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VlachosGroup / pMuTT

Python Multiscale Thermochemistry Toolbox (pMuTT)
https://vlachosgroup.github.io/pMuTT/
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get_EoRT_act calculates HoRT_act #187

Open googhgoo opened 3 years ago

googhgoo commented 3 years ago

Version of pMuTT 1.2.21

Describe the bug Hello, When we use get_EoRT_act to calculate activation energy, it actually calculates get_HoRT to calculate activation energy. This maybe due to the difference in the philosophy. When I use this function, I was more interested in the experimentally obtained value, which is the raw electronic energy terms + the zero point energy terms, but this function calculates enthalpy of activation instead, which is not necessarily technically correct. I think this need a clarification.

Another way to explain this is that, get_EoRT_act is the same as get_HoRT_act. These should not be the same values.

jonlym commented 3 years ago

Hey Geun. Sorry for the delay. For some reason I stopped getting Github notifications.

I agree that I think it's a difference in philosophy. We wanted to use transition-state theory, which dictates the Ea is related to ΔH_TS and the A is related to ΔS_TS. See the exact formula we used here in the get_EoRT_act docstring. This has the added benefit of working with empirical objects that do not have electronic/vibrational properties.

We could add an option to get specifically the electronic + ZPE terms. Although not ideal, until a new version comes out you could calculate it using: Ea = reaction.get_EoRT_state(state='ts', include_ZPE=True) - reaction.get_EoRT_state(state='reactants', include_ZPE=True))

googhgoo commented 3 years ago

Ea is related to ΔH_TS and the A is related to ΔS_TS.

Is this true? When we get Ea from experiment using Arrhenius plot, aren't we only getting E0+ZPE? When we get slope (-Ea/R), the T is completely out, so Ea obtained using Arrhenius plot is different than ΔH_TS.

So technically, A is related q_TS/q_IS, terms of which exclude E0+ZPE. I get that we are working with transition state theory most of the time, but I think it can be confusing for some people.