Isomerization reaction dynamics

Benjamin, I. Pohorille, A., Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular dynamics study, J. Chem. Phys. 1993, 98, 236-242... 

From stochastic molecnlar dynamics calcnlations on the same system, in the viscosity regime covered by the experiment, it appears that intra- and intennolecnlar energy flow occur on comparable time scales, which leads to the conclnsion that cyclohexane isomerization in liquid CS2 is an activated process [99]. Classical molecnlar dynamics calcnlations [104] also reprodnce the observed non-monotonic viscosity dependence of ic. Furthennore, they also yield a solvent contribntion to the free energy of activation for tlie isomerization reaction which in liquid CS, increases by abont 0.4 kJ moC when the solvent density is increased from 1.3 to 1.5 g cm T Tims the molecnlar dynamics calcnlations support the conclnsion that the high-pressure limit of this unimolecular reaction is not attained in liquid solntion at ambient pressure. It has to be remembered, though, that the analysis of the measnred isomerization rates depends critically on the estimated valne of... 

Schroeder J and Troe J 1993 Soivent effects in the dynamics of dissociation, recombination and isomerization reactions Activated Barrier Crossing ed G R Fieming and P Hanggi (Singapore Worid Scientific) p 206... 

Detailed reaction dynamics not only require that reagents be simple but also that these remain isolated from random external perturbations. Theory can accommodate that condition easily. Experiments have used one of three strategies. (/) Molecules ia a gas at low pressure can be taken to be isolated for the short time between coUisions. Unimolecular reactions such as photodissociation or isomerization iaduced by photon absorption can sometimes be studied between coUisions. (2) Molecular beams can be produced so that motion is not random. Molecules have a nonzero velocity ia one direction and almost zero velocity ia perpendicular directions. Not only does this reduce coUisions, it also aUows bimolecular iateractions to be studied ia intersecting beams and iacreases the detail with which unimolecular processes that can be studied, because beams facUitate dozens of refined measurement techniques. (J) Means have been found to trap molecules, isolate them, and keep them motionless at a predetermined position ia space (11). Thus far, effort has been directed toward just manipulating the molecules, but the future is bright for exploiting the isolated molecules for kinetic and dynamic studies. 

Recently, Eisenthal and coworkers have developed time-resolved surface second harmonic techniques to probe dynamics of polar solvation and isomerization reactions occurring at liquid liquid, liquid air, and liquid solid interfaces [22]. As these experiments afford subpicosecond time resolution, they are analogous to ultrafast pump probe measurements. Specifically, they excite a dye molecule residing at the interface and follow its dynamics via the resonance enhance second harmonic signal. 

There are, however, still some unsolved, important questions103 about this fundamental reaction, of great relevance in dense interstellar clouds, where it could well be the source of the C3H and C3 species detected there. These unsolved questions are (a) what is the branching ratio for formation of the two isomeric C3H species, Z-C3H and C-C3H, and how does it vary with Ec (b) How do the detailed reaction dynamics and the branching ratio for C3H and C3 formation vary with Ec ... 

Pohorille, A. Wilson, M.A. Isomerization reactions at aqueous interfaces, in Reaction Dynamics in Clusters and Condensed Phases — The Jerusalem Symposia on Quantum Chemistry and Biochemistry, lortner, J. Levine, R. Pullman, B., Eds., vol. 26. Kluwer Dordrecht, 1993, p. 207... 

The several theoretical and/or simulation methods developed for modelling the solvation phenomena can be applied to the treatment of solvent effects on chemical reactivity. A variety of systems - ranging from small molecules to very large ones, such as biomolecules [236-238], biological membranes [239] and polymers [240] -and problems - mechanism of organic reactions [25, 79, 223, 241-247], chemical reactions in supercritical fluids [216, 248-250], ultrafast spectroscopy [251-255], electrochemical processes [256, 257], proton transfer [74, 75, 231], electron transfer [76, 77, 104, 258-261], charge transfer reactions and complexes [262-264], molecular and ionic spectra and excited states [24, 265-268], solvent-induced polarizability [221, 269], reaction dynamics [28, 78, 270-276], isomerization [110, 277-279], tautomeric equilibrium [280-282], conformational changes [283], dissociation reactions [199, 200, 227], stability [284] - have been treated by these techniques. Some of these... 

In addition to charge transfer processes, calculations of adsorption free energy and of isomerization reaction equilibrium and dynam-... 

Achieving control over microscopic dynamics of molecules with external fields has long been a major goal in chemical reaction dynamics. This goal stimulated the development of quantum control schemes, which have been applied with spectacular results to unimolecular reactions, such as photodissociation or isomerization reactions. Attaining control over bimolecular reactions in a gas has proven to be a much bigger challenge. 

Interestingly, in the experiments devoted solely to computational chemistry, molecular dynamics calculations had the highest representation (96-98). The method was used in simulations of simple liquids, (96), in simulations of chemical reactions (97), and in studies of molecular clusters (98). One experiment was devoted to the use of Monte Carlo methods to distinguish between first and second-order kinetic rate laws (99). One experiment used DFT theory to study two isomerization reactions (100). 

H. Hamaguchi I would like to comment on the stilbene photoisomerization in solution. We recently found an interesting linear relationship between the dephasing time of the central double-bond stretch vibration of Si franj-stilbene, which was measured by time-resolved Raman spectroscopy, and the rate of isomerization in various solutions. Although the linear relationship has not been established in an extensive range of the isomerization rate, I can point out that the vibrational dephasing time measured by Raman spectroscopy is an important source of information on the solvent-induced vibrational dynamics relevant to the reaction dynamics in solution. 

Cis-trans isomerization in benzylideneaniline (PhCH=NPh) has been found by computation to involve a single TS, and conformers leading to each isomer have been identified. However, kinetic selectivity of the two conformers depends on the reaction dynamics.23... 

Since his arrival at McMaster in 1988, Randall Dumont has focused on statistical theories and their origin in quantum and classical mechanics. His interests include the development of Monte Carlo implementations of statistical theory wherein dynamical processes are simulated by random walks on potential energy surfaces. The breakdown of statistical theory and the appearance of nonexponential population decay are also topics of his ongoing investigations. Other questions of interest are the incorporation of quantum effects into statistical theory and the effects of collisions on reaction processes. He has a special interest in argon cluster evaporation in vacuum197 and in the description of simple isomerization reactions.198 His other interests include the semiclassical description of classically unallowed processes such as tunneling.199... 

Reactivity is an intriguing aspect of these complexes not only because of the previously mentioned unique bonding mode, but also because these complexes can serve as good models for surface-bound divalent silicon and germanium species. Unfortunately, only a limited number of the reactions with small molecules and catalytic reactions have been reported so far. In contrast, the dynamic behaviors and isomerization reactions of these complexes, which give plentiful information about their chemical properties, are well documented. 

The potential energy surface for the isomerization reaction HCN —> CNH used below was proposed by Murrell, Carter, and Halonen [65]. A contour plot of this potential energy surface is presented in Fig. 36. The two local minima correspond clearly to HCN and CNH. Although there are quantitative differences between this potential energy surface and others, all of the surfaces are sufficiently similar that the qualitative character of the classical dynamics that each surface supports is the same. 

Up to moderately high energy ( 179%) of the activation barrier for reactant product in the Are isomerization reaction, the fates of most trajectories can be predicted more accurately by Eq. (11) as the order of perturbation calculation increases, except just in the vicinity of the (approximate) stable invariant manifolds (e.g., see Eig. 5), and that the transmission coefficient K observed in the configurational space can also be reproduced by the dynamical propensity rule without any elaborate trajectory calculation (see Eig. 6). Our findings indicate that almost all observed deviations from unity of the conventional transmission coefficient k may be due to the choice of the reaction coordinate whenever the k arises from the recrossings, and most transitions in chemical... 

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