Overview: parameters and analysis
*********************************

COSMO-RS AMSview Sigma profile COSMO-SAC COSMO surface


Step 1: Start AMScrs
====================

For this tutorial it is convenient to start with an empty directory,
for example, with the name Tutorial. You should start AMSjobs and move
to the Tutorial directory:

   Start amsjobs
   Click on the Tutorial folder icon
   Select **SCM → COSMO-RS**
 [image]

This AMScrs window consists of the following main parts:

* the menu bar with the menu commands

* on the left: a list of compounds and the possibility to add
  compounds

* on the right: some properties for the selected compound

This is the so called **List of Added Compounds**, which is the window
you will get if you select **Compounds → List of Added Compounds**.

If you run the COSMO-RS GUI the first time, you will be asked if you
would want to download and install the COSMO-RS compound database:

[image]

The download of such databases is handled by AMSpackages. It is
recommended to download the COSMO-RS compound database. On the other
hand, for this tutorial, it is not necessary that the COSMO-RS
compound database is downloaded.


Step 2: Add Compounds
=====================

In tutorial 1 it was shown how to make ADF COSMO result files. In this
tutorial we will use some pre-made ADF COSMO result files. These files
can be found in the directory "$AMSHOME/examples/COSMO-
RS/Parameters_and_Analysis". Copy these COSMO result files
(water.coskf, methanol.coskf, ethanol.coskf, and benzene.coskf) to the
directory Tutorial. As the names suggest, these are COSMO result files
of water, methanol, ethanol, and benzene, respectively.

Note that these COSKF (.coskf) files contain only the part of an
ordinary TAPE21 (.t21) file which is needed in a COSMO-RS calculation.
These COSKF files can only partly be used in AMSview, for example.

   Press 'Add' for 'Add Compound(s)' in the left window
 [image]

A file select box will open, that looks like (may look different on
different platforms)

[image]

or

[image]

   Select **Files of type** (or **Filter**) **→ COSMO kf file (*.coskf)**
   Select multiple files: benzene.coskf, ethanol.coskf, methanol.coskf and water.coskf
   Click 'Open'

On the right side of the **List of Added Compounds** you can find some
data that was written from the last file that was opened, in this case
water.coskf. It is also possible to add some pure compound input data
here, although this is not required in this particlar case. However,
for some other types of compounds, user input is required at this
point. We will encounter an example of this in the next step.

[image]


Step 3: Set pure compound parameters
====================================

In the COSMO-RS model [1] there is a ring correction term. This is
important for, for example, the benzene molecule, which has 6 ring
atoms. However, it is really required only when the vapor pressure of
the compound is going to be computed (either because that is
explicitly requested or because it is used in predicting partial vapor
pressures in a mixture or gas/liquid partitioning coefficients).

For some properties, like solubility of a solid, one can or one has to
include some pure compound properties in the left window of the **List
of Added Compounds** for a selected compound.

It is possible to save this pure compound data in as a new COSKF file
(or COSMO file).

   Click in the left window (in the **List of Added Compounds**) benzene
   Press 'Generate' for 'Nring' in the right window
 [image]

To save this data in a .coskf file:

   Click in the left window (in the **List of Added Compounds**) benzene
   Press 'Save As' at the top of the right window
   Enter the name 'benzene' in the 'Filename' field

If you have followed this tutorial from the start then you will
overwrite an existing benzene.coskf file. You will be asked if you
want to to that, click 'Yes'. The writing can take some time,
especially for larger compounds. During this time the COSMO-RS GUI is
not available for other actions.

Notice that there are 'Estimate' buttons to estimate some pure
compound properties. The method that is used for the estimation is a
group contribution method. If you press all 'Generate' and 'Estimate'
buttons, you will see something like the following for benzene:

[image]

Note that some of the estimates are less accurate, such as the
estimated melting point of small molecules.


Step 4: COSMO-RS, COSMO-SAC, and UNIFAC parameters
==================================================

You can easily change between the COSMO-RS, COSMO-SAC, and UNIFAC
method that is going to be used in the calculation by selecting
**Method → COSMO-RS**, **Method → COSMO-SAC**, or **Method → UNIFAC**.
Here we will use COSMO-RS, since ADF was parametrized for this method.

   Select **Method → COSMO-RS**

**Expert option: set COSMO-RS parameters**

   Select **Method → COSMO-RS**
   Select **Method → Parameters**
 [image]

Default 'ADF combi2005' COSMO-RS parameters are selected, which are
ADF optimized COSMO-RS parameters. See also a discussion of the COSMO-
RS  parameters in the COSMO-RS manual. If you select the 'Klamt'
option for 'Use: ... COSMO-RS parameters', the optimized parameters
are chosen, which are optimized by Klamt et al., see ref. [1].

**Expert option: set COSMO-SAC parameters**

   Select **Method → COSMO-SAC**
   Select **Method → Parameters**
 [image]

The 2013-ADF COSMO-SAC parameters were optimized for use with ADF. See
also a discussion of the COSMO-SAC parameters in the COSMO-RS manual.

**Expert option: set UNIFAC parameters**

   Select **Method → UNIFAC**
   Select **Method → Parameters**
 [image]

The UNIFAC implementation needs a SMILES string to generate the groups
in a compound. The generation of SMILES strings is not done
automatically.

   **Compounds → List of Added Compounds**
   Click in the left window (in the **List of Added Compounds**) water
   Press 'Generate' for 'SMILES' in the right window
   Click in the left window (in the **List of Added Compounds**) ethanol
   Press 'Generate' for 'SMILES' in the right window
   Click in the left window (in the **List of Added Compounds**) methanol
   Press 'Generate' for 'SMILES' in the right window
   Click in the left window (in the **List of Added Compounds**) benzene
   Press 'Generate' for 'SMILES' in the right window

For example, for benzene, the SMILES string 'c1ccccc1' should be
generated (by Openbabel). You should double check the SMILES string
generated, especially for charged systems, radicals, and inorganic
compounds.

[image]

For the rest of the tutorial the COSMO-RS method will be used:

   Select **Method → COSMO-RS**


Step 5: Visualize the COSMO surface: AMSview
============================================

You can use AMSview to have a look at the COSMO surface, and the COSMO
surface charge density. This is possible if the COSMO result file of
the compound is a .coskf file or a .t21 file.

Note:

  The AMSview module was redesigned in AMS2026. If you use an older
  version, follow the older tutorial.

   Select **Compounds → List of Added Compounds**
   Click on the left side 'water'
   Press on the right side 'Show 3D'
   An AMSview window should pop-up
   In AMSview, select **Properties → COSMO: Surface Charge Density → on COSMO surface (reconstructed)**
   If the side panel is not visible, select **View → Layout → Toggle controls**
   Click on the black triangle next to "COSMO surface". This reveals some more options.
   Select **Colormap → Rainbow**

Then you will see something like:

[image]

The red part represents positive COSMO charge density (the underlying
molecular charge is negative), the blue part negative COSMO charge
density (the underlying molecular charge is positive). You can also
look at the COSMO surface points themselves.

   Select **Add → COSMO: Surface Charge Density → on COSMO surface points**
   In the controls click on the black triangle in front of 'COSMO surface points' to show the details
   Select **Colormap → Rainbow**
   In the controls click on the black triangle in front of 'COSMO surface points' to hide the details
   Hide the sidebar with **View → Layout → Toggle controls**
 [image]

The small spheres represent the COSMO surface points that are used for
the construction of the COSMO surface.

Next we will close this AMSview window.

   Select the AMSview window 'water'
   Select **File → Close Job**
   Select the COSMO-RS GUI window

AMSview has many options to change the look of the picture.

   Select **Compounds → List of Added Compounds**
   Click on the left side 'methanol'
   Press on the right side 'Show 3D'
   An AMSview window should pop-up
   In AMSview, select **Properties → COSMO: Surface Charge Density → on COSMO surface (reconstructed)**
   If the side panel is not visible, select **View → Layout → Toggle controls**
   Check  **View → Anti-Alias**
   In the controls click on the arrow in front of 'COSMO surface' to show the details
   Change the Opacity to 70
   Select **Colormap → Rainbow**
 [image]

Next we will close this AMSview window.

   Select the AMSview window 'methanol'
   Select **File → Close Job**
   Select the COSMO-RS GUI window

Optionally you can change the default settings for the colormap that
is used in AMSview

   Select **SCM → Preferences → Module → AMSview**
   Select **Colormap → Rainbow**


Step 6: Analysis: The sigma profile
===================================

The \sigma-profile shows the amount of surface area for a given COSMO
charge density.

   In the COSMO-RS GUI window, select **Analysis → Sigma Profile Pure Compounds**
   Check the '+' button to add 'benzene', 'ethanol', 'methanol', and 'water'
 [image]

   Select **File → Save As**
   Enter the name 'tutorial2' in the 'Filename' field
   Select **File → Run**

The sigma profiles (\sigma-profile) of the four pure compounds will be
shown in a graph and in a table in the right part of the window. The
whole window can be resized. The relative size of the left part of the
window compared to the right part can be changed if you move the
divider that is in between these parts. In the right part of the
window you can also change the relative size of the upper part
compared to the lower part if you move the divider that is in between
these parts.

[image]

With default settings, if you click in the graph you can zoom (right
mouse, or Command-Left (drag up or down)), or translate (left mouse)
the graph. If you click in the graph window at the left or below the
axes, a popup window will appear in which you can set details for the
graph window.

Note that the \sigma-profile depends on the method (COSMO-RS or COSMO-
SAC) that was used in the calculation. Here we have used COSMO-RS.  In
this case the \sigma-profile depends on the actual value for r_av
(r_av ), which is one of the COSMO-RS parameters, see one of the
previous steps.

You can also look at the hydrogen bonding part of the \sigma-profile.

   Select **Graph → Y axes → hydrogen bonding (HB) part sigma profile**
 [image]


Step 7: Analysis: The sigma potential
=====================================

   Select **Analysis → Sigma Potential Pure Compounds**
   Check the '+' button to add 'benzene', 'ethanol', 'methanol', and 'water'
   Press 'Run'

The sigma potentials (\sigma-potential) of the four pure compounds
will be shown in a graph and in a table in the right part of the
window. The \sigma-potential depends on the temperature of a compound.
Here the temperature is set to 25 °C (298.15 K).

[image]

If you double-click on the x-axis in the graph, you can customize the
look of the graph on the "Curves" panel in the window that pops up.

Note that the \sigma-potential is not calculated for values of the
COSMO charge density that are non-existent on the COSMO surface of a
certain compound.

[image]

-[ References ]-

[1] A. Klamt, V. Jonas, T. Bürger and J.C. Lohrenz,  *Refinement and
    Parametrization of COSMO-RS.*  J. Phys. Chem. A 102, 5074 (1998)
