Proton transfer, computational

Outer sphere electron transfer (e.g., [11-19,107,160-162]), ion transfer [10,109,163,164] and proton transfer [165] are among the reactions near electrodes and the hquid/liquid interface which have been studied by computer simulation. Much of this work has been reviewed recently [64,111,125,126] and will not be repeated here. All studies involve the calculation of a free energy profile as a function of a spatial or a collective solvent coordinate. 

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]. 

As in the case of benzothiazoles and benzimidazoles, the excited-state proton transfer in 2-(2 -hydroxyphenyl)benzoxazole was studied both experimentally and computationally. The results closely resemble the observations for the other species The cw-enol form is preferred in the Sq ground state and the cw-keto form in the 5i excited state. Moreover, the proton transfer appears to be due to vibrational relaxation rather than thermal activation, suggesting that the aromatic ring has an impact on the transfer reaction of these systems [95JPC12456, 99JST255]. 

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... 

Comparison of Barrier Heights (BH) in kcal mol for the Proton Transfer in Malonaldehyde Computed by Different Quantum Chemical Methods... 

The detailed mechanism of this enantioselective transformation remains under investigation.178 It is known that the acidic carboxylic group is crucial, and the cyclization is believed to occur via the enamine derived from the catalyst and the exocyclic ketone. A computational study suggested that the proton transfer occurs through a TS very similar to that described for the proline-catalyzed aldol reaction (see page 132).179... 

The TS proposed for these proline-catalyzed reactions is very similar to that for the proline-catalyzed aldol addition (see p. 132). In the case of imines, however, the aldehyde substituent is directed toward the enamine double bond because of the dominant steric effect of the (V-aryl substituent. This leads to formation of syn isomers, whereas the aldol reaction leads to anti isomers. This is the TS found to be the most stable by B3LYP/6-31G computations.199 The proton transfer is essentially complete at the TS. As with the aldol addition TS, the enamine is oriented anti to the proline carboxy group in the most stable TS. 

Table 13-6. Computed total energy differences [kcal/mol] and distances [A] for the proton transfer in malonaldehyde enol (6-311++G(d,p) basis). 

Gao J, Wong K-Y, Major DT (2008) Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. J Comput... 

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. 

With the RPA model it has been possible to simulate many sets of CPA/alumina data mentioned in the literature [18], with the same set of unadjusted parameters (PZC, K and K2, OH density). Since pH shifts in the presence and the absence of CPA adsorption on alumina [23] and PTA adsorption on silica [19] are similar, it can be concluded that metal and proton transfer are independent in these systems. Thus the pH shift model can be used in concert with the RPA model not only to predict metal uptake, but also to compute final pH from the initial pH of the contacting solutions [18,28],... 

The computational results show that transition structures derived from hydroperoxo Re complexes lie slightly higher in energy than those obtained for the corresponding peroxo complexes, nevertheless their involvement in the epoxidation reaction cannot be excluded. However, for neither MoVI nor Revn evidence Get alone preference) for hydroperoxo reaction pathways is as clear as for TiIV complexes. Of course, more complex mechanisms involving intermolecular proton transfer and/or hydrogen bonded intermediates may change this picture to some extent. 

The empirical valence bond (EVB) approach introduced by Warshel and co-workers is an effective way to incorporate environmental effects on breaking and making of chemical bonds in solution. It is based on parame-terizations of empirical interactions between reactant states, product states, and, where appropriate, a number of intermediate states. The interaction parameters, corresponding to off-diagonal matrix elements of the classical Hamiltonian, are calibrated by ab initio potential energy surfaces in solu-fion and relevant experimental data. This procedure significantly reduces the computational expenses of molecular level calculations in comparison to direct ab initio calculations. The EVB approach thus provides a powerful avenue for studying chemical reactions and proton transfer events in complex media, with a multitude of applications in catalysis, biochemistry, and PEMs. 

Molecular modeling of PT at dense interfacial arrays of protogenic surface groups in PEMs needs ab initio quantum mechanical calculations. In spite of fhe dramafic increase in computational capabilihes, it is still "but a dream" to perform full ab initio calculations of proton and water transport within realistic pores or even porous networks of PEMs. This venture faces two major obstacles structural complexity and the rarity of proton transfer events. The former defines a need for simplified model systems. The latter enforces the use of advanced compufahonal techniques that permit an efficient sampling of rare evenfs. ... 

A density functional theory computational approach has been used " to investigate the [1,5]-hydrogen shift in (z)-penta-l,3-diene. Ab initio calculations of the activation barriers to proton transfer in nitrogen derivatives have been computed and these values used to show that the proton transfer in pyrazole is formally a... 

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