Posts Tagged ‘dynamics’
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.
The 1st Meeting of the Working Group 2 of the COST Action CM1204 XLIC took place at the Mercure Omaha beach Hotel situated in Port-en-Bessin, Lower Normandy, France from 24th to 27th February 2014. This meeting brought together experts from different disciplines (physics, chemistry, experience, theory) to discuss aspects of the stability of highly excited and highly charged molecules in the gas phase and their reactivity (for example interaction with other molecules and formation of new species through isomerization and/or fragmentation).
The format of the meeting was based on 24 talks (20’) with long discussion time (10’), 2 poster sections (with 23 posters) and free time for discussion. Seven talks were given by young researchers. The number of participants was around 50 persons.
We hope that this Meeting gave the opportunities exchange scientific ideas and results, to initiate new collaborations and to integrate in particular young researchers in the research community.Alicja Domaracka and Henning Zettergren
The Meeting Chairs
- 1st WG2 meeting (Port-en-Bessin, Feb. 2014) - Book of abstracts (2434 downloads)
- WG2 meeting web site
Post-transition state chemical dynamics for gas phase reactivity of dications
Our aim is to understand reaction mechanisms that characterize reactivity of dications in the gas phase, in particular complexes formed by a divalent metal (Ca, Sr for example) and an organic molecule. Two general pathways are possible, Coulomb explosion and neutral loss and chemical dynamics simulations are performed to understand weather and when reactivity proceeds through a statistical or to a non-statistical mechanism, and how the metal affects the reactivity.
Post-transition state dynamics were able to explain the difference in reactivity found between the two systems, in particular the Sr2+ + formamide reaction channel was found to be much more probable than the analogous Ca2+ + formamide one when starting from a particular transition state. Another particular result was obtained by analyzing the reaction pathways dealing to [Ca(H2O)]2+ that proceeds to a different and fast pathway with respect to what obtained from PES study. This pathway was not observed for related Sr2+ system, confirming experimental results.
We are now planning to perform detailed analysis on wave-function character and bond character across the two reaction pathways to couple the dynamical differences with chemical differences. Furthermore, we decided to run a fourth (and probably last) set of chemical dynamics simulations from another transition state. Finally, we are setting up publications related to the project, and in particular thanks to the ad hoc analysis tools provided during the visit, we are rationalizing all post-transition state dynamics results to show how this approach can be complementary to the usual PES approach.