In this work, we present a theoretical study of the mechanism of double proton transfer in formamide, formamide-thioformamide and thioformamide dimers. The reaction mechanisms were analyzed in terms of the energy profile and novel concepts such as the reaction force profile and reaction electronic flux, along with local electronic properties such as NBO analysis. All systems were characterized computationally using DFT/B3LYP 6-311G** on Gaussian09. These results show that the electronic processes take place mostly in the transition state for all the systems; in the formamide and thioformamide dimers, electron transfer has a synchronic nature, while the electron transfer is asynchronic in the formamide-thioformamide dimer.

Methyl transfer reactions play an important role in biology and are catalyzed by various enzymes. Here, the influence of the molecular environment on the reaction mechanism was studied using advanced ab initio methods, implicit solvation models and QM/MM molecular dynamics simulations. Various conceptual DFT and electronic structure descriptors identified different processes along the reaction coordinate e.g. electron transfer. The results show that the polarity of the solvent increases the energy required for the electron transfer and that this spontaneous process is located in the transition state region identified by the (mean) reaction force analysis and takes place through the bonds which are broken and formed. The inclusion of entropic contributions and hydrogen bond interactions in QM/MM molecular dynamics simulations with a validated DFTB3 Hamiltonian yields activation barriers in good agreement with the experimental values in contrast to the values obtained using two implicit solvation models.

In this study, we present an atomic decomposition, in principle exact, at any point on a given reaction path, of the molecular energy, reaction force and reaction flux, which is based on Bader's atoms-in-molecules theory and on Pendás' interacting quantum atoms scheme. This decomposition enables the assessment of the importance and the contribution of each atom or molecular group to these global properties, and may cast the light on the physical factors governing bond formation or bond breaking. The potential use of this partition is finally illustrated by proton transfers in model biological systems.

The mechanism of Menshutkin reaction, NH(3) + CH(3)Cl = [CH(3)-NH(3)]+ + Cl-, has been thoroughly studied in both gas and solvent (H(2)O and cyclohexane) phase. It has been found that solvents favor the reaction, both thermodynamically and kinetically. The electronic activity that drives the mechanism of the reaction was identified, fully characterized, and associated to specific chemical events, bond forming/breaking processes, by means of the reaction electronic flux. This led to a complete picture of the reaction mechanism that was independently confirmed by natural bond-order analysis and the dual descriptor for chemical reactivity and selectivity along the reaction path.

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