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:
Maybe this makes sense, as I don´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:
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:
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?
