conformation search

User 2371d77fed

28-02-2016 15:28:34

Hi,

I would like to to use the conformer plugin of Marvin to determine the potential conformers of a non-linear compound. I would have two questions: 1.) the program perform a geometric optimization for the molecule before the calculation?

2.) what means exactly the Dreiding energy that you receive using the Marvin conformer plugin? It means the E(total)=E(steric) or it contains the translation and rotation energy of the molecule also, which results E(total)=ΔfH°(enthaply of formation) = 3 /2RT + 3 /2RT + RT + bond energy + steric energy + torsional increments.

Thank you very much for your help.

Best Regards,

Joe

ChemAxon d51151248d

29-02-2016 16:02:45

Hi,

Here are the answers for your questions:

1, We don't perform any geometry optimization before generating conformers.

2, The Dreiding force field energy only contains energy contributions for the internal motions of the molecule (internal degrees of freedom), like bonds, angle, torsional angles. Here is a good reference for the Dreiding force field:

http://www.wag.caltech.edu/publications/sup/pdf/256.pdf

I hope this helps,

Daniel