Peptide bond formation is a crucial chemical process that dominates most biological mechanisms and is claimed to be a governing factor in the origin of life. Dipeptides made from glycine are studied computationally via Density Functional Theory (DFT) using two different basis sets. This reaction was investigated from both a thermodynamic and kinetic point of view. The effect of explicit assistance via the introduction of discrete solvent molecules was investigated. Water, methanol, and cyclohexane were all employed as solvent media in addition to gas to investigate their effects on the mechanism of peptide bond formation. This computational investigation revealed that methanol is slightly better than water to leverage peptide bond formation both kinetically and thermodynamically, while cyclohexane, a non-polar and non-protic solvent, is the least effective after gas as a medium of solvation. Energetic results in the gas environment are very close to those obtained in polar and protic solvents, suggesting that peptide bonds can be formed under interstellar conditions.

The tautomeric equilibrium of benzimidazolone and benzimidazolthione have been studied by the density functional theory method using the CAM-B3LYP functional together with the 6-311G(d,p) basis set. Two separate mechanisms have been investigated: a direct intramolecular transfer using the polarizable continuum model and an indirect proton transfer assisted by a molecule of solvent (C6H12, H2O, CH3OH, and H2O2). In both cases, the results obtained indicate that ketone and thione are the most stable forms. However, the enhanced height of the activation barrier for the four-center mechanisms describing the tautomerism reaction as a direct intramolecular transfer implicates a relatively disadvantaged process. The participation of a polar protic solvent molecule allows the lowering of the activation energy barrier. Potential energy profiles of keto-enol and thio-enol tautomerism assisted by methanol and water are very different. The former one describes a concerted mechanism but the latter does not because it is associated with asynchronous processes that take place during the thio-enol tautomerism.

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A DFT study of hexene hydrogenation catalysed by the RuH(CO)(Cl)(PCy3)2 complex is presented. The investigation explores the feasibility of two different mechanisms: the first exploits a single phosphine complex and the second uses a two phosphines complex. The energy barriers involving a hydrogen transfer have a ten kcal.mol-1 higher than the one obtained through the single-phosphine mechanism. These results confirm the experimental hypothesis claiming that the departure of a phosphine is favourable at the beginning of the reaction which is the substitution of the catalyst model RuHCl(CO)(PMe3)2 by the real catalyst RuHCl(CO)(PCy3)2 shows no significant influence on the energetic barriers of hexene hydrogenation mechanism. The most important step of the mechanism is the kinetically determining step. The heterolytic cleavage of ruthenium-complexed H2 molecule leads to the generation of two Ru-H bonds and the oxidation of the ruthenium from Ru(II) to Ru(IV). The energy profile of this step is not relative to an elementary reaction because a shouldering is observed after the transition state. This results in an unusual gradient norm profile with five extrema. This is a direct consequence of the asynchronous nature of the different processes taking place during this step. In the case of the model complex RuHCl(CO)(IMes)(PMe3) with IMes = ( N , N '-bis( mesityl)imidazol-2-ylidene), an increase of the free enthalpy of activation is observed during the kinetically determining step, which is in agreement with the experimental work.