I have some systems and I want to study whether any reaction is feasible among them. In order to do that I want to study the possible transition states and activation energy barrier using Gaussian 09. How can I do that?
Thanks in advance.
Based on your explanation the free energy calculations can help you more than transition states in the beginning.
There is an simple command as the CBS-QB3 which yields many data about the possibility of your mentioned reaction such as:
(1) The total electronic energy as defined by the compound model, including the zero-point energy scaled by the factor defined in the model.
(2) The total electronic energy plus the internal thermal energy, which comes directly from the thermo-chemistry output in the frequency part of the output.
(3)The scaled zero-point energy is included.
(4)The total electronic energy
(5) CBS-QB3 Free Energy which is the total electronic energy and zero-point energy
of course for any accurate details, then you can use the command of PES SCAN
and consider the exited states
To sumamarize: gaussian (and any other qm software) allows you to estimate the energy barrier and free energy barrier of any reaction. In order to get such estimate you need to obtain the optimized geometry (stationary point) of reactants andm in a separate job, the optimized geometry of the transition state (another stationary point) + it would be good to also obtain the optimized geometry of the products. So it's a geometry optimziation jobs for each stationary point + freqency calculations, which accomplish two things: 1) provide a proof that your optimized structure is a true minimum for reactants and products (zero imaginary frequencies) nad true transition state (one imaginary frequency corresponding to the reaction coordinate you're looking for) and 2) give you the thermodynamic quantities at given temperature, so you can estimate the entropy contribution and obtain Gibbs free energy, instead of simple, internal energy.
Gaussian (and any other qm software) is, however, not a black box and requires certain knowledge about the reaction you're looking for, since the starting geometries have to as close to the true ones as possible. It's not possible to simply ask - what reaction are possible for my system. You need to have chemical knowledge of the system and suggest (by building corresponding geometries of transition states and products) which particular reactions following which particular mechanisms are energetically feasible. So, in other words, gaussian won't be able to suggest you any reactions, but if you have some particular reactions following particular mechanisms in mind, gaussian may answer if they're probable under certain conditions or not and estimate reaction rates.
Must-read: http://www.gaussian.com/g_whitepap/thermo.htm
If you have optimized structure of your pre-reaction complex(RC) and product, you can generate guess from them. To do that follow the steps below below:-
1. Open RC and product in the separate window in gaussview
2. Copy structure of product and paste--> Add to mol group in RC window.
3. Use opt=(calcfc,qst2) to generate guess for TS.
4. After successful completion resultant structure must be optimized again by opt=(calcfc,TS, noeigentest). This will give you true transition state.
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