Reaction Mechanisms in Chemistry, We Sometimes Find That Looking At
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Chapter 12 Lecture Notes
Chemical Kinetics “The study of speeds of reactions and the nanoscale pathways or rearrangements by which atoms and molecules are transformed to products” Chapter 13: Chemical Kinetics: Rates of Reactions © 2008 Brooks/Cole 1 © 2008 Brooks/Cole 2 Reaction Rate Reaction Rate Combustion of Fe(s) powder: © 2008 Brooks/Cole 3 © 2008 Brooks/Cole 4 Reaction Rate Reaction Rate + Change in [reactant] or [product] per unit time. Average rate of the Cv reaction can be calculated: Time, t [Cv+] Average rate + Cresol violet (Cv ; a dye) decomposes in NaOH(aq): (s) (mol / L) (mol L-1 s-1) 0.0 5.000 x 10-5 13.2 x 10-7 10.0 3.680 x 10-5 9.70 x 10-7 20.0 2.710 x 10-5 7.20 x 10-7 30.0 1.990 x 10-5 5.30 x 10-7 40.0 1.460 x 10-5 3.82 x 10-7 + - 50.0 1.078 x 10-5 Cv (aq) + OH (aq) → CvOH(aq) 2.85 x 10-7 60.0 0.793 x 10-5 -7 + + -5 1.82 x 10 change in concentration of Cv Δ [Cv ] 80.0 0.429 x 10 rate = = 0.99 x 10-7 elapsed time Δt 100.0 0.232 x 10-5 © 2008 Brooks/Cole 5 © 2008 Brooks/Cole 6 1 Reaction Rates and Stoichiometry Reaction Rates and Stoichiometry Cv+(aq) + OH-(aq) → CvOH(aq) For any general reaction: a A + b B c C + d D Stoichiometry: The overall rate of reaction is: Loss of 1 Cv+ → Gain of 1 CvOH Rate of Cv+ loss = Rate of CvOH gain 1 Δ[A] 1 Δ[B] 1 Δ[C] 1 Δ[D] Rate = − = − = + = + Another example: a Δt b Δt c Δt d Δt 2 N2O5(g) 4 NO2(g) + O2(g) Reactants decrease with time. -
Solvent Effects on Structure and Reaction Mechanism: a Theoretical Study of [2 + 2] Polar Cycloaddition Between Ketene and Imine
J. Phys. Chem. B 1998, 102, 7877-7881 7877 Solvent Effects on Structure and Reaction Mechanism: A Theoretical Study of [2 + 2] Polar Cycloaddition between Ketene and Imine Thanh N. Truong Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, UniVersity of Utah, Salt Lake City, Utah 84112 ReceiVed: March 25, 1998; In Final Form: July 17, 1998 The effects of aqueous solvent on structures and mechanism of the [2 + 2] cycloaddition between ketene and imine were investigated by using correlated MP2 and MP4 levels of ab initio molecular orbital theory in conjunction with the dielectric continuum Generalized Conductor-like Screening Model (GCOSMO) for solvation. We found that reactions in the gas phase and in aqueous solution have very different topology on the free energy surfaces but have similar characteristic motion along the reaction coordinate. First, it involves formation of a planar trans-conformation zwitterionic complex, then a rotation of the two moieties to form the cycloaddition product. Aqueous solvent significantly stabilizes the zwitterionic complex, consequently changing the topology of the free energy surface from a gas-phase single barrier (one-step) process to a double barrier (two-step) one with a stable intermediate. Electrostatic solvent-solute interaction was found to be the dominant factor in lowering the activation energy by 4.5 kcal/mol. The present calculated results are consistent with previous experimental data. Introduction Lim and Jorgensen have also carried out free energy perturbation (FEP) theory simulations with accurate force field that includes + [2 2] cycloaddition reactions are useful synthetic routes to solute polarization effects and found even much larger solvent - formation of four-membered rings. -
Reaction Mechanism
Reaction Mechanism A detailed sequence of steps for a reaction Reasonable mechanism: 1. Elementary steps sum to the overall reaction 2. Elementary steps are physically reasonable 3. Mechanism is consistent with rate law and other experimental observations (generally found from rate limiting (slow) step(s) A mechanism can be supported but never proven NO2 + CO NO + CO2 2 Observed rate = k [NO2] Deduce a possible and reasonable mechanism NO2 + NO2 NO3 + NO slow NO3 + CO NO2 + CO2 fast Overall, NO2 + CO NO + CO2 Is the rate law for this sequence consistent with observation? Yes Does this prove that this must be what is actually happening? No! NO2 + CO NO + CO2 2 Observed rate = k [NO2] Deduce a possible and reasonable mechanism NO2 + NO2 NO3 + NO slow NO3 + CO NO2 + CO2 fast Overall, NO2 + CO NO + CO2 Is the rate law for this sequence consistent with observation? Yes Does this prove that this must be what is actually happening? No! Note the NO3 intermediate product! Arrhenius Equation Temperature dependence of k kAe E/RTa A = pre-exponential factor Ea= activation energy Now let’s look at the NO2 + CO reaction pathway* (1D). Just what IS a reaction coordinate? NO2 + CO NO + CO2 High barrier TS for step 1 Reactants: Lower barrier TS for step 2 NO2 +NO2 +CO Products Products Bottleneck NO +CO2 NO +CO2 Potential Energy Step 1 Step 2 Reaction Coordinate NO2 + CO NO + CO2 NO22 NO NO 3 NO NO CO NO CO 222In this two-step reaction, there are two barriers, one for each elementary step. The well between the two transition states holds a reactive intermediate. -
Photoionization Studies of Reactive Intermediates Using Synchrotron
Photoionization Studies of Reactive Intermediates using Synchrotron Radiation by John M.Dyke* School of Chemistry University of Southampton SO17 1BJ UK *e-mail: [email protected] 1 Abstract Photoionization of reactive intermediates with synchrotron radiation has reached a sufficiently advanced stage of development that it can now contribute to a number of areas in gas-phase chemistry and physics. These include the detection and spectroscopic study of reactive intermediates produced by bimolecular reactions, photolysis, pyrolysis or discharge sources, and the monitoring of reactive intermediates in situ in environments such as flames. This review summarises advances in the study of reactive intermediates with synchrotron radiation using photoelectron spectroscopy (PES) and constant-ionic-state (CIS) methods with angular resolution, and threshold photoelectron spectroscopy (TPES), taking examples mainly from the recent work of the Southampton group. The aim is to focus on the main information to be obtained from the examples considered. As future research in this area also involves photoelectron-photoion coincidence (PEPICO) and threshold photoelectron-photoion coincidence (TPEPICO) spectroscopy, these methods are also described and previous related work on reactive intermediates with these techniques is summarised. The advantages of using PEPICO and TPEPICO to complement and extend TPES and angularly resolved PES and CIS studies on reactive intermediates are highlighted. 2 1.Introduction This review is organised as follows. After an Introduction to the study of reactive intermediates by photoionization with fixed energy photon sources and synchrotron radiation, a number of Case Studies are presented of the study of reactive intermediates with synchrotron radiation using angle resolved PES and CIS, and TPE spectroscopy. -
Fundamentals of Theoretical Organic Chemistry Lecture 9
Fund. Theor. Org. Chem 1 SE Fundamentals of Theoretical Organic Chemistry Lecture 9 1 Fund. Theor. Org. Chem 2 SE 2.2.2 Electrophilic substitution The reaction which takes place between a reactant with an electronegative carbon and an electropositive reagent forming a polarized covalent bond is called electrophilic. In addition, if substitution occurs (i.e. there is a similar polarized covalent bond on the electronegative carbon, which breaks up during the reaction, so the reagent „substitutes” the „old” group or the leaving group) then this specific reaction is called electrophilic substitution. The electronegative carbon is called the reaction centre. In general, the good reactant are molecules having electronegative carbons like aromatic compounds, alkenes and other compounds containing electron-rich double bonds. These are called Lewis bases. On the contrary, good electrophilic reagents are electron poor compounds/molecule groups like acid-halides, which easily form covalent bond with an electronegative centre, thus creating a new molecule. These are often referred to as Lewis acids. According to molecular orbital (MO) theory the driving force for the electrophilic substitution (SE) is a Lewis complex formation involving the LUMO of the Lewis Acid Reagent and the HOMO of the Lewis Base Reactant. Reactant Reagent LUMO LUMO HOMO Lewis base Lewis acid Lewis complex Types of reactions: There are four types of reactions as illustrated below: 2 Fund. Theor. Org. Chem 3 SE Table. 2.2.2-1. Saturated Aromatic SE1 SE1 (Ar) SE2 SE2 (Ar) SE reaction on saturated atom: (1)Unimolecular electrophilic substitution (SE1): The reaction proceeds in two steps. After the departure of the leaving group, the negatively charged reaction intermediate will combine with the reagent. -
Ochem ACS Review 23 Aryl Halides
ACS Review Aryl Halides 1. Which one of the following has the weakest carbon-chlorine bond? A. I B. II C. III D. IV 2. Which compound in each of the following pairs is the most reactive to the conditions indicated? A. I and III B. I and IV C. II and III D. II and IV 3. Which of the following reacts at the fastest rate with potassium methoxide (KOCH 3) in methanol? A. fluorobenzene B. 4-nitrofluorobenzene C. 2,4-dinitrofluorobenzene D. 2,4,6-trinitrofluorobenzene 4. Which of the following reacts at the fastest rate with potassium methoxide (KOCH 3) in methanol? A. fluorobenzene B. p-nitrofluorobenzene C. p-fluorotoluene D. p-bromofluorobenzene 5. Which of the following is the kinetic rate equation for the addition-elimination mechanism of nucleophilic aromatic substitution? A. rate = k[aryl halide] B. rate = k[nucleophile] C. rate = k[aryl halide][nucleophile] D. rate = k[aryl halide][nucleophile] 2 6. Which of the following is not a resonance form of the intermediate in the nucleophilic addition of hydroxide ion to para -fluoronitrobenzene? A. I B. II C. III D. IV 7. Which chlorine is most susceptible to nucleophilic substitution with NaOCH 3 in methanol? A. #1 B. #2 C. #1 and #2 are equally susceptible D. no substitution is possible 8. What is the product of the following reaction? A. N,N-dimethylaniline B. para -chloro-N,N-dimethylaniline C. phenyllithium (C 6H5Li) D. meta -chloro-N,N-dimethylaniline 9. Which one of the reagents readily reacts with bromobenzene without heating? A. -
Bsc Chemistry
Subject Chemistry Paper No and Title 05, ORGANIC CHEMISTRY-II (REACTION MECHANISM-I) Module No and Title 15, The Neighbouring Mechanism, Neighbouring Group Participation by π and σ Bonds Module Tag CHE_P5_M15 CHEMISTRY PAPER :5, ORGANIC CHEMISTRY-II (REACTION MECHANISM-I) MODULE: 15 , The Neighbouring Mechanism, Neighbouring Group Participation by π and σ Bonds TABLE OF CONTENTS 1. Learning Outcomes 2. Introduction 3. NGP Participation 3.1 NGP by Heteroatom Lone Pairs 3.2 NGP by alkene 3.3 NGP by Cyclopropane, Cyclobutane or a Homoallyl group 3.4 NGP by an Aromatic Ring 4. Neighbouring Group Participation on SN2 Reactions 5. Neighbouring Group Participation on SN1 Reactions 6. Neighbouring Group and Rearrangement 7. Examples 8. Summary CHEMISTRY PAPER :5, ORGANIC CHEMISTRY-II (REACTION MECHANISM-I) MODULE: 15 , The Neighbouring Mechanism, Neighbouring Group Participation by π and σ Bonds 1. Learning Outcomes After studying this module, you shall be able to Know about NGP reaction Learn reaction mechanism of NGP reaction Identify stereochemistry of NGP reaction Evaluate the factors affecting the NGP reaction Analyse Phenonium ion, NGP by alkene, and NGP by heteroatom. 2. Introduction The reaction centre (carbenium centre) has direct interaction with a lone pair of electrons of an atom or with the electrons of s- or p-bond present within the parent molecule but these are not in conjugation with the reaction centre. A distinction is sometimes made between n, s and p- participation. An increase in rate due to Neighbouring Group Participation (NGP) is known as "anchimeric assistance". "Synartetic acceleration" happens to be the special case of anchimeric assistance and applies to participation by electrons binding a substituent to a carbon atom in a β- position relative to the leaving group attached to the α-carbon atom. -
Chapter 14 Chemical Kinetics
Chapter 14 Chemical Kinetics Learning goals and key skills: Understand the factors that affect the rate of chemical reactions Determine the rate of reaction given time and concentration Relate the rate of formation of products and the rate of disappearance of reactants given the balanced chemical equation for the reaction. Understand the form and meaning of a rate law including the ideas of reaction order and rate constant. Determine the rate law and rate constant for a reaction from a series of experiments given the measured rates for various concentrations of reactants. Use the integrated form of a rate law to determine the concentration of a reactant at a given time. Explain how the activation energy affects a rate and be able to use the Arrhenius Equation. Predict a rate law for a reaction having multistep mechanism given the individual steps in the mechanism. Explain how a catalyst works. C (diamond) → C (graphite) DG°rxn = -2.84 kJ spontaneous! C (graphite) + O2 (g) → CO2 (g) DG°rxn = -394.4 kJ spontaneous! 1 Chemical kinetics is the study of how fast chemical reactions occur. Factors that affect rates of reactions: 1) physical state of the reactants. 2) concentration of the reactants. 3) temperature of the reaction. 4) presence or absence of a catalyst. 1) Physical State of the Reactants • The more readily the reactants collide, the more rapidly they react. – Homogeneous reactions are often faster. – Heterogeneous reactions that involve solids are faster if the surface area is increased; i.e., a fine powder reacts faster than a pellet. 2) Concentration • Increasing reactant concentration generally increases reaction rate since there are more molecules/vol., more collisions occur. -
Reaction Kinetics in Organic Reactions
Autumn 2004 Reaction Kinetics in Organic Reactions Why are kinetic analyses important? • Consider two classic examples in asymmetric catalysis: geraniol epoxidation 5-10% Ti(O-i-C3H7)4 O DET OH * * OH + TBHP CH2Cl2 3A mol sieve OH COOH5C2 L-(+)-DET = OH COOH5C2 * OH geraniol hydrogenation OH 0.1% Ru(II)-BINAP + H2 CH3OH P(C6H5)2 (S)-BINAP = P(C6 H5)2 • In both cases, high enantioselectivities may be achieved. However, there are fundamental differences between these two reactions which kinetics can inform us about. 1 Autumn 2004 Kinetics of Asymmetric Catalytic Reactions geraniol epoxidation: • enantioselectivity is controlled primarily by the preferred mode of initial binding of the prochiral substrate and, therefore, the relative stability of intermediate species. The transition state resembles the intermediate species. Finn and Sharpless in Asymmetric Synthesis, Morrison, J.D., ed., Academic Press: New York, 1986, v. 5, p. 247. geraniol hydrogenation: • enantioselectivity may be dictated by the relative reactivity rather than the stability of the intermediate species. The transition state may not resemble the intermediate species. for example, hydrogenation of enamides using Rh+(dipamp) studied by Landis and Halpern (JACS, 1987, 109,1746) 2 Autumn 2004 Kinetics of Asymmetric Catalytic Reactions “Asymmetric catalysis is four-dimensional chemistry. Simple stereochemical scrutiny of the substrate or reagent is not enough. The high efficiency that these reactions provide can only be achieved through a combination of both an ideal three-dimensional structure (x,y,z) and suitable kinetics (t).” R. Noyori, Asymmetric Catalysis in Organic Synthesis,Wiley-Interscience: New York, 1994, p.3. “Studying the photograph of a racehorse cannot tell you how fast it can run.” J. -
Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling
Article pubs.acs.org/JCTC Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations Matthew J. Varga and Steven D. Schwartz* Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States *S Supporting Information ABSTRACT: In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems. ■ INTRODUCTION staging method from the Chandler group.10 Another method that uses an energy gap formalism like QCP is a hybrid Particle transfer plays a crucial role in a breadth of enzymatic ff reactions, including hydride, hydrogen atom, electron, and quantum-classical approach of Hammes-Schi er and co-work- 1 ers, which models the transferring particle nucleus as a proton-coupled electron transfer reactions. -
Linking Chemical Reaction Intermediates of the Click Reaction to Their Molecular Diffusivity
1 Linking chemical reaction intermediates of the click reaction to their molecular diffusivity Tian Huang,a Bo Li,a Huan Wang,b* and Steve Granicka,c* a Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, South Korea b College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China c Departments of Chemistry and Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea Abstract Bipolar reactions have been provoked by reports of boosted diffusion during chemical and enzymatic reactions. To some, it is intuitively reasonable that relaxation to truly Brownian motion after passing an activation barrier can be slow, but to others the notion is so intuitively unphysical that they suspect the supporting experiments to be artifact. Here we study a chemical reaction according to whose mechanism some intermediate species should speed up while others slow down in predictable ways, if the boosted diffusion interpretation holds. Experimental artifacts would do not know organic chemistry mechanism, however. Accordingly, we scrutinize the absolute diffusion coefficient (D) during intermediate stages of the CuAAC reaction (copper- catalyzed azide-alkyne cycloaddition click reaction), using proton pulsed field-gradient nuclear magnetic resonance (PFG-NMR) to discriminate between the diffusion of various reaction intermediates. For the azide reactant, its D increases during reaction, peaks at the same time as peak reaction rate, then returns to its initial value. For the alkyne reagent, its D decreases consistent with presence of the intermediate large complexes formed from copper catalyst and its ligand, except for the 2Cu-alk complex whose more rapid D may signify that this species is the 2 real reactive complex. -
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.