Implicit Solvation

Accurate predictions in quantum chemical calculations require consideration and understanding of the effects of solvents on chemical systems. Solvation, the interaction between molecules and solvents, strongly influences their behavior. In computational chemistry, solvation effects are incorporated through two main approaches: explicit solvation, in which solvent molecules are explicitly included, and implicit solvation, in which the solvent is treated as a continuum or dielectric medium surrounding the solute molecule. Implicit solvation models simplify the computational complexity by treating the solvent as a continuous medium.

This tutorial focuses specifically on implicit solvation in WEASEL, while explicit solvation is covered separately in another tutorial available :ref:`here<explicitsolv>.

How to sepcify the solvent in WEASEL

By default, WEASEL simulations are carried out in implicit water solvent.

Other solvents can be chosen with the following argument:

weasel example.xyz -solvent Octanol

The available solvents are:

Keyword	Solvent option
-solvent	Water, Acetonitrile, Acetone, Ammonia, Benzene, Ethanol, Methanol, CH2Cl2, CCl4, DMF, DMSO, Pyridine, THF, Chloroform, Hexane, Octanol, Cyclohexane, Toluene, Protein

Note

It is common practice in biomolecular modeling to model protein structures as cluster models. In such cases, in order to mimic the effect of screening charges in the protein environment, it is common practice to use a dielectric constant of 4. This can be achieved in WEASEL calculations with the solvent option Protein.

Important

It can be useful to carry out multiple simulations on a single structure but using different solvents. In such a case it can be useful to additionally use the solvent name as label, e.g.

weasel structure.xyz -solvent acetonitrile -label acetonitrile

in order to prevent overwriting the previous results.

Gas phase calculations

Also gas phase calculations can be carried out. This is requested with the following argument:

weasel structure.mol2 -gas

Solvents in workflows

Different workflows each have their own default solvents (depending on the method, and following the usual standard experimental setups).

The default solvent can be exchanged by another solvent via the command line using the -solvent keyword:

weasel water.xyz -W UVVis -solvent acetonitrile -label acetonitrile

Note

If your lab setting is different to our defaults you can define new workflows and adapt the workflow-dependent default solvent in the corresponding workflow configuration file.

Solvent models

By default the CPCM implicit solvation model is used. Another option is to use the SMD model with the -smd keyword:

weasel water.xyz -W UVVis -solvent acetonitrile -smd