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Details

Building Solvent Shells

Solvation of starting structures can be done using presto's pre-loaded solvents, shown below. The dipole moment and polarizibility have been benchmarked to experiment for some commonly used solvents. In general, the dipole moment is slightly overestimated by GFN2-xtb and GFN0-xtb. (To convert polarizability from a.u. to Å3, multiply by 0.5293 = 0.148.)

Solvent Keyword Dipole (Exp./GFN2/GFN0, D) Polariz. (Exp./GFN2/GFN0, Å3)
Acetonitrile acetonitrile 3.92 / 5.77 / 3.85 4.28 / 4.40 / 4.36
Benzene benzene
Chloroform chloroform 1.01 / 1.47 / 1.20 8.13 / 8.09 / 8.09
Cyclohexane cyclohexane
Dichloroethane (gauche conformer) dce_gauche
Dichloroethane (anti conformer) dce_anti
Dichloromethane dcm 1.60 / 1.79 / 1.77 6.66 / 6.19 / 6.18
Dibutyl Ether dibutylether
Diethyl Ether ether 1.15 / 1.79 / 1.71 ??? / 8.37 / 8.47
Diisopropyl Ether diisopropylether 1.13 / 1.91 / 1.92 ??? / 11.82 / 11.97
Dioxane dioxane
Ethanol ethanol
Ethyl Acetate ethyl_acetate 1.78 / 4.03 / 2.56 8.62 / 8.67 / 8.59
n-Hexane hexanes
Methanol methanol 1.70 / 1.57 / 1.91 3.21 / 3.18 / 3.20
Tetrahydrofuran thf 1.63 / 1.55 / 2.03 7.88 / 7.80 / 7.64
Toluene toluene 0.33 / 0.55 / 0.51 11.86 / 11.83 / 11.77
Water water 1.86 / 1.81 / 2.22 1.50 / 1.41 / 1.40
Xenon xenon

Solvation can be performed by the Python script scripts/solvate.py. To use solvate.py, PACKMOL must be accessible via the bash command packmol. (You may wish to define an appropriate bash alias.) The output of python solvate.py --help is reproduced here:

usage: solvate.py [-h] [--file FILE] [--solvent SOLVENT [SOLVENT ...]]
                      [--num NUM [NUM ...]] [--output OUTPUT]

A script to solvate arbitrary xyz files, generating spheres of realistic
solvent density.

optional arguments:
  -h, --help            show this help message and exit
  --file FILE, -f FILE  xyz file containing the desired input structure to
                        solvate.
  --solvent SOLVENT [SOLVENT ...], -s SOLVENT [SOLVENT ...]
                        solvents to use (specified by name, multiple arguments
                        allowed).
  --num NUM [NUM ...], -n NUM [NUM ...]
                        number of each solvent to add. same order as list of
                        solvents.
  --output OUTPUT, -o OUTPUT
                        desired output xyz file.

Running solvate.py is straightforward, and requires only a starting .xyz file:

$ python scripts/build_input.py -f test/static/PhF.xyz -o solvated.xyz -s benzene -n 50

solvate.py will compute the volume of the solute automatically and then choose an appropriate sphere size, placing the solute in the center. The output .xyz file will always contain the solute first, and can be visualized with Avogadro, CYLView, or other software prior to the start of the simulation.