Energies used in cxcalc

Hello,

I am trying to find the lowest energy conformers using cxcalc.Therefore, I applied the programs

- conformers

- lowestenergyconformer

- mmff94optimizedstructure

to the sampe *.sdf file attached to this post. However, I obtain totally different energies in all cases. The "conformers" routine identifies the lowest energy conformer with 26.67, whereas the "lowestenergyconformer" routine gives 26.81 and the "mmff94optimizedstructure" routine results in -57.08. I expect the latter number to be in kcal/mole, but I could not find any hint on the unit of the other results. Therefore, could it be that the units are different, or why does the mmff94-routine give much lower energies. In the online documentation "mmff94" routine is said to identify the lowest energy conformer, so where is the difference to the other routines?

Thank you very much for your help.

Best regards,

Manuel

Hi Manuel,

The unit for the returned energy in all the three cases are kcal/mol. The reason for the energy difference is that 'conformers' and 'leconformer' uses our own version of the DREIDING force field and 'mmff94optimizedstructure' uses the industry standard MMFF94 force field.

It is a known fact that the energy values calculated for the same structure with different force fields cannot be compared because different force fields generally uses different constants and energy terms.

Generally the only  valid comparison can be to compare the energy values of multiple conformers of the same structure calculated with the same force field.

You used the following options for cxcalc:

• 
  

  conformers

  
  

The cxcalc with this option returns more conformers. All corresponds to a local energy minimum on the potential energy surface. These conformers expected to be some of the lowest and also diverse enough.

• 
  

  lowestenergyconformer

  
  

The cxcalc with this option returns the most stable, the lowest energy conformer found.

• 
  

  mmff94optimizedstructure

  
  

Generates a single structure in 3D or uses the original if in 3D. Then performs a geometry optimization on this structure and returns the obtained energy.

 

Hope this helps.

Cheers

Adrian

Dear Adrain,

thank you very much for the comprehensive answer, so I guess I will use the "leconformer" option for my task. However, I still have another question on the zero-point of the energy used in this case (so the DREIDING force field) to get an idea of the energy level.

Are the numbers I get heats of formation at 0K without zero point energies? Or is there a different zero point?

Thanks a lot for your help.

Best regards,

Manuel

Malli wrote:

Dear Adrain, thank you very much for the comprehensive answer, so I guess I will use the "leconformer" option for my task. However, I still have another question on the zero-point of the energy used in this case (so the DREIDING force field) to get an idea of the energy level. Are the numbers I get heats of formation at 0K without zero point energies? Or is there a different zero point? Thanks a lot for your help. Best regards, Manuel

Hi Manuel,

zero point energy is a term frequently used in quantum mechanics or quantum chemistry. What we have here is a force field energy based on empirical functions. Energy terms of the such are frequently decomposed to a kinetic and a potential energy part.

Imagine a 3D coordinate system where two axes are molecular coordinates and the third is the energy. This is like a hilly landscape or a map with height coloring. In this analogy the potential energy surface this hilly ground  level. During the geometry optimization process the point, which describes the current status of the coordinates of the molecule, is moved on this ground level to reach a local energy minimum (or if we are lucky the global).   Whenever extra kinetic energy is added to the system this point floats above the ground level.

we might see an analogy beetween the zero point energy and the local minimum value of the potential energy in a sense that in that point the kinetic energy is zero.However  I am not sure this analogy is not used in the literature.

This was just a qualitiative and short answer. If you are interested in this field in more detail you can consult any computational chemistry textbook.

Cheers,

Adrian