Using pseudo potentials in your project
Adding the PP
In your project you should not use PPs on all the atoms, only use PP only on the heavy atoms. There is an easy way to do this by directly editing the *.gjf or *.com file that Gaussian reads.
Build your molecule as you normally would, but in the basis set selection choose "GEN" and then add the keywords "pseudo=cards gfinput" to the additional commands line. Then save the file, do not submit it! You are going to add some extra information.
I have set-up a demo file for AsMe3 and the file looks like this:
%chk=asme3.chk # b3lyp/gen geom=connectivity pseudo=cards gfinput AsMe3 optimisation using pp and basis sets 0 1 As -0.25054466 0.64270152 0.00000000 C -1.24054466 2.35743181 0.00000000 H -0.66227355 3.10313962 0.50440301 H -1.41887795 2.66631387 -1.00880579 H -2.17548229 2.22948873 0.50440280 C 1.71293214 0.63316184 0.25508406 H 1.94954423 1.03676382 1.21738347 H 2.07611581 -0.37123904 0.19045826 H 2.17420672 1.22880548 -0.50474119 C -1.22402145 -1.06248910 -0.25508406 H -0.73996948 -1.63925293 -1.01530585 H -1.22643826 -1.61255000 0.66269977 H -2.23172722 -0.85715587 -0.55049452 1 2 1.0 6 1.0 10 1.0 2 3 1.0 4 1.0 5 1.0 3 4 5 6 7 1.0 8 1.0 9 1.0 7 8 9 10 11 1.0 12 1.0 13 1.0 11 12 13
Now we have to specify the basis sets for all atoms and the pseudo-potential for the As atom. This is done after the coordinates and connectivity information. I have an example below for the AsMe3 molecule where I want a PP on the As but not on the C or H atoms:
12 (this is the bottom of the connectivity information) 13 As 0 LanL2DZ **** C H 0 6-311G(d,p) **** As 0 LanL2DZ
the general format is the following:
coordinates
(blank line)
atomic symbol (space) 0 (zero)
pseudo-potential basis set
**** (four stars)
atomic symbols (space) 0 (zero)
normal basis set
**** (four stars)
(blank line)
atomic symbol (space) 0 (zero)
pseudo-potential
(blank line) important!
So now my whole file looks like this:
%chk=asme3.chk # b3lyp/gen geom=connectivity pseudo=cards gfinput AsMe3 optimisation using pp and basis sets 0 1 As -0.25054466 0.64270152 0.00000000 C -1.24054466 2.35743181 0.00000000 H -0.66227355 3.10313962 0.50440301 H -1.41887795 2.66631387 -1.00880579 H -2.17548229 2.22948873 0.50440280 C 1.71293214 0.63316184 0.25508406 H 1.94954423 1.03676382 1.21738347 H 2.07611581 -0.37123904 0.19045826 H 2.17420672 1.22880548 -0.50474119 C -1.22402145 -1.06248910 -0.25508406 H -0.73996948 -1.63925293 -1.01530585 H -1.22643826 -1.61255000 0.66269977 H -2.23172722 -0.85715587 -0.55049452 1 2 1.0 6 1.0 10 1.0 2 3 1.0 4 1.0 5 1.0 3 4 5 6 7 1.0 8 1.0 9 1.0 7 8 9 10 11 1.0 12 1.0 13 1.0 11 12 13 As 0 LanL2DZ **** C H 0 6-311G(d,p) **** As 0 LanL2DZ
A problem with some PP!
There apears to be a problem with some PP, in that the NBO analysis will not open properly in gaussview. If this happens to you, take your optimised geometry (checked with frequency analysis) and then run a single point all electron calculation with the NBO option. This means you remove the opt and freq keywords and just do an energy calculation, with the same basis set that you have used for all the other atoms. For example if I was to do this for the AsMe3 molecule above I would have B3LYP/6-311G(d,p), set up just like we did for the BH3 molecule. The geometry however MUST be that of the optimised structure.Alternative
You can explicitly give the PP as in the following, where I have replaced the LANL2DZ with the explicit basis set and PP taken from the Basis set exchange site.
As 0
S 2 1.00
0.9635000 -2.6709549
0.5427000 2.9387892
S 1 1.00
0.1407000 1.0000000
P 2 1.00
2.0840000 -0.1137100
0.3224000 1.0380266
P 1 1.00
0.1020000 1.0000000
****
C H 0
6-311G(d,p)
****
AS 0
AS-ECP 3 28
f potential
5
1 375.4748803 -28.0000000
2 72.6554769 -198.3687357
2 15.9162677 -60.4563798
2 4.6420251 -22.3188274
2 1.4789182 -2.1638290
s-f potential
5
0 105.8853870 3.0000000
1 62.5951846 31.8486777
2 34.5017431 200.9958215
2 10.3758594 102.6387604
2 2.5379347 34.1845359
p-f potential
5
0 37.6471440 5.0000000
1 17.2034665 24.2505747
2 18.9075709 48.9174963
2 6.8153452 66.5332259
2 2.0611853 19.6577666
d-f potential
5
0 52.0731335 3.0000000
1 28.0037824 23.3460712
2 14.7051208 80.7854919
2 4.7973194 40.2681347
2 1.1062763 4.8332790