I would like to calculate the reaction kinetics using gaussian. The reactants are two molecules that form amide bond and resultant is polyamide.
What would be the transition state in this reaction?
Dear Nikhil Maroli ,
It is not clear from your question that which are the two molecules you wanted to study. Consider a simple amide bond formation; the reaction is happening between CH3C(O)OH and CH3NH2. Two molecules react with each other and give CH2C(O)NHCH3 and H2O, which is happening through a four-member transition state (see the figure). In the transition state, C5-N13, O7-H14 bonds form, and C5-O7, N13-H14 bonds break. Of course, the product is not a polyamide. You can change the CH3 groups on both acid and amine with desirable substituents and try yourself.
I hope the explanation helps!
Dear Vipin,
That is the perfect answer I was looking for. Do you recommend any tutorial/material to study the reaction kinetics through gaussian. basically, I have to predict which reaction is most fast/probable by comparing rate constant/related parameters.
Dear Nikhil Maroli ,
I have given a link below where Dr. Turbasu Sengupta has described the transition state calculations with many useful links.
Link: https://www.researchgate.net/post/How_can_I_calculate_the_Transition_state_on_gaussian_and_construct_the_energy_profile
If you want to compare two reactions with multiple steps, obtain all the transition states involved in those two reactions, and then calculate each barrier. Usually, you can compare the rate-determining step barrier (highest barrier) of one reaction with another; the lower barrier reaction proceeds faster than, the higher barrier reaction.
Suppose you want to compare two catalysts' efficiency. In that case, a better way is to calculate the TOF (turn over frequency) from the values you already obtained than merely comparing two rate-determining transition states. Please read the following article by Prof. Shaik and Prof. Kozuch, which is very helpful.
Link: https://pubs.acs.org/doi/10.1021/ar1000956
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