Polymers
********

COSMO-RS Polymers Activity coefficient Vapor pressure log P Gas
solubility Flory-Huggins χ

The COSMO-RS program can also be used to calculate thermodynamic
properties of polymers and polymer-containing mixtures.  The theory
and equations behind this are described in the COSMO-RS documentation.
This tutorial will focus on practical details of performing
calculations with polymers in the COSMO-RS GUI.

This tutorial expects that that you are familiar with setting COSMO-RS
parameters and pure compound data (see the COSMO-RS overview tutorial:
parameters and analysis), doing COSMO-RS calculations (see the COSMO-
RS overview tutorial: properties), and that the COSMO-RS compound
database ADFCRS-2018 has been installed already (see the COSMO-RS
compound database tutorial).


The ADFCRS Polymer Database
===========================

The COSMO-RS Polymer Database contains >200 structures of common
polymers, all represented as the central unit of a trimer as described
in the COSMO-RS manual.  Because the simplest procedure used to
generate the structure of a monomer still requires the calculation of
a trimer, it is recommended to use the polymer database for this
tutorial as adding user-defined polymers will likely be time-consuming
(minutes-days, depending on the size of the polymer).

To quickly get started with polymers in COSMO-RS, download the COSMO-
RS Polymer Database.  More information about the database can be found
here.


Selecting/inputting database compounds
======================================

After downloading and unzipping the database, open the COSMO-RS GUI
AMScrs.  To use the database in COSMO-RS, follow the steps shown
below.

   Open a new COSMO-RS GUI window
   Select **Compounds → Add Compound(s)**
   Navigate to the Polymer Database directory
   Click on **monomers.compoundlist** and select **Open**

Note:

  Polymeric compounds can also be added by SMILES string.  Be sure to
  input a polymer in CurlySMILES format.  One can read the CurlySMILES
  paper for more thorough coverage, but the CurlySMILES format is
  fairly self-explanatory.  For example, in CurlySMILES polyethylene
  is "C{-}C{n+}" and polysytrene is "C{-}C{n+}(c1ccccc1)".  These
  examples show that the atoms that are part of the polymerization are
  marked with "{-}" and "{n+}" identifiers.


Inputting your own polymers (optional)
======================================

It is also possible to input new polymers to the database and use
these structures as you would any polymer in the database.  As for all
new compound inputs, there are two ways of doing this.


Method 1: Using ADF
-------------------

This is the standard method for using compounds not already present in
the database.  This method requires an ADF and COSMO calculation, but
polymer calculations can require a lot of atoms, sometimes making
these calculations expensive.  For this method, we must first perform
a geometry optimization and then a single point COSMO calculation.
The required steps for this calculation are as follows:

   Start AMSinput (**SCM → New Input**)
   Select **Task → COSMO-RS Compound**
   Input the structure of a single monomer unit of your polymer
   Add dummy ("Xx") atoms corresponding to where the monomer is attached to other monomers in the polymeric structure
   Go to **Model → Solvation**
   click "Generate" next to "COSKF trimer"
   Save/run your input file

We will illustrate the process of new polymer input using polyethylene
below:

**(1) Select Task → COSMO-RS Compound, Input the monomer structure**

[image: alternate text][image]

**(2) Select the atoms that should be replaced by other monomer units
in the full polymer. Click on Atoms → Change Atom Type and replace the
atoms with "Xx"**.  Note: depending on how you have inputted the
structure, you may have to add these atoms.  Be sure to check that all
of the correct atoms are present.  Select multiple atoms by holding
the "Shift" key and clicking.

[image]

**(3) Go to Model → Solvation and click "Generate" next to "COSKF
trimer"**

[image]

**(3.1) (Optional, but recommended) Right click the** [image:
PreOptimTool][image] **and select GFN1-xTB**.  This will start a pre-
optimization with DFTB method and can provide a good initial geometry
for the subsequent ADF calculation.

[image]

**(4) Go back to the ADF panel and select Task: COSMO-RS Compound save
your input file**

[image]

**(5) Run the job (File → Run).  After running the job, open the newly
created .coskf file in the COSMO-RS GUI.**  Note that depending on the
order of opening GUI windows the .coskf file may already have been
opened by the COSMOS-RS GUI. You can see the COSMO surface by first
selecting your new compound on the **Compounds → List of added
compounds** window.  Then press the "Show 3D" button, which opens an
AMSview window.  From AMSview, click **Properties → COSMO: Surface
Charge Density → On COSMO surface points**.  This could produce the
image below:

[image]


Method 2: Using FastSigma to estimate a polymer's sigma profile
---------------------------------------------------------------

Because ADF calculations for large polymers can be expensive, it is
sometimes preferred to estimate the necessary parameters to perform a
COSMO-RS calculation.  This can be done with the FastSigma tool
available from the GUI or the command line.  To use this tool from the
COSMO-RS GUI, use the following steps:

   Select **Compounds → List of added compounds**
   Under 'Add Compound using FastSigma' field, choose "FS1" in the Model
   Type the CurlySMILES for polystyrene "C{-}C{n+}(c1ccccc1)" in the SMILES
   Click Add next to the SMILES section and save the file

The above steps should involve the following (main) step:

[image]


Inputting necessary property values
===================================

In the rest of the tutorial only polymers from the polymer database
will be used.


Polymer/Average Molecular Weight
--------------------------------

Because polymers of the same type can come in many lengths, it is
important to be able to adjust the average molecular weight of a
polymer.  This is done from the compounds menu: **Compounds → List of
Added Compounds.**  Below, we show an example of setting the average
molecular weight for Poly(ether_ether_sulfone) (PEES):

[image]

Additionally, to specify that a compound should be treated like a
polymer, the Polymer box should be checked (shown in the image above).
The number of repeat units will be set to the average molecular weight
divided by the molar mass of the compound (the compound is assumed to
the be monomer). Note that a default value of 10000 g/mol is used if
no input is given.


Density
-------

Due to a modified combinatorial term for polymers, **densities are
required for every species** in a calculation involving any polymers.
In the ADFCRS database, many polymers already have a recommended
density value, which should provide reasonable results under standard
temperature and pressure conditions.  However, it is well-known that
for many polymers these density values can be sensitive to temperature
and solvent.  In these cases -- or in cases where there is no
recommended density value given -- the density can be input from the
compounds menu: **Compounds → List of Added Compounds.**

Here, we show an example of inputting the density for
Poly(ether_ether_sulfone) (PEES):

[image]

Note:

  Many polymers in the Polymer Database already have a given
  experimental density value.  This value is automatically used for
  the calculation if the user does not input a different value for
  density.  These experimental values come from the the Polymer
  Database Website.


Example polymer calculations
============================

Polymers can be used just like other compounds in COSMO-RS/-SAC: they
are simply selected as pure components or components of a mixture.  If
any polymers are present in the system (as indicated by the **Polymer
flag on the List of Added Compounds menu**), then a number of special
properties will be calculated.  Because polymer calculations are done
just like calculations for small molecules, this tutorial will cover a
few example calculations without going into the details of every
possible type of calculation.  For a comprehensive tutorial about
different problem types with the COSMO-RS GUI, we redirect the reader
here.

Note:

  To simplify the examples, the molecular weight of the polymer has
  not been specified. As a result, a default value of 10,000 g/mol
  will be used to calculate the special properties.


Activity coefficients
---------------------

For this calculation, we estimate the activity coefficients in a
Poly(ethylene)/Benzene mixture.  Because this is a calculation
involving polymers, we will need the density of both Poly(ethylene)
and Benzene.  There is a recommended value of Poly(ethylene) given
(0.852), so we can use that value.  For Benzene, we'll enter a value
of 0.876.  Use the following summary of steps to perform the
calculation:

   **Compounds → List of Added Compounds**
   Select Benzene
   Set Density to 0.876
   **Properties → Activity Coefficients**
   Select **2 Components**
   Select **Mass fraction**
   Select Poly(ethylene) and Benzene
   Set mass fraction of Poly(ethylene) to 0.5
   Set mass fraction of Benzene to 0.5
   Click **Run**
   Click OK to the 'Warning: no solutes found'

The result of this calculation is the following:

[image]

Notice that some non-standard properties are given: weight fraction
activity coefficient (= mass fraction activity coefficient), volume
fraction activity coefficient, and Flory-Huggins \chi.


Vapor pressure of a mixture
---------------------------

Now, we will estimate the vapor pressure of a mixture of
Poly(dimethylsiloxane), Methanol, and n-Hexane.  Use the following
summary of steps to perform the calculation:

   **Compounds → List of Added Compounds**
   Select Methanol
   Set Density to 0.792
   Click **Estimate** next to Vapor pressure equation
   Select Hexane
   Set Density to 0.655
   Click **Estimate** next to Vapor pressure equation
   **Properties → Vapor pressure mixture**
   Select **3 Components**
   Select **Mass fraction**
   Select Poly(dimethylsiloxane), Methanol, and Hexane
   Set mass fraction of Poly(dimethylsiloxane) to 0.5
   Set mass fraction of Methanol to 0.25
   Set mass fraction of Hexane to 0.25
   Adjust the temperature range from 298.15 K to 398.15 K
   Click **Run**

The result of this calculation is the following:

[image]

Note that estimated properties are calculated with the Property
estimation tools


Partition Coefficients (LogP)
-----------------------------

Now, we'll calculate the partition coefficient of Methanol between a
water and poly(ethylene) phase.

   **Compounds → List of Added Compounds**
   Select Methanol
   Set Density to 0.792
   Select Water
   Set Density to 1.0
   **Properties → Partition Coefficients (LogP)**
   **User Defined 2 components**
   Select Poly(ethylene) and Water
   Set mole fraction Poly(ethylene) to 1.0 in phase 1
   Set mole fraction Water to 1.0 in phase 2
   Select Methanol in the *Solutes (infinite dilute)* box
   Click **Run**

The output of this calculation is shown below:

[image]


Solubility in Pure Solvents
---------------------------

In this example, we'll calculate the solubility of Hexane gas in
Poly(styrene) over the temperature range 398.15 K to 498.15 K and over
the pressure range 1.0 bar to 4.0 bar.

   **Compounds → List of Added Compounds**
   Select Hexane
   Set Density to 0.655
   Click **Estimate** next to Vapor pressure equation
   **Properties → Solubility in Pure Solvents**
   Select Poly(styrene) in *Pure Compound Solvents*
   Select Hexane as the *Solute*
   Select **Gas** for the solute type
   Set the temperature range from 398.15 K to 498.15 K
   Set the number of steps for pressure to 3
   Set the pressure range from 1.0 bar to 4.0 bar
   Click **Run**
   Click **Graph → Y axes → Solubilty (g/L solvent)**
 [image]


Binary Mixture and Flory-Huggins \chi
-------------------------------------

In this example, we will calculate binary mixture properties
(including the \chi) over the entire range of compositions.  We will
do this for a binary mixture of Benzene and Poly(ethyl_ethylene) and
use COSMO-SAC (the 2013-ADF Xiong parameters).

   **Compounds → List of Added Compounds**
   Select Benzene
   Set Density to 0.876
   **Method → COSMO-SAC**
   **Method → Parameters**
   Select the **2013-ADF Xiong** parameters
   **Properties → Binary Mixture VLE/LLE**
   Select Poly(ethyl_ethylene) as Compound 1
   Select Benzene as Compound 2
   Select **Mass Fraction**
   Click **Run**
   Click **Graph → X axes → w1: mass fraction 1**
   Click **Graph → Y axes → Flory-Huggins 𝛘**

The result of this calculation is the following:

[image]
