Solution reactions, potential energy calculations

Figure 10. Calculated potential energies in the gas phase (bottom) and potentials of mean force in aqueous solution (top) for the Adjj reaction of OH + H2C-O. Solid lines...

GH Theory was originally developed to describe chemical reactions in solution involving a classical nuclear solute reactive coordinate x. The identity of x will depend of course on the reaction type, i.e., it will be a separation coordinate in an SnI unimolecular ionization and an asymmetric stretch in anSN2 displacement reaction. To begin our considerations, we can picture a reaction free energy profile in the solute reactive coordinate x calculated via the potential of mean force Geq(x) -the system free energy when the system is equilibrated at each fixed value of x, which would be the output of e.g. equilibrium Monte Carlo or Molecular Dynamics calculations [25] or equilibrium integral equation methods [26], Attention then focusses on the barrier top in this profile, located at x. ... 

In chapter 3, Profs. A. Gonzalez-Lafont, Lluch and Bertran present an overview of Monte Carlo simulations for chemical reactions in solution. First of all, the authors briefly review the main aspects of the Monte Carlo methodology when it is applied to the treatment of liquid state and solution. Special attention is paid to the calculations of the free energy differences and potential energy through pair potentials and many-body corrections. The applications of this methodology to different chemical reactions in solution are... 

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. 

Hynes et al. [298] and later Schell et al. [272] have developed a numerical simulation method for the recombination of iodine atoms in solution. The motions of iodine atoms was governed by a Langevin equation, though spatially dependent friction coefficients could be introduced to increase solvent structure. The force acting on iodine atoms was obtained from the mutual potential energy of interaction, represented by a Morse potential and the solvent static potential of mean force. The solvent and iodine atoms were regarded as hard spheres. The probability of reaction was calculated by following many trajectories until reaction had occurred or was most improbable. The importance of the potential of... 

The process of mutation by tautomerization is similar to the excited-state process described here. If a misprint induced by a tautomer takes place during replication, then an error is recorded. Because reaction path calculations of DNA base pairs show similar potential-energy characteristics to those discussed here, we anticipate being able to explore the relevance of tautomerization dynamics to mutagenesis. In this area, we are currently examining these and other systems, also in solutions. 

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