C-H bond lengths in MarvinSpace

When I display H atoms in MarvinSpace, is MarvinSpace taking into account the lowest vibrational energy level of the C-H bond when it places the H atoms?

Hi Bob,

It's not the lowest, it is one of the low energy conformers. According to our benchmarks the RMSD of this one and the crystal structure is 1.6A on average.

Would you prefer the lowest energy conformer as default? or an option to get the lowest energy one?

 

Regards,

Miklos

I'm not talking about conformers.  The C-H bond has a ground state vibration even at 0 K, so its effective bond length is longer than the bond length given by the bottom of the energy well in the E vs. bond length energy diagram.  My question is, does MarvinSpace use the C-H bond length as measured at the bottom of the well, or does it use the C-H bond length at the maximum amplitude of the lowest vibrational energy level, or does it use some other value?

Hi Bob,

Clean3d is used for structure generation, if a 2D structure is imported into MarvinSpace. The 3D structure generation does not take into account the molecular vibrations and its effect on the bond lengths. A geometry optimized minimal energy structure is created based on the Dreiding force field. However the MMFF94 will be introduced as the new default force field for the structure generation in the 5.12 release.

Do you experience unnatural bond length in the generated 3D structure?

Kind regards,

Adrian

No, we don't experience unnatural bond lengths.  We just wanted to know what bond lengths you were using.  Now we know.  Thanks for the response.