Is it possible to compare the energies of two different but structurally similar molecules?
For example, if we perform a simple opt/freq calculation on a small tripeptide with the amino acids Alanine-Glycine-Alanine and the energy is -150,000 and we do the same thing for the peptide Alanine-Alanine-Alanine and the energy is -200,000, could we say that the Alanine-Alanine-Alanine peptide is more stable. Or does the fact that they have different atoms make any energy comparisons impossible?
'More stable' is a hard term to pin down! It is dependent on the environment that the molecule is held in. Having said that, one way to compare 'stability' is to calculate the energy of formation by calculating the energies of the atoms in their natural state at room temperature/pressure and subtracting that from the energy of the molecule.
Mr.Kastner,
The comparative analysis can be done only if the N-particles are the same. In your systems they are not.
'More stable' is a hard term to pin down! It is dependent on the environment that the molecule is held in. Having said that, one way to compare 'stability' is to calculate the energy of formation by calculating the energies of the atoms in their natural state at room temperature/pressure and subtracting that from the energy of the molecule.
Mat Tolladay. I really appreciate your answer and would like to try it! Would I perform an energy calculation for each atom type that I used in my system using the same method and basis set as I did on the larger molecule?
You would need to calculate the energy of atoms in a natural state at room temperature/pressure. O2 for oxygen, H2 for hydrogen, graphite for carbon and so on. Use the same method, basis set and such like. The link below gives an example of this method in use.
https://10.1021/nl0708922
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