Hi,
I am working on an organic pesticide molecule, thiram. For DFT calculations, I have constructed a thiram molecule in GaussView 5.0.8 and submitted my job to Gaussian 09 working in Tyrone Cluster of Indian Institute of Science, Bangalore. After optimization thiram molecule got split into two separate molecules. I am unable to avoid this bond breaking of the thiram molecule. Can anyone please suggest how to stop this breaking of the bond?
Thanks in advance!
(PS: I am attaching a screenshot of the input file (.gjf) and optimized output file (.out) herewith.)
Dear Shreyas Parbat,
GaussView shows (or not) chemical bonds based in distances. There is a threshold value (different for each element) and, if the distance between two atoms is lower than that value, GaussView will show a bond. It is the same for multiple bonds: the reason why you see a "single" or a "double" or "aromatic"...It is because the distance is between those threshold values.
So, do not check GaussView to say that there is a chemical bond. Chemical bonds are electron densities, not "springs". If you want to check the bond order, I recommend you to perform a Natural Bond Orbital analysis (https://gaussian.com/population/).
Hope it helps,
Fernando
Dear Shreyas Parbat,
GaussView shows (or not) chemical bonds based in distances. There is a threshold value (different for each element) and, if the distance between two atoms is lower than that value, GaussView will show a bond. It is the same for multiple bonds: the reason why you see a "single" or a "double" or "aromatic"...It is because the distance is between those threshold values.
So, do not check GaussView to say that there is a chemical bond. Chemical bonds are electron densities, not "springs". If you want to check the bond order, I recommend you to perform a Natural Bond Orbital analysis (https://gaussian.com/population/).
Hope it helps,
Fernando
Shreyas Parbat , No bond shown between sulfur atoms in GaussView, may means that the optimized bond length is larger than default distance defined in GaussView. In this case, you can simply visualize it using "Bond distances" window. On the other hand, absence of S-S bond , may signify an optimization problem caused for example by the used method/basis set. So, I suggest conducting a Frequency calculation. No imaginary frequency is sufficient to ensure that your structure is truly minimized. Additionally, you can check the mode of S-S, the bond may be broken if you cannnot find S-S translational mode in output file.
Dr. Melek Hajji and Dr. Fernando Aguilar-Galindo , Thanks for answering the question.
The threshold concept was quite interesting. Thanks for enlightening me on this.
I tried "opt+freq" calculation and yes, the simulation did terminate without calculating actual results. I have again simulated the same molecule. This time it terminated normally and gave me Raman Spectra, But the spectra are not matching with literature. Can you please help me out with this?
- Badges
- Science topic