Hello. I just started using Avogadro 1.2. I need to select one type of optimization UFF, Ghemical etc. Can someone tell the difference between these types of energies and why for one molecule the values are different. Thank you.
The difference between the different force fields can be found in many places, including the manual: Molecular Mechanics & Force Fields - Avogadro
Suffice to say if you can, use MMFF94 or GAFF for general organics and UFF otherwise.
The reason the energies will be different is because they’re relatively simple methods. Depending on what interactions are taken into account and the parameter, you will get different energies. Force fields don’t account for true quantum chemical interactions.
Thank you for the reply.
I read this but was hoping for more detailed information.
So if a molecule has a lower energy than another one it means the first is more stable?
I put 1 benzene molecule and optimized. Then I put 2 molecules of benzene on the screen the energy generated by both molecules is lower than the double of 1 molecule. Any explanation.?
Thank you and best regards.
No. In most cases, for example, having more bonds means a lower energy, since bonding is favorable. That doesn’t mean that a larger molecule is necessarily “more stable.”
I wouldn’t compare force field energies between multiple molecules.
Sure. That just implies that there are favorable intermolecular interactions … which is of course true. Benzene forms liquids and at the right temperature freezes. So benzene molecules interact favorably.
Thank you very much for the response.
The energy gain from interacting 2 or more molecules could be used to assess the type of adsorption/absorption or organic and inorganic molecules?
Thank you so much.
Regards.
I would not trust force field energies.
Would you like to help me and suggest a software to do adsorption studies on organic and inorganic molecules, preferably for windows. Thank you so much in advance.
That’s an incredibly broad question and far beyond my particular expertise.
- it depends a lot on the specifics of molecules involved
- it depends on the type of surface
- it depends on how accurate you want the answer
I’d suggest posing a much more specific question at the Matter Modeling Stack Exchange (e.g., give some specific examples that you might want to study).
In general, it may be difficult to do molecular adsorption studies on an individual PC in a reasonable time period. Generally DFT methods for surface-molecule interactions take hours to days depending on the specifics.