I am the new one who is using gaussian 9w software. While studying the geometry optimization of SDS (sodium dodecyl sulfate) using the DFT method and B3LYP level basis set 6-31G(d,p) using Gaussview 6 the optimized structure of SDS molecule however shows a fragmented structure of SDS with the Na atom out of the molecule. kindly help with the process to find an optimized SDS molecular structure
If Na goes to an unreasonable location during the optimization, the initial occupation of orbitals may be unfavorable. So you might want to perform a single-point calculation of your starting geometry first, then check the orbital occupations and then perform the actual optimization.
An alternative would be to use a preoptimized structure for the anion, so optimize it first without the Na+ (don't forget to set the charge) and then add Na. Often it is easier for QC software to optimize both the orbitals and the geometry if the initial structure is already close to the truth.