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The final "blank card" or blank line at the end is required and must not be omit
ted.
--Manually create a .gjf file by typing this and saving as [Ar.gjf]
%chk=C:\Users\TempUser1\Desktop\Ar.chk
# HF/STO-3G
Ar test calculation
0 1
Ar
--Start the job in Gaussian or GaussView (no difference as GaussView will call Gau
ssian anyway)
But if running from GaussView, make sure to close any other instances of Gaussia
n first.
Gaussian
File > Open [Ar.gjf] > Check-Route > RUN >> [Ar.out] will be output
GaussView
File > Open [Ar.gjf] > Calculate > Gaussian Calculation Setup > Submit >> [Ar.lo
g] output
or close New Molecule window and open a new one (File > New > Create Mol
ecule Group)
In the (grey) Main Panel...
Click the [6C] icon to choose an element from the periodic table display
Select oxygen, and below, select the fragment with two single bonds
Because hydrogens are automatically attached to the dangling bonds, this
gives H2O
Now H2O is displayed in the Main Panel but there's nothing in the New Mo
lecule Window
In the (purple) New Molecule window...
Click ONCE to add single-bonded oxygen with hydrogens attached, i.e. H2O
Click on Bond Length tool, then click on O and click on H > can change b
ond length
Click on Bond Angle tool, then click on H,O,H in turn > can change bond
angle too
(Don't worry about messing up the lengths and angles because we can easi
ly clean up!)
In the (grey) Main Panel...
Clean [brush icon]
Symmetrize [mirror plane icon] (the symmetry C2v / C1 now shows at the
bottom)
Clean corrects all bond lengths and angles to "typical" values.
However, note that this is not necessarily the true molecular ge
ometry!
Symmetrize chooses a coordinate system that gives highest molecu
lar symmetry.
This can help to speed up calculations as some integrals can be
re-used.
Calculate > Gaussian Calculation Setup
Job Type
Method
tral singlet
Title
Link 0
cify > 2
Energy
Ground State Hartree-Fock Default Spin, STO-3G
! check that the charge and spin are correct. H2O is neu
water STO-3G energy
Memory Limit > Specify > 1 GB;
SOLVATION
The calculations we have performed so far are in the gas phase (the molecules ar
e isolated).
We can introduce explicit solvation by adding in more molecules but this is comp
utationally
expensive. Instead, more commonly used is *implicit* solvation wherein the solve
nt is treated
as a continuous medium or continuum, rather than individual molecules.
We can set up a calculation using the Onsager solvation model (spherical dipole
molecule).
Run an energy calculation with additional keyword "volume" >> output will contai
n the line:
"Recommended a0 for SCRF calculation = X angstrom ( Y bohr)"
Here, a0 is the solute radius estimated by a Monte Carlo procedure.
Now remove the keyword "volume" and add in keyword "scrf=dipole" (to call the On
sager model).
Save this input file as .gjf but do not run the calculation yet.
Edit the file in a word-processing software and add in two lines after the final
blank card:
[solute radius a0 in Angstrom] [solvent dielectric constant]
[blank card]
At this point the Onsager solvation calculation is ready to be run.
The energy calculated for the solvated molecule can be compared with its gas pha
se energy to
determine the solvation energy. Of course, the same level of theory should be us
ed for both.
! Note that the geometry of the molecule should be *optimized* in the gas phase,
and again in
the solvent, for the result to be more accurate. Optimization will be discussed
in part 2.
**Tip - Onsager solvation model really sucks! Choose something more decent from
the drop-down
menu in Gaussian Calculation Setup > Solvation > Model. The default model is PCM
, and other
even better models such as CPCM and SMD can be selected. The default solvent is
water (but
H-bonding is not taken into account as these are all implicit solvation models).