Alkenes and Alkynes
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Prebiological Evolution and the Metabolic Origins of Life
Prebiological Evolution and the Andrew J. Pratt* Metabolic Origins of Life University of Canterbury Keywords Abiogenesis, origin of life, metabolism, hydrothermal, iron Abstract The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. The initial protometabolism was based on positive feedback loops associated with in situ carbon fixation in which the initial protometabolites modified the catalytic capacity and mobility of metal-based catalysts, especially iron-sulfur centers. A number of selection mechanisms, including catalytic efficiency and specificity, hydrolytic stability, and selective solubilization, are proposed as key determinants for autocatalytic reproduction exploited in protometabolic evolution. This evolutionary process led from autocatalytic networks within preexisting compartments to discrete, reproducing, mobile vesicular protocells with the capacity to use soluble sugar phosphates and hence the opportunity to develop nucleic acids. Fidelity of information transfer in the reproduction of these increasingly complex autocatalytic networks is a key selection pressure in prebiological evolution that eventually leads to the selection of nucleic acids as a digital information subsystem and hence the emergence of fully functional chemotons capable of Darwinian evolution. 1 Introduction: Chemoton Subsystems and Evolutionary Pathways Living cells are autocatalytic entities that harness redox energy via the selective catalysis of biochemical transformations. -
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 . -
Nucleophilic Aromatic Substitution
NUCLEOPHILIC AROMATIC SUBSTITUTION Ms. Prerana Sanas M.Pharm (Pharmceutical Chemistry) Asst.Professor, NCRD’s Sterling Institute of Pharmacy Nerul Navi Mumbai Nucleophilic aromatic substitution results in the substitution of a halogen X on a benzene ring by a nucleophile (:Nu– ). Aryl halides undergo a limited number of substitution reactions with strong nucleophiles. NAS occurs by two mechanisms i) Bimoleccular displacement (Addition –Elimination) ii) Benzyne Formation( Elimination –Addition) 7/5/2019 Ms.Prerana Sanas 2 Bimolecular displacement (Addition – Elimination) Aryl halides with strong electron-withdrawing groups (such as NO2) on the ortho or para positions react with nucleophiles to afford substitution products. For example, treatment of p-chloronitrobenzene with hydroxide (– OH) affords p-nitrophenol by replacement of Cl by OH. Nucleophilic aromatic substitution occurs with a variety of strong nucleophiles, including – OH, – OR, – NH2, – SR, and in some cases, neutral nucleophiles such as NH3 and RNH2 . 7/5/2019 Ms.Prerana Sanas 3 Mechanism…… The mechanism of these reactions has two steps: Step i) Addition of the nucleophile (:Nu– ) forms a resonance-stabilized carbanion with a new C – Nu bond—three resonance structures can be drawn. • Step [1] is rate-determining since the aromaticity of the benzene ring is lost. In Step ii) loss of the leaving group re-forms the aromatic ring. This step is fast because the aromaticity of the benzene ring is restored. 7/5/2019 Ms.Prerana Sanas 4 Factors affecting Bimolecular displacement Increasing the number of electron-withdrawing groups increases the reactivity of the aryl halide. Electron-withdrawing groups stabilize the intermediate carbanion, and by the Hammond postulate, lower the energy of the transition state that forms it. -
Chemical Kinetics HW1 (Kahn, 2010)
Chemical Kinetics HW1 (Kahn, 2010) Question 1. (6 pts) A reaction with stoichiometry A = P + 2Q was studied by monitoring the concentration of the reactant A as a function of time for eighteen minutes. The concentration determination method had a maximum error of 6 M. The following concentration profile was observed: Time (min) Conc (mM) 1 0.9850 2 0.8571 3 0.7482 4 0.6549 5 0.5885 6 0.5183 7 0.4667 8 0.4281 9 0.3864 10 0.3557 11 0.3259 12 0.3037 13 0.2706 14 0.2486 15 0.2355 16 0.2188 17 0.2111 18 0.1930 Determine the reaction order and calculate the rate constant for decomposition of A. What can be said about the mechanism or molecularity of this reaction? Question 2. (4 pts) Solve problem 2 on pg 31 in your textbook (House) using both linear and non-linear regression. Provide standard errors for the rate constant and half-life based on linear and non-linear fits. Below is the data set for your convenience: dataA = {{0, 0.5}, {10, 0.443}, {20,0.395}, {30,0.348}, {40,0.310}, {50,0.274}, {60,0.24}, {70,0.212}, {80,0.190}, {90,0.171}, {100,0.164}} Question 3. (3 pts) Solve problem 3 on pg 32 in your textbook (House). Question 4. (7 pts) The authors of the paper “Microsecond Folding of the Cold Shock Protein Measured by a Pressure-Jump Technique” suggest that the activated state of folding of CspB follows Hammond- type behavior. -
Organic Chemistry PEIMS Code: N1120027 Abbreviation: ORGCHEM Number of Credits That May Be Earned: 1/2-1
Course: Organic Chemistry PEIMS Code: N1120027 Abbreviation: ORGCHEM Number of credits that may be earned: 1/2-1 Brief description of the course (150 words or less): Organic chemistry is an introductory course that is designed for the student who intends to continue future study in the sciences. The student will learn the concepts and applications of organic chemistry. Topics covered include aliphatic and aromatic compounds, alcohols, aldehydes, ketones, acids, ethers, amines, spectra, and stereochemistry. A brief introduction into biochemistry is also provided. The laboratory experiments will familiarize the student with the important laboratory techniques, specifically spectroscopy. Traditional high school chemistry courses focus on the inorganic aspects of chemistry whereas organic chemistry introduces the student to organic compounds and their properties, mechanisms of formations, and introduces the student to laboratory techniques beyond the traditional high school chemistry curriculum. Essential Knowledge and Skills of the course: (a) General requirements. This course is recommended for students in Grades 11-12. The recommended prerequisite for this course is AP Chemistry. (b) Introduction. Organic chemistry is designed to introduce students to the fundamental concepts of organic chemistry and key experimental evidence and data, which support these concepts. Students will learn to apply these data and concepts to chemical problem solving. Additionally, students will learn that organic chemistry is still evolving by reading about current breakthroughs in the field. Finally, students will gain appreciation for role that organic chemistry plays in modern technological developments in diverse fields, ranging from biology to materials science. (c) Knowledge and skills. (1) The student will be able to write both common an IUPAC names for the hydrocarbon. -
Lecture 5 Diastereoselective Addition Into Carbonyl Compounds
Lecture 5 Diastereoselective Addition into Carbonyl Compounds Containing α-Stereogenic Centres Learning outcomes: by the end of this lecture, and after answering the associated problems, you will be able to: 1. use the Felkin-Anh T.S. to predict the stereochemical outcome of reactions carried out on carbonyl compounds that possess an α-stereogenic centre; 2. rationalise the preferential adoption of a Felkin-Anh T.S. in nucleophilic addition reactions on steric and stereoelectronic grounds; 3. understand how the presence of an α-electron-withdrawing substituent affects the Felkin-Anh T.S.; 4. use the Felkin-Anh T.S. to prepare 1,2-syn diols from α-alkoxy ketones; 5. use the Cram chelation model to prepare 1,2-anti diols from α-alkoxy ketones. Stereoselective Addition of Nucleophiles into Ketones and Aldehydes containing α- Stereogenic Centres The addition of a nucleophile into a chiral ketone or aldehyde provides diastereoisomers. When the stereogenic centres in the substrate are close to the reacting carbonyl group (e.g. 1,2-disposed), then it is often possible to exploit this stereochemical information to control the stereoselectivity of the addition reaction. This method for controlling the stereochemical outcome of a reaction is known as substrate control. A number of models have been developed for predicting the stereochemical outcome of this type of reaction. Felkin-Anh Model Consider a carbonyl compound containing an α-stereogenic centre in which the three substituents at the α-site are well differentiated in size: O HO Nu Nu OH RL Nu RL RL R R R S M S M S RM R R R R R RS = small substituent RM = medium-sized substituent RL = large substituent Of the two diastereoisomeric alcohol addition products, one will be formed to a greater extent than the other. -
HISTORICAL ASPECTS of ORGANIC CHEMISTRY TEACHING (On the Example of Chemistry Direction of Higher Educational Institutions)
Journal of Critical Reviews ISSN- 2394-5125 Vol 7, Issue 13, 2020 CONCEPTUAL - HISTORICAL ASPECTS OF ORGANIC CHEMISTRY TEACHING (on the example of chemistry direction of Higher educational institutions) Rajabov Khudayor Madrimovich Uzbekistan, Khorasm region, Rajabov Khudayor Madrimovich, Doctor of philosophy (PhD) on pedagogical sciences, Urganch State University E-mail: [email protected] Received: 16.04.2020 Revised: 18.05.2020 Accepted: 13.06.2020 Abstract. The article reveals the historical approach on the teaching of organic chemistry in pedagogical universities. The development of modern trends and general competencies of students on the basis of historical approach, the creation of educational motivation, the focus on independent research and training of creative specialists are the most important directions. In this regard, it is important to improve the technology for organizing the educational process on the basis of historical principles in the system of training future chemistry teachers, to improve the mechanisms on the methodological support, to fulfill the system of competencies and cyclic diagnostics. Keywords: historical approach, organic chemistry, conceptual - historical aspects, professional competence, principle of historicism, methodology, self-improvement, innovation, non-historical, positive attitude, extracurricular activities. © 2020 by Advance Scientific Research. This is an open-access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) DOI: http://dx.doi.org/10.31838/jcr.07.13.129 -
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. -
The Arene–Alkene Photocycloaddition
The arene–alkene photocycloaddition Ursula Streit and Christian G. Bochet* Review Open Access Address: Beilstein J. Org. Chem. 2011, 7, 525–542. Department of Chemistry, University of Fribourg, Chemin du Musée 9, doi:10.3762/bjoc.7.61 CH-1700 Fribourg, Switzerland Received: 07 January 2011 Email: Accepted: 23 March 2011 Ursula Streit - [email protected]; Christian G. Bochet* - Published: 28 April 2011 [email protected] This article is part of the Thematic Series "Photocycloadditions and * Corresponding author photorearrangements". Keywords: Guest Editor: A. G. Griesbeck benzene derivatives; cycloadditions; Diels–Alder; photochemistry © 2011 Streit and Bochet; licensee Beilstein-Institut. License and terms: see end of document. Abstract In the presence of an alkene, three different modes of photocycloaddition with benzene derivatives can occur; the [2 + 2] or ortho, the [3 + 2] or meta, and the [4 + 2] or para photocycloaddition. This short review aims to demonstrate the synthetic power of these photocycloadditions. Introduction Photocycloadditions occur in a variety of modes [1]. The best In the presence of an alkene, three different modes of photo- known representatives are undoubtedly the [2 + 2] photocyclo- cycloaddition with benzene derivatives can occur, viz. the addition, forming either cyclobutanes or four-membered hetero- [2 + 2] or ortho, the [3 + 2] or meta, and the [4 + 2] or para cycles (as in the Paternò–Büchi reaction), whilst excited-state photocycloaddition (Scheme 2). The descriptors ortho, meta [4 + 4] cycloadditions can also occur to afford cyclooctadiene and para only indicate the connectivity to the aromatic ring, and compounds. On the other hand, the well-known thermal [4 + 2] do not have any implication with regard to the reaction mecha- cycloaddition (Diels–Alder reaction) is only very rarely nism. -
NEW TANDEM REACTIONS INVOLVING NUCLEOPHILIC AROMATIC SUBSTITUTION by JAMES ERVIN SCHAMMERHORN III Associates of Science Murray
NEW TANDEM REACTIONS INVOLVING NUCLEOPHILIC AROMATIC SUBSTITUTION By JAMES ERVIN SCHAMMERHORN III Associates of Science Murray State College Tishomingo, Oklahoma 2003 Bachelor of Science in Chemistry Oklahoma State University Stillwater, Oklahoma 2006 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May, 2011 1 NEW TANDEM REACTIONS INVOLVING NUCLEOPHILIC ARMOMATIC SUBSTITUTION Thesis Approved: Dr. Richard Bunce Thesis Adviser Dr. K. Darrell Berlin Dr. Ziad El-Rassi Dr. Nicholas Materer Dr. Andrew Mort Dr. Mark E. Payton Dean of the Graduate College ii ACKNOWLEDGMENTS I would like to express my sincere gratitude to Dr. R. A. Bunce, my research advisor, my graduate committee chairman and my friend. I have learned many valuable lessons working alongside him in his research laboratory. His ability to teach both organic theory and laboratory techniques have been instrumental in my research at Oklahoma State University. I am immensely thankful for his support, guidance and patience to me during the course of this research. His unique sense of humor always makes me laugh and makes it a joy to come to lab. I would also like to thank my committee members, Drs. K. D. Berlin, Z. El Rassi, N. F. Materer, and A. J. Mort their acceptance to be on my committee. Their insights into research and graduate life have been invaluable during my graduate career. I am especially grateful to Dr. Berlin for sharing his wealth of organic chemistry knowledge with me during the course of my research. Also, to Dr. -
Aromatic Compounds
OCR Chemistry A Aromatic Compounds Aromatic Compounds Naming Aromatic compounds contain one or more benzene rings (while aliphatic compounds do not contain benzene rings). Another term for a compound containing a benzene ring is arene. The basic benzene ring, C6H6 is commonly represented as a hexagon with a ring inside. You should be aware that there is a hydrogen at each corner although this is not normally shown. N.B. it is OK to use benzene in this form in structural formulae too! Arenes occur naturally in many substances, and are present in coal and crude oil. Aspirin, for example, is an aromatic compound, an arene: HO O O CH 3 O Naming of substances based on benzene follows familiar rules: CH Br NO 3 2 benzene methylbenzene bromobenzene nitrobenzene Numbers are needed to identify the positions of substituents. The carbons around the ring are numbered from 1-6 consecutively and the name which gives the lowest number(s) is chosen: CH3 CH3 Cl Br Cl Br 2-bromomethylbenzene 4-bromomethylbenzene 1,2-dichlorobenzene Cl Cl Cl 1,3,5-trichlorobenzene Page 1 OCR Chemistry A Aromatic Compounds Determining the structure of benzene (historical) 1825 – substance first isolated by Michael Faraday, who also determined its empirical formula as CH 1834 – RFM of 78 and molecular formula of C6H6 determined H H H C C C Much speculation over the structure. Many suggested structures like: C C C H H H 1865 – Kekulé publishes suggestion of a ring with alternating double and single bonds: H H C H C C displayed C C skeletal H C H H This model persisted until 1922, but not all chemists accepted the structure because it failed to explain the chemical and physical properties of benzene fully: if C=C bonds were present as Kekulé proposed, then benzene would react like alkenes. -
Introduction to Alkenes and Alkynes in an Alkane, All Covalent Bonds
Introduction to Alkenes and Alkynes In an alkane, all covalent bonds between carbon were σ (σ bonds are defined as bonds where the electron density is symmetric about the internuclear axis) In an alkene, however, only three σ bonds are formed from the alkene carbon -the carbon thus adopts an sp2 hybridization Ethene (common name ethylene) has a molecular formula of CH2CH2 Each carbon is sp2 hybridized with a σ bond to two hydrogens and the other carbon Hybridized orbital allows stronger bonds due to more overlap H H C C H H Structure of Ethylene In addition to the σ framework of ethylene, each carbon has an atomic p orbital not used in hybridization The two p orbitals (each with one electron) overlap to form a π bond (p bonds are not symmetric about the internuclear axis) π bonds are not as strong as σ bonds (in ethylene, the σ bond is ~90 Kcal/mol and the π bond is ~66 Kcal/mol) Thus while σ bonds are stable and very few reactions occur with C-C bonds, π bonds are much more reactive and many reactions occur with C=C π bonds Nomenclature of Alkenes August Wilhelm Hofmann’s attempt for systematic hydrocarbon nomenclature (1866) Attempted to use a systematic name by naming all possible structures with 4 carbons Quartane a alkane C4H10 Quartyl C4H9 Quartene e alkene C4H8 Quartenyl C4H7 Quartine i alkine → alkyne C4H6 Quartinyl C4H5 Quartone o C4H4 Quartonyl C4H3 Quartune u C4H2 Quartunyl C4H1 Wanted to use Quart from the Latin for 4 – this method was not embraced and BUT has remained Used English order of vowels, however, to name the groups