxylic acids are discussed. 17.1 NOMENCLATURE O X The longest continuous chain that contains the ±CH group provides the base name for aldehydes. The -e ending of the corresponding alkane name is replaced by -al, and sub- stituents are specified in the usual way. It is not necessary to specify the location of O X the ±CH group in the name, since the chain must be numbered by starting with this group as C-1. The suffix -dial is added to the appropriate alkane name when the com- pound contains two aldehyde functions.* * The -e ending of an alkane name is dropped before a suffix beginning with a vowel (-al) and retained be- fore one beginning with a consonant (-dial). 654 Back Forward Main Menu TOC Study Guide TOC Student OLC MHHE Website 17.1 Nomenclature 655 CH3 O O O O CH3CCH2CH2CH CH2 CHCH2CH2CH2CH HCCHCH CH3 4,4-Dimethylpentanal 5-Hexenal 2-Phenylpropanedial When a formyl group (±CHœO) is attached to a ring, the ring name is followed by the suffix -carbaldehyde. -
Reactions of Aromatic Compounds Just Like an Alkene, Benzene Has Clouds of Electrons Above and Below Its Sigma Bond Framework
Reactions of Aromatic Compounds Just like an alkene, benzene has clouds of electrons above and below its sigma bond framework. Although the electrons are in a stable aromatic system, they are still available for reaction with strong electrophiles. This generates a carbocation which is resonance stabilized (but not aromatic). This cation is called a sigma complex because the electrophile is joined to the benzene ring through a new sigma bond. The sigma complex (also called an arenium ion) is not aromatic since it contains an sp3 carbon (which disrupts the required loop of p orbitals). Ch17 Reactions of Aromatic Compounds (landscape).docx Page1 The loss of aromaticity required to form the sigma complex explains the highly endothermic nature of the first step. (That is why we require strong electrophiles for reaction). The sigma complex wishes to regain its aromaticity, and it may do so by either a reversal of the first step (i.e. regenerate the starting material) or by loss of the proton on the sp3 carbon (leading to a substitution product). When a reaction proceeds this way, it is electrophilic aromatic substitution. There are a wide variety of electrophiles that can be introduced into a benzene ring in this way, and so electrophilic aromatic substitution is a very important method for the synthesis of substituted aromatic compounds. Ch17 Reactions of Aromatic Compounds (landscape).docx Page2 Bromination of Benzene Bromination follows the same general mechanism for the electrophilic aromatic substitution (EAS). Bromine itself is not electrophilic enough to react with benzene. But the addition of a strong Lewis acid (electron pair acceptor), such as FeBr3, catalyses the reaction, and leads to the substitution product. -
AROMATIC NUCLEOPHILIC SUBSTITUTION-PART -2 Electrophilic Substitution
Dr. Tripti Gangwar AROMATIC NUCLEOPHILIC SUBSTITUTION-PART -2 Electrophilic substitution ◦ The aromatic ring acts as a nucleophile, and attacks an added electrophile E+ ◦ An electron-deficient carbocation intermediate is formed (the rate- determining step) which is then deprotonated to restore aromaticity ◦ electron-donating groups on the aromatic ring (such as -OH, -OCH3, and alkyl) make the reaction faster, since they help to stabilize the electron-poor carbocation intermediate ◦ Lewis acids can make electrophiles even more electron-poor (reactive), increasing the reaction rate. For example FeBr3 / Br2 allows bromination to occur at a useful rate on benzene, whereas Br2 by itself is slow). In fact, a substitution reaction does occur! (But, as you may suspect, this isn’t an electrophilic aromatic substitution reaction.) In this substitution reaction the C-Cl bond breaks, and a C-O bond forms on the same carbon. The species that attacks the ring is a nucleophile, not an electrophile The aromatic ring is electron-poor (electrophilic), not electron rich (nucleophilic) The “leaving group” is chlorine, not H+ The position where the nucleophile attacks is determined by where the leaving group is, not by electronic and steric factors (i.e. no mix of ortho– and para- products as with electrophilic aromatic substitution). In short, the roles of the aromatic ring and attacking species are reversed! The attacking species (CH3O–) is the nucleophile, and the ring is the electrophile. Since the nucleophile is the attacking species, this type of reaction has come to be known as nucleophilic aromatic substitution. n nucleophilic aromatic substitution (NAS), all the trends you learned in electrophilic aromatic substitution operate, but in reverse.