Showing papers on "Transition state published in 1988"

Femtosecond real‐time probing of reactions. II. The dissociation reaction of ICN

Abstract: Experimental results obtained for the dissociation reaction ICN^*→[I⋅⋅⋅CN]^(‡*)→I+CN using femtosecond transition‐state spectroscopy (FTS) are presented. The process of the I–CN bond breaking is clocked, and the transition states of the reaction are observed in real time. From the clocking experiments, a "dissociation" time of 205±30 fs was measured and was related to the length scale of the potential. The transition states live for only ∼50 fs or less, and from the observed transients we deduce some characteristics of the relevant potential energy surfaces (PES). These FTS experiments are discussed in relation to both classical and quantum mechanical models of the dynamical motion, including features of the femtosecondcoherence and alignment of fragments during recoil. The observations are related to the radial and angular properties of the PES.

A diabatic reaction path Hamiltonian

Abstract: A reaction path Hamiltonian is constructed that is based on a straight‐line, least motion path that interpolates linearly between equilibrium reactant and product geometries of the molecular system. Conservation of linear and angular momentum are correctly accounted for. The resulting Hamiltonian has a Cartesian‐type kinetic energy, the Coriolis coupling terms originally present in the kinetic energy having been transformed to potential energy coupling (hence the term ‘‘diabatic’’ reaction path Hamiltonian). Curvature coupling terms that appear in the original reaction path Hamiltonian, which is based on the minimum energy reaction path, are absent here because the present reaction path is straight. This new, diabatic reaction path Hamiltonian should be especially useful for describing H‐atom transfer reactions in polyatomic systems, a case for which the minimum energy reaction path provides a poor description.

A dynamical theory of unimolecular ionic dissociation reactions in polar solvents

Abstract: A dynamical theory for the rates of unimolecular dissociations in polar solvents is constructed. Two classes of dissociation reactions, with dipolar and ionic transition states, are considered, and the theory is illustrated for a generalized continuum model water solvent. The rate of charge variation along the reaction coordinate is found to play a central role. Deviations from equilibrium solvation transition state theory predictions are found and discussed. Two nonequilibrium solvation regimes—nonadiabatic solvation and polarization caging—occur, and their appearance is connected to whether the solvated transition state has a reactant‐like or product‐like charge distribution.

Unimolecular reaction rate theory for highly flexible transition states: use of conventional coordinates

Abstract: An alternative method for implementing RRKM theory for unimolecular reactions with highly flexible transition states is described using conventional coordinates. The number of available states for motion in the transition state state N_(EJ) is determined via an appropriate average over the absolute space orientations and body-fixed momenta of the two fragments. The results of calculations of N_(EJ) for the C_2H_6 → 2CH_3 reaction (or alternatively for the corresponding recombination reaction) obtained from the present expression are shown to be equivalent numerically to those obtained previously by Wardlaw and Marcus.

Do supra-antara paths really exist for 2 + 2 cycloaddition reactions? Analytical computation of the MC-SCF Hessians for transition states of ethylene with ethylene, singlet oxygen, and ketene

Abstract: The "transition structures" for the 2, + 2, cycloaddition of ethylene with ethylene, with singlet 02, and with ketene have been determined by MC-SCF gradient methods. The subsequent characterization of these critical points by analytical Hessian computation shows that in each case the critical point is a saddle point of index 2 (Le., there are two imaginary vibrational frequencies). Thus, the results show that the supra-antara reaction path may not exist at all for 2 + 2 cycloadditions.

Determination of the intrinsic reaction coordinate: Comparison of gradient and local quadratic approximation methods

Abstract: The determination of the intrinsic reaction coordinate (IRC) by gradient methods often fails or is very inefficient when gradients vary markedly between coordinates as occurs in asymptotic regions of bimolecular surfaces. The alternative local quadratic approximation (LQA) approach, based on second derivatives of the surface, is shown to be generally accurate and efficient.

Double many-body expansion of molecular potential energy functions and the role of long-range forces in the rates of chemical reactions

Abstract: A review is given of the double many-body expansion (DMBE) of molecular potential energy functions and of the role of long-range forces - these being properly described in the DMBE - in the rates of chemical reactions. The O+OH→O2+H and H+H2→H2+H reactions are discussed. New thermal rate coefficients for the former reaction are also reported from the assumption of loose transition states.

Unimolecular reaction rate theory for highly flexible transition states. 2. Conventional coordinate formulas for the various possible fragment combinations: miscellaneous topics

Abstract: A method for using conventional coordinates in the implementation of RRKM theory for unimolecular dissociations was described in part 1 of this series, for the case where both fragment molecules are nonlinear. The corresponding formalism for all possible types of fragments, atomic, linear, and nonlinear fragments and their combinations, is presented here. Also discussed analytically is the tendency, in a unimolecular dissociation, for the position of the transition state to move to shorter fragment-fragment separation distances with increasing total energy E. This tendency has marked consequences, including increasing deviation of rate constants from those of phase space theory with increasing E and, in the case of fragment-fragment recombination, a corresponding tendency for high-pressure rate constants to decrease with increasing temperature. Two other topics considered in this paper are the case of two minima in the variational calculation and the role of the repulsive potential energy curves in the unimolecular dissociations under consideration.

Consequences of molecular recognition in the S1-S2 intersubsite region of papain for catalytic-site chemistry. Change in pH-dependence characteristics and generation of an inverse solvent kinetic isotope effect by introduction of a P1-P2 amide bond into a two-protonic-state reactivity probe

Abstract: 1. The pH-dependences of the second-order rate constant (k) for the reactions of papain (EC 3.4.22.2) with 2-(acetamido)ethyl 2'-pyridyl disulphide and with ethyl 2-pyridyl disulphide and of k for the reaction of benzimidazol-2-ylmethanethiol (as a minimal model of cysteine proteinase catalytic sites) with the former disulphide were determined in aqueous buffers at 25 degrees C at I 0.1. 2. Of these three pH-k profiles only that for the reaction of papain with 2-(acetamido)ethyl 2'-pyridyl disulphide has a rate maximum at pH approx. 6; the others each have a rate minimum in this pH region and a rate maximum at pH 4, which is characteristic of reactions of papain with other 2-pyridyl disulphides that do not contain a P1-P2 amide bond in the non-pyridyl part of the molecule. 3. The marked change in the form of the pH-k profile consequent upon introduction of a P1-P2 amide bond into the probe molecule for the reaction with papain but not for that with the minimal catalytic-site model is interpreted in terms of the induction by binding of the probe in the S1-S2 intersubsite region of the enzyme of a transition-state geometry in which nucleophilic attack by the -S- component of the catalytic site is assisted by association of the imidazolium ion component with the leaving group. 4. The greater definition of the rate maximum in the pH-k profile for the reaction of papain with an analogous 2-pyridyl disulphide reactivity probe containing both a P1-P2 amide bond and a potential occupant for the S2 subsite [2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide [Brocklehurst, Kowlessur, O'Driscoll, Patel, Quenby, Salih, Templeton, Thomas & Willenbrock (1987) Biochem. J. 244, 173-181]) suggests that a P2-S2 interaction substantially increases the population of transition states for the imidazolium ion-assisted reaction. 5. The overall kinetic solvent 2H-isotope effect at pL 6.0 was determined to be: for the reaction of papain with 2,2'-dipyridyl disulphide, 0.96 (i.e. no kinetic isotope effect), for its reaction with the probe containing only the P1-P2 amide bond, 0.75, for its reaction with the probe containing both the P1-P2 amide bond and the occupant for the S2 subsite, 0.61, and for kcat./Km for its catalysis of the hydrolysis of N-methoxycarbonylglycine 4-nitrophenyl ester, 0.67.(ABSTRACT TRUNCATED AT 400 WORDS)

Ab initio structures of transition states in electrophilic addition reactions of molecular halogens with ethene

Abstract: The fluorination of ethene occurs via a four-centred transition state, while chlorination and bromination give zwitterionic three-centred transition states.

Destabilized carbenium ions: secondary and tertiary α-carbomethoxybenzyl cations

Abstract: The secondary α-carbomethoxybenzyl cations a and the tertiary α-carbomethoxybenzyl cations d have been generated by electron impact-induced fragmentation from appropriately α-substituted methyl phenylacetate and 2-phenylpropionates 1–4 The ions a and d are further examples of destabilized carbenium ions with a push–pull substitution at the carbenium ion centre The characteristic reaction of these ions is a rearrangement by a 1,2-shift of the methoxy group concomitant to the elimination of CO This rearrangement reaction is associated with a very large and non-statistical kinetic energy release (a : T50 = 570 meV; d : T50 = 760 meV), which is attributed to tight transition states along the reaction coordinates corresponding to the three-membered cyclic oxonium ions b and h, respectively The tertiary ion d can be distinguished from its more stable isomers f and g by the mass-analysed ion kinetic energy and collisional activation spectra The investigation of specifically deuterated analogues of ions d and g reveals an isomerization of d to g via a species protonated at the phenyl group but no equilibration between d and g This isomerization exhibits a large isotope effect for the hydrogen transfer, indicating similar energy barriers for the isomerization and for the CO elimination of d

Potential energy surfaces for the reaction silicon + water

Abstract: The potential energy surfaces for the reactions of silicon atom (/sup 1/D and /sup 3/P) with the water molecule were calculated by ab initio self-consistent field (SCF) methods. The transition states for the insertion of silicon atom into the O-H bond of water were also calculated by the multiconfigurational SCF method. It is found that the crossing point of the singlet and triplet surfaces along the insertion reaction paths is near the transition state for the triplet rearrangement from the Si:OH/sub 2/ complex to HSiOH. The potential energy surfaces for the 1,2-hydrogen migration HSiOH /leftrightarrow/ H/sub 2/SiO in the singlet and triplet states and the hydrogen (H/sub 2/) elimination from HSiOH and H/sub 2/SiO were also investigated.

Solvation energies of ions and ionic transition states from studies of gas-phase ion–molecule reactions and equilibria

Abstract: Gas-phase ion–molecule reaction equilibrium measurements of reactions such as proton transfer and electron transfer have provided gas-phase thermochemical data for thousands of ions which are of importance also in solution The solvation energies of such ions can be evaluated via Born-type cycles provided that the supporting thermochemical data for the liquid solvents are available The resulting solvation enthalpies and free energies can be analysed on the basis of gas-phase data providing the sequential energy release in the initial solvation of the ion M± by solvent molecules S1 in the gas phase: M±(Sl)n–1+ Sl = M±(Sl)n, where the ΔG°n–1,n and ΔH°n–1,n are obtained from measurements of the gas-phase equilibria As examples of this approach the hydration of NH+4 and H3O+ are examined Data for the solvation of radical anions of substituted benzenes and quinones are given also Kinetic studies of gas-phase ion–molecule reactions provide energetics for the key points of the reaction coordinate Comparisons of the reaction coordinates in the gas phase and solution lead, via Born cycles, to solvation energies of the transition states Data are provided for the nucleophilic displacement reactions: Cl–+ CH3Br →(ClCH3Br)–→ ClCH3+ Br– and F–+ C6F6→ C6F–7→ C6F6+ F–

Theoretical studies on the reaction mechanism of ketene dimerization reactions

Abstract: The dimerization reactions of ketene in the gas phase to form cyclobutane-1,3-dione, diketene, or 2,4-dimethylene-1,3-dioxetane have been studied theoretically. The geometries of the reactants, products and the transition states of the above three reactions are optimized by an ab initio method. Single point energies are obtained at the MP2/4–31G level, using STO-3G geometries. The calculated activation barriers are 29.8, 35.1 and 61.2 kcal mol −1 , respectively. The orbital symmetry rule and frontier molecular orbital theory are used to elucidate the modes of approach of the reactants. In addition, the intrinsic reaction coordinate (IRC) based on the MINDO/3 method is used to trace the reaction pathways. No intermediate is found along the IRC of any reaction. All the reactions are concerted ones.

Theoretical investigations of the structural and chemical properties of hydrazinecarboxamide and hydrazinecarbothioamide

Abstract: Ab-initio MO calculations at the 3-21G//3-21G level were performed on hydrazinecarboxamide and hydrazinecarbothioamide and on their protonated forms (at the hydrazinic amino group). The two molecules show very close structural characteristics and similar behaviour for the process of internal rotation around the different bonds. For the ground-states of the free-bases the E -form turns out to be the more stable one, while the Z -form is more stable in the case of the cations. The energy difference between conformers indicates that, in physical conditions where an equilibrium is possible, the amount of one form should predominate. These trends are in agreement with a number of experimental results, especially those relative to hydrazinecarbothioamide, which is accurately known. In the bases the barriers for internal rotation around the CN bonds are higher for the amino than for the hydrazino group and in the sulphur higher than in the oxygen compound, yet the transition states occur for almost perpendicular conformations. For the cations two transition states are found, one in the proximity of the perpendicular conformation and the other at the planar E -conformation, separated by a flat minimum. The energy barriers in the cations are lower than in the corresponding bases. The calculated properties enable a homogeneous picture of the chemical behaviour of these molecules to be drawn, even in the absence of exhaustive experimental studies.

Rotational barriers of some CH2X radicalar compounds

Abstract: An analysis of the rotation barriers appearing in CH2X radicals (X= CH3, NH2, OH, COH, CHCH2) has been performed by theoretical calculations at different levels of accuracy (SCF, full MP4, CISD) and with the 6-31G and 6-31G** basis sets. When the transition state undergoes important structural changes, correlation must be introduced onto the largest basis set. The equilibrium structures are stabilized by the appearance of a three electron bond, while the transition states remain close to the conventional structure of the parent molecule. This “third electron” comes preferentially from a double bond or from a nitrogen lone pair. The oxygen substituent induces a small barrier which disappears in the ethyl radical.

Potential energy surfaces of cycloaddition reactions

Abstract: Cycloadditions reactions can be used to obtain compounds of various ring sizes. Although they have been largely investigated experimentally, considerable controversy still surrounds their mechanism. To improve the understanding of these reactions the potential energy surfaces of the following series of cycloadditions have been computed: [2+2] cycloadditions (H 2 CCH 2 + H 2 CCH 2 , H 2 CO + H 2 CO, H 2 CCH 2 + O 2 ); Diels—Alder reaction (H 2 CCHCHCH 2 + H 2 CCH 2 ); 1,3 dipolar cycloadditions (HCNO + HCCH, HCNO + H 2 CCH 2 , H 2 CNHO + H 2 CCH 2 ). The computations were performed using the ab initio MC-SCF method, which allows treatment of both concerted and non-concerted paths on an equal footing. All the critical points of the surface were optimized using analytic gradient methods and characterized by computing the Hessian matrix by finite differences of the gradients. All surfaces are investigated at minimal (STO-3G) and extended (4-31G) levels. The results of these computations indicate that: (i) for a [2+2] cycloaddition only step-wise reaction paths exist, involving diradicaloid transition states and intermediates; (ii) for the Diels—Alder reaction, the concerted synchronous pathway appears to be preferred over non-synchronous concerted or non-conccerted pathways; (iii) for the 1,3 dipolar cycloadditions the concerted pathway is preferred over the non-concerted pathway involving a diradical intermediate.

Kinetics and mechanism of the reaction of 2,3-dimethoxy-1,4-naphthoquinone with alkoxide ions in alcoholic solvents

Abstract: The reaction of 2,3-dimethoxy-1,4-naphthoquinone with ethoxide, n-propoxide, n-butoxide, and isopropoxide ion in the respective alcohols as solvents has been subjected to kinetic study. The reaction leads to 2,3-dialkoxy-1,4-naphthoquinones (2a–d) through 2-alkoxy-3-methoxy-1,4-naphthoquinones (3a–d) as intermediates. Catalytic behaviour by the alkoxide ions is observed. Rate constants and activation parameters have been measured for the two steps. The nucleophilic rate constants are related to the acidity of the respective alcohols, leading to linear behaviour in log k–ET(30) plots. Activation parameters of the two steps are discussed in terms of stabilization of reactants and transition states and the differences between the first and second substitution in terms of the effect of the sustituent in the vicinal position.

Ab initio SCF calculations of 3P Mg and Be atom activation of methane

Abstract: In studying the insertion of metal atoms into CH bonds, ab initio molecular orbital calculations were used to obtain the energies and geometries of the reaction products methylmagnesium hydride (CH3MgH) and methylberyllium hydride (CH3BeH). The two species were successfully geometry-optimized in their respective ground states and in their lowest-lying excited triplet states: 7a113e1 for the Mg-system (3-21G) and 5a112e1 for the Be-species (3-21G, 6-31G*). In both systems it was revealed that the excited states behaved like two weakly interacting species, the metal hydride and methyl radical moieties. This was in contrast to the ground state molecules which exhibited much shorter metal—carbon bonds. Investigations of possible reaction pathways involving different approaches of the 3P Mg and Be atoms with respect to a methane molecule were carried out. No transition states or meta-stable species were found for any one of four specific approaches examined at the 3-21G level of sophistication but energy minima were obtained for each geometry in the context of restricted symmetry.

Theoretical Investigations of the Structural and Chemical Properties of Hydrazinecarboxamide and Hydrazinecarbothioamide

Abstract: Ab-initio MO calculations at the 3-21G//3-21G level were performed on hydrazinecarboxamide and hydrazinecarbothioamide and on their protonated forms (at the hydrazinic amino group). The two molecules show very close structural characteristics and similar behaviour for the process of internal rotation around the different bonds. For the ground-states of the free-bases the E -form turns out to be the more stable one, while the Z -form is more stable in the case of the cations. The energy difference between conformers indicates that, in physical conditions where an equilibrium is possible, the amount of one form should predominate. These trends are in agreement with a number of experimental results, especially those relative to hydrazinecarbothioamide, which is accurately known. In the bases the barriers for internal rotation around the CN bonds are higher for the amino than for the hydrazino group and in the sulphur higher than in the oxygen compound, yet the transition states occur for almost perpendicular conformations. For the cations two transition states are found, one in the proximity of the perpendicular conformation and the other at the planar E -conformation, separated by a flat minimum. The energy barriers in the cations are lower than in the corresponding bases. The calculated properties enable a homogeneous picture of the chemical behaviour of these molecules to be drawn, even in the absence of exhaustive experimental studies.

Extra polar interactions in the transition states of the cross cycloadditions of differently substituted trifluorostyrenes: 1. Kinetics of the cycloaddition of p-trifluoromethyltrifluorostyrene and p-methoxytrifluorostyrene

Abstract: The rate constants for cross-cycloaddition and homo-cycloaddition reactions of p-methoxytrifluorostyrene and p-trifluoromethyltrifluorostyrene have been measured at 110–160°C with the help of the “KINETICS-I” computer programm. Our data, particularly the π function values (1.4–1.9) which are defined by eq 10 and related to the tendency of cross-cycloaddition, reveal that very likly there is an extra polar interaction in the transition state of the cross-cycloaddition reaction between donor- and acceptor-substituted trifluorostyrenes.

Kinetics and Mechanism of the Reaction of 2,3-Dimethoxy-1,4-naphthoquinone with Alkoxide Ions in Alcoholic Solvents

Abstract: The reaction of 2,3-dimethoxy-1,4-naphthoquinone with ethoxide, n-propoxide, n-butoxide, and isopropoxide ion in the respective alcohols as solvents has been subjected to kinetic study. The reaction leads to 2,3-dialkoxy-1,4-naphthoquinones (2a–d) through 2-alkoxy-3-methoxy-1,4-naphthoquinones (3a–d) as intermediates. Catalytic behaviour by the alkoxide ions is observed. Rate constants and activation parameters have been measured for the two steps. The nucleophilic rate constants are related to the acidity of the respective alcohols, leading to linear behaviour in log k–ET(30) plots. Activation parameters of the two steps are discussed in terms of stabilization of reactants and transition states and the differences between the first and second substitution in terms of the effect of the sustituent in the vicinal position.

The Mechanisms of Nucleophilic Substitution at the Main Group Elements and Design of Intramolecular Tautomeric Systems

Abstract: The general principles of the construction of 1,j-tautomeric sigmatropic systems developed in the previous chapters are here applied to predict novel compounds of this type. Furthermore, they are used for the analysis of the intramolecular dynamics of recently-obtained tautomeric systems based on transfer reactions of heavy atomic groups. Mechanisms of the elementary stages at which the transition states are formed, which determine the stereochemical outcome and the magnitude of the activation barrier of 1,j-sigmatropic reactions, are examined in greater detail. The data obtained are then used for the structural modelling of the tautomeric compounds that are sterically adjusted to mimic the configuration of the reaction centers in the reactive zone of the potential energy surface.

Theoretical Studies on the Reaction Mechanism of Ketene Dimerization Reactions

Abstract: The dimerization reactions of ketene in the gas phase to form cyclobutane-1,3-dione, diketene, or 2,4-dimethylene-1,3-dioxetane have been studied theoretically. The geometries of the reactants, products and the transition states of the above three reactions are optimized by an ab initio method. Single point energies are obtained at the MP2/4–31G level, using STO-3G geometries. The calculated activation barriers are 29.8, 35.1 and 61.2 kcal mol −1 , respectively. The orbital symmetry rule and frontier molecular orbital theory are used to elucidate the modes of approach of the reactants. In addition, the intrinsic reaction coordinate (IRC) based on the MINDO/3 method is used to trace the reaction pathways. No intermediate is found along the IRC of any reaction. All the reactions are concerted ones.

Thiopyrylium Cations as Appropriate Compounds for the Quantitative Evaluation of ipso‐Substituent Effects.

Abstract: The kinetic and equilibrium constants for the reaction of 2,6-diphenyl-4-X-thiopyrylium cations (X = H, Ph, But, or OMe) with methoxide ion to yield the corresponding 2H- and 4H-adducts have been determined in MeOH at 25 °C. The completion of an analogous study for 2,4,6-triphenylpyrylium ion is also reported. The equilibrium data allow the quantitative evaluation, in free energy terms, of ipso-effects relative to H (OMe, ca.–12; Butca. 0; Ph ca. 10 kJ mol–1). The estimate of the gem-dimethoxy stabilisation is in accordance with a previous estimate based on data referring to the formation of negatively charged Meisenheimer adducts. Although steric interactions between the geminal groups seem to be negligible in the final adducts, the kinetics data suggest that they occur in the transition states. This observation further supports our previous hypothesis of an ion-pair-like transition state for this class of reactions.