Is it possible to combine two separate molecular groups created in Gaussian software into a single large molecule? If so how can we do it?
Thanks in advance!
Dear Devi,
With the word "combine" you mean react or you are referring to add one molecule to the other image?
-The solution in the first one is build directly the molecule, but if they are a optimized structures, then you can perform a SCAN calculation in order to see how they can react to the given reaction A+B=C. (see guide)
-The solution to the other option is to copy (control+c). Then if you go to the option (image1) you will see your structure. Then, for example, you can make left-click to the atom which you want to use as link (if it is attached to the other molecule) or you can click somewhere in the drawing panel.
PD: If it is a "reaction" or interaction of two fragments, remember the BSSE effect or long-range effects if you are using DFT methods.
I hope it helps you,
Joaquim Rius
Technical Report Gaussian Guide. Section 1. Optimization and Frequency Calculations
Dear Devi,
another, more "primitive", so to say, approach would be to use the Z-matrix editor within the Molden software (which is free) and to build the combined structure from two fragments of your interest. However, in this case you would have to optimize the final structure, because if you would use the optimized structure of the one fragment, another fragment, when you add it, might differ significantly from the optimized structure.
Best regards,
Aleksey.
Dear Devi,
I agree with the answers of my previous two peers, however, I suggest to do the following:
1-Build your two fragments in the same file using ArgusLab
2-Minimize both of them (together) by UFF (installed within Arguslab)
3-Write the input file and save it as ------.GJF
4-Run a single point calculation by AM, PM3 or any other methods.
5-View the output file using Molden and connect the two fragments by changing the distance between the atoms of interest.Then you can start optimization by AM1 and ending with DFT calculation with the appropriate basis set.
ArgusLab and Molden prograns are free downloaded programs.
Hoping this will be helpful,
Rafik
I found this link so i share it here maybe someone will need it
https://joaquinbarroso.com/2015/05/20/efficient-use-of-the-clipboard-on-gaussview/
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