Nature of the Transition Structure for Alkene Epoxidation By
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Transition State Theory. I
MIT OpenCourseWare http://ocw.mit.edu 5.62 Physical Chemistry II Spring 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. 5.62 Spring 2007 Lecture #33 Page 1 Transition State Theory. I. Transition State Theory = Activated Complex Theory = Absolute Rate Theory ‡ k H2 + F "! [H2F] !!" HF + H Assume equilibrium between reactants H2 + F and the transition state. [H F]‡ K‡ = 2 [H2 ][F] Treat the transition state as a molecule with structure that decays unimolecularly with rate constant k. d[HF] ‡ ‡ = k[H2F] = kK [H2 ][F] dt k has units of sec–1 (unimolecular decay). The motion along the reaction coordinate looks ‡ like an antisymmetric vibration of H2F , one-half cycle of this vibration. Therefore k can be approximated by the frequency of the antisymmetric vibration ν[sec–1] k ≈ ν ≡ frequency of antisymmetric vibration (bond formation and cleavage looks like antisymmetric vibration) d[HF] = νK‡ [H2] [F] dt ! ‡* $ d[HF] (q / N) 'E‡ /kT [ ] = ν # *H F &e [H2 ] F dt "#(q 2 N)(q / N)%& ! ‡ $ ‡ ‡* ‡ (q / N) ' q *' q *' g * ‡ K‡ = # trans &) rot ,) vib ,) 0 ,e-E kT H2 qH2 ) q*H2 , gH2 gF "# (qtrans N) %&( rot +( vib +( 0 0 + ‡ Reaction coordinate is antisymmetric vibrational mode of H2F . This vibration is fully excited (high T limit) because it leads to the cleavage of the H–H bond and the formation of the H–F bond. For a fully excited vibration hν kT The vibrational partition function for the antisymmetric mode is revised 4/24/08 3:50 PM 5.62 Spring 2007 Lecture #33 Page 2 1 kT q*asym = ' since e–hν/kT ≈ 1 – hν/kT vib 1! e!h" kT h! Note that this is an incredibly important simplification. -
Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium Sp
Article Cite This: Biochemistry 2019, 58, 1246−1259 pubs.acs.org/biochemistry Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium sp. TCM1 † † † ‡ ‡ Andrew N. Bigley, Dao Feng Xiang, Tamari Narindoshvili, Charlie W. Burgert, Alvan C. Hengge,*, † and Frank M. Raushel*, † Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States ‡ Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States *S Supporting Information ABSTRACT: Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phospho- triesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organo- phosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic hydrolysis mechanism of Sb-PTE, the pH dependence of the reaction and the effects of changing the solvent viscosity were determined. These experiments were complemented by measurement of the primary and ff ff secondary 18-oxygen isotope e ects on substrate hydrolysis and a determination of the e ects of changing the pKa of the leaving group on the magnitude of the rate constants for hydrolysis. Collectively, the results indicated that a single group must be ionized for nucleophilic attack and that a separate general acid is not involved in protonation of the leaving group. -
Lecture Outline a Closer Look at Carbocation Stabilities and SN1/E1 Reaction Rates We Learned That an Important Factor in the SN
Lecture outline A closer look at carbocation stabilities and SN1/E1 reaction rates We learned that an important factor in the SN1/E1 reaction pathway is the stability of the carbocation intermediate. The more stable the carbocation, the faster the reaction. But how do we know anything about the stabilities of carbocations? After all, they are very unstable, high-energy species that can't be observed directly under ordinary reaction conditions. In protic solvents, carbocations typically survive only for picoseconds (1 ps - 10–12s). Much of what we know (or assume we know) about carbocation stabilities comes from measurements of the rates of reactions that form them, like the ionization of an alkyl halide in a polar solvent. The key to connecting reaction rates (kinetics) with the stability of high-energy intermediates (thermodynamics) is the Hammond postulate. The Hammond postulate says that if two consecutive structures on a reaction coordinate are similar in energy, they are also similar in structure. For example, in the SN1/E1 reactions, we know that the carbocation intermediate is much higher in energy than the alkyl halide reactant, so the transition state for the ionization step must lie closer in energy to the carbocation than the alkyl halide. The Hammond postulate says that the transition state should therefore resemble the carbocation in structure. So factors that stabilize the carbocation also stabilize the transition state leading to it. Here are two examples of rxn coordinate diagrams for the ionization step that are reasonable and unreasonable according to the Hammond postulate. We use the Hammond postulate frequently in making assumptions about the nature of transition states and how reaction rates should be influenced by structural features in the reactants or products. -
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. -
Glossary of Terms Used in Photochemistry, 3Rd Edition (IUPAC
Pure Appl. Chem., Vol. 79, No. 3, pp. 293–465, 2007. doi:10.1351/pac200779030293 © 2007 IUPAC INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY ORGANIC AND BIOMOLECULAR CHEMISTRY DIVISION* SUBCOMMITTEE ON PHOTOCHEMISTRY GLOSSARY OF TERMS USED IN PHOTOCHEMISTRY 3rd EDITION (IUPAC Recommendations 2006) Prepared for publication by S. E. BRASLAVSKY‡ Max-Planck-Institut für Bioanorganische Chemie, Postfach 10 13 65, 45413 Mülheim an der Ruhr, Germany *Membership of the Organic and Biomolecular Chemistry Division Committee during the preparation of this re- port (2003–2006) was as follows: President: T. T. Tidwell (1998–2003), M. Isobe (2002–2005); Vice President: D. StC. Black (1996–2003), V. T. Ivanov (1996–2005); Secretary: G. M. Blackburn (2002–2005); Past President: T. Norin (1996–2003), T. T. Tidwell (1998–2005) (initial date indicates first time elected as Division member). The list of the other Division members can be found in <http://www.iupac.org/divisions/III/members.html>. Membership of the Subcommittee on Photochemistry (2003–2005) was as follows: S. E. Braslavsky (Germany, Chairperson), A. U. Acuña (Spain), T. D. Z. Atvars (Brazil), C. Bohne (Canada), R. Bonneau (France), A. M. Braun (Germany), A. Chibisov (Russia), K. Ghiggino (Australia), A. Kutateladze (USA), H. Lemmetyinen (Finland), M. Litter (Argentina), H. Miyasaka (Japan), M. Olivucci (Italy), D. Phillips (UK), R. O. Rahn (USA), E. San Román (Argentina), N. Serpone (Canada), M. Terazima (Japan). Contributors to the 3rd edition were: A. U. Acuña, W. Adam, F. Amat, D. Armesto, T. D. Z. Atvars, A. Bard, E. Bill, L. O. Björn, C. Bohne, J. Bolton, R. Bonneau, H. -
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 -
Spring 2013 Lecture 13-14
CHM333 LECTURE 13 – 14: 2/13 – 15/13 SPRING 2013 Professor Christine Hrycyna INTRODUCTION TO ENZYMES • Enzymes are usually proteins (some RNA) • In general, names end with suffix “ase” • Enzymes are catalysts – increase the rate of a reaction – not consumed by the reaction – act repeatedly to increase the rate of reactions – Enzymes are often very “specific” – promote only 1 particular reaction – Reactants also called “substrates” of enzyme catalyst rate enhancement non-enzymatic (Pd) 102-104 fold enzymatic up to 1020 fold • How much is 1020 fold? catalyst time for reaction yes 1 second no 3 x 1012 years • 3 x 1012 years is 500 times the age of the earth! Carbonic Anhydrase Tissues ! + CO2 +H2O HCO3− +H "Lungs and Kidney 107 rate enhancement Facilitates the transfer of carbon dioxide from tissues to blood and from blood to alveolar air Many enzyme names end in –ase 89 CHM333 LECTURE 13 – 14: 2/13 – 15/13 SPRING 2013 Professor Christine Hrycyna Why Enzymes? • Accelerate and control the rates of vitally important biochemical reactions • Greater reaction specificity • Milder reaction conditions • Capacity for regulation • Enzymes are the agents of metabolic function. • Metabolites have many potential pathways • Enzymes make the desired one most favorable • Enzymes are necessary for life to exist – otherwise reactions would occur too slowly for a metabolizing organis • Enzymes DO NOT change the equilibrium constant of a reaction (accelerates the rates of the forward and reverse reactions equally) • Enzymes DO NOT alter the standard free energy change, (ΔG°) of a reaction 1. ΔG° = amount of energy consumed or liberated in the reaction 2. -
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. -
Chapter 7 - Alkenes and Alkynes I
Andrew Rosen Chapter 7 - Alkenes and Alkynes I 7.1 - Introduction - The simplest member of the alkenes has the common name of ethylene while the simplest member of the alkyne family has the common name of acetylene 7.2 - The (E)-(Z) System for Designating Alkene Diastereomers - To determine E or Z, look at the two groups attached to one carbon atom of the double bond and decide which has higher priority. Then, repeat this at the other carbon atom. This system is not used for cycloalkenes - If the two groups of higher priority are on the same side of the double bond, the alkene is designated Z. If the two groups of higher priority are on opposite sides of the double bond, the alkene is designated E - Hydrogenation is a syn/cis addition 7.3 - Relative Stabilities of Alkenes - The trans isomer is generally more stable than the cis isomer due to electron repulsions - The addition of hydrogen to an alkene, hydrogenation, is exothermic (heat of hydrogenation) - The greater number of attached alkyl groups, the greater the stability of an alkene 7.5 - Synthesis of Alkenes via Elimination Reactions, 7.6 - Dehydrohalogenation of Alkyl Halides How to Favor E2: - Reaction conditions that favor elimination by E1 should be avoided due to the highly competitive SN 1 mechanism - To favor E2, a secondary or tertiary alkyl halide should be used - If there is only a possibility for a primary alkyl halide, use a bulky base - Use a higher concentration of a strong and nonpolarizable base, like an alkoxide - EtONa=EtOH favors the more substituted double bond -
Reactions of Alkenes and Alkynes
05 Reactions of Alkenes and Alkynes Polyethylene is the most widely used plastic, making up items such as packing foam, plastic bottles, and plastic utensils (top: © Jon Larson/iStockphoto; middle: GNL Media/Digital Vision/Getty Images, Inc.; bottom: © Lakhesis/iStockphoto). Inset: A model of ethylene. KEY QUESTIONS 5.1 What Are the Characteristic Reactions of Alkenes? 5.8 How Can Alkynes Be Reduced to Alkenes and 5.2 What Is a Reaction Mechanism? Alkanes? 5.3 What Are the Mechanisms of Electrophilic Additions HOW TO to Alkenes? 5.1 How to Draw Mechanisms 5.4 What Are Carbocation Rearrangements? 5.5 What Is Hydroboration–Oxidation of an Alkene? CHEMICAL CONNECTIONS 5.6 How Can an Alkene Be Reduced to an Alkane? 5A Catalytic Cracking and the Importance of Alkenes 5.7 How Can an Acetylide Anion Be Used to Create a New Carbon–Carbon Bond? IN THIS CHAPTER, we begin our systematic study of organic reactions and their mecha- nisms. Reaction mechanisms are step-by-step descriptions of how reactions proceed and are one of the most important unifying concepts in organic chemistry. We use the reactions of alkenes as the vehicle to introduce this concept. 129 130 CHAPTER 5 Reactions of Alkenes and Alkynes 5.1 What Are the Characteristic Reactions of Alkenes? The most characteristic reaction of alkenes is addition to the carbon–carbon double bond in such a way that the pi bond is broken and, in its place, sigma bonds are formed to two new atoms or groups of atoms. Several examples of reactions at the carbon–carbon double bond are shown in Table 5.1, along with the descriptive name(s) associated with each. -
Computational Analysis of the Mechanism of Chemical Reactions
Computational Analysis of the Mechanism of Chemical Reactions in Terms of Reaction Phases: Hidden Intermediates and Hidden Transition States ELFI KRAKA* AND DIETER CREMER Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314 RECEIVED ON JANUARY 9, 2009 CON SPECTUS omputational approaches to understanding chemical reac- Ction mechanisms generally begin by establishing the rel- ative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening spe- cies via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by- step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an effi- cient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mech- anism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase.