Proton-transfer reactions model

There is little direct information about the magnitude of secondary kinetic isotope effects in proton-transfer reactions. Model calculations predict that in the absence of changes in force constants the effect of deuterium substitution on atoms adjacent to the reaction site should not exceed 1-2%. Moderately large effects have been observed when several atoms are substituted. Thus the transfer of a proton from the ketones... 

Figure A3.8.3 Quantum activation free energy curves calculated for the model A-H-A proton transfer reaction described 45. The frill line is for the classical limit of the proton transfer solute in isolation, while the other curves are for different fully quantized cases. The rigid curves were calculated by keeping the A-A distance fixed. An important feature here is the direct effect of the solvent activation process on both the solvated rigid and flexible solute curves. Another feature is the effect of a fluctuating A-A distance which both lowers the activation free energy and reduces the influence of the solvent. The latter feature enliances the rate by a factor of 20 over the rigid case.

Many computational studies in heterocyclic chemistry deal with proton transfer reactions between different tautomeric structures. Activation energies of these reactions obtained from quantum chemical calculations need further corrections, since tunneling effects may lower the effective barriers considerably. These effects can either be estimated by simple models or computed more precisely via the determination of the transmission coefficients within the framework of variational transition state calculations [92CPC235, 93JA2408]. 

The approach presented above is referred to as the empirical valence bond (EVB) method (Ref. 6). This approach exploits the simple physical picture of the VB model which allows for a convenient representation of the diagonal matrix elements by classical force fields and convenient incorporation of realistic solvent models in the solute Hamiltonian. A key point about the EVB method is its unique calibration using well-defined experimental information. That is, after evaluating the free-energy surface with the initial parameter a , we can use conveniently the fact that the free energy of the proton transfer reaction is given by... 

ALL-ATOM MODELS FOR PROTON TRANSFER REACTIONS IN ENZYMES... 

Proton transfer reactions, 143-144, 144 activation energy, 149,164 all-atom models for, 146-148 Cys 25-His 159 in papain, 140-143 computer program for EVB calculations, 150-151... 

All-Atom Models for Proton Transfer Reactions in Enzymes, 146... 

Below we will use Eq. (16), which, in certain models in the Born-Oppenheimer approximation, enables us to take into account both the dependence of the proton tunneling between fixed vibrational states on the coordinates of other nuclei and the contribution to the transition probability arising from the excited vibrational states of the proton. Taking into account that the proton is the easiest nucleus and that proton transfer reactions occur often between heavy donor and acceptor molecules we will not consider here the effects of the inertia, nonadiabaticity, and mixing of the normal coordinates. These effects will be considered in Section V in the discussion of the processes of the transfer of heavier atoms. 

A formalism similar to that used for partially adiabatic proton transfer reactions was applied in the calculation of the transition probability. This model of the diffusion jump is similar to the model of the diffusion of light defects in solids which was first considered in Ref. 62. 

Borgis D, Hynes JT (1991) Molecular-dynamics simulation for a model nonadiabatic proton transfer reaction in solution. J Chem Phys 94 3619-3628... 

The values of ks/kp for partitioning of carbocations are most conveniently determined as the ratio of the yields of products from the competing nucleophile addition and proton transfer reactions (equation 1 derived for Scheme 2). The determination of these product yields has been simplified in recent years by the application of high-pressure liquid chromatography (HPLC). Typically, the product peaks from an HPLC analysis are detected and quantified by UV-vis spectroscopy. In cases where the absorbance of reactants and products is small, substrates may be prepared with a chromophore placed at a sufficient distance so that its effects on the intrinsic reactivity of the carbocationic center are negligible. For example, the aliphatic substrates [1]-Y have proved to be very useful in studies of the reactions of the model tertiary carbocation [1+].21,23... 

However, a closer inspection of the experimental data reveals several differences. For ion-transfer reactions the transfer coefficient a can take on any value between zero and one, and varies with temperature in many cases. For outer-sphere electron-transfer reactions the transfer coefficient is always close to 1/2, and is independent of temperature. The behavior of electron-transfer reactions could be explained by the theory presented in Chapter 6, but this theory - at least in the form we have presented it - does not apply to ion transfer. It can, in fact, be extended into a model that encompasses both types of reactions [7], though not proton-transfer reactions, which are special because of the strong interaction of the proton with water and because of its small mass. 

The reaction of ammonia and hydrogen chloride in the gas phase has been the subject of several studies in the last 30 years [56-65], The interest in this system is mainly that it represents a simple model for proton transfer reactions, which are important for many chemical and biological processes. Moreover, in the field of atmospheric sciences, this reaction has been considered as a prototype system for investigation of particle formation from volatile species [66,67], Finally, it is the reaction chosen as a benchmark on the ability, of quantum chemical computer simulations, to realistically simulate a chemical process, its reaction path and, eventually, its kinetics. 

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