Browsing by Subject "Free energy perturbation"

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    Comprehensive study of the chemical reactions resulting from the decomposition of chloroform in alkaline aqueous solution.
    (2009-11) Mews, Jorge Estevez
    Chloroform (CHCl3) is a volatile liquid, which has a rather slow rate of decomposition in ground water. It is a known carcinogen and one of the most common contaminants found at toxic waste sites. The dominant degradation process for chloroform in both the atmosphere and the groundwater is the reaction with the hydroxyl radical or hydroxide ion. This process triggers a sequence of reactions which ultimately yield carbon monoxide, hydrogen chloride, and formic acid. The rate of chloroform degradation is considerably larger in solution than that in the gas phase and it increases dramatically with increasing pH. However, only one of the viable reactions had been studied previously at a high level of theory in solution. It is of great interest to gain a deeper understanding of the decomposition reaction mechanism. Quantum mechanical methods are well suited for studying the mechanism of organic reactions. However, a full quantum mechanical treatment of the entire fluid system is not computationally feasible. In this work, combined quantum mechanical and molecular mechanical (QM/MM) methods are used for studying chemical reactions in condensed phases. In these calculations, the solute molecules are treated quantum mechanically (QM), whereas the solvent molecules are approximated by empirical (MM) potential energy functions. The use of quantum mechanics and statistical sampling simulation is necessary to determine the reaction free energy profile. In the present study, the ab initio Hartree-Fock theory along with the 3-21G basis set was used in the quantum mechanical calculations to elucidate the reaction pathways of chloroform decomposition, with a focus on basic reaction conditions. Statistical mechanical Monte Carlo approach was then applied in molecular mechanical simulations, employing the empirical TIP3P model for water. We employed state-of-the-art electronic structure methods to determine the gas-phase inter-nuclear potential energy profile for all the relevant reactions. Each gas-phase potential energy profile obtained at a high level of theory was used as a post-correction of the corresponding reaction free energy profile in aqueous solution. A detailed picture of the actual mechanism driving the decomposition pathway of chloroform has emerged from these simulations.