Showing papers on "Transition state published in 1991"

Interpolated variational transition-state theory: Practical methods for estimating variational transition-state properties and tunneling contributions to chemical reaction rates from electronic structure calculations

Abstract: In many cases, variational transition states for a chemical reaction are significantly displaced from a saddle point because of zero‐point and entropic effects that depend on the reaction coordinate Such displacements are often controlled by the competition between the potential energy along the minimum‐energy reaction path and the energy requirements of one or more vibrational modes whose frequencies show a large variation along the reaction path In calculating reaction rates from potential‐energy functions we need to take account of these factors and—especially at lower temperatures—to include tunneling contributions, which also depend on the variation of vibrational frequencies along a reaction path To include these effects requires more information about the activated complex region of the potential‐energy surface than is required for conventional transition‐state theory In the present article we show how the vibrational and entropic effects of variational transition‐state theory and the effective potentials and effective masses needed to calculate tunneling probabilities can be estimated with a minimum of electronic structure information, thereby allowing their computation at a higher level of theory than would otherwise be possible As examples, we consider the reactions OH+H2, CH3+H2, and Cl+CH4 and some of their isotopic analogs We find for Cl+CH4→HCl+CH3 that the reaction rate is greatly enhanced by tunneling under conditions of interest for atmospheric chemistry

Comparison of biradical formation between enediyne and enyne-allene. Ab initio CASSCF and MRSDCI study

Abstract: We theoretically compared energetics of the Bergman-type biradical formation between enediyne and enyne-allene. The structures of transition states as well as reactants and products for the reaction of (Z)-hexa-1,5-diyn-3-ene (1) and (Z)-hepta-1,2,4-trien-6-yne (3) are determined at the CASSCF level. Energy calculations at the CASSCF and the MRSDCI level show that the reaction of enyne-allene 3 is more exothermic and its activation energy is lower than that of enediyne 1, consistent with the experiments

Protein engineering in analysis of protein folding pathways and stability

Abstract: Publisher Summary This chapter discusses the way the folding process of a protein can be examined using a combination of equilibrium and kinetic experiments and protein engineering. A specific interaction that stabilizes the folded structure is deleted by a small nondisruptive mutation. The energetic contribution of the interaction to the stability of folding of the protein is measured from equilibrium unfolding experiments, usually by urea-mediated denaturation. The next step is to make kinetic measurements on the folding and unfolding of wild type and mutant proteins. This can be used to measure the effects the mutations have on the stability of other forms of the protein, such as the transition state of the rate-determining step in unfolding and, possibly, intermediates present on the folding pathway. This is performed by constructing the free energy profile for the reaction. The energy of the transition state is determined from the unfolding rate constant using transition state theory and the energy of intermediates by the ratio of unfolding and refolding constants. In practice, transition state theory is used quantitatively only to measure the differences in energy between transition states of wild-type and mutant enzymes and not the absolute value.

Van der Waals Complexes in 1,3-Dipolar Cycloaddition Reactions: Ozone-Ethylene

Abstract: Microwave spectra of O3-CH2=CHz, O3-CDz=CHz, 03-trans-CHD=CHD, and O,-cis-CHD=CHD have been observed with a pulsed-beam Fabry-Perot cavity, Fourier transform microwave spectrometer. Internal motions in the van der Waals complex give two states for the normal, 1 ,I-dideuterated and trans-I ,2-dideuterated isotopic forms. The C-type transitions of the two states for the isotopic species above, as well as the one observed isotopic form of 03-cis-CHD=CHD, independently fit to an asymmetric top Watson Hamiltonian. Stark effect measurements for 03-CHz=CHz giye wLa = 0.017 (I) D and p, = 0.466 (2) D. The microwave data are only consistent with a structure having C, symmetry in which the nearly parallel planes of ethylene and ozone have a center of mass separation of R,, = 3.290 (3) A. Ab initio calculations at the MP4 level indicate that the preferred geometry corresponds to small tilts of the ozone and ethylene planes, which place an exo-oriented pair of hydrogens toward the terminal oxygens of ozone. Both the theoretical and microwave results suggest the tunneling splitting arises at least in part from a 180' rotation of ethylene about its Cz axis, which is perpendicular to the ethylene plane. I ,3-Dipolar cycloaddition theory, orbital symmetry rules, and ab initio calculations of the complex and transition states are used to argue that 03-CH2=CH2 lies in a shallow minimum on the reaction coordinate prior to the transition state in the reaction of ozone plus ethylene, which produces the primary product 1,2,3-trioxolane.

Theoretical studies of inorganic and organometallic reaction mechanisms. 2. The trans effect in square-planar platinum(II) and rhodium(I) substitution reactions

Abstract: Ab initio calculations with an effective core potential have been used to study the mechanism of substitution reactions for square-planar transition-metal complexes. Pseudo-trigonal-bipyramidal transition states with rather small entering-ligand to metal to leaving-ligand angles were found for the substitution reactions investigated in this paper. The stability of the transition state is determined by both σ and π effects of the ligands

Energy and structure of the transition states in the reaction OH + CO → H + CO2

Abstract: Two, quite different, experimental studies have been carried out on the reaction between OH and CO at low total pressures. In the first, rate constants have been determined at 82 and 106 K. At the lower temperature, measurements were made at 2 and 5 Torr total pressure, yielding k=(1.0 ± 0.12)× 10–13 cm3 molecule–1 s–1 and (0.91 ± 0.1)× 10–13 cm3 molecule–1 s–1, respectively. At 106 K and 4 Torr, k=(0.98 ± 0.08)× 10–13 cm3 molecule–1 s–1. Theoretical considerations show that the reaction must be in its low-pressure limit, yielding H + CO2, and that the vibrational ground-state adiabatic barrier to formation of HOCO must be <200 cm–1, significantly lower than estimated previously.In the second series of experiments, a tunable diode laser has been used to observe transient absorptions on transitions in the ν3 infrared bands of the CO2 product of the reaction, when it is initiated by flash photolysis at room temperature. There is no excitation of the ν3 mode, and the overall vibrational distribution corresponds to an averaged vibrational energy yield of only 6%. It is concluded that energy is released largely as repulsion following passage through a transition state in which the OCO angle is ca. 171° and the O—C, C—O bond distances are very similar to those in isolated CO2.

Global Control of Suprathreshold Reactivity by Quantized Transition States

Abstract: The authors present evidence that the accurate quantum mechanical probability of the reaction of H with H{sub 2} is globally controlled by quantized transition states up to very high energies. The quantized transition states produce steplike features in the cumulative reaction probability curves that are analyzed up to energies of 1.6 eV; the analysis clearly associates these steps (or thresholds) with quantized dynamical bottlenecks that control the passage of reactive flux to products. They have assigned bend and stretch quantum numbers to the modes orthogonal to the reaction coordinate for all these transition states on the basis of threshold energies of semiclassical vibrationally adiabatic potential energy curves and vibrationally specific cumulative reaction probability densities.

Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach

Abstract: A new approach is proposed for the determination of transition states and reaction paths for conformational transitions. The method makes use of adiabatic energy surfaces in the space of ‘‘essential’’ degrees of freedom of the molecule. The reduced dimensionality of this space, compared to the full Cartesian space, offers improved computational efficiency and should allow determination of exact reaction paths in systems much larger than those currently amenable to study in Cartesian space. A procedure to obtain reaction paths and free energy profiles in solution is also proposed. The free energy profile along the path in solution is calculated utilizing a free energy perturbation method with constrains and perturbations in internal coordinate space. Applications to a conformational transition of the alanine dipeptide and the folding transition of a model reverse turn in water are presented. For the reverse turn, the sequential flip of dihedral angles reported by Czerminsky and Elber on a similar peptide [...

Crotonase-catalyzed beta-elimination is concerted: a double isotope effect study.

Abstract: Determining the sequence of bond cleavages, and consequently the nature of intermediates, in enzyme-catalyzed reactions is a major goal of mechanistic enzymology. When significant primary isotope effects on V/K are observed for two different bond cleavages, both bonds may be broken in the same transition state or they can reflect two different transition states that are of nearly identical energy and consequently both are partially rate limiting. For the crotonase-catalyzed dehydration of 3-hydroxybutyrylpantetheine, the primary D(V/K) and 18(V/K) are 1.60 and 1.053 [Bahnson, B. J., & Anderson, V. E. (1989) Biochemistry 28, 4173-4181], respectively. In this case, double isotope effects can discriminate between the two possibilities [Hermes, J. D., Roeske, C. A., O'Leary, M. H., & Cleland, W. W. (1982) Biochemistry 21, 5106-5114; Belasco, J. G., Albery, W. J., & Knowles, J. R. (1983) J. Am. Chem. Soc. 105, 2475-2477]. The ratio of the alpha-secondary D(V/K) for the hydration of crotonylpantetheine catalyzed by crotonase in H2O and D2O has been determined to be 1.003 +/- 0.006. The invariance of the alpha-secondary effect where the chemical reaction is completely rate determining requires that both bond cleavages be concerted or that the substitution of 2H at the primary position not significantly alter the partitioning of a hypothetical carbanion. The observation of a solvent discrimination isotope effect determined from the relative incorporation of 2H from 50% D2O of 1.60 +/- 0.03, identical with the primary D(V/K), and the determination that the rate of exchange of the abstracted proton with solvent proceeds at less than 3% of the overall reaction rate also fail to provide evidence for a carbanion intermediate and are consistent with a concerted reaction. Identical primary D(V/K)s determined in H2O and D2O indicate that there is not a significant solvent isotope effect on C-O bond cleavage. The isotope ratios determined in these studies were performed by negative ion chemical ionization whole molecule mass spectrometry of the pentafluorobenzyl esters, a new method whose validity is established by comparison with previously determined kinetic and equilibrium isotope effects.

Theoretical Studies of Inorganic and Organometallic Reaction Mechanisms. 3. The Origin of the Difference in the Barrier for the Kinetic and Thermodynamic Products for the Oxidative Addition of Dihydrogen to a Square-Planar Iridium Complex

Abstract: The stereoselective oxidative addition of H2 to IrCl(CO)(dppe) was examined with ab initio theoretical techniques. Reaction coordinates for the two pathways to addition which lead to the formation of the two isomers were constructed from geometry optimization calculations and were augmented by significant portions of the potential energy surfaces near the transition states. The analysis of the Laplacian of the total charge densities revealed that as the complexes evolve from four-coordinate to six-coordinate species, the ligands in the plane of addition move past regions of charge concentration around the metal center. Electron withdrawing ligands in the plan of addition reduce this repulsive interaction by delocalizing a portion of the electronic charge. Electron-donor ligands are unable to function in this capacity and therefore contribute to the repulsive interaction of the five-coordinate transition state to a greater extent. The influence of electron correlation on the reaction coordinates was examined and found not to significantly alter the conclusions based on the single-determinant calculations.

Transition states from molecular symmetry groups: Analysis of non-rigid acetylene trimer

Abstract: We demonstrate that Longuet-Higgins' molecular symmetry (MS) group for describing non-rigid molecules allows deduction of the transition state for an intramolecular rearrangement and that the level of symmetry of the transition state is governed by very simple rules. Key pieces of information are the order of the MS group and the number of distinctly labelled forms represented by it. We also show that the local symmetry at stationary points on the potential energy surface is important and introduce natural definitions of narcissistic reactions and pathways using the laboratory-fixed inversion operation, giving examples of each. Inspection of normal modes is used to depict motion across the potential energy surface between a minimum-energy structure and a transition state. This analysis is applied to acetylene trimer, a recently observed van der Waals cluster. We elucidate the relationships between the stationary points identified by our earlier ab initio work. There are two transition state structures tha...

Negative-ion photodetachment as a probe of bimolecular transition states: the F + H2 reaction

Abstract: The transition-state region of the F + H2, F + D2 and F + HD reactions has been studied by photoelectron spectroscopy of the negative ions FH–2, FD–2 and FDH–. Photodetachment of these anions can access three electronic states of the neutral, but transitions to the ground-state potential-energy surface for the reaction can be observed selectively by adjusting the polarization of the photodetachment laser. Under these conditions, the FH–2 spectrum is similar to the recent simulation by Zhang and Miller which used the T5a potential-energy surface for the F + H2 reaction. The spectra of all three isotopic anions are interpreted by comparison to previous reactive scattering calculations. This comparison strongly suggests that several of the peaks in the photoelectron spectra are due to transitions to scattering resonances.

Ab initio study of the insertion reaction of magnesium into the carbon-halogen bond of fluoro- and chloromethane

Abstract: Theoretical calculations using self-consistent field (SCF) and Moller-Plessett perturbation theory, up to fourth order (MP4), have been carried out on the gas-phase Mg+CH 3 X→CH 3 MgX Grignard reaction surface for X=F and Cl. The transition-state energies, geometries, and vibrational frequencies for both reactions are presented and compared to the smaller Mg+HX→HMgX reaction. The transition states for both X=F and X=Cl are found to process C s symmetry and to be almost identical in structure. The activation energy for the Mg + fluoromethane reaction is found to be 31.2 kcal-mol −1 , while that for the chloromethane reaction is substantially higher, at 39.4 kcal.mol −1 , calculated at the MP4SDTQ level by using the 6-311G(d,p) basis. The intrinsic reaction coordinate has been followed down from the transition state toward both reactants and product for the Mg + CH 3 F→CH 3 MgF reaction, confirming the connection of these points on the potential surface

Effects of water on combustion kinetics at high pressure

Abstract: The effect of water on reaction mechanisms in high pressure combustion has been studied theoretically using the quantum chemical BAC-MP4 method combined with the Peng-Robinson equation of state to treat non-ideal gas effects. Transition state structures involving additional water molecules have been calculated using the BAC-MP4 method for the water gas shift reaction CO+H 2 O→CO 2 +H 2 going via the formic acid, HCOOH, intermediate. The resulting transition states can be stabilized due to water solvation effects. The magnitude of the Gibbs energy changes due to solvation were calculated using the Peng-Robinson equation of state. The results indicate large lowerings of the activation energies for the reaction when additional water molecules are included in the reaction mechanism. Also, we find that the transition state structures possess significant ionic character which leads to substantial stabilization due to the presence of surrounding water molecules. The temperature and pressure dependence of these effects are discussed with respect to the chemical mechanisms in combustion processes.

Quantum Chemistry of Organic Compounds: Mechanisms of Reactions

Abstract: 1 Potential Energy Surfaces of Chemical Reactions.- 1.1 Introduction. Mechanism of Chemical Reaction and Quantum Chemistry.- 1.2 Choice of a Coordinate System and the Representation of a PES.- 1.3 Topography of the PES and Properties of a Reacting System.- 1.3.1 Critical Points.- 1.3.2 The Regions of the Minima on the PES.- 1.3.2.1 Vibrational Spectrum of Molecules.- 1.3.2.2 Calculation of Thermodynamic Functions of Molecules.- 1.3.2.3 Topological Definition of Molecular Structure.- 1.3.2.4 Structural Diagrams.- 1.3.3 Saddle Points on the PES. Transition States.- 1.3.3.1 Localization of the Transition States on the PES.- 1.3.3.2 Symmetry Selection Rules for Transition State Structures.- 1.3.3.3 Calculation of Activation Parameters of Reactions and of Kinetic Isotopic Effects.- 1.3.4 Pathway of a Chemical Reaction.- 1.3.4.1 Ambiguity of the Definition.- 1.3.4.2 A More Accurate Definition of the MERP and the Reaction Coordinate.- 1.3.4.3 Symmetry Demands on the Reaction Path.- 1.3.4.4 Chiral and Achiral Pathways of Degenerate Reactions.- 1.3.5 Empirical Correlations of the Reaction Pathways.- 1.3.5.1 Molecular Vibrations and the Reaction Coordinate.- 1.3.5.2 The Principle of Least-Motion.- 1.3.5.3 Structural Correlations of the Pathways of Chemical Reactions.- 1.4 Dynamic Approach.- 1.5 Tunnelling Effects in Chemical Reactions.- 1.6 Description of Nonadiabatic Reactions.- References.- 2 Quantum Chemical Methods for Calculating Potential Energy Surfaces.- 2.1 General Requirements upon the Methods for Calculating Potential Energy Surfaces.- 2.2 Nonempirical (ab initio) Methods. The Hartree-Fock Method.- 2.2.1 Closed Electron Shells.- 2.2.2 Open Electron Shells.- 2.2.3 Basis Sets of Atomic Orbitals.- 2.2.4 Electron Correlation.- 2.2.5 The Problem of Stability of Hartree-Fock Solutions.- 2.3 Semiempirical Methods.- 2.3.1 The Extended Huckel Method.- 2.3.2 Semiempirical Selfconsistent Field Methods.- 2.3.2.1 The CNDO/2 Method.- 2.3.2.2 The MINDO/3 Method.- 2.3.2.3 The MNDO Method.- 2.3.2.4 The AM1 Method.- References.- 3 Effects of the Medium.- 3.1 A General Scheme for Calculating the Solvation Effects.- 3.2 Macroscopic Approximation.- 3.2.1 General Theory.- 3.2.2 Model Hamiltonians in the Macroscopic Approximation.- 3.2.2.1 Model Hamiltonian in the Kirkwood Approximation.- 3.2.2.2 A Model Hamiltonian Based on the Born Formula. Scheme of Solvatons.- 3.2.2.3 The Scheme of Virtual Charges.- 3.2.2.4 The Theory of Selfconsistent Reactive Field.- 3.3 Discrete Representation of Solvent Molecules. Model Hamiltonians in the Microscopic Approximation.- 3.4 Specific Features of the Supermolecular Approach in Studies of Solvation Effects.- 3.5 Statistical Methods for Studying Solutions.- References.- 4 Orbital Interactions and the Pathway of a Chemical Reaction.- 4.1 The Role of Frontier Orbitals.- 4.2 Theory of Orbital Interactions.- 4.3 Components of the Interaction Energy of a Reacting System in a Transition State.- 4.4 Isolobal Analogy.- References.- 5 Substitution Reaction.- 5.1 Nucleophilic Substitution at a Tetrahedral Carbon Atom.- 5.1.1 The SN2 Reactions.- 5.1.1.1 Stereochemistry of the Reactions.- 5.1.1.2 Reaction Coordinate and the Structure of the Transition State.- 5.1.1.3 Energetics and Stoichiometric Mechanism of the Gas-Phase SN2 Reactions.- 5.1.1.4 Effect of the Solvent.- 5.1.1.5 Reactions with Retention of Configuration of the Carbon Atom.- 5.1.2 The SN1 Reactions.- 5.2 Electrophilic Substitution at the Tetrahedral Carbon Atom.- 5.3 Nucleophilic Substitution at the Carbon Atom of the Carbonyl Group.- 5.3.1 The Stoichiometric Mechanism.- 5.3.2 Homogeneous Catalysis.- 5.3.3 Stereochemistry of the Reaction.- 5.3.3.1 The Direction of Nucleophilic Attack and Orbital Steering.- 5.3.3.2 Stereochemical Control of the Breakdown of the Tetrahedral Adduct.- 5.4 Aromatic Electrophilic Substitution Reactions.- 5.5 Nucleophilic Substitution at the Nitrogen, Phosphorus, and Sulfur Centers.- 5.5.1 Substitution at the Nitrogen Atom of Nitroso- and Nitro-Groups.- 5.5.2 Substitution at the Dicoordinate Sulfur Atom.- 5.5.3 Substitution at Tricoordinate Sulfur and Phosphorus Centers.- 5.5.4 Substitution at Tetracoordinate Phosphorus.- 5.5.5 Substitution at Pentacoordinate Phosphorus.- 5.5.6 Inclusion of the Polytopal Rearrangements of Intermediates in the Overall Reaction Scheme.- References.- 6 Addition Reactions.- 6.1 Electrophilic Additions to Multiple Bonds.- 6.2 Nucleophilic Addition to Alkenes.- 6.3 Nucleophilic Addition to a Triple Bond.- References.- 7 Low-Energy Barrier Reactions. Structural Modelling.- 7.1 The Principle of Correspondence Between Structures of the Initial and the Transition State of Reaction.- 7.2 Nucleophilic Rearrangements and Tautomerizations.- 7.3 Cyclization Reactions.- 7.4 Topochemical Reactions.- References.- 8 Radical Reactions.- 8.1 Specific Features of the Theoretical Analysis of Radical Reactions.- 8.2 Free-Radical Reactions.- 8.2.1 Bond-Cleavage and Addition Reactions.- 8.2.2 Radical Substitution Reactions at the Tetrahedral Carbon Atom.- 8.3 Reactions with Formation of Biradicals.- 8.4 The Reactions of Carbenes.- 8.4.1 Addition to the Double Carbon-Carbon Bond.- 8.4.2 Insertion into ?-Bonds.- References.- 9 Electron and Proton Transfer Reactions.- 9.1 Electron Transfer Reactions.- 9.1.1 Single Electron Transfer Reactions in Organic Chemistry.- 9.1.2 Elementary Act of Electron Transfer.- 9.1.3 Theoretical Studies of the Mechanism of SRN1 Reactions.- 9.2 Proton Transfer Reactions.- 9.2.1 Potential Energy Curves and Activation Barriers.- 9.2.2 Stereochemistry.- 9.2.3 Proton Transfer in Systems with the Intramolecular Hydrogen Bonding.- 9.2.4 The Tunnelling Mechanism in Proton Transfer Reactions.- 9.2.5 Double Proton Migrations.- References.- 10 Pericyclic Reactions.- 10.1 Reactions of Cycloaddition.- 10.1.1 [2 + 2]-Cycloaddition.- 10.1.2 [4 + 2]-Cycloaddition.- 10.2 Electrocyclic Reactions.- 10.3 Sigmatropic Rearrangements.- 10.4 Haptotropic Rearrangements.- 10.5 Ion-Radical Pericyclic Reactions.- References.- List of Abbreviations.

Potential energy surface for unimolecular dissociation and rearrangement reactions of the ground electronic state of HFCO

Abstract: The potential energy surface of the HFCO molecule in its electronic ground state has been investigated with ab initio method, at levels up to MP4(SDTQ)/6‐311G**//MP2/6‐31G*. At the highest level, the barrier height for molecular dissociation (HFCO→HF+CO) was calculated to be 46.9 kcal/mol with a zero‐point energy correction, in good agreement with an experimental estimate and a recent theoretical result. The intrinsic reaction coordinate (IRC) for molecular dissociation was traced and the coupling between the IRC and normal modes as well as that among the normal modes was analyzed along the IRC. The analysis is consistent with the mode specificity of recently observed quasistable vibrational states of HFCO above the dissociation limit. Almost all possible stationary points on the potential surface of the HFCO system have been located, including the rearrangement and atomic dissociation products and transition states, as well as van der Waals complexes. These are compared with the H2CO system. All the spec...

Temperature dependence of the rates of conformational changes reported by fluorescein 5'-isothiocyanate modification of H+,K(+)- and Na+,K(+)-ATPases.

Abstract: Stopped-flow fluorometry has been used to measure the forward and reverse rates of the conformational change from E1 to E2 in the fluorescein-modified proton and sodium pumps (1) as a function of Na+ and K+ concentrations to verify the proposed mechanism of ion interaction with the enzymes and (2) as a function of temperature to gain insight into the nature of the conformational transition. (1) The fluorescence changes caused by Na+ and K+ are consistent with rapid competitive binding of the two ions to the E1 conformations of the enzymes followed by rate-limiting transitions between E1K and E2K. (2) Reaction coordinate diagrams for the E1K to E2K transitions in the H,K-ATPase and Na,K-ATPase are qualitatively similar. Enthalpy barriers to reaction are partially compensated by increased entropy in the transition states. However, there are striking quantitative differences between the two enzymes. The E2K to E1K reaction of the H,K-ATPase is more than 2 orders of magnitude faster (tau 1/2 = 6 ms at 22 degrees C) than the reverse rate of the Na,K-ATPase transition (tau 1/2 = 1.6 s), explaining repeated failure to detect a K(+)-"occluded" form of the H,K-enzyme. The E2K conformer of the Na,K-ATPase is 3 orders of magnitude more stable than E1K, while the E1K and E2K conformations of the H,K-ATPase are nearly equivalent energetically.

Molecular Orbital Approach to Antioxidant Mechanisms of Phenols by an Ab Initio Study

Abstract: An ab initio molecular orbital theory has been applied to a study of the hydrogen abstractions of phenolic antioxidants in the chain process of autoxidation. The optimum structures of phenols, of peroxides, and of those compounds in the transition states were obtained with a Hartree–Fock/STO-3G basis set. From the values of enthalpy (ΔH) and activation energy (Ea) obtained, it was found that the rates of the reaction of peroxyl radical with phenolic antioxidant were faster than those with organic substrate in the propagation, and that the effect of the aromatic ring of the antioxidants not only stabilized a product state but also decreased an energy level in the transition state. The para-substituent effect that an electron-releasing substituent increased the antioxidant activity, whereas an electron-withdrawing one decreased it, was recognized. The relationship between ΔH and Ea values followed the Evans–Polanyi rule. The transition states in the hydrogen abstractions with lower Ea values prefer reactant...

1.1 – Ene Reactions with Alkenes as Enophiles

Abstract: The thermal reaction of an alkene having an allylic hydrogen (an ‘ene’) with a compound containing a double or triple bond (enophile) to form a new bond with migration of the ene double bond and 1,5-hydrogen shift is referred to as the ene reaction (equation 1). The ene reaction is mechanistically related to the much better known Diels–Alder reaction since both reactions can be concerted, proceeding through cyclic transition states involving six electrons.1–5Stepwise ene reactions proceeding through either a diradical or zwitterionic intermediate are also known. Ene reactions proceed most readily when the enophile, like the dienophile in a Diels–Alder reaction, is electron deficient. Similarly, the ene, like the diene in the Diels–Alder reaction, should be electron rich. Although the exact order depends upon the enophile and reaction conditions, the relative reactivity of alkenes as ene components has typically been found to be 1,1-di- > tri- > tetra- > mono- > 1,2-disubstituted. Unfortunately, ene reactions typically occur at higher temperatures than related Diels–Alder reactions, limiting the synthetic utility of the ene reaction.

Transition-state switchings for single potential well ionic dissociations

Abstract: Microcanonical variational transition state theory calculations were applied to the reaction C6HsBr'' C6H5+ + Br' in bromobenzene. Calculations were compared with experimental results for C6HS+ time-resolved photoionization efficiency curves and available k ( E ) data for this system. Calculations demonstrate, in agreement with previous results for CHI'', that multiple transition states are possible for single-well potintials of ionic systems. However, comparison with experiments indicates the dominance of the orbiting transition state over a wide energy range above threshold. Further extension of k ( E ) measurements to higher energies is recommended, in order to be able to confidently rule out transition-state switching to a tight transition state as E increases.

Variational transition state theory : a simple model for dissociation and recombination reactions of small species

Abstract: A simple interaction potential is deduced for calculating rates of unimolecular and recombination reactions involving simple fission transition states (e.g., CH3OH --> CH3 + OH and its reverse recombination reaction), based on the Gorin notion of two independent moieties (CH3 and OH in the preceding example) plus an interaction made up of a Morse potential and two independent sinusoidally hindered rotors. The hindrance potential is in accord with accurate quantum calculations for such systems. Implementation of this potential in RRKM theory leads to a simple extension of the conventional direct-count algorithm. Variational transition state theory can then be easily employed to calculate rate coefficients with minimal computational resources. The results obtained compare favorably with those from more "act (and more complex) formulations, and from experiment, for cases where both moieties are comparatively small. However, for large moieties (e.g., a tert-butyl group), results are very sensitive to the assumed values for the van der Waals radii, and the method cannot be employed in such cases.

An ab initio study of the reaction of atomic hydrogen with sulfur dioxide

Abstract: The potential energy surface for H(1 2S)+SO2 has been investigated computationally in order to study the catalytic removal of atomic hydrogen in flames by sulfur dioxide. HF/3–21G(*) and MP2/3–21G(*) levels of theory were employed to locate stationary points, which were then characterized by calculation of the vibrational frequencies. Some geometries were also optimized with the 6–31G* basis set. Two adducts HOSO and HSO2, with H bonded to O or S, respectively, were studied. Energies were estimated at the optimized geometries using spin‐projected MP4/6–31G* calculations, which show that planar cis HOSO is more stable than Cs HSO2. An H–OSO bond energy of 109 kJ mol−1 is predicted. By contrast HSO2 is predicted to be 25 kJ mol−1 endothermic with respect to H+SO2, and is insufficiently stable to be significant in combustion chemistry. Transition states were located and the information used to derive the kinetics of H+SO2+Ar⇄HOSO+Ar from 298 to 2000 K. An unusually large energy barrier to recombination, of a...

Theoretical investigation of the dimerization of ketene: does the 2S + 2A cycloaddition reaction exist?

Abstract: Ab initio quantum mechanical methods have been used to study the dimerization of ketene to form diketene and 1,3-cyclobutanedione. Molecular structures for reactants, products, and transition states of the above reactions have been determined at the self-consistent-field (SCF) level of theory with a double-ζ plus polarization (DZ+P) basis set. Relative energies of stationary points have been predicted at the single and double excitation configuration interaction (CISD) level of theory. At the DZ+P SCF level of theory, the formation of 1,3-cyclobutanedione is predicted to proceed through an unsymmetrical transition state and has a classical barrier height of 36 kcal/mol. The formation of diketene also proceeds through an unsymmetrical transition state and is predicted to have a barrier height of 32 kcal/mol. Inclusion of electron correlation and zero-point vibrational energy yields an estimate of 26 kcal/mol for the latter barrier. Neither transition state is consistent with the 2S+2A cycloaddition reaction mechanism

Theoretical studies on the mechanism of conversion of androgens to estrogens by aromatase.

Abstract: Semiempirical molecular orbital calculations (AM1) were used to model several possible reaction mechanisms for the third oxidation of the aromatase-catalyzed conversion of androgens to estrogens. The reaction mechanisms considered are based on the assumption that the third oxidation is initiated by 1 beta-hydrogen atom abstraction. Homolytic cleavage of the C10-C19 bond was modeled for both the 3-keto and 2-en-3-ol forms of the androgen 1-radicals. The addition of a protein nucleophile to the 19-oxo intermediate was also considered, and -OCH3, -SCH3, and -NHCH3 were used to represent the Ser, Cys, and Lys adducts. The transition states were estimated and optimized from the reaction coordinates obtained by constraining and increasing the C10-C19 bond lengths. The enthalpies of activation range from 14 to 21 kcal and are approximately 2 kcal lower for cleavage of the enol form. Given the tendency for AM1 to overestimate activation energies, all reactions may be energetically accessible. Other reactions modeled include a homolytic cleavage reaction from a thioether radical cation and the direct additions of oxygen radical compounds to the carbonyl of the 1-radical-2-en-3-ol-19-oxo androgen. A mechanism is proposed in which the 19-oxo intermediate is subject to initial nucleophilic attack by the protein. Since rotation of the 19-carbonyl can bring the oxygen within 2.1 A of the 2 beta-hydrogen, the formation of a tetrahedral intermediate can occur with concomitant removal of the 2 beta-proton. Enolization activates the C1-position for hydrogen atom abstraction, since the resulting radical is resonance stabilized.(ABSTRACT TRUNCATED AT 250 WORDS)

The chemical reaction molecular dynamics method and the dynamic transition state: Proton transfer reaction in the formamidine and water solvent system

Abstract: The chemical reaction mechanism in solution is analyzed by using the chemical reaction molecular dynamics (CRMD) method where a solute molecule and a few solvent molecules are regarded as a supermolecule and the chemical reaction dynamics can be analyzed in a time-dependent way on the intrasupermolecular potential surface. We have examined a proton transfer reaction, the formamidine-water system, and focused on the dynamic effect in the chemical reaction after considering the static «electronic» solvent effect. Two schemes, the constant-temperature scheme (CTS) and the constant-energy scheme (CES), have been employed, and a new type of critical state, named the dynamic transition state (DTS), was found by the appearance of a cusp in the hydrogen-bonding correlation function (HBCF). The cusp is due to the stopping of change in the O-H bond length, which produces a water molecule in the product region. In the CES, alternately modulated oscillation appeared, which is a characteristic in triatomic systems and should play an important role in energy flow in solution

Directions of theoretical and experimental investigations into the mechanisms of heterogeneous catalysis

Abstract: The roles of the atomic structure and the electronic structure of the active surface sites in bonding of reactants and causing bond breaking or bond formation have been the focus of theoretical studies. In addition to calculations on static systems, usually clusters, modelling of the transition states and the dynamics of elementary reaction steps (adsorption, dissociation, surface diffusion, desorption) have been performed. Variations of electronic structure of elements across the periodic table have been shown to be responsible for the unique importance of transition metals in catalysis. Experimental studies utilize catalysts with well-characterized structure (zeolites, crystal surfaces) and information about surface structure, composition and chemical bonding of adsorbates becomes available on the molecular level. Deliberate alteration of catalyst structure, surface composition by alloying and electronic structure by addition of electron donor and electron acceptor promoters have been utilized to modify reaction rates and selectivity. This way many of the molecular ingredients of heterogeneous catalytic reactions have been identified. In recent years evidence has been accumulating that indicates periodic and long term restructuring of the catalyst surface as necessary for chemical change and reaction turnover. These findings point to the need of time resolved studies and in-situ investigations of both the substrate and the adsorbate sides of the surface chemical bonds simultaneously on a time scale shorter than the reaction turnover frequency. Close collaboration between theorists and experimentalists is essential if we are to succeed in designing heterogeneous catalysts.

Mechanism and site selectivity in the Diels-Alder reaction between protoanemonin and butadiene. A theoretical study

Abstract: The Diels-Alder reaction between protoanemonin and butadiene has been theoretically studied by means of the semiempirical MNDO and AM1 methods. With use of the results obtained, the experimentally observed site selectivity is discussed regarding the mechanism of the process and the nature of the transition states. It is concluded that this reaction probably proceeds via a diradical intermediate

On the use of isovalued surfaces to determine molecule shape and reaction pathways.

Abstract: Novel insights into local molecule structure and reactivity can be gained from viewing isovalued surfaces of the molecular electron density, electrostatic potential and molecular orbitals rendered as colored, 3-D objects. For example, drawing positive and negative electrostatic isopotential surfaces partitions the molecule into regions subject to nucleophilic or electrophilic attack. Similarly, coloring isodensity surfaces to indicate the magnitude of the gradient of the electron density maps the molecule surface into regions of high and low electronegativity. A basic understanding of reaction mechanisms can also come from viewing and manipulating isovalued surfaces. A theory of molecular interactions, based upon second-order perturbation theory, provides for the decomposition of the intermolecular interaction energy into steric, electrostatic and orbital interactions. Color figures illustrate the docking of reactant molecular densities, electrostatic potentials and orbitals on low-energy pathways. The figures are used to visualize the steric, electrostatic and orbital contributions to molecular interaction energy. The visualization not only identifies low-energy reaction pathways, but it frequently reveals local interactions which determine the magnitude of the total interaction energy. Similar insight is not easily obtained by simple evaluation of the total interaction energy. Approximate transition states, built from structures along low-energy approach pathways, are excellent starting points for transition state searches.

Molecular dynamics study of a model isomerization reaction at the liquid–vapor interface of a Lennard‐Jones fluid

Abstract: The dynamics of a model isomerization reaction at the liquid–vapor interface of a Lennard‐Jones fluid is studied using molecular dynamics simulation and is compared to the same reaction in bulk liquid. The reaction system consists of two atoms moving in a double well potential between a compact and an extended state. The potential of mean force and the dynamical friction are evaluated for the reaction in the bulk and at the interface, and are used to estimate the effects on the rate of the reaction. The transition from the bulk to the interface reduces both the friction along the reaction coordinate and the activation barrier for the transition from the compact to the extended state. The rate of the reaction at the interface can be larger than the rate in the bulk by a factor of ≊2, depending on the system’s potential parameters. These effects on the rate of the reaction can be understood in terms of the density variation in going from the bulk to the interface.