Posts Tagged ‘DFT’
Doubly charged metal ions Reactivity with peptides. An ab initio molecular dynamics perspective
A good knowledge of the interaction of formamide, as a suitable model of a peptide function, with alkaline-earth doubly charged metal ions is important to understand many aspects of the behavior of proteins at the molecular level. This motivated the study of such interactions from both the experimental and the theoretical viewpoints, the dynamical aspects being crucial to rationalize the experimental results (See Fig. 1)
Figure 1: In CID processes alternative trajectories (pink curve) to the minimum energy path may be accessible leading to non-thermodinamically favored products.
The first step focused on a thorough assessment of the model to be used in the ab initio molecular dynamics simulations of the [M(formamide)]2+, M=Ca and Sr, unimolecular reactivity. This assessment included 21 different functionals, and was carried out to account simultaneously for geometries, energetics and kinetics (by means of RRKM rate constants). The subsequent ab initio molecular dynamics simulations provide us with an atomic level description of the reaction mechanism (Fig. 2), which explains the preferential loss of formamide, for both Ca2+ and Sr2+containing systems, in spite of being the more endothermic processes. We could also explain the lower reactivity of the heavier metal and account for most of the other products of both reactions, either associated to Coulomb explosions or neutral loss.
Figure 2: Evolution with time of the natural charges and some representative distances for a trajectory yielding a Coulomb explosion product.
The aforementioned assessment will be published in Phys. Chem. Chem. Phys. The ab initio molecular dynamics simulation performed after the assessment will form the body of a second publication which was almost finished during the STSM. One of the most important conclusions of the analysis of the dynamical results was the necessity of doing post-TS dynamics to actually explain the formation of some products when the reactive processes are too slow. This will be the objective of our immediate work, which will show the importance of the bifurcations on the potential energy surface, that can only be accounted for through the aforementioned post-TS dynamics.