I am working of a reaction CH2 + CH2NH CH3CHNH. Before reacting those molecules I should form pre-reaction complex to have proper reference of energy to calculate barrier to the reaction (energy of the transition state - energy of pre-reaction complex). My seniors told me I should keep molecules at the sum of van der wall radius of atoms between which bond is supposed to form and then optimise. I suppose to get a structure in which molecules attract each other(distance between them decreases). If failed then look for another orientation. Is that correct ? if the distance increase by amount say 0.25 Å is that can be assumed pre-reaction complex
Dear Keshav,
In order to locate the pre-reaction complex you should run a reaction coordinate method using DFT or ab initio in which you approach the two reacting centers in increment of 0.1 A. Generally, in your case, you should observe a local minimum before reaching the transition state. this local minimum is the pre-reaction complex geometry.
Place the two reactants such that the distance between the two reacting centers is 4 angstrum to find the global minimum (GM) structure of the system, then run a reaction coordinate method such that the distance is decreased in increment of 0. 1 A (it is suggested to calculate about 20-25 steps in order to reach to the geometry of the products).
For an example, I suggest that you read the publication entitled "Enhancement of bimolecular reactivity by a pre-reaction van der Waals complex: The case of F + H2O → HF + HO " published in Chemical Science 4(2):629-632 · January 2013 which describes a similar study to yours:
https://www.researchgate.net/publication/255765412_Enhancement_of_bimolecular_reactivity_by_a_pre-reaction_van_der_Waals_complex_The_case_of_F_H2O_HF_HO
Another study which may be beneficial is the one entitled " Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-6" published Published online before print May 2, 2016, doi: 10.1073/pnas.1523362113 PNAS May 17, 2016 vol. 113 no. 20 5514-5519:
http://www.pnas.org/content/113/20/5514.abstract
Hoping this will be helpful,
Rafik
Article Enhancement of bimolecular reactivity by a pre-reaction van ...
thank you, Oleg B. Gadzhiev for your valuable answer. I will read all the articles you suggest and cite them if relevant for my work specially article 2.
- Badges
- Science topic