COSMO result files
******************

COSMO-RS ADF FastSigma

If you already have COSMO result files for all the compounds that you
are interested in you can skip this tutorial, without problems of
continuity. For example, ADF has a database of COSMO result files, the
COSMO-RS compound database ADFCRS-2018.

The purpose of this tutorial is to teach you how to make data for a
compound using the ADF program such that it can be read by COSMO-RS.
COSMO-RS expects so called COSMO result files, which are results of
quantum mechanical calculation using COSMO. In ADF such a COSMO result
file is called a TAPE21 (.t21) file, RKF (.rkf), or a COSKF (.coskf)
file. For example the COSMO-RS compound database ADFCRS-2018 consists
of .coskf files. In other programs such a file could be called a
.cosmo file. For example, at https://design.che.vt.edu  one may find a
database of .cosmo files, which were made with a different program.
Note that the optimal COSMO-RS parameters may depend on the program
chosen.

Please read through the first GUI tutorial before starting with this
tutorial. Even better: try using the AMS-GUI yourself, especially the
Getting started Tutorial.

In this tutorial an ADF COSMO result file and a MOPAC COSMO result
file will be made.  We will also use the program "FastSigma" to
quickly estimate the sigma profile of molecules from SMILES strings.

For ADF COSMO-RS calculations the recommended choice is to use ADF
COSMO result files. For very fast calculations, in which one avoids
doing a quantum mechanical calculation for a compound, the "FastSigma"
method is recommended.


Step 1: Start AMSinput
======================

For this tutorial we prefer to work in a separate directory, for
example a directory called Tutorial, as was explained in the Getting
started Tutorial.

Start AMSjobs (in your home directory), and move to the Tutorial
directory:

   Start AMSjobs
   If the Tutorial directory does not exist, **File → New Directory**, and create a directory called Tutorial
   Click on the Tutorial folder icon

Next start AMSinput using the SCM menu.

   Select the **SCM → New input** menu command.


Step 2: Create the molecule
===========================

First we construct a water molecule, and preoptimize its geometry:

   Select the O-tool by clicking on [image: OTool][image]
   Click somewhere in the drawing area to create an oxygen atom
   Select the pointer-tool by clicking on [image: PointerTool][image]
   Click once in empty space so nothing is selected
   Select **Atoms → Add Hydrogen**
   Click the preoptimizer button [image: PreOptimTool][image]
   Symmetrize the system by clicking on [image: SymmTool][image]

By symmetrizing the system ADF will use symmetry. Your water molecule
should look something like this:

[image]


Step 3: ADF COSMO result file
=============================

The next step is to optimize the gas geometry using ADF, and perform
the ADF COSMO calculation at the optimized gas phase geometry, using
**Task: COSMO-RS Compound**.

   On the **main panel**, set **Task → COSMO-RS Compound**
 [image]

For your information, the proper settings for the gas phase geometry
optimization are: the Becke Perdew exchange correlation functional
(GGA:BP86), use of the scalar relativistic ZORA Hamiltonian, a TZP
small core basis set (for Iodine a TZ2P small core basis set), and an
integration accuracy with a normal quality. Like for Iodine, for
heavier elements than Krypton, a TZ2P small core basis set is
recommended. Note that these settings were used for the optimization
of the COSMO-RS parameters.

In the version after **AMS2025**, an additional densf calculation can
be enabled to determine the hydrogen bond center used in COSMO-SAC
DHB-ADF MESP method.

   Click on the [image: MoreBtn][image] button next to the Task
 [image]

If **H-bond center from MESP** is set to 'Yes', the hydrogen bond
center will additionally be determined from the local minima of the
molecular electrostatic potential (MESP), calculated from the
potentials in the densf calculation.

If **Single Point** is set to 'Yes', a single point calculation will
be performed instead of geometry optimization for the gas phase
calculation, which is useful when an optimized structure is already
available.

With the proper options selected, now run ADF:

   Select **File → Run**
   In the file select box, choose a name for your file (for example 'water')
   and click 'Save'

Now ADF will start automatically, and you can follow the calculation:
AMSjobs will show the progress of the calculation with the last few
lines of the logfile.

   Wait until the optimization and ADF-COSMO calculation are ready (should take very little time)
   Click the [image: UpdateMolecule][image] button, which will have appeared in the right hand panel, to update the coordinates

Now the geometry of the water molecule is the optimized one, and the
ADF COSMO calculation has been performed. The result file water.coskf,
which is an ADF COSMO result file, can be used as input for a COSMO-RS
calculation.

Note that a .coskf file is not a complete .rkf file. For example, if
one has such a .coskf file, only the COSMO surface charge density can
be viewed with AMSview. Thus a .coskf file is mostly useful for COSMO-
RS calculations.

More details on parameters used in the COSMO calculation can be found
in the run script: **Details → Run Script**. See also the COSMO-RS
manual.


Step 4: Lowest Conformer
========================

In standard COSMO-RS theory, one uses one COSMO result file for one
molecule in conjunction with the conformer with the lowest energy.
Note, however, that sometimes molecules behave in solution in ways
that are not accurately captured by the “one-molecule-one-structure”
paradigm of standard COSMO-RS theory. For more information, see the
tutorial COSMO-RS with multi-species components, where multiple
conformers, multimers, dissociated and associated molecules are
discussed.

The AMS-GUI does have some basic support for handling conformers. This
includes the generation of conformers and the refinement of conformers
using different theoretical methods, see the AMS-GUI tutorial on
Conformers for more details. In the step in this tutorial where the
structures of the conformers are refined, one can use ADF with the
Task 'COSMO-RS Compound'. Next one can select the conformer with the
lowest energy to be used as an ADF COSMO result file.

Note that this step does not involve a calculation, but only shows one
way to find the lowest conformer.

Alternatively, you can generate the lowest conformer and multiple
conformers by utilizing the "ADFCOSMORSCompound" class and
"ADFCOSMORSConfJob" class through Python scripting. You can find more
information and examples in the documentation links provided:
ADFCOSMORSCompound class and ADFCOSMORSConfJob. Before running the
Python script, please ensure that you have completed the necessary
environment setup by referring to the Getting Started with scripting.


Step 5: Polymers with ADF
=========================

The AMS-GUI supports the making of a polymer. However, the calculation
of a full polymer is very expensive. Instead of this very expensive
calculation, here an "average monomer" COSMO result file is
calculated. The full polymer result could then be calculated by
multiplying the "average monomer" result by a factor equal to the
number of repeat units in the polymer.

In this step ADF is used to generate a COSMO result file for a
polymer. One can also use the approximate, but much faster,
"FastSigma" method, described in step 7.

Here, a trimer is calculated from 3 units of the monomer, in which the
trimer is capped with 2 methyl groups. Next an ADF COSMO result file
is generated, in which only the COSMO charges of the center monomer
will be used in the COSMO-RS calculations.

   Select the **SCM → New input** menu command.
   Select **Builders → Polymer Builder** (before AMS2026: **Edit → Polymer...**)
   Click the **Add monomer:** search box
   Enter 'styrene' (without quotes)
 [image]

   Select 'styrene' from the pull-down menu

This will create a Polystyrene monomer. The 2 dummy atoms will later
be replaced with 2 other monomers to form a Polystyrene trimer.

[image]

Next we will not use the Polymer builder window, but instead use a
specialized button that generates a trimer, adds 2 methyls as capping
groups, and selects the center monomer atoms as so called 'COSKF
atoms'.

   Click the **Close** button at the bottom of the Polymer builder window
   Select **Task → COSMO-RS Compound**
   Go to the **Model → Solvation** panel
   Click the 'COSKF trimer:' **Generate** button
 [image]

If one would select **File → Run** an "average monomer" COSMO result
file would be created, which an be used for polymer calculations. The
calculation can take up quite some time, therefore we skip this part
in this step.


Step 6: MOPAC COSMO result file
===============================

Note this step is presented here only for completeness. One can skip
this step, since we do not recommend to use MOPAC to generate COSMO
result files.

MOPAC is a faster method than ADF for the generation of COSMO result
files. However, we recommend to use the "FastSigma" program described
in the next step, if you want get an estimate of a COSMO result file
very quickly and which has a better quality.

A MOPAC COSMO result file can be created in almost the same way as an
ADF COSMO result file.  We will change the program from ADF to MOPAC,
and select the COSMO solvation method.

   Select the **SCM → New input** menu command.
   Create a water molecule
   Select [image: ADFPanel][image] **→** [image: MopacPanel][image]
   Select **Model → Solvation**
   Tick the **Use COSMO** checkbox
   Select **CRS** from the **Solvent** dropdown menu
 [image]

For sake of clarity we will save the COSMO calculation under a
different name, and run the calculation

   Select the 'Save As...' command from the 'File' menu
   In the file select box, choose 'water_mopac' as name for your file and click 'Save'
   Select **File → Run**
   Wait until the optimization is ready (should take very little time)
   Click the [image: UpdateMolecule][image] button, which will have appeared in the right hand panel, to update the coordinates

After the calculation has finished the file
water_mopac.results/mopac.coskf, which is a MOPAC COSMO result file,
can be used as input for a COSMO-RS calculation.

Note that MOPAC is a semi-empirical quantum chemistry program, whereas
ADF is based on density functional theory (DFT). Thus the MOPAC COSMO
result files will not be of the same quality as the ADF COSMO result
files.


Step 7: FastSigma: estimating sigma profiles for use with COSMO-RS/-SAC
=======================================================================

FastSigma  is a program that estimates information in a COSMO result
file without doing an expensive DFT calculation.  Practically
speaking, this that in the timeframe of milliseconds, "FastSigma" can
estimate a sigma profile and other required molecular descriptors used
to perform COSMO-RS/-SAC calculations.

See also:

  The FastSigma Documentation is a useful resource for additional
  calculation types and more general information.

In the GUI, "FastSigma" can be used for compounds with a SMILES string
or an .xyz file. In this example, we use Ibuprofen, which is
represented in the SMILES string "CC(Cc1ccc(cc1)[C@@H](C(=O)O)C)C".

Note that for a polymer one would need as input a so called
CurlySMILES string, which for example, for Polystyrene is
"C{-}C{n+}(c1ccccc1)", see the COSMO-RS polymers tutorial for more
details.

   Select the **SCM → COSMO-RS** menu command.
   Select **No** if the question **Install ADF COSMO-RS Database** pops up
   (Remark: it is not a problem to install the database, it will just take some time)
   Select **Compounds → List of Added Compounds**
   For **Add Compound using FastSigma → SMILES**
   Enter "CC(Cc1ccc(cc1)[C@@H](C(=O)O)C)C" for Ibuprofen
   Select **FS1** as the Model
   Select the **Add** button at the right of the SMILES string
   In the pop-up in the file select box, choose a name for your file (for example 'ibuprofen')
 [image]

In the right part of the COSMO-RS GUI window one should see something
like:

[image]

FastSigma does not create a COSMO surface, but creates a so called
sigma-profile, which can be used in COSMO-RS calculations. The
parameters in FastSigma are fitted to COSMO-RS sigma-profiles of
organic closed shell neutral molecules. The created sigma-profile can
not be used in COSMO-SAC calculations. The created file contains a
SMILES string, thus it can be used in UNIFAC calculations. Note that
is is not recommended to be used for radicals or charged molecules.

Important:

  To use the "SG1" method instead of "FS1", users will have to first
  download the **Subgraph Sigma Profile Estimation (SG1) Database**
  (molsg_sg1db) using the AMS Package Manager.

One can visualize the molecule in 2D (a .html file will be created)
with

   Press 'Show 2D' at the top of the right window
   In the pop-up in the file select box, choose a name for your html file (for example 'ibuprofen')
 [image]

Openbabel is used to translate the SMILES string into a picture.
