Posts Tagged ‘chemical reactivity’
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 first meeting of the Working Group 3 will take place in Birmingham Apr. 14th – 16th 2014.
The Working group focuses on the control of chemical reactivity using laser light. There will be 5 sessions covering control strategies, strong field control, measuring the evolving system, control in the condensed phase and applications. Contributions from young scientists are encouraged: as a talk or as a poster.
Registration will be open Feb. 15th.
For further details see www.stchem.bham.ac.uk/~worthgrp/xlic_wg3_2014
STSM by Cristina Sanz-Sanz, Department of Physical Chemistry, Universidad Autónoma de Madrid with Graham Worth, School of Chemistry, University of Birmingham
On September 23rd, 2013 (10 days)
From SPAIN to UNITED KINGDOM
Fitting of field dependent potential energy curves, spin-orbit and elements of the dipole moment matrix of the first 36 states of IBr
The control of the photodissociation of IBr through a curve crossing was studied in the group of Prof. Stolow using the dynamic Stark effect. Until now, theoretical simulations have used a reduced model including just 3 electronic states. However, the system consists on 36 electronic states dissociating to the ground states of atoms. We have computed and fitted the 36 potential energy curves, spin-orbit and elements of the dipole matrix for several electric field strengths and orientations. Those curves will be used in the dynamical calculations to reproduce the experiment.
The electronic structure calculation programs do not maintain the phase of the wavefunction and it translates into jumps in the spin-orbit and transition dipole moment curves. In order to use these curves in dynamical calculation programs the curves have to be fitted. Because of the sudden changes in the curves normal fitting methods do not work. We have used an optimization method to smooth out the spin-orbit and transition dipoles.
During the STSM visit we finished with the fittings of the potential energy curves, spin-orbit couplings and the elements of the dipole moment matrix for several electric field strengths and orientations. The dynamical calculations will be done using MCTDH package and we created the input files and fittings required for the wavepacket calculations. A test calculation was done for a free field example using the 36 spin-orbit states. In addition, we wrote the outline of the first publication of a series of works that will include the global fittings of potential energy curves, spin-orbit couplins and dipole moment matrix.