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I tried to generate a density surface (the one from red to blue) for Clothianidin, but GaussView 6 gives me errors. I am using GaussView 6.0 without Gaussian installed on the same machine. Gaussian16 is installed on a server, where I can optimize my structure or generate cubes.

To make it short: What files e.g. only optimization or frequency do I need to use for cubegen? Do I need cubegen Density=SCF and cubegen Potential=SCF? What else do I need?

My Attempt(s)

So what I did was to optimize my structure and generate a fchk file using formcheck e.g. formchk -2 Clothianidin_opt2.chk. I also tried formcheck -3 which ended with the same results. Then I generated a cubefile using cubegen 1 Density=SCF Clothianidin_opt2.fchk Clothianidin_opt2.cube 80 h which resulted in this:

>  Clothianidin_aug-cc-pvTZ Rotamer1 Density=SCF  Electron density from
> Total SCF Density    23  -14.508446   -9.185611   -8.060497    1   108
> 0.299772    0.000000    0.000000    70    0.000000    0.299772    0.000000    67    0.000000    0.000000    0.299772    17   17.000000    9.411010   -0.663572    0.080443
>     6    6.000000    6.208134   -0.939150    0.357091
>     7    7.000000    4.714953   -1.379204   -1.492821
>     6    6.000000    2.271291   -1.496183   -0.658306
>     6    6.000000    1.905644   -1.138093    1.850851    16   16.000000    4.789064   -0.613814    3.284518
>     6    6.000000   -0.527227   -1.167258    3.303661
>     7    7.000000   -2.715471   -1.279566    1.698451
>     6    6.000000   -3.701916    0.716798    0.488475
>     7    7.000000   -5.898175    0.857682   -0.699938
>     7    7.000000   -7.493805   -1.150643   -0.668691
>     8    8.000000   -6.873423   -3.221607    0.238729
>     8    8.000000   -9.537711   -0.789805   -1.617011
>     7    7.000000   -2.349769    2.873389    0.479663
>     1    1.000000   -0.490259    2.708699    0.792811
>     6    6.000000   -3.201984    5.101774   -0.861255
>     1    1.000000   -3.310255    4.779762   -2.885485
>     1    1.000000   -5.063000    5.637655   -0.204045
>     1    1.000000   -1.880202    6.615397   -0.473743
>     1    1.000000   -3.836257   -2.821282    1.639883
>     1    1.000000   -0.589188   -2.808413    4.534685
>     1    1.000000   -0.638050    0.488941    4.524813
>     1    1.000000    0.780564   -1.861533   -1.991145
>   6.19673E-11  8.83004E-11  1.23586E-10  1.69934E-10  2.29631E-10  3.05069E-10
>   3.98654E-10  5.12710E-10  6.49378E-10  8.10526E-10  9.97653E-10  1.21180E-09
>   1.45346E-09  1.72240E-09  2.01751E-09  2.33654E-09  2.67583E-09  3.03002E-09
>   3.39182E-09  3.75190E-09  4.09899E-09  4.42026E-09  4.70199E-09  4.93048E-09
>   5.09323E-09  5.18010E-09  5.18441E-09  5.10381E-09  4.94065E-09  4.70197E-09
>   4.39892E-09  4.04581E-09  3.65884E-09  3.25473E-09  2.84941E-09  2.45690E-09
>   2.08855E-09  1.75259E-09  1.45411E-09  1.19523E-09  9.75599E-10  7.92931E-10
>   6.43632E-10  5.23354E-10  4.27493E-10  3.51563E-10  2.91469E-10  2.43659E-10
>   2.05198E-10  1.73763E-10  1.47592E-10  1.25405E-10  1.06307E-10  8.96951E-11
>   7.51744E-11  6.24857E-11  5.14501E-11  4.19301E-11  3.38038E-11  2.69509E-11
>   2.12473E-11  1.65642E-11  1.27715E-11  9.74160E-12  7.35311E-12  5.49453E-12
>   4.06627E-12 ...

Does this makes sense having density that small e.g. E-11 ?

Anyway back to GaussView I opened the fchk file, clicked on Results/Surfaces/Contours... loaded the cube file above via cube actions, clicked on surface actions and new mapped surface, used type ESP with density matrix SCF and gained the warning:

Surface map failed! Executing Gaussian cubegen job

Giving me this: density cube

Maybe this makes sense, as I donĀ“t have Gaussian installed on this machine. So I generated another cube using cubegen 1 Potential=SCF Clothianidin_opt2.fchk Clothianidin_opt2b.cube 80 h which resulted in this:

>  Clothianidin_aug-cc-pvTZ Rotamer1 Potential=SCF  Electrostatic
> potential from Total SCF Density    23  -14.508446   -9.185611  
> -8.060497    1   108    0.299772    0.000000    0.000000    70    0.000000    0.299772    0.000000    67    0.000000    0.000000    0.299772    17   17.000000    9.411010   -0.663572    0.080443
>     6    6.000000    6.208134   -0.939150    0.357091
>     7    7.000000    4.714953   -1.379204   -1.492821
>     6    6.000000    2.271291   -1.496183   -0.658306
>     6    6.000000    1.905644   -1.138093    1.850851    16   16.000000    4.789064   -0.613814    3.284518
>     6    6.000000   -0.527227   -1.167258    3.303661
>     7    7.000000   -2.715471   -1.279566    1.698451
>     6    6.000000   -3.701916    0.716798    0.488475
>     7    7.000000   -5.898175    0.857682   -0.699938
>     7    7.000000   -7.493805   -1.150643   -0.668691
>     8    8.000000   -6.873423   -3.221607    0.238729
>     8    8.000000   -9.537711   -0.789805   -1.617011
>     7    7.000000   -2.349769    2.873389    0.479663
>     1    1.000000   -0.490259    2.708699    0.792811
>     6    6.000000   -3.201984    5.101774   -0.861255
>     1    1.000000   -3.310255    4.779762   -2.885485
>     1    1.000000   -5.063000    5.637655   -0.204045
>     1    1.000000   -1.880202    6.615397   -0.473743
>     1    1.000000   -3.836257   -2.821282    1.639883
>     1    1.000000   -0.589188   -2.808413    4.534685
>     1    1.000000   -0.638050    0.488941    4.524813
>     1    1.000000    0.780564   -1.861533   -1.991145  -1.06018E-02 -1.08792E-02 -1.11586E-02 -1.14393E-02 -1.17201E-02 -1.19998E-02  -1.22773E-02 -1.25511E-02 -1.28196E-02 -1.30811E-02 -1.33340E-02 -1.35761E-02  -1.38057E-02 -1.40206E-02 -1.42187E-02 -1.43979E-02 -1.45561E-02 -1.46913E-02  -1.48016E-02 -1.48852E-02 -1.49406E-02 -1.49664E-02 -1.49615E-02 -1.49252E-02  -1.48570E-02 -1.47568E-02 -1.46249E-02 -1.44619E-02 -1.42688E-02 -1.40468E-02  -1.37975E-02 -1.35228E-02 -1.32247E-02 -1.29054E-02 -1.25673E-02 -1.22130E-02  -1.18448E-02 -1.14654E-02 -1.10770E-02 -1.06823E-02 -1.02833E-02 -9.88236E-03  -9.48137E-03 -9.08220E-03 -8.68652E-03 -8.29583E-03 -7.91145E-03 -7.53453E-03  -7.16607E-03 -6.80689E-03 -6.45767E-03 -6.11895E-03 -5.79116E-03 -5.47460E-03  -5.16946E-03 -4.87585E-03 -4.59380E-03 -4.32327E-03 -4.06415E-03 -3.81627E-03  -3.57945E-03 -3.35343E-03 -3.13795E-03 -2.93273E-03 -2.73743E-03 -2.55175E-03  -2.37535E-03 ...

Loaded this cube to surfaces and was able to click on electrostatical potential / surface actions and new mapped surface / use an existing cube, select electron density, pressed ok and gained the warning:

Surface build failed!  Reading cube file Writing Grid Data Reading
Grid Point Line Number 10215 No data to plot. IsoValue may be out of range.

I played with the isovalues and always got the same message.

Then I tried to use cubegen density=SCF with the freq=raman file of the optimized structure resulting in this:

>  Clothianidin_aug-cc-pvTZ Rotamer1 Density=SCF  Electron density from
> Total SCF Density    23  -14.720430   -9.389071   -9.369187    1   107
> 0.302641    0.000000    0.000000    71    0.000000    0.302641    0.000000    67    0.000000    0.000000    0.302641    17   17.000000    9.246225    0.463788   -1.228247
>     6    6.000000    6.098476   -0.120440   -0.826692
>     7    7.000000    4.468003   -0.079914   -2.611440
>     6    6.000000    2.117989   -0.628869   -1.685338
>     6    6.000000    1.962729   -1.087829    0.829228    16   16.000000    4.934572   -0.817273    2.148065
>     6    6.000000   -0.325160   -1.742793    2.367719
>     7    7.000000   -2.640963   -1.518183    0.966174
>     6    6.000000   -3.828287    0.674504    0.513435
>     7    7.000000   -6.126859    1.010551   -0.413585
>     7    7.000000   -7.613589   -1.022699   -0.899286
>     8    8.000000   -6.814014   -3.220296   -0.730685
>     8    8.000000   -9.749694   -0.540506   -1.540856
>     7    7.000000   -2.588956    2.823436    1.083883
>     1    1.000000   -0.703004    2.708938    1.198058
>     6    6.000000   -3.665831    5.286456    0.570168
>     1    1.000000   -3.940101    5.595358   -1.440374
>     1    1.000000   -5.483984    5.454605    1.491321
>     1    1.000000   -2.389744    6.701318    1.317225
>     1    1.000000   -3.686129   -3.045921    0.507781
>     1    1.000000   -0.196125   -3.682799    3.025270
>     1    1.000000   -0.406044   -0.555342    4.049952
>     1    1.000000    0.532873   -0.676284   -2.957095
>   8.65666E-12  1.19103E-11  1.60910E-11  2.13384E-11  2.77799E-11  3.55358E-11
>   4.47422E-11  5.55998E-11  6.84525E-11  8.38973E-11  1.02912E-10  1.26981E-10
>   1.58181E-10  1.99184E-10  2.53147E-10  3.23428E-10  4.13162E-10  5.24687E-10
>   6.58923E-10  8.14781E-10  9.88751E-10  1.17477E-09  1.36449E-09  1.54787E-09
>   1.71421E-09  1.85331E-09  1.95667E-09  2.01854E-09  2.03656E-09  2.01193E-09
>   1.94910E-09  1.85500E-09  1.73801E-09  1.60684E-09  1.46951E-09  1.33263E-09
>   1.20097E-09  1.07742E-09  9.63253E-10  8.58505E-10  7.62493E-10  6.74248E-10
>   5.92858E-10  5.17660E-10  4.48295E-10  3.84672E-10  3.26856E-10  2.74956E-10
>   2.29016E-10  1.88955E-10  1.54538E-10  1.25389E-10  1.01018E-10  8.08750E-11
>   6.43859E-11  5.09952E-11  4.01908E-11  3.15191E-11  2.45908E-11  1.90788E-11
>   1.47128E-11  1.12713E-11  8.57358E-12  6.47230E-12  4.84729E-12  3.60048E-12
>   2.65197E-12 ...

Loaded this cube to surfaces, which gave me a second but different electron density:

Surfaces 3 cubes loaded

Then I was able to click on (the Raman) electron density / surface actions and new mapped surface / use an existing cube, select (the first optimized) electron density, pressed ok and gained finally no errors resulting in this:

electron density of clo

Well, I was expecting a bit more red, especially there are oxygens and nitrogens in that molecule. So I changed the values of minus and plus 1.981e-2 to e-5 and everything in between, changing the colors of the surface but still not as expected.

Do you have a hint for me?

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1 Answer 1

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Finally found the solution:

After optimizing the structure I needed to generate an electron density cube like this:

cubegen 1 Density=SCF Clothianidin_opt2.fchk Clothianidin_opt2_dens.cube 80 h

Then I calculated the Electrostatic potential using the density of SCF like this:

cubegen 1 Potential=SCF Clothianidin_opt2.fchk Clothianidin_opt2_pot.cube 80 h

After this was done I loaded the fchk file of the optimized structure (in my case Clothianidin_opt2.fchk) into GaussView, clicked on Results/Surfaces/Contours... loaded both cube files above via cube actions, selected "Electron density from Total SCF Density", clicked on surface actions and Use an existing cube, selected the only cube available, which was the "Electrostatic potential from total SCF Density" and confirmed with ok.

select surfaces

Now this gave me the right surface, where I only needed to adjust the neg and pos values for coloring:

MEP of Clo

Finished!

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