I'm attepting to do NICS analysis on a reaction intermediate, but currently the molecule is oriented in a random way and the aromatic ring I want to analyse is not in the XY plane. Does anyone know how to reorient the coordinates of a molecule in gaussview without changing their relative positions? Currently the only way I've thought of is manually changing the cartesian coordinated but am hoping there's a method that won't require hours of labourious manual atom movements
Dear Joe Higham ,
I don't know how to do this with Gaussview. Nevertheless, I could suggest you to use Avogadro (free) to do this.
I personally have Avogadro 1.2.0 that, from my point of view is better than the second one.
I joined two images to illustrate how to do this easily with this software:
1. The first one shows you the module I use (two arrows, at the top left). You can choose two atoms and choose an axis on which you want to align.
2. As an illustration on Benzene, I choose to align along 'x' and that is the *.xyz file I obtained.
With the new geometry you optimized, from Gaussview, just register the geometry in *.pdb, *.mol2 or *.xyz file so that you can open it with Avogadro then. Thus you can align as you wish, register the new geometry and use Gaussian to make a single point energy with the keyword "nosymm".
If you generate a *.chk file, you can obtain a *.fchk file from it or, generate also *.wfn and *.wfx file.
If you are interested, I remember Multiwfn (free) is able to help you also for this purpose (I join also an image in the discussion).
Hope this could help you!
Multiwfn (http://sobereva.com/multiwfn) is able to evaluate NICS_ZZ for nonplanar or tilted ring, you need to input magnetic shielding tensor calculated by quantum chemistry code, see Section 3.100.24 of Multiwfn manual for detail.
Another way is to use Multiwfn to put the ring of interest to XY plane first. Just load your geometry into Multiwfn, enter main function 300 and select subfunction 7, you can find an option "11 Make the plane defined by selected atoms parallel to a Cartesian plane". Use it to make the ring of interest parallel to XY plane, then use corresponding option in the menu to export the current coordinate. After that, you can conduct NICS_ZZ analysis as usual based on the exported geometry (If you are a Gaussian user, do not forget to add "nosymm" keyword in NMR task to prevent automatic reorientation).
If you have any question I will explain further.
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