I am using Gaussian to perform excited-state calculations on a coumarin derivative. In the input file, I have drawn the molecule correctly. The output files always come out with altered bonds (single bonds become doubles, doubles become singles, dashed bonds added in, etc.). Most importantly, Gaussian continuously is adding 5 bonds to a carbon atom on an aromatic ring. It is turning the dashed bonds of the aromatic ring into solid double bonds, and still keeping the bond to the proton. Does anyone have experience with this issue or have ideas on how to fix it?
For reference, I have been using the CIS method with 6-31g (d,p). I have tried CIS 6-311g, tried freezing all of the impacted bonds, and tried using all other methods, none of which have worked.
Hi Hailey, there is some debate over what precisely a "chemical bond" is actually defined as/by in quantum mechanics, and therefore also in quantum chemistry. I won't address this debate now, other than to say that there are no chemical bonds defined within configuration interaction singles theory (CIS).
What you *do* have in CIS is an electronic wavefunction and energy defined by the electronic Schrodinger equation, and (within the Born-Oppenheimer approximation) this creates a nuclear potential energy surface that can be used to optimize the position of the atoms in your molecule into positions that normally match quite well with the positions one would expect from theories about bonding in chemistry. But again, no bonds were actually used to do that in CIS.
I would therefore assume that the bonds you are observing are actually being generated by some other piece of molecular visualization software, which is probably making tacit assumptions about how and when to draw a "bond" (ie. a line between two atoms) based on how far apart the various atoms are. These "bonds" are essentially just there for aesthetic and descriptive purposes only, and don't directly relate to the CIS calculation.
Excited state electronics, and therefore "bonding" in as far as it is actually defined, can get rather complicated, but you are essentially free to draw whatever lines between atoms that you think are the most descriptive or representative of what the underlying electronic structure actually is when creating images to show other people. Doing so doesn't misrepresent anything about the quantum mechanical CIS calculation you are reporting, and you shouldn't feel constrained by the somewhat arbitrary, or at least very average, choice for the default settings of your visualization software.
I hope that helps,
Magnus.
I absolutely agree with Magnus, whose comment I recommend. Gaussian does not create or erase bonds. Bonds are depicted by visualisation software based on bond distances and on standard covalent bond values. I would add that sometimes erroneous basis set specifications (especially regarding pseudo potentials) lead to oddly short distances, resulting (in the visualisation) in an increase of the number of bonds.
In case you wish to evaluate bonds at QM level you should evaluate bond indexes, for example at Wiberg or Mayer level. But this is another problem, I suppose.
Gaussian doesn't any create bonds and the visualisation software is used to depicted the bond due to covalent bond and bond distances
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