I like to perform a DFT Study on Tetramethylthiuramdisulfid. So I made a structure optimization for my start structur with PW6B95D3/aug-cc-pvtz to get a good structure to begin my dihedral scan to get a PES. The optimization terminated without errors, so I set up my 2 dimension scan. To get the result in a reasonable time, I worked with the combination of b3lyp/6-311++g(df,3p). The scan terminated also without any errors but when I visualize the structures there are a lot of conformers which "break" the disulfide bridge in the middle of the molecule. This is the job file for my scan job of Tetramethylthiuramdisulfid

#p opt=modredundant b3lyp/6-311++g(df,3p) nosymm


0 1
C                 -1.74592187   -0.85849184   -3.04571889
H                 -1.40943008   -1.30350450   -3.97938373
H                 -2.02299710    0.17009508   -3.24009808
H                 -2.59989913   -1.40635258   -2.66575731
C                 -0.71925406   -2.00684947   -1.11257147
H                  0.28707357   -2.34094083   -0.90110803
H                 -1.26310648   -2.82213958   -1.57474097
H                 -1.21061914   -1.72818310   -0.18319845
N                 -0.69637471   -0.89790505   -2.04320925
C                  0.24194475    0.03232282   -2.07621742
S                  0.48458418    1.13895429   -3.28209220
S                  1.50073028    0.30966253   -0.86090974
S                  1.25923450   -0.62165388    0.97873412
C                 -0.11055416    0.26088441    1.73601358
S                 -1.19921450    1.13723172    0.86384763
N                 -0.17557323    0.07031831    3.05850714
C                  0.82479554   -0.69237907    3.78321945
H                  0.64244558   -0.58545917    4.84382283
H                  0.78278163   -1.74952893    3.52785139
H                  1.82221281   -0.32440612    3.56290405
C                 -1.30366309    0.62423516    3.78483310
H                 -1.30718364    1.70769026    3.71156759
H                 -2.23638330    0.26687372    3.35848443
H                 -1.23069336    0.32351632    4.82194412

D 16 14 13 12 S 11 30.0
D 14 13 12 10 S 11 30.0

Is the job running well and the visualization has a problem made by gaussview? I read earlier that sometimes gaussview can not show binding proper. Or do I need more functions for my basisset? To simulate the disulfide bridge better?


Without seeing the result of the scan, my guess would be that it is a visualization problem with gaussview, and it has nothing to do with the calculation. Gaussview detects bonds by the distance between two atoms, and sometimes it does not show up, even though the distance is right.

You can try two things—first, in the frames where you can't see the bonds, check the S-S distance: if it's the same as the other frames where the bond is showing, then your calculation is right. Second, you can use another visualisation software, and see if it renders the bond.

I don't think that your basis set is so bad that your S-S covalent bond will break, that would not happen even with smaller basis sets than what you have used. Although adding an extra d-polarization function wouldn't hurt, but that's just my personal opinion.

  • $\begingroup$ Thanks, this comment helped me well. So I checked the bond length of the C-S, S-S, and S-C bonds. They are always around 1.8 Â for the S-C bond and 2.1 Â for the Disulfide bridge. I tried to open my .log and .fchk file of the scan job with avogadro, but I just can see the starting structure. How can I get the other scanned structures in avogadro? $\endgroup$ – Andrea Apr 8 at 6:20
  • $\begingroup$ @Andrea Huh, I thought Avogadro would be able to read all the geometries, I also tried it on my laptop and it doesn't work, so I guess I was wrong. Could you try Gabedit or GaussSum maybe? One of them has to work. Otherwise, as a last resort you would have to manually lift out coordinates from the log file. In any case, as the S-S distance is almost same in every frame, I would say your calculation ran correctly. $\endgroup$ – Shoubhik R Maiti Apr 8 at 9:30

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.