The rate constant of the NH3 + H -NH2 + H2 reaction was calculated using the nonvariational transition-state theory for the temperature range 500-2000 K. The quality of the theoretical barrier height depends on the amount of correlation energy taken into account, on the post-MP4 corrections, and on the spin decontamination when radicals are involved. The quadratic configuration interaction (QCI) method gives values higher than the perturbational post-MP4 SAC4/A1 method. The basis set superposition error and the sources of thermal corrections (theoretical or experimental) have minor importance. We found that the two rate constants using the SAC4/A1 and QCI barriers represent an upper and lower bound, respectively, to the available experimental values.

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A theoretical study is described of chemical reactions in solution by means of molecular dynamics simulations, with solute-solvent interaction potentials derived from AMBER van der Waals parameters and QM/MM electrostatic charges in solution. The solvent is used as the reaction coordinate, and the free energy curves to calculate the properties related to the reaction mechanism. The proposed scheme is applied to the tautomerization process in aqueous solution for some amino acids H(2)NCHR-COOH (with R = H being glycine, R = CH(3) alanine, R = CH(2)OH serine, and R = CH(2)COOH aspartic acid), focusing on the role of the solvent in the reaction (assisted versus unassisted mechanisms) and on the effect of the hydrophilic/hydrophobic character of the radical R on the activation and reaction energies.

Free energy of the tautomeric equilibrium A-T ! A*-T* between the canonical and noncanonical DNA base equilibrium in aqueous solution was theoretically determined by applying electronic structure methods (at the M06-2X-PCM/6-31111G(d,p) level) and steered molecular dynamic simulations. Concerted and stepwise mechanisms were considered for the double proton transfer in an effort to explain the anomalous behavior of this system where an unfavorable process without a transition state can be observed depending on the level of calculation used. Of the different mechanisms used in the simulations, the stepwise mechanism, in which the first step implies the transference of a proton from thymine to adenine, and a second step with the transference of a different proton from adenine to thymine, was the only one that showed two transition states and a reaction intermediate. However, a concerted and stepwise mechanism has similar kinetic and thermodynamic behavior, with similar reaction and activation energies. Simple proton transfer was more favorable for the transference of the hydrogen from the adenine to the thymine. The inclusion of an aqueous medium in this study only slightly modified these energies, but the barrier energy was higher when the solvent was described as a discrete medium. Transition states and intermediate structures were analyzed at molecular dynamic level. K E Y W O R D Sadenine-thymine, electronic structure calculation, proton transfer in solution, steered molecular dynamic simulations, tautomeric equilibrium, thermodynamic properties