I am new to Gaussian and I want to optimize graphene using DFT. After the geometry optimization, it has been severely changed, and some bonds were set as double and triple.
Why am I unable to get the structural values similar to the input structure?
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8$\begingroup$ Please post your input file. $\endgroup$– DSVACommented Jul 14, 2017 at 12:47
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3$\begingroup$ Possible reasons: wrong input files / unreasonable edge effects $\endgroup$– GregCommented Jul 14, 2017 at 15:20
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$\begingroup$ Thank you for your interest. I didn't know how to post a input file so that I have sent a google drive link. drive.google.com/file/d/0B3OwbLbmgat8YXRRX1huNHhNV2M/… $\endgroup$– MariappanCommented Jul 17, 2017 at 11:32
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1 Answer
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The decision for a bond to be visually represented as a single, double, or triple bond in a molecular visualization program (e.g. GaussView) is based on rather arbitrary distance rules that often do not represent the actual bond order. Unless you are investigating the bond order in other ways (e.g. Wiberg bond index), what you're seeing for the bond order is nothing more than a guess. If you switch visualization programs, you'll likely find the bond orders to change.
If, indeed, the actual geometry of the graphene is completely unphysical after the geometry optimization, here are some questions to ask yourself:
How good is the initial structure you gave the optimization algorithm? Are you using a template graphene structure that should be close to the final geometry? If you made it "from scratch", it would be worthwhile to apply symmetry to your structure prior to running the calculation in Gaussian.
How have you terminated your graphene? You say you're using Gaussian, so I doubt you are using periodic methods. Have you terminated all dangling bonds with hydrogens, for instance?
In line with Point #2, what is the size of your graphene "cluster" model? Perhaps the cluster you chose is too small.
Ensure you don't have various input file errors (e.g charge/multiplicity).
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$\begingroup$ Dear Argon, Thank you for your comments. Yes, It may be the reason of input files. I gave it by drawn using chemdraw then save it as gaussian input file. Isn't right? I have deleted all the hydrogen atoms manually. I really didn't know how to give optimized algorithm without get successful optimization. There are 54 atoms in my geometry of graphene structure. Isn't enough size? Thanks in advance. $\endgroup$ Commented Jul 17, 2017 at 10:41
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1$\begingroup$ Nobody is going to be able to help you directly unless you post your input file or at least the atomic coordinates. It sounds like the initial geometry could have been very poor if you made it in ChemDraw. Did you at least visualize it beforehand in a program like Avogadro or GaussView to confirm it looks correct? Also, as I mentioned, you likely need to artificially terminate the undercoordinated C atoms with H atoms. If you just consider a small graphene cluster of 54 atoms, you need to terminate the cluster where it would normally continue periodically, otherwise the coordination is off. $\endgroup$– ArgonCommented Jul 17, 2017 at 12:52
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$\begingroup$ Thank you for your reply. Yes, I have visualized and verified using GAISSVIEW prior to run calculation. It was pretty good to view, all the bonds are single. Sorry, I am new to this forum also. I didn't know how to upload a input file. The characters also very limited here so i could not copy and paste the input coordinates also. I am unable to know how to overcome this issue. $\endgroup$ Commented Jul 19, 2017 at 8:36