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I am using Gaussian 16 to optimize a paraquat molecule on top of a bulk of gold atoms. Some of these gold atoms are frozen, so I use the option opt=modredundant. I also want to use different basis sets for the calculation of different atoms. I found the option of using gen. My root section is as follows:

%cpu=48-63
%mem=50GB
%chk=paraquat+goldbulk1656.chk
#p opt=modredundant b3lyp/gen nosymm int=ultrafine

After the root section, I specify the title, charge, and multiplicity. The .gjf file includes the coordinates for the atoms and the information on which atoms should be frozen (e.g. X 54 F).

Do I put the code to specify the basis sets after the coordinates, after the frozen atoms, or at the very end of the .gjf file?

H C N 0
aug-cc-PVTZ

Au 0
lanl2dz

Thank you for your answers!

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(1) int=ultrafine is the default option for g16, so there is no need to write it.

(2) You need to use genecp rather than gen since LANL2DZ for Au includes ECP. gen can only deal with all-electron basis set. Alternatively, gen pseudo=read will also work.

(3) aug-cc-pVTZ may be unnecessarily large for a DFT computation. If your "paraquat molecule" is neutral, i.e. net charge is zero, the basis set def2-TZVP is enough (If you want to change it to def2-TZVP, note that def2-TZVP is used in papers/reference, but def2TZVP is used in Gaussian input file).

(4) The functional B3LYP cannot deal with dispersion or weak interactions correctly. In your case "a paraquat molecule on top of a bulk of gold atoms", such interactions should be important. You are recommended to use B3LYP-D3(BJ), which should be written as B3LYP em=GD3BJ. If combined with genecp, it turns into B3LYP genecp em=GD3BJ or B3LYP/genecp em=GD3BJ.

(5) Since there may be many gold atoms to be frozen, it becomes tedious if you use opt=modredundant. You can try another way of freezing, for example,

C  0  0.0   0.0   0.0
H  0  0.0   0.0   1.0
Au -1 0.0   0.0   5.0
...
Au -1 0.0  10.0   6.0

H C N 0
def2TZVP
****
Au 0
LANL2DZ
****

Au 0
LANL2DZ

where -1 after the element means frozen during geometry optimizations, and 0 means its position can be optimized. Do not write opt=modredundant if you adopt this way of freezing atoms. Besides, the usage of mixed basis set is shown above. Remember to type two blank lines after the final LANL2DZ, Gaussian needs blank lines to detect where it is the end of a file.

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    $\begingroup$ As an additional comment, there are other functionals that handle dispersion and B3LYP-D3(BJ) is not the only option. Almost any functional can be used with dispersion corrections and I am skeptical that B3LYP will be good for this system with a bulk Au fragment. $\endgroup$
    – Tristan Maxson
    Aug 25, 2022 at 14:57
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    $\begingroup$ You are right, @TristanMaxson, B3LYP or B3LYP-D3(BJ) is not a good choice for this system. I was assuming that if he/she wants to use B3LYP, then D3(BJ) should be added. But using another functional with D3 correction may be better. $\endgroup$
    – jxzou
    Aug 26, 2022 at 4:34
  • $\begingroup$ Thank you very much for the long and detailed answer! Is there any reason you put "AU 0 LANDL2DZ" two times in a row at the end? $\endgroup$
    – Anastasia Bitter
    Sep 1, 2022 at 9:34
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    $\begingroup$ @AnastasiaBitter, the first LANL2DZ tells Gaussian program to load the LANL2DZ basis set for Au, while the second LANL2DZ tell Gaussian program to load the LANL2 ECP for Au (actually, the second LANL2DZ can be simply written as LANL2). If the second LANL2 is missing, the calculation is wrong (although Gaussian may not abort). $\endgroup$
    – jxzou
    Sep 1, 2022 at 11:24

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