I am trying to generate the optimised structure of cation- 1-Butyl-3-methylimidazolium (Bmim) in GAMESS. I used the basis set of 6-31 G (d,p) and GAMESS was successful with the "Eqilibrium Geometry Located". I went on to run Hessian with the optimised structure using the same basis set. On analysis of the output in MacMolplt, I find that the double bond has been shifted and is different from my input. I have attached the input of the molecule from Avogadro and the optimised structure. Please help in solving the issue.
Mrs/Miss/Mr. Sundaram,
Which program you have use in preparing your inputs?
Looking at your two pictures, it appears to me that the positive charge has been delocalized at bit causing that double bond and two singles on that imidazole ring to change to three singles. That does not matter. The program uses bond distances to determine what bond type it shows between any two atoms. If you want the double bond in your picture where it was before you can (1) put the atom numbering on the atoms of the molecule and then (2) open the Subwindow (on wxMacMolPlt) Bonds and find the two atom labels and change the designation from single to double. Be assured the picture is just eye candy and the bonding shown does not affect the answers you are interested in. In fact, if you go into Gaussian and indicate no bonds between all of the atoms in the molecule and run an optimization, you get the same optimized geometry as when you put the bonds in. I suspect that a MM or semiempirical calculation may depend on the bond designations, but as long as you are running an HF or DFT calculation I would ignore the difference between the input and output bonding types. Like I said above, if you think someone is going to question your results because of the missing double bond from your input you can change the appearance of the bonding types. I wouldn't do that - but that is just me.
Dear Dr. Ivanova,
Thanks for taking your time to look into my concern. I used Avogadro v 1.2 to generate .inp fie for GAMESS
Dear Prof. Dr. Lieb,
Thanks a lot for your time and detailed explanation. As long as it does not affect the results, I guess I can proceed with the present optimised structure.
Thanks again!!!
Vidya.
Hi Vidya,
You are welcome. Oh, and one more thing. If you get a negative frequency, that will be the test of whether you are not a an optimimum (local) geometry. The negative frequency means is that the force constant is negative making the frequency imaginary. The negative force constant means you are on a transition state. You may already know this, but I thought I would mention it anyway. Happy computing{:^)
Fortunately, the vibrational frequencies are all positive and I have ended up with the minimum and not the transition state. I just reassured it. Thanks again Prof. Dr. Lieb!!! With your message taken, I am doubly sure:)
Vidya.
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